bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of changes in physical activity on frequency of hospitalization in chronic obstructive pulmonary disease
Authors: Esteban Cristóbal , Arostegui Inmaculada , Aburto Myriam , Moraza Javier , Quintana José M. , Aizpiri Susana , Basualdo Luis V. , Capelastegui Alberto 
Published: February 2014

AbstractBackground and objectiveTo evaluate whether changes in regular physical activity (PA) in patients with chronic obstructive pulmonary disease (COPD) affect the rate of hospitalizations for COPD exacerbation (eCOPD).MethodsFive hundred forty‐three ambulatory clinic patients being treated for COPD were prospectively identified. PA was self‐reported by patients, and the level was established by the distance they walked (km/day) at least 3 days per week. Hospitalizations were recorded from hospital databases. All patients with at least a 2‐year follow‐up after enrolment were included in the analysis. The response variable was the number of hospitalizations for eCOPD within the 3‐year period from 2 to 5 years after study enrolment.ResultsThree hundred ninety‐one survivors were studied. Mean forced expiratory volume in 1 s was 52% (±14%) of the predicted value. Patients who maintained a lower level of PA had an increased rate of hospitalization (odds ratio 1.901; 95% confidence interval 1.090–3.317). After having had the highest level of PA, those patients who decreased their PA in the follow‐up showed an increasing rate of hospitalizations (odds ratio 2.134; 95% confidence interval 1.146–3.977).ConclusionsPatients with COPD with a low level of PA or who reduced their PA over time were more likely to experience a significant increase in the rate of hospitalization for eCOPD. Changes to a higher level of PA or maintaining a moderate or high level of PA over time, with a low intensity activity such as walking for at least 3–6 km/day, could reduce the rate of hospitalizations for eCOPD.
Comments on Quantum Probability Theory
Authors: Sloman Steven 
Published: January 2014

AbstractQuantum probability theory (QP) is the best formal representation available of the most common form of judgment involving attribute comparison (inside judgment). People are capable, however, of judgments that involve proportions over sets of instances (outside judgment). Here, the theory does not do so well. I discuss the theory both in terms of descriptive adequacy and normative appropriateness.
Quantum and Concept Combination, Entangled Measurements, and Prototype Theory
Authors: Aerts Diederik 
Published: January 2014

AbstractWe analyze the meaning of the violation of the marginal probability law for situations of correlation measurements where entanglement is identified. We show that for quantum theory applied to the cognitive realm such a violation does not lead to the type of problems commonly believed to occur in situations of quantum theory applied to the physical realm. We briefly situate our quantum approach for modeling concepts and their combinations with respect to the notions of “extension” and “intension” in theories of meaning, and in existing concept theories.
Regulated Oligomerization Induces Uptake of a Membrane Protein into COPII Vesicles Independent of Its Cytosolic Tail
Authors: Springer Sebastian , Malkus Per , Borchert Britta , Wellbrock Ursula , Duden Rainer , Schekman Randy 
Published: January 2014

Export of transmembrane proteins from the endoplasmic reticulum (ER) is driven by directed incorporation into coat protein complex II (COPII)‐coated vesicles. The sorting of some cargo proteins into COPII vesicles was shown to be mediated by specific interactions between transmembrane and COPII‐coat‐forming proteins. But even though some signals for ER exit have been identified on the cytosolic domains of membrane proteins, the general signaling and sorting mechanisms of ER export are still poorly understood. To investigate the role of cargo protein oligomer formation in the export process, we have created a transmembrane fusion protein that – owing to its FK506‐binding protein domains – can be oligomerized in isolated membranes by addition of a small‐molecule dimerizer. Packaging of the fusion protein into COPII vesicles is strongly enhanced in the presence of the dimerizer, demonstrating that the oligomeric state is an ER export signal for this membrane protein. Surprisingly, the cytosolic tail is not required for this oligomerization‐dependent effect on protein sorting. Thus, an alternative mechanism, such as membrane bending, must account for ER export of the fusion protein.
Pure Exporter: Theory and Evidence from China
Authors: Lu Jiangyong , Lu Yi , Tao Zhigang 
Published: January 2014

AbstractThis article provides the first evidence about pure exporters (i.e. firms exporting all of their output to the foreign market) – a phenomenon overlooked and cannot be explained in the existing literature. It then offers a theoretical analysis of the existence and behaviour of pure exporters. In particular, pure exporters arise when the export market is sufficiently large – a situation more likely to hold in developing countries as opposed to large developed countries, and their productivity levels are above those of nonexporters, but below those of firms having both domestic sales and export. These theoretical predictions are borne out in a data of Chinese manufacturing firms for the period of 1998–2005.
Performance of the BioPlex 2200 Flow Immunoassay in Critical Cases of Serodiagnosis of Toxoplasmosis
Authors: Guigue Nicolas , Menotti Jean , Hamane Samia , Derouin Francis , Garin Yves Jean-François 
Published: January 2014

ABSTRACT

The BioPlex 2200 automated analyzer (Bio-Rad Laboratories, Hercules, CA) is a recently developed multiplex analyzer that enables the detection of anti-
Toxoplasma
, -rubella, and -cytomegalovirus antibodies in the same assay. The aim of this study was to compare this new technology (using the BioPlex 2200 ToRC IgG/IgM kit) in critical cases of serodiagnosis of toxoplasmosis (acute, chronic, or congenital infections and cases with discrepant results) to the technologies used in our routine practice, i.e., the Platelia IgG/IgM enzyme-linked immunosorbent assays (ELISAs) (Bio-Rad Laboratories) and the Toxo-Screen direct agglutination assay (bioMérieux, Lyon, France). Overall, most cases of false-positive/negative results obtained with the Platelia IgG or Toxo-Screen assay were corrected by the BioPlex 2200 ToRC IgG (87.5%). Furthermore, the analysis of 35 sequences of sera showed a trend toward a more rapid decrease of IgM titers by BioPlex 2200 than by Platelia. These results for IgM detection can be explained by a weaker detection of residual IgM. Indeed, among 23 serum samples from patients with probable past infection with long-lasting IgM (Platelia M positive and IgG avidity index, ≥0.5), the BioPlex 2200
Toxoplasma
IgM assay was positive for only 11 serum samples. In our panel of critical cases comprising 156 serum and 6 cord blood samples from 103 patients with acute, chronic, or congenital infection, the BioPlex 2200 IgG assay was a sensitive (97.8%) and specific (91.3%) method for IgG detection. The high specificity (97.4%) of IgM detection combined with the shorter kinetics of IgM titers may considerably reduce the number of residual IgM detections, thus yielding more precise diagnoses of acute infections.
Multiplex High-Resolution Melting Analysis as a Diagnostic Tool for Detection of Plasmid-Mediated AmpC β-Lactamase Genes
Authors: Geyer Chelsie N. , Hanson Nancy D. 
Published: January 2014

ABSTRACT

High-resolution melting (HRM) analysis can be a diagnostic tool to evaluate the presence of resistance genes with the added bonus of discriminating sequence modifications. A real-time, multiplex PCR assay using HRM was designed for the detection of plasmid-mediated
ampC
genes. The specificity and sensitivity of this assay were 96% and 100%, respectively.
Simultaneous Detection of Five Enteric Viruses Associated with Gastroenteritis by Use of a PCR Assay: a Single Real-Time Multiplex Reaction and Its Clinical Application
Authors: Jiang Yixiang , Fang Lin , Shi Xiaolu , Zhang Hailong , Li Yinghui , Lin Yiman , Qiu Yaqun , Chen Qingliang , Li Hui , Zhou Li , Hu Qinghua 
Published: January 2014

ABSTRACT
We developed a highly sensitive reverse transcription and multiplex real-time PCR (rtPCR) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups I and II; sapovirus genogroups I, II, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. In comparison to monoplex rtPCR assays, the sensitivities and specificities of the multiplex rtPCR ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clinical stool specimens.
Specific Noninvasive Detection of Leishmania donovani in Desquamated Buccal Cell Swab Samples from Human Visceral Leishmaniasis-HIV Coinfected Patients
Authors: Das Sushmita , Halder Avishek , Rabidas Vidya Nand , Mandal Abhishek , Das Pradeep 
Published: January 2014

ABSTRACT
Diagnosis of human immunodeficiency virus (HIV) infection with visceral leishmaniasis (VL) coinfection is challenging. Specific diagnosis of VL in HIV-coinfected patients was evaluated by molecular methods in desquamated buccal swab samples, demonstrating 86.3% sensitivity and 98.3% specificity in controls. This test holds significant potential for development as a noninvasive diagnostic tool for VL in HIV-coinfected patients.
Tools for Detection of Mycoplasma amphoriforme: a Primary Respiratory Pathogen?
Authors: Ling Clare L. , Oravcova Katarina , Beattie Thomas F. , Creer Dean D. , Dilworth Paul , Fulton Naomi L. , Hardie Alison , Munro Michelle , Pond Marcus , Templeton Kate , Webster David , Workman Sarita , McHugh Timothy D. , Gillespie Stephen H. 
Published: January 2014

ABSTRACT

Mycoplasma amphoriforme
is a recently described organism isolated from the respiratory tracts of patients with immunodeficiency and evidence of chronic infection. Novel assays for the molecular detection of the organism by real-time quantitative PCRs (qPCRs) targeting the uracil DNA glycosylase gene (
udg
) or the 23S rRNA gene are described here. The analytical sensitivities are similar to the existing conventional
M. amphoriforme
16S rRNA gene PCR, with the advantage of being species specific, rapid, and quantitative. By using these techniques, we demonstrate the presence of this organism in 17 (19.3%) primary antibody-deficient (PAD) patients, 4 (5%) adults with lower respiratory tract infection, 1 (2.6%) sputum sample from a patient attending a chest clinic, and 23 (0.21%) samples submitted for viral diagnosis of respiratory infection, but not in normal adult control subjects. These data show the presence of this microorganism in respiratory patients and suggest that
M. amphoriforme
may infect both immunocompetent and immunocompromised people. Further studies to characterize this organism are required, and this report provides the tools that may be used by other research groups to investigate its pathogenic potential.
Real-Time PCR Assay for Detection of
blaZ
Genes in Staphylococcus aureus Clinical Isolates
Authors: Pereira Lynette A. , Harnett Gerald B. , Hodge Meredith M. , Cattell Julia A. , Speers David J. 
Published: January 2014

ABSTRACT

The Clinical and Laboratory Standards Institute recommends consideration of
blaZ
gene testing for cases of serious
Staphylococcus aureus
infection. Conventional PCR methods have demonstrated superior sensitivity and specificity to phenotypic tests. To our knowledge, this is the first description of real-time PCR detection of the
blaZ
gene.
Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients with Hospital Readmissions
Authors: Eghbaria Saleh , Schnitser Kathy , Danial-Farran Nada , Keness Yoram , Bisharat Naiel 
Published: January 2014

ABSTRACT

It is unclear whether patients colonized with methicillin-resistant
Staphylococcus aureus
(MRSA) continue to harbor the same genotype during hospital readmissions. We characterized 140 MRSA strains isolated from 33 persistent MRSA carriers with hospital readmissions. Nearly half of the patients continued to harbor the same genotype, and the rest acquired different genotypes. Among 25 patients who received eradication therapy, 16 (64%) were colonized with MRSA strains exhibiting different genotypes from the preexisting one.
Specific Sequence of a Beta Turn in Human La Protein May Contribute to Species Specificity of Hepatitis C Virus
Authors: Kumar Anuj , Manna Asit Kumar , Ray Upasana , Mullick Ranajoy , Basu Gautam , Das Saumitra , Roy Siddhartha 
Published: January 2014

ABSTRACT

Human La protein is known to be an essential host factor for translation and replication of hepatitis C virus (HCV) RNA. Previously, we have demonstrated that residues responsible for interaction of human La protein with the HCV internal ribosomal entry site (IRES) around the initiator AUG within stem-loop IV form a β-turn in the RNA recognition motif (RRM) structure. In this study, sequence alignment and mutagenesis suggest that the HCV RNA-interacting β-turn is conserved only in humans and chimpanzees, the species primarily known to be infected by HCV. A 7-mer peptide corresponding to the HCV RNA-interacting region of human La inhibits HCV translation, whereas another peptide corresponding to the mouse La sequence was unable to do so. Furthermore, IRES-mediated translation was found to be significantly high in the presence of recombinant human La protein
in vitro
in rabbit reticulocyte lysate. We observed enhanced replication with HCV subgenomic and full-length replicons upon overexpression of either human La protein or a chimeric mouse La protein harboring a human La β-turn sequence in mouse cells. Taken together, our results raise the possibility of creating an immunocompetent HCV mouse model using human-specific cell entry factors and a humanized form of La protein.

IMPORTANCE
Hepatitis C virus is known to infect only humans and chimpanzees under natural conditions. This has prevented the development of a small-animal model, which is important for development of new antiviral drugs. Although a number of human-specific proteins are responsible for this species selectivity and some of these proteins—-mostly entry factors—-have been identified, full multiplication of the virus in mouse cells is still not possible. In this study, we show that a turn in the human La protein that is responsible for the interaction with the viral RNA is highly specific for the human sequence. Replacement of the corresponding mouse sequence with the human sequence allows the mouse La to behave like its human counterpart and support viral growth in the mouse cell efficiently. This observation, in combination with previously identified cell entry factors, should open up the possibility of creating a mouse model of hepatitis C.
Inhibition of Hepatitis C Virus in Chimeric Mice by Short Synthetic Hairpin RNAs: Sequence Analysis of Surviving Virus Shows Added Selective Pressure of Combination Therapy
Authors: Dallas Anne , Ilves Heini , Ma Han , Chin Daniel J. , MacLachlan Ian , Klumpp Klaus , Johnston Brian H. 
Published: January 2014

ABSTRACT

We have recently shown that a cocktail of two short synthetic hairpin RNAs (sshRNAs), targeting the internal ribosome entry site of hepatitis C virus (HCV) formulated with lipid nanoparticles, was able to suppress viral replication in chimeric mice infected with HCV GT1a by up to 2.5 log
10
(H. Ma et al., Gastroenterology 146:63–66.e5,
http://dx.doi.org/10.1053/j.gastro.2013.09.049
) Viral load remained about 1 log
10
below pretreatment levels 21 days after the end of dosing. We have now sequenced the HCV viral RNA amplified from serum of treated mice after the 21-day follow-up period. Viral RNA from the HCV sshRNA-treated groups was altered in sequences complementary to the sshRNAs and nowhere else in the 500-nucleotide sequenced region, while the viruses from the control group that received an irrelevant sshRNA had no mutations in that region. The ability of the most commonly selected mutations to confer resistance to the sshRNAs was confirmed
in vitro
by introducing those mutations into HCV-luciferase reporters. The mutations most frequently selected by sshRNA treatment within the sshRNA target sequence occurred at the most polymorphic residues, as identified from an analysis of available clinical isolates. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNA interference (RNAi) mechanism of action.

IMPORTANCE
This study presents a detailed analysis of the impact of treating a hepatitis C virus (HCV)-infected animal with synthetic hairpin-shaped RNAs that can degrade the virus's RNA genome. These RNAs can reduce the viral load in these animals by over 99% after 1 to 2 injections. The study results confirm that the viral rebound that often occurred a few weeks after treatment is due to emergence of a virus whose genome is mutated in the sequences targeted by the RNAs. The use of two RNA inhibitors, which is more effective than use of either one by itself, requires that any resistant virus have mutations in the targets sites of both agents, a higher hurdle, if the virus is to retain the ability to replicate efficiently. These results demonstrate a direct antiviral activity with effective HCV suppression, demonstrate the added selective pressure of combination therapy, and confirm an RNAi mechanism of action.
Role of Phosphatidylserine Receptors in Enveloped Virus Infection
Authors: Morizono Kouki , Chen Irvin S. Y. 
Published: January 2014

ABSTRACTWe recently demonstrated that a soluble protein, Gas6, can facilitate viral entry by bridging viral envelope phosphatidylserine to Axl, a receptor tyrosine kinase expressed on target cells. The interaction between phosphatidylserine, Gas6, and Axl was originally shown to be a molecular mechanism through which phagocytes recognize phosphatidylserine exposed on dead cells. Since our initial report, several groups have confirmed that Axl/Gas6, as well as other phosphatidylserine receptors, facilitate entry of dengue, West Nile, and Ebola viruses. Virus binding by viral envelope phosphatidylserine is now a viral entry mechanism generalized to many families of viruses. In addition to Axl/Gas6, various molecules are known to recognize phosphatidylserine; however, the effects of these molecules on virus binding and entry have not been comprehensively evaluated and compared. In this study, we examined most of the known human phosphatidylserine-recognizing molecules, including MFG-E8, TIM-1, -3, and -4, CD300a, BAI1, and stabilin-1 and -2, for their abilities to facilitate virus binding and infection. Using pseudotyped lentiviral vectors, we found that a soluble phosphatidylserine-binding protein, MFG-E8, enhances transduction. Cell surface receptors TIM-1 and -4 also enhance virus binding/transduction. The extent of enhancement by these molecules varies, depending on the type of pseudotyping envelope proteins. Mutated MFG-E8, which binds viral envelope phosphatidylserine without bridging virus to cells, but, surprisingly, not annexin V, which has been used to block phagocytosis of dead cells by concealing phosphatidylserine, efficiently blocks these phosphatidylserine-dependent viral entry mechanisms. These results provide insight into understanding the role of viral envelope phosphatidylserine in viral infection.IMPORTANCEEnvelope phosphatidylserine has previously been shown to be important for replication of various envelope viruses, but details of this mechanism(s) were unclear. We were the first to report that a bifunctional serum protein, Gas6, bridges envelope phosphatidylserine to a cell surface receptor, Axl. Recent studies demonstrated that many envelope viruses, including vaccinia, dengue, West Nile, and Ebola viruses, utilize Axl/Gas6 to facilitate their entry, suggesting that the phosphatidylserine-mediated viral entry mechanism can be shared by various enveloped viruses. In addition to Axl/Gas6, various molecules are known to recognize phosphatidylserine; however, the effects of these molecules on virus binding and entry have not been comprehensively evaluated and compared. In this study, we examined most human phosphatidylserine-recognizing molecules for their abilities to facilitate viral infection. The results provide insights into the role(s) of envelope phosphatidylserine in viral infection, which can be applicable to the development of novel antiviral reagents that block phosphatidylserine-mediated viral entry.
Development of Continuous Cell Culture of Brown Planthopper To Trace the Early Infection Process of Oryzaviruses in Insect Vector Cells
Authors: Chen Hongyan , Zheng Limin , Mao Qianzhuo , Liu Qifei , Jia Dongsheng , Wei Taiyun 
Published: January 2014

ABSTRACT

Rice ragged stunt virus (RRSV), an oryzavirus in the family
Reoviridae
, is transmitted by the brown planthopper,
Nilaparvata lugens
, in a persistent-propagative manner. Here, we established a continuous cell line of brown planthopper to investigate the mechanism underlying the formation of the viroplasm, the putative site for viral replication and assembly, during infection of RRSV in its insect vector cells. Within 24 h of viral infection of cultured cells, the viroplasm had formed and contained the viral nonstructural proteins Pns6 and Pns10, known to be constituents of viroplasm. Core capsid protein P3, core particles, and newly synthesized viral RNAs were accumulated inside the viroplasm, while outer capsid protein P8 and virions were accumulated at the periphery of the viroplasm, confirming that the viroplasm induced by RRSV infection was the site for viral replication and assembly. Pns10 formed viroplasm-like inclusions in the absence of viral infection, suggesting that the viroplasm matrix was largely composed of Pns10. Pns6 was recruited in the viroplasm by direct interaction with Pns10. Core capsid protein P3 was recruited to the viroplasm through specific association with Pns6. Knockdown of Pns6 and Pns10 expression using RNA interference inhibited viroplasm formation, virion assembly, viral protein expression, and viral double-stranded RNA synthesis. Thus, the present study shows that both Pns6 and Pns10 of RRSV play important roles in the early stages of viral life cycle in its insect vector cells, by recruiting or retaining components necessary for viral replication and assembly.

IMPORTANCE
The brown planthopper, a commonly distributed pest of rice in Asia, is the host of numerous insect endosymbionts, and the major vector of two rice viruses (RRSV and rice grassy stunt virus). For the first time, we successfully established the continuous cell line of brown planthopper. The unique uniformity of brown planthopper cells in the monolayer can support a consistent, synchronous infection by endosymbionts or viral pathogens, improving our understanding of molecular insect-microbe interactions.