bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilingual creativity on China's Internet
Authors: ZHANG WEI 
Published: May 2015

ABSTRACTPrevious research in China has shown that Chinese‐English code‐mixing is gaining popularity on China's online social network sites. This study investigates the practice of multilingual language play onShanghai Release, an official microblog account set up by the municipal government of Shanghai. Based on the observation of the day‐to‐day weather messages onShanghai Release, as well as the comments posted by the participating netizens over a period of two years, the study reports on a range of strategies employed in the practice of multilingual language play, that involves bending, breaking, and blending the conventional ‘rules’ of Putonghua, English, and Shanghai dialect usage. The findings suggest that through such practices the municipal government web microbloggers posting onShanghai Releasehave constructed a distinct new professional identity, which aims to establish rapport with its audience, through the ludic construction of mixed‐code messages to its Internet public.
Writing in English in China: An autobiographical essay
Authors: ZHANG LIJIA 
Published: May 2015

ABSTRACTAs one of the few Chinese writers in mainland China writing prose in English, Lijia Zhang presents an autobiographical account of her decision to write and publish in the English language. This paper describes how Lijia Zhang first taught herself English, as she perceived the language as offering her an ‘escape’ from working as a factory worker in Nanjing to how she finally established herself as a published author writing in the English language. This paper also presents Lijia Zhang's personal reflections on the reasons why she writes in English, and also how she ‘weaves’ Chinese expressions and concepts in her use of the English language in her writing. Lijia Zhang's much‐acclaimed memoir on coming of age in China, Socialism is great: A worker's memoir of the new China, was published in 2008, and has been translated into Dutch, Italian, French and Portuguese. The memoir has been also been translated into Korean and her first novel Lotus is to be published by Henry Holt in February 2017.
English in China: A contemporary bibliography
Authors: BOLTON KINGSLEY , BOTHA WERNER , ZHANG WEI 
Published: May 2015

ABSTRACTThe list of research publications presented here is a contemporary bibliography, providing details of research articles, books, and other research outputs that were published between 2003 and 2015. The main focus of this bibliography is major works published internationally as well as in core journals from the People's Republic of China (PRC). Despite the problems concerning the representativeness of this current bibliography, the authors hope that the following list of references will usefully complement the research articles in this special issue on ‘English in contemporary China’. It is intended that the present bibliography will complement the earlier bibliographical article by Adamson et al. (), and serve as a guide for current and future research in this field.
Prediction of healing progress of pressure ulcers by distribution analysis of protein markers on necrotic tissue: A retrospective cohort study
Authors: Kitamura Aya , Yoshida Mikako , Minematsu Takeo , Nakagami Gojiro , Iizaka Shinji , Fujita Hideki , Naito Ayumi , Takahashi Kazuo , Mori Taketoshi , Sanada Hiromi 
Published: May 2015

ABSTRACTPredicting the short‐term healing progress of pressure ulcers is important for providing timely and appropriate intervention. Although there are some prediction methods available, these are unsuitable for ulcers with abundant necrotic tissue. We aimed to elucidate the relationship between necrotic tissue alteration and protein distributions on ulcers to establish a new prediction method. Thirty‐eight pressure ulcers were retrospectively analyzed. Protein distributions on necrotic tissue were evaluated by the wound blotting at three levels: marker protein positivity, signal patterns (speckled, heterogeneous, or homogeneous), and the occupation of heterogeneous pattern. Peroxidase, alkaline phosphatase, tumor necrosis factor α, and matrix metalloproteinase‐2 were used as marker proteins. One‐week necrotic tissue alteration was classified as liquefaction or nonliquefaction, and associations with protein distributions were analyzed. The peroxidase positivity was significantly higher in the liquefaction than in the nonliquefaction (p = 0.031). In peroxidase‐positive samples, the proportion of nonliquefaction samples was significantly higher in the heterogeneous pattern (p = 0.029). In the heterogeneous‐patterned samples, the proportion of samples with an occupation values greater than the median value tended to be higher in the nonliquefaction (p = 0.087). There was no significant relationship between liquefaction and other markers. Peroxidase positivity predicts 1‐week liquefaction of necrotic tissue, while a heterogeneous pattern indicates nonliquefaction.
Comparative Efficacy of Feline Leukemia Virus (FeLV) Inactivated Whole-Virus Vaccine and Canarypox Virus-Vectored Vaccine during Virulent FeLV Challenge and Immunosuppression
Authors: Patel M. , Carritt K. , Lane J. , Jayappa H. , Stahl M. , Bourgeois M. 
Published: May 2015

ABSTRACTFour vaccines for feline leukemia virus (FeLV) are available in the United States. This study's purpose was to compare the efficacy of Nobivac feline 2-FeLV (an inactivated, adjuvanted whole-virus vaccine) and PureVax recombinant FeLV (a live, canarypox virus-vectored vaccine) following FeLV challenge. Cats were vaccinated at 9 and 12 weeks with Nobivac feline 2-FeLV (group A,n= 11) or PureVax recombinant FeLV (group B,n= 10). Group C (n= 11) comprised unvaccinated controls. At 3 months postvaccination, cats were immunosuppressed and challenged with FeLV-A/61E. The outcomes measured were persistent antigenemia at 12 weeks postchallenge (PC) and proviral DNA and viral RNA at 3 to 9 weeks PC. Persistent antigenemia was observed in 0 of 11 cats in group A, 5 of 10 cats in group B, and 10 of 11 cats in group C. Group A was significantly protected compared to those in groups B (P< 0.013) and C (P< 0.0001). No difference was found between groups B and C (P> 0.063). The preventable fraction was 100% for group A and 45% for group B. At 9 weeks PC, proviral DNA and viral RNA were detected 1 of 11 cats in group A, 6 of 10 cats in group B, and 9 of 11 cats in group C. Nucleic acid loads were significantly lower in group A than in group C (P< 0.01). Group A had significantly lower proviral DNA loads than group B at weeks 6 to 9 (P< 0.02). The viral RNA loads were significantly lower in group A than in group B at weeks 7 to 9 (P< 0.01). The results demonstrate that Nobivac feline 2-FeLV-vaccinated cats were fully protected against persistent antigenemia and had significantly smaller amounts of proviral DNA and plasma viral RNA loads than PureVax recombinant FeLV-vaccinated cats and unvaccinated controls.
Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
Authors: Brown Amanda C. , Bryant Josephine M. , Einer-Jensen Katja , Holdstock Jolyon , Houniet Darren T. , Chan Jacqueline Z. M. , Depledge Daniel P. , Nikolayevskyy Vladyslav , Broda Agnieszka , Stone Madeline J. , Christiansen Mette T. , Williams Rachel , McAndrew Michael B. , Tutill Helena , Brown Julianne , Melzer Mark , Rosmarin Caryn , McHugh Timothy D. , Shorten Robert J. , Drobniewski Francis , Speight Graham , Breuer Judith 
Published: May 2015

ABSTRACT

The rapid identification of antimicrobial resistance is essential for effective treatment of highly resistant
Mycobacterium tuberculosis
. Whole-genome sequencing provides comprehensive data on resistance mutations and strain typing for monitoring transmission, but unlike for conventional molecular tests, this has previously been achievable only from cultures of
M. tuberculosis
. Here we describe a method utilizing biotinylated RNA baits designed specifically for
M. tuberculosis
DNA to capture full
M. tuberculosis
genomes directly from infected sputum samples, allowing whole-genome sequencing without the requirement of culture. This was carried out on 24 smear-positive sputum samples, collected from the United Kingdom and Lithuania where a matched culture sample was available, and 2 samples that had failed to grow in culture.
M. tuberculosis
sequencing data were obtained directly from all 24 smear-positive culture-positive sputa, of which 20 were of high quality (>20× depth and >90% of the genome covered). Results were compared with those of conventional molecular and culture-based methods, and high levels of concordance between phenotypical resistance and predicted resistance based on genotype were observed. High-quality sequence data were obtained from one smear-positive culture-negative case. This study demonstrated for the first time the successful and accurate sequencing of
M. tuberculosis
genomes directly from uncultured sputa. Identification of known resistance mutations within a week of sample receipt offers the prospect for personalized rather than empirical treatment of drug-resistant tuberculosis, including the use of antimicrobial-sparing regimens, leading to improved outcomes.
Competitive Homogeneous Immunoassay for Rapid Serodiagnosis of Hantavirus Disease
Authors: Hepojoki Satu , Rusanen Juuso , Hepojoki Jussi , Nurmi Visa , Vaheri Antti , Lundkvist Åke , Hedman Klaus , Vapalahti Olli 
Published: May 2015

ABSTRACT
In this study, we describe a competitive homogeneous immunoassay that makes use of Förster resonance energy transfer (FRET) in rapid detection of pathogen-specific antibodies. The assay principle is based on competition between a monoclonal antibody (MAb) and serum antibodies to a given antigen. In the assay, named competitive FRET immunoassay (CFRET-IA), the FRET signal is induced if MAb carrying a donor label binds to an acceptor-labeled antigen. Specific antibodies in serum compete for antigen binding, resulting in reduced FRET signal. The proof-of-principle for the assay was obtained using donor-labeled Puumala virus nucleocapsid protein (PUUV-N) and acceptor-labeled anti-PUUV-N MAb. The assay was evaluated by analyzing 329 clinical samples comprising 101 from individuals with acute PUUV infection, 42 from individuals with past infection, and 186 from individuals with PUUV-seronegative sera, and the results were compared to those of reference tests. The rapid serodiagnostic test we introduced herein performed with 100% sensitivity and 99% specificity for diagnosing acute hantavirus disease.
Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci
Authors: van Tonder Andries J. , Bray James E. , Roalfe Lucy , White Rebecca , Zancolli Marta , Quirk Sigríður J. , Haraldsson Gunnsteinn , Jolley Keith A. , Maiden Martin C. J. , Bentley Stephen D. , Haraldsson Ásgeir , Erlendsdóttir Helga , Kristinsson Karl G. , Goldblatt David , Brueggemann Angela B. 
Published: May 2015

ABSTRACT
The pneumococcus is a leading pathogen infecting children and adults. Safe, effective vaccines exist, and they work by inducing antibodies to the polysaccharide capsule (unique for each serotype) that surrounds the cell; however, current vaccines are limited by the fact that only a few of the nearly 100 antigenically distinct serotypes are included in the formulations. Within the serotypes, serogroup 6 pneumococci are a frequent cause of serious disease and common colonizers of the nasopharynx in children. Serotype 6E was first reported in 2004 but was thought to be rare; however, we and others have detected serotype 6E among recent pneumococcal collections. Therefore, we analyzed a diverse data set of ∼1,000 serogroup 6 genomes, assessed the prevalence and distribution of serotype 6E, analyzed the genetic diversity among serogroup 6 pneumococci, and investigated whether pneumococcal conjugate vaccine-induced serotype 6A and 6B antibodies mediate the killing of serotype 6E pneumococci. We found that 43% of all genomes were of serotype 6E, and they were recovered worldwide from healthy children and patients of all ages with pneumococcal disease. Four genetic lineages, three of which were multidrug resistant, described ∼90% of the serotype 6E pneumococci. Serological assays demonstrated that vaccine-induced serotype 6B antibodies were able to elicit killing of serotype 6E pneumococci. We also revealed three major genetic clusters of serotype 6A capsular sequences, discovered a new hybrid 6C/6E serotype, and identified 44 examples of serotype switching. Therefore, while vaccines appear to offer protection against serotype 6E, genetic variants may reduce vaccine efficacy in the longer term because of the emergence of serotypes that can evade vaccine-induced immunity.
Detection of Group A Streptococcus in Pharyngeal Swab Specimens by Use of the AmpliVue GAS Isothermal Helicase-Dependent Amplification Assay
Authors: Faron Matthew L. , Ledeboer Nathan A. , Granato Paul , Daly Judy A. , Pierce Kristina , Pancholi Preeti , Uphoff Timothy S. , Buchan Blake W. 
Published: May 2015

ABSTRACT

We evaluated the clinical performance (sensitivity and specificity) of the AmpliVue group A
Streptococcus
(GAS) isothermal helicase-dependent amplification assay using 1,192 pharyngeal swab specimens. AmpliVue GAS assay results were compared to the results of routine throat cultures on selective streptococcal blood agar plates. The sensitivity and specificity of the AmpliVue GAS assay were 98.3% (95% confidence interval [CI], 95 to 100%) and 93.2% (95% CI, 91 to 95%), respectively.
Commentary: Assessing Airway Microbiota in Cystic Fibrosis: What More Should Be Done?
Authors: LiPuma John J. 
Published: May 2015

ABSTRACT

The use of culture-independent methods has deepened our appreciation of the complexity of the bacterial communities that typically reside in the airways of persons with cystic fibrosis (CF). New insights into how changes in the structure of these communities relate to lung disease progression will likely raise expectations for more in-depth microbiologic analysis of CF respiratory specimens. An article in this issue of the
Journal of Clinical Microbiology
(W. G. Flight, A. Smith, C. Paisey, J. R. Marchesi, M. J. Bull, P. J. Norville, K. J. Mutton, A. K. Webb, R. J. Bright-Thomas, A. M. Jones, and E. Mahenthiralingam, J Clin Microbiol 53:2022–2029, 2015,
http://dx.doi.org/10.1128/JCM.00432-15
) describes the application of a culture-independent approach to the assessment of CF airway microbiota.
The Nuclear DNA Sensor IFI16 Acts as a Restriction Factor for Human Papillomavirus Replication through Epigenetic Modifications of the Viral Promoters
Authors: Lo Cigno Irene , De Andrea Marco , Borgogna Cinzia , Albertini Silvia , Landini Manuela M. , Peretti Alberto , Johnson Karen E. , Chandran Bala , Landolfo Santo , Gariglio Marisa 
Published: May 2015

ABSTRACT
The human interferon-inducible IFI16 protein, an innate immune sensor of intracellular DNA, was recently demonstrated to act as a restriction factor for human cytomegalovirus (HCMV) and herpes simplex virus 1 (HSV-1) infection by inhibiting both viral-DNA replication and transcription. Through the use of two distinct cellular models, this study provides strong evidence in support of the notion that IFI16 can also restrict human papillomavirus 18 (HPV18) replication. In the first model, an immortalized keratinocyte cell line (NIKS) was used, in which the IFI16 protein was knocked down through the use of small interfering RNA (siRNA) technology and overexpressed following transduction with the adenovirus IFI16 (AdVIFI16) vector. The second model consisted of U2OS cells transfected by electroporation with HPV18 minicircles. In differentiated IFI16-silenced NIKS-HPV18 cells, viral-load values were significantly increased compared with differentiated control cells. Consistent with this, IFI16 overexpression severely impaired HPV18 replication in both NIKS and U2OS cells, thus confirming its antiviral restriction activity. In addition to the inhibition of viral replication, IFI16 was also able to reduce viral transcription, as demonstrated by viral-gene expression analysis in U2OS cells carrying episomal HPV18 minicircles and HeLa cells. We also provide evidence that IFI16 promotes the addition of heterochromatin marks and the reduction of euchromatin marks on viral chromatin at both early and late promoters, thus reducing both viral replication and transcription. Altogether, these results argue that IFI16 restricts chromatinized HPV DNA through epigenetic modifications and plays a broad surveillance role against viral DNA in the nucleus that is not restricted to herpesviruses.

IMPORTANCE
Intrinsic immunity is mediated by cellular restriction factors that are constitutively expressed and active even before a pathogen enters the cell. The host nuclear factor IFI16 acts as a sensor of foreign DNA and an antiviral restriction factor, as recently demonstrated by our group for human cytomegalovirus (HCMV) and herpes simplex virus 1 (HSV-1). Here, we provide the first evidence that IFI16 inhibits HPV18 replication by repressing viral-gene expression and replication. This antiviral restriction activity was observed in immortalized keratinocytes transfected with the religated genomes and in U2OS cells transfected with HPV18 minicircles, suggesting that it is not cell type specific. We also show that IFI16 promotes the assembly of heterochromatin on HPV DNA. These changes in viral chromatin structure lead to the generation of a repressive state at both early and late HPV18 promoters, thus implicating the protein in the epigenetic regulation of HPV gene expression and replication.
The Minor Capsid Protein VP11 of Thermophilic Bacteriophage P23-77 Facilitates Virus Assembly by Using Lipid-Protein Interactions
Authors: Pawlowski Alice , Moilanen Anni M. , Rissanen Ilona A. , Määttä Juha A. E. , Hytönen Vesa P. , Ihalainen Janne A. , Bamford Jaana K. H. 
Published: May 2015

ABSTRACT

Thermus thermophilus
bacteriophage P23-77 is the type member of a new virus family of icosahedral, tailless, inner-membrane-containing double-stranded DNA (dsDNA) viruses infecting thermophilic bacteria and halophilic archaea. The viruses have a unique capsid architecture consisting of two major capsid proteins assembled in various building blocks. We analyzed the function of the minor capsid protein VP11, which is the third known capsid component in bacteriophage P23-77. Our findings show that VP11 is a dynamically elongated dimer with a predominantly α-helical secondary structure and high thermal stability. The high proportion of basic amino acids in the protein enables electrostatic interaction with negatively charged molecules, including nucleic acid and large unilamellar lipid vesicles (LUVs). The plausible biological function of VP11 is elucidated by demonstrating the interactions of VP11 with
Thermus
-derived LUVs and with the major capsid proteins by means of the dynamic-light-scattering technique. In particular, the major capsid protein VP17 was able to link VP11-complexed LUVs into larger particles, whereas the other P23-77 major capsid protein, VP16, was unable to link VP11-comlexed LUVs. Our results rule out a previously suggested penton function for VP11. Instead, the electrostatic membrane association of VP11 triggers the binding of the major capsid protein VP17, thus facilitating a controlled incorporation of the two different major protein species into the assembling capsid.

IMPORTANCE
The study of thermophilic viruses with inner membranes provides valuable insights into the mechanisms used for stabilization and assembly of protein-lipid systems at high temperatures. Our results reveal a novel way by which an internal membrane and outer capsid shell are linked in a virus that uses two different major protein species for capsid assembly. We show that a positive protein charge is important in order to form electrostatic interactions with the lipid surface, thereby facilitating the incorporation of other capsid proteins on the membrane surface. This implies an alternative function for basic proteins present in the virions of other lipid-containing thermophilic viruses, whose proposed role in genome packaging is based on their capability to bind DNA. The unique minor capsid protein of bacteriophage P23-77 resembles in its characteristics the scaffolding proteins of tailed phages, though it constitutes a substantial part of the mature virion.
Transcriptome Profiling of the Virus-Induced Innate Immune Response in Pteropus vampyrus and Its Attenuation by Nipah Virus Interferon Antagonist Functions
Authors: Glennon Nicole B. , Jabado Omar , Lo Michael K. , Shaw Megan L. 
Published: May 2015

ABSTRACT

Bats are important reservoirs for several viruses, many of which cause lethal infections in humans but have reduced pathogenicity in bats. As the innate immune response is critical for controlling viruses, the nature of this response in bats and how it may differ from that in other mammals are of great interest. Using next-generation transcriptome sequencing (mRNA-seq), we profiled the transcriptional response of
Pteropus vampyrus
bat kidney (PVK) cells to Newcastle disease virus (NDV), an avian paramyxovirus known to elicit a strong innate immune response in mammalian cells. The
Pteropus
genus is a known reservoir of Nipah virus (NiV) and Hendra virus (HeV). Analysis of the 200 to 300 regulated genes showed that genes for interferon (IFN) and antiviral pathways are highly upregulated in NDV-infected PVK cells, including genes for beta IFN, RIG-I, MDA5, ISG15, and IRF1. NDV-infected cells also upregulated several genes not previously characterized to be antiviral, such as RND1, SERTAD1, CHAC1, and MORC3. In fact, we show that MORC3 is induced by both IFN and NDV infection in PVK cells but is not induced by either stimulus in human A549 cells. In contrast to NDV infection, HeV and NiV infection of PVK cells failed to induce these innate immune response genes. Likewise, an attenuated response was observed in PVK cells infected with recombinant NDVs expressing the NiV IFN antagonist proteins V and W. This study provides the first global profile of a robust virus-induced innate immune response in bats and indicates that henipavirus IFN antagonist mechanisms are likely active in bat cells.

IMPORTANCE
Bats are the reservoir host for many highly pathogenic human viruses, including henipaviruses, lyssaviruses, severe acute respiratory syndrome coronavirus, and filoviruses, and many other viruses have also been isolated from bats. Viral infections are reportedly asymptomatic or heavily attenuated in bat populations. Despite their ecological importance to viral maintenance, research into their immune system and mechanisms for viral control has only recently begun. Nipah virus and Hendra virus are two paramyxoviruses associated with high mortality rates in humans and whose reservoir is the
Pteropus
genus of bats. Greater knowledge of the innate immune response of
P. vampyrus
bats to viral infection may elucidate how bats serve as a reservoir for so many viruses.
Presence of a
trs
-Like Motif Promotes Rep-Mediated Wild-Type Adeno-Associated Virus Type 2 Integration
Authors: Petri Karl , Gabriel Richard , Agundez Leticia , Fronza Raffaele , Afzal Saira , Kaeppel Christine , Linden R. Michael , Henckaerts Els , Schmidt Manfred 
Published: May 2015

ABSTRACT

High-throughput integration site (IS) analysis of wild-type adeno-associated virus type 2 (wtAAV2) in human dermal fibroblasts (HDFs) and HeLa cells revealed that juxtaposition of a Rep binding site (RBS) and terminal resolution site (
trs
)-like motif leads to a 4-fold-increased probability of wtAAV integration. Electrophoretic mobility shift assays (EMSAs) confirmed binding of Rep to off-target RBSs. For the first time, we show Rep protein off-target nicking activity, highlighting the importance of the nicking substrate for Rep-mediated integration.