bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient satisfaction and outcome using emergency care practitioners in New Zealand
Authors: Swain Andrew H , Al‐Salami Manar , Hoyle Sarah R , Larsen Peter D 
Published: January 2012

AbstractObjective: A patient satisfaction survey was undertaken in the Kapiti District of the Wellington Region to ascertain patients' experience and opinions of New Zealand's first extended care paramedic (ECP) service before consideration is given to extending it to other locations within the region. Patient outcomes were also analysed for 1 week following ECP care.Methods: One hundred patients, 50 attended by ECPs and 50 by standard emergency ambulance service paramedics, were interviewed by an independent assessor, either in person or by phone according to patient preference. The questionnaire was aimed at comparing the experience of both groups of patients, dividing them into those treated at home and those transferred to the ED. ED and general practice records were then reviewed to determine whether the ECP‐treated patients attended either facility within 7 days and why.Results: Patients were very satisfied with their experience of both groups of paramedics but expressed a clear desire to be treated at home if possible. Of the 50 ECP‐treated patients, 11 were transferred directly to the ED. Only one clinical complication arose over the next 7 days in those treated in the community: a seizure in a patient with refractory epilepsy.Conclusion: The avoidance of unnecessary transfers to hospital is beneficial to patients, the ambulance service and the ED. This study demonstrates that patients are very satisfied with their assessment and treatment by ECPs, endorsing the proposal that the scheme should be extended across the Wellington Region, and perhaps New Zealand.
Diagnosis and treatment of seminal vesicle cysts
Authors: He Qun , Yang Yong , Xia Ming 
Published: January 2012

Aim:  To deepen the understanding of patients with seminal vesicle cysts for correct diagnosis and treatment.Patients and Methods:  Five patients with seminal vesicle cysts were treated over the period January 1996–May 2010. Their symptoms, diagnostic results, treatment and outcomes were analysed retrospectively. The mean age of these patients at diagnosis was 35 years (range: 20–45). Symptoms included haematospermia in three patients, urinary frequency in three patients, perineal malaise in four patients, infertility in three patients, pain after ejaculation in three patients, scrotal pain in three patients and dysuria in one patient. Cysts were palpable in four patients on digital rectal examination. All patients underwent intravenous urography and cystoscopy. Some patients received ultrasonography, computed tomography (CT) scanning, magnetic resonance imaging (MRI) or vasovesiculography. The size of the masses ranged from 3.8 cm × 3 cm × 2.6 cmto approximately 9.6 cm × 5.2 cm × 5 cm. Final open surgery consisted of vesiculectomy in two patients and laparoscopic excision of a partial seminal vesical cyst in three patients.Results:  The postoperative course was uneventful, except for one patient who complained of ureter pain. All patients were free of symptoms after open surgery.Conclusions:  Seminal vesicle cysts are rare, but should be considered in men with haematospermia and otherwise inexplicable bladder irritation symptoms, perineal discomfort or other genitourinary complaints of unknown aetiology. Diagnosis consists of digital rectal examination, transrectal and abdominal ultrasonography, CT scanning and MRI. Laparoscopic excision of seminal vesical cysts produced excellent results.
Avian Composition Co‐varies with Floristic Composition and Soil Nutrient Concentration in Amazonian Upland Forests
Authors: Pomara Lars Y. , Ruokolainen Kalle , Tuomisto Hanna , Young Kenneth R. 
Published: January 2012

AbstractSpatial heterogeneity in the plant species composition of tropical forests is expected to influence animal species abundance and composition because vegetation constitutes the primary habitat feature for forest animals. Floristic variation is tied to variation in soils, so edaphic properties should ultimately influence animal species composition as well. The study of covariation in floristic and faunistic turnover has been hindered by the difficulty of completing coordinated surveys in hyperdiverse tropical communities, but this can be overcome with the use of a few plant taxa that function as surrogates for general floristic turnover. We used avian and plant transect surveys and soil sampling in a western Amazonian upland (terra firme) forest landscape to test whether spatial variation in bird community composition is associated with floristic turnover and corresponding edaphic gradients. Partial Mantel tests and Non‐metric Multidimensional Scaling showed floristic distinctiveness between two forest types closely associated with differences in soil cation concentrations, and differences in both floristic composition and cation concentrations were further linked to compositional differences in avian species, independent of geographic distances among sites. Ten percent of bird species included in Indicator Species Analyses showed significant associations with one of the two forest types. The upland forest types that we sampled, each corresponding to a different geological formation, are intermediate relative to edaphically extreme environments in the region. Models of avian diversification should take into account this environmental heterogeneity, as should conservation planning approaches that aim to represent faunal diversity.Abstract in Spanish is available in the online version of this article.
A comparative study of ecological specialization estimators
Authors: Poisot Timothée , Canard Elsa , Mouquet Nicolas , Hochberg Michael E. 
Published: January 2012

Summary1. Ecological specialization is a unifying concept in the biological sciences. While there are reliable ways to characterize specificity at individual and community levels, the evaluation of population and species‐level measures is lacking. There is a need for such assessments given that populations and species are the relevant scales for most ecological and evolutionary processes.2. Using examples of simulated and empirical data sets of bipartite networks representing a continuum of biological interactions, we evaluate six indices of specificity in terms of their robustness to incomplete sampling and information they extract from data.3. Robustness differed between the measures and in their ability to differentiate specialists and generalists along a full continuum. On the empirical data sets, indices were less separated by their informativity than on the simulated data sets, which may be due to the heterogeneity of the former.4. Based on these different evaluations for species‐level (or population‐level) specificity, we recommend the use of Resource range when no quantitative data are available and Paired Difference Index otherwise. These results will assist both applied and fundamental researchers in the characterization and interpretation of species specificity.
RNETLOGO: an R package for running and exploring individual‐based models implemented in NETLOGO
Authors: Thiele Jan C. , Kurth Winfried , Grimm Volker 
Published: January 2012

Summary1. NetLogo is a free software platform for implementing individual‐based and agent‐based models. However, NetLogo’s support of systematic design, performance and analysis of simulation experiments is limited. The statistics software R includes such support.2. RNetLogo is an R package that links R and NetLogo: any NetLogo program can be controlled and run from R and model results can be transferred back to R for statistical analyses. RNetLogo includes 16 functions, which are explained and demonstrated in the user manual and tutorial. The design of RNetLogo was inspired by a similar link between Mathematica and NetLogo.3. RNetLogo is a powerful tool for making individual‐based modelling more efficient and less ad hoc. It links two fast growing user communities and constitutes a new interface for integrating descriptive statistical analyses and individual‐based modelling.
Effects of a randomized maintenance intervention on adiposity and metabolic risk factors in overweight minority adolescents
Authors: Davis J. N. , Ventura E. E. , Tung A. , Munevar M. A. , Hasson R. E. , Byrd‐Williams C. , Vanni A. K. , Spruijt‐Metz D. , Weigensberg M. , Goran M. I. 
Published: January 2012

SummaryObjectiveThe objective of this study was to assess the effects of a maintenance programme (monthly newsletters vs. monthly group classes and telephone behavioural sessions) on obesity and metabolic disease risk at 1 year in overweight minority adolescents.MethodsAfter a 4‐month nutrition and strength training intervention, 53 overweight Latino and African–American adolescents (15.4 ± 1.1 years) were randomized into one of two maintenance groups for 8 months: monthly newsletters (n = 23) or group classes (n = 30; monthly classes + individualized behavioural telephone sessions). The following outcomes were measured at months 4 (immediately following the intense intervention) and 12: height, weight, blood pressure, body composition via BodPod™ (Life Measurement Instruments, Concord, CA, USA), lipids and glucose/insulin indices via frequently sampled intravenous glucose tolerance test.ResultsThere were no significant group by time interactions for any of the health outcomes. There were significant time effects in several outcomes for both groups from months 4 to 12: bench press and leg press decreased by 5% and 14%, respectively (P = 0.004 & P = 0.01), fasting insulin and acute insulin response decreased by 26% and 16%, respectively (P < 0.001 & P = 0.046); while high‐density lipoprotein cholesterol and insulin sensitivity improved by 5% and 14% (P = 0.042 & P = 0.039).ConclusionsNewsletters as opposed to group classes may suffice as follow‐up maintenance programmes to decrease type 2 diabetes and cardiovascular risk in overweight minority adolescents.
Failure of the Smallpox Vaccine To Develop a Skin Lesion in Vaccinia Virus-Naïve Individuals Is Related to Differences in Antibody Profiles before Vaccination, Not After
Authors: Tan Xiaolin , Chun Sookhee , Pablo Jozelyn , Felgner Philip , Liang Xiaowu , Davies D. Huw 
Published: January 2012

ABSTRACTSuccessful vaccination against smallpox with conventional vaccinia virus is usually determined by the development of a vesicular skin lesion at the site of vaccinia inoculation, called a “take.” Although previous vaccination is known to be associated with attenuation of the take, the immunology that underlies a no-take in vaccinia-naïve individuals is not well understood. We hypothesized that antibody profiling of individuals before and after receiving vaccinia virus would reveal differences between takes and no-takes that may help better explain the phenomenon. Using vaccinia virus proteome microarrays and recombinant protein enzyme-linked immunosorbent assays (ELISAs), we first examined the antibody response in vaccinia-naïve individuals that failed to take after receiving different doses of the replication-competent DryVax and Aventis Pasteur (APSV) smallpox vaccines. Most that received diluted vaccine failed to respond, although four no-takes receiving diluted vaccine and four receiving undiluted vaccine mounted an antibody response. Interestingly, their antibody profiles were not significantly different from those of controls that did show a take. However, we did find elevated antibody titers in no-takes prior to receiving DryVax that were significantly different from those of takes. Although the sample size studied was small, we conclude the failure to take in responders correlates with preexisting immunity of unknown etiology that may attenuate the skin reaction in a way similar to previous smallpox vaccination.
Effects of Decontamination, DNA Extraction, and Amplification Procedures on the Molecular Diagnosis of Mycobacterium ulcerans Disease (Buruli Ulcer)
Authors: Affolabi Dissou , Sanoussi N′Dira , Vandelannoote Koen , Odoun Mathieu , Faïhun Frank , Sopoh Ghislain , Anagonou Séverin , Portaels Françoise , Eddyani Miriam 
Published: January 2012

ABSTRACT

We compared two DNA extraction methods (a semiautomated method using a Maxwell kit and a modified Boom method) and three amplification procedures (a single-step PCR, a nested PCR, and a real-time quantitative PCR) on 74 surgical tissue specimens from patients with clinically suspected Buruli ulcer. All of these procedures were compared before and after decontamination. We observed that, among the procedures tested, real-time PCR after the modified Boom extraction method or a single-run PCR assay after the Maxwell 16 extraction method, performed on nondecontaminated suspensions, are the best for the molecular diagnosis of
Mycobacterium ulcerans
disease.
Clostridium difficile Testing Algorithms Using Glutamate Dehydrogenase Antigen and C. difficile Toxin Enzyme Immunoassays with C. difficile Nucleic Acid Amplification Testing Increase Diagnostic Yield in a Tertiary Pediatric Population
Authors: Ota Kaede V. , McGowan Karin L. 
Published: January 2012

ABSTRACT

We evaluated the performance of the rapid C. diff Quik Chek Complete's glutamate dehydrogenase antigen (GDH) and toxin A/B (CDT) tests in two algorithmic approaches for a tertiary pediatric population: algorithm 1 entailed initial testing with GDH/CDT followed by loop-mediated isothermal amplification (LAMP), and algorithm 2 entailed GDH/CDT followed by cytotoxicity neutralization assay (CCNA) for adjudication of discrepant GDH-positive/CDT-negative results. A true positive (TP) was defined as positivity by CCNA or positivity by LAMP plus another test (GDH, CDT, or the Premier
C. difficile
toxin A and B enzyme immunoassay [P-EIA]). A total of 141 specimens from 141 patients yielded 27 TPs and 19% prevalence. Sensitivity, specificity, positive predictive value, and negative predictive value were 56%, 100%, 100%, and 90% for P-EIA and 81%, 100%, 100%, and 96% for both algorithm 1 and algorithm 2. In summary, GDH-based algorithms detected
C. difficile
infections with superior sensitivity compared to P-EIA. The algorithms allowed immediate reporting of half of all TPs, but LAMP or CCNA was required to confirm the presence or absence of toxigenic
C. difficile
in GDH-positive/CDT-negative specimens.
Persistent Bloodstream Infection with Kocuria rhizophila Related to a Damaged Central Catheter
Authors: Moissenet Didier , Becker Karsten , Mérens Audrey , Ferroni Agnès , Dubern Béatrice , Vu-Thien Hoang 
Published: January 2012

ABSTRACT

A case of persistent bloodstream infection with
Kocuria rhizophila
related to a damaged central venous catheter in a 3-year-old girl with Hirschsprung's disease is reported. The strain was identified as
K. rhizophila
by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Arbitrarily primed PCR analysis showed a clonal strain. The repeated septic episodes were resolved with the catheter repair.
Identification of Optimal Epitopes for Plasmodium falciparum Rapid Diagnostic Tests That Target Histidine-Rich Proteins 2 and 3
Authors: Lee Nelson , Gatton Michelle L. , Pelecanos Anita , Bubb Martin , Gonzalez Iveth , Bell David , Cheng Qin , McCarthy James S. 
Published: January 2012

ABSTRACT

Rapid diagnostic tests (RDTs) represent important tools to diagnose malaria infection. To improve understanding of the variable performance of RDTs that detect the major target in
Plasmodium falciparum
, namely, histidine-rich protein 2 (HRP2), and to inform the design of better tests, we undertook detailed mapping of the epitopes recognized by eight HRP-specific monoclonal antibodies (MAbs). To investigate the geographic skewing of this polymorphic protein, we analyzed the distribution of these epitopes in parasites from geographically diverse areas. To identify an ideal amino acid motif for a MAb to target in HRP2 and in the related protein HRP3, we used a purpose-designed script to perform bioinformatic analysis of 448 distinct gene sequences from
pfhrp2
and from 99 sequences from the closely related gene
pfhrp3
. The frequency and distribution of these motifs were also compared to the MAb epitopes. Heat stability testing of MAbs immobilized on nitrocellulose membranes was also performed. Results of these experiments enabled the identification of MAbs with the most desirable characteristics for inclusion in RDTs, including copy number and coverage of target epitopes, geographic skewing, heat stability, and match with the most abundant amino acid motifs identified. This study therefore informs the selection of MAbs to include in malaria RDTs as well as in the generation of improved MAbs that should improve the performance of HRP-detecting malaria RDTs.
Comparison of Three Assays for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in SurePath Pap Samples and the Role of Pre- and Postcytology Testing
Authors: Chernesky M. , Jang D. , Portillo E. , Smieja M. , Kapala J. , Doucette C. , Sumner J. , Ewert R. , MacRitchie C. , Gilchrist J. 
Published: January 2012

ABSTRACT

Chlamydia trachomatis
and
Neisseria gonorrhoeae
are common causes of sexually transmitted infections, and there is interest in screening SurePath liquid-based Pap (L-Pap) samples with Aptima Combo 2 (AC2), Amplicor (AMP), and ProbeTec ET (PT) assays. SurePath L-Pap samples and a cervical swab (CS) were collected from 394 women attending health clinics in Hamilton and Toronto, ON, Canada. L-Pap samples were tested with the three assays prior to being processed for cytology, and the CS sample was tested with AC2. The prevalence of
C. trachomatis
was 8.9%, and that of
N. gonorrhoeae
was 1.5%. By using the positives from CS testing, as well as CS negatives corresponding to L-Pap samples that tested positive in 2 of 3 assays, the sensitivities of AC2, AMP, and PT for
C. trachomatis
in precytology samples were calculated to be 97.1% (34 of 35 positive samples were detected), 91.4% (32 of 35 were detected), and 77.1% (27 of 35 were detected), respectively. Six women were infected with
N. gonorrhoeae
. After cytology processing, the results of testing the remaining liquid in the L-Pap vial and the cell-enriched fraction for
C. trachomatis
by AC2 showed positive agreements of 98.9% (kappa [
k
], 0.93) and 98.7% (
k
, 0.92), respectively, with the results of testing precytology L-Pap samples. Although all testing showed high specificity, testing for
C. trachomatis
by AC2 was significantly more sensitive than testing by PT for SurePath samples (
P
= 0.02). Newer versions of AMP (Cobas 4800) and PT (Q

x

with XTR technology) need published evaluations for detecting
C. trachomatis
and
N. gonorrhoeae
in L-Pap samples.
C. trachomatis
testing can be performed with similar results on pre- and postcytology SurePath samples.
Multilocus Sequence Typing and Phylogenetic Analysis of Propionibacterium acnes
Authors: Kilian Mogens , Scholz Christian F. P. , Lomholt Hans B. 
Published: January 2012

ABSTRACTPropionibacterium acnesis a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associateP. acneswith prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two multilocus sequence typing (MLST) schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78P. acnesgenomes and their gene contents. Further support for a basically clonal population structure ofP. acnesand a scenario of the global spread of epidemic clones ofP. acneswas obtained. Compared to the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/), which is based on nine genes, offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential.
Sensing of RNA Viruses: a Review of Innate Immune Receptors Involved in Recognizing RNA Virus Invasion
Authors: Jensen Søren , Thomsen Allan Randrup 
Published: January 2012

ABSTRACT
Our knowledge regarding the contribution of the innate immune system in recognizing and subsequently initiating a host response to an invasion of RNA virus has been rapidly growing over the last decade. Descriptions of the receptors involved and the molecular mechanisms they employ to sense viral pathogen-associated molecular patterns have emerged in great detail. This review presents an overview of our current knowledge regarding the receptors used to detect RNA virus invasion, the molecular structures these receptors sense, and the involved downstream signaling pathways.
Role of Ubiquitin in Parainfluenza Virus 5 Particle Formation
Authors: Harrison Megan S. , Schmitt Phuong Tieu , Pei Zifei , Schmitt Anthony P. 
Published: January 2012

ABSTRACTUbiquitin is important for the budding of many retroviruses and other enveloped viruses, but the precise role of ubiquitin in virus budding remains unclear. Here, we characterized the ubiquitination of the matrix (M) protein of a paramyxovirus, parainfluenza virus 5 (PIV5). The PIV5 M protein (but not the PIV5 nucleocapsid protein) was found to be targeted for monoubiquitination in transfected mammalian cells. Major sites of ubiquitin attachment identified by mass spectrometry analysis were lysine residues at amino acid positions 79/80, 130, and 247. The cumulative mutation of lysine residues 79, 80, and 130 to arginines led to an altered pattern of M protein ubiquitination and impaired viruslike particle (VLP) production. However, the cumulative mutation of lysine residues 79, 80, 130, and 247 to arginines restored M protein ubiquitination and VLP production, suggesting that ubiquitin is attached to alternative sites on the M protein when the primary ones have been removed. Additional lysine residues were targeted for mutagenesis based on the UbiPred algorithm. An M protein with seven lysine residues changed to arginines exhibited altered ubiquitination and poor VLP production. A recombinant virus encoding an M protein with seven lysines mutated was generated, and this virus exhibited a 6-fold-reduced maximum titer, with the defect being attributed mainly to the budding of noninfectious particles. The recombinant virus was assembly deficient, as judged by the redistribution of viral M and hemagglutinin-neuraminidase proteins in infected cells. Similar assembly defects were observed for the wild-type (wt) virus after treatment with a proteasome inhibitor. Collectively, these findings suggest that the monoubiquitination of the PIV5 M protein is important for proper virus assembly and for the budding of infectious particles.