bluuebunny/crossref_metadata_2025_split huggingface dataset:
Russell, His Paradoxes, and Cantor's Theorem: Part II
Authors: Klement Kevin C. 
Published: January 2010

AbstractSequel to Part I. In these articles, I describe Cantor's power‐class theorem, as well as a number of logical and philosophical paradoxes that stem from it, many of which were discovered or considered (implicitly or explicitly) in Bertrand Russell's work. These include Russell's paradox of the class of all classes not members of themselves, as well as others involving properties, propositions, descriptive senses, class‐intensions and equivalence classes of coextensional properties. Part II addresses Russell's own various attempts to solve these paradoxes, including strategies that he considered and rejected (limitation of size, the zigzag theory, etc.), as well as his own final views whereupon many purported entities that, if reified, lead to these contradictions, must not be genuine entities, but ‘logical fictions’ or ‘logical constructions’ instead.
Colonisation credit in recent wet heathland butterfly communities
Authors: CRISTOFOLI SARA , MAHY GRÉGORY 
Published: December 2009

Abstract.  1. Wet heathlands and closely associated habitats (e.g. bogs and poor fens) have been highly fragmented over the last two centuries. These habitats nowadays benefit from large‐scale restoration projects, for which the success should be evaluated.2. Recently, the concept of colonisation credit (the number of species yet to colonise a patch) was proposed as a spatially explicit framework to assess recovery in species richness following restoration. In this study, we estimated the colonisation credit of wet heathland butterfly communities in Southern Belgium. The method was applied separately to generalist and specialist species for two reference dates (new patches <25 years old and new patches 25–55 years old).3. Only a marginally significant colonisation credit was detected for generalist species. In contrast, we found a significant colonisation credit for specialists, although this was due to a very limited number of strict specialist species. Butterfly community composition differed only marginally between patch age classes.4. As a general trend, butterfly communities exhibit a rapid response (<25 years) to landscape structure modification. However, conservation and restoration actions should urgently target strict specialists, exhibiting colonisation limitation in new habitat patches. A lack of colonisation credit for plant communities in the same landscape suggests that restoration of wet heathlands may be successful in the short term for various taxonomic groups.
Genotypes Coding for Low Serum Levels of Mannose-Binding Lectin Are Underrepresented among Individuals Suffering from Noninfectious Systemic Inflammatory Response Syndrome
Authors: Smithson Alex , Perello Rafael , Aibar Jesus , Espinosa Gerard , Tassies Dolors , Freire Carolina , Castro Pedro , Suarez Belen , Lozano Francisco , Nicolas Josep-Maria 
Published: December 2009

ABSTRACTGene polymorphisms, giving rise to low serum levels of mannose-binding lectin (MBL) or MBL-associated protease 2 (MASP2), have been associated with an increased risk of infections. The objective of this study was to assess the outcome of intensive care unit (ICU) patients with systemic inflammatory response syndrome (SIRS) regarding the existence of functionally relevantMBL2andMASP2gene polymorphisms. The study included 243 ICU patients with SIRS admitted to our hospital, as well as 104 healthy control subjects.MBL2andMASP2single nucleotide polymorphisms were genotyped using a sequence-based typing technique. No differences were observed regarding the frequencies of low-MBL genotypes (O/O and XA/O) andMASP2polymorphisms between patients with SIRS and healthy controls. Interestingly, ICU patients with a noninfectious SIRS had a lower frequency for low-MBL genotypes and a higher frequency for high-MBL genotypes (A/A and A/XA) than either ICU patients with an infectious SIRS or healthy controls. The existence of low- or /high-MBL genotypes or aMASP2polymorphism had no impact on the mortality rates of the included patients. The presence of high-MBL-producing genotypes in patients with a noninfectious insult is a risk factor for SIRS and ICU admission.
Proof of Principle for Successful Characterization of Methicillin-Resistant Coagulase-Negative Staphylococci Isolated from Skin by Use of Raman Spectroscopy and Pulsed-Field Gel Electrophoresis
Authors: Willemse-Erix H. F. M. , Jachtenberg J. , Barutçi H. , Puppels G. J. , van Belkum A. , Vos M. C. , Maquelin K. 
Published: December 2009

ABSTRACT
Coagulase-negative staphylococci (CNS) are among the most frequently isolated bacterial species in clinical microbiology, and most CNS-related infections are hospital acquired. Distinguishing between these frequently multiple-antibiotic-resistant isolates is important for both treatment and transmission control. In this study we used isolates of methicillin-resistant coagulase-negative staphylococci (MR-CNS) that were selected from a large surveillance study of the direct spread of MR-CNS. This strain collection was used to evaluate (i) Raman spectroscopy as a typing tool for MR-CNS isolates and (ii) diversity between colonies with identical and different morphologies. Reproducibility was high, with 215 of 216 (99.5%) of the replicate samples for 72 isolates ending up in the same cluster. The concordance with pulsed-field gel electrophoresis (PFGE)-based clusters was 94.4%. We also confirm that the skin of patients can be colonized with multiple MR-CNS types at the same time. Morphological differences between colonies from a single patient sample correlated with differences in Raman and PFGE types. Some morphologically indistinguishable colonies revealed different Raman and PFGE types. This indicates that multiple MR-CNS colonies should be examined to obtain a complete insight into the prevalence of different types and to be able to perform an accurate transmission analysis. Here we show that Raman spectroscopy is a reproducible typing system for MR-CNS isolates. It is a tool for screening variability within a collection of isolates. Because of the high throughput, it enables the analysis of multiple colonies per patient, which will enhance the quality of clinical and epidemiological studies.
Results of the Abbott RealTi
m
e HIV-1 Assay for Specimens Yielding “Target Not Detected” Results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test
Authors: Babady N. Esther , Germer Jeffrey J. , Yao Joseph D. C. 
Published: December 2009

ABSTRACT

No significantly discordant results were observed between the Abbott RealTi
m
e HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding “target not detected” results by CTM.
Italian National Survey of Blood Donors: External Quality Assessment (EQA) of Syphilis Testing
Authors: Vulcano Francesca , Milazzo Luisa , Volpi Sabrina , Battista Mara Maria , Barca Alessandra , Hassan Hamisa Jane , Pimpinelli Fulvia , Giampaolo Adele 
Published: December 2009

ABSTRACT

The detection of syphilis among blood donors may reveal high-risk sexual behavior, which can go unreported at the time of donor selection and compromise the safety of the donated blood. In Italy, blood is collected, tested, and distributed by transfusion services (TSs), which also perform outpatient transfusions. Although the TSs must screen for syphilis by law, there are no indications of the specific type of method to be used, generating discrepancies in the results obtained by the different TSs. To determine the proficiency of the TSs in screening for syphilis, we performed an external quality assessment (EQA). The EQA was based on two shipments of serum panels; 133 and 118 of the 326 existing TSs participated in the first and second shipments, respectively. Each panel consisted of both positive and negative serum samples. The results confirmed that the use of a single nontreponemal test (the Venereal Disease Research Laboratory [VDRL] and the rapid plasma reagin [RPR] tests) is the least sensitive means of identifying samples that are positive for syphilis antibodies. We also found that the interpretation of the results of manual techniques, such as the RPR test, the VDRL test, the
Treponema pallidum
hemagglutination (TPHA) assay, and the
T. pallidum
particle agglutination (TPPA) assay, can vary greatly among different TSs and operators. Total Ig enzyme immunoassays (EIAs) are the most sensitive. However, the determination of syphilis on the basis of the results of a single test is not sufficient for an accurate screening; and all blood units should thus be assessed by two distinct treponemal tests, that is, a total Ig EIA and the TPHA or the TPPA assay.
Clonal Distribution of Disease-Associated and Healthy Carrier Isolates ofNeisseria meningitidisbetween 1983 and 2005 in Cuba
Authors: Climent Yanet , Yero Daniel , Martinez Isabel , Martín Alejandro , Jolley Keith A. , Sotolongo Franklin , Maiden Martin C. J. , Urwin Rachel , Pajón Rolando 
Published: December 2009

ABSTRACTIn response to epidemic levels of serogroup B meningococcal disease in Cuba during the 1980s, the VA-MENGOC-BC vaccine was developed and introduced into the National Infant Immunization Program in 1991. Since then the incidence of meningococcal disease in Cuba has returned to the low levels recorded before the epidemic. A total of 420Neisseria meningitidisstrains collected between 1983 and 2005 in Cuba were analyzed by multilocus sequence typing (MLST). The set of strains comprised 167 isolated from disease cases and 253 obtained from healthy carriers. By MLST analysis, 63 sequence types (STs) were identified, and 32 of these were reported to be a new ST. The Cuban isolates were associated with 12 clonal complexes; and the most common were ST-32 (246 isolates), ST-53 (86 isolates), and ST-41/44 (36 isolates). This study also showed that the application of VA-MENGOC-BC, the Cuban serogroup B and C vaccine, reduced the frequency and diversity of hypervirulent clonal complexes ST-32 (vaccine serogroup B type-strain) and ST-41/44 and also affected other lineages. Lineages ST-8 and ST-11 were no longer found during the postvaccination period. The vaccine also affected the genetic composition of the carrier-associated meningococcal isolates. The number of carrier isolates belonging to hypervirulent lineages decreased significantly after vaccination, and ST-53, a sequence type common in carriers, became the predominant ST.
Application of Truncated Immunodominant Polypeptide from Hepatitis E Virus (HEV) ORF2 in an Assay To Exclude Nonspecific Binding in Detecting Anti-HEV Immunoglobulin M
Authors: Pan Jin-Shun , Zhang Kui , Zhou Jinyong , Wu Chao , Zhuang Hui , Zhou Yi-Hua 
Published: December 2009

ABSTRACT
The diagnosis of recent hepatitis E virus (HEV) infection depends on serologic testing for anti-HEV IgM; however, false-positive results may occur. In the present study, we cloned the ORF2 fragment of genotype 4 HEV and demonstrated that a subregion covering amino acids 459 to 607 in ORF2 forms the immunodominant B-cell epitopes, as it does in genotype 1 viruses. Truncation of several residues from either the N or C terminus of the polypeptide abolished the reactivity of anti-HEV from naturally infected persons. By the combination of high reactivity of the immunodominant polypeptide and poor reactivity of the truncated polypeptide, we established an indirect enzyme-linked immunosorbent assay (ELISA) to detect anti-HEV IgM. In this assay, all 37 sera that were HEV RNA positive reacted with the immunodominant polypeptide but not with the truncated one, and none of 159 sera from healthy persons reacted with either of the polypeptides. In retesting of 117 sera that originally tested positive for anti-HEV IgM, using a Genelabs kit, only 34 were positive and 83 were negative. Western blot analyses and other experiments strongly indicated that these 83 discordant sera were negative for anti-HEV IgM. Furthermore, among the 117 sera, 5 reacted with both the immunodominant and truncated polypeptides, with comparable optical densities at 450 nm. However, their reactivity was demonstrated to result from nonspecific binding. Together, the data indicate that the poor reactivity of a truncated ORF2 polypeptide can be used to exclude nonspecific binding in the detection of anti-HEV IgM.
Cytospin-Enhanced Immunofluorescence and Impact of Sample Quality on Detection of Novel Swine Origin (H1N1) Influenza Virus
Authors: Landry Marie L. , Ferguson David 
Published: December 2009

ABSTRACT

Nasopharyngeal swabs (
n
= 601) from 278 adult and 323 pediatric patients were tested within 24 h of receipt by cytospin-enhanced direct immunofluorescence antibody testing (DFA) and real-time reverse transcriptase PCR (RT-PCR) using the CDC assay. Cytospin-enhanced DFA detected 230 (84.6%) of 272 swine influenza A PCR-positive results overall but 25 (92.6%) of 27 positive results in patients less than 5 years old and 208 (96.7%) of 215 positive samples with cycle threshold values of <26.
Computational Analysis Identifies Human Adenovirus Type 55 as a Re-Emergent Acute Respiratory Disease Pathogen
Authors: Walsh Michael P. , Seto Jason , Jones Morris S. , Chodosh James , Xu Wenbo , Seto Donald 
Published: December 2009

ABSTRACT
Novel human adenoviruses (HAdVs) arise from genome recombination. Analysis of HAdV type 55 from an outbreak in China shows a hexon recombination between HAdV-B11 and HAdV-B14, resulting in a genome that is 97.4% HAdV-B14. Sporadic appearances as a re-emergent pathogen and misidentification as “HAdV-B11a” are due to this partial hexon.
Multilocus Sequence Typing of
Clostridium difficile
Authors: Griffiths David , Fawley Warren , Kachrimanidou Melina , Bowden Rory , Crook Derrick W. , Fung Rowena , Golubchik Tanya , Harding Rosalind M. , Jeffery Katie J. M. , Jolley Keith A. , Kirton Richard , Peto Tim E. , Rees Gareth , Stoesser Nicole , Vaughan Alison , Walker A. Sarah , Young Bernadette C. , Wilcox Mark , Dingle Kate E. 
Published: December 2009

ABSTRACT

A robust high-throughput multilocus sequence typing (MLST) scheme for
Clostridium difficile
was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes and 102 isolates from recent clinical samples. A total of 49 PCR ribotypes were represented overall. All isolates were typed by MLST and yielded 40 sequence types (STs). A web-accessible database was set up (
http://pubmlst.org/cdifficile/
) to facilitate the dissemination and comparison of
C. difficile
MLST genotyping data among laboratories. MLST and PCR ribotyping were similar in discriminatory abilities, having indices of discrimination of 0.90 and 0.92, respectively. Some STs corresponded to a single PCR ribotype (32/40), other STs corresponded to multiple PCR ribotypes (8/40), and, conversely, the PCR ribotype was not always predictive of the ST. The total number of variable nucleotide sites in the concatenated MLST sequences was 103/3,501 (2.9%). Concatenated MLST sequences were used to construct a neighbor-joining tree which identified four phylogenetic groups of STs and one outlier (ST-11; PCR ribotype 078). These groups apparently correlate with clades identified previously by comparative genomics. The MLST scheme was sufficiently robust to allow direct genotyping of
C. difficile
in total stool DNA extracts without isolate culture. The direct (nonculture) MLST approach may prove useful as a rapid genotyping method, potentially benefiting individual patients and informing hospital infection control.
Evidence of Emergence of New GGII.4 Norovirus Variants from Gastroenteritis Outbreak Survey in France during the 2007-to-2008 and 2008-to-2009 Winter Seasons
Authors: Belliot Gaël , Kamel A. H. , Estienney M. , Ambert-Balay K. , Pothier P. 
Published: December 2009

ABSTRACT
Analysis of 316 outbreaks of gastroenteritis in France from September 2007 through March 2009 showed that genogroup II.4 (GGII.4) noroviruses were predominant and mostly belonged to the 2006b variant. However, the new GGII.4 variants, variant 2008 and the newly discovered Cairo variant from the Middle East, were also detected. The epidemiological survey suggests that these new variants might become the next predominant strains.
Emergence of SCC
mec
Type IV and SCC
mec
Type V Methicillin-Resistant
Staphylococcus aureus
Containing the Panton-Valentine Leukocidin Genes in a Large Academic Teaching Hospital in Central Switzerland: External Invaders or Persisting Circulators?
Authors: Valsesia Giorgia , Rossi Marco , Bertschy Sonja , Pfyffer Gaby E. 
Published: December 2009

ABSTRACT

The hospital epidemiology of methicillin-resistant
Staphylococcus aureus
(MRSA) has changed in the past few years due to the encroachment of community-associated MRSA (CA-MRSA) strains into health care settings. MRSA strains that were isolated during a 2-year period from patients of the Luzerner Kantonsspital were analyzed to elucidate their epidemiology. Moreover, extended surveillance of individuals who were contacts of those patients was carried out for 6 months to identify the routes of spread and to assess the quality of the infection control measures used in our setting. Patient data were collected to distinguish CA-MRSA strains from health care-associated MRSA (HA-MRSA) strains by epidemiological criteria, as defined by the Centers for Disease Control and Prevention (CDC). On the basis of the CDC definition, the majority of the strains were considered to be HA-MRSA. However, 87% of them belonged to staphylococcal cassette chromosome
mec
(SCC
mec
) types IV and V, which are traditionally associated with CA-MRSA. Surprisingly, classical nosocomial SCC
mec
types I and II represented a minority, whereas SCC
mec
type III was completely absent. By PFGE analysis, four predominant clonal lineages and 21 highly variable sporadic genotypes were detected. Twenty-eight percent of the MRSA strains studied carried the genes encoding the Panton-Valentine leukocidin (PVL), of which 21% and 83% were associated with SCC
mec
types IV and V, respectively. Among 289 contact individuals screened for MRSA carriage throughout the extended surveillance, a single secondary patient was discovered. The possibility of nosocomial transmission could be excluded. The high proportions of SCC
mec
type IV and V strains as well as PVL-positive strains suggest strong infiltration of CA-MRSA into our institution. Moreover, the low endemic prevalence of MRSA demonstrates that current infection control measures are sufficient to limit its spreading and the emergence of large epidemic outbreaks.
Sequence-Based Identification of Filamentous Basidiomycetous Fungi from Clinical Specimens: a Cautionary Note
Authors: Romanelli Anna M. , Sutton Deanna A. , Thompson Elizabeth H. , Rinaldi Michael G. , Wickes Brian L. 
Published: December 2009

ABSTRACT
The species-level identification of sterile and/or arthroconidium-forming filamentous fungi presumed to be basidiomycetes based upon morphological or physiological features alone is usually not possible due to the limited amount of hyphal differentiation. Therefore, a reliable molecular approach capable of the unambiguous identification of clinical isolates is needed. One hundred sixty-eight presumptive basidiomycetes were screened by sequence analysis of the internal transcribed spacer (ITS) and D1/D2 ribosomal DNA regions in an effort to obtain a species identification. Through the use of this approach, identification of a basidiomycetous fungus to the species level was obtained for 167/168 of the isolates. However, comparison of the BLAST results for each isolate for both regions revealed that only 28.6% (48/168) of the isolates had the same species identification by use of both the ITS and the D1/D2 regions, regardless of the percent identity. At the less stringent genus-only level, the identities for only 48.8% (82/168) of the isolates agreed for both regions. Investigation of the causes for this low level of agreement revealed that 14% of the species lacked an ITS region deposit and 16% lacked a D1/D2 region deposit. Few GenBank deposits were found to be complete for either region, with only 8% of the isolates having a complete ITS region and 10% having a complete D1/D2 region. This study demonstrates that while sequence-based identification is a powerful tool for many fungi, sequence data derived from filamentous basidiomycetes should be interpreted carefully, particularly in the context of missing or incomplete GenBank data, and, whenever possible, should be evaluated in light of compatible morphological features.
MIC Quality Control Guidelines and Disk Diffusion Test Optimization for CEM-101, a Novel Fluoroketolide
Authors: Jones Ronald N. , Ross James E. , Rhomberg Paul R. 
Published: December 2009

ABSTRACT
The development of diagnostic susceptibility tests for CEM-101, a new fluoroketolide, was addressed by structured studies to determine the optimal disk diffusion test concentration and effects of various testing conditions or supplements and to establish the quality control (QC) ranges for reference broth microdilution tests. The 15-μg CEM-101 disk was selected, and MIC ranges for a total of four QC organisms were proposed, with only three doubling dilutions each that included 95.6 to 99.7% of values reported from the eight-laboratory investigation.
Efficacy of Multivalent Adenovirus-Based Vaccine against Simian Immunodeficiency Virus Challenge
Authors: Casimiro Danilo R. , Cox Kara , Tang Aimin , Sykes Kara J. , Feng Meizhen , Wang Fubao , Bett Andrew , Schleif William A. , Liang Xiaoping , Flynn Jessica , Tobery Timothy W. , Wilson Keith , Finnefrock Adam , Huang Lingyi , Vitelli Salvatore , Lin Jing , Patel Deepa , Davies Mary-Ellen , Heidecker Gwendolyn J. , Freed Daniel C. , Dubey Sheri , O'Connor David H. , Watkins David I. , Zhang Zhi-Qiang , Shiver John W. 
Published: December 2009

ABSTRACTThe prophylactic efficacies of several multivalent replication-incompetent adenovirus serotype 5 (Ad5) vaccines were examined in rhesus macaques using an intrarectal high-dose simian immunodeficiency virus SIVmac239 challenge model. Cohorts ofMamu-A*01+/B*17−Indian rhesus macaques were immunized with one of several combinations of Ad5 vectors expressing Gag, Pol, Nef, and Env gp140; for comparison, aMamu-A*01+cohort was immunized using the Ad5 vector alone. There was no sign of immunological interference between antigens in the immunized animals. In general, expansion of the antigen breadth resulted in more favorable virological outcomes. In particular, the order of efficacy trended as follows: Gag/Pol/Nef/Env ≈ Gag/Pol > Gag ≈ Gag/Pol/Nef > Nef. However, the precision in ranking the vaccines based on the study results may be limited by the cohort size, and as such, may warrant additional testing. The implications of these results in light of the recent discouraging results of the phase IIb study of the trivalent Ad5 HIV-1 vaccine are discussed.