bluuebunny/crossref_metadata_2025 huggingface dataset:
Early experience on simultaneous mastectomy and video‐assisted thoracoscopic surgery lobectomy via mastectomy incision
Authors: Chong Charing Ching‐Ning , Wan Innes Yuk‐Pui , Ng Calvin Sze‐Hang , Hsin Michael Kuan‐Yew , Leung Siu‐Lan , Chan Wing‐Cheong
Published: October 2009

Aim:  To assess the feasibility of simultaneous video‐assisted thoracoscopic surgery (VATS) lobectomy and mastectomy via the same incision in patients with synchronous primary carcinoma of the ipsilateral breast and lung.

Methods:  The patient was first positioned supine and modified radical mastectomy for the breast carcinoma was carried out in the standard way. After that, the mastectomy wound was partially closed and the patient was then turned into a full right decubitus position. Camera and instrument ports were inserted and a utility thoracotomy was made through the mastectomy wound. VATS lobectomy was then carried out.

Results:  From December 2007 to December 2008, three patients with synchronous primary breast and lung tumour received simultaneous mastectomy and VATS lobectomy through a single mastectomy incision in our institute. There was no operation‐related mortality. The median operation time was 253 min (range 246–345 min) and the median blood loss was 250 mL (range 110–300 mL). All except one patient had uneventful postoperative recovery and deep vein thrombosis was noted in one patient.

Conclusion:  Simultaneous lobectomy through the mastectomy incision is a safe and feasible treatment option for ipsilateral pulmonary and breast lesion with encouraging outcome.
Povidone‐iodine wound irrigation: A word of caution
Authors: Wong Randolph H.L. , Hung Emily C.W. , Wong Vivien W.Y. , Wan Innes Y.P. , Ng Calvin S.H. , Wan Song , Underwood Malcolm J.
Published: October 2009

Iodine‐based disinfectants are widely used by various surgical specialties to prevent and treat wound infection; however, its detrimental effects are often overlooked. We hereby report a dialysis‐dependent renal failure patient with clinical manifestation of systemic iodine toxicity after irrigation of an infected mediastinal wound with povidone‐iodine solution. Further study is required to determine the systemic absorption and side‐effect profile of povidone‐iodine especially when used for irrigation of deep body structures.
Value of monitoring postoperative intra‐abdominal drainage fluid for the diagnosis of postoperative pancreatic fistula: Results of a prospective study in 134 patients
Authors: Shi Chenye , Jin Dayong , Xu Bin , Lou Wenhui
Published: October 2009

Objective:  To evaluate the value of monitoring postoperative intra‐abdominal drainage in the diagnosis and treatment of postoperative pancreatic fistula (POPF).

Methods:  Intra‐abdominal drainage adjacent to the pacreaticoenteric anastomosis was prospectively collected from 134 patients accepted for pancreatic surgery in our department between November 2005 and August 2007 to determine the concentration of amylase and bacteriology. Also, the clinical outcome of each patient was recorded. The international study group definition was used to diagnose POPF.

Results:  The overall incidence of POPF was 39.6% in 53 patients diagnosed as POPF, among which 50 patients (37.3%, 50/134) were graded as I/II of POPF. The rising trend of the amylase level in the drainage fluid (P = 0.001), the texture of the pancreatic remnant (P = 0.042), and the amylase level on the 3rd and 7th postoperative days demonstrated good diagnostic values in univariate analysis (P < 0.001). The amylase value in drains on the 3rd postoperative day (POD3) and the 7th postoperative day (POD7) were the predicting factors (P < 0.001) of POPF by multivariate analysis.

Conclusions:  The amylase values in drains on the 3rd postoperative day and on the 7th postoperative day (POD7) were both valuable factors in the diagnoses of POPF. It is very important to monitor the dynamic change of amylase concentration in the drainage, not the result of a single test. These clinical factors could help us to detect the incidence of POPF earlier.
Are we doing too many surveillance colonoscopies on colonic adenoma? A 4‐year study on a major colorectal cancer screening hospital
Authors: Leung Edmund , Hughes Paul , McKay Stephen , Wong Ling
Published: October 2009

Introduction:  The British Society of Gastroenterology (BSG) has set clear guidelines on post‐polypectomy surveillance colonoscopy for adenomatous polyps. The present study aims to determine whether these guidelines were adhered to in a screening unit, where colonoscopy is offered to anyone between 50 and 69 with positive faecal occult blood testing.

Methods:  All patients (asymptomatic and symptomatic) who underwent surveillance colonoscopy were retrospectively included between 2003 and 2006. Surveillance colonoscopy was carried out as a follow‐up examination to a patient previously found to have adenoma(s), malignancy, strong family history or history of inflammatory bowel disease. Patients with no evidence of adenomas on their baseline or any repeat colonoscopy were excluded. Information relating polyp number, size and histology was collected, and their subsequent schedule colonoscopy was then compared with the BSG guidelines.

Results:  Of the 1856 colonoscopies carried out, 779 cases of polyps were detected after exclusion criteria (478 symptomatic, 301 screened cases). In the symptomatic cohort, 344 cases (72%), whereas in the screened cohort, 242 cases (80%) were compliant with the BSG guidelines (P < 0.01). Reasons for non‐compliance were premature follow up, late follow up, follow up occurring when not indicated, follow up not occurring when indicated, and the use of flexible sigmoidoscopy for follow up.

Conclusion:  Too many surveillance colonoscopies were performed in our unit. Targeting the reasons for non‐compliance could potentially reduce workload and improve efficiency in an over‐stretched colonoscopy unit.
Implementation of Standardized Nomenclature in the Electronic Medical Record
Authors: Klehr Joan , Hafner Jennifer , Spelz Leah Mylrea , Steen Sara , Weaver Kathy
Published: October 2009

PURPOSE.  To describe a customized electronic medical record documentation system which provides an electronic health record, Epic, which was implemented in December 2006 using standardized taxonomies for nursing documentation.

DATA SOURCES.  Descriptive data is provided regarding the development, implementation, and evaluation processes for the electronic medical record system. Nurses used standardized nursing nomenclature including NANDA‐I diagnoses, Nursing Interventions Classification, and Nursing Outcomes Classification in a measurable and user‐friendly format using the care plan activity.

CONCLUSIONS AND IMPLICATIONS.  Key factors in the success of the project included close collaboration among staff nurses and information technology staff, ongoing support and encouragement from the vice president/chief nursing officer, the ready availability of expert resources, and nursing ownership of the project. Use of this evidence‐based documentation enhanced institutional leadership in clinical documentation.
Problems Expressed by Caregivers of Children With Fetal Alcohol Spectrum Disorder
Authors: Caley Linda M. , Winkelman Theresa , Mariano Kathleen
Published: October 2009

PURPOSE.  The purpose of this study was to determine if use of a standardized classification system could help identify potential nursing sensitive problems for caregivers of children with fetal alcohol spectrum disorder (FASD).

METHOD.  This study is a secondary analysis of data obtained from transcripts of public testimonies. Content analysis was conducted using a standardized classification system. The sample consisted of 376 statements from electronic transcripts of first person testimonies given by 48 caregivers of children with FASD in four states.

FINDINGS.  Forty‐eight caregivers expressed a total of 53 signs and symptoms. The majority was in the problem areas: communication with community resources, caretaking/parenting, mental health, and income.

CONCLUSIONS AND IMPLICATIONS FOR NURSING PRACTICE.  Using a nursing classification system, investigators were able to identify nursing sensitive problems expressed by caregivers of children with FASD. The information from this study can be used in future studies to confirm or revise the signs/symptoms identified in this study.
Repair of a type IV Monteggia fracture in a foal
Authors: Jalim SL , McKinnon AO , Russell TM
Published: October 2009

A Monteggia fracture is a humero‐radial luxation combined with a fracture of the ulna. It is a rare injury, infrequently reported in the horse. This case report describes the surgical repair of such a fracture in a 4‐month‐old filly.
Veterinarians' preferences for anticonvulsant drugs for treating seizure disorders in dogs and cats
Authors: Kluger EK , Malik R , Govendir M
Published: October 2009

Objective To identify veterinarians' approaches and concerns when managing canine and feline patients with acute and chronic seizure disorders.

Design Cross‐sectional survey.

Method A questionnaire was distributed to veterinarians to determine how many dogs and cats they were actively treating for seizures, their anticonvulsant drug (ACD) preferences for treating acute and chronic seizure disorders and whether serum anticonvulsant concentrations and/or biochemical analytes were routinely measured. Additional questions involved the respondent's year and place of graduation and identified concerns they faced when managing patients with seizure disorders.

Results Phenobarbitone was the most commonly used ACD for managing chronic seizure disorders in both dogs and cats, with 82% of respondents using a combination of phenobarbitone and potassium bromide to manage refractory seizure disorders in dogs. Most respondents (96%) felt comfortable managing seizures in dogs, but only 63% were comfortable managing affected cats. Routine monitoring of serum ACD concentrations and of liver biochemical analytes was performed routinely by 71% and 45% of respondents, respectively. Of the respondents, 86% graduated from Australian universities and of these 53% had graduated after 1985.

Conclusion Veterinarians identified when to commence medication, whether regular monitoring of serum ACD concentrations and liver enzyme activity was necessary, and if the cost was justified. Veterinarians also identified the need to balance dose rates and side‐effects by using combination therapy, and the importance of providing accurate information to clients about what to expect in terms of seizure control for their pet.
Gender and the Civil Rights Movement
Authors: Van Delinder Jean
Published: October 2009

This study outlines how gender relations and gender differences come into play in the civil rights movement – the national movement to transform American race relations in the 1950s and 1960s. Social movement scholarship on the civil rights movement emphasizes dramatic mass mobilizations and charismatic leadership, both distinctively masculine enterprises. This emphasis overlooks the subtle and underappreciated dynamics of gender in shaping cultures of protest and resistance. Consideration of gender and gender roles in the private and public spheres provides a more nuanced understanding of protest strategies and the formulation of resistance in direct action. Gendered patterns related to movement participation, mobilization, leadership, strategies and ideologies also bring into focus how local issues shaped regional variations in civil rights initiatives. Finally, gender symbolism and culture deepen our understanding of non‐violent direct action as a moral, emancipatory performance, serving to blur the physical boundaries enacted by civil restraint.
Documentary at a Crossroads: Reality TV and the Hybridization of Small‐Screen Documentary
Authors: Mast Jelle
Published: October 2009

Today, as tendencies of popularization and hybridization have fundamentally redefined conventional notions of (small) screen documentary, the genre (re‐)emerges as a particularly appealing topic of scholarly research. This article elaborates some of the main strands of the multifaceted debate about these ongoing developments, thereby focusing on the ‘reality TV’ phenomenon, which is probably the most notable, yet also most controversial embodiment of the shifting that takes place. Discussing key positions regarding the problem of labeling and definition, questions of documentary values, and ethical issues, it is argued that a comprehensive, nuanced approach based on profound conceptualizations as well as empirical research into production and reception contexts are invaluable in making an astute assessment of the popular hybrid documentary.
Social Aspects of Genetic Testing Technologies
Authors: Tutton Richard
Published: October 2009

Since the early days of the Human Genome Project, there has been increasing social scientific research that promises to elucidate the social implications, aspects or dimensions of research on human, animal and plant genetics. This paper discusses the literature on the social aspects of different types of genetic testing technologies and their applications in the contexts of clinical medicine, biomedical research, personal and family genealogy, and criminal justice. Although there are many differences in the practices, purposes and organization of these technologies across such contexts, this paper shows that social scientists’ understandings of their social aspects centers on individual and collective experiences of how genetic testing technologies operate in practice.
Saproxylic beetle assemblages in artificially created high‐stumps of spruce (Picea abies) and birch (Betula pendula/pubescens) – does the surrounding landscape matter?
Authors: ABRAHAMSSON MARKUS , JONSELL MATS , NIKLASSON MATS , LINDBLADH MATTS
Published: October 2009

Abstract.  1. To create high‐stumps (snags) is a common conservation action during final felling in Swedish production forests. However, many wood‐living beetle species are only found in certain areas with higher overall biodiversity, so called hotspots. It has been argued that it is efficient to concentrate conservation efforts to hotspots.

2. The saproxylic beetle fauna was sampled on ten clearcuts inside hotspots and ten clearcuts outside the hotspots. They were collected with window traps mounted on 2‐ and 4‐year‐old spruce and birch high‐stumps. We also used environmental data (e.g. tree species composition) to confirm differences between the surroundings of two, the clearcut types.

3. High‐stumps on the hotspot clearcuts did not attract more saproxylic beetle species, or red‐listed species, than high‐stumps outside the hotspots. The environmental data showed that the clearcuts differed in several important aspects, for instance, were there a higher proportion of broadleaved trees around the hotspot compared with the clearcuts outside the hotspots. In a Canonical Correspondence Analysis, the proportion of coniferous and broadleaved forest was an important explanatory variables. The hotspot variable did contribute significantly in explaining the beetle composition on the birch high‐stumps, but not on the spruce high‐stumps.

4. In general, the study suggests that concentrating high‐stumps to hotspot areas will not benefit more species. However, the result indicates birch high‐stumps could be prioritised in a biologically rich landscape. The hotspot effect may be more noticeable in the future as the high‐stumps decay and their importance for late successional species increase.
Effects of logging on fire regimes in moist forests
Authors: Lindenmayer David B. , Hunter Malcolm L. , Burton Philip J. , Gibbons Philip
Published: October 2009

Does logging affect the fire proneness of forests? This question often arises after major wildfires, but data suggest that answers differ substantially among different types of forest. Logging can alter key attributes of forests by changing microclimates, stand structure and species composition, fuel characteristics, the prevalence of ignition points, and patterns of landscape cover. These changes may make some kinds of forests more prone to increased probability of ignition and increased fire severity. Such forests include tropical rainforests where fire was previously extremely rare or absent and other moist forests where natural fire regimes tend toward low frequency, stand replacing events. Relationships between logging and fire regimes are contingent on forest practices, the kind of forest under consideration, and the natural fire regime characteristic of that forest. Such relationships will influence both the threat of fire to human life and infrastructure and biodiversity conservation. We therefore argue that conservation scientists must engage in debates about fire and logging to provide an environmental context to guide considered actions.
Lab Experiments Are a Major Source of Knowledge in the Social Sciences
Authors: Falk Armin , Heckman James J.
Published: October 2009

Experimental Economics

The disciplines of social science, with the notable exception of psychology, have traditionally steered clear of laboratory. The field of economics, and in particular econometrics, has amassed an imposing arsenal of quantitative and statistical methods for analyzing observational data in assessing economic theory and in making causal inferences. More recently, laboratory experiments carried out under controlled conditions and randomized field experiments carried out under natural conditions have gained some currency as complementary approaches.Falk and Heckman(p.535) review the strengths and shortfalls of these recent developments.
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
Authors: Walsh David A. , Zaikova Elena , Howes Charles G. , Song Young C. , Wright Jody J. , Tringe Susannah G. , Tortell Philippe D. , Hallam Steven J.
Published: October 2009

Life in Dead Zones

Oxygen minimum zones, or oceanic “dead zones,” are expanding. Marine dead zone expansion and intensification results in amplification of biological nitrogen and greenhouse gas production, with implications for marine fisheries' productivity and for climate balance. Little is known about the microbial communities mediating the underlying biogeochemistry of dead zones.

Walsh
et al.

(p.
578
) present metagenomic analyses of a ubiquitous, abundant, and uncultivated bacterium in oceanic dead zones. Similar bacteria, related to chemoautotrophic gill symbionts of deep-sea clams and mussels, play a role in sulfide detoxification in African shelf waters. Reconstruction of the carbon and energy metabolism of this enigmatic lineage revealed a metabolic repertoire mediating carbon sequestration, sulfur-detoxification, and biological nitrogen loss in oxygen-deficient oceanic waters.
Pathogenesis of Chytridiomycosis, a Cause of Catastrophic Amphibian Declines
Authors: Voyles Jamie , Young Sam , Berger Lee , Campbell Craig , Voyles Wyatt F. , Dinudom Anuwat , Cook David , Webb Rebecca , Alford Ross A. , Skerratt Lee F. , Speare Rick
Published: October 2009

Croaking Frogs

The global amphibian decline has been attributed, among other causes, to an amphibian skin disease chytridiomycosis caused by the fungus
Batrachochytrium dendrobatidis
. However, how this pathogen causes mortality has been unclear.

Voyles
et al.

(p.
582
) show that this superficial skin infection may lead to cardiac failure owing to changes caused by lowered ion transport through the skin and consequent electrolyte reduction in the blood.
Parallel Pursuit of Near-Term and Long-Term Climate Mitigation
Authors: Jackson Stacy C.
Published: October 2009

Two separate treaties are needed to address the unique climate roles of long-lived versus medium- and short-lived pollutants.
Characterization of a Rhodium(I) σ-Methane Complex in Solution
Authors: Bernskoetter Wesley H. , Schauer Cynthia K. , Goldberg Karen I. , Brookhart Maurice
Published: October 2009

Methane Loosely Bound

For the most part, molecular bonds involve sharing of electrons between two discrete atoms. In certain cases, however, a third atom can also attract a portion of the electron density without fully cleaving the bond. Such loose complexes between C-H bonds and transition metals are often invoked as short-lived intermediates in metal-catalyzed reactions of hydrocarbons, though they are rarely observed directly.

Bernskoetter
et al.

(p.
553
) glimpse this coordination motif for methane (CH
4
) and rhodium (Rh) using low-temperature nuclear magnetic resonance spectroscopy after protonation of an Rh-CH
3
precursor. Kinetics measurements revealed a half-life of just over 80 minutes at −87°C.
The Passions of Meteorite Seekers
The Fallen Sky
An Intimate History of Shooting Stars

by Christopher Cokinos

Tarcher (Penguin), New York, 2009. 528 pp. $27.95, C$35. ISBN 9781585427208.
Authors: Lauretta Dante S.
Published: October 2009

Cokinos weaves together an account of meteorites, a history of meteorite hunters, and his own travels in the footsteps of collectors and researchers.
Exasperated by Copyright

Moral Panics and the Copyright Wars
by William Patry

Oxford University Press, Oxford, 2009. 290 pp. $29.95, £16.99. ISBN 9780195385649.
Authors: Samuelson Pamela
Published: October 2009

Patry argues that copyright is a utilitarian government program (rather than a moral or property right) and thus should be shaped so as to effectively encourage learning and the creation of new works.
Life and Death Play Out on the Skins of Frogs
Authors: Pennisi Elizabeth
Published: October 2009

On page
582
of this week's issue of
Science
, researchers go a long way toward solving the mystery of how a fungal infection has been killing amphibians worldwide. They find that the fungus,
Batrachochytrium dendrobatidis
, causes such severe electrolyte imbalances that the frog's heart stops.
Scientists Line Up Against Dam That Would Alter Protected Wetlands
Authors: Jiao Li
Published: October 2009

Scientists concerned about the ecological effects of a proposed dam across the northern end of Poyang Lake, 27 kilometers from the Yangtze River, were encouraged by the State Council's recent order that critics and the dam's backers thrash out their differences in Beijing.
Archaeologists Alarmed by Turkey's Proposed Dig Rules
Authors: Balter Michael
Published: October 2009

Archaeologists fear that proposed new rules governing foreign-led excavations in Turkey could make it very difficult for foreigners to dig in the country. The draft regulations could require that each excavation season last at least 4 months and that a Turkish co-director be appointed for each dig.
The Colossus of Europe
Authors: Bhattacharjee Yudhijit
Published: October 2009

The European Extremely Large Telescope will outsize the U.S. entries in its class, the Thirty Meter Telescope and the Giant Magellan Telescope, by a fair margin, with a primary mirror 42 meters in diameter.
Another Biofuels Drawback: The Demand for Irrigation
Authors: Service Robert F.
Published: October 2009

New U.S. mandates are prompting farmers to plant more corn in areas of the country that require irrigation. The move could trigger water shortages and water-quality problems.
Sex and Social Structure
Authors: Pennisi Elizabeth
Published: October 2009

Behavioral ecologists are discovering that social roles in bees may recapitulate the reproductive life cycle of solitary females.
Negative Correlation of Distributions of
Streptococcus cristatus
and
Porphyromonas gingivalis
in Subgingival Plaque
Authors: Wang Bing-yan , Wu Jie , Lamont Richard J. , Lin Xinghua , Xie Hua
Published: October 2009

Porphyromonas gingivalis
is one of the major causative agents of adult periodontitis. One of the features of this periodontal pathogen is its ability to attach to a variety of oral bacterial surfaces and to colonize subgingival dental plaque. We have shown that
Streptococcus cristatus
CC5A inhibits expression of
fimA
, a gene encoding the major protein subunit of long fimbriae in
P. gingivalis
; as a result,
S. cristatus
interrupts formation of
P. gingivalis
biofilms. Here we further demonstrate that the inhibitory activity of
S. cristatus
affects multiple strains of
P. gingivalis
and that optimal inhibitory activity correlates with levels of arginine deiminase expression in
S. cristatus
. More strikingly, the impact of
S. cristatus
on
P. gingivalis
colonization was revealed by comparing levels of
P. gingivalis
and
S. cristatus
in subgingival dental plaque. Spearman correlation analysis indicated a negative correlation between the distributions of
S. cristatus
and
P. gingivalis
(
r
= −0.57;
P
< 0.05). These data suggest that some early colonizers of dental plaque, such as
S. cristatus
, may be beneficial to the host by antagonizing the colonization and accumulation of periodontal pathogens such as
P. gingivalis
.
Improved Selective Isolation of
Bordetella pertussis
by Use of Modified Cyclodextrin Solid Medium
Authors: Ohtsuka Masayuki , Kikuchi Ken , Shundo Kazuya , Okada Kenji , Higashide Masato , Sunakawa Keisuke , Hiramatsu Keiichi
Published: October 2009

We have developed a modified cyclodextrin solid (MCS) medium using the selective antibiotic cefdinir. MCS medium exhibited higher sensitivity (95.6%; any culture-positive sample as reference) and greater inhibition of nasopharyngeal flora than did Bordet-Gengou agar (65.2%,
P
= 0.009) or cyclodextrin solid medium (39.1%,
P
< 0.001).
Rhizomucor variabilis
var.
regularior
and
Hormographiella aspergillata
Infections in a Leukemic Bone Marrow Transplant Recipient with Refractory Neutropenia
Authors: Abuali Mayssa M. , Posada Roberto , Del Toro Gustavo , Roman Elizabeth , Ramani Rama , Chaturvedi Sudha , Chaturvedi Vishnu , LaBombardi Vincent J.
Published: October 2009

Rhizomucor variabilis
and
Hormographiella aspergillata
rarely cause human infections. This report details a fatal case of a 14-year-old female with leukemia posthematopoietic cell transplant and relapse with refractory pancytopenia. The patient first developed
an
R. variabilis
var.
regularior
palate infection and later developed a cutaneous
H. aspergillata
infection while on posaconazole and caspofungin therapy.
Multicenter Comparison of Two Norovirus ORF2-Based Genotyping Protocols
Authors: Mattison Kirsten , Grudeski Elsie , Auk Brian , Charest Hugues , Drews Steven J. , Fritzinger Angela , Gregoricus Nicole , Hayward Stephen , Houde Alain , Lee Bonita E. , Pang Xiaoli L. , Wong Julie , Booth Tim F. , Vinjé Jan
Published: October 2009

Point source norovirus outbreaks can be difficult to track due to high background levels of the virus in the environment and the limited strain variation in some genotyping regions. However, rapid and accurate source identification can limit the spread of a foodborne outbreak and reduce the number of cases. Harmonization of genotyping assays is critical for enabling the rapid exchange of sequence data nationally and internationally. Several regions of the genome have been proposed for this purpose, but no consensus has been reached. In the present study, two standardized genotyping protocols (region C and region D) were evaluated by nine laboratories in Canada and the United States, using a coded panel of 96 fecal specimens representing 22 different norovirus genotypes. Overall, region C typing had a success rate of 78% compared to 52% for region D; however, region D provides greater nucleotide sequence diversity for identifying new GII.4 variant strains. Significant differences in the genotyping success rate were observed among the nine participating laboratories (10% to 100%) and among the different genotypes (6% to 100%). For several genogroup II strains, reduced region D amplification correlated directly with mismatches between primer sequences and the template. Based on overall performance, we recommend the region C protocol for routine genotyping of noroviruses, while the region D protocol may be useful for identifying new GII.4 variants. Standardized genotyping protocols will enable rapid exchange of outbreak and sequence data through electronic norovirus surveillance networks.
Subtyping of
emm
1 Group A Streptococci Causing Invasive Infections in France
Authors: Bidet P. , Lesteven E. , Doit C. , Liguori S. , Mariani-Kurkdjian P. , Bonacorsi S. , Bingen E.
Published: October 2009

By combining PCR amplification of toxin-encoding genes and
sic
gene sequencing, we distinguished 24 genotypes among 47 M/
emm
1 group A streptococci isolated from children and adults in France in 9 cases of infection comprising four clusters and 38 unrelated invasive infection cases used as controls.
(CGG)
4
-Based PCR as a Novel Tool for Discrimination of Uropathogenic
Escherichia coli
Strains: Comparison with Enterobacterial Repetitive Intergenic Consensus-PCR
Authors: Adamus-Bialek Wioletta , Wojtasik Arkadiusz , Majchrzak Marta , Sosnowski Marek , Parniewski Pawel
Published: October 2009

Urinary tract infections are one of the most frequent bacterial diseases in humans, and
Escherichia coli
is most often the relevant pathogen. A specific pathotype of
E. coli
, known as uropathogenic
E. coli
(UPEC), often causes serious and difficult-to-treat infections of the urinary tract. We propose a new single-tube screening tool that uses an (N)
6
(CGG)
4
primer to generate fingerprint profiles that allow rapid discrimination and epidemiology of this group of bacteria. We found 71 different CGG-PCR profiles among 127
E. coli
strains, while enterobacterial repetitive intergenic consensus (ERIC)-PCR of the same group yielded only 28 profiles. Additionally, the (CGG)
4
-based PCR test turned out to be very effective for clustering UPEC strains exhibiting multiple virulence genes and usually belonging to the B2 phylogenetic group, and it separated these strains from
E. coli
strains lacking most of the UPEC-specific virulence factors. Since the reproducibility of the CGG-PCR screen is higher than that of ERIC-PCR, our test should be a valuable means of increasing the discriminatory power of current UPEC typing schemes.
Delineation of a New Species of the
Borrelia burgdorferi
Sensu Lato Complex,
Borrelia americana
sp. nov
Authors: Rudenko Nataliia , Golovchenko Maryna , Lin Tao , Gao Lihui , Grubhoffer Libor , Oliver James H.
Published: October 2009

Analysis of borrelia isolates collected from ticks, birds, and rodents from the southeastern United States revealed the presence of well-established populations of
Borrelia burgdorferi
sensu stricto,
Borrelia bissettii
,
Borrelia carolinensis
, and
Borrelia
sp. nov. Multilocus sequence analysis of five genomic loci from seven samples representing
Borrelia
sp. nov. isolated from nymphal
Ixodes minor
collected in South Carolina showed their close relatedness to California strains known as genomospecies 1 and separation from any other known species of the
B. burgdorferi
sensu lato complex. One nucleotide difference in the size of the 5S-23S intergenic spacer region, one substitution in 16S rRNA gene signature nucleotides, and silent nucleotide substitutions in sequences of the gene encoding flagellin and the gene
p66
clearly separate
Borrelia
sp. nov. isolates from South Carolina into two subgroups. The sequences of isolates of each subgroup share the same restriction fragment length polymorphism patterns of the 5S-23S intergenic spacer region and contain unique signature nucleotides in the 16S rRNA gene. We propose that seven
Borrelia
sp. nov. isolates from South Carolina and two California isolates designated as genomospecies 1 comprise a single species, which we name
Borrelia americana
sp. nov. The currently recognized geographic distribution of
B. americana
is South Carolina and California. All strains are associated with
Ixodes pacificus
or
Ixodes minor
and their rodent and bird hosts.
Multicenter Comparative Evaluation of Five Commercial Methods for
Toxoplasma
DNA Extraction from Amniotic Fluid
Authors: Yera H. , Filisetti D. , Bastien P. , Ancelle T. , Thulliez P. , Delhaes L.
Published: October 2009

Over the past few years, a number of new nucleic acid extraction methods and extraction platforms using chemistry combined with magnetic or silica particles have been developed, in combination with instruments to facilitate the extraction procedure. The objective of the present study was to investigate the suitability of these automated methods for the isolation of
Toxoplasma gondii
DNA from amniotic fluid (AF). Therefore, three automated procedures were compared to two commercialized manual extraction methods. The MagNA Pure Compact (Roche), BioRobot EZ1 (Qiagen), and easyMAG (bioMérieux) automated procedures were compared to two manual DNA extraction kits, the QIAamp DNA minikit (Qiagen) and the High Pure PCR template preparation kit (Roche). Evaluation was carried out with two specific
Toxoplasma
PCRs (targeting the 529-bp repeat element), inhibitor search PCRs, and human beta-globin PCRs. The samples each consisted of 4 ml of AF with or without a calibrated
Toxoplasma gondii
RH strain suspension (0, 1, 2.5, 5, and 25 tachyzoites/ml). All PCR assays were laboratory-developed real-time PCR assays, using either TaqMan or fluorescent resonance energy transfer probes. A total of 1,178 PCRs were performed, including 978
Toxoplasma
PCRs. The automated and manual methods were similar in sensitivity for DNA extraction from
T. gondii
at the highest concentration (25
Toxoplasma gondii
cells/ml). However, our results showed that the DNA extraction procedures led to variable efficacy in isolating low concentrations of tachyzoites in AF samples (<5
Toxoplasma gondii
cells/ml), a difference that might have repercussions since low parasite concentrations in AF exist and can lead to congenital toxoplasmosis.
Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage ofMycobacterium tuberculosisin Israel Originating Predominantly in Sub-Saharan Africa
Authors: Freidlin Paul J. , Goldblatt Drora , Kaidar-Shwartz Hasia , Rorman Efrat
Published: October 2009

As part of the Israel National Program for Prevention and Control of Tuberculosis, the molecular epidemiology of new tuberculosis cases is monitored. Prospective screening showed that about 20% of all new cases of culture-positive tuberculosis (43 of 222) in Israel in the year 2008 were caused by certainMycobacterium tuberculosisstrains of the central Asian (CAS) spoligotype lineage. The identity and similarity of these strains by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing form a lineage we call PETRA for polymorphic at locus ETR A. The name PETRA was given to 79 strains we have found since the year 2000, because the largest number of strains with MIRU-VNTR profiles identical other than at locus A formed three groups, including 5 of 10 strains that had deleted the ETR A region from their genomes. No PETRA strain was found to be multiple drug resistant (resistant to both isoniazid and rifampin [rifampicin]). Most patients (75% [58 of 77 patients of known origin]) infected with PETRA were of sub-Saharan African origins. The genotypes associated with the 79 PETRA lineage strains presented in this paper suggest that the PETRA lineage is a large, major contributor to new tuberculosis cases in Israel.
Determination of Echinocandin MICs for
Candida
Species in Less than 8 Hours: Comparison of the Rapid Susceptibility Assay with the Clinical and Laboratory Standards Institute's Broth Microdilution Assay
Authors: Hazen Kevin C. , Dirks Dawn , Masuoka James
Published: October 2009

The echinocandins prevent fungal cell wall synthesis by inhibiting β-1,3-glucan synthesis, a significant glucose-consuming process. Previous studies suggested that echinocandin inhibitory activity is evident within 1 h of exposure. We hypothesized that a susceptibility assay based on glucose consumption may provide clinically useful MICs rapidly. The rapid susceptibility assay (RSA), which provides MICs in less than 8 h, was compared with the standard broth microdilution susceptibility assay (Clinical and Laboratory Standards Institute, document M27-A3, 2008) for 56
Candida
species strains. Variables which are known to influence MICs determined by the M27-A3 method were also assessed for their effects on the RSA results. Excellent agreement (>90%) between the results of the RSA and M27-A3 methods was achieved for all three FDA-approved echinocandins (micafungin, caspofungin, and anidulafungin).
Candida lusitaniae
strains were responsible for most of the discordant results. Assay variables such as the test medium, the age of the inoculum culture, and the presence of human serum affected MIC results from the RSA and the M27-A3 method similarly. The RSA is equivalent to the standard M27-A3 method for determining echinocandin MICs for
Candida
species. The RSA provides MIC results in less than 8 h and can be applied to old and young yeast colonies. The assay could potentially provide clinically useful MICs on the same day that yeast growth from a specimen is first detected on solid medium.
Multiplex PCR To Diagnose Bloodstream Infections in Patients Admitted from the Emergency Department with Sepsis
Authors: Tsalik Ephraim L. , Jones Daphne , Nicholson Bradly , Waring Lynette , Liesenfeld Oliver , Park Lawrence P. , Glickman Seth W. , Caram Lauren B. , Langley Raymond J. , van Velkinburgh Jennifer C. , Cairns Charles B. , Rivers Emanuel P. , Otero Ronny M. , Kingsmore Stephen F. , Lalani Tahaniyat , Fowler Vance G. , Woods Christopher W.
Published: October 2009

Sepsis is caused by a heterogeneous group of infectious etiologies. Early diagnosis and the provision of appropriate antimicrobial therapy correlate with positive clinical outcomes. Current microbiological techniques are limited in their diagnostic capacities and timeliness. Multiplex PCR has the potential to rapidly identify bloodstream infections and fill this diagnostic gap. We identified patients from two large academic hospital emergency departments with suspected sepsis. The results of a multiplex PCR that could detect 25 bacterial and fungal pathogens were compared to those of blood culture. The results were analyzed with respect to the likelihood of infection, sepsis severity, the site of infection, and the effect of prior antibiotic therapy. We enrolled 306 subjects with suspected sepsis. Of these, 43 were later determined not to have infectious etiologies. Of the remaining 263 subjects, 70% had sepsis, 16% had severe sepsis, and 14% had septic shock. The majority had a definite infection (41.5%) or a probable infection (30.7%). Blood culture and PCR performed similarly with samples from patients with clinically defined infections (areas under the receiver operating characteristic curves, 0.64 and 0.60, respectively). However, blood culture identified more cases of septicemia than PCR among patients with an identified infectious etiology (66 and 46, respectively;
P
= 0.0004). The two tests performed similarly when the results were stratified by sepsis severity or infection site. Blood culture tended to detect infections more frequently among patients who had previously received antibiotics (
P
= 0.06). Conversely, PCR identified an additional 24 organisms that blood culture failed to detect. Real-time multiplex PCR has the potential to serve as an adjunct to conventional blood culture, adding diagnostic yield and shortening the time to pathogen identification.
Serum (1-3)-β-
d
-Glucan as a Tool for Diagnosis of
Pneumocystis jirovecii
Pneumonia in Patients with Human Immunodeficiency Virus Infection or Hematological Malignancy
Authors: Desmet Stefanie , Van Wijngaerden Eric , Maertens Johan , Verhaegen Jan , Verbeken Eric , De Munter Paul , Meersseman Wouter , Van Meensel Britt , Van Eldere Johan , Lagrou Katrien
Published: October 2009

(1-3)-β-
d
-Glucan (BG) reactivity was tested in serum samples from 28 patients with human immunodeficiency virus infection or a hematological malignancy and
Pneumocystis jirovecii
pneumonia (PCP) and 28 control patients. The sensitivity and specificity of BG detection with the Fungitell assay for PCP were 100 and 96.4%, respectively, using a cutoff value of 100 pg/ml. Serum BG testing looks promising for the noninvasive diagnosis of PCP. Our data suggest that a higher cutoff value for the diagnosis of PCP than for the diagnosis of invasive aspergillosis or candidiasis could be used safely and will improve the specificity of the test.
Microbiological Characteristics of Community-Associated
Staphylococcus aureus
Causing Uncomplicated Bacteremia and Infective Endocarditis
Authors: Chi Chia-Yu , Wang Shih-Min , Lin Chia-Chun , Liu Ching-Chuan
Published: October 2009

Staphylococcus aureus
is an important cause of community-associated bacteremia (SAB) and infective endocarditis (IE). No significant differences in distribution or frequency of genes encoding virulence factors, including genes encoding adhesins, were found between isolates from the IE and SAB groups (12 IE and 10 SAB patients).
Outbreak of Acute Respiratory Disease Caused by
Mycoplasma pneumoniae
on Board a Deployed U.S. Navy Ship
Authors: Sliman Joseph A. , Metzgar David , Asseff David C. , Coon Robert G. , Faix Dennis J. , Lizewski Stephen
Published: October 2009

We identified 179 cases of acute respiratory illness including 50 cases of radiographically confirmed pneumonia over the course of 4 months on a deployed U.S. Navy vessel. Laboratory tests showed
Mycoplasma pneumoniae
to be the etiological agent. This report represents the first published description of a shipboard outbreak of this pathogen.
Changes in Multidrug Resistance of Enteric Bacteria following an Intervention To Reduce Antimicrobial Resistance in Dairy Calves
Authors: Kaneene John B. , Warnick Lorin D. , Bolin Carole A. , Erskine Ronald J. , May Katherine , Miller RoseAnn
Published: October 2009

An intervention study was conducted to determine whether discontinuing the feeding of milk replacer medicated with oxytetracycline and neomycin to preweaned calves reduced antimicrobial resistance in
Salmonella
,
Campylobacter
, and
Escherichia coli
bacteria. Results demonstrated that the intervention did reduce multidrug resistance in these bacteria but that other factors also influenced multidrug resistance.
MKRN1 Induces Degradation of West Nile Virus Capsid Protein by Functioning as an E3 Ligase
Authors: Ko Aram , Lee Eun-Woo , Yeh Jung-Yong , Yang Mi-Ran , Oh Wonkyung , Moon Jin-San , Song Jaewhan
Published: October 2009

West Nile virus capsid protein (WNVCp) displays pathogenic toxicity via the apoptotic pathway. However, a cellular mechanism protective against this toxic effect has not been observed so far. Here, we identified Makorin ring finger protein 1 (MKRN1) as a novel E3 ubiquitin ligase for WNVCp. The cytotoxic effects of WNVCp as well as its expression levels were inhibited in U2OS cells that stably expressed MKRN1. Immunoprecipitation analyses revealed an interaction between MKRN1 and WNVCp. Domain analysis indicated that the C terminus of MKRN1 and the N terminus of WNVCp were required for the interaction. MKRN1 could induce WNVCp ubiquitination and degradation in a proteasome-dependent manner. Interestingly, the WNVCp mutant with amino acids 1 to 105 deleted WNVCp was degraded by MKRN1, whereas the mutant with amino acids 1 to 90 deleted was not. When three lysine sites at positions 101, 103, and 104 of WNVCp were replaced with alanine, MKRN1-mediated ubiquitination and degradation of the mutant were significantly inhibited, suggesting that these sites are required for the ubiquitination. Finally, U2OS cell lines stably expressing MKRN1 were resistant to cytotoxic effects of WNV. In contrast, cells depleted of MKRN1 were more susceptible to WNVCp cytotoxicity. Confirming this, overexpression of MKRN1 significantly reduced, but depletion of MKRN1 increased, WNV proliferation in 293T cells. Taken together, our results suggest that MKRN1 can protect cells from WNV by inducing WNVCp degradation.
Hepatitis C Virus-Linked Mitochondrial Dysfunction Promotes Hypoxia-Inducible Factor 1α-Mediated Glycolytic Adaptation
Authors: Ripoli Maria , D'Aprile Annamaria , Quarato Giovanni , Sarasin-Filipowicz Magdalena , Gouttenoire Jérôme , Scrima Rosella , Cela Olga , Boffoli Domenico , Heim Markus H. , Moradpour Darius , Capitanio Nazzareno , Piccoli Claudia
Published: October 2009

Hepatitis C virus (HCV) infection induces a state of oxidative stress by affecting mitochondrial-respiratory-chain activity. By using cell lines inducibly expressing different HCV constructs, we showed previously that viral-protein expression leads to severe impairment of mitochondrial oxidative phosphorylation and to major reliance on nonoxidative glucose metabolism. However, the bioenergetic competence of the induced cells was not compromised, indicating an efficient prosurvival adaptive response. Here, we show that HCV protein expression activates hypoxia-inducible factor 1 (HIF-1) by normoxic stabilization of its α subunit. In consequence, expression of HIF-controlled genes, including those coding for glycolytic enzymes, was significantly upregulated. Similar expression of HIF-controlled genes was observed in cell lines inducibly expressing subgenomic HCV constructs encoding either structural or nonstructural viral proteins. Stabilization and transcriptional activation of HIF-1α was confirmed in Huh-7.5 cells harboring cell culture-derived infectious HCV and in liver biopsy specimens from patients with chronic hepatitis C. The HCV-related HIF-1α stabilization was insensitive to antioxidant treatment. Mimicking an impairment of mitochondrial oxidative phosphorylation by treatment of inducible cell lines with oligomycin resulted in stabilization of HIF-1α. Similar results were obtained by treatment with pyruvate, indicating that accumulation of intermediate metabolites is sufficient to stabilize HIF-1α. These observations provide new insights into the pathogenesis of chronic hepatitis C and, possibly, the HCV-related development of hepatocellular carcinoma.
Human Cytomegalovirus Gene UL21a Encodes a Short-Lived Cytoplasmic Protein and Facilitates Virus Replication in Fibroblasts
Authors: Fehr Anthony R. , Yu Dong
Published: October 2009

The human cytomegalovirus (HCMV) gene UL21a was recently annotated by its conservation in chimpanzee cytomegalovirus. Two large-scale mutagenic analyses showed that mutations in overlapping UL21a/UL21 resulted in a severe defect of virus growth in fibroblasts. Here, we characterized UL21a and demonstrated its role in HCMV infection. We mapped a UL21a-specific transcript of ∼600 bp that was expressed with early kinetics. UL21a encoded pUL21a, a protein of ∼15 kDa, which was unstable and localized predominantly to the cytoplasm during HCMV infection or when expressed alone. Interestingly, pUL21a was drastically stabilized in the presence of proteasome inhibitor MG132, but its instability was independent of a functional ubiquitin-mediated pathway, suggesting that pUL21a underwent proteasome-dependent, ubiquitin-independent degradation. A UL21a deletion virus was attenuated in primary human newborn foreskin fibroblasts (HFFs) and embryonic lung fibroblasts (MRC-5), whereas a marker-rescued virus and mutant viruses lacking the neighboring or overlapping genes UL20, UL21, or UL21.5-UL23 replicated at wild-type levels. The growth defect of UL21a-deficient virus in MRC-5 cells was more pronounced than that in HFFs. At a high multiplicity of infection, the UL21a deletion virus synthesized viral proteins with wild-type kinetics but had a two- to threefold defect in viral DNA replication. More importantly, although pUL21a was not detected in the virion, progeny virions produced by the mutant virus were ∼10 times less infectious than wild-type virus, suggesting that UL21a is required for HCMV to establish efficient productive infection. We conclude that UL21a encodes a short-lived cytoplasmic protein and facilitates HCMV replication in fibroblasts.