bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement between allergen‐specific IgE assays and ensuing immunotherapy recommendations from four commercial laboratories in theUSA
Authors: Plant Jon D. , Neradelik Moni B. , Polissar Nayak L. , Fadok Valerie A. , Scott Brian A. 
Published: January 2014

BackgroundCanine allergen‐specificIgEassays in theUSAare not subjected to an independent laboratory reliability monitoring programme.Hypothesis/ObjectivesThe aim of this study was to evaluate the agreement of diagnostic results and treatment recommendations of four serum IgE assays commercially available in theUSA.MethodsReplicate serum samples from 10 atopic dogs were submitted to each of four laboratories for allergen‐specific IgE assays (ACTT®,VARLLiquid Gold,ALLERCEPT®and Greer®Aller‐g‐complete®). The interlaboratory agreement of standard, regional panels and ensuing treatment recommendations were analysed with the kappa statistic (κ) to account for agreement that might occur merely by chance. Six comparisons of pairs of laboratories and overall agreement among laboratories were analysed for ungrouped allergens (as tested) and also with allergens grouped according to reported cross‐reactivity and taxonomy.ResultsThe overall chance‐corrected agreement of the positive/negative test results for ungrouped and grouped allergens was slight (κ = 0.14 and 0.13, respectively). Subset analysis of the laboratory pair with the highest level of diagnostic agreement (κ = 0.36) found slight agreement (κ = 0.13) for ungrouped plants and fungi, but substantial agreement (κ = 0.71) for ungrouped mites. The overall agreement of the treatment recommendations was slight (κ = 0.11). Altogether, 85.1% of ungrouped allergen treatment recommendations were unique to one laboratory or another.Conclusions and clinical importanceOur study indicated that the choice of IgE assay may have a major influence on the positive/negative results and ensuing treatment recommendations.
Prior‐based artifact correction (PBAC) in computed tomography
Authors: Heußer Thorsten , Brehm Marcus , Ritschl Ludwig , Sawall Stefan , Kachelrieß Marc 
Published: January 2014

Purpose:Image quality in computed tomography (CT) often suffers from artifacts which may reduce the diagnostic value of the image. In many cases, these artifacts result from missing or corrupt regions in the projection data, e.g., in the case of metal, truncation, and limited angle artifacts. The authors propose a generalized correction method for different kinds of artifacts resulting from missing or corrupt data by making use of available prior knowledge to perform data completion.Methods:The proposed prior‐based artifact correction (PBAC) method requires prior knowledge in form of a planning CT of the same patient or in form of a CT scan of a different patient showing the same body region. In both cases, the prior image is registered to the patient image using a deformable transformation. The registered prior is forward projected and data completion of the patient projections is performed using smooth sinogram inpainting. The obtained projection data are used to reconstruct the corrected image.Results:The authors investigate metal and truncation artifacts in patient data sets acquired with a clinical CT and limited angle artifacts in an anthropomorphic head phantom data set acquired with a gantry‐based flat detector CT device. In all cases, the corrected images obtained by PBAC are nearly artifact‐free. Compared to conventional correction methods, PBAC achieves better artifact suppression while preserving the patient‐specific anatomy at the same time. Further, the authors show that prominent anatomical details in the prior image seem to have only minor impact on the correction result.Conclusions:The results show that PBAC has the potential to effectively correct for metal, truncation, and limited angle artifacts if adequate prior data are available. Since the proposed method makes use of a generalized algorithm, PBAC may also be applicable to other artifacts resulting from missing or corrupt data.
Dosimetric characterization and output verification for conical brachytherapy surface applicators. Part II. High dose rate 192Ir sources
Authors: Fulkerson Regina K. , Micka John A. , DeWerd Larry A. 
Published: January 2014

Purpose:Historically, treatment of malignant surface lesions has been achieved with linear accelerator based electron beams or superficial x‐ray beams. Recent developments in the field of brachytherapy now allow for the treatment of surface lesions with specialized conical applicators placed directly on the lesion. Applicators are available for use with high dose rate (HDR)192Ir sources, as well as electronic brachytherapy sources. Part I of this paper discussed the applicators used with electronic brachytherapy sources. Part II will discuss those used with HDR 192Ir sources. Although the use of these applicators has gained in popularity, the dosimetric characteristics have not been independently verified. Additionally, there is no recognized method of output verification for quality assurance procedures with applicators like these.Methods:This work aims to create a cohesive method of output verification that can be used to determine the dose at the treatment surface as part of a quality assurance/commissioning process for surface applicators used with HDR electronic brachytherapy sources (Part I) and192Ir sources (Part II). Air‐kerma rate measurements for the 192Ir sources were completed with several models of small‐volume ionization chambers to obtain an air‐kerma rate at the treatment surface for each applicator. Correction factors were calculated using MCNP5 and EGSnrc Monte Carlo codes in order to determine an applicator‐specific absorbed dose to water at the treatment surface from the measured air‐kerma rate. Additionally, relative dose measurements of the surface dose distributions and characteristic depth dose curves were completed in‐phantom.Results:Theoretical dose distributions and depth dose curves were generated for each applicator and agreed well with the measured values. A method of output verification was created that allows users to determine the applicator‐specific dose to water at the treatment surface based on a measured air‐kerma rate.Conclusions:The novel output verification methods described in this work will reduce uncertainties in dose delivery for treatments with these kinds of surface applicators, ultimately improving patient care.
The first clinical implementation of electromagnetic transponder‐guided MLC tracking
Authors: Keall Paul J. , Colvill Emma , O’Brien Ricky , Ng Jin Aun , Poulsen Per Rugaard , Eade Thomas , Kneebone Andrew , Booth Jeremy T. 
Published: January 2014

Purpose:We report on the clinical process, quality assurance, and geometric and dosimetric results of the first clinical implementation of electromagnetic transponder‐guided MLC tracking which occurred on 28 November 2013 at the Northern Sydney Cancer Centre.Methods:An electromagnetic transponder‐based positioning system (Calypso) was modified to send the target position output to in‐house‐developed MLC tracking code, which adjusts the leaf positions to optimally align the treatment beam with the real‐time target position. Clinical process and quality assurance procedures were developed and performed. The first clinical implementation of electromagnetic transponder‐guided MLC tracking was for a prostate cancer patient being treated with dual‐arc VMAT (RapidArc). For the first fraction of the first patient treatment of electromagnetic transponder‐guided MLC tracking we recorded the in‐room time and transponder positions, and performed dose reconstruction to estimate the delivered dose and also the dose received had MLC tracking not been used.Results:The total in‐room time was 21 min with 2 min of beam delivery. No additional time was needed for MLC tracking and there were no beam holds. The average prostate position from the initial setup was 1.2 mm, mostly an anterior shift. Dose reconstruction analysis of the delivered dose with MLC tracking showed similar isodose and target dose volume histograms to the planned treatment and a 4.6% increase in the fractional rectal V60. Dose reconstruction without motion compensation showed a 30% increase in the fractional rectal V60 from that planned, even for the small motion.Conclusions:The real‐time beam‐target correction method, electromagnetic transponder‐guided MLC tracking, has been translated to the clinic. This achievement represents a milestone in improving geometric and dosimetric accuracy, and by inference treatment outcomes, in cancer radiotherapy.
Mammographic compression after breast conserving therapy: Controlling pressure instead of force
Authors: de Groot J. E. , Broeders M. J. M. , Branderhorst W. , den Heeten G. J. , Grimbergen C. A. 
Published: January 2014

Purpose:X‐ray mammography is the primary tool for early detection of breast cancer and for follow‐up after breast conserving therapy (BCT). BCT‐treated breasts are smaller, less elastic, and more sensitive to pain. Instead of the current force‐controlled approach of applying the same force to each breast, pressure‐controlled protocols aim to improve standardization in terms of physiology by taking breast contact area and inelasticity into account. The purpose of this study is to estimate the potential for pressure protocols to reduce discomfort and pain, particularly the number of severe pain complaints for BCT‐treated breasts.Methods:A prospective observational study including 58 women having one BCT‐treated breast and one untreated nonsymptomatic breast, following our hospitalˈs 18 decanewton (daN) compression protocol was performed. Breast thickness, applied force, contact area, mean pressure, breast volume, and inelasticity (mean E‐modulus) were statistically compared between the within‐women breast pairs, and data were used as predictors for severe pain, i.e., scores 7 and higher on an 11‐point Numerical Rating Scale. Curve‐fitting models were used to estimate how pressure‐controlled protocols affect breast thickness, compression force, and pain experience.Results:BCT‐treated breasts had on average 27% smaller contact areas, 30% lower elasticity, and 30% higher pain scores than untreated breasts (allp < 0.001). Contact area was the strongest predictor for severe pain (p < 0.01). Since BCT‐treatment is associated with an average 0.36 dm2 decrease in contact area, as well as increased pain sensitivity, BCT‐breasts had on average 5.3 times higher odds for severe pain than untreated breasts. Model estimations for a pressure‐controlled protocol with a 10 kPa target pressure, which is below normal arterial pressure, suggest an average 26% (range 10%–36%) reduction in pain score, and an average 77% (range 46%–95%) reduction of the odds for severe pain. The estimated increase in thickness is +6.4% for BCT breasts.Conclusions:After BCT, women have hardly any choice in avoiding an annual follow‐up mammogram. Model estimations show that a 10 kPa pressure‐controlled protocol has the potential to reduce pain and severe pain particularly for these women. The results highly motivate conducting further research in larger subject groups.
Effects of Examiner Strength on Reliability of Hip-Strength Testing Using a Handheld Dynamometer
Authors: Krause David A. , Neuger Mathew D. , Lambert Kimberly A. , Johnson Amanda E. , DeVinny Heather A. , Hollman John H. 
Published: January 2014

Context:Hip-muscle impairments are associated with a variety of lower-extremity dysfunctions. Accurate assessment in the clinical setting can be challenging due to the strength of hip muscles relative to examiner strength.Objective:To examine the influence of examiner strength and technique on manual hip-strength testing using a handheld dynamometer.Design:Repeated measures.Setting:Research laboratory.Participants:30 active adults (age 24 ± 1.4 y).Interventions:Three examiners of different strength performed manual muscle tests (MMT) in 2 different positions for hip extension, abduction, and external rotation using a MicroFet handheld dynamometer. Examiner strength was quantified via a 1-repetition-maximum leg press and chest press with a Keiser A420 pneumatic resistance machine.Main Outcome Measures:Intrarater reliability (ICC3,1), interrater reliability (ICC2,1), and measured torque values.Results:Intrarater reliability for all measurements ranged from .82 to .97. Interrater reliability ranged from .81 to .98. Main effects for hip extension revealed a significant difference in torque values between examiners and between techniques. For the short-lever hip-abduction and seated hip-external-rotation tests, there was a significant difference between examiners. There was no significant difference in measured torque values between examiners with the long-lever hip-abduction or the prone hip-external-rotation tests.Conclusions:MMT of the hip may be performed with high reliability by examiners of different strength. To obtain valid MMT measurements of hip muscles, examiners must consider their own strength and testing techniques employed. The authors recommend a long-lever technique for hip abduction and a prone position for testing hip external rotation to minimize the influence of examiner strength. Both positions appear to provide mechanical advantages to the examiner compared with the alternative techniques. The authors are unable to recommend a preferred hip-extension-testing technique to minimize the influence of examiner strength.
Kinematic Analysis of Selected Reach Directions of the Star Excursion Balance Test Compared With the Y-Balance Test
Authors: Fullam Karl , Caulfield Brian , Coughlan Garrett F. , Delahunt Eamonn 
Published: January 2014

Context:The Star Excursion Balance Test (SEBT) and the Y-Balance Test (YBT) have 3 common reach directions: anterior (ANT), posteromedial (PM), and posterolateral (PL). Previous research has indicated that reach-distance performance on the ANT reach direction of the SEBT differs from that on the YBT. Kinematic patterns associated with the ANT reach direction of the SEBT and YBT need to be investigated to fully understand this difference, along with the PM and PL reach directions, to deduce any kinematic discrepancies between the 2 balance tests.Objective:To compare and contrast the kinematic patterns associated with test performance on the reach directions common to the SEBT and YBT.Design:Controlled laboratory study.Setting:University laboratory.Participants:15 healthy male (age 23.33 ± 2.02 y, height 1.77 ± 0.04 m, body mass 80.00 ± 9.03 kg) and 14 healthy female (age 21.14 ± 1.66 y, height 1.63 ± 0.06 m, body mass 59.58 ± 7.61 kg) volunteers.Intervention:Each participant performed 3 trials of the ANT, PM, and PL reach directions of the SEBT and YBT on their dominant leg.Main Outcome Measures:Sagittal-plane lower-limb kinematic profiles were recorded using a 3-D motion-analysis system. Reach distances were also recorded for each reach direction.Results:A significant main effect (P < .05) was observed for test condition with participants reaching farther on the ANT reach direction of the SEBT compared with the YBT. While reaching in the ANT direction participants were characterized by a more flexed position of the hip joint at the point of maximum reach on the YBT (27.94° ± 13.84°) compared with the SEBT (20.37° ± 18.64°).Conclusions:Based on these observed results, the authors conclude that test performance on the SEBT and YBT differ in terms of dynamic neuromuscular demands, as evidenced by differences in reach distances achieved in the ANT reach direction and associated test kinematic profile.
Effect of Gender on the Quadriceps-to-Hamstrings Coactivation Ratio During Different Exercises
Authors: Harput Gulcan , Soylu A. Ruhi , Ertan Hayri , Ergun Nevin , Mattacola Carl G. 
Published: January 2014

Context:Coactivation ratio of quadriceps to hamstring muscles (Q:H) and medial to lateral knee muscles (M:L) contributes to the dynamic stability of the knee joint during movement patterns recommended during rehabilitation and important for daily function.Objective:To compare the quadriceps-to-hamstring and medial-to-lateral knee muscles' coactivation ratios between men and women during the following closed kinetic chain exercises performed on a balance board: forward lunge, side lunge, single-leg stance, and single-leg squat.Design:Cross-sectional.Participants:20 healthy subjects (10 female and 10 male).Main Outcome Measures:Surface electromyography was used to measure the activation level of quadriceps (vastus lateralis and medialis) and hamstrings (biceps femoris and medial hamstrings) during forward- and side-lunge, single-leg-stance, and single-leg-squat exercises. Subjects were instructed during each exercise to move into the test position and to hold that position for 15 s. EMG was recorded during the 15-s isometric period where subjects tried to maintain a “set” position while the foot was on a balance board. Analysis of variance was used for statistical analysis.Results:There was a significant exercise-by-gender interaction for Q:H ratio (F3,48 = 6.63, P = .001), but the exercise-by-gender interaction for M:L ratio was not significant (F3,48 = 1.67, P = .18). Women showed larger Q:H ratio in side-lunge exercises than men (P = .002). Both genders showed larger M:L and lower Q:H ratio in a single-leg-stance exercise than in the other exercises.Conclusions:The results indicate that the forward- and side-lunge and single-leg-squat exercises should not be recommended as exercise where a balanced coactivation between quadriceps and hamstring muscles is warranted. Single-leg-stance exercise could be used when seeking an exercise where the ratio is balanced for both women and men.
Concurrent and Discriminant Validity of the Star Excursion Balance Test for Military Personnel With Lateral Ankle Sprain
Authors: Bastien Maude , Moffet Hélène , Bouyer Laurent , Perron Marc , Hébert Luc J. , Leblond Jean 
Published: January 2014

The Star Excursion Balance Test (SEBT) has frequently been used to measure motor control and residual functional deficits at different stages of recovery from lateral ankle sprain (LAS) in various populations. However, the validity of the measure used to characterize performance—the maximal reach distance (MRD) measured by visual estimation—is still unknown.Objectives:To evaluate the concurrent validity of the MRD in the SEBT estimated visually vs the MRD measured with a 3D motion-capture system and evaluate and compare the discriminant validity of 2 MRD-normalization methods (by height or by lower-limb length) in participants with or without LAS (n = 10 per group).Results:There is a high concurrent validity and a good degree of accuracy between the visual estimation measurement and the MRD gold-standard measurement for both groups and under all conditions. The Cohen d ratios between groups and MANOVA products were higher when computed from MRD data normalized by height.Conclusion:The results support the concurrent validity of visual estimation of the MRD and the use of the SEBT to evaluate motor control. Moreover, normalization of MRD data by height appears to increase the discriminant validity of this test.
Whole-Genome Sequencing of Salmonella enterica subsp.
enterica
Serovar Cubana Strains Isolated from Agricultural Sources
Authors: Benahmed Faiza H. , Gopinath Gopal R. , Wang Hua , Jean-Gilles Beaubrun Junia , Grim Christopher , Cheng Chorng-Ming , McClelland Michael , Ayers Sherry , Abbott Jason , Desai Prerak , Frye Jonathan G. , Weinstock George , Hammack Thomas S. , Hanes Darcy E. , Rasmussen Mark A. , Davidson Maureen K. 
Published: January 2014

ABSTRACT

We report the draft genomes of
Salmonella enterica
subsp.
enterica
serovar Cubana strain CVM42234, isolated from chick feed in 2012, and
S
. Cubana strain 76814, isolated from swine in 2004. The genome sizes are 4,975,046 and 4,936,251 bp, respectively.
Metagenome Sequencing of the Prokaryotic Microbiota of the Hypersaline and Meromictic Soap Lake, Washington
Authors: Hawley Erik R. , Hess Matthias 
Published: January 2014

ABSTRACT
Soap Lake is a small saline lake in central eastern Washington that is sharply stratified into two layers. In addition to being highly alkaline (~pH 10), Soap Lake also contains high concentrations of sulfide. Here, we report the community profile of the prokaryotic microbiota associated with Soap Lake surface water.
Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium
Authors: Wang Xinxin , Jin Decai , Zhou Lisha , Wu Liang , An Wei , Chen Yu , Zhao Lin 
Published: January 2014

ABSTRACT

Brevibacillus panacihumi
strain W25 was isolated from hydrocarbon-contaminated saline soil. Here, we report the 5.5-Mb draft genome sequence of this strain, which may provide insights into the mechanism of microbial hydrocarbon degradation in saline environments.
Genome Sequence of Pyrethroid-Degrading Bacterium Rhodopseudomonas palustris Strain JSC-3b
Authors: Zhang Songbai , Luo Xiangwen , Cheng Ju'e , Peng Jing , Zhang Deyong , Liu Yong 
Published: January 2014

ABSTRACT

Rhodopseudomonas palustris
strain JSC-3b is a facultative, thermophilic bacterium, which was isolated from water in a canal adjacent to a vegetable field. Strain JSC-3b biodegrades several varieties of pyrethroid residues effectively through cometabolic pathways. Here, we present the genome sequence of this biodegrader.
Nuclear structure and reaction properties ofNe,MgandSiisotopes with RMF densities
Authors: Panda R. N. , Sharma Mahesh K. , Patra S. K. 
Published: January 2014

We have studied nuclear structure and reaction properties of Ne , Mg and Si isotopes, using relativistic mean field (RMF) densities, in the framework of Glauber model. Total reaction cross-section σRfor Ne isotopes on12C target have been calculated at incident energy 240 MeV. The results are compared with the experimental data and with the recent theoretical study [W. Horiuchi et al., Phys. Rev. C 86, 024614 (2012)]. Study of σRusing deformed densities have shown a good agreement with the data. We have also predicted total reaction cross-section σRfor Ne , Mg and Si isotopes as projectiles and12C as target at different incident energies.
Synergies of phosphatidylserine and protein disulfide isomerase in tissue factor activation
Authors: Ruf Wolfram , Langer Florian 
Published: January 2014

SummaryTissue factor (TF), the cellular receptor and cofactor for factor VII/VIIa, initiates haemostasis and thrombosis. Initial tissue distribution studies suggested that TF was sequestered from the circulation and only present at perivascular sites. However, there is now clear evidence that TF also exists as a blood-borne form with critical contributions not only to arterial thrombosis following plaque rupture and to venous thrombosis following endothelial perturbation, but also to various other clotting abnormalities associated with trauma, infection, or cancer. Because thrombin generation, fibrin deposition, and platelet aggregation in the contexts of haemostasis, thrombosis, and pathogen defence frequently occur without TF de novo synthesis, considerable efforts are still directed to understanding the molecular events underlying the conversion of predominantly non-coagulant or cryptic TF on the surface of haematopoietic cells to a highly procoagulant molecule following cellular injury or stimulation. This article will review some of the still controversial mechanisms implicated in cellular TF activation or decryption with particular focus on the coordinated effects of outer leaflet phosphatidylserine exposure and thiol-disulfide exchange pathways involving protein disulfide isomerase (PDI). In this regard, our recent findings of ATP-triggered stimulation of the purinergic P2X7 receptor on myeloid and smooth muscle cells resulting in potent TF activation and shedding of procoagulant microparticles as well as of rapid monocyte TF decryption following antithymocyte globulin-dependent membrane complement fixation have delineated specific PDIdependent pathways of cellular TF activation and thus illustrated additional and novel links in the coupling of inflammation and coagulation.