bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Many Sputum Culture Results Do We Need To Monitor Multidrug-Resistant-Tuberculosis (MDR-TB) Patients during Treatment?
Authors: Janssen Saskia , Padanilam Xavier , Louw Rianna , Mahanyele Russel , Coetzee Gerrit , Hänscheid Thomas , Leenstra Tjalling , Grobusch Martin P. 
Published: December 2012

ABSTRACT
Discharge of a hospital patient after a single negative sputum culture may save money when treating multidrug-resistant tuberculosis. However, after initial sputum conversion in 336 South Africans, 11.6% and 5.4% reconverted after 1 and 2 months, respectively. These findings endorse the WHO definitions of 2 negative cultures taken ≥30 days apart after sputum culture conversion.
Virulence Determinants of Pandemic A(H1N1)2009 Influenza Virus in a Mouse Model
Authors: Uraki Ryuta , Kiso Maki , Shinya Kyoko , Goto Hideo , Takano Ryo , Iwatsuki-Horimoto Kiyoko , Takahashi Kazuo , Daniels Rod S. , Hungnes Olav , Watanabe Tokiko , Kawaoka Yoshihiro 
Published: December 2012

ABSTRACT
A novel swine-origin H1N1 influenza virus [A(H1N1)pdm09 virus] caused the 2009 influenza pandemic. Most patients exhibited mild symptoms similar to seasonal influenza, but some experienced severe clinical signs and, in the worst cases, died. Such differences in symptoms are generally associated with preexisting medical conditions, but recent reports indicate the possible involvement of viral factors in clinical severity. To better understand the mechanism of pathogenicity of the A(H1N1)pdm09 virus, here, we compared five viruses that are genetically similar but were isolated from patients with either severe or mild symptoms. In a mouse model, A/Norway/3487/2009 (Norway3487) virus exhibited greater pathogenicity than did A/Osaka/164/2009 (Osaka164) virus. By exploiting reassortant viruses between these two viruses, we found that viruses possessing the hemagglutinin (HA) gene of Norway3487 in the genetic background of Osaka164 were more pathogenic in mice than other reassortant viruses, indicating a role for HA in the high virulence of Norway3487 virus. Intriguingly, a virus possessing HA, NA, and NS derived from Norway3487 exhibited greater pathogenicity in mice in concert with PB2 and PB1 derived from Osaka164 than did the parental Norway3487 virus. These findings demonstrate that reassortment between A(H1N1)pdm09 viruses can lead to increased pathogenicity and highlight the need for continued surveillance of A(H1N1)pdm09 viruses.
Identification and Structural Characterization of a Broadly Neutralizing Antibody Targeting a Novel Conserved Epitope on the Influenza Virus H5N1 Hemagglutinin
Authors: Du Lanying , Jin Lei , Zhao Guangyu , Sun Shihui , Li Junfeng , Yu Hong , Li Ye , Zheng Bo-Jian , Liddington Robert C. , Zhou Yusen , Jiang Shibo 
Published: December 2012

ABSTRACT
The unabated circulation of the highly pathogenic avian influenza A virus/H5N1 continues to be a serious threat to public health worldwide. Because of the high frequency of naturally occurring mutations, the emergence of H5N1 variants with high virulence has raised great concerns about the potential transmissibility of the virus in humans. Recent studies have shown that laboratory-mutated or reassortant H5N1 viruses could be efficiently transmitted among mammals, particularly ferrets, the best animal model for humans. Thus, it is critical to establish effective strategies to combat future H5N1 pandemics. In this study, we identified a broadly neutralizing monoclonal antibody (MAb), HA-7, that potently neutralized all tested strains of H5N1 covering clades 0, 1, 2.2, 2.3.4, and 2.3.2.1 and completely protected mice against lethal challenges of H5N1 viruses from clades 1 and 2.3.4. HA-7 specifically targeted the globular head of the H5N1 virus hemagglutinin (HA). Using electron microscopy technology with three-dimensional reconstruction (3D-EM), we discovered that HA-7 bound to a novel and highly conserved conformational epitope that was centered on residues 81 to 83 and 117 to 122 of HA1 (H5 numbering). We further demonstrated that HA-7 inhibited viral entry during postattachment events but not at the receptor-binding step, which is fully consistent with the 3D-EM result. Taken together, we propose that HA-7 could be humanized as an effective passive immunotherapeutic agent for antiviral stockpiling for future influenza pandemics caused by emerging unpredictable H5N1 strains. Our study also provides a sound foundation for the rational design of vaccines capable of inducing broad-spectrum immunity against H5N1.
Attenuation of the Adaptive Immune Response in Rhesus Macaques Infected with Simian Varicella Virus Lacking Open Reading Frame 61
Authors: Meyer Christine , Kerns Amelia , Haberthur Kristen , Dewane Jesse , Walker Joshua , Gray Wayne , Messaoudi Ilhem 
Published: December 2012

ABSTRACTVaricella zoster virus (VZV) is a neurotropic alphaherpesvirus that causes chickenpox during primary infection and establishes latency in sensory ganglia. Infection of rhesus macaques (RM) with the homologous simian varicella virus (SVV) recapitulates hallmarks of VZV infection. We have shown that an antisense transcript of SVV open reading frame 61 (ORF61), a viral transactivator, was detected most frequently in latently infected RM sensory ganglia. In this study, we compared disease progression, viral replication, immune response, and the establishment of latency following intrabronchial infection with a recombinant SVV lacking ORF61 (SVVΔORF61) to those following infection with wild-type (WT) SVV. Varicella severity and viral latency within sensory ganglia were comparable in RMs infected with SVVΔORF61 and WT SVV. In contrast, viral loads, B and T cell responses, and plasma inflammatory cytokine levels were decreased in RMs infected with SVVΔORF61. To investigate the mechanisms underlying the reduced adaptive immune response, we compared acute SVV gene expression, frequency and proliferation of dendritic cell (DC) subsets, and the expression of innate antiviral genes in bronchoalveolar lavage (BAL) samples. The abundance of SVV transcripts in all kinetic classes was significantly decreased in RMs infected with SVVΔORF61. In addition, we detected a higher frequency and proliferation of plasmacytoid dendritic cells in BAL fluid at 3 days postinfection in RMs infected with SVVΔORF61, which was accompanied by a slight increase in type I interferon gene expression. Taken together, our data suggest that ORF61 plays an important role in orchestrating viral gene expressionin vivoand interferes with the host antiviral interferon response.
Frequent Cross-Species Transmission of Parvoviruses among Diverse Carnivore Hosts
Authors: Allison Andrew B. , Kohler Dennis J. , Fox Karen A. , Brown Justin D. , Gerhold Richard W. , Shearn-Bochsler Valerie I. , Dubovi Edward J. , Parrish Colin R. , Holmes Edward C. 
Published: December 2012

ABSTRACT
Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.
The Kaposi's Sarcoma-Associated Herpesvirus ORF34 Protein Binds to HIF-1α and Causes Its Degradation via the Proteasome Pathway
Authors: Haque Muzammel , Kousoulas Konstantin G. 
Published: December 2012

ABSTRACT

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi's sarcoma (KS) and two other lymphoproliferative disorders, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). Kaposi's sarcoma is a highly vascular tumor, and recently both hypoxia-inducible factor 1α (HIF-1α) and HIF-2α were detected in KS samples, indicating a role of HIFs in the KSHV life cycle. Previously, we showed that ORF34, a lytic gene of unassigned function, was activated by hypoxia and that ORF34 transcription was upregulated by both HIFs (M. Haque, D. A. Davis, V. Wang, I. Widmer, and R. Yarchoan, J Virol.
77:
6761–6768, 2003). In the present study, we show that coexpression of ORF34 with HIF-1αm (degradation-resistant HIF-1α) caused substantial reduction in HIF-1α-dependent transcription, as evidenced by reporter assays. Two-way immunoprecipitation experiments revealed that ORF34 physically interacted with HIF-1αm in transient expression experiments. Deletion analysis revealed that three different ORF34 domains interacted with the amino-terminal domain of HIF-1α. Also, purified HIF-1α and ORF34 proteins interacted with each other. The observed transcriptional inhibition of HIF-1α-dependent promoters was attributed to degradation of HIF-1α after binding with ORF34, since the overall amount of wild-type HIF-1α but not the degradation-resistant one (HIF-1αm) was reduced in the presence of ORF34. Moreover, ORF34 caused degradation of HIF-1α in a dose-dependent manner. Inhibition of the ubiquitin-dependent pathway by the chemical proteasome inhibitor MG132 prevented HIF-1α degradation in the presence of ORF34. These results show that ORF34 binds to HIF-1α, leading to its degradation via the proteasome-dependent pathway.
Design Requirements for Interfering Particles To Maintain Coadaptive Stability with HIV-1
Authors: Rouzine Igor M. , Weinberger Leor S. 
Published: December 2012

ABSTRACTDefective interfering particles (DIPs) are viral deletion mutants lacking essential transacting or packaging elements and must be complemented by wild-type virus to propagate. DIPs transmit through human populations, replicating at the expense of the wild-type virus and acting as molecular parasites of viruses. Consequently, engineered DIPs have been proposed as therapies for a number of diseases, including human immunodeficiency virus (HIV). However, it is not clear if DIP-based therapies would face evolutionary blocks given the high mutation rates and high within-host diversity of lentiviruses. Divergent evolution of HIV and DIPs appears likely since natural DIPs have not been detected for lentiviruses, despite extensive sequencing of HIVs and simian immunodeficiency viruses (SIVs). Here, we tested if the apparent lack of lentiviral DIPs is due to natural selection and analyzed which molecular characteristics a DIP or DIP-based therapy would need to maintain coadaptive stability with HIV-1. Using a well-established mathematical model of HIV-1 in a host extended to include its replication in a single cell and interference from DIP, we calculated evolutionary selection coefficients. The analysis predicts that interference by codimerization between DIPs and HIV-1 genomes is evolutionarily unstable, indicating that recombination between DIPs and HIV-1 would be selected against. In contrast, DIPs that interfere via competition for capsids have the potential to be evolutionarily stable if the capsid-to-genome production ratio of HIV-1 is >1. Thus, HIV-1 variants that attempt to “starve” DIPs to escape interference would be selected against. In summary, the analysis suggests specific experimental measurements that could address the apparent lack of naturally occurring lentiviral DIPs and specifies how therapeutic approaches based on engineered DIPs could be evolutionarily robust and avoid recombination.
Hypervariable Domains of nsP3 Proteins of New World and Old World Alphaviruses Mediate Formation of Distinct, Virus-Specific Protein Complexes
Authors: Foy Niall J. , Akhrymuk Maryna , Akhrymuk Ivan , Atasheva Svetlana , Bopda-Waffo Alain , Frolov Ilya , Frolova Elena I. 
Published: December 2012

ABSTRACT
Alphaviruses are a group of single-stranded RNA viruses with genomes of positive polarity. They are divided into two geographically isolated groups: the Old World and the New World alphaviruses. Despite their similar genome organizations and virion structures, they differ in many aspects of pathogenesis and interaction with the host cell. Here we present new data highlighting previously unknown differences between these two groups. We found that nsP3 proteins of Sindbis virus (SINV) and Venezuelan equine encephalitis virus (VEEV) form cytoplasmic complexes with different morphologies and protein compositions. Unlike the amorphous aggregates formed by SINV nsP3 and other Old World alphavirus-specific nsP3s, VEEV nsP3 forms unique, large spherical structures with striking symmetry. Moreover, VEEV nsP3 does not interact with proteins previously identified as major components of SINV nsP3 complexes, such as G3BP1 and G3BP2. Importantly, the morphology of the complexes and the specificity of the interaction with cellular proteins are largely determined by the hypervariable domain (HVD) of nsP3. Replacement of the VEEV nsP3 HVD with the corresponding domain of SINV nsP3 rendered this protein capable of interaction with G3BPs. Conversely, replacement of the SINV nsP3 HVD with that of VEEV abolished SINV nsP3's interaction with G3BPs. The replacement of natural HVDs with those from heterologous viruses did not abrogate virus replication, despite these fragments demonstrating very low levels of sequence identity. Our data suggest that in spite of the differences in morphology and composition of the SINV- and VEEV-specific nsP3 complexes, it is likely that they have similar functions in virus replication and modification of the cellular environment.
Helicobacter pylori Peptidoglycan Modifications Confer Lysozyme Resistance and Contribute to Survival in the Host
Authors: Wang Ge , Lo Leja F. , Forsberg Lennart S. , Maier Robert J. 
Published: December 2012

ABSTRACT

The prominent host muramidase lysozyme cleaves bacterial peptidoglycan (PG), and the enzyme is abundant in mucosal secretions. The lytic enzyme susceptibility of Gram-negative bacteria and mechanisms they use to thwart lytic enzyme activity are poorly studied. We previously characterized a
Helicobacter pylori
PG modification enzyme, an N-deacetylase (PgdA) involved in lysozyme resistance. In this study, another PG modification enzyme, a putative PG O-acetyltransferase (PatA), was identified. Mass spectral analysis of the purified PG demonstrated that a
patA
strain contained a greatly reduced amount of acetylated muropeptides, indicating a role for PatA in
H. pylori
PG O-acetylation. The PG modification mutant strains (
pgdA
,
patA
, or
pgdA patA
) were more susceptible to lysozyme killing than the parent, but this assay required high lysozyme levels (up to 50 mg/ml). However, addition of host lactoferrin conferred lysozyme sensitivity to
H. pylori
, at physiologically relevant concentrations of both host components (3 mg/ml lactoferrin plus 0.3 mg/ml lysozyme). The
pgdA patA
double mutant strain was far more susceptible to lysozyme/lactoferrin killing than the parent. Peptidoglycan purified from a
pgdA patA
mutant was five times more sensitive to lysozyme than PG from the parent strain, while PG from both single mutants displayed intermediate sensitivity. Both sensitivity assays for whole cells and for purified PGs indicated that the modifications mediated by PgdA and PatA have a synergistic effect, conferring lysozyme tolerance. In a mouse infection model, significant colonization deficiency was observed for the double mutant at 3 weeks postinoculation. The results show that PG modifications affect the survival of a Gram-negative pathogen.

IMPORTANCE
Pathogenic bacteria evade host antibacterial enzymes by a variety of mechanisms, which include resisting lytic enzymes abundant in the host. Enzymatic modifications to peptidoglycan (PG, the site of action of lysozyme) are a known mechanism used by Gram-positive bacteria to protect against host lysozyme attack. However, Gram-negative bacteria contain a thin layer of PG and a recalcitrant outer membrane permeability barrier to resist lysis, so molecular modifications to cell wall structure in order to combat lysis remain largely unstudied. Here we show that two
Helicobacter pylori
PG modification enzymes (PgdA and PatA) confer a clear protective advantage to a Gram-negative bacterium. They protect the bacterium from lytic enzyme degradation, albeit via different PG modification activities. Many pathogens are Gram negative, so some would be expected to have a similar cell wall-modifying strategy. Understanding such strategies may be useful for combating pathogen growth.
Experimental Infections of the Reservoir Species Peromyscus leucopus with Diverse Strains of Borrelia burgdorferi, a Lyme Disease Agent
Authors: Baum Elisabeth , Hue Fong , Barbour Alan G. 
Published: December 2012

ABSTRACTThe rodentPeromyscus leucopusis a major natural reservoir for the Lyme disease agentBorrelia burgdorferiand a host for its vectorIxodes scapularis. At various locations in northeastern United States 10 to 15 B. burgdorferistrains coexist at different prevalences in tick populations. We asked whether representative strains of high or low prevalence differed in their infections ofP. leucopus. After 5 weeks of experimental infection of groups with each of 6 isolates, distributions and burdens of bacteria in tissues were measured by quantitative PCR, and antibodies toB. burgdorferiwere evaluated by immunoblotting and protein microarray. All groups of animals were infected in their joints, ears, tails, and hearts, but overall spirochete burdens were lower in animals infected with low-prevalence strains. Animals were similar regardless of the infecting isolate in their levels of antibodies to whole cells, FlaB, BmpA, and DbpB proteins, and the conserved N-terminal region of the serotype-defining OspC proteins. But there were strain-specific antibody responses to full-length OspC and to plasmid-encoded VlsE, BBK07, and BBK12 proteins. Sequencing of additional VlsE genes revealed substantial diversity within some pairs of strains but near-identical sequences within other pairs, which otherwise differed in theirospCalleles. The presence or absence of full-length bbk07 and bbk12 genes accounted for the differences in antibody responses. We propose that forB. burgdorferi, there is selection in reservoir species for (i) sequence diversity, as for OspC and VlsE, and (ii) the presence or absence of polymorphisms, as for BBK07 and BBK12.IMPORTANCEHumans are dead-end hosts forBorreliaagents of Lyme disease (LD), and, thus, irrelevant for the pathogens’ maintenance. Many reports of human cases and laboratory mouse infections exist, but less is known about infection and immunity in natural reservoirs, such as the rodentPeromyscus leucopus. We observed that high- and low-prevalence strains ofBorrelia burgdorferiwere capable of infectingP. leucopusbut elicited different patterns of antibody responses. Antibody reactivities to the VlsE protein were as type-specific as previously characterized reactivities to serotype-defining OspC proteins. In addition, the low-prevalence strains lacked full-length genes for two proteins that (i) are encoded by a virulence-associated plasmid in some high-prevalence strains and (ii) LD patients and field-captured rodents commonly have antibodies to. Immune selection against these genes may have led to null phenotype lineages that can infect otherwise immune hosts but at the cost of reduced fitness and lower prevalence.
De-differentiation of papillary thyroid carcinoma into squamous cell carcinoma. A case of coexistence within an excised neck lesion
Authors: Evans William David George 
Published: December 2012

An 80-year-old man with papillary thyroid carcinoma of the neck underwent surgery and radioiodide therapy. He presented 11 years later with a lesion adjudged from fine needle aspiration to be a squamous cell carcinoma (SCC). Histological analysis of the excised mass revealed a lymph node overwhelmed with papillary thyroid carcinoma and moderately differentiated SCC thought to have transformed from papillary cells. A very small number of similar transformations specifically involving the ‘tall cell variant’ of papillary carcinoma transforming to spindle cell carcinoma have been reported previously. This case report demonstrates clear images of this rare occurrence and briefly considers factors leading to de-differentiation. The clinician should consider possible transformation from papillary thyroid cancer in cases of SCC of the head and neck as this variation may be more aggressive.
Evaluation of the filter paper IP-10 tests in school children after exposure to tuberculosis: a prospective cohort study with a 4-year follow-up
Authors: Tuuminen Tamara , Salo Eeva , Kotilainen Hannele , Ruhwald Morten 
Published: December 2012

ObjectivesThe prevalence of active tuberculosis (TB) is low in Finland, but outbreaks do occur. Following exposure national guidelines recommend either tuberculosis skin test or interferon-γ-release assay-testing of asymptomatic children. The aim of this study was to compare QuantiFERON-TB Gold In-Tube test (QFT) and interferon-γ-inducible protein (IP-10) release assay for detection ofMycobacterium tuberculosisinfection following exposure to TB in a primary school.DesignA prospective cohort study.SettingSchool children in Helsinki, Finland.ParticipantsTwo siblings of the index case and 58 classmates exposed toM tuberculosis.InterventionAll the children were screened using the QFT, which was used to guide preventive treatment. All those exposed were followed up through the national TB registry.Outcome measuresIP-10 was measured in plasma supernatants from the QFT test supernatants and in plasma dried and stored for 1 year on filter paper. IP-10 test results were calculated using preset algorithms for positive and indeterminate tests. The negative predictive values of the tests were assessed.ResultsAt an initial screening 2 months after the debut of symptoms in the index case, QFT was positive in two children; 56 tests were negative; one was indeterminate and one was borderline. IP-10 showed a perfect concordance between the dried plasma spot and plasma method; two children were IP-10 positive and two were IP-10 indeterminate. There were two (3%) discordant results between the QFT and IP-10 tests. Four children converted to positive QFT at a 1–3 month follow-up. None of the QFT negative/borderline children developed TB in the 4-year period since exposure.ConclusionsWe demonstrated that IP-10 and QFT perform comparably as screening tools for infection withM tuberculosisin a contact investigation. IP-10 determined in dried plasma spots was at par with IP-10 determined in plasma, which further supports the usefulness of this alternative approach.