bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Two Multilocus Variable-Number Tandem-Repeat Methods and Pulsed-Field Gel Electrophoresis for Differentiating Highly Clonal Methicillin-Resistant
Staphylococcus aureus
Isolates
Authors: Holmes A. , Edwards G. F. , Girvan E. K. , Hannant W. , Danial J. , Fitzgerald J. R. , Templeton K. E. 
Published: August 2010

ABSTRACT

In the United Kingdom, EMRSA-15 and EMRSA-16 account for the majority (∼90%) of nosocomial methicillin-resistant
Staphylococcus aureus
(MRSA) infections. Currently, the standard typing technique, pulsed-field gel electrophoresis (PFGE), is laborious and insufficient for discriminating between closely related subtypes of EMRSA-15 and -16. The objective of the present study was to compare the usefulness of multilocus variable-number tandem-repeat fingerprinting (MLVF) and multilocus variable-number tandem-repeat analysis (MLVA) with PFGE for subtyping these highly clonal MRSA lineages. A panel of 85 MRSA isolates (41 EMRSA-15, 20 EMRSA-16, and 24 MRSA isolates with diverse PFGE patterns) was investigated. In addition, a further 29 EMRSA-15s with identical PFGE patterns from two geographically linked but epidemiologically distinct outbreaks and several sporadic cases were analyzed. PFGE, MLVF, and MLVA resolved 66 (Simpson's index of diversity [SID] = 0.984), 51 (SID = 0.95), and 42 (SID = 0.881) types, respectively, among the 85 MRSA isolates. MLVF was more discriminatory than MLVA for EMRSA-15 and -16 strains, but both methods had comparable discriminatory powers for distinguishing isolates in the group containing diverse PFGE types. MLVF was comparable to PFGE for resolving the EMRSA-15s but had a lower discriminatory power for the EMRSA-16s. MLVF and MLVA resolved the 29 isolates with identical PFGE patterns into seven and six subtypes, respectively. Importantly, both assays indicated that the two geographically related outbreaks were caused by distinct subtypes of EMRSA-15. Taken together, the data suggest that both methods are suitable for identifying and tracking specific subtypes of otherwise-indistinguishable MRSA. However, due to its greater discriminatory power, MLVF would be the most suitable alternative to PFGE for hospital outbreak investigations.
Rapid Molecular Identification of Pathogenic Yeasts by Pyrosequencing Analysis of 35 Nucleotides of Internal Transcribed Spacer 2
Authors: Borman Andrew M. , Linton Christopher J. , Oliver Debra , Palmer Michael D. , Szekely Adrien , Johnson Elizabeth M. 
Published: August 2010

ABSTRACT
Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures.
Comparison of Midturbinate Flocked-Swab Specimens with Nasopharyngeal Aspirates for Detection of Respiratory Viruses in Children by the Direct Fluorescent Antibody Technique
Authors: Faden Howard 
Published: August 2010

ABSTRACT
Paired nasopharyngeal aspirate (NPA) and midturbinate flocked-swab specimens from 153 children with respiratory symptoms were examined by the direct fluorescent antibody (DFA) technique. Seventy-four infants (49%) had a viral infection documented by DFA. The flocked-swab specimens had 93% sensitivity and 96.7% agreement with the NPA specimens, with a kappa coefficient of 93.4% (95% confidence interval, 0.877, 0.991).
Characterization of Essential Domains and Plasticity of the Classical Swine Fever Virus Core Protein
Authors: Riedel Christiane , Lamp Benjamin , Heimann Manuela , Rümenapf Till 
Published: August 2010

ABSTRACT

Pestiviruses are pathogens of cloven-hoofed animals, belonging to the
Flaviviridae
. The pestiviral particle consists of a lipid membrane containing the three envelope glycoproteins E
rns
, E1, and E2 and a nucleocapsid of unknown symmetry, which is composed of the Core protein and the viral positive-sense RNA genome. The positively charged pestiviral Core protein consists of 86 to 89 amino acids. To analyze the organization of essential domains, N- and C-terminal truncations, as well as internal deletions, were introduced into the Core coding sequence in the context of an infectious cDNA clone of classical swine fever virus strain Alfort. Amino acids 179 to 180, 194 to 198, and 208 to 212 proved to be of special importance for the generation of progeny virus. The results of transcomplementation of a series of C-terminally truncated Core molecules indicate the importance of Ala
255
at the C terminus. The plasticity of Core protein was examined by the construction of concatemeric arrays of Core coding regions and the insertion of up to three yellow fluorescent protein (YFP) genes between two Core genes. Even a Core fusion protein with more than 10-fold-increased molecular mass was integrated into the viral particle and supported the production of infectious progeny virus. The unexpected plasticity of Core protein brings into question the formation of a regular icosahedric particle and supports the idea of a histone-like protein-RNA interaction. All viruses with a duplicated Core gene were unstable and reverted to the wild-type sequence. Interestingly, a nonviable YFP-Core construct was rescued by a mutation within the C-terminal domain of the nonstructural protein NS3.
The African Swine Fever Virus DP71L Protein Recruits the Protein Phosphatase 1 Catalytic Subunit To Dephosphorylate eIF2α and Inhibits CHOP Induction but Is Dispensable for These Activities during Virus Infection
Authors: Zhang Fuquan , Moon Alice , Childs Kay , Goodbourn Stephen , Dixon Linda K. 
Published: August 2010

ABSTRACT
The African swine fever virus (ASFV) DP71L protein is present in all isolates as either a short form of 70 to 72 amino acids or a long form of about 184 amino acids, and both of these share sequence similarity to the C-terminal domain of the herpes simplex virus ICP34.5 protein and cellular protein GADD34. In the present study we expressed DP71L in different mammalian cells and demonstrated that DP71L causes dephosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2α) in resting cells and during chemical-induced endoplasmic reticulum stress and acts to enhance expression of cotransfected reporter genes. We showed that DP71L binds to all the three isoforms (α, β, and γ) of the protein phosphatase 1 catalytic subunit (PP1c) and acts by recruiting PP1c to eIF2α. We also showed that DP71L inhibits the induction of ATF4 and its downstream target, CHOP. We investigated the eIF2α phosphorylation status and induction of CHOP in porcine macrophages infected by two ASFV field isolates, Malawi Lil20/1 and Benin 97/1, and two DP71L deletion mutants, MalawiΔNL and E70ΔNL. Our results showed that deletion of the DP71L gene did not cause an increase in the level of eIF2α phosphorylation or induction of CHOP, indicating that DP71L is not the only factor required by the virus to control the phosphorylation level of eIF2α during infection. We therefore hypothesize that ASFV has other mechanisms to prevent the eIF2α phosphorylation and the subsequent protein synthesis inhibition.
Transcriptomic Analysis Reveals a Mechanism for a Prefibrotic Phenotype in STAT1 Knockout Mice during Severe Acute Respiratory Syndrome Coronavirus Infection
Authors: Zornetzer Gregory A. , Frieman Matthew B. , Rosenzweig Elizabeth , Korth Marcus J. , Page Carly , Baric Ralph S. , Katze Michael G. 
Published: August 2010

ABSTRACT

Severe acute respiratory syndrome coronavirus (SARS-CoV) infection can cause the development of severe end-stage lung disease characterized by acute respiratory distress syndrome (ARDS) and pulmonary fibrosis. The mechanisms by which pulmonary lesions and fibrosis are generated during SARS-CoV infection are not known. Using high-throughput mRNA profiling, we examined the transcriptional response of wild-type (WT), type I interferon receptor knockout (IFNAR1
−/−
), and STAT1 knockout (STAT1
−/−
) mice infected with a recombinant mouse-adapted SARS-CoV (rMA15) to better understand the contribution of specific gene expression changes to disease progression. Despite a deletion of the type I interferon receptor, strong expression of interferon-stimulated genes was observed in the lungs of IFNAR1
−/−
mice, contributing to clearance of the virus. In contrast, STAT1
−/−
mice exhibited a defect in the expression of interferon-stimulated genes and were unable to clear the infection, resulting in a lethal outcome. STAT1
−/−
mice exhibited dysregulation of T-cell and macrophage differentiation, leading to a T
H
2-biased immune response and the development of alternatively activated macrophages that mediate a profibrotic environment within the lung. We propose that a combination of impaired viral clearance and T-cell/macrophage dysregulation causes the formation of prefibrotic lesions in the lungs of rMA15-infected STAT1
−/−
mice.
Genotype-Specific Neutralization and Protection by Antibodies against Dengue Virus Type 3
Authors: Brien James D. , Austin S. Kyle , Sukupolvi-Petty Soila , O'Brien Katie M. , Johnson Syd , Fremont Daved H. , Diamond Michael S. 
Published: August 2010

ABSTRACTDengue viruses (DENV) comprise a family of related positive-strand RNA viruses that infect up to 100 million people annually. Currently, there is no approved vaccine or therapy to prevent infection or diminish disease severity. Protection against DENV is associated with the development of neutralizing antibodies that recognize the viral envelope (E) protein. Here, with the goal of identifying monoclonal antibodies (MAbs) that can function as postexposure therapy, we generated a panel of 82 new MAbs against DENV-3, including 24 highly neutralizing MAbs. Using yeast surface display, we localized the epitopes of the most strongly neutralizing MAbs to the lateral ridge of domain III (DIII) of the DENV type 3 (DENV-3) E protein. While several MAbs functioned prophylactically to prevent DENV-3-induced lethality in a stringent intracranial-challenge model of mice, only three MAbs exhibited therapeutic activity against a homologous strain when administered 2 days after infection. Remarkably, no MAb in our panel protected prophylactically against challenge by a strain from a heterologous DENV-3 genotype. Consistent with this, no single MAb neutralized efficiently the nine different DENV-3 strains used in this study, likely because of the sequence variation in DIII within and between genotypes. Our studies suggest that strain diversity may limit the efficacy of MAb therapy or tetravalent vaccines against DENV, as neutralization potency generally correlated with a narrowed genotype specificity.
Soluble HLA-G Inhibits Myeloid Dendritic Cell Function in HIV-1 Infection by Interacting with Leukocyte Immunoglobulin-Like Receptor B2
Authors: Huang Jinghe , Burke Patrick , Yang Yue , Seiss Katherine , Beamon Jill , Cung Thai , Toth Ildiko , Pereyra Florencia , Lichterfeld Mathias , Yu Xu G. 
Published: August 2010

ABSTRACT
Dendritic cells represent a specialized class of professional antigen-presenting cells that are responsible for priming and maintaining antigen-specific effector cell responses and regulating immune activation by cytokine secretion. In HIV-1 infection, myeloid dendritic cells are highly dysfunctional, but mechanisms contributing to their functional alterations are not well defined. Here, we show that soluble molecules of the nonclassical major histocompatibility complex class Ib (MHC-Ib) antigen HLA-G are highly upregulated in the plasma during progressive HIV-1 infection, while levels of membrane-bound HLA-G surface expression on dendritic cells, monocytes, and T cells only slightly differ among HIV-1 progressors, HIV-1 elite controllers, and HIV-1-negative persons. These elevated levels of soluble HLA-G in progressive HIV-1 infection likely result from increased secretion of intracellularly stored HLA-G molecules in monocytes and dendritic cells and contribute to a functional disarray of dendritic cells by inhibiting their antigen-presenting properties, while simultaneously enhancing their secretion of proinflammatory cytokines. Interestingly, we observed that these immunoregulatory effects of soluble HLA-G were mainly mediated by interactions with the myelomonocytic HLA class I receptor leukocyte immunoglobulin-like receptor B2 (LILRB2; ILT4), while binding of soluble HLA-G to its alternative high-affinity receptor, LILRB1 (ILT2), appeared to be less relevant for its immunomodulatory functions on dendritic cells. Overall, these results demonstrate a critical role for soluble HLA-G in modulating the functional characteristics of professional antigen-presenting cells in progressive HIV-1 infection and suggest that soluble HLA-G might represent a possible target for immunotherapeutic interventions in HIV-1-infected persons.
A Novel Chemoimmunomodulating Property of Docetaxel: Suppression of Myeloid-Derived Suppressor Cells in Tumor Bearers
Authors: Kodumudi Krithika N. , Woan Karrune , Gilvary Danielle L. , Sahakian Eva , Wei Sheng , Djeu Julie Y. 
Published: August 2010

Abstract
Purpose: Myeloid-derived suppressor cells (MDSC) accumulate in tumor-bearing hosts and are associated with immune suppression. To date, there have only been few studies that evaluate the direct effect of chemotherapeutic agents on MDSCs. Agents that inhibit MDSCs may be useful in the treatment of patients with various cancers.
Experimental Design: We investigated the in vivo effects of docetaxel on immune function in 4T1-Neu mammary tumor-bearing mice to examine if a favorable immunomodulatory effect accompanies tumor suppression. Primary focus was on the differentiation status of MDSCs and their ability to modulate T-cell responses.
Results: Docetaxel administration significantly inhibited tumor growth in 4T1-Neu tumor-bearing mice and considerably decreased MDSC proportion in the spleen. The treatment also selectively increased CTL responses. Docetaxel-pretreated MDSCs cocultured with OT-II splenocytes in the presence of OVA323-339 showed OT-II–specific CD4 activation and expansion in vitro. In characterizing the phenotype of MDSCs for M1 (CCR7) and M2 [mannose receptor (CD206)] markers, MDSCs from untreated tumor bearers were primarily MR+ with few CCR7+ cells. Docetaxel treatment polarized MDSCs toward an M1-like phenotype, resulting in 40% of MDSCs expressing CCR7 in vivo and in vitro, and macrophage differentiation markers such as MHC class II, CD11c, and CD86 were upregulated. Interestingly, docetaxel induced cell death selectively in MR+ MDSCs while sparing the M1-like phenotype. Finally, inhibition of signal transducer and activator of transcription 3 may in part be responsible for the observed results.
Conclusions: These findings suggest potential clinical benefit for the addition of docetaxel to current immunotherapeutic protocols. Clin Cancer Res; 16(18); 4583–94. ©2010 AACR.
A systematic review of arm activity measures for children with hemiplegic cerebral palsy
Authors: Klingels K. , Jaspers E. , Van de Winckel A. , De Cock P. , Molenaers G. , Feys H. 
Published: August 2010

Objective: To identify psychometrically sound and clinically feasible assessments of arm activities in children with hemiplegic cerebral palsy for implementation in research and clinical practice. Data sources: PubMed, CINAHL, Cochrane Library, Web of Science and reference lists of relevant articles were searched. Review methods: A systematic search was performed based on the following inclusion criteria: (1) evaluative tools at the activity level according to the International Classification of Functioning, Disability and Health; (2) previously used in studies including children with hemiplegic cerebral palsy aged 2-18 years; (3) at least one aspect of reliability and validity in children with cerebral palsy should be established. Descriptive information, psychometric properties and clinical utility were reviewed. Results: Eighteen assessments were identified of which 11 met the inclusion criteria: eight functional tests and three questionnaires. Five functional tests were condition-specific, three were generic. All functional tests measure different aspects of activity, including unimanual capacity and performance during bimanual tasks. The questionnaires obtain information about the child’s abilities at home or school. The reliability and validity have been established, though further use in clinical trials is necessary to determine the responsiveness. Conclusions: To obtain a complete view of what the child can do and what the child actually does, we advise a capacity-based test (Melbourne Assessment of Unilateral Upper Limb Function), a performance-based test (Assisting Hand Assessment) and a questionnaire (Abilhand-Kids). This will allow outcome differentiation and treatment guidance for the arm in children with cerebral palsy.
Long-term effects of an expanded cardiac rehabilitation programme after myocardial infarction or coronary artery bypass surgery: a five-year follow-up of a randomized controlled study
Authors: Plüss Catrine Edström , Billing Ewa , Held Claes , Henriksson Peter , Kiessling Anna , Karlsson Monica Rydell , Wallen Håkan N 
Published: August 2010

Objective: To investigate the long-term effect of expanded cardiac rehabilitation on a composite end-point, consisting of cardiovascular death, myocardial infarction or readmission for cardiovascular disease, in patients with coronary artery disease. Design: Single-centre prospective randomized controlled trial. Setting: University hospital. Subjects: Two hundred and twenty-four patients with acute myocardial infarction or undergoing coronary artery by-pass grafting. Intervention: Patients were randomized to expanded cardiac rehabilitation (a one-year stress management programme, increased physical training, staying at a ‘patient hotel’ for five days after the event, and cooking sessions), or to standard cardiac rehabilitation. Main measures: Data on cardiovascular death, myocardial infarction, readmission for cardiovascular disease and days at hospital for cardiovascular reasons were obtained from national registries of the Swedish National Board of Health and Welfare. Results: The primary end-point occurred in 121 patients altogether (54%). The number of cardiovascular events were reduced in the expanded rehabilitation group compared with the standard cardiac rehabilitation (53 patients (47.7%) versus 68 patients (60.2%); hazard ratio 0.69; P =  0.049). This was mainly because of a reduction of myocardial infarctions in the expanded rehabilitation group. During the five years 12 patients (10.8%) versus 23 patients (20.3%); hazard ratio 0.47; P =  0.047 had a myocardial infarction. Days at hospital for cardiovascular reasons were significantly reduced in patients who received expanded cardiac rehabilitation (median 6 days) compared with standard cardiac rehabilitation (median 10 days; P =  0.02). Conclusion: Expanded cardiac rehabilitation after acute myocardial infarction or coronary artery bypass grafting reduces cardiovascular morbidity and days at hospital for cardiovascular reasons.
Biomechanical Measures during Landing and Postural Stability Predict Second Anterior Cruciate Ligament Injury after Anterior Cruciate Ligament Reconstruction and Return to Sport
Authors: Paterno Mark V. , Schmitt Laura C. , Ford Kevin R. , Rauh Mitchell J. , Myer Gregory D. , Huang Bin , Hewett Timothy E. 
Published: August 2010

Background Athletes who return to sport participation after anterior cruciate ligament reconstruction (ACLR) have a higher risk of a second anterior cruciate ligament injury (either reinjury or contralateral injury) compared with non—anterior cruciate ligament— injured athletes. Hypotheses Prospective measures of neuromuscular control and postural stability after ACLR will predict relative increased risk for a second anterior cruciate ligament injury. Study Design Cohort study (prognosis); Level of evidence, 2. Methods Fifty-six athletes underwent a prospective biomechanical screening after ACLR using 3-dimensional motion analysis during a drop vertical jump maneuver and postural stability assessment before return to pivoting and cutting sports. After the initial test session, each subject was followed for 12 months for occurrence of a second anterior cruciate ligament injury. Lower extremity joint kinematics, kinetics, and postural stability were assessed and analyzed. Analysis of variance and logistic regression were used to identify predictors of a second anterior cruciate ligament injury. Results Thirteen athletes suffered a subsequent second anterior cruciate ligament injury. Transverse plane hip kinetics and frontal plane knee kinematics during landing, sagittal plane knee moments at landing, and deficits in postural stability predicted a second injury in this population (C statistic = 0.94) with excellent sensitivity (0.92) and specificity (0.88). Specific predictive parameters included an increase in total frontal plane (valgus) movement, greater asymmetry in internal knee extensor moment at initial contact, and a deficit in single-leg postural stability of the involved limb, as measured by the Biodex stability system. Hip rotation moment independently predicted second anterior cruciate ligament injury (C = 0.81) with high sensitivity (0.77) and specificity (0.81). Conclusion Altered neuromuscular control of the hip and knee during a dynamic landing task and postural stability deficits after ACLR are predictors of a second anterior cruciate ligament injury after an athlete is released to return to sport.