bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome: Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes
Authors: Dresang Lindsay R. , Vereide David T. , Sugden Bill 
Published: January 2009

ABSTRACT
We identified binding sites for Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) in the human genome using chromatin immunoprecipitation and microarrays. The sequences for these newly identified sites were used to generate a position-weighted matrix (PWM) for EBNA1's DNA-binding sites. This PWM helped identify additional DNA-binding sites for EBNA1 in the genomes of EBV, Kaposi's sarcoma-associated herpesvirus, and cercopithecine herpesvirus 15 (CeHV-15) (also called herpesvirus papio 15). In particular, a homologue of the Rep* locus in EBV was predicted in the genome of CeHV-15, which is notable because Rep* of EBV was not predicted by the previously developed consensus sequence for EBNA1's binding DNA. The Rep* of CeHV-15 functions as an origin of DNA synthesis in the EBV-positive cell line Raji; this finding thus builds on a set of DNA-binding sites for EBNA1 predicted in silico.
Inhibition of the Ubiquitin-Proteasome System Prevents Vaccinia Virus DNA Replication and Expression of Intermediate and Late Genes
Authors: Satheshkumar P. S. , Anton Luis C. , Sanz Patrick , Moss Bernard 
Published: January 2009

ABSTRACTThe ubiquitin-proteasome system has a central role in the degradation of intracellular proteins and regulates a variety of functions. Viruses belonging to several different families utilize or modulate the system for their advantage. Here we showed that the proteasome inhibitors MG132 and epoxomicin blocked a postentry step in vaccinia virus (VACV) replication. When proteasome inhibitors were added after virus attachment, early gene expression was prolonged and the expression of intermediate and late genes was almost undetectable. By varying the time of the removal and addition of MG132, the adverse effect of the proteasome inhibitors was narrowly focused on events occurring 2 to 4 h after infection, the time of the onset of viral DNA synthesis. Further analyses confirmed that genome replication was inhibited by both MG132 and epoxomicin, which would account for the effect on intermediate and late gene expression. The virus-induced replication of a transfected plasmid was also inhibited, indicating that the block was not at the step of viral DNA uncoating. UBEI-41, an inhibitor of the ubiquitin-activating enzyme E1, also prevented late gene expression, supporting the role of the ubiquitin-proteasome system in VACV replication. Neither the overexpression of ubiquitin nor the addition of an autophagy inhibitor was able to counter the inhibitory effects of MG132. Further studies of the role of the ubiquitin-proteasome system for VACV replication may provide new insights into virus-host interactions and suggest potential antipoxviral drugs.
Herpes Simplex Virus UL12.5 Targets Mitochondria through a Mitochondrial Localization Sequence Proximal to the N Terminus
Authors: Corcoran Jennifer A. , Saffran Holly A. , Duguay Brett A. , Smiley James R. 
Published: January 2009

ABSTRACT

The herpes simplex virus type 1 (HSV-1) gene
UL12
encodes a conserved alkaline DNase with orthologues in all herpesviruses. The HSV-1 UL12 gene gives rise to two separately promoted 3′ coterminal mRNAs which encode distinct but related proteins: full-length UL12 and UL12.5, an amino-terminally truncated form that initiates at UL12 codon 127. Full-length UL12 localizes to the nucleus where it promotes the generation of mature viral genomes from larger precursors. In contrast, UL12.5 is predominantly mitochondrial and acts to trigger degradation of the mitochondrial genome early during infection. We examined the basis for these very different subcellular localization patterns. We confirmed an earlier report that the amino-terminal region of full-length UL12 is required for nuclear localization and provide evidence that multiple nuclear localization determinants are present in this region. In addition, we demonstrate that mitochondrial localization of UL12.5 relies largely on sequences located between UL12 residues 185 and 245 (UL12.5 residues 59 to 119). This region contains a sequence that resembles a typical mitochondrial matrix localization signal, and mutations that reduce the positive charge of this element severely impaired mitochondrial localization. Consistent with matrix localization, UL12.5 displayed a detergent extraction profile indistinguishable from that of the matrix protein cyclophilin D. Mitochondrial DNA depletion required the exonuclease activity of UL12.5, consistent with the idea that UL12.5 located within the matrix acts directly to destroy the mitochondrial genome. These results clarify how two highly related viral proteins are targeted to different subcellular locations with distinct functional consequences.
Evolution of the Sabin Vaccine into Pathogenic Derivatives without Appreciable Changes in Antigenic Properties: Need for Improvement of Current Poliovirus Surveillance
Authors: Yakovenko Maria L. , Korotkova Ekaterina A. , Ivanova Olga E. , Eremeeva Tatyana P. , Samoilovich Elena , Uhova Iryna , Gavrilin Gene V. , Agol Vadim I. 
Published: January 2009

ABSTRACT
The Sabin oral polio vaccine (OPV) may evolve into pathogenic viruses, causing sporadic cases and outbreaks of poliomyelitis. Such vaccine-derived polioviruses (VDPV) generally exhibit altered antigenicity. The current paradigm to distinguish VDPV from OPV and wild polioviruses is to characterize primarily those poliovirus isolates that demonstrate deviations from OPV in antigenic and genetic intratypic differentiation (ITD) tests. Here we report on two independent cases of poliomyelitis caused by VDPVs with “Sabin-like” properties in several ITD assays. The results suggest the existence of diverse pathways of OPV evolution and necessitate improvement of poliovirus surveillance, which currently potentially misses this class of VDPV.
Comparisons of CD8+T Cells Specific for Human Immunodeficiency Virus, Hepatitis C Virus, and Cytomegalovirus Reveal Differences in Frequency, Immunodominance, Phenotype, and Interleukin-2 Responsiveness
Authors: Jagannathan Prasanna , Osborne Christine M. , Royce Cassandra , Manion Maura M. , Tilton John C. , Li Li , Fischer Steven , Hallahan Claire W. , Metcalf Julia A. , McLaughlin Mary , Pipeling Matthew , McDyer John F. , Manley Thomas J. , Meier Jeffery L. , Altman John D. , Hertel Laura , Davey Richard T. , Connors Mark , Migueles Stephen A. 
Published: January 2009

ABSTRACTTo better understand the components of an effective immune response to human immunodeficiency virus (HIV), the CD8+T-cell responses to HIV, hepatitis C virus (HCV), and cytomegalovirus (CMV) were compared with regard to frequency, immunodominance, phenotype, and interleukin-2 (IL-2) responsiveness. Responses were examined in rare patients exhibiting durable immune-mediated control over HIV, termed long-term nonprogressors (LTNP) or elite controllers, and patients with progressive HIV infection (progressors). The magnitude of the virus-specific CD8+T-cell response targeting HIV, CMV, and HCV was not significantly different between LTNP and progressors, even though their capacity to proliferate to HIV antigens was preserved only in LTNP. In contrast to HIV-specific CD8+T-cell responses of LTNP, HLA B5701-restricted responses within CMV pp65 were rare and did not dominate the total CMV-specific response. Virus-specific CD8+T cells were predominantly CD27+45RO+for HIV and CD27−45RA+for CMV; however, these phenotypes were highly variable and heavily influenced by the degree of viremia. Although IL-2 induced significant expansions of CMV-specific CD8+T cells in LTNP and progressors by increasing both the numbers of cells entering the proliferating pool and the number of divisions, the proliferative capacity of a significant proportion of HIV-specific CD8+T cells was not restored with exogenous IL-2. These results suggest that immunodominance by HLA B5701-restricted cells is specific to HIV infection in LTNP and is not a feature of responses to other chronic viral infections. They also suggest that poor responsiveness to IL-2 is a property of HIV-specific CD8+T cells of progressors that is not shared with responses to other viruses over which immunologic control is maintained.
Determinants Flanking the CD4 Binding Loop Modulate Macrophage Tropism of Human Immunodeficiency Virus Type 1 R5 Envelopes
Authors: Duenas-Decamp Maria José , Peters Paul J. , Burton Dennis , Clapham Paul R. 
Published: January 2009

ABSTRACTHuman immunodeficiency virus type 1 R5 viruses vary extensively in phenotype. Thus, R5 envelopes (env) in the brain tissue of individuals with neurological complications are frequently highly macrophage-tropic. Macrophage tropism correlates with the capacity of the envelope to exploit low CD4 levels for infection. In addition, the presence of an asparagine at residue 283 within the CD4 binding site has been associated with brain-derived envelopes, increased env-CD4 affinity, and enhanced macrophage tropism. Here, we identify additional envelope determinants of R5 macrophage tropism. We compared highly macrophage-tropic (B33) and non-macrophage-tropic (LN40) envelopes from brain and lymph node specimens of one individual. We first examined the role of residue 283 in macrophage tropism. Introduction of N283 into LN40 (T283N) conferred efficient macrophage infectivity. In contrast, substitution of N283 for the more conserved threonine in B33 had little effect on macrophage infection. Thus, B33 carried determinants for macrophage tropism that were independent of N283. We prepared chimeric B33/LN40 envelopes and used site-directed mutagenesis to identify additional determinants. The determinants of macrophage tropism that were identified included residues on the CD4 binding loop flanks that were proximal to CD4 contact residues and residues in the V3 loop. The same residues affected sensitivity to CD4-immunoglobulin G inhibition, consistent with an altered env-CD4 affinity. We predict that these determinants alter exposure of CD4 contact residues. Moreover, the CD4 binding loop flanks are variable and may contribute to a general mechanism for protecting proximal CD4 contact residues from neutralizing antibodies. Our results have relevance for env-based vaccines that will need to expose critical CD4 contact residues to the immune system.
Abrogation of the Postmitotic Checkpoint Contributes to Polyploidization in Human Papillomavirus E7-Expressing Cells
Authors: Heilman Susan A. , Nordberg Joshua J. , Liu Yingwang , Sluder Greenfield , Chen Jason J. 
Published: January 2009

ABSTRACT
High-risk types of human papillomavirus (HPV) are considered the major causative agents of cervical carcinoma. The transforming ability of HPV resides in the E6 and E7 oncogenes, yet the pathway to transformation is not well understood. Cells expressing the oncogene E7 from high-risk HPVs have a high incidence of polyploidy, which has been shown to occur as an early event in cervical carcinogenesis and predisposes the cells to aneuploidy. The mechanism through which E7 contributes to polyploidy is not known. It has been hypothesized that E7 induces polyploidy in response to mitotic stress by abrogating the mitotic spindle assembly checkpoint. It was also proposed that E7 may stimulate rereplication to induce polyploidy. We have tested these hypotheses by using human epithelial cells in which E7 expression induces a significant amount of polyploidy. We find that E7-expressing cells undergo normal mitoses with an intact spindle assembly checkpoint and that they are able to complete cytokinesis. Our results also exclude DNA rereplication as a major mechanism of polyploidization in E7-expressing cells upon microtubule disruption. Instead, we have shown that while normal cells arrest at the postmitotic checkpoint after adaptation to the spindle assembly checkpoint, E7-expressing cells replicate their DNA and propagate as polyploid cells. Thus, abrogation of the postmitotic checkpoint leads to polyploidy formation in E7-expressing human epithelial cells. Our results suggest that downregulation of pRb is important for E7 to induce polyploidy and abrogation of the postmitotic checkpoint.
Differentially Stimulated CD4+T Cells Display Altered Human Immunodeficiency Virus Infection Kinetics: Implications for the Efficacy of Antiviral Agents
Authors: Vatakis Dimitrios N. , Nixon Christopher C. , Bristol Gregory , Zack Jerome A. 
Published: January 2009

ABSTRACTThe activation state of CD4+T cells plays a crucial role in the establishment of a productive human immunodeficiency virus infection. Here, we show that T cells stimulated for 1 day demonstrated delayed kinetics of viral reverse transcription and integration compared to cells stimulated for 2 days prior to infection. As a result, the efficiency of reverse transcription and integration inhibitors differs in these differentially stimulated cells. These studies increase our understanding of how T cells support viral replication and provide insight regarding the efficiency of antiretroviral therapy in lymphoid compartments.
An approach for detecting prosodic phrase boundaries in spoken english
Authors: Brierley Claire , Atwell Eric 
Published: January 2009

Prosodic phrasing is the means by which speakers of any given language break up an utterance into meaningful chunks. The term "prosody" itself refers to the tune or intonation of an utterance, and therefore prosodic phrases literally signal the end of one tune and the beginning of another. This study uses phrase break annotations in the Aix-MARSEC corpus of spoken English as a "gold standard" for measuring the degree of correspondence between prosodic phrases and the discrete syntactic grouping of prepositional phrases, where the latter is defined via a chunk parsing rule using nltk_lite's regular expression chunk parser.
A three-way comparison is also introduced between the "gold standard" chunk parsing rule and human judgment in the form of intuitive predictions about phrasing. Results show that even with a discrete syntactic grouping and a small sample of text, problems may arise for this rule-based method due to uncategorical behavior in parts of speech. Lack of correspondence between intuitive prosodic phrases and corpus annotations highlights the optional nature of certain boundary types. Finally, there are clear indications, supported by corpus annotations, that significant prosodic phrase boundaries occur within sentences and not just at full stops.
Classification of manual abilities in children with cerebral palsy under 5 years of age: how reliable is the Manual Ability Classification System?
Authors: Plasschaert VFP , Ketelaar M. , Nijnuis MG , Enkelaar L. , Gorter JW 
Published: January 2009

Objective: To assess the interobserver reliability of the Manual Ability Classification System (MACS) in young children (age 1—5 years) with cerebral palsy. Design: Interobserver reliability study. Setting: A cross-sectional study of a hospital-based population of children with cerebral palsy. Subjects: Thirty children, 18 boys and 12 girls between 1 and 5 years of age (mean age 2.5 years ± 14.2 SD, Gross Motor Function Classification System level I—IV). Measures: the children were classified by means of the MACS by two independent observers. Interobserver reliability was analysed using Cohen's kappa. Results: Overall interobserver reliability of the MACS for children aged 1—5 years was moderate, with a linear weighted kappa (κ) of 0.62 (95% confidence interval (CI) 0.49—0.76). According to the generally accepted categories of agreement, reliability was moderate for children under 2 years of age (κ = 0.55), and good for children between 2 and 5 years of age (κ = 0.67). Conclusion: Classification of manual ability of young children with cerebral palsy is possible between 2 and 5 years of age. For children younger than 2 years old, it should be done with caution. Further development of the MACS for children under 5 years of age is recommended with an emphasis on age-appropriate descriptions of manual abilities.
Mesenchymal stem/progenitor cells promote the reconstitution of exogenous hematopoietic stem cells in Fancg−/− mice in vivo
Authors: Li Yan , Chen Shi , Yuan Jin , Yang Yanzhu , Li Jingling , Ma Jin , Wu Xiaohua , Freund Marcel , Pollok Karen , Hanenberg Helmut , Goebel W. Scott , Yang Feng-Chun 
Published: January 2009

AbstractFanconi anemia (FA) is a heterogeneous genetic disorder characterized by bone marrow failure and complex congenital anomalies. Although mutations in FA genes result in a characteristic phenotype in the hematopoietic stem/progenitor cells (HSPCs), little is known about the consequences of a nonfunctional FA pathway in other stem/progenitor cell compartments. Given the intense functional interactions between HSPCs and the mesenchymalmicroenvironment, we investigated the FA pathway on the cellular functions of murine mesenchymal stem/progenitor cells (MSPCs) and their interactions with HSPCs in vitro and in vivo. Here, we show that loss of the murine homologue of FANCG (Fancg) results in a defect in MSPC proliferation and in their ability to support the adhesion and engraftment of murine syngeneic HSPCs in vitro or in vivo. Transplantation of wild-type (WT) but not Fancg−/− MSPCs into the tibiae of Fancg−/− recipient mice enhances the HSPC engraftment kinetics, the BM cellularity, and the number of progenitors per tibia of WT HSPCs injected into lethally irradiated Fancg−/− recipients. Collectively, these data show that FA proteins are required in the BM microenvironment to maintain normal hematopoiesis and provide genetic and quantitative evidence that adoptive transfer of WT MSPCs enhances hematopoietic stem cell engraftment.
Inhibition of monocyte-derived inflammatory cytokines by IL-25 occurs via p38 Map kinase–dependent induction of Socs-3
Authors: Caruso Roberta , Stolfi Carmine , Sarra Massimiliano , Rizzo Angelamaria , Fantini Massimo C. , Pallone Francesco , MacDonald Thomas T. , Monteleone Giovanni 
Published: January 2009

Abstract
IL-25, a member of the IL-17 cytokine family, is known to enhance Th2-like responses associated with increased serum levels of IgE, IgG1, IgA, blood eosinophilia, and eosinophilic infiltrates in various tissues. However, IL-25 also abrogates inflammatory responses driven by Th17 cells. However, the cell types that respond to IL-25 and the mechanisms by which IL-25 differentially regulates immune reactions are not well explored. To identify potential targets of IL-25, we initially examined IL-25 receptor (IL-25R) in human peripheral blood cells. IL-25R was predominantly expressed by CD14+ cells. We next assessed the functional role of IL-25 in modulating the response of CD14+ cells to various inflammatory signals. CD14+ cells responded to IL-25 by down-regulating the synthesis of inflammatory cytokines induced by toll-like receptor (TLR) ligands and inflammatory cytokines. Inhibition of cytokine response by IL-25 occurred via a p38 Map kinase–driven Socs-3–dependent mechanism. In vivo, IL-25 inhibited monocyte-derived cytokines and protected against LPS-induced lethal endotoxemia in mice. These data indicate that IL-25 is a negative regulator of monocyte proinflammatory cytokine responses, which may have therapeutic implications.
First acute haemodynamic study of soluble guanylate cyclase stimulator riociguat in pulmonary hypertension
Authors: Grimminger F. , Weimann G. , Frey R. , Voswinckel R. , Thamm M. , Bölkow D. , Weissmann N. , Mück W. , Unger S. , Wensing G. , Schermuly R. T. , Ghofrani H.A. 
Published: January 2009

Pulmonary hypertension (PH) is associated with impaired production of the vasodilator nitric oxide (NO). Riociguat (BAY 63-2521; Bayer Healthcare AG, Wuppertal, Germany) acts directly on soluble guanylate cyclase, stimulating the enzyme and increasing sensitivity to low NO levels. The present study evaluates riociguat safety, tolerability and efficacy in patients with moderate-to-severe PH (pulmonary arterial hypertension, distal chronic thromboembolic PH or PH with mild to moderate interstitial lung disease).The optimal tolerated dose was identified by incremental dosing in four patients with PH; pharmacodynamic and pharmacokinetic parameters were assessed following single-dose administration (2.5 mg or 1 mg) in 10 and five patients with PH, respectively. All subjects (n = 19) were analysed for safety and tolerability.Riociguat had a favourable safety profile at single doses ≤2.5 mg. It significantly improved pulmonary haemodynamic parameters and cardiac index in patients with PH in a dose-dependent manner, to a greater extent than inhaled NO. Although riociguat also had significant systemic effects and showed no pulmonary selectivity, mean systolic blood pressure remained >110 mmHg.The present report is the first to describe the use of riociguat in patients with pulmonary hypertension. The drug was well-tolerated and superior to nitric oxide in efficacy and duration. Riociguat, therefore, has potential as a novel therapy for pulmonary hypertension and warrants further investigation.
Effect of sildenafil on acrolein-induced airway inflammation and mucus production in rats
Authors: Wang T. , Liu Y. , Chen L. , Wang X. , Hu X-R. , Feng Y-L. , Liu D-S. , Xu D. , Duan Y-P. , Lin J. , Ou X-M. , Wen F-Q. 
Published: January 2009

Airway inflammation with mucus overproduction is a distinguishing pathophysiological feature of many chronic respiratory diseases. Phosphodiesterase (PDE) inhibitors have shown anti-inflammatory properties. In the present study, the effect of sildenafil, a potent inhibitor of PDE5 that selectively degrades cyclic guanosine 3′,5′-monophosphate (cGMP), on acrolein-induced inflammation and mucus production in rat airways was examined.Rats were exposed to acrolein for 14 and 28 days. Sildenafil or distilled saline was administered intragastrically prior to acrolein exposure. Bronchoalveolar lavage fluid (BALF) was acquired for cell count and the detection of pro-inflammatory cytokine levels. Lung tissue was examined for cGMP content, nitric oxide (NO)-metabolite levels, histopathological lesion scores, goblet cell metaplasia and mucin production.The results suggested that sildenafil pretreatment reversed the significant decline of cGMP content in rat lungs induced by acrolein exposure, and suppressed the increase of lung NO metabolites, the BALF leukocyte influx and pro-inflammatory cytokine release. Moreover, sildenafil pretreatment reduced acrolein-induced Muc5ac mucin synthesis at both mRNA and protein levels, and attenuated airway inflammation, as well as epithelial hyperplasia and metaplasia.In conclusion, sildenafil could attenuate airway inflammation and mucus production in the rat model, possibly through the nitric oxide/cyclic guanosine 3′,5′-monophosphate pathway, and, thus, might have a therapeutic potential for chronic airway diseases.