bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta‐data flag several cryptic species
Authors: ASGHARIAN HOSSEINALI , SAHAFI HOMAYOUN HOSSEINZADEH , ARDALAN ARIA ASHJA , SHEKARRIZ SHAHROKH , ELAHI ELAHE 
Published: February 2011

AbstractWe provide cytochrome c oxidase subunit 1 (COI) barcode sequences of fishes of the Nayband National Park, Persian Gulf, Iran. Industrial activities, ecological considerations and goals of The Fish Barcode of Life campaign make it crucial that fish species residing in the park be identified. To the best of our knowledge, this is the first report of barcoding data on fishes of the Persian Gulf. We examined 187 individuals representing 76 species, 56 genera and 32 families. The data flagged potentially cryptic species of Gerres filamentosus and Plectorhinchus schotaf. 16S rDNA data on these species are provided. Exclusion of these two potential cryptic species resulted in a mean COI intraspecific distance of 0.18%, and a mean inter‐ to intraspecific divergence ratio of 66.7. There was no overlap between maximum Kimura 2‐parameter distances among conspecifics (1.66%) and minimum distance among congeneric species (6.19%). Barcodes shared among species were not observed. Neighbour‐joining analysis showed that most species formed cohesive sequence units with little variation. Finally, the comparison of 16 selected species from this study with meta‐data of conspecifics from Australia, India, China and South Africa revealed high interregion divergences and potential existence of six cryptic species. Pairwise interregional comparisons were more informative than global divergence assessments with regard to detection of cryptic variation. Our analysis exemplifies optimal use of the expanding barcode data now becoming available.
Quality of life of eye amputated patients
Authors: Rasmussen Marie L. R. , Ekholm Ola , Prause Jan U. , Toft Peter B. 
Published: February 2011

Abstract.Purpose:  To evaluate eye‐amputated patients’ health‐related quality of life, perceived stress, self‐rated health, job separation because of illness or disability and socioeconomic position.Methods:  Patients were recruited from a tertiary referral centre situated in Copenhagen. Inclusion criteria were eye amputation, i.e. evisceration, enucleation, orbital exenteration or secondary implantation of an orbital implant during the period 1996–2003, and participation in a previous investigation (2005).In total, 159 eye‐amputated patients were included, and completed a self‐administered questionnaire containing health‐related quality of life (SF‐36), the perceived stress scale and answered questions about self‐rated health, job changes because of illness or disability and socioeconomic status. These results were compared with findings from the Danish Health Interview Survey 2005.Results:  The eye‐amputated patients had significantly (p < 0.05) lower scores (poorer health) on all SF‐36 subscales and more perceived stress compared to the general population. In all, 43.3% of the patients rated their health as excellent or very good compared to 52.1% of the general population. In total, 25% of the study population has retired or changed to a part‐time job because of eye disease.The percentage of eye amputated patients, who were divorced or separated, was twice as high as in the general population.Conclusion:  The impact of an eye amputation is considerable. The quality of life, perceived stress and self‐rated health of many eye‐amputated patients are drastically changed. Eye amputation has a marked negative influence on job separation because of illness or disability and on socioeconomic position.
Fair Value Accounting and Stewardship*
Authors: Rashad Abdel‐Khalik A. 
Published: February 2011

AbstractCurrent standards define fair value as the market price at which an asset could be sold or a liability could be settled in the normal course of business. Setting aside measurement issues, assessing the relevance of exit values has intensified in recent years as fair value becomes a pervasive component of accounting regulation. The current debate about accounting measurement is framed in terms of making a choice between fair value and historical cost. In this article I argue that this is not a correct framing of the issues; knowledge of fair value alone cannot help investors to evaluate stewardship, because they would not know how much resources the management had sacrificed to obtain that fair value. To properly evaluate stewardship, investors need both types of information, historical cost and fair value.Using this information, a rate‐of‐return‐like index of stewardship quality is proposed. This commentary concludes with a statement about three significant drawbacks of relying solely on fair value accounting.
A semi‐Markov model to assess reliably survival patterns from birth to death in free‐ranging populations
Authors: Choquet Rémi , Viallefont Anne , Rouan Lauriane , Gaanoun Kamel , Gaillard Jean‐Michel 
Published: February 2011

Summary1. Semi‐Markov models explicitly define the distribution of waiting time duration and have been used as a convenient framework for modelling the time spent in one physiological state in previous biological studies.2. Here, we focus on the modelling of the time spent within a life‐cycle stage (e.g. juvenile, adult and old) by individuals over their lifetime from Capture–Mark–Recapture data, which are commonly used to estimate demographic parameters in free‐ranging populations.3. We propose a parametric model (1) with a semi‐Markov state, (2) associated to a hazard function and (3) accounting for imperfect detection to assess reliably survival patterns from birth to death.4. These models indeed outperform models with a linear trend or a quadratic form, often selected as the best model for survival in capture–recapture studies.5. Moreover, our approach offers the first opportunity to estimate statistically rather than visually the age of the onset of actuarial senescence, associated with confidence intervals.6. The application of this new approach to the detailed long‐term study of survival in roe deer at Trois Fontaines (France) illustrates the relevance of semi‐Markov models to assess survival patterns from birth to death.
Histoplasma Antigen Clearance during Treatment of Histoplasmosis in Patients with AIDS Determined by a Quantitative Antigen Enzyme Immunoassay
Authors: Hage Chadi A. , Kirsch Emily J. , Stump Timothy E. , Kauffman Carol A. , Goldman Mitchell , Connolly Patricia , Johnson Philip C. , Wheat L. Joseph , Baddley John W. 
Published: February 2011

ABSTRACTClearance ofHistoplasmaantigen has been used as a marker for response to treatment of progressive disseminated histoplasmosis (PDH) in patients with AIDS. Advancements inHistoplasmaantigen detection permit accurate quantification of antigen concentration. We compared the clearance of antigenemia and antigenuria during effective treatment of PDH. Urine and serum specimens were serially collected from patients with AIDS who were successfully treated for PDH as part of two prospective clinical trials. Samples were stored frozen until they were tested in the quantitativeHistoplasmaantigen enzyme immunoassay. The kinetics of antigen clearance during the first 12 weeks of therapy were assessed in urine and serum during treatment with liposomal or deoxycholate amphotericin B followed by itraconazole and, in a separate analysis, in patients receiving only itraconazole. Latent class growth analysis was performed to define patterns of antigen clearance over time. In patients receiving amphotericin B, antigen levels declined the most during the first 2 weeks of treatment and antigenemia decreased more rapidly than antigenuria (5.90 ng/ml per week versus 4.21 ng/ml per week, respectively;P= 0.09). Mean reductions of antigen levels from baseline at weeks 2 and 12 were greater in sera than in urine: 11.26 ng/ml versus 7.65 ng/ml (P= 0.0948) and 18.52 ng/ml versus 14.64 ng/ml (P= 0.0440), respectively. In patients who received itraconazole alone, most of the decline in antigenuria occurred later during treatment and was overall slower than that seen with amphotericin B (P< 0.0001). Results of latent class growth modeling showed two distinct trajectories for each parameter. With effective therapy,Histoplasmaantigenemia decreases more rapidly than antigenuria, providing a more sensitive early laboratory marker for response to treatment. Antigenuria declines earlier with amphotericin B than with itraconazole.
Comparison of Western Immunobloting to an Enzyme-Linked Immunosorbent Assay for the Determination of Anti-Bordetella pertussis Antibodies
Authors: Merrigan Stephen D. , Welch Ryan J. , Litwin Christine M. 
Published: February 2011

ABSTRACTDuringBordetella pertussisinfection, it has been established that an increase of anti-pertussis toxin (PT) and anti-filamentous hemagglutinin (FHA) antibodies occurs. Immunoblots from two manufacturers using FHA and PT antigens were compared with an enzyme-linked immunosorbent assay (ELISA) that used both FHA and PT. One manufacturer used two concentrations of PT bands for the IgG immunoblot, calibrated to the World Health Organization standard for PT in international units (IU/ml), 100 IU/ml (PT-100) and 8 IU/ml (PT). The second immunoblot kit measured antibodies to a single calibrated PT band. Both kits measured IgA antibodies, and one additionally measured IgM antibodies. Two of 41 (5%) ELISA IgM positives were confirmed positive by IgM immunoblotting, suggesting poor specificity of the IgM ELISA. The agreements of the IgG and IgA immunoblots with the ELISA ranged from 72.5% to 85.3%, with only 38 to 51% of IgA positives confirmed by immunoblotting and only 61 to 68% of IgG positives confirmed by immunoblotting. The two immunoblots correlated well with each other, with 91.7% and 94.3% agreement for IgG and IgA, respectively. When the FHA band was used with the PT band as the criterion for positivity, significant differences existed in specificity compared to the ELISA (IgG, 84.1% versus 33.3%; IgA, 82.4% versus 71.0%). When the positive IgA immunoblots (evidence of natural recent infection) were compared to the positive PT-100 IgG immunoblots (evidence of recent infection or vaccination), the PT-100 blot showed a 71% sensitivity in detecting natural recent infection.B. pertussisimmunoblots, alone or in combination with ELISAs, can aid in the diagnosis ofB. pertussisinfection.
Parvovirus among Patients with Cytopenia of Unknown Origin in Brazil: a Case-Control Study
Authors: de Oliveira Garcia Sheila , Neto Walter Kleine , da Costa Antonio Charlys , Sanabani Sabri Saeed , Mendrone Alfredo , Pereira Juliana , Sabino Ester Cerdeira 
Published: February 2011

ABSTRACT
The molecular prevalence of human parvovirus B19V (B19V) in bone marrow (BM) samples from 120 cases with cytopenias of unknown etiology was compared with that in samples from 45 BM donors (control group 1) and 120 oncohematological patients (control group 2) to determine the role that B19V genotypes may play in unexplained cytopenias. Of the 285 participants, the BM samples of 39 (13.7%) contained B19V DNA (21 with genotype 1, 5 with genotype 2, and 13 with genotype 3). The prevalences of B19V were similar between case and control subjects (15.0% versus 12.7%, respectively). Genotypes 2 and 3 were associated with older age and were detected in similar proportions between case and control group 2 subjects. The results of this study do not support a role for B19V genotype variants in the etiology of unexplained cytopenias.
Adenoid Reservoir for Pathogenic Biofilm Bacteria
Authors: Nistico L. , Kreft R. , Gieseke A. , Coticchia J. M. , Burrows A. , Khampang P. , Liu Y. , Kerschner J. E. , Post J. C. , Lonergan S. , Sampath R. , Hu F. Z. , Ehrlich G. D. , Stoodley P. , Hall-Stoodley L. 
Published: February 2011

ABSTRACT

Biofilms of pathogenic bacteria are present on the middle ear mucosa of children with chronic otitis media (COM) and may contribute to the persistence of pathogens and the recalcitrance of COM to antibiotic treatment. Controlled studies indicate that adenoidectomy is effective in the treatment of COM, suggesting that the adenoids may act as a reservoir for COM pathogens. To investigate the bacterial community in the adenoid, samples were obtained from 35 children undergoing adenoidectomy for chronic OM or obstructive sleep apnea. We used a novel, culture-independent molecular diagnostic methodology, followed by confocal microscopy, to investigate the
in situ
distribution and organization of pathogens in the adenoids to determine whether pathogenic bacteria exhibited criteria characteristic of biofilms. The Ibis T5000 Universal Biosensor System was used to interrogate the extent of the microbial diversity within adenoid biopsy specimens. Using a suite of 16 broad-range bacterial primers, we demonstrated that adenoids from both diagnostic groups were colonized with polymicrobial biofilms.
Haemophilus influenzae
was present in more adenoids from the COM group (
P
= 0.005), but there was no significant difference between the two patient groups for
Streptococcus pneumoniae
or
Staphylococcus aureus
. Fluorescence
in situ
hybridization, lectin binding, and the use of antibodies specific for host epithelial cells demonstrated that pathogens were aggregated, surrounded by a carbohydrate matrix, and localized on and within the epithelial cell surface, which is consistent with criteria for bacterial biofilms.
Comparison of BD Bactec Plus Blood Culture Media to VersaTREK Redox Blood Culture Media for Detection of Bacterial Pathogens in Simulated Adult Blood Cultures Containing Therapeutic Concentrations of Antibiotics
Authors: Miller Nancy S. , Rogan Dagmar , Orr Beverley L. , Whitney Dana 
Published: February 2011

ABSTRACT
Antibiotic neutralization in blood culture media from two automated systems was evaluated by measuring the recovery of organisms and times to detection in simulated cultures. Overall, BD Bactec Plus media (Bactec FX system) outperformed TREK 80 ml Redox media (VersaTREK system), although results suggest a relative rather than an absolute increased rate of recovery for the Bactec media.
Comparison of the DiversiLab Repetitive Element PCR System with
spa
Typing and Pulsed-Field Gel Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus
Authors: Babouee B. , Frei R. , Schultheiss E. , Widmer A. F. , Goldenberger D. 
Published: February 2011

ABSTRACT

The emergence of methicillin-resistant
Staphylococcus aureus
(MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with
spa
typing,
spa
clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into
spa
clonal complexes resulted in 3 clusters:
spa
-CC 067/548,
spa
-CC 008, and
spa
-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE,
spa
typing, DL typing, and
spa
clonal clustering, respectively. DL typing and
spa
clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to
spa
type t008 and
spa
-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and
spa
typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns.
Detection of Hemagglutinin Variants of the Pandemic Influenza A (H1N1) 2009 Virus by Pyrosequencing
Authors: Levine Marnie , Sheu Tiffany G. , Gubareva Larisa V. , Mishin Vasiliy P. 
Published: February 2011

ABSTRACTFor influenza viruses, pyrosequencing has been successfully applied to the high-throughput detection of resistance markers in genes encoding the drug-targeted M2 protein and neuraminidase. In this study, we expanded the utility of this assay to the detection of multiple receptor binding variants of the hemagglutinin protein of influenza viruses directly in clinical specimens. Specifically, a customized pyrosequencing protocol that permits detection of virus variants with the D, G, N, or E amino acid at position 222 in the hemagglutinin of the 2009 pandemic influenza A (H1N1) virus was developed. This customized pyrosequencing protocol was applied to the analysis of 241 clinical specimens. The use of the optimized nucleotide dispensation order allowed detection of mixtures of variants in 10 samples (4.1%) which the standard cyclic nucleotide dispensation protocol failed to detect. The optimized pyrosequencing protocol is expected to provide a more accurate tool in the analysis of virus variant composition.
Both Nonstructural Proteins NS1 and NS2 of Pneumonia Virus of Mice are Inhibitors of the Interferon Type I and Type III Responses In Vivo
Authors: Heinze Britta , Frey Stefanie , Mordstein Markus , Schmitt-Gräff Anette , Ehl Stephan , Buchholz Ursula J. , Collins Peter L. , Staeheli Peter , Krempl Christine D. 
Published: February 2011

ABSTRACT
Infection of mice with pneumonia virus of mice (PVM) provides a convenient experimental pathogenesis model in a natural host for a human respiratory syncytial virus-related virus. Extending our previous work showing that the PVM nonstructural (NS) proteins were pathogenicity factors in mice, we identify both the NS1 and NS2 proteins as antagonists of alpha/beta interferon (IFN-α/β) and IFN-λ by use of recombinant PVM (rPVM) with single and combined deletions of the NS proteins (ΔNS1, ΔNS2, and ΔNS1 ΔNS2). Wild-type and NS deletion PVMs were evaluated for growth and pathogenesis by infecting knockout mice that lack functional receptors to IFN-α/β, IFN-λ, or both. The absence of the receptor to IFN-α/β (IFNAR) or IFN-λ (interleukin-28 receptor α chain [IL-28Rα]) individually did not reverse the attenuated virulence of the NS deletion viruses although loss of IFNAR partially restored replication efficiency. When both receptors were deleted, replication and virulence were largely rescued for rPVM ΔNS1 and were significantly but not completely rescued for rPVM ΔNS2. As for rPVM ΔNS1 ΔNS2, the effect was mostly limited to partial enhancement of replication. This indicates that both IFN-α/β and IFN-λ contributed to restricting the NS deletion viruses, with the former playing the greater role. Interestingly, the replication and virulence of wild-type PVM were completely unaffected by the presence or absence of functional receptors to IFN-α/β and IFN-λ, indicating that both systems are strongly suppressed during infection. However, pretreatment of mice with IFN-α/β was protective against lethal rPVM challenge, whereas pretreatment with IFN-λ delayed but did not prevent disease and, in some cases, reduced mortality. The fact that virulence of rPVM lacking NS2 was not recovered completely when both interferon receptors were deleted suggests that NS2 may have further functions outside the IFN system.
Restriction of Porcine Endogenous Retrovirus by Porcine APOBEC3 Cytidine Deaminases
Authors: Dörrschuck Eva , Fischer Nicole , Bravo Ignacio G. , Hanschmann Kay-Martin , Kuiper Heidi , Spötter Andreas , Möller Ronny , Cichutek Klaus , Münk Carsten , Tönjes Ralf R. 
Published: February 2011

ABSTRACT

Xenotransplantation of porcine cells, tissues, and organs shows promise to surmount the shortage of human donor materials. Among the barriers to pig-to-human xenotransplantation are porcine endogenous retroviruses (PERV) since functional representatives of the two polytropic classes, PERV-A and PERV-B, are able to infect human embryonic kidney cells
in vitro
, suggesting that a xenozoonosis
in vivo
could occur. To assess the capacity of human and porcine cells to counteract PERV infections, we analyzed human and porcine APOBEC3 (A3) proteins. This multigene family of cytidine deaminases contributes to the cellular intrinsic immunity and act as potent inhibitors of retroviruses and retrotransposons. Our data show that the porcine
A3
gene locus on chromosome 5 consists of the two single-domain genes
A3Z2
and
A3Z3
. The evolutionary relationships of the
A3Z3
genes reflect the evolutionary history of mammals. The two
A3
genes encode at least four different mRNAs: A3Z2, A3Z3, A3Z2-Z3, and A3Z2-Z3 splice variant A (SVA). Porcine and human A3s have been tested toward their antiretroviral activity against PERV and murine leukemia virus (MuLV) using novel single-round reporter viruses. The porcine A3Z2, A3Z3 and A3Z2-Z3 were packaged into PERV particles and inhibited PERV replication in a dose-dependent manner. The antiretroviral effect correlated with editing by the porcine A3s with a trinucleotide preference for 5′ TGC for A3Z2 and A3Z2-Z3 and 5′ CAC for A3Z3. These results strongly imply that human and porcine A3s could inhibit PERV replication
in vivo
, thereby reducing the risk of infection of human cells by PERV in the context of pig-to-human xenotransplantation.
In Vivo
Fitness Associated with High Virulence in a Vertebrate Virus Is a Complex Trait Regulated by Host Entry, Replication, and Shedding
Authors: Wargo Andrew R. , Kurath Gael 
Published: February 2011

ABSTRACT

The relationship between pathogen fitness and virulence is typically examined by quantifying only one or two pathogen fitness traits. More specifically, it is regularly assumed that within-host replication, as a precursor to transmission, is the driving force behind virulence. In reality, many traits contribute to pathogen fitness, and each trait could drive the evolution of virulence in different ways. Here, we independently quantified four viral infection cycle traits, namely, host entry, within-host replication, within-host coinfection fitness, and shedding,
in vivo
, in the vertebrate virus
Infectious hematopoietic necrosis virus
(IHNV). We examined how each of these stages of the viral infection cycle contributes to the fitness of IHNV genotypes that differ in virulence in rainbow trout. This enabled us to determine how infection cycle fitness traits are independently associated with virulence. We found that viral fitness was independently regulated by each of the traits examined, with the largest impact on fitness being provided by within-host replication. Furthermore, the more virulent of the two genotypes of IHNV we used had advantages in all of the traits quantified. Our results are thus congruent with the assumption that virulence and within-host replication are correlated but suggest that infection cycle fitness is complex and that replication is not the only trait associated with virulence.