bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoautotrophic–heterotrophic biofilm communities: a laboratory incubator designed for growing axenic diatoms and bacteria in defined mixed‐species biofilms
Authors: Buhmann Matthias , Kroth Peter G. , Schleheck David 
Published: December 2011

SummaryBiofilm communities in the euphotic zone of aquatic habitats comprise photoautotrophic microorganisms, such as diatoms, green algae and cyanobacteria, which produce the organic carbon that fuels the life of a heterotrophic contingent of microorganisms, mostly bacteria. Such photoautotrophic–heterotrophic mixed‐species biofilms have received little attention in biofilm research due to a lack of suitable pure‐culture laboratory model systems. However, they offer important insight into microbial population dynamics and community interactions during a biofilm‐developmental process that shapes highly structured, extremely well‐adapted microbial landscapes. Here, we report on the development of a sterile incubation chamber for growing and monitoring axenic phototrophic biofilms, i.e. a sterilizable, illuminated, continuous‐flow system for a routine work with pure cultures. The system has been designed to simulate the growth conditions in the shallow, littoral zone of aquatic habitats (horizontal surface, submerged in water, illuminated, aerated). Additional features of the concept include automated photometrical monitoring of biofilm density (as biofilm turbidity), analysis via confocal microscopy, direct harvesting of cells, and options to control illumination, flow velocity, and composition of culture fluid. The application of the system was demonstrated in growth experiments using axenic diatom biofilms, or axenic diatom biofilms co‐cultivated with different bacterial strains isolated from epilithic biofilms of an oligotrophic freshwater lake.
A Knowledge-based Diagnostic Clinical Decision Support System for Musculoskeletal Disorders of the Shoulder for Use in a Primary Care Setting
Authors: Farmer Nicholas , Schilstra Maria J. 
Published: December 2011

Background Twenty percent of cases seen by primary care clinicians (general practitioners; GPs) are musculoskeletal in nature, and approximately one-quarter of these are shoulder complaints. GPs are increasingly overloaded with clinical information and unfamiliarity with current research can easily lead to misdiagnosis and, in turn, to unnecessary test requests or onward specialist referrals. Well-designed diagnostic clinical decision support systems (CDSS) have been shown to facilitate clinical decision-making and reduce diagnostic errors. However, no CDSS have been developed or tested for musculoskeletal disorders. Methods We have developed a prototype knowledge-based diagnostic CDSS for musculoskeletal shoulder conditions. The CDSS uses Bayesian reasoning to diagnose six common musculoskeletal shoulder pathologies, based on current evidence and expert opinion. The CDSS was tested by comparing its diagnostic outcome against 50 case studies with known diagnosis by radiological imaging. Results The CDSS diagnostic validity and reliability was shown to be 88% with a Kappa value of 0.85 to a confidence level of 99% compared to known diagnosis by radiological imaging. Conclusions The results suggest that a Bayesian network-based CDSS is a promising instrument in the diagnosis of musculoskeletal shoulder conditions, having been shown to be valid and reliable for 50 case studies.
Cathepsin K Expression and Activity in Canine Osteosarcoma
Authors: Schmit J.M. , Pondenis H.C. , Barger A.M. , Borst L.B. , Garrett L.D. , Wypij J.M. , Neumann Z.L. , Fan T.M. 
Published: December 2011

BackgroundCathepsin K (CatK) is a lysosomal protease with collagenolytic activity, and its secretion by osteoclasts is responsible for degrading organic bone matrix. People with pathologic bone resorption have higher circulating CatK concentrations.HypothesisCanine osteosarcoma (OS) cells will possess CatK, and its secretion will be cytokine inducible. Circulating CatK concentrations will be increased in dogs with OS, and will be a surrogate marker of bone resorption.AnimalsFifty‐one dogs with appendicular OS and 18 age‐ and weight‐matched healthy control dogs.MethodsIn a prospective study, expressions of CatK mRNA and protein were investigated in OS cells. The inducible secretion and proteolytic activity of CatK from OS cells was assessed in vitro. Serum CatK concentrations were quantified in normal dogs and dogs with OS and its utility as a bone resorption marker was evaluated in dogs with OS treated with palliative radiation and antiresorptive agents.ResultsCanine OS cells contain preformed CatK within cytoplasmic vesicles. In OS cells, TGFβ1 induced the secretion of CatK, which degraded bone‐derived type I collagen in vitro. CatK concentrations were higher in dogs with OS than healthy dogs (11.3 ± 5.2 pmol/L versus 8.1 ± 5.0 pmol/L, P = .03). In a subset of dogs with OS, pretreatment CatK concentrations gradually decreased after palliative radiation and antiresorptive treatment, from 9.3 ± 3.2 pmol/L to 5.0 ± 3.1 pmol/L, P = .03.Conclusions and Clinical ImportanceCanine OS is associated with pathologic bone resorption, and CatK inhibitors might aid in the management of canine OS‐related malignant osteolysis.
The influence of mare numbers, ejaculation frequency and month on the fertility of Thoroughbred stallions
Authors: ALLEN W. R. , WILSHER S. 
Published: December 2011

SummaryReason for performing the study: Although considerable variation in per cycle pregnancy rates exists between Thoroughbred (TB) stallions, there is little information on factors that may influence this figure.Objective: To assess the influence of month, mare numbers and mating frequency on the fertility of TB stallions standing on studfarms in East Anglia, England.Methods: The daily breeding records of 31 TB stallions mating 3034 mares on 4851 occasions during the 2010 season were surveyed and related to first scan pregnancy rates. The influences of mare book size, month, number of matings per day and mating frequency or abstinence on per mating pregnancy rates were analysed.Results: The overall per mating pregnancy rate for all the stallions was 59.6%, but for individual stallions the figures ranged from 19.0% to 80.1%. The first mating occurred on 9 February and the last on 24 July and the per mating pregnancy rate per month was significantly reduced in June and July. The number of mares mated by individual stallions ranged from 15 to 161, giving a mean overall workload of 160 matings per 100 mares. The per mating pregnancy rate was not related to book size, the number of matings in the season or the mating frequency per day. However, some stallions showed differences in per mating pregnancy rate related to month or the number of ejaculations in the preceding 3 days.Conclusions: The majority of TB stallions are able to maintain good fertility despite large books of mares. However, 5 of the 31 stallions surveyed showed a per mating pregnancy rate of ≤50%.Potential relevance: This survey has identified wide differences between the per mating pregnancy rate in TB stallions. Identification of the factors involved through more comprehensive surveys would provide useful information for mare and stallion owners.
Epilepsy in horses: Aetiological classification and predictive factors
Authors: Lacombe V. A. , Mayes M. , Mosseri S. , Reed S. M. , Fenner W. R. , Ou H. T. 
Published: December 2011

SummaryReasons for performing the study:In contrast with reports in man and small animals, a systematic classification of seizures in horses is lacking.Objectives:The purpose of this study was to classify seizures based on their aetiology and to characterise epilepsy in 104 horses presented for seizures at the Ohio State University Veterinary Medical Center between 1988 and 2009.Methods:In a retrospective observational study, seizures were classified by aetiology based on history, clinical observations, diagnostic investigations (e.g. electroencephalograms, cerebrospinal fluid and computed tomography imaging of the head) andpost mortemexaminations, when available. Univariate and multivariate logistic regression analyses were performed.Results:Epilepsy (i.e. 2 or more recurrent seizures) was identified in 70% of cases, and further classified as symptomatic (i.e. structural brain pathology, 35.6% of cases), cryptogenic (i.e. unknown, 54.8% of cases) and idiopathic (i.e. suspected genetic predisposition, 2.7% of cases). Normal neurological examination on admission, the presence of seizures unprovoked by any identified factors and paroxysmal epileptiform activity on electroencephalogram recordings were all strongly (P<0.05) correlated with epilepsy on univariate analysis. For a horse with generalised seizures, the odds of having epilepsy was 7 times lower compared with a similar horse with partial seizures (P<0.05) in multivariate modelling.Conclusions:Seizure aetiology was symptomatic or cryptogenic in most horses, whereas reactive seizures and idiopathic epilepsy were less common.Potential relevance:This study is the first attempt to classify seizures and to characterise epilepsy in a referral‐based equine population. Predictive factors of epilepsy in horses were similar to those reported in other species and may assist the clinician with the early diagnosis of epilepsy.
Role of Universal 16S rRNA Gene PCR and Sequencing in Diagnosis of Prosthetic Joint Infection
Authors: Marín M. , Garcia-Lechuz J. M. , Alonso P. , Villanueva M. , Alcalá L. , Gimeno M. , Cercenado E. , Sánchez-Somolinos M. , Radice C. , Bouza E. 
Published: December 2011

ABSTRACT
The etiological diagnosis of prosthetic joint infection (PJI) requires the isolation of microorganisms from periprosthetic samples. Microbiological cultures often yield false-positive and false-negative results. 16S rRNA gene PCR combined with sequencing (16SPCR) has proven useful for diagnosing various infections. We performed a prospective study to compare the utility of this approach with that of culture to diagnose PJI using intraoperative periprosthetic samples. We analyzed 176 samples from 40 patients with PJI and 321 samples from 82 noninfected patients using conventional culture and 16SPCR. Three statistical studies were undertaken following a previously validated mathematical model: sample-to-sample analysis, calculation of the number of samples to be studied, and calculation of the number of positive samples necessary to diagnose PJI. When only the number of positive samples is taken into consideration, a 16SPCR-positive result in one sample has good specificity and positive predictive value for PJI (specificity, 96.3%; positive predictive value, 91.7%; and likelihood ratio [LR], 22), while 3 positive cultures with the same microorganism are necessary to achieve similar specificity. The best combination of results for 16SPCR was observed when 5 samples were studied and the same microorganism was detected in 2 of them (sensitivity, 94%; specificity, 100%; and LR, 69.62). The results for 5 samples with 2 positive cultures were 96% and 82%, respectively, and the likelihood ratio was 1.06. 16SPCR is more specific and has a better positive predictive value than culture for diagnosis of PJI. A positive 16SPCR result is largely suggestive of PJI, even when few samples are analyzed; however, culture is generally more sensitive.
Performance of Different Mono- and Multiplex Nucleic Acid Amplification Tests on a Multipathogen External Quality Assessment Panel
Authors: Loens K. , van Loon A. M. , Coenjaerts F. , van Aarle Y. , Goossens H. , Wallace P. , Claas E. J. C. , Ieven M. 
Published: December 2011

ABSTRACT

An external quality assessment (EQA) panel consisting of a total of 48 samples in bronchoalveolar lavage (BAL) fluid or transport medium was prepared in collaboration with Quality Control for Molecular Diagnostics (QCMD) (
www.qcmd.org
). The panel was used to assess the proficiency of the three laboratories that would be responsible for examining the 6,000 samples to be collected in the GRACE Network of Excellence (
www.grace-lrti.org
). The main objective was to decide on the best-performing testing approach for the detection of influenza viruses A and B, parainfluenza virus types 1 to 3, respiratory syncytial virus (RSV), human metapneumovirus, coronavirus, rhinovirus, adenovirus,
Chlamydophila pneumoniae
,
Mycoplasma pneumoniae
, and
Legionella pneumophila
by nucleic acid amplification techniques (NAATs). Two approaches were chosen: (i) laboratories testing samples using their in-house procedures for extraction and amplification and (ii) laboratories using their in-house amplification procedures on centrally extracted samples. Furthermore, three commercially available multiplex NAAT tests—the ResPlex (Qiagen GmbH, Hilden, Germany), RespiFinder plus (PathoFinder, Maastricht, The Netherlands), and RespiFinder Smart 21 (PathoFinder) tests—were evaluated by examination of the same EQA panel by the manufacturer. No large differences among the 3 laboratories were noticed when the performances of the assays developed in-house in combination with the in-house extraction procedures were compared. Also, the extraction procedure (central versus local) had little effect on performance. However, large differences in amplification efficacy were found between the commercially available tests; acceptable results were obtained by using the PathoFinder assays.
Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni
Authors: Taboada Eduardo N. , Ross Susan L. , Mutschall Steven K. , MacKinnon Joanne M. , Roberts Michael J. , Buchanan Cody J. , Kruczkiewicz Peter , Jokinen Cassandra C. , Thomas James E. , Nash John H. E. , Gannon Victor P. J. , Marshall Barbara , Pollari Frank , Clark Clifford G. 
Published: December 2011

ABSTRACT

Campylobacter
spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance- and outbreak-based epidemiologic investigations of
Campylobacter
spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for
C. jejuni
. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID = 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID = 0.873) and sequence type (ID = 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for
C. jejuni
subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations.
Prospective Evaluation of Clinical and Biological Markers To Predict the Outcome of Invasive Pulmonary Aspergillosis in Hematological Patients
Authors: Bergeron Anne , Porcher Raphaël , Menotti Jean , Poirot Jean Louis , Chagnon Karine , Vekhoff Anne , Cornet Muriel , Isnard Françoise , Raffoux Emmanuel , Brethon Benoit , Lacroix Claire , Touratier Sophie , Latgé Jean Paul , Bouges-Michel Claire , Tazi Abdellatif , Derouin Francis , Ribaud Patricia , Sulahian Annie 
Published: December 2011

ABSTRACTEarly evaluation of treatment efficacy in invasive aspergillosis (IA), a leading cause of morbidity and mortality in hematological patients, remains a challenge. We conducted a prospective study to evaluate the performance of different markers in predicting the outcome of patients with IA. Both clinical and biological criteria were assessed 7, 14, 21, and 45 days after inclusion in the study, and mortality was assessed at day 60. The association between baseline data and their evolution and the day 45 response to treatment was analyzed. A total of 57 patients (4 with proven, 44 with probable, and 9 with possible aspergillosis according to the revised EORTC/MSG [European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group] definitions) were included. At day 45, 30 patients (53%) were determined to be responders, 25 (44%) were nonresponders, and 2 were not able to be evaluated. Twenty patients died within the 60 days of follow-up. We found that a poor day 45 outcome was associated with patients who had high baseline serum galactomannan (GM) antigen levels and those receiving steroids at the time of IA. A consistently negative serum GM index was associated with a good outcome, and the day 14 clinical evaluation was predictive of the day 45 outcome. No association was found betweenAspergillusantibodies or DNA detection and patients' outcome. We conclude that the GM index value at diagnosis of IA, GM index kinetics, and clinical evaluation at day 14 are good markers for predicting the outcome of patients with IA and should be taken into account for adapting antifungal treatment.
International Circumpolar Surveillance Interlaboratory Quality Control Program for Serotyping Haemophilus influenzae and Serogrouping Neisseria meningitidis, 2005 to 2009
Authors: Tsang Raymond S. W. , Rudolph Karen , Lovgren Marguerite , Bekal Sadjia , Lefebvre Brigitte , Lambertsen Lotte , Zulz Tammy , Bruce Michael 
Published: December 2011

ABSTRACT

The International Circumpolar Surveillance (ICS) program was initiated in 1999 to conduct population-based surveillance for invasive pneumococcal disease in select regions of the Arctic. The program was expanded to include the surveillance of invasive diseases caused by
Neisseria meningitidis
and
Haemophilus influenzae
. An interlaboratory quality control (QC) program to monitor laboratory proficiencies in the serogrouping of
N. meningitidis
and serotyping of
H. influenzae
strains was codeveloped by the Arctic Investigations Program (Anchorage, AK) and the Public Health Agency of Canada National Microbiology Laboratory (Winnipeg, Manitoba, Canada) and introduced into the ICS program in 2005. Other participating laboratories included the Provincial Laboratory for Public Health (Edmonton, Alberta, Canada), Laboratoire Santé Publique du Québec (Sainte-Anne-de-Bellevue, Québec, Canada), and Statens Serum Institut (Copenhagen, Denmark). From 2005 through 2009, 50 isolates (24
N. meningitidis
and 26
H. influenzae
isolates) were distributed among the five participating laboratories. The overall serogroup concordance for
N. meningitidis
strains was 92.3% (96/104), without including three isolates that were found to express both serogroup Y and W135 specificities. Concordant results were obtained for serogroups A, B, C, and Y among all laboratories. Discrepancies were observed most frequently for serogroups W135, X, Z, and 29E. The overall serotype concordance for
H. influenzae
was 98% (125/127 attempts). The two discrepant results involved a serotype c strain and a serotype e strain, and in both cases, the serotypeable
H. influenzae
isolates were misidentified as being nontypeable. These data demonstrate a high degree of concordance for serogroup and serotype determinations of
N. meningitidis
and
H. influenzae
isolates, respectively, among the five laboratories participating in this quality control program.
Identification of Infectious Agents in Onychomycoses by PCR-Terminal Restriction Fragment Length Polymorphism
Authors: Verrier Julie , Pronina Marina , Peter Corinne , Bontems Olympia , Fratti Marina , Salamin Karine , Schürch Stéphanie , Gindro Katia , Wolfender Jean-Luc , Harshman Keith , Monod Michel 
Published: December 2011

ABSTRACTA fast and reliable assay for the identification of dermatophyte fungi and nondermatophyte fungi (NDF) in onychomycosis is essential, since NDF are especially difficult to cure using standard treatment. Diagnosis is usually based on both direct microscopic examination of nail scrapings and macroscopic and microscopic identification of the infectious fungus in culture assays. In the last decade, PCR assays have been developed for the direct detection of fungi in nail samples. In this study, we describe a PCR-terminal restriction fragment length polymorphism (TRFLP) assay to directly and routinely identify the infecting fungi in nails. Fungal DNA was easily extracted using a commercial kit after dissolving nail fragments in an Na2S solution.Trichophytonspp., as well as 12 NDF, could be unambiguously identified by the specific restriction fragment size of 5′-end-labeled amplified 28S DNA. This assay enables the distinction of different fungal infectious agents and their identification in mixed infections. Infectious agents could be identified in 74% (162/219) of cases in which the culture results were negative. The PCR-TRFLP assay described here is simple and reliable. Furthermore, it has the possibility to be automated and thus routinely applied to the rapid diagnosis of a large number of clinical specimens in dermatology laboratories.
Prevalence and Characterization of Staphylococcus aureus, Including Methicillin-Resistant Staphylococcus aureus, Isolated from Bulk Tank Milk from Minnesota Dairy Farms
Authors: Haran K. P. , Godden S. M. , Boxrud D. , Jawahir S. , Bender J. B. , Sreevatsan S. 
Published: December 2011

ABSTRACT

Staphylococcus aureus
is a common causative agent of bovine mastitis in dairy herds. The emergence of methicillin-resistant
Staphylococcus aureus
(MRSA) in hospitals as well as the community is a significant and costly public health concern.
S. aureus
-related bovine mastitis is a common reason for therapeutic and/or prophylactic use of antibiotics on dairy farms. In this study, herd prevalence of
S. aureus
, including MRSA, was estimated from bulk tank milk (BTM) from Minnesota farms. A total of 150 pooled BTM samples from 50 farms, collected over 3 seasons (spring, summer, and fall of 2009), were assessed. Herd prevalence of methicillin-susceptible
S. aureus
(MSSA) was 84%, while MRSA herd prevalence was 4%. A total of 93 MSSA isolates and 2 MRSA isolates were recovered from 150 BTM samples. Antibiotic susceptibility testing of
S. aureus
isolates showed pansusceptibility in 54 isolates, resistance to a single antibiotic class in 21 isolates, resistance to two antibiotic classes in 13 isolates, and resistance to ≥3 antibiotics classes and thus multidrug resistance in 5 isolates. The two MRSA isolates displayed resistance to β-lactams, cephalosporins, and lincosamides and were multiresistant. Staphylococcal protein A gene (
spa
) typing identified
spa
types t529 and t034 most frequently among methicillin-susceptible isolates, while t121 was observed in MRSA isolates. Seven isolates, including the two MRSA isolates, produced staphylococcal enterotoxins B, C, D, and E on overnight culture. MRSA isolates were further genotyped using multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Of the 2 MRSA isolates, one had a composite genotype profile of MLST ST 5-PFGE USA100-unknown
spa
type, which has been reported among hospital-associated MRSA isolates, while the second isolate carried the MLST ST 8-PFGE USA300-
spa
type t121 genotype, commonly identified among community-associated MRSA isolates. These results suggest that MRSA genotypes associated with hospitals and community can be isolated from milk at very low rates.