bluuebunny/crossref_metadata_2025_split huggingface dataset:
Field Evaluation of Dried Blood Spots for Routine HIV-1 Viral Load and Drug Resistance Monitoring in Patients Receiving Antiretroviral Therapy in Africa and Asia
Authors: Monleau Marjorie , Aghokeng Avelin F. , Eymard-Duvernay Sabrina , Dagnra Anoumou , Kania Dramane , Ngo-Giang-Huong Nicole , Touré-Kane Coumba , Truong Lien X. T. , Chaix Marie-Laure , Delaporte Eric , Ayouba Ahidjo , Peeters Martine 
Published: December 2013

ABSTRACT
Dried blood spots (DBS) can be used in developing countries to alleviate the logistic constraints of using blood plasma specimens for viral load (VL) and HIV drug resistance (HIVDR) testing, but they should be assessed under field conditions. Between 2009 and 2011, we collected paired plasma-DBS samples from treatment-experienced HIV-1-infected adults in Burkina Faso, Cameroon, Senegal, Togo, Thailand, and Vietnam. The DBS were stored at an ambient temperature for 2 to 4 weeks and subsequently at −20°C before testing. VL testing was performed on the plasma samples and DBS using locally available methods: the Abbott m2000rt HIV-1 test, generic G2 real-time PCR, or the NucliSENS EasyQ version 1.2 test. In the case of virological failure (VF), i.e., a plasma VL of ≥1,000 copies/ml, HIVDR genotyping was performed on paired plasma-DBS samples. Overall, we compared 382 plasma-DBS sample pairs for DBS VL testing accuracy. The sensitivities of the different assays in different laboratories for detecting VF using DBS varied from 75% to 100% for the m2000rt test in labs B, C, and D, 91% to 93% for generic G2 real-time PCR in labs A and F, and 85% for the NucliSENS test in lab E. The specificities varied from 82% to 97% for the m2000rt and NucliSENS tests and reached only 60% for the generic G2 test. The NucliSENS test showed good agreement between plasma and DBS VL but underestimated the DBS VL. The lowest agreement was observed for the generic G2 test. Genotyping was successful for 96/124 (77%) DBS tested, and 75/96 (78%) plasma-DBS pairs had identical HIVDR mutations. Significant discrepancies in resistance interpretations were observed in 9 cases, 6 of which were from the same laboratory. DBS can be successfully used as an alternative to blood plasma samples for routine VL and HIVDR monitoring in African and Asian settings. However, the selection of an adequate VL measurement method and the definition of the VF threshold should be considered, and laboratory performance should be monitored.
Comparison of Conventional PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Arcobacter Species
Authors: Wang Xiaoyu , Seo Dong Joo , Lee Min Hwa , Choi Changsun 
Published: December 2013

ABSTRACT

This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of
Arcobacter
species. Specific primers targeting the 23S ribosomal RNA gene were used to detect
Arcobacter butzleri
,
Arcobacter cryaerophilus
, and
Arcobacter skirrowii
. The specificity of the LAMP primer set was assessed using DNA samples from a panel of
Arcobacter
and
Campylobacter
species, and the sensitivity was determined using serial dilutions of
Arcobacter
species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction
in vitro
. Whereas multiplex PCR showed cross-reactivity with
Campylobacter
species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of
Arcobacter
species.
Pork Meat as a Potential Source of Salmonella enterica subsp. arizonae Infection in Humans
Authors: Evangelopoulou Grammato , Kritas Spyridon , Govaris Alexander , Burriel Angeliki R. 
Published: December 2013

ABSTRACT

Salmonella enterica
subsp.
arizonae
was isolated from 13 of 123 slaughtered pigs in central Greece. The samples cultured were feces, ileum tissue, mesenteric lymph nodes, and gallbladder swabs. A total of 74 isolates from 492 samples were identified as
Salmonella
spp. by use of standard laboratory culture media and two commercial micromethods and by use of a polyvalent slide agglutination test for the detection of O and H antigens. Among them were 19 (25.68%) suspected to be
S. enterica
subsp.
arizonae
according to analysis with standard laboratory culture media. Of those, 14 were identified as
S. enterica
subsp.
arizonae
by the API 20E (bioMérieux, France) and the Microgen GnA+B-ID (Microgen Bioproducts, Ltd., United Kingdom) identification systems. All the isolates were tested for resistance to 23 antimicrobials. Strains identified as
S. enterica
subsp.
arizonae
were resistant to 17 (70.8%) antibiotics. The highest proportions of resistance were observed for sulfamethoxazole-trimethoprim (71.4%), tetracycline (71.4%), ampicillin (64.3%), and amoxicillin (57.1%). Two isolates were resistant to aztreonam (7.1%) and tigecycline (7.1%), used only for the treatment of humans. Thus, pork meat may play a role in the transmission of antibiotic-resistant
S. enterica
subsp.
arizonae
to human consumers. This is the first report of
S. enterica
subsp.
arizonae
isolation from pigs.
Brain Abscess Caused by Ureaplasma urealyticum in an Adult Patient
Authors: Deetjen Philipp , Maurer Christoph , Rank Andreas , Berlis Ansgar , Schubert Sören , Hoffmann Reinhard 
Published: December 2013

ABSTRACT

Ureaplasma urealyticum
is a fastidious bacterium usually residing in the female genitourinary tract. We present an exceedingly complicated case of a brain abscess secondary to mastoiditis by
U. urealyticum
in an adult hypogammaglobulinemic patient after rituximab treatment 3 years earlier.
Ablation of Nectin4 Binding Compromises CD46 Usage by a Hybrid Vesicular Stomatitis Virus/Measles Virus
Authors: Liu Yu-Ping , Russell Samuel P. , Ayala-Breton Camilo , Russell Stephen J. , Peng Kah-Whye 
Published: December 2013

ABSTRACT
Measles virus (MV) immunosuppression is due to infection of SLAM-positive immune cells, whereas respiratory shedding and virus transmission are due to infection of nectin4-positive airway epithelial cells. The vaccine lineage MV strain Edmonston (MV-Edm) acquired an additional tropism for CD46 which is the basis of its oncolytic specificity. VSVFH is a vesicular stomatitis virus (VSV) encoding the MV-Edm F and H entry proteins in place of G. The virus spreads faster than MV-Edm and is highly fusogenic and a potent oncolytic. To determine whether ablating nectin4 tropism from VSVFH might prevent shedding, increasing its safety profile as an oncolytic, or might have any effect on CD46 binding, we generated VSVFH viruses with H mutations that disrupt attachment to SLAM and/or nectin4. Disruption of nectin4 binding reduced release of VSVFH from the basolateral side of differentiated airway epithelia composed of Calu-3 cells. However, because nectin4 and CD46 have substantially overlapping receptor binding surfaces on H, disruption of nectin4 binding compromised CD46 binding and greatly diminished the oncolytic potency of these viruses on human cancer cells. Thus, our results support continued preclinical development of VSVFH without ablation of nectin4 binding.
Infection of Myofibers Contributes to Increased Pathogenicity during Infection with an Epidemic Strain of Chikungunya Virus
Authors: Rohatgi Anjali , Corbo Joseph C. , Monte Kristen , Higgs Stephen , Vanlandingham Dana L. , Kardon Gabrielle , Lenschow Deborah J. 
Published: December 2013

ABSTRACT

Chikungunya virus (CHIKV) is an alphavirus transmitted by mosquitoes that is known to cause severe arthritis and myositis in affected patients. The ongoing epidemic began in eastern Africa in 2004 and then spread to islands of the Indian Ocean, India, and Southeast Asia, ultimately afflicting millions. During this outbreak, more severe disease manifestations, including fatalities, have been documented. The reasons for this change in pathogenesis are multifactorial but likely include mutations that have arisen in the viral genome which could alter disease pathogenesis. To test this hypothesis, we used a murine model of CHIKV to compare the disease pathogeneses of two recombinant strains of CHIKV, the first derived from the La Reunion outbreak in 2006 (LR2006 OPY1) and the second isolated from Senegal in 1983 (37997). While the two strains exhibited similar growth in mammalian cells
in vitro
, we observed more severe clinical disease and pathology in mice infected with the LR2006 OPY1 strain of CHIKV, which included prolonged viremia and elevated viral titers and persistence in the muscle, resulting in devastating myonecrosis. Both CHIKV strains infected connective tissue fibroblasts of the muscle, but only the LR2006 OPY1 strain replicated within myofibers
in vivo
, despite similar growth of the two strains in these cell types
in vitro
. However, when the 37997 strain was administered directly into muscle, myofiber infection was comparable to that in LR2006 OPY1-infected mice. These results indicate that differences in the ability of the strain of CHIKV to establish infection in myofibers may contribute to the increased disease severity.

IMPORTANCE
CHIKV is an emerging pathogen that causes significant morbidity. Little is known about the pathogenesis of the disease, and this study suggests that the ability of a recent epidemic strain to infect myofibers results in increased disease severity. Better understanding of how CHIKV causes disease contributes to the ultimate goal of creating therapeutics to alleviate the impact of this debilitating virus.
STAT1 Interaction with E3-14.7K in Monocytes Affects the Efficacy of Oncolytic Adenovirus
Authors: Spurrell Emma , Gangeswaran Rathi , Wang Pengju , Cao Fengyu , Gao Dongling , Feng Baisui , Wold William , Tollefson Ann , Lemoine Nicholas R. , Wang Yaohe 
Published: December 2013

ABSTRACT

Oncolytic viruses based on adenovirus type 5 (Ad5) have been developed as a new class of therapeutic agents for cancers that are resistant to conventional therapies. Clinical experience shows that these agents are safe, but virotherapy alone has not achieved long-term cure in cancer patients. The vast majority of oncolytic adenoviruses used in clinical trials to date have deletion of the E3B genes. It has been demonstrated that the antitumor potency of the E3B-deleted mutant (
dl
309) is inferior to adenovirus with E3B genes intact. Tumors treated with
dl
309 show markedly greater macrophage infiltration than E3B-intact adenovirus. However, the functional mechanisms for this were not previously known. Here, we demonstrate that deletion of E3B genes increases production of chemokines by monocytes after adenovirus infection and increases monocyte migration. The E3B 14,700-Da protein (E3B-14.7K) inhibits STAT1 function by preventing its phosphorylation and nuclear translocation. The STAT1 inhibitor, fludarabine, rescues the effect of E3B-14.7K deletion by downregulating target chemokine expression in human and murine monocytes and results in an enhanced antitumor efficacy with
dl
309
in vivo
. These findings have important implications for clinical use of E3B-deleted oncolytic adenovirus and other E3B-deleted adenovirus vector-based therapy.
Structural Basis for HIV-1 Neutralization by 2F5-Like Antibodies m66 and m66.6
Authors: Ofek Gilad , Zirkle Brett , Yang Yongping , Zhu Zhongyu , McKee Krisha , Zhang Baoshan , Chuang Gwo-Yu , Georgiev Ivelin S. , O'Dell Sijy , Doria-Rose Nicole , Mascola John R. , Dimitrov Dimiter S. , Kwong Peter D. 
Published: December 2013

ABSTRACT
Antibodies m66.6 and 2F5 are the only effective human HIV-1-neutralizing antibodies reported thus far to recognize the N-terminal region of the membrane-proximal external region (MPER) of the gp41 subunit of the HIV-1 envelope glycoprotein. Although 2F5 has been extensively characterized, much less is known about antibody m66.6 or antibody m66, a closely related light-chain variant. Here, we report the crystal structure of m66 in complex with its gp41 epitope, along with unbound structures of m66 and m66.6. We used mutational and binding analyses to decipher antibody elements critical for their recognition of gp41 and determined the molecular basis that underlies their neutralization of HIV-1. When bound by m66, the N-terminal region of the gp41 MPER adopts a conformation comprising a helix, followed by an extended loop. Comparison of gp41-bound m66 to unbound m66.6 identified three light-chain residues of m66.6 that were confirmed through mutagenesis to underlie the greater breadth of m66.6-mediated virus neutralization. Recognition of gp41 by m66 also revealed similarities to antibody 2F5 both in the conformation of crucial epitope residues as well as in the angle of antibody approach. Aromatic residues at the tip of the m66.6 heavy-chain third complementarity-determining region, as in the case of 2F5, were determined to be critical for virus neutralization in a manner that correlated with antibody recognition of the MPER in a lipid context. Antibodies m66, m66.6, and 2F5 thus utilize similar mechanistic elements to recognize a common gp41-MPER epitope and to neutralize HIV-1.
Sirtuin 1 Regulates Hepatitis B Virus Transcription and Replication by Targeting Transcription Factor AP-1
Authors: Ren Ji-Hua , Tao Ying , Zhang Zhen-Zhen , Chen Wei-Xian , Cai Xue-Fei , Chen Ke , Ko Ben C. B. , Song Chun-Li , Ran Long-Kuan , Li Wan-Yu , Huang Ai-Long , Chen Juan 
Published: December 2013

ABSTRACT
Chronic hepatitis B virus (HBV) infection is a major risk factor for liver cirrhosis and hepatocellular carcinoma. Nevertheless, the molecular mechanism of HBV replication remains elusive. SIRT1 is a class III histone deacetylase that is a structure component of the HBV cccDNA minichromosome. In this study, we found by using microarray-based gene expression profiling analysis that SIRT1 was upregulated in HBV-expressing cells. Gene silencing of SIRT1 significantly inhibited HBV DNA replicative intermediates, 3.5-kb mRNA, and core protein levels. In contrast, the overexpression of SIRT1 augmented HBV replication. Furthermore, SIRT1 enhanced the activity of HBV core promoter by targeting transcription factor AP-1. The c-Jun subunit of AP-1 was bound to the HBV core promoter region, as demonstrated by using a chromatin immunoprecipitation assay. Mutation of AP-1 binding site or knockdown of AP-1 abolished the effect of SIRT1 on HBV replication. Finally, SIRT1 inhibitor sirtinol also suppressed the HBV DNA replicative intermediate, as well as 3.5-kb mRNA. Our study identified a novel host factor, SIRT1, which may facilitate HBV replication in hepatocytes. These data suggest a rationale for the use of SIRT1 inhibitor in the treatment of HBV infection.
Unification of the Globally Distributed Spindle-Shaped Viruses of the Archaea
Authors: Krupovic Mart , Quemin Emmanuelle R. J. , Bamford Dennis H. , Forterre Patrick , Prangishvili David 
Published: December 2013

ABSTRACT

Viruses with spindle-shaped virions are abundant in diverse environments. Over the years, such viruses have been isolated from a wide range of archaeal hosts. Evolutionary relationships between them remained enigmatic, however. Here, using structural proteins as markers, we define familial ties among these “dark horses” of the virosphere and segregate all spindle-shaped viruses into two distinct evolutionary lineages, corresponding to
Bicaudaviridae
and
Fuselloviridae
. Our results illuminate the utility of structure-based virus classification and bring additional order to the virosphere.
Hantavirus Gn and Gc Glycoproteins Self-Assemble into Virus-Like Particles
Authors: Acuña Rodrigo , Cifuentes-Muñoz Nicolás , Márquez Chantal L. , Bulling Manuela , Klingström Jonas , Mancini Roberta , Lozach Pierre-Yves , Tischler Nicole D. 
Published: December 2013

ABSTRACT
How hantaviruses assemble and exit infected cells remains largely unknown. Here, we show that the expression of Andes (ANDV) and Puumala (PUUV) hantavirus Gn and Gc envelope glycoproteins lead to their self-assembly into virus-like particles (VLPs) which were released to cell supernatants. The viral nucleoprotein was not required for particle formation. Further, a Gc endodomain deletion mutant did not abrogate VLP formation. The VLPs were pleomorphic, exposed protrusions and reacted with patient sera.
Encephalomyocarditis Virus Leader Is Phosphorylated by CK2 and Syk as a Requirement for Subsequent Phosphorylation of Cellular Nucleoporins
Authors: Basta Holly A. , Bacot-Davis Valjean R. , Ciomperlik Jessica J. , Palmenberg Ann C. 
Published: December 2013

ABSTRACT

Encephalomyocarditis virus
and
Theilovirus
are species in the
Cardiovirus
genus of the
Picornaviridae
family. For all cardioviruses, the viral polyprotein is initiated with a short Leader (L) protein unique to this genus. The nuclear magnetic resonance (NMR) structure of L
E
from encephalomyocarditis virus (EMCV) has been determined. The protein has an NH
2
-proximal CHCC zinc finger, a central linker, and a contiguous, highly acidic motif. The theiloviruses encode the same domains, with one or two additional, COOH-proximal domains, characteristic of the human Saffold viruses (SafV) and Theiler's murine encephalomyelitis viruses (TMEV), respectively. The expression of a cardiovirus L, in recombinant form, or during infection/transfection, triggers an extensive, cell-dependent, antihost phosphorylation cascade, targeting nucleoporins (Nups) that form the hydrophobic core of nuclear pore complexes (NPC). The consequent inhibition of active nucleocytoplasmic trafficking is potent and prevents the host from mounting an effective antiviral response. For this inhibition, the L proteins themselves must be phosphorylated. In cells (extracts or recombinant form), L
E
was shown to be phosphorylated at Thr
47
and Tyr
41
. The first reaction (Thr
47
), catalyzed by casein kinase 2 (CK2), is an obligatory precedent to the second event (Tyr
41
), catalyzed by spleen tyrosine kinase (Syk). Site mutations in L
E
, or kinase-specific inhibitors, prevented L
E
phosphorylation and subsequent Nup phosphorylation. Parallel experiments with L
S
(SafV-2) and L
T
(TMEV BeAn) proteins confirmed the general cardiovirus requirement for L phosphorylation, but CK2 was not the culpable kinase. It is likely that L
S
and L
T
are both activated by alternative kinases in different cell types, probably reactive within the Theilo-specific domains.

IMPORTANCE
An understanding of the diverse methods used by viruses to interfere with cellular processes is important because they can teach us how to control virus infections. This report shows how viruses in the same genus use different cellular enzymes to phosphorylate their proteins. If these processes are interfered with, the viruses are severely disabled.
Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotypes
Authors: Pope Welkin H. , Anders Kirk R. , Baird Madison , Bowman Charles A. , Boyle Michelle M. , Broussard Gregory W. , Chow Tiffany , Clase Kari L. , Cooper Shannon , Cornely Kathleen A. , DeJong Randall J. , Delesalle Veronique A. , Deng Lisa , Dunbar David , Edgington Nicholas P. , Ferreira Christina M. , Weston Hafer Kathleen , Hartzog Grant A. , Hatherill J. Robert , Hughes Lee E. , Ipapo Khristina , Krukonis Greg P. , Meier Christopher G. , Monti Denise L. , Olm Matthew R. , Page Shallee T. , Peebles Craig L. , Rinehart Claire A. , Rubin Michael R. , Russell Daniel A. , Sanders Erin R. , Schoer Morgan , Shaffer Christopher D. , Wherley James , Vazquez Edwin , Yuan Han , Zhang Daiyuan , Cresawn Steven G. , Jacobs-Sera Deborah , Hendrix Roger W. , Hatfull Graham F. 
Published: December 2013

ABSTRACT

Genomic analysis of a large set of phages infecting the common host
Mycobacterium smegmatis
mc
2
155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode.

IMPORTANCE
The bacteriophage population is vast, dynamic, and old and plays a central role in bacterial pathogenicity. We know surprisingly little about the genetic diversity of the phage population, although metagenomic and phage genome sequencing indicates that it is great. Probing the depth of genetic diversity of phages of a common host,
Mycobacterium smegmatis
, provides a higher resolution of the phage population and how it has evolved. Three new phages constituting a new cluster M further expand the diversity of the mycobacteriophages and introduce novel features. As such, they provide insights into phage genome architecture, virion structure, and gene regulation at the transcriptional and translational levels.
Evasion of Antiviral Immunity through Sequestering of TBK1/IKKε/IRF3 into Viral Inclusion Bodies
Authors: Wu Xiaodong , Qi Xian , Qu Bingqian , Zhang Zerui , Liang Mifang , Li Chuan , Cardona Carol J. , Li Dexin , Xing Zheng 
Published: December 2013

ABSTRACT

Cells are equipped with pattern recognition receptors (PRRs) such as the Toll-like and RIG-I-like receptors that mount innate defenses against viruses. However, viruses have evolved multiple strategies to evade or thwart host antiviral responses. Viral inclusion bodies (IBs), which are accumulated aggregates of viral proteins, are commonly formed during the replication of some viruses in infected cells, but their role in viral immune evasion has rarely been explored. Severe fever with thrombocytopenia syndrome (SFTS) is an emerging febrile illness caused by a novel phlebovirus in the
Bunyaviridae
. The SFTS viral nonstructural protein NSs can suppress host beta interferon (IFN-β) responses. NSs can form IBs in infected and transfected cells. Through interaction with tank-binding kinase 1 (TBK1), viral NSs was able to sequester the IKK complex, including IKKε and IRF3, into IBs, although NSs did not interact with IKKε or IRF3 directly. When cells were infected with influenza A virus, IRF3 was phosphorylated and active phosphorylated IRF3 (p-IRF3) was translocated into the nucleus. In the presence of NSs, IRF3 could still be phosphorylated, but p-IRF3 was trapped in cytoplasmic IBs, resulting in reduced IFN-β induction and enhanced viral replication. Sequestration of the IKK complex and active IRF3 into viral IBs through the interaction of NSs and TBK1 is a novel mechanism for viral evasion of innate immunity.
Vitamin D receptor gene polymorphisms and the risk of rickets among Asians: a meta-analysis
Authors: Mao Song , Huang Songming 
Published: December 2013

This article has been retracted. Dr Songming Huang has advised that although he agreed to be listed as the correspondence author he should not have been named as a co-author of this publication because he made no contributions to it.He and Song Mao have asked for the article to be retracted on the ground that data included in it and its conclusions are to a significant degree the same as those previously published in Chin J Evid Based Pediatr 2011;6:4.