bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of a real‐time PCR assay for the detection of Aeromonas salmonicida
Authors: Keeling S E , Brosnahan C L , Johnston C , Wallis R , Gudkovs N , McDonald W L 
Published: November 2012

AbstractA real‐time PCR assay using a molecular beacon was developed and validated to detect the vapA (surface array protein) gene in the fish pathogen, Aeromonas salmonicida. The assay had 100% analytical specificity and analytical sensitivities of 5 ± 0 fg (DNA), 2.2 × 104 ± 1 × 104 CFU g−1 (without enrichment) and 40 ± 10 CFU g−1 (with enrichment) in kidney tissue. The assay was highly repeatable and proved to be robust following equivalency testing using a different real‐time PCR platform. Following analytical validation, diagnostic specificity was determined using New Zealand farmed Chinook salmon, Oncorhynchus tshawytscha (Walbaum), (n = 750) and pink shubunkin, Carassius auratus (L.) (n = 157). The real‐time PCR was run in parallel with culture and all fish tested were found to be negative by both methods for A. salmonicida, resulting in 100% diagnostic specificity (95% confidence interval). The molecular beacon real‐time PCR system is specific, sensitive and a reproducible method for the detection of A. salmonicida. It can be used for diagnostic testing, health certification and active surveillance programmes.
Use of agent‐based modelling to predict benefits of cleaner fish in controlling sea lice, Lepeophtheirus salmonis, infestations on farmed Atlantic salmon, Salmo salar L.
Authors: Groner M L , Cox R , Gettinby G , Revie C W 
Published: November 2012

AbstractSea lice, Lepeophtheirus salmonis, are ectoparasites of farmed and wild salmonids. Infestations can result in significant morbidity and mortality of hosts in addition to being costly to control. Integrated pest management programmes have been developed to manage infestations, and in some salmon farming areas, these programmes include the use of wrasse. Wrasse prey upon the parasitic life stages of L. salmonis and can be stocked on farms at varying densities. Despite considerable variation in the usage of wrasse, there are few quantitative estimates of how well they can control sea lice and how best to optimize their use. To explore at what densities wrasse should be stocked in order to meet specific control targets, we built an individual‐based model that simulates sea lice infestation patterns on a representative salmonid host. Sea lice can be controlled through the use of chemical treatments as well as by wrasse predators. We found that the wrasse can effectively control sea lice, and the densities of wrasse needed for effective control depend upon the source of the infestation and the targeted level of control. Effective usage of wrasse can result in decreased use of chemical treatments and improved control of sea lice.
Interrater agreement, reliability and validity of the Glamorgan Paediatric Pressure Ulcer Risk Assessment Scale
Authors: Kottner Jan , Kenzler Martina , Wilborn Doris 
Published: November 2012

Aims and objectivesTo determine (1) What is the degree of interrater agreement and reliability of Glamorgan scale item and sum scores? and (2) Are Glamorgan scale sum scores valid?BackgroundPressure ulcer risk assessment scales are recommended for use in clinical practice. For paediatric patients, 12 instruments are currently described. Empirical evidence about the performance of Glamorgan scale scores in clinical practice is limited.DesignAn observational validation study was conducted on a paediatric cardiac unit of a large university hospital in Germany in April and May 2010.MethodsChildren were assessed simultaneously and independently by varying convenience samples of three nurses per assessment situation. Pressure ulcer risk was measured by the Glamorgan scale and a 100 mm Visual Analogue Scale (VAS). Proportions of agreement (po), multirater kappa and intraclass correlation coefficients were calculated.ResultsThirty children were rated by 27 nurses. Median children's age was 5·5 years. Agreement among item scores was high, whereas reliability coefficients of item scores were low. Interrater reliability for the Glamorgan scale sum scores was higher than for VAS scores. Correlation between both scales was moderate.ConclusionsHigh agreement among item scores indicates that nurses are able to make precise judgements. The low interrater reliability of item and sum scores indicates that nurses were unable to differentiate the rated children based on their item and sum scores, thus providing little additional clinical relevant information about pressure ulcer risk in this setting.Relevance to clinical practiceThe Glamorgan scale and the VAS are unable to make clear distinctions in a low‐risk setting. Therefore, it is unlikely that the tools in this setting provide additional information for clinical decision making. Both tools are not recommended for daily use.
Bruxism defined and graded: an international consensus
Authors: Lobbezoo F. , Ahlberg J. , Glaros A. G. , Kato T. , Koyano K. , Lavigne G. J. , de Leeuw R. , Manfredini D. , Svensson P. , Winocur E. 
Published: November 2012

SummaryTo date, there is no consensus about the definition and diagnostic grading of bruxism. A written consensus discussion was held among an international group of bruxism experts as to formulate a definition of bruxism and to suggest a grading system for its operationalisation. The expert group defined bruxism as a repetitive jaw‐muscle activity characterised by clenching or grinding of the teeth and/or by bracing or thrusting of the mandible. Bruxism has two distinct circadian manifestations: it can occur during sleep (indicated as sleep bruxism) or during wakefulness (indicated as awake bruxism). For the operationalisation of this definition, the expert group proposes a diagnostic grading system of ‘possible’, ‘probable’ and ‘definite’ sleep or awake bruxism. The proposed definition and grading system are suggested for clinical and research purposes in all relevant dental and medical domains.
Enzymatic Characterization ofCorynespora cassiicolaIsolates Using theAPI‐ZYM®System
Authors: de Oliveira Rodrigo Cardoso , de Oliveira Ricardo Ribeiro , de Marchi Bordon Caroline , Tessmann Dauri José , Schwan‐Estrada Kátia Regina Freitas , Vida João Batista 
Published: November 2012

AbstractCorynespora cassiicola(Berk. &Curt.) Wei is an important phytopathogenic fungus, and different isolates show great diversity in their reproductive structures. Therefore, the aim of this study was to evaluate the potential of theAPI‐ZYM®system as an auxiliary tool in the polyphasic approach ofC. cassiicolaidentification. FiveC. cassiicolaisolates from different host plants and onePseudocercospora griseolaisolate were tested. A typical enzymatic pattern was obtained, with eight enzymes being produced by all fiveC. cassiicolaisolates. An intraspecific differentiation was also found. Certain enzymes produced, such as α‐glucosidase, β‐glucosidase and α‐mannosidase, may be related to pathogenic processes, acting in the degradation of the structural components of the host cells.
A translocator‐specific export signal establishes the translocator–effector secretion hierarchy that is important for type III secretion system function
Authors: Tomalka Amanda G. , Stopford Charles M. , Lee Pei‐Chung , Rietsch Arne 
Published: November 2012

SummaryType III secretion systems are used by many Gram‐negative pathogens to directly deliver effector proteins into the cytoplasm of host cells. To accomplish this, bacteria secrete translocator proteins that form a pore in the host‐cell membrane through which the effector proteins are then introduced into the host cell. Evidence from multiple systems indicates that the pore‐forming translocator proteins are exported before effectors, but how this secretion hierarchy is established is unclear. Here we used the Pseudomonas aeruginosa translocator protein PopD as a model to identify its export signals. The N‐terminal secretion signal and chaperone, PcrH, are required for export under all conditions. Two novel signals in PopD, one proximal to the chaperone binding site and one at the very C‐terminus of the protein, are required for export of PopD before effector proteins. These novel export signals establish the translocator–effector secretion hierarchy, which in turn, is critical for the delivery of effectors into host cells.
Erythema nodosum induced by kerion celsi of the scalp in a child: a case report and mini‐review of literature
Authors: Castriota Marina , Ricci Francesco , Paradisi Andrea , Fossati Barbara , De Simone Clara , Capizzi Rodolfo , Guerriero Cristina 
Published: November 2012

SummaryA 9‐year‐old girl, presented with a 4‐week history of an inflammatory suppurative plaque, 8 cm in diameter, localised in the occipital area of the scalp. Mycological direct examination showed ectoendothrix invasion of the hair and Trichophyton mentagrophytes was isolated. Oral therapy with griseofulvin 25 mg kg−1 day−1 was prescribed, but after 2 weeks of treatment appeared multiple erythematous subcutaneous nodules localised in the legs. Erythema nodosum (EN) was confirmed by histological examination of a nodule and then we combined therapy with 1 mg Kg−1 day−1 of prednisone. At the remission of the panniculitis, which occurred in about 10 days, the steroid therapy was suspended, while the orally administered griseofulvin continued for 6 weeks until full recovery. EN is the most frequent clinical form of acute nodular panniculitis and it is considered an epiphenomenon relative to various infectious and non‐infectious stimuli. The association of EN with dermatophytosis of the scalp is infrequent, with only 15 cases reported in the Literature.
Management of Parkinson's Disease medication in acutely admitted patients
Authors: Sathyababu Renay , Chan Edmund , Dhakam Zahid 
Published: November 2012

AbstractThis project aimed to identify problems in the management of Parkinson's Disease (PD) medications in those acutely admitted to the medical ward. Errors in prescription of medications are due to difficulties in conversion of formulation of medications to suit different needs, lack of awareness of help available amongst junior doctors and lack of awareness of trust guidance. Drug charts were audited over two weeks on medical wards. Dosing, frequency, formulation, and any difficulties in the administration were noted. A survey of junior doctors regarding their knowledge of PD management was also undertaken. The effects of our interventions (creation of summary guidance made available on wards, advice regarding where to obtain prescription information, and teaching sessions) were evaluated using a survey and audit. There was improved accuracy in PD prescriptions, improved confidence in switching formulation, increased awareness of trust guidance and the consequences of missed doses of PD medications. However there was no improvement in knowledge about appropriate resources used to make correct prescriptions. Increased education and training is required to continue improvement in prescription accuracy and awareness of where to seek help, to improve patient safety.
Improving illiterate patients understanding and adherence to discharge medications
Authors: Clayton Matthew , Syed Faizan , Rashid Amjid , Fayyaz Umer 
Published: November 2012

AbstractAdherence to a hospital discharge medication regime is crucial for successful treatment and to avoid increasing rates of drug resistance. A patient's success in adhering to their medication regime is dependent on many social, cultural, economic, illness and therapy-related factors, and these are often more pronounced in the developing world. Anecdotal evidence in Services Hospital, Lahore (Pakistan) suggested that the relatively high levels of illiteracy in the patient population was a major factor in poor adherence. Baseline measurement revealed that 48% of all the hospital's patients were illiterate with just 5%-12% of illiterate patients being able to interpret their handwritten discharge prescription after leaving hospital. Unsurprisingly follow-up clinics reported very poor adherence. This quality improvement project intervened by designing a new discharge prescription proforma which used pictures and symbols rather than words to convey the necessary information. Repeated surveys demonstrated large relative increases in comprehension of the new proformas amongst illiterate patients with between 23%-35% of illiterate patients understanding the new proformas.
Polarimetric Signatures above the Melting Layer in Winter Storms: An Observational and Modeling Study
Authors: Andrić Jelena , Kumjian Matthew R. , Zrnić Dušan S. , Straka Jerry M. , Melnikov Valery M. 
Published: November 2012

AbstractPolarimetric radar observations above the melting layer in winter storms reveal enhanced differential reflectivity ZDR and specific differential phase shift KDP, collocated with reduced copolar correlation coefficient ρhv; these signatures often appear as isolated “pockets.” High-resolution RHIs and vertical profiles of polarimetric variables were analyzed for a winter storm that occurred in Oklahoma on 27 January 2009, observed with the polarimetric Weather Surveillance Radar-1988 Doppler (WSR-88D) in Norman. The ZDR maximum and ρhv minimum are located within the temperature range between −10° and −15°C, whereas the KDP maximum is located just below the ZDR maximum. These signatures are coincident with reflectivity factor ZH that increases toward the ground. A simple kinematical, one-dimensional, two-moment bulk microphysical model is developed and coupled with electromagnetic scattering calculations to explain the nature of the observed polarimetric signature. The microphysics model includes nucleation, deposition, and aggregation and considers only ice-phase hydrometeors. Vertical profiles of the polarimetric radar variables (ZH, ZDR, KDP, and ρhv) were calculated using the output from the microphysical model. The base model run reproduces the general profile and magnitude of the observed ZH and ρhv and the correct shape (but not magnitude) of ZDR and KDP. Several sensitivity experiments were conducted to determine if the modeled signatures of all variables can match the observed ones. The model was incapable of matching both the observed magnitude and shape of all polarimetric variables, however. This implies that some processes not included in the model (such as secondary ice generation) are important in producing the signature.
The Role of Cloud Microphysics Parameterization in the Simulation of Mesoscale Convective System Clouds and Precipitation in the Tropical Western Pacific
Authors: Van Weverberg K. , Vogelmann A. M. , Lin W. , Luke E. P. , Cialella A. , Minnis P. , Khaiyer M. , Boer E. R. , Jensen M. P. 
Published: November 2012

Abstract
This paper presents a detailed analysis of convection-permitting cloud simulations, aimed at increasing the understanding of the role of parameterized cloud microphysics in the simulation of mesoscale convective systems (MCSs) in the tropical western Pacific (TWP). Simulations with three commonly used bulk microphysics parameterizations with varying complexity have been compared against satellite-retrieved cloud properties. An MCS identification and tracking algorithm was applied to the observations and the simulations to evaluate the number, spatial extent, and microphysical properties of individual cloud systems. Different from many previous studies, these individual cloud systems could be tracked over larger distances because of the large TWP domain studied.
The analysis demonstrates that the simulation of MCSs is very sensitive to the parameterization of microphysical processes. The most crucial element was found to be the fall velocity of frozen condensate. Differences in this fall velocity between the experiments were more related to differences in particle number concentrations than to fall speed parameterization. Microphysics schemes that exhibit slow sedimentation rates for ice aloft experience a larger buildup of condensate in the upper troposphere. This leads to more numerous and/or larger MCSs with larger anvils. Mean surface precipitation was found to be overestimated and insensitive to the microphysical schemes employed in this study. In terms of the investigated properties, the performances of complex two-moment schemes were not superior to the simpler one-moment schemes, since explicit prediction of number concentration does not necessarily improve processes such as ice nucleation, the aggregation of ice crystals into snowflakes, and their sedimentation characteristics.
A Cumulus Cloud Microphysics Parameterization for Cloud-Resolving Models
Authors: Kogan Yefim 
Published: November 2012

Abstract
A microphysical parameterization for shallow cumulus and boundary layer stratocumulus clouds has been developed. Similar to the Khairoutdinov and Kogan parameterization for stratocumulus clouds, the new parameterization is based on an explicit microphysical large-eddy simulation (LES) model as a data source and benchmark for comparison. The predictions of the bulk model using the new parameterization were tested in simulations of shallow cumulus and boundary layer stratocumulus clouds; in both cases the new parameterization matched the predictions of the explicit microphysics LES quite accurately. These results show the importance of the choice of the dataset in parameterization development and the need for it to be balanced by realistic dynamic conditions. The strong sensitivity to representation of rain evaporation is also demonstrated. Accurate formulation of this process, tuned for the case of cumulus convection, has substantially improved precision of rain production.
On the Use of Doppler Radar–Derived Wind Fields to Diagnose the Secondary Circulations of Tornadoes
Authors: Nolan David S. 
Published: November 2012

Abstract
A number of studies in recent years have used wind fields derived from portable Doppler radars in combination with the ground-based velocity track display (GBVTD) technique to diagnose the primary (tangential) and secondary (radial and vertical) circulations in tornadoes. These analyses indicate very strong vertical motions in the vortex core, in some cases with updrafts and downdrafts exceeding 100 m s−1. In addition, many of the analyses indicate strong radial outflow at low levels and in the vicinity of the low-level tangential wind maximum. This paper shows that strong outward motion at this location cannot be consistent with a tornado circulation that lasts more than a few minutes. In addition, using data from numerical simulations as truth, it is shown that using observed radial velocities to diagnose vertical velocities greatly overestimates the intensity of downward motion in the core for two reasons: neglect of the mass flux into the core through the swirling boundary layer, and the likely positive bias in low-level radial velocities due to the centrifuging of debris. Possible methods for accounting for these errors are briefly discussed.
Coarse Graining the Vorticity Equation in the ECMWF Integrated Forecasting System: The Search for Kinetic Energy Backscatter
Authors: Shutts G. J. 
Published: November 2012

Abstract
Stochastic kinetic energy backscatter parameterization schemes are now widely used in ensemble prediction systems to account for random error associated with excessive dissipation and unrepresented energy backscatter in numerical weather prediction models. This dissipation arises from numerical advection schemes and explicit diffusion terms and is also implicit in some parameterization schemes. In the absence of a backscatter theory applicable to the convective scale and mesoscale, current parameterization methods are based on simple heuristic models designed to scale the energy input in proportion to a suitable measure of net energy dissipation rate. Free parameters in the formulation of backscatter tend to be tuned for the optimal performance of ensemble prediction systems, yet other forms of uncertainty represented in these forecasting systems make that task harder. Results are presented here from a study that aims to characterize the form and magnitude of kinetic energy backscatter within a global spectral framework. This is achieved by comparing a high-resolution “truth” model with a spectrally truncated version of the model for which the effect of the missing scales of motion is to be gauged. Energy exchange between these omitted scales and the resolved scales of the truncated representation is computed for the dominant terms in the vorticity equation. It is found that although there is a nonlocal spectral energy flux to low wavenumbers due to the purely rotational part of the flow, it is much smaller than the dissipative effect associated with terms involving the divergent part of the flow. Biharmonic horizontal diffusion is found to contribute significantly as an energy sink across the entire wavenumber spectrum.
Anatomy of an Extreme Event
Authors: Hoerling Martin , Kumar Arun , Dole Randall , Nielsen-Gammon John W. , Eischeid Jon , Perlwitz Judith , Quan Xiao-Wei , Zhang Tao , Pegion Philip , Chen Mingyue 
Published: November 2012

Abstract
The record-setting 2011 Texas drought/heat wave is examined to identify physical processes, underlying causes, and predictability. October 2010–September 2011 was Texas’s driest 12-month period on record. While the summer 2011 heat wave magnitude (2.9°C above the 1981–2010 mean) was larger than the previous record, events of similar or larger magnitude appear in preindustrial control runs of climate models. The principal factor contributing to the heat wave magnitude was a severe rainfall deficit during antecedent and concurrent seasons related to anomalous sea surface temperatures (SSTs) that included a La Niña event. Virtually all the precipitation deficits appear to be due to natural variability. About 0.6°C warming relative to the 1981–2010 mean is estimated to be attributable to human-induced climate change, with warming observed mainly in the past decade. Quantitative attribution of the overall human-induced contribution since preindustrial times is complicated by the lack of a detected century-scale temperature trend over Texas. Multiple factors altered the probability of climate extremes over Texas in 2011. Observed SST conditions increased the frequency of severe rainfall deficit events from 9% to 34% relative to 1981–2010, while anthropogenic forcing did not appreciably alter their frequency. Human-induced climate change increased the probability of a new temperature record from 3% during the 1981–2010 reference period to 6% in 2011, while the 2011 SSTs increased the probability from 4% to 23%. Forecasts initialized in May 2011 demonstrate predictive skill in anticipating much of the SST-enhanced risk for an extreme summer drought/heat wave over Texas.