bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abundance of Multiple High-Risk Human Papillomavirus (HPV) Infections Found in Cervical Cells Analyzed by Use of an Ultrasensitive HPV Genotyping Assay
Authors: Schmitt Markus , Dondog Bolormaa , Waterboer Tim , Pawlita Michael , Tommasino Massimo , Gheit Tarik 
Published: October 2009

ABSTRACT
PCR methods enable the detection of a large variety of human papillomavirus (HPV) genotypes that infect the anogenital tract. However, PCR with consensus primers, general primers, and, to a lesser extent, broad-spectrum primers may underrepresent the true prevalence of HPV, especially the true prevalence of multiple infections. We compared the rate of HPV positivity determined by a broad-spectrum PCR with primers BSGP5+ and BSGP6+ (BS-PCR) coupled to an established bead-based multiplex HPV genotyping (MPG) assay with the rate of HPV positivity determined by a multiplex PCR with type-specific primers (TS-PCR) coupled to a newly developed MPG assay for 735 selected cervical scraping samples. While the primers used for the BS-PCR are located within the L1 region of the HPV genome, the primers used for the TS-PCR target the E7 gene. The overall rates of positivity for the 19 HPV types included in both assays were 60.9% and 72.2% by the BS-PCR and the TS-PCR, respectively, and the two assays found multiple infections in 34.8% and 58.0% of the specimens, respectively. Both HPV detection assays allowed the semiquantitative detection of HPV types and identified the same dominant HPV type in 66.6% of the multiple infections. In conclusion, the TS-PCR-MPG assay significantly increased the rate of detection of HPV DNA and the number of infections with multiple HPV types detected and demonstrated that the prevalence of low-copy-number HPV infections in the anogenital tract may be strongly underestimated by conventional HPV amplification methods, especially in cases of multiple infections. As a consequence, PCR-TS-MPG appears to be highly suited for analysis of the significance of multiple infections in the development of cervical cancer and for the study the natural history and the latency of HPV.
Diversity of Human Parechoviruses Isolated from Stool Samples Collected from Thai Children with Acute Gastroenteritis
Authors: Pham Ngan Thi Kim , Trinh Quang Duy , Khamrin Pattara , Maneekarn Niwat , Shimizu Hideaki , Okitsu Shoko , Mizuguchi Masashi , Ushijima Hiroshi 
Published: October 2009

ABSTRACT
A total of 82 fecal specimens which were known to be negative for rotavirus, adenovirus, norovirus, sapovirus, and astrovirus and which were collected from infants and children with acute gastroenteritis in Chiang Mai, Thailand, from January to December 2005 were screened for human parechovirus (HPeV). HPeV was detected by reverse transcription-PCR with a primer pair that amplified the 5′ untranslated region of its genome and was genotyped by sequencing of the VP1 region. HPeV was detected in 12 of 82 specimens tested, and the detection rate was found to be 14.6%. The capsid VP1 gene was successfully sequenced from nine of the HPeV strains detected. The HPeV strains studied clustered into four different genotypes, HPeV genotype 1 (HPeV1) to HPeV4, and the majority of the strains studied (five strains) belonged to HPeV1. This is the first finding of HPeV from children with acute gastroenteritis in Thailand. In addition, the diversity of the Thai HPeV strains was also noted.
Multiplex PCR-Ligation Detection Reaction Assay for Simultaneous Detection of Drug Resistance and Toxin Genes from
Staphylococcus aureus
,
Enterococcus faecalis
, and
Enterococcus faecium
Authors: Granger K. , Rundell M. S. , Pingle M. R. , Shatsky R. , Larone D. H. , Golightly L. M. , Barany F. , Spitzer E. D. 
Published: October 2009

ABSTRACT

A multiplex PCR-ligation detection reaction (PCR-LDR) assay was developed for rapid detection of methicillin, tetracycline, and vancomycin resistance, as well as toxic shock toxin and Panton-Valentine leukocidin. The assay was tested on 470 positive blood culture bottles containing
Staphylococcus aureus
or enterococci. PCR-LDR exhibited a sensitivity and specificity of ≥98% for all components except tetracycline resistance, which had a sensitivity of 94.7%. Rapid and sensitive detection of antimicrobial resistance and virulence genes could help guide therapy and appropriate infection control measures.
Molecular Epidemiology of Genogroup II-Genotype 4 Noroviruses in the United States between 1994 and 2006
Authors: Zheng Du-Ping , Widdowson Marc-Alain , Glass Roger I. , Vinjé Jan 
Published: October 2009

ABSTRACT
Human noroviruses (NoVs) of genogroup II, genotype 4 (GII.4) are the most common strains detected in outbreaks of acute gastroenteritis worldwide. To gain insight into the epidemiology and genetic variation of GII.4 strains, we analyzed 773 NoV outbreaks reported to the CDC from 1994 to 2006. Of these NoV outbreaks, 629 (81.4%) were caused by GII viruses and 342 (44.2%) were caused by GII.4 strains. The proportion of GII.4 outbreaks increased from 5% in 1994 to 85% in 2006, but distinct annual differences were noted, including sharp increases in 1996, 2003, and 2006 each associated with newly emerging GII.4 strains. Sequence analysis of the full-length VP1 gene of GII.4 strains identified in this study and from GenBank segregated these viruses into at least 9 distinct subclusters which had 1.3 to 3.2% amino acid variation between strains in different subclusters. We propose that GII.4 subclusters be defined as having >5% sequence variation between strains. Our data confirm other studies on the rapid emergence and displacement of highly virulent GII.4 strains.
Comparison of BD GeneOhm Cdiff Real-Time PCR Assay with a Two-Step Algorithm and a Toxin A/B Enzyme-Linked Immunosorbent Assay for Diagnosis of Toxigenic
Clostridium difficile
Infection
Authors: Kvach Elizabeth J. , Ferguson David , Riska Paul F. , Landry Marie L. 
Published: October 2009

ABSTRACT

The BD GeneOhm Cdiff assay, a real-time PCR assay for the detection of the
Clostridium difficile
toxin B (
tcdB
) gene, was compared with the toxin A/B (Tox A/B) II enzyme-linked immunosorbent assay (ELISA) and a two-step algorithm which includes a C. Diff Chek-60 glutamate dehydrogenase (GDH) antigen assay followed by cytotoxin neutralization. Four hundred liquid or semisolid stool samples submitted for diagnostic
C. difficile
testing, 200 GDH antigen positive and 200 GDH antigen negative, were selected for analysis. All samples were tested by the C. Diff Chek-60 GDH antigen and cytotoxin neutralization assays, the Tox A/B II ELISA, and the BD GeneOhm Cdiff assay. Specimens with discrepant results were tested by toxigenic culture as an independent “gold standard.” Of 200 GDH-positive samples, 71 were positive by the Tox A/B II ELISA, 88 were positive by the two-step method, 93 were positive by PCR, and 96 were positive by the GDH antigen assay only. Of 200 GDH-negative samples, 3 were positive by PCR only. Toxigenic culture was performed for 41 samples with discrepant results, and 39 were culture positive. Culture resolution of discrepant results showed the Tox A/B II assay to have detected 70 (66.7%), the two-step method to have detected 87 (82.9%), and PCR to have detected 96 (91.4%) of 105 true positives. The BD GeneOhm Cdiff assay was more sensitive in detecting toxigenic
C. difficile
than the Tox A/B II assay (
P
< 0.0001); however, the difference between PCR and the two-step method was not significant (
P
= 0.1237). Enhanced sensitivity and rapid turnaround time make the BD GeneOhm Cdiff assay an important advance in the diagnosis of toxigenic
C. difficile
infection.
Analysis of Herpes Simplex Virus Type 1 DNA Packaging Signal Mutations in the Context of the Viral Genome
Authors: Tong Lily , Stow Nigel D. 
Published: October 2009

ABSTRACT

The minimal signal required for the cleavage and packaging of replicated concatemeric herpes simplex virus type 1 (HSV-1) DNA corresponds to an approximately 200-bp fragment, Uc-DR1-Ub, spanning the junction of the genomic L and S segments. Uc and Ub occupy positions adjacent to the L and S termini and contain motifs (
pac
2 and
pac
1, respectively) that are conserved near the ends of other herpesvirus genomes. We have used homologous Red/ET recombination in
Escherichia coli
to introduce wild-type and specifically mutated Uc-DR1-Ub fragments into an ectopic site of a cloned HSV-1 genome from which the resident packaging signals had been previously deleted. The resulting constructs were transfected into mammalian cells, and their abilities to replicate and become encapsidated, generate Uc- and Ub-containing terminal fragments, and give rise to progeny virus were assessed. In general, the results obtained agree well with previous observations made using amplicons and confirm roles for the
pac
2 T element in the initiation of DNA packaging and for the GC-rich motifs flanking the
pac
1 T element in termination. In contrast to a previous report, the sequence of the DR1 element was also crucial for DNA packaging. Following repair of the resident packaging signals in mammalian cells, recombination occurred at high frequency in progeny virus between the repaired sequences and mutated Uc-DR1-Ub inserts. This restored the ability of mutated Uc-DR1-Ub inserts to generate terminal fragments, although these were frequently larger than expected from simple repair of the original lesion.
Polymorphisms in the putative micro-RNA-binding sites of mesothelin gene are associated with serum levels of mesothelin-related protein
Authors: Cristaudo Alfonso , Foddis Rudy , Bonotti Alessandra , Simonini Silvia , Vivaldi Agnese , Guglielmi Giovanni , Bruno Rossella , Landi Debora , Gemignani Federica , Landi Stefano 
Published: October 2009

BackgroundSerum mesothelin, also known as soluble mesothelin-related protein (SMRP), reportedly shows increased levels in epithelial-type malignant pleural mesothelioma, but sometimes also arrives at high values in healthy asbestos-exposed subjects.ObjectivesThis study aimed to investigate whether single nucleotide polymorphisms in the 3′untranslated region (3′UTR) of the mesothelin-encoded gene (MSLN) are associated with the SMRP levels measured in serum.MethodsThe 3′UTR of the mesothelin gene was genotyped in 59 healthy asbestos-exposed subjects, selected on the basis of their SMRP levels. Direct sequencing did not show any new polymorphism, but enabled us to genotype two known SNPs (rs1057147, rs57272256). Differences in the mean values of SMRP in wild-type and variant heterozygote groups were calculated.ResultsHigh levels of SMRP in healthy asbestos-exposed subjects were significantly associated with polymorphism rs1057147 (G<A). Regarding rs57272256, there was no statistically significant difference between wild-type and heterozygote groups.Our study suggests that rs1057147 polymorphism can affect mesothelin expression. Although these data need to be confirmed with a larger number of cases, this study warrants further research in order to better understand the relationship between mesothelin polymorphisms and SMRP.
Changes in methyl mercury concentrations in zooplankton from four experimental reservoirs with differing amounts of carbon in the flooded catchmentsThis paper is part of the series “Forty Years of Aquatic Research at the Experimental Lakes Area”.
Authors: Hall Britt D. , Cherewyk Katharine A. , Paterson Michael J. , Bodaly R. (Drew) A. 
Published: October 2009

Methyl mercury (MeHg) concentrations in zooplankton were compared from four experimental reservoirs at the Experimental Lakes Area in northwestern Ontario, Canada, to test the hypothesis that increases in concentrations of MeHg in zooplankton would be proportional to C availability. The experimental reservoirs included three upland reservoirs flooded between 1999 and 2003 that differed in amounts of flooded organic terrestrial C (high, medium, and low C) and an experimental reservoir created over a wetland–peatland complex in 1993. After flooding, MeHg in zooplankton increased from <100 ng·g dry weight–1in inflow source waters to >500 ng·g dry weight–1in all reservoirs. In the first two years of flooding, MeHg in zooplankton was not correlated with amounts of flooded C, but the rates of decline in mean annual concentrations were negatively correlated with the amount of C stored in flooded catchments. Concentrations of MeHg in zooplankton were highly correlated with MeHg concentrations in unfiltered water, with reductions in bioaccumulation associated with increases in dissolved organic C and decreases in pH. Overall, our results suggest that reservoir designs that minimize the amount of flooded terrestrial C should result in shorter periods of elevated MeHg in the food web.
Benthic algal communities: recovery from experimental acidificationThis paper is part of the series “Forty Years of Aquatic Research at the Experimental Lakes Area”.
Authors: Turner Michael A. , Findlay David L. , Baulch Helen M. , Armstrong Llwellyn M. , Kasian Susan E. M. , McNicol Donald K. , Vinebrooke Rolf D. 
Published: October 2009

Chemical recovery is hypothesized to promote rapid recovery of benthic algal communities in formerly acidified lakes; this expectation needs modification. We evaluated the hypothesis in a small lake (L302S) in the boreal forest of northwestern Ontario, Canada, during a decade of pH recovery following a prior decade of experimental acidification from pH 6.7 to 4.5. To account for regional changes during the study, we also studied a nearby reference lake (L239). Taxonomic changes in the epilithon (biofilm on rock surfaces) included persistently lower cyanobacterial biomass following its acidification-related decline and increases in both diatoms and greens. Epilithic metabolic recovery was incomplete because the acidification-induced increase in respiration continued, although the prior decline in photosynthesis was reversed. Unexpectedly, blooms of metaphytic filamentous green algae occurred at higher pH during recovery than during acidification. Although several community attributes recovered fully, recovery of many aggregate functional and taxonomic properties lagged improvements in pH. Divergence was greater at the taxonomic than at the functional level. Despite pH recovery, potential causes of incomplete algal recovery include incomplete chemical recovery and the persistent absence of functionally important biota. Our findings counter the assumption that ecological recovery mirrors the pathway of damage caused by a human stressor.
Assimilation of freshwater salmonid aquaculture waste by native aquatic biotaThis paper is part of the series “Forty Years of Aquatic Research at the Experimental Lakes Area”.
Authors: Kullman Marilynn A. , Kidd Karen A. , Podemski Cheryl L. , Paterson Michael J. , Blanchfield Paul J. 
Published: October 2009

An experimental finfish aquaculture farm was operated in a small lake at the Experimental Lakes Area in northwestern Ontario, Canada. In this study, we used the distinct and enriched carbon and nitrogen isotope ratios (δ13C and δ15N) of rainbow trout ( Oncorhynchus mykiss ) feed and waste to determine whether the operation provided a novel source of energy for native biota. For 1 year prior to and for 3 years during the cage culture, we collected littoral, pelagic, and profundal invertebrates and minnows from the experimental and reference lakes. In both the second and third years of aquaculture, there was a significant increase in δ15N of all organisms sampled in the experimental lake; mean δ15N values of littoral, pelagic, and profundal invertebrates and minnows shifted towards the signature of the fish feed by up to 4.2‰. Significant increases in δ13C of up to 2.6‰ were observed in Mysis , profundal chironomids, and minnows but not in littoral invertebrates or zooplankton. Aquaculture waste became a progressively more important component of minnow diets over the course of this study. The dissolved and (or) particulate wastes of the cage operation became a novel source of energy for the native biota in this experimental lake.
Late Devonian tetrapod habitats indicated by palaeosols in Pennsylvania
Authors: Retallack G.J. , Hunt R.R. , White T.S. 
Published: October 2009

Abstract:

Late Devonian (Famennian) tetrapods from the Duncannon Member of the Catskill Formation, near Hyner (Pennsylvania, USA) have been found within palaeosols that offer a new line of evidence for their ancient environments. Hyner has yielded at least two fossil tetrapod species,
Hynerpeton basseti
and
Densignathus rowei
. Subhumid Vertisol palaeosols and semiarid Aridisol palaeosols alternate at Hyner, as in other Catskill Formation sedimentary cycles attributed to Milankovitch-eccentricity periods (100 ka). Tetrapods were found in palaeosols of subhumid, not semiarid, phases of 100 ka palaeoclimate cycles. In addition, palaeosols at Hyner record an unusually warm and wet climatic episode compared with other palaeosols of the Catskill Formation, and correlated with the European
Annulata
black shale event. Tetrapod bones are cracked and disarticulated in red palaeosols of an oxbow lake margin, as if victims of dry-season death, decay, and subaerial weathering. Vegetation-choked swales and floodplains would have afforded shelter from 3–4 m long predatory fish (
Hyneria lindae
) of open water, and offered food of large dead fish, small live fish, arachnids, myriapods and scorpions. If these early tetrapods lived on land at all, it was during wet seasons of feeding and breeding, rather than fatally dry seasons.

Supplementary material:

Chemical data are available at
http://www.geolsoc.org.uk/SUP18373
.
Exhumation of an active magmatic–hydrothermal system in a resurgent caldera environment: the example of Ischia (Italy)
Authors: Sbrana A. , Fulignati P. , Marianelli P. , Boyce A.J. , Cecchetti A. 
Published: October 2009

Abstract:

Ischia is a rare case of a well-exposed caldera system that has experienced rapid recent resurgence, which can be used to dissect the anatomy of an otherwise inaccessible active hydrothermal system developed in a caldera-forming environment. Integrated analyses of melt and fluid inclusions, mineralogy and stable isotopic compositions of pumices, tuffs and syenitic xenoliths of the Ischia volcanic system provide strong physico-chemical constraints on the shallow magmatic reservoir and the hydrothermal system. The hydrothermal system has been exposed by the rapid uplift of the Mt. Epomeo resurgent block. The engine of the hydrothermal system of Ischia can be identified in the shallow magmatic system (at around 2 km depth) that hosts hot (
c
. 1000 °C) trachytic magma. The hydrothermal system developed principally within thick intracaldera ignimbrite deposits, and extended to a depth of at least 1 km, defining a series of facies characterized by associations of alteration mineral assemblages typical of a seawater-dominated high-temperature geothermal system.

Supplementary material:

Sample descriptions and analytical methods are available at
http://www.geolsoc.org.uk/SUP18371
.
The gravity fields of Palawan and New Caledonia: insights into the subsurface geometries of ophiolites
Authors: Milsom John , Barretto Jenny , Aguda Nancy , Bringas Dennis , Ho Romeo , Aitchison Jonathan 
Published: October 2009

Abstract:
New gravity data from Palawan, in the western Philippines, emphasize resemblances to New Caledonia. On both islands, ophiolites derived from root zones just offshore rest on basal surfaces that change abruptly in depth by as much as 5 km. The subsurface geometries of these thrust sheets are as important to an understanding of their emplacement histories as are their exposure patterns.
Global Neoproterozoic petroleum systems: the emerging potential in North Africa
Authors: Craig Jonathan , Thurow Juergen , Thusu Bindra , Whitham Andy , Abutarruma Yousef 
Published: October 2009

Abstract

The Neoproterozoic Eon is relatively poorly known from a petroleum perspective, despite the existence of producing, proven and potential plays in many parts of the world. In tectonic, climatic and petroleum systems terms, the Neoproterozoic to Early Cambrian period can be divided into three distinct phases: a Tonian to Early Cryogenian phase, prior to about 750 Ma, dominated by the formation, stabilization and initial break-up of the supercontinent of Rodinia; a mid Cryogenian to Early Ediacaran phase (
c
. 750–600 Ma) including the major global-scale ‘Sturtian’ and ‘Marinoan’ glaciations and a mid Ediacaran to Early Cambrian (
c
. post 600 Ma) phase corresponding with the formation and stabilization of the Gondwana Supercontinent. There is increasing evidence that deposition of many mid to late Neoproterozoic (to Early Palaeozoic) organic-rich units was triggered by strong post-glacial sea level rise on a global scale, following the ‘Snowball Earth’ type glaciations, coupled with basin development and rifting on a more local scale.

Fieldwork in North Africa including the Taoudenni Basin in Mauritania, Algeria and Mali; the Anti-Atlas region of Morocco and the Cyrenaica, Kufra and Murzuk basins in Libya has added to the understanding of reservoir, source and seal relationships and confirmed the widespread presence of Precambrian stromatolitic carbonate units of potential reservoir facies. Current research on the chronostratigraphy, distribution and quality of source rocks, controls on reservoir quality and distribution of seals in the Precambrian–Early Cambrian hydrocarbon plays throughout South America, North Africa, the Middle East and the Indian Subcontinent is documented in this Special Publication.
Distribution of Infracambrian rocks and the hydrocarbon potential within the Murzuq and Al Kufrah basins, NW Africa
Authors: Aziz Abdussalam , Ghnia Sadeg 
Published: October 2009

Abstract
This paper presents an overview of the distribution of the Infracambrian rocks within the Murzuq and Al Kufrah basins obtained by integrating existing data and new outcrop and subsurface data, and discusses the implications for the regional depositional setting and hydrocarbon potential.
In the Murzuq Basin the Infracambrian units comprise volcaniclastics, metasediments and fine- to medium-grained sandstones with an average thickness of 61 m, reflecting a proximal, clastic-dominated depositional system.
In the Al Kufrah Basin carbonate facies in Jabal Arkanu (eastern margin) indicate that the distal facies may become organic-rich. Interpreted seismic lines reveal Infracambrian graben systems similar to those found elsewhere that provide good hydrocarbon source rocks in petroliferous basins.
Potential for oil and gas in the Proterozoic carbonates (Sirban Limestone) of Jammu, northern India
Authors: Bhat G. M. , Ram Ghara , Koul Sumita 
Published: October 2009

AbstractThe Proterozoic Sirban Limestone of Jammu in northern India contains an assemblage of Neoproterozoic microflora comparable to other such assemblages from different Proterozoic oil- and gas-bearing carbonate successions in India, Morocco and Siberia. The stromatolitic Sirban Limestone succession is composed of lamina-scale organic-rich source rocks, limestone units with good-quality reservoir characteristics and seal horizons that together constitute the basic physical elements of a petroleum system. A reworked microfloral assemblage of Neoproterozoic age is also recovered from the unconformably overlying Subathu Formation (Eocene) from the area. Somein situelements of this assemblage, including a few genera, were also recovered from the Sirban Limestone. This reworked assemblage may be related either to upwards migration of hydrocarbons from deeper sediments or, more likely, to the existence of the Sirban Limestone and younger Neoproterozoic formations as a positive area that sourced the microflora to the Eocene Subathu Basin.