bluuebunny/crossref_metadata_2025 huggingface dataset:
Disparities Between Two Common Data Sources on Hospital Nurse Staffing
Authors: Jiang H. Joanna , Stocks Carol , Wong Cindy J.
Published: May 2006

Purpose: To compare nurse staffing measures derived from two widely used data sources: the American Hospital Association (AHA) Annual Survey of Hospitals and the California Office for Statewide Health Planning and Development (OSHPD).

Design: Descriptive cross‐sectional study with measures of nurse staffing level and skill mix constructed from each database for 372 nonfederal, acute care hospitals in California.

Methods: Discrepancies in nurse staffing estimates between the two databases were examined. Relationships of nurse staffing with risk‐adjusted patient outcomes (decubitus ulcer, failure to rescue, and mortality) were assessed through multivariate analyses and compared for nursing measures derived from the two databases.

Findings: For small, rural, or nonteaching hospitals, AHA reported substantially higher registered nurse (RN) hours per patient day than did OSHPD. RN proportion among licensed nurses matched most closely in the two databases. RN hours per patient day derived from both databases showed significant inverse relationships with decubitus ulcer and mortality, and the association was stronger for the measure based on the OSHPD data. RN proportion derived from the OSHPD data was significantly associated with all three patient outcomes, but the AHA measure had a significant relationship only with decubitus ulcer.

Conclusions: Compared with the AHA survey, the OSHPD data on hospital nurse staffing appear to be more complete and also were more closely associated with patient outcomes. Efforts to refine the AHA survey as a national database for nurse staffing will significantly enhance the capacity for monitoring nurse workforce and its effect on quality of care.
Optimal CINAHL Search Strategies for Identifying Therapy Studies and Review Articles
Authors: Wong Sharon S.‐L. , Wilczynski Nancy L. , Haynes R. Brian
Published: May 2006

Purpose: To design optimal search strategies for locating sound therapy studies and review articles in CINAHL in the year 2000.

Design and Methods: An analytic survey was conducted, comparing hand searches of 75 journals with retrievals from CINAHL for 5,020 candidate search terms and 17,900 combinations for therapy and 5,977 combinations for review articles. All articles were rated with purpose and quality indicators. Candidate search strategies were used in CINAHL, and the retrievals were compared with results of the hand searches. The proposed search strategies were treated as “diagnostic tests” for sound studies and the manual review of the literature was treated as the “gold standard.” Operating characteristics of the search strategies were calculated.

Findings: Of the 1,383 articles about treatment, 506 (36.6%) met basic criteria for scientific merit and 127 (17.9%) of the 711 articles classified as a review met the criteria for systematic reviews. For locating sound treatment studies, a three‐term strategy maximized sensitivity at 99.4% but with compromised specificity at 58.3%, and a two‐term strategy maximized specificity at 98.5% but with compromised sensitivity at 52.0%. For detecting systematic reviews, a three‐term strategy maximized sensitivity at 91.3% while keeping specificity high at 95.4%, and a single‐term strategy maximized specificity at 99.6% but with compromised sensitivity at 42.5%. Three‐term search strategies optimizing sensitivity and specificity achieved these values over 91% for detecting sound treatment studies and over 76% for detecting systematic reviews.

Conclusions: Search strategies combining indexing terms and text words can achieve high sensitivity and specificity for retrieving sound treatment studies and review articles in CINAHL.
Literary History’s Alternate Groove: The Expectations of Periodization and Seventeenth‐Century Literary Culture
Authors: Ezell Margaret
Published: May 2006

This piece investigates the possibilities of periodization and its labels for the mid‐ and later seventeenth century, historical decades which have always posed certain problems for those in search of literary period names. The Interregnum as a historical period has very clear boundaries, but supposedly little literary merit. The standard literary histories of the seventeenth century emphasized continuity with earlier Stuart court literary culture and suggested to us that literature, too, was defeated by a Puritan aesthetic, the “Cavalier winter.” The Restoration is typically represented as a clean break with the Interregnum. This “rupture” model creates the expectation that literary culture comes back in from the cold and the countryside; it also privileges certain forms of literature associated with the new court culture. This has hindered the perception of such diverse contemporary writers as John Milton, John Bunyan, and Aphra Behn as emerging from the same period. While the war years and the Interregnum have been recently become the focus of literary study of alternative radical voices – women’s religious discourse, radical political discourse, and the creation of the genres of journalism – this essay looks at yet another Interregnum literary culture, of the reading habits of the middle class, or artisan consumer. “Literature” is a commercial commodity as well as a cultural one. Leaving aside periodization as a means to assist in evaluating artistic merit, this essay instead uses it to define a discreet slice of time to explore in terms of what was being written and what was being printed and sold, in other words to provide a time frame for a descriptive overview of literary production and consumption.
Samson’s “Rousing Motions”: What They Are, How They Work, and Why They Matter
Authors: DuRocher Richard
Published: May 2006

Before going to the Temple of Dagon with the Philistian Officer near the climax of Milton’s Samson Agonistes, Samson tells the uncomprehending Chorus to “Be of good courage.” For, he assures them, “I begin to feel / Some rousing motions in me which dispose / To something extraordinary my thoughts” (1381–3). Samson’s motivation for his decision to enter the temple, together with his catastrophic act of pulling down the temple upon the Philistian nobility, and “inevitably” upon himself, has become the flashpoint of voluminous debate about Samson Agonistes in recent Milton criticism. This essay aims to contribute to this critical conversation by exploring precisely what Milton and his readers would have understood by the “rousing motions” that Samson reports feeling at this pivotal moment. Seventeenth‐century readers would have recognized Samson’s “motions” as the part of the so‐called system of “faculty psychology” responsible for the feelings. Beyond scrutinizing Milton’s text, I examine contextual support from ancient and early modern sources toward understanding Samson’s “motions” and their workings. As well as reviewing the theory of emotions expounded by Aristotle in the Rhetoric and Nicomachean Ethics, I describe the modifications to that theory propounded by the Protestant reformer Philip Melanchthon, as well as the nuanced approach to dealing with affective volatility developed by the Cambridge theologian William Fenner. Milton and these Protestant writers share three essential convictions: they locate the emotions within a comprehensive model of the mental faculties; they assert the power of the human agent, typically through the will, to control – in Milton’s phrase, “to temper and reduce to just measure”– their potentially overwhelming power; and, most significant of all, they regard the emotions as the specific point of interaction between God, typically in the form of the Spirit, and the aspiring spirits of the human being. This last claim in particular addresses a question raised by several recent commentators on Samson Agonistes, namely, whether Samson’s impulse to act comes from himself or from God.
Women Writers in World War II
Authors: Maslen Elizabeth
Published: May 2006

This article covers the period 1939 to 1945, looking at women writers and their work throughout the Second World War. It explores their writing in the context of the jobs they were, in many cases, called upon to do over that time, and also examines the subjects they chose to write about. It attempts to answer certain central questions, as, for instance, was there a difference between generations in the way women wrote and the issues that concerned them; did they look outside the war situation for their subject matter or did they engage? Readers are pointed to leading research on women’s writing in the war years, to biographies, and to primary texts.
The early effects of chronic hypoxia on the cardiovascular system in the rat: role of nitric oxide
Authors: Walsh Martin P. , Marshall Janice M.
Published: May 2006

Experiments were performed under Saffan anaesthesia on normoxic (N) rats and on chronically hypoxic rats exposed to 12% O2 for 1, 3 or 7 days (1, 3 or 7CH rats): N rats routinely breathed 21% O2 and CH rats 12% O2. The 1, 3 and 7CH rats showed resting hyperventilation relative to N rats, but baseline heart rate (HR) was unchanged and arterial blood pressure (ABP) was lowered. Femoral vascular conductance (FVC) was increased in 1 and 3CH rats, but not 7CH rats. When 1–7CH rats were acutely switched to breathing 21% O2 for 5 min, ABP increased and FVC decreased, consistent with removal of a hypoxic dilator stimulus that is waning in 7CH rats. We propose that this is because the increase in haematocrit and vascular remodelling in skeletal muscle help restore the O2 supply. The increases in FVC evoked by acute hypoxia (8% O2 for 5 min) and by infusion for 5 min of α‐calcitonin gene‐related peptide (α‐CGRP), which are NO‐dependent, were particularly accentuated in 1CH, relative to N rats. The NO synthesis inhibitor l‐NAME increased ABP, decreased HR and greatly reduced FVC, and attenuated increases in FVC evoked by acute hypoxia and α‐CGRP, such that baselines and responses were similar in N and 1–7CH rats. We propose that in the first few days of chronic hypoxia there is tonic NO‐dependent vasodilatation in skeletal muscle that is associated with accentuated dilator responsiveness to acute hypoxia and dilator substances that are NO ‐dependent.
Neurosteroid modulation of respiratory rhythm in rats during the perinatal period
Authors: Ren Jun , Greer John J.
Published: May 2006

Neurosteroids regulate neuronal excitability and are expressed at particularly high levels in the CNS during the perinatal period. Further, neurosteroid levels are increased by a variety of stressors including hypoxia, asphyxia, parturition, ethanol exposure and infection. One mechanism by which neurosteroids regulate neuronal activity is by negative or positive modulation of GABAAreceptor function. Perinatal respiration is strongly modulated by GABAergic synaptic drive, and GABA release is increased during hypoxia to contribute to hypoxia‐induced depression of neonatal ventilation. Here, we usein vitroandin vivorat models to test the hypothesis that GABAAreceptor‐mediated modulation of perinatal respiration is markedly influenced by the presence of neurosteroids. The principal finding of this study was that the efficacy of GABAAreceptor‐mediated modulation of respiratory membrane potential and rhythmogenesis is markedly enhanced by allopregnanolone and depressed by dehydroepiandrosterone sulphate. These data demonstrate that the modulation of breathing via GABAAreceptor activation will be determined by the overall balance of negative and positive neurosteroid modulators within respiratory nuclei. This adds a level of complexity that must be considered when examining the depression of breathing in mammals associated with various behavioural states and pathogenic conditions such as apnoea and sudden death suspected to be associated with central respiratory dysfunction.
Developing a head for energy sensing: AMP‐activated protein kinase as a multifunctional metabolic sensor in the brain
Authors: Ramamurthy Santosh , Ronnett Gabriele V.
Published: May 2006

The 5′‐adenosine monophosphate‐activated protein kinase (AMPK) is a metabolic and stress sensor that has been functionally conserved throughout eukaryotic evolution. Activation of the AMPK system by various physiological or pathological stimuli that deplete cellular energy levels promotes activation of energy restorative processes and inhibits energy consumptive processes. AMPK has a prominent role not only as a peripheral sensor of energy balance, but also in the CNS as a multifunctional metabolic sensor. Recent work suggests that AMPK plays an important role in maintaining whole body energy balance by coordinating feeding behaviour through the hypothalamus in conjunction with peripheral energy expenditure. In addition, brain AMPK is activated by energy‐poor conditions induced by hypoxia, starvation, and ischaemic stroke. Under these conditions, AMPK is activated as a protective response in an attempt to restore cellular homeostasis. However in vivo, it appears that the overall consequence of activation of AMPK is more complex than previously imagined, in that over‐activation may be deleterious rather than neuroprotective. This review discusses recent findings that support the role of AMPK in brain as a multidimensional energy sensor and the consequences of its activation or inhibition under physiological and pathological states.
Ca2+–calmodulin‐dependent protein kinase expression and signalling in skeletal muscle during exercise
Authors: Rose Adam J. , Kiens Bente , Richter Erik A.
Published: May 2006

Ca2+ signalling is proposed to play an important role in skeletal muscle function during exercise. Here, we examined the expression of multifunctional Ca2+–calmodulin‐dependent protein kinases (CaMK) in human skeletal muscle and show that CaMKII and CaMKK, but not CaMKI or CaMKIV, are expressed. Furthermore, the effect of exercise duration and intensity on skeletal muscle CaMKII activity and phosphorylation of downstream targets was examined. Eight healthy men exercised at ∼67% of peak pulmonary O2 uptake with muscle samples taken at rest and after 1, 10, 30, 60 and 90 min of exercise. Ten other men exercised for three consecutive 10 min bouts at 35%, 60% and 85% with muscle samples taken at rest, at the end of each interval and 30 min post‐exercise. There was a rapid and transient increase in autonomous CaMKII activity and CaMKII phosphorylation at Thr287 in skeletal muscle during exercise. Furthermore, the phosphorylation of phospholamban (PLN) at Thr17, which was identified as a CaMKII substrate in skeletal muscle, was rapidly (< 1 min) increased by exercise, and remained phosphorylated 5‐fold above basal level during 90 min of exercise. The phosphorylation of serum response factor at Ser103, a putative CaMKII substrate, was higher after 30 min of exercise. PLN phosphorylation at Thr17 was higher with increasing exercise intensities. These data indicate that CaMKII is the major multifunctional CaMK in skeletal muscle and its activation occurs rapidly and is sustained during continuous exercise, with the activation being greater during intense exercise.
On the problem of (dis)charging a capacitor through a lamp
Authors: Ross Robert , Venugopal Prasad
Published: May 2006

The traditional analysis of RC circuits with constant resistance fails to adequately account for the charging characteristics of a capacitor in series with a lamp. We find that a simple model for the changing resistance of the lamp provides a good fit to the time-varying current in the circuit. This experiment can readily be performed in an introductory physics laboratory.
The magnetic dipole interaction as measured by spring dynamometers
Authors: Castañer Ramón , Medina José M. , Cuesta-Bolao María J.
Published: May 2006

We present a simple experiment to measure the magnetic dipole moment of a magnet using two identical magnets and spring dynamometers. The experiment illustrates the concept of a dipole field, as well as the interaction between two magnetic dipoles. The validity of the magnetic dipole approximation is discussed. The experiment also makes it possible to obtain the remanent magnetization of rare earth magnets.
Comment on "Evidence for Positive Epistasis in HIV-1"
Authors: Wang Kai , Mittler John E. , Samudrala Ram
Published: May 2006

Bonhoeffer
et al
. (Reports, 26 November 2004, p. 1547) presented evidence for positive epistasis in a clinical data set of HIV-1 mutants and corresponding fitness values. We demonstrate that biases in the original and simulated data sets may lead to erroneous evidence for epistasis. More rigorous statistical tests must be used to account for such biases before one can infer epistasis.
Response to Comment on "Evidence for Positive Epistasis in HIV-1"
Authors: Bonhoeffer Sebastian , Chappey Colombe , Parkin Neil T. , Whitcomb Jeannette M. , Petropoulos Christos J.
Published: May 2006

Wang
et al
. analyzed artificially biased data to show that our results can be explained by a bias against sequences with low fitness. We explicitly acknowledged this potential caveat in our original study. Showing that an artificially introduced bias can produce a spurious signal of positive epistasis does not demonstrate that such bias exists in our original data.
Impaired Control of IRES-Mediated Translation in X-Linked Dyskeratosis Congenita
Authors: Yoon Andrew , Peng Guang , Brandenburg Yves , Zollo Ornella , Xu Wei , Rego Eduardo , Ruggero Davide
Published: May 2006

The
DKC1
gene encodes a pseudouridine synthase that modifies ribosomal RNA (rRNA).
DKC1
is mutated in people with X-linked dyskeratosis congenita (X-DC), a disease characterized by bone marrow failure, skin abnormalities, and increased susceptibility to cancer. How alterations in ribosome modification might lead to cancer and other features of the disease remains unknown. Using an unbiased proteomics strategy, we discovered a specific defect in IRES (internal ribosome entry site)–dependent translation in

Dkc1
m

mice and in cells from X-DC patients. This defect results in impaired translation of messenger RNAs containing IRES elements, including those encoding the tumor suppressor p27(Kip1) and the antiapoptotic factors Bcl-xL and XIAP (X-linked Inhibitor of Apoptosis Protein). Moreover,

Dkc1
m

ribosomes were unable to direct translation from IRES elements present in viral messenger RNAs. These findings reveal a potential mechanism by which defective ribosome activity leads to disease and cancer.
Molecular Sorting by Electrical Steering of Microtubules in Kinesin-Coated Channels
Authors: van den Heuvel Martin G. L. , de Graaff Martijn P. , Dekker Cees
Published: May 2006

Integration of biomolecular motors in nanoengineered structures raises the intriguing possibility of manipulating materials on nanometer scales. We have managed to integrate kinesin motor proteins in closed submicron channels and to realize active electrical control of the direction of individual kinesin-propelled microtubule filaments at Y junctions. Using this technique, we demonstrate molecular sorting of differently labeled microtubules. We attribute the steering of microtubules to electric field–induced bending of the leading tip. From measurements of the orientation-dependent electrophoretic motion of individual, freely suspended microtubules, we estimate the net applied force on the tip to be in the picoNewton range and we infer an effective charge of 12 e
–
per tubulin dimer under physiological conditions.
Biomarker Evidence for a Major Preservation Pathway of Sedimentary Organic Carbon
Authors: Hebting Y. , Schaeffer P. , Behrens A. , Adam P. , Schmitt G. , Schneckenburger P. , Bernasconi S. M. , Albrecht P.
Published: May 2006

Hydrogenation processes leading from biomolecules to fossil biomarkers in anoxic sediments are crucial for the preservation of organic matter. However, these processes are still poorly understood. The present identification of several reduced carotenoids in recent sediments attests that these processes operate at the earliest stages of diagenesis without structural or stereochemical specificity, implying a nonbiological reduction pathway. Sulfur species (e.g., H
2
S) are the hydrogen donors involved in such reduction, as demonstrated with laboratory experiments. These reactions allow the preservation of abundant organic carbon in the rock record.
Effect of Apolipoprotein E on the Cerebral Load of Latent Herpes Simplex Virus Type 1 DNA
Authors: Burgos Javier S. , Ramirez Carlos , Sastre Isabel , Valdivieso Fernando
Published: May 2006

Herpes simplex virus type 1 (HSV-1) is neurotropic and enters a latent state lasting the lifetime of the host. This pathogen has recently been proposed as a risk factor for Alzheimer's disease (AD) in conjunction with apolipoprotein E4 (ApoE4). In a murine acute infection model, we showed that viral neuroinvasiveness depends directly on the overall ApoE dosage and especially on the presence of isoform ApoE4. If an interaction between ApoE and HSV-1 is involved in AD, it may occur during latency rather than during acute infection. Certainly, ApoE plays an important role in late-onset AD, i.e., at a time in life when the majority of people harbor HSV-1 in their nervous system. In the present work, wild-type, APOE knockout, APOE3, and APOE4 transgenic mice were used to analyze the influence of the ApoE profile on the levels of latent virus DNA. The knockout mice had significantly lower concentrations of the virus in the nervous system than the wild-type mice, while the APOE4 mice had very high levels in the brain compared to the APOE3 animals. ApoE4 seems to facilitate HSV-1 latency in the brain much more so than ApoE3. The APOE dosage correlated directly with the HSV-1 DNA concentration in the brain, strengthening the hypothesis that HSV-1, together with ApoE, might be involved in AD.
Evidence for Potent Autologous Neutralizing Antibody Titers and Compact Envelopes in Early Infection with Subtype C Human Immunodeficiency Virus Type 1
Authors: Li Bing , Decker Julie M. , Johnson Roy W. , Bibollet-Ruche Frederic , Wei Xiping , Mulenga Joseph , Allen Susan , Hunter Eric , Hahn Beatrice H. , Shaw George M. , Blackwell Jerry L. , Derdeyn Cynthia A.
Published: May 2006

Information about neutralizing antibody responses in subtype C-infected individuals is limited, even though this viral subtype causes the majority of AIDS cases worldwide. Here we compared the course and magnitude of the autologous neutralizing antibody (NAb) response against viral envelope (Env) glycoproteins present during acute and early infection with subtypes B and C human immunodeficiency virus type 1 (HIV-1). NAb responses were evaluated in 6 subtype B-infected and 11 subtype C-infected subjects over a mean evaluation period of 25 months using a pseudovirus reporter gene assay. All subjects in the C cohort were infected through heterosexual contact, while five of the six subjects in the B cohort were infected via male-to-male contact. The kinetics and magnitude of the NAb responses varied among subjects in the B and C cohorts; however, the median 50% inhibitory concentration (IC
50
titer) reached by antibody in the plasma of subtype C-infected subjects, overall, was 3.5-fold higher than in the subtype B-infected subjects (
P
= 0.06). The higher titers of NAbs in the C cohort were associated with viruses having significantly shorter amino acid length (
P
= 0.002) in the V1 to V4 region of the surface Env glycoprotein, gp120, compared to the B cohort. Despite the potency of the autologous subtype C NAb response, it was not directed against cross-neutralizing epitopes. These data demonstrate that subtype C Envs elicit a potent yet restricted NAb response early in infection that frequently reaches IC
50
titers in excess of 1:1,000 and suggest that clade-specific differences may exist in Env immunogenicity or susceptibility to neutralization.
Molecular Determinants of Substrate Specificity for Semliki Forest Virus Nonstructural Protease
Authors: Lulla Aleksei , Lulla Valeria , Tints Kairit , Ahola Tero , Merits Andres
Published: May 2006

The C-terminal cysteine protease domain of Semliki Forest virus nonstructural protein 2 (nsP2) regulates the virus life cycle by sequentially cleaving at three specific sites within the virus-encoded replicase polyprotein P1234. The site between nsP3 and nsP4 (the 3/4 site) is cleaved most efficiently. Analysis of Semliki Forest virus-specific cleavage sites with shuffled N-terminal and C-terminal half-sites showed that the main determinants of cleavage efficiency are located in the region preceding the cleavage site. Random mutagenesis analysis revealed that amino acid residues in positions P4, P3, P2, and P1 of the 3/4 cleavage site cannot tolerate much variation, whereas in the P5 position most residues were permitted. When mutations affecting cleavage efficiency were introduced into the 2/3 and 3/4 cleavage sites, the resulting viruses remained viable but had similar defects in P1234 processing as observed in the in vitro assay. Complete blockage of the 3/4 cleavage was found to be lethal. The amino acid in position P1′ had a significant effect on cleavage efficiency, and in this regard the protease markedly preferred a glycine residue over the tyrosine natively present in the 3/4 site. Therefore, the cleavage sites represent a compromise between protease recognition and other requirements of the virus life cycle. The protease recognizes at least residues P4 to P1′, and the P4 arginine residue plays an important role in the fast cleavage of the 3/4 site.
Lepidopteran Ortholog of
Drosophila
Breathless Is a Receptor for the Baculovirus Fibroblast Growth Factor
Authors: Katsuma Susumu , Daimon Takaaki , Mita Kazuei , Shimada Toru
Published: May 2006

The
Bombyx mori
nucleopolyhedrovirus (BmNPV) encodes a gene homologous to the mammalian fibroblast growth factor (FGF) family. We report the cloning of
B. mori
and
Spodoptera frugiperda
orthologous genes (
Bmbtl
and
Sfbtl
, respectively) of
Drosophila melanogaster breathless
(
btl
) encoding a receptor for Branchless/FGF and show that these genes encode the receptor for a baculovirus-encoded FGF (vFGF). Sequence analysis showed that BmBtl is composed of 856 amino acid residues, which potentially encodes a 97.3-kDa polypeptide and shares structural features and sequence similarities with the FGF receptor family. Reverse transcription-PCR experiments showed that
Bmbtl
was abundantly expressed in the trachea and midgut in
B. mori
larvae, with moderate expression observed in the hemocytes and the
B. mori
cultured cell line BmN. We generated Sf-9 cells that stably expressed His-tagged BmBtl. Western blot analysis revealed that BmBtl was an ∼110-kDa protein. Immunoprecipitation experiments showed that BmNPV vFGF markedly phosphorylated BmBtl in Sf-9 cells. In addition, we found that BmBtl overexpression enhanced the migration activity for BmNPV vFGF. Furthermore, we generated Sf-9 cells in which
Sfbtl
was knocked down by transfection with double-strand RNA-expressing plasmids. In these cells, cell motility triggered by vFGF was markedly reduced. These results strongly suggest that the Btl orthologs, BmBtl and SfBtl, are the receptors for vFGF, which mediate vFGF-induced host cell chemotaxis.
Gamma Interferon Plays a Crucial Early Antiviral Role in Protection against West Nile Virus Infection
Authors: Shrestha Bimmi , Wang Tian , Samuel Melanie A. , Whitby Kevin , Craft Joe , Fikrig Erol , Diamond Michael S.
Published: May 2006

West Nile virus (WNV) causes a severe central nervous system (CNS) infection in humans, primarily in the elderly and immunocompromised. Prior studies have established an essential protective role of several innate immune response elements, including alpha/beta interferon (IFN-α/β), immunoglobulin M, γδ T cells, and complement against WNV infection. In this study, we demonstrate that a lack of IFN-γ production or signaling results in increased vulnerability to lethal WNV infection by a subcutaneous route in mice, with a rise in mortality from 30% (wild-type mice) to 90% (IFN-γ
−/−
or IFN-γR
−/−
mice) and a decrease in the average survival time. This survival pattern in IFN-γ
−/−
and IFN-γR
−/−
mice correlated with higher viremia and greater viral replication in lymphoid tissues. The increase in peripheral infection led to early CNS seeding since infectious WNV was detected several days earlier in the brains and spinal cords of IFN-γ
−/−
or IFN-γR
−/−
mice. Bone marrow reconstitution experiments showed that γδ T cells require IFN-γ to limit dissemination by WNV. Moreover, treatment of primary dendritic cells with IFN-γ reduced WNV production by 130-fold. Collectively, our experiments suggest that the dominant protective role of IFN-γ against WNV is antiviral in nature, occurs in peripheral lymphoid tissues, and prevents viral dissemination to the CNS.
Modulation of Kaposi's Sarcoma-Associated Herpesvirus Infection and Replication by MEK/ERK, JNK, and p38 Multiple Mitogen-Activated Protein Kinase Pathways during Primary Infection
Authors: Pan Hongyi , Xie Jianping , Ye Fengchun , Gao Shou-Jiang
Published: May 2006

Kaposi's sarcoma-associated herpesvirus (KSHV) is etiologically associated with Kaposi's sarcoma, a dominant AIDS-related tumor of endothelial cells, and several other lymphoproliferative malignancies. While activation of the phosphatidylinositol 3-kinase-protein kinase C-MEK-ERK pathway is essential for KSHV infection, we have recently shown that KSHV also activates JNK and p38 mitogen-activated protein kinase (MAPK) pathways during primary infection (J. Xie, H. Y. Pan, S. Yoo, and S.-J. Gao, J. Virol. 79:15027-15037, 2005). Here, we found that activation of both JNK and p38 pathways was also essential for KSHV infection. Inhibitors of all three MAPK pathways reduced KSHV infectivity in both human umbilical vein endothelial cells (HUVEC) and 293 cells. These inhibitory effects were dose dependent and occurred at the virus entry stage of infection. Consistently, inhibition of all three MAPK pathways with dominant-negative constructs reduced KSHV infectivity whereas activation of the ERK pathway but not the JNK and p38 pathways enhanced KSHV infectivity. Importantly, inhibition of all three MAPK pathways also reduced the yield of infectious virions during KSHV productive infection of HUVEC. While the reduction of infectious virions was in part due to the reduced infectivity, it was also the result of direct modulation of KSHV lytic replication by the MAPK pathways. Accordingly, KSHV upregulated the expression of RTA (Orf50), a master transactivator of KSHV lytic replication, and activated its promoter during primary infection. Furthermore, KSHV activation of RTA promoter during primary infection was modulated by all three MAPK pathways, predominantly through their downstream target AP-1. Together, these results indicate that, by modulating multiple MAPK pathways, KSHV manipulates the host cells to facilitate its entry into the cells and postentry productive lytic replication during primary infection.
Lipid-Mediated Introduction of Hepatitis B Virus Capsids into Nonsusceptible Cells Allows Highly Efficient Replication and Facilitates the Study of Early Infection Events
Authors: Rabe Birgit , Glebe Dieter , Kann Michael
Published: May 2006

The hepatitis B virus (HBV) is an enveloped DNA virus which is highly infectious in vivo. In vitro, only primary hepatocytes of humans andTupaia belangerior the novel HepaRG cell line are susceptible to HBV, but infection is inefficient and study of early infection events in single cells is unsatisfactory. Since hepatoma cells replicate the virus efficiently after transfection, this limited infection efficiency must be related to the initial entry phase. Here, we describe the lipid-based delivery of HBV capsids into nonsusceptible cells, circumventing the natural entry pathway. Successful infection was monitored by observing the emergence of the nuclear viral covalently closed circular DNA and the production of progeny virus and subviral particles. Lipid-mediated transfer initiated productive infection that was at least 100-fold more effective than infection of permissive cell cultures. High-dose capsid transfer showed that the uptake was not receptor limited and allowed the intracellular transport of capsids and genomes to be examined microscopically. The addition of inhibitors confirmed an entry pathway by fusion of the lipid with the plasma membrane. By indirect immune fluorescence and native fluorescence in situ hybridization, we followed the pathway of capsids and viral genomes in individual cells. We observed an active microtubule-dependent capsid transfer to the nucleus and a subsequent release of the viral genomes exclusively into the karyoplasm. Lipid-mediated transfer of viral capsids thus appears to allow efficient introduction of genetic information into target cells, facilitating studies of early infection events which are otherwise impeded by the small number of viruses entering the cell.
Ebola Virus VP24 Binds Karyopherin α1 and Blocks STAT1 Nuclear Accumulation
Authors: Reid St. Patrick , Leung Lawrence W. , Hartman Amy L. , Martinez Osvaldo , Shaw Megan L. , Carbonnelle Caroline , Volchkov Viktor E. , Nichol Stuart T. , Basler Christopher F.
Published: May 2006

Ebola virus (EBOV) infection blocks cellular production of alpha/beta interferon (IFN-α/β) and the ability of cells to respond to IFN-α/β or IFN-γ. The EBOV VP35 protein has previously been identified as an EBOV-encoded inhibitor of IFN-α/β production. However, the mechanism by which EBOV infection inhibits responses to IFNs has not previously been defined. Here we demonstrate that the EBOV VP24 protein functions as an inhibitor of IFN-α/β and IFN-γ signaling. Expression of VP24 results in an inhibition of IFN-induced gene expression and an inability of IFNs to induce an antiviral state. The VP24-mediated inhibition of cellular responses to IFNs correlates with the impaired nuclear accumulation of tyrosine-phosphorylated STAT1 (PY-STAT1), a key step in both IFN-α/β and IFN-γ signaling. Consistent with this proposed function for VP24, infection of cells with EBOV also confers a block to the IFN-induced nuclear accumulation of PY-STAT1. Further, VP24 is found to specifically interact with karyopherin α1, the nuclear localization signal receptor for PY-STAT1, but not with karyopherin α2, α3, or α4. Overexpression of VP24 results in a loss of karyopherin α1-PY-STAT1 interaction, indicating that the VP24-karyopherin α1 interaction contributes to the block to IFN signaling. These data suggest that VP24 is likely to be an important virulence determinant that allows EBOV to evade the antiviral effects of IFNs.
Group B Coxsackievirus Diabetogenic Phenotype Correlates with Replication Efficiency
Authors: Kanno Toru , Kim Kisoon , Kono Ken , Drescher Kristen M. , Chapman Nora M. , Tracy Steven
Published: May 2006

Group B coxsackieviruses can initiate rapid onset type 1 diabetes (T1D) in old nonobese diabetic (NOD) mice. Inoculating high doses of poorly pathogenic CVB3/GA per mouse initiated rapid onset T1D. Viral protein was detectable in islets shortly after inoculation in association with beta cells as well as other primary islet cell types. The virulent strain CVB3/28 replicated to higher titers more rapidly than CVB3/GA in the pancreas and in established beta cell cultures. Exchange of 5′-nontranslated regions between the two CVB3 strains demonstrated a variable impact on replication in beta cell cultures and suppression of in vivo replication for both strains. While any CVB strain may be able to induce T1D in prediabetic NOD mice, T1D onset is linked both to the viral replication rate and infectious dose.
Measles Virus V Protein Inhibits p53 Family Member p73
Authors: Cruz Cristian D. , Palosaari Heidi , Parisien Jean-Patrick , Devaux Patricia , Cattaneo Roberto , Ouchi Toru , Horvath Curt M.
Published: May 2006

Paramyxovirus V proteins function as host interference factors that inactivate antiviral responses, including interferon. Characterization of cellular proteins that copurify with ectopically expressed measles virus V protein has revealed interactions with DNA binding domains of p53 family proteins, p53 and p73. Specific transcriptional assays reveal that expression of measles virus V cDNA inhibits p73, but not p53. Expression of measles virus V cDNA can delay cell death induced by genotoxic stress and also can decrease the abundance of the proapoptotic factor PUMA, a p73 target. Recombinant measles virus with an engineered deficiency in V protein is capable of inducing more severe cytopathic effects than the wild type, implicating measles virus V protein as an inhibitor of cell death. These findings also suggest that p73-PUMA signaling may be a previously unrecognized arm of cellular innate antiviral immunity.
Differentially Regulated Interferon Response Determines the Outcome of Newcastle Disease Virus Infection in Normal and Tumor Cell Lines
Authors: Krishnamurthy Sateesh , Takimoto Toru , Scroggs Ruth Ann , Portner Allen
Published: May 2006

Newcastle disease virus (NDV) is a negative-strand RNA virus with oncolytic activity against human tumors. Its effectiveness against tumors and safety in normal tissue have been demonstrated in several clinical studies. Here we show that the spread of NDV infection is drastically different in normal cell lines than in tumor cell lines and that the two cell types respond differently to beta interferon (IFN-β) treatment. NDV rapidly replicated and killed HT-1080 human fibrosarcoma cells but spread poorly in CCD-1122Sk human skin fibroblast cells. Pretreatment with endogenous or exogenous IFN-β completely inhibited NDV replication in normal cells but had little or no effect in tumor cells. Thus, the outcome of NDV infection appeared to depend on the response of uninfected cells to IFN-β. To investigate their differences in IFN responsiveness, we analyzed and compared the expression and activation of components of the IFN signal transduction pathway in these two types of cells. The levels of phosphorylated STAT1 and STAT2 and that of the ISGF3 complex were markedly reduced in IFN-β-treated tumor cells. Moreover, cDNA microarray analysis revealed significantly fewer IFN-regulated genes in the HT-1080 cells than in the CDD-1122Sk cells. This finding suggests that tumor cells demonstrate a less-than-optimum antiviral response because of a lesion in their IFN signal transduction pathway. The rapid spread of NDV in HT-1080 cells appears to be caused by their deficient expression of anti-NDV proteins upon exposure to IFN-β.
Epstein-Barr Virus Protein Kinase BGLF4 Is a Virion Tegument Protein That Dissociates from Virions in a Phosphorylation-Dependent Process and Phosphorylates the Viral Immediate-Early Protein BZLF1
Authors: Asai Risa , Kato Ai , Kato Kentaro , Kanamori-Koyama Mikiko , Sugimoto Ken , Sairenji Takeshi , Nishiyama Yukihiro , Kawaguchi Yasushi
Published: May 2006

Epstein-Barr virus (EBV) BGLF4 is a viral protein kinase that is expressed in the lytic phase of infection and is packaged in virions. We report here that BGLF4 is a tegument protein that dissociates from the virion in a phosphorylation-dependent process. We also present evidence that BGLF4 interacts with and phosphorylates BZLF1, a key viral regulator of lytic infection. These conclusions are based on the following observations. (i) In in vitro tegument release assays, a significant fraction of BGLF4 was released from virions in the presence of physiological NaCl concentrations. (ii) Addition of physiological concentrations of ATP and MgCl
2
to virions enhanced BGLF4 release, but phosphatase treatment of virions significantly reduced BGLF4 release. (iii) A recombinant protein containing a domain of BZLF1 was specifically phosphorylated by purified recombinant BGLF4 in vitro, and BGLF4 altered BZLF1 posttranslational modification in vivo. (iv) BZLF1 was specifically coimmunoprecipitated with BGLF4 in 12-
O
-tetradecanoylphorbol-13-acetate-treated B95-8 cells and in COS-1 cells transiently expressing both of these viral proteins. (v) BGLF4 and BZLF1 were colocalized in intranuclear globular structures, resembling the viral replication compartment, in Akata cells treated with anti-human immunoglobulin G. Our results suggest that BGLF4 functions not only in lytically infected cells by phosphorylating viral and cellular targets but also immediately after viral penetration like other herpesvirus tegument proteins.
Expression Profiles of Bovine Adeno-Associated Virus and Avian Adeno-Associated Virus Display Significant Similarity to That of Adeno-Associated Virus Type 5
Authors: Qiu Jianming , Cheng Fang , Pintel David J.
Published: May 2006

We present the first detailed expression profiles of nonprimate-derived adeno-associated viruses, namely, bovine adeno-associated virus (B-AAV) and avian adeno-associated virus (A-AAV), which were obtained after the infection of cell lines derived from their natural hosts. In general, the profiles of B-AAV and A-AAV were quite similar to that of AAV5; however, both exhibited features found for AAV2 as well. Like adeno-associated virus type 5 (AAV5), B-AAV and A-AAV utilized an internal polyadenylation site [(pA)p]; however, it was used to greater relative levels by B-AAV than by A-AAV. Similar to AAV5, >99% of B-AAV RNAs generated from upstream promoters were polyadenylated at (pA)p and hence not spliced. In contrast, ca. 50% of the A-AAV RNAs generated from upstream promoters read through (pA)p, as seen for AAV2. However, A-AAV generated lower levels of spliced P5 and P19 products than does AAV2, suggesting that A-AAV generates lower relative levels of Rep 68 and Rep 40. An additional difference in the expression profile of these viruses was that B-AAV generated a greater level of ITR-initiated RNAs than did A-AAV or AAV5. In addition, we demonstrate that, like AAV2, transactivation of transcription of the capsid-gene promoter of B-AAV required both adenovirus and targeting of its Rep protein to the transcription template; however, expression of the capsid-gene promoter of A-AAV was, like AAV5, largely independent of both adenovirus and its Rep proteins.
Expressed sequence tag analysis in tef (Eragrostis tef(Zucc) Trotter)
Authors: Yu Ju-Kyung , Sun Qi , Rota Mauricio La , Edwards Hugh , Tefera Hailu , Sorrells Mark E
Published: May 2006

Tef (Eragrostis tef (Zucc.) Trotter) is the most important cereal crop in Ethiopia; however, there is very little DNA sequence information available for this species. Expressed sequence tags (ESTs) were generated from 4 cDNA libraries: seedling leaf, seedling root, and inflorescence of E. tef and seedling leaf of Eragrostis pilosa, a wild relative of E. tef. Clustering of 3603 sequences produced 530 clusters and 1890 singletons, resulting in 2420 tef unigenes. Ap prox imately 3/4 of tef unigenes matched protein or nucleotide sequences in public databases. Annotation of unigenes associated 68% of the putative tef genes with gene ontology categories. Identification of the translated unigenes for conserved protein domains revealed 389 protein family domains (Pfam), the most frequent of which was protein kinase. A total of 170 ESTs containing simple sequence repeats (EST-SSRs) were identified and 80 EST-SSR markers were developed. In addition, 19 single-nucleotide polymorphism (SNP) and (or) insertion–deletion (indel) and 34 intron frag ment length polymorphism (IFLP) markers were developed. The EST database and molecular markers generated in this study will be valuable resources for further tef genetic research.Key words: tef, Ethiopian cereal crop, EST, molecular markers.
Potential pitfalls in the quantitative molecular detection ofEscherichia coliO157:H7 in environmental matrices
Authors: Artz Rebekka R.E , Avery Lisa M , Jones Davey L , Killham Ken
Published: May 2006

The detection sensitivity and potential interference factors of a commonly used assay based on real-time polymerase chain reaction (PCR) for Escherichia coli O157:H7 using eae gene-specific primers were assessed. Animal wastes and soil samples were spiked with known replicate quantities of a nontoxigenic strain of E. coli O157:H7 in a viable or dead state and as unprotected DNA. The detection sensitivity and accuracy of real-time PCR for E. coli O157:H7 in animal wastes and soil is low compared to enrichment culturing. Nonviable cells and unprotected DNA were shown to produce positive results in several of the environmental samples tested, leading to potential overestimates of cell numbers due to prolonged detection of nonviable cells. This demonstrates the necessity for the specific calibration of real-time PCR assays in environmental samples. The accuracy of the eae gene–based detection method was further evaluated over time in a soil system against an activity measurement, using the bioluminescent properties of an E. coli O157:H7 Tn5luxCDABE construct. The detection of significant numbers of viable but nonculturable (VBNC) as well as nonviable and possibly physically protected cells as shown over a period of 90 days further complicates the use of real-time PCR assays for quick diagnostics in environmental samples and infers that enrichment culturing is still required for the final verification of samples found positive by real-time PCR methods.Key words: Escherichia coli O157:H7, real-time PCR, animal waste, soil, VBNC.
The effect of broadleaved woodland on Chalk groundwater resources
Authors: Roberts J. , Rosier P.
Published: May 2006

The impact of broadleaved woodland on chalk groundwater resources, in Hampshire, UK, was assessed with a comparative study of beech woodland at Black Wood near Micheldever and grass at Bridgets Farm near Winchester. At both sites, parallel estimates of evaporation and detailed studies of the changes in soil water content and the direction of water movement were made.

Beneath both sites, a reduction in soil water content was observed during the summer to a depth of 6 m. However, total water potential measurements showed that upward movement of water was only occurring in the upper 2 m of the profile, whilst drainage was occurring below this point. Drainage continued even when soil moisture deficits existed in the upper part of the profile. Seasonal differences between woodland and grass do exist, however annual differences in evaporation and drainage are insignificant.

The similarity of evaporation from and drainage below the broadleaved woodland and grass sites contrasts markedly with several other studies that show greater drying below woodland. Unlike other comparisons, this study was made within a large block of woodland and both sites were on chalk. The relevance of woodland size and chalk substrate are discussed.
Selection of potential reactive materials for a permeable reactive barrier for remediating acidic groundwater in acid sulphate soil terrains
Authors: Golab A.N. , Peterson M.A. , Indraratna B.
Published: May 2006

A permeable reactive barrier is being designed to remediate leachate from acid sulphate soils. The current research relates to testing of alkaline materials for use in the barrier, with an emphasis on waste materials. Thirteen alkaline materials including recycled concrete, limestone, calcite-bearing zeolitic breccia, blast furnace slag, lime and fly ash were tested. The batch tests involved several phases, such as leaching in deionized water to characterize the soluble components of the materials and the pH that each material could achieve. Another phase involved testing with acidic water (pH 3) to determine the acid leachable components of the materials and the pH after neutralization. The pH achieved by each reactive material was controlled by the reaction kinetics of the dominant alkaline mineral. The concretes, fly ash, and air-cooled blast furnace slag (ACBFS) all achieved a pH that is consistent with the dissolution of lime (pH 11 to 12). The limestone and zeolitic breccias all achieved a pH consistent with the dissolution of calcite (pH
c
. 7.4). Based on the results of the batch tests, a short-list of materials was selected that included a recycled concrete, ACBFS, three zeolitic breccias and limestone. The short-listed materials were examined for exhaustion of neutralizing ability by repeatedly replacing the acidic water and monitoring the resultant pH. The precipitates that formed during this process were analysed to characterize the chemical reactions that occurred during the tests. Based on the results, the recycled concrete was selected for testing in columns that will simulate flow conditions through the barrier.