bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Highly Prevalent Hepatitis B Virus Coinfection among HIV-Seropositive Persons in Ghana
Authors: Geretti Anna Maria , Patel Mauli , Sarfo Fred Stephen , Chadwick David , Verheyen Jens , Fraune Maria , Garcia Ana , Phillips Richard Odame 
Published: July 2010

ABSTRACTSimple hepatitis B surface antigen (HBsAg) tests may facilitate ascertainment of hepatitis B virus (HBV) infection in settings with high endemicity but limited infrastructure. We evaluated two rapid HBsAg tests and characterized HBV coinfection in a Ghanaian HIV-positive cohort. Samples from 838 patients were tested by the rapid assays Determine and Vikia and the reference assays Architect, Murex version 3, and Liaison Ultra. The assays were also evaluated using the 2nd International Standard, a seroconversion panel, and two mutant panels. HBsAg-positive samples underwent HBV DNA quantification by real-time PCR and surface and polymerase gene population sequencing. Overall, 140/838 patients (16.7%; 95% confidence interval, 14.2 to 19.2%) were HBsAg positive, and of these, 103/140 (73.6%) were e-antigen negative and 118/140 (84.3%) showed an HBV DNA level of >14 IU/ml (median, 8,279 IU/ml). Assay sensitivities and specificities were as follows: Architect, 97.9 and 99.6%; Liaison, 97.1 and 99.4%; Murex, 98.6 and 99.3%; Determine, 69.3 and 100%; and Vikia, 70.7 and 100%. With Determine, the limit of detection was >1.5 to 3.4 HBsAg IU/ml, and the median HBV DNA loads were 598 and 10,905 IU/ml in Determine-negative and -positive samples, respectively (P= 0.0005). Results were similar with the Vikia assay. HBV DNA sequencing indicated infection with genotype E in 82/86 (95.3%) patients. HBsAg mutations affected assay performance, including a T123A mutant that escaped detection by Architect. Major drug resistance mutations were observed in 4/86 patients (4.6%). The prevalence of HBV coinfection was high in this HIV-positive Ghanaian cohort. The two rapid assays identified HBsAg-positive patients at risk for liver disease with high specificity, albeit with only moderate sensitivity.
Clinical and Economic Outcomes for Patients with Health Care-Associated
Staphylococcus aureus
Pneumonia
Authors: Shorr Andrew F. , Haque Nadia , Taneja Charu , Zervos Marcus , Lamerato Lois , Kothari Smita , Zilber Sophia , Donabedian Susan , Perri Mary Beth , Spalding James , Oster Gerry 
Published: July 2010

ABSTRACT

While the increasing importance of methicillin-resistant
Staphylococcus aureus
(MRSA) as a pathogen in health care-associated
S. aureus
pneumonia has been documented widely, information on the clinical and economic consequences of such infections is limited. We retrospectively identified all patients admitted to a large U.S. urban teaching hospital between January 2005 and May 2008 with pneumonia and positive blood or respiratory cultures for
S. aureus
within 48 h of admission. Among these patients, those with suspected health care-associated pneumonia (HCAP) were identified using established criteria (e.g., recent hospitalization, admission from nursing home, or hemodialysis). Subjects were designated as having methicillin-resistant (MRSA) or methicillin-susceptible (MSSA) HCAP, based on initial
S. aureus
isolates. Initial therapy was designated “appropriate” versus “inappropriate” based on the expected susceptibility of the organism to the regimen received. We identified 142 patients with evidence of
S. aureus
HCAP. Their mean (standard deviation [SD]) age was 64.5 (17) years. Eighty-seven patients (61%) had initial cultures that were positive for MRSA. Most (∼90%) patients received appropriate initial antibiotic therapy (86% for MRSA versus 91% for MSSA;
P
= 0.783). There were no significant differences between MRSA and MSSA HCAP patients in mortality (29% versus 20%, respectively), surgery for pneumonia (22% versus 20%), receipt of mechanical ventilation (60% versus 58%), or admission to the intensive care unit (79% versus 76%). Mean (SD) total charges per admission were universally high ($98,170 [$94,707] for MRSA versus $104,121 [$91,314]) for MSSA [
P
= 0.712]). Almost two-thirds of patients admitted to hospital with
S. aureus
HCAP have evidence of MRSA infection.
S. aureus
HCAP, irrespective of MRSA versus MSSA status, is associated with significant mortality and high health care costs, despite appropriate initial antibiotic therapy.
The Genome Segments of a Group D Rotavirus Possess Group A-Like Conserved Termini but Encode Group-Specific Proteins
Authors: Trojnar Eva , Otto Peter , Roth Bernhard , Reetz Jochen , Johne Reimar 
Published: July 2010

ABSTRACT
Rotaviruses are a leading cause of viral acute gastroenteritis in humans and animals. They are grouped according to gene composition and antigenicity of VP6. Whereas group A, B, and C rotaviruses are found in humans and animals, group D rotaviruses have been exclusively detected in birds. Despite their broad distribution among chickens, no nucleotide sequence data exist so far. Here, the first complete genome sequence of a group D rotavirus (strain 05V0049) is presented, which was amplified using sequence-independent amplification strategies and degenerate primers. Open reading frames encoding homologues of rotavirus proteins VP1 to VP4, VP6, VP7, and NSP1 to NSP5 were identified. Amino acid sequence identities between the group D rotavirus and the group A, B, and C rotaviruses varied between 12.3% and 51.7%, 11.0% and 23.1%, and 9.5% and 46.9%, respectively. Segment 10 of the group D rotavirus has an additional open reading frame. Generally, phylogenetic analysis indicated a common evolution of group A, C, and D rotaviruses, separate from that of group B. However, the NSP4 sequence of group C has only very low identities in comparison with cogent sequences of all other groups. The avian group A NSP1 sequences are more closely related to those of group D than those of mammalian group A rotaviruses. Most interestingly, the nucleotide sequences at the termini of the 11 genome segments are identical between group D and group A rotaviruses. Further investigations should clarify whether these conserved structures allow an exchange of genome segments between group A and group D rotaviruses.
Protein Kinase R Is Responsible for the Phosphorylation of eIF2α in Rotavirus Infection
Authors: Rojas Margarito , Arias Carlos F. , López Susana 
Published: July 2010

ABSTRACT
The eukaryotic initiation translation factor 2 (eIF2) represents a key point in the regulation of protein synthesis. This factor delivers the initiator Met-tRNA to the ribosome, a process that is conserved in all eukaryotic cells. Many types of stress reduce global translation by triggering the phosphorylation of the α subunit of eIF2, which reduces the formation of the preinitiation translation complexes. Early during rotavirus infection, eIF2α becomes phosphorylated, and even under these conditions viral protein synthesis is not affected, while most of the cell protein synthesis is blocked. Here, we found that the kinase responsible for the phosphorylation of eIF2α in rotavirus-infected cells is PKR, since in mouse embryonic fibroblasts deficient in the kinase domain of PKR, or in MA104 cells where the expression of PKR was knocked down by RNA interference, eIF2α was not phosphorylated upon rotavirus infection. The viral component responsible for the activation of PKR seems to be viral double-stranded RNA, which is found in the cytoplasm of infected cells, outside viroplasms. Taken together, these results suggest that rotaviruses induce the PKR branch of the interferon system and have evolved a mechanism to translate its proteins, surpassing the block imposed by eIF2α phosphorylation.
Myosin Va Enhances Secretion of Herpes Simplex Virus 1 Virions and Cell Surface Expression of Viral Glycoproteins
Authors: Roberts Kari L. , Baines Joel D. 
Published: July 2010

ABSTRACT
The final step in the egress of herpes simplex virus (HSV) virions requires virion-laden vesicles to bypass cortical actin and fuse with the plasma membrane, releasing virions into the extracellular space. Little is known about the host or viral proteins involved. In the current study, we noted that the conformation of myosin Va (myoVa), a protein known to be involved in melanosome and secretory granule trafficking to the plasma membrane in melanocytes and neuroendocrine cells, respectively, was altered by 4 h after infection with HSV-1 such that an N-terminal epitope expected to be masked in its inactive state was rendered immunoreactive. Wild-type myoVa localized throughout the cytoplasm and to a limited extent in the nuclei of HSV-infected cells. Two different dominant negative myoVa molecules containing cargo-binding domains but lacking the lever arms and actin-binding domains colocalized with markers of the trans-Golgi network (TGN). Expression of dominant negative myoVa isoforms reduced secretion of HSV-1 infectivity into the medium by 50 to 75%, reduced surface expression of glycoproteins B, M, and D, and increased intracellular virus infectivity to levels consistent with increased retention of virions in the cytoplasm. These data suggest that myoVa is activated during HSV-1 infection to help transport virion- and glycoprotein-laden vesicles from the TGN, through the cortical actin, to the plasma membrane. We cannot exclude a role for myoVa in promoting fusion of these vesicles with the inner surface of the plasma membrane. These data also indicate that myoVa is involved in exocytosis in human epithelial cells as well as other cell types.
The 7a Accessory Protein of Severe Acute Respiratory Syndrome Coronavirus Acts as an RNA Silencing Suppressor
Authors: Karjee Sumona , Minhas Ankita , Sood Vikas , Ponia Sanket S. , Banerjea Akhil C. , Chow Vincent T. K. , Mukherjee Sunil K. , Lal Sunil K. 
Published: July 2010

ABSTRACT

RNA silencing suppressors (RSSs) are well studied for plant viruses but are not well defined to date for animal viruses. Here, we have identified an RSS from a medically important positive-sense mammalian virus,
Severe acute respiratory syndrome coronavirus
. The viral 7a accessory protein suppressed both transgene and virus-induced gene silencing by reducing the levels of small interfering RNA (siRNA). The suppression of silencing was analyzed by two independent assays, and the middle region (amino acids [aa] 32 to 89) of 7a was responsible for suppression. Finally, the RNA suppression property and the enhancement of heterologous replicon activity by the 7a protein were confirmed for animal cell lines.
Two Overlapping Domains of a Lyssavirus Matrix Protein That Acts on Different Cell Death Pathways
Authors: Larrous Florence , Gholami Alireza , Mouhamad Shahul , Estaquier Jérôme , Bourhy Hervé 
Published: July 2010

ABSTRACTThe lyssavirus matrix (M) protein induces apoptosis. The regions of the M protein that are essential for triggering cell death pathways are not yet clearly defined. We therefore compared the M proteins from two viruses that have contrasting characteristics in terms of cellular apoptosis: a genotype 3 lyssavirus, Mokola virus (MOK), and a genotype 1 rabies virus isolated from a dog from Thailand (THA). We identified a 20-amino-acid fragment (corresponding to positions 67 to 86) that retained the cell death activities of the full-length M protein from MOK via both the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and inhibition of cytochromecoxidase (CcO) activity. We found that the amino acids at positions 77 and 81 have an essential role in triggering these two cell death pathways. Directed mutagenesis demonstrated that the amino acid at position 77 affects CcO activity, whereas the amino acid at position 81 affects TRAIL-dependent apoptosis. Mutations in the full-length M protein that compromised induction of either of these two pathways resulted in delayed apoptosis compared with the time to apoptosis for the nonmutated control.
Structure of the Recombinant Alphavirus Western Equine Encephalitis Virus Revealed by Cryoelectron Microscopy
Authors: Sherman Michael B. , Weaver Scott C. 
Published: July 2010

ABSTRACT

Western equine encephalitis virus (WEEV;
Togaviridae
,
Alphavirus
) is an enveloped RNA virus that is typically transmitted to vertebrate hosts by infected mosquitoes. WEEV is an important cause of viral encephalitis in humans and horses in the Americas, and infection results in a range of disease, from mild flu-like illnesses to encephalitis, coma, and death. In addition to spreading via mosquito vectors, human WEEV infections can potentially occur directly via aerosol transmission. Due to its aerosol infectivity and virulence, WEEV is thus classified as a biological safety level 3 (BSL-3) agent. Because of its highly infectious nature and containment requirements, it has not been possible to investigate WEEV's structure or assembly mechanism using standard structural biology techniques. Thus, to image WEEV and other BSL-3 agents, we have constructed a first-of-its-kind BSL-3 cryoelectron microscopy (cryoEM) containment facility. cryoEM images of WEEV were used to determine the first three-dimensional structure of this important human pathogen. The overall organization of WEEV is similar to those of other alphaviruses, consistent with the high sequence similarity among alphavirus structural proteins. Surprisingly, the nucleocapsid of WEEV, a New World virus, is more similar to the Old World alphavirus Sindbis virus than to other New World alphaviruses.
Divergent Evolution in Reverse Transcriptase (RT) of HIV-1 Group O and M Lineages: Impact on Structure, Fitness, and Sensitivity to Nonnucleoside RT Inhibitors
Authors: Tebit Denis M. , Lobritz Michael , Lalonde Matthew , Immonen Taina , Singh Kamlendra , Sarafianos Stefanos , Herchenröder Ottmar , Kräusslich Hans-Georg , Arts Eric J. 
Published: July 2010

ABSTRACT
Natural evolution in primate lentiviral reverse transcriptase (RT) appears to have been constrained by the necessity to maintain function within an asymmetric protein composed of two identical primary amino acid sequences (66 kDa), of which one is cleaved (51 kDa). In this study, a detailed phylogenetic analysis now segregates groups O and M into clusters based on a cysteine or tyrosine residue located at position 181 of RT and linked to other signature residues. Divergent evolution of two group O (C181 or Y181) and the main (Y181 only) HIV-1 lineages did not appreciably impact RT activity or function. Group O RT structural models, based on group M subtype B RT crystal structures, revealed that most evolutionarily linked amino acids appear on a surface-exposed region of one subunit while in a noncatalytic RT pocket of the other subunit. This pocket binds nonnucleoside RT inhibitors (NNRTI); therefore, NNRTI sensitivity was used to probe enzyme differences in these group O and M lineages. In contrast to observations showing acquired drug resistance associated with fitness loss, the C181Y mutation in the C181 group O lineage resulted in a loss of intrinsic NNRTI resistance and was accompanied by fitness loss. Other mutations linked to the NNRTI-resistant C181 lineage also resulted in altered NNRTI sensitivity and a net fitness cost. Based on RT asymmetry and conservation of the intricate reverse transcription process, millions of years of divergent primate lentivirus evolution may be constrained to discrete mutations that appear primarily in the nonfunctional, solvent-accessible NNRTI binding pocket.
Inhibition of the Ubiquitin-Proteasome System Affects Influenza A Virus Infection at a Postfusion Step
Authors: Widjaja Ivy , de Vries Erik , Tscherne Donna M. , García-Sastre Adolfo , Rottier Peter J. M. , de Haan Cornelis A. M. 
Published: July 2010

ABSTRACT
We have demonstrated that influenza A virus (IAV) RNA synthesis depends on the ubiquitin-proteasome system. IAV replication was reduced both by proteasome inhibitors and in E36ts20 cells, which contain the thermolabile ubiquitin-activating enzyme E1. While virus entry was not affected in E36ts20 cells, the proteasome inhibitor MG132 retained viral particles in the cytoplasm. Addition-removal experiments of MG132 in combination with bafilomycin A1, a well-established inhibitor of IAV entry and fusion, showed that MG132 affected IAV infection at a postfusion step. This was confirmed by the lack of inhibition of IAV entry by proteasome inhibitors in a virus-like particle fusion assay.
Inhibition of Encephalomyocarditis Virus and Poliovirus Replication by Quinacrine: Implications for the Design and Discovery of Novel Antiviral Drugs
Authors: Gasparian Alexander V. , Neznanov Nickolay , Jha Sujata , Galkin Oleksandr , Moran John J. , Gudkov Andrei V. , Gurova Katerina V. , Komar Anton A. 
Published: July 2010

ABSTRACT
The 9-aminoacridine (9AA) derivative quinacrine (QC) has a long history of safe human use as an antiprotozoal and antirheumatic agent. QC intercalates into DNA and RNA and can inhibit DNA replication, RNA transcription, and protein synthesis. The extent of QC intercalation into RNA depends on the complexity of its secondary and tertiary structure. Internal ribosome entry sites (IRESs) that are required for initiation of translation of some viral and cellular mRNAs typically have complex structures. Recent work has shown that some intercalating drugs, including QC, are capable of inhibiting hepatitis C virus IRES-mediated translation in a cell-free system. Here, we show that QC suppresses translation directed by the encephalomyocarditis virus (EMCV) and poliovirus IRESs in a cell-free system and in virus-infected HeLa cells. In contrast, IRESs present in the mammalian p53 transcript that are predicted to have less-complex structures were not sensitive to QC. Inhibition of IRES-mediated translation by QC correlated with the affinity of binding between QC and the particular IRES. Expression of viral capsid proteins, replication of viral RNAs, and production of virus were all strongly inhibited by QC (and 9AA). These results suggest that QC and similar intercalating drugs could potentially be used for treatment of viral infections.
Retargeting of Adenovirus Vectors through Genetic Fusion of a Single-Chain or Single-Domain Antibody to Capsid Protein IX
Authors: Poulin Kathy L. , Lanthier Robert M. , Smith Adam C. , Christou Carin , Risco Quiroz Milagros , Powell Karen L. , O'Meara Ryan W. , Kothary Rashmi , Lorimer Ian A. , Parks Robin J. 
Published: July 2010

ABSTRACT
Adenovirus (Ad) vectors are the most commonly used system for gene therapy applications, due in part to their ability to infect a wide array of cell types and tissues. However, many therapies would benefit from the ability to target the Ad vector only to specific cells, such as tumor cells for cancer gene therapy. In this study, we investigated the utility of capsid protein IX (pIX) as a platform for the presentation of single-chain variable-fragment antibodies (scFv) and single-domain antibodies (sdAb) for virus retargeting. We show that scFv can be displayed on the capsid through genetic fusion to native pIX but that these molecules fail to retarget the virus, due to improper folding of the scFv. Redirecting expression of the fusion protein to the endoplasmic reticulum (ER) results in correct folding of the scFv and allows it to recognize its epitope; however, ER-targeted pIX-scFv was incorporated into the Ad capsid at a very low level which was not sufficient to retarget virus infection. In contrast, a pIX-sdAb construct was efficiently incorporated into the Ad capsid and enhanced virus infection of cells expressing the targeted receptor. Taken together, our data indicate that pIX is an effective platform for presentation of large targeting polypeptides on the surface of the virus capsid, but the nature of the ligand can significantly affect its association with virions.
Infection by Discordant Strains of HIV-1 Markedly Enhances the Neutralizing Antibody Response against Heterologous Virus
Authors: Powell Rebecca L. R. , Kinge Thompson , Nyambi Phillipe N. 
Published: July 2010

ABSTRACT

High-risk cohorts in East Africa and the United States show rates of dual HIV-1 infection—the concomitant or sequential infection by two HIV-1 strains—of 50% to 100% of those of primary infection, and our normal-risk HIV-positive cohort in Cameroon exhibits a rate of dual infection of 11% per year, signifying that these infections are not exceptional. Little is known regarding the effect of dual infections on host immunity, despite the fact that they provide unique opportunities to investigate how the immune response is affected when challenged with diverse HIV-1 antigens. Using heterologous primary isolates, we have shown here that dual HIV-1 infection by genetically distant strains correlates with significantly increased potency and breadth of the anti-HIV-1 neutralizing antibody response. When the neutralization capacities of sequential plasma obtained before and after the dual infection of 4 subjects were compared to those of matched plasma obtained from 23 singly infected control subjects, a significant increase in the neutralization capacity of the sequential sample was found for 16/28 dually infected plasma/virus pairs, while only 4/159 such combinations for the control subjects exhibited a significant increase (
P
< 0.0001). Similarly, there was a significant increase in the plasma dilution capable of neutralizing 50% of virus (IC
50
) for 18/24 dually infected plasma/virus pairs, while 0/36 controls exhibited such an increase (
P
< 0.0001). These results demonstrate that dual HIV-1 infection broadens and strengthens the anti-HIV-1 immune response, suggesting that vaccination schemes that include polyvalent, genetically divergent immunogens may generate highly protective immunity against any HIV-1 challenge strain.
ALTERNATING SUM FORMULAE FOR THE DETERMINANT AND OTHER LINK INVARIANTS
Authors: DASBACH OLIVER T. , FUTER DAVID , KALFAGIANNI EFSTRATIA , LIN XIAO-SONG , STOLTZFUS NEAL W. 
Published: July 2010

A classical result states that the determinant of an alternating link is equal to the number of spanning trees in a checkerboard graph of an alternating connected projection of the link. We generalize this result to show that the determinant is the alternating sum of the number of quasi-trees of genus j of the dessin of a non-alternating link. Furthermore, we obtain formulas for coefficients of the Jones polynomial by counting quantities on dessins. In particular, we will show that the jth coefficient of the Jones polynomial is given by sub-dessins of genus less or equal to j.
THORN-FORKING AS LOCAL FORKING
Authors: ADLER HANS 
Published: July 2010

We introduce the notion of a preindependence relation between subsets of the big model of a complete first-order theory, an abstraction of the properties which numerous concrete notions such as forking, dividing, thorn-forking, thorn-dividing, splitting or finite satisfiability share in all complete theories. We examine the relation between four additional axioms (extension, local character, full existence and symmetry) that one expects of a good notion of independence. We show that thorn-forking can be described in terms of local forking if we localize the number k in Kim's notion of "dividing with respect to k" (using Ben-Yaacov's "k-inconsistency witnesses") rather than the forking formulas. It follows that every theory with an M-symmetric lattice of algebraically closed sets (in Teq) is rosy, with a simple lattice theoretical interpretation of thorn-forking.