From text to codings: intercoder reliability assessment in qualitative content analysis

BACKGROUND: High intercoder reliability (ICR) is required in qualitative content analysis for assuring quality when more than one coder is involved in data analysis. The literature is short of standardized procedures for ICR procedures in qualitative content analysis. OBJECTIVE: To illustrate how ICR assessment can be used to improve codings in qualitative content analysis. METHODS: Key steps of the procedure are presented, drawing on data from a qualitative study on patients' perspectives on low back pain. RESULTS: First, a coding scheme was developed using a comprehensive inductive and deductive approach. Second, 10 transcripts were coded independently by two researchers, and ICR was calculated. A resulting kappa value of .67 can be regarded as satisfactory to solid. Moreover, varying agreement rates helped to identify problems in the coding scheme. Low agreement rates, for instance, indicated that respective codes were defined too broadly and would need clarification. In a third step, the results of the analysis were used to improve the coding scheme, leading to consistent and high-quality results. DISCUSSION: The quantitative approach of ICR assessment is a viable instrument for quality assurance in qualitative content analysis. Kappa values and close inspection of agreement rates help to estimate and increase quality of codings. This approach facilitates good practice in coding and enhances credibility of analysis, especially when large samples are interviewed, different coders are involved, and quantitative results are presented.

Prognostic importance of anaemia in HIV type-1-infected patients starting antiretroviral therapy: collaborative analysis of prospective cohort studies

BACKGROUND: In HIV type-1-infected patients starting highly active antiretroviral therapy (HAART), the prognostic value of haemoglobin when starting HAART, and of changes in haemoglobin levels, are not well defined. METHODS: We combined data from 10 prospective studies of 12,100 previously untreated individuals (25% women). A total of 4,222 patients (35%) were anaemic: 131 patients (1.1%) had severe (<8.0 g/dl), 1,120 (9%) had moderate (male 8.0-<11.0 g/dl and female 8.0- < 10.0 g/dl) and 2,971 (25%) had mild (male 11.0- < 13.0 g/ dl and female 10.0- < 12.0 g/dl) anaemia. We separately analysed progression to AIDS or death from baseline and from 6 months using Weibull models, adjusting for CD4+ T-cell count, age, sex and other variables. RESULTS: During 48,420 person-years of follow-up 1,448 patients developed at least one AIDS event and 857 patients died. Anaemia at baseline was independently associated with higher mortality: the adjusted hazard ratio (95% confidence interval) for mild anaemia was 1.42 (1.17-1.73), for moderate anaemia 2.56 (2.07-3.18) and for severe anaemia 5.26 (3.55-7.81). Corresponding figures for progression to AIDS were 1.60 (1.37-1.86), 2.00 (1.66-2.40) and 2.24 (1.46-3.42). At 6 months the prevalence of anaemia declined to 26%. Baseline anaemia continued to predict mortality (and to a lesser extent progression to AIDS) in patients with normal haemoglobin or mild anaemia at 6 months. CONCLUSIONS: Anaemia at the start of HAART is an important factor for short- and long-term prognosis, including in patients whose haemoglobin levels improved or normalized during the first 6 months of HAART.

Statistical analysis of personal radiofrequency electromagnetic field measurements with nondetects

Exposimeters are increasingly applied in bioelectromagnetic research to determine personal radiofrequency electromagnetic field (RF-EMF) exposure. The main advantages of exposimeter measurements are their convenient handling for study participants and the large amount of personal exposure data, which can be obtained for several RF-EMF sources. However, the large proportion of measurements below the detection limit is a challenge for data analysis. With the robust ROS (regression on order statistics) method, summary statistics can be calculated by fitting an assumed distribution to the observed data. We used a preliminary sample of 109 weekly exposimeter measurements from the QUALIFEX study to compare summary statistics computed by robust ROS with a naïve approach, where values below the detection limit were replaced by the value of the detection limit. For the total RF-EMF exposure, differences between the naïve approach and the robust ROS were moderate for the 90th percentile and the arithmetic mean. However, exposure contributions from minor RF-EMF sources were considerably overestimated with the naïve approach. This results in an underestimation of the exposure range in the population, which may bias the evaluation of potential exposure-response associations. We conclude from our analyses that summary statistics of exposimeter data calculated by robust ROS are more reliable and more informative than estimates based on a naïve approach. Nevertheless, estimates of source-specific medians or even lower percentiles depend on the assumed data distribution and should be considered with caution.

Analysis of key molecules of the innate immune system in mammary epithelial cells isolated from marker-assisted and conventionally selected cattle

Mastitis is the most prevalent infectious disease in dairy herds. Breeding programs considering mastitis susceptibility were adopted as approaches to improve udder health status. In recent decades, conventional selection criteria based on phenotypic characteristics such as somatic cell score in milk have been widely used to select animals. Recently, approaches to incorporate molecular information have become feasible because of the detection of quantitative trait loci (QTL) affecting mastitis resistance. The aims of the study were to explore molecular mechanisms underlying mastitis resistance and the genetic mechanisms underlying a QTL on Bos taurus chromosome 18 found to influence udder health. Primary cell cultures of mammary epithelial cells from heifers that were selected for high or low susceptibility to mastitis were established. Selection based on estimated pedigree breeding value or on the basis of marker-assisted selection using QTL information was implemented. The mRNA expression of 10 key molecules of the innate immune system was measured using quantitative real-time PCR after 1, 6, and 24 h of challenge with heat-inactivated mastitis pathogens (Escherichia coli and Staphylococcus aureus) and expression levels in the high and low susceptibility groups were compared according to selection criteria. In the marker-assisted selection groups, mRNA expression in cells isolated from less-susceptible animals was significantly elevated for toll-like receptor 2, tumor necrosis factor-alpha, IL-1beta, IL-6, IL-8, RANTES (regulated upon activation, normal t-cell expressed and secreted), complement factor C3, and lactoferrin. In the estimated pedigree breeding value groups, mRNA expression was significantly elevated only for V-rel reticuloendotheliosis viral oncogene homolog A, IL-1 beta, and RANTES. These observations provide first insights into genetically determined divergent reactions to pathogens in the bovine mammary gland and indicate that the application of QTL information could be a successful tool for the selection of animals resistant to mastitis.

Accounting for baseline differences and measurement error in the analysis of change over time

If change over time is compared in several groups, it is important to take into account baseline values so that the comparison is carried out under the same preconditions. As the observed baseline measurements are distorted by measurement error, it may not be sufficient to include them as covariate. By fitting a longitudinal mixed-effects model to all data including the baseline observations and subsequently calculating the expected change conditional on the underlying baseline value, a solution to this problem has been provided recently so that groups with the same baseline characteristics can be compared. In this article, we present an extended approach where a broader set of models can be used. Specifically, it is possible to include any desired set of interactions between the time variable and the other covariates, and also, time-dependent covariates can be included. Additionally, we extend the method to adjust for baseline measurement error of other time-varying covariates. We apply the methodology to data from the Swiss HIV Cohort Study to address the question if a joint infection with HIV-1 and hepatitis C virus leads to a slower increase of CD4 lymphocyte counts over time after the start of antiretroviral therapy.

An analysis of variance type method to describe and compare steady states in clinical data

Identifying and comparing different steady states is an important task for clinical decision making. Data from unequal sources, comprising diverse patient status information, have to be interpreted. In order to compare results an expressive representation is the key. In this contribution we suggest a criterion to calculate a context-sensitive value based on variance analysis and discuss its advantages and limitations referring to a clinical data example obtained during anesthesia. Different drug plasma target levels of the anesthetic propofol were preset to reach and maintain clinically desirable steady state conditions with target controlled infusion (TCI). At the same time systolic blood pressure was monitored, depth of anesthesia was recorded using the bispectral index (BIS) and propofol plasma concentrations were determined in venous blood samples. The presented analysis of variance (ANOVA) is used to quantify how accurately steady states can be monitored and compared using the three methods of measurement.

When to start antiretroviral therapy in children aged 2-5 years: a collaborative causal modelling analysis of cohort studies from southern Africa

BACKGROUND There is limited evidence on the optimal timing of antiretroviral therapy (ART) initiation in children 2-5 y of age. We conducted a causal modelling analysis using the International Epidemiologic Databases to Evaluate AIDS-Southern Africa (IeDEA-SA) collaborative dataset to determine the difference in mortality when starting ART in children aged 2-5 y immediately (irrespective of CD4 criteria), as recommended in the World Health Organization (WHO) 2013 guidelines, compared to deferring to lower CD4 thresholds, for example, the WHO 2010 recommended threshold of CD4 count <750 cells/mm(3) or CD4 percentage (CD4%) <25%. METHODS AND FINDINGS ART-naïve children enrolling in HIV care at IeDEA-SA sites who were between 24 and 59 mo of age at first visit and with ≥1 visit prior to ART initiation and ≥1 follow-up visit were included. We estimated mortality for ART initiation at different CD4 thresholds for up to 3 y using g-computation, adjusting for measured time-dependent confounding of CD4 percent, CD4 count, and weight-for-age z-score. Confidence intervals were constructed using bootstrapping. The median (first; third quartile) age at first visit of 2,934 children (51% male) included in the analysis was 3.3 y (2.6; 4.1), with a median (first; third quartile) CD4 count of 592 cells/mm(3) (356; 895) and median (first; third quartile) CD4% of 16% (10%; 23%). The estimated cumulative mortality after 3 y for ART initiation at different CD4 thresholds ranged from 3.4% (95% CI: 2.1-6.5) (no ART) to 2.1% (95% CI: 1.3%-3.5%) (ART irrespective of CD4 value). Estimated mortality was overall higher when initiating ART at lower CD4 values or not at all. There was no mortality difference between starting ART immediately, irrespective of CD4 value, and ART initiation at the WHO 2010 recommended threshold of CD4 count <750 cells/mm(3) or CD4% <25%, with mortality estimates of 2.1% (95% CI: 1.3%-3.5%) and 2.2% (95% CI: 1.4%-3.5%) after 3 y, respectively. The analysis was limited by loss to follow-up and the unavailability of WHO staging data. CONCLUSIONS The results indicate no mortality difference for up to 3 y between ART initiation irrespective of CD4 value and ART initiation at a threshold of CD4 count <750 cells/mm(3) or CD4% <25%, but there are overall higher point estimates for mortality when ART is initiated at lower CD4 values. Please see later in the article for the Editors' Summary.

Discontinuous Galerkin finite element approximation of quasilinear elliptic boundary value problems II: Strongly monotone quasi-Newtonian flows

In this article, we develop the a priori and a posteriori error analysis of hp-version interior penalty discontinuous Galerkin finite element methods for strongly monotone quasi-Newtonian fluid flows in a bounded Lipschitz domain Ω ⊂ ℝd, d = 2, 3. In the latter case, computable upper and lower bounds on the error are derived in terms of a natural energy norm, which are explicit in the local mesh size and local polynomial degree of the approximating finite element method. A series of numerical experiments illustrate the performance of the proposed a posteriori error indicators within an automatic hp-adaptive refinement algorithm.

Different Prognostic Value of Functional Right Ventricular Parameters in Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia

BACKGROUND -The value of standard two-dimensional transthoracic echocardiographic (TTE) parameters for risk stratification in patients with arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D) is controversial. METHODS AND RESULTS -We investigated the impact of right ventricular fractional area change (FAC) and tricuspid annulus plane systolic excursion (TAPSE) for prediction of major adverse cardiovascular events (MACE) defined as the occurrence of cardiac death, heart transplantation, survived sudden cardiac death, ventricular fibrillation, sustained ventricular tachycardia or arrhythmogenic syncope. Among 70 patients who fulfilled the 2010 ARVC/D Task Force Criteria and underwent baseline TTE, 37 (53%) patients experienced a MACE during a median follow-up period of 5.3 (IQR 1.8-9.8) years. Average values for FAC, TAPSE, and TAPSE indexed to body surface area (BSA) decreased over time (p=0.03 for FAC, p=0.03 for TAPSE and p=0.01 for TAPSE/BSA, each vs. baseline). In contrast, median right ventricular end-diastolic area (RVEDA) increased (p=0.001 vs. baseline). Based on the results of Kaplan-Meier estimates, the time between baseline TTE and experiencing MACE was significantly shorter for patients with FAC <23% (p<0.001), TAPSE <17mm (p=0.02) or right atrial (RA) short axis/BSA ≥25mm/m(2) (p=0.04) at baseline. A reduced FAC constituted the strongest predictor of MACE (hazard ratio 1.08 per 1% decrease; 95% confidence interval 1.04-1.12; p<0.001) on bivariable analysis. CONCLUSIONS -This long-term observational study indicates that TAPSE and dilation of right-sided cardiac chambers are associated with an increased risk for MACE in ARVC/D patients with advanced disease and a high risk for adverse events. However, FAC is the strongest echocardiographic predictor of adverse outcome in these patients. Our data advocate a role for TTE in risk stratification in patients with ARVC/D, although our results may not be generalizable to lower risk ARVC/D cohorts.

Value of different follow-up strategies to assess the efficacy of circumferential pulmonary vein ablation for the curative treatment of atrial fibrillation.

BACKGROUND The objective of this study was to compare transtelephonic ECG every 2 days and serial 7-day Holter as two methods of follow-up after atrial fibrillation (AF) catheter ablation for the judgment of ablation success. Patients with highly symptomatic AF are increasingly treated with catheter ablation. Several methods of follow-up have been described, and judgment on ablation success often relies on patients' symptoms. However, the optimal follow-up strategy objectively detecting most of the AF recurrences is yet unclear. METHODS Thirty patients with highly symptomatic AF were selected for circumferential pulmonary vein ablation. During follow-up, a transtelephonic ECG was transmitted once every 2 days for half a year. Additionally, a 7-day Holter was recorded preablation, after ablation, after 3 and 6 months, respectively. With both, procedures symptoms and actual rhythm were correlated thoroughly. RESULTS A total of 2,600 transtelephonic ECGs were collected with 216 of them showing AF. 25% of those episodes were asymptomatic. On a Kaplan-Meier analysis 45% of the patients with paroxysmal AF were still in continuous SR after 6 months. Simulating a follow-up based on symptomatic recurrences only, that number would have increased to 70%. Using serial 7-day ECG, 113 Holter with over 18,900 hours of ECG recording were acquired. After 6 months the percentage of patients classified as free from AF was 50%. Of the patients with recurrences, 30-40% were completely asymptomatic. The percentage of asymptomatic AF episodes stepwise increased from 11% prior ablation to 53% 6 months after. CONCLUSIONS The success rate in terms of freedom from AF was 70% on a symptom-only-based follow-up; using serial 7-day Holter it decreased to 50% and on transtelephonic monitoring to 45%, respectively. Transtelephonic ECG and serial 7-day Holter were equally effective to objectively determine long-term success and to detect asymptomatic patients.

Beyond the tree of texts: Building an empirical model of scribal variation through graph analysis of texts and stemmata

Stemmatology, or the reconstruction of the transmission history of texts, is a field that stands particularly to gain from digital methods. Many scholars already take stemmatic approaches that rely heavily on computational analysis of the collated text (e.g. Robinson and O’Hara 1996; Salemans 2000; Heikkilä 2005; Windram et al. 2008 among many others). Although there is great value in computationally assisted stemmatology, providing as it does a reproducible result and allowing access to the relevant methodological process in related fields such as evolutionary biology, computational stemmatics is not without its critics. The current state-of-the-art effectively forces scholars to choose between a preconceived judgment of the significance of textual differences (the Lachmannian or neo-Lachmannian approach, and the weighted phylogenetic approach) or to make no judgment at all (the unweighted phylogenetic approach). Some basis for judgment of the significance of variation is sorely needed for medieval text criticism in particular. By this, we mean that there is a need for a statistical empirical profile of the text-genealogical significance of the different sorts of variation in different sorts of medieval texts. The rules that apply to copies of Greek and Latin classics may not apply to copies of medieval Dutch story collections; the practices of copying authoritative texts such as the Bible will most likely have been different from the practices of copying the Lives of local saints and other commonly adapted texts. It is nevertheless imperative that we have a consistent, flexible, and analytically tractable model for capturing these phenomena of transmission. In this article, we present a computational model that captures most of the phenomena of text variation, and a method for analysis of one or more stemma hypotheses against the variation model. We apply this method to three ‘artificial traditions’ (i.e. texts copied under laboratory conditions by scholars to study the properties of text variation) and four genuine medieval traditions whose transmission history is known or deduced in varying degrees. Although our findings are necessarily limited by the small number of texts at our disposal, we demonstrate here some of the wide variety of calculations that can be made using our model. Certain of our results call sharply into question the utility of excluding ‘trivial’ variation such as orthographic and spelling changes from stemmatic analysis.

Illegitimate tasks associated with higher cortisol levels among male employees when subjective health is relatively low: an intra-individual analysis

Objectives Illegitimate tasks refer to tasks that do not conform to what can appropriately be expected from an employee. Violating role expectations, they constitute “identity-stressors”, as one’s professional role tends to become part of one’s identity. The current study investigated the impact of illegitimate tasks on salivary cortisol. We analyzed data on an intra-individual level, that is, by examining fluctuations in illegitimate tasks and cortisol within individuals. Furthermore, we investigated the moderating role of perceived health, expecting that illegitimate tasks evoke stronger reactions when perceived health is relatively poor. Methods Illegitimate tasks, salivary cortisol, and perceived health were assessed in each of three waves (time lag: 6 months) in a sample of 104 male employees. Data were analyzed by multilevel analysis using group mean centering. Results Controlling for social stressors, work interruptions, and emotional stability, the experience of more illegitimate tasks was associated with increased cortisol release if personal health resources were low compared to one’s mean value of perceived health. Results cannot be explained by inter-individual differences. Conclusions This is the first study showing that illegitimate tasks predict a biological indicator of stress, thus confirming and extending previous research on illegitimate tasks. The moderating role of perceived health confirms its importance as a personal resource, implying augmented vulnerability when perceived health is below its usual value. It is plausible to assume that increased stress reactions due to relatively poor health may further weaken available personal resources. Both avoiding illegitimate tasks and restoring personal health seem to be crucial.

Prognostic value of the Geneva prediction rule in patients with pulmonary embolism

BACKGROUND Assessment of pre-test probability of pulmonary embolism (PE) and prognostic stratification are two widely recommended steps in the management of patients with suspected PE. Some items of the Geneva prediction rule may have a prognostic value. We analyzed whether the initial probability assessed by the Geneva rule was associated with the outcome of patients with PE. METHODS In a post-hoc analysis of a multicenter trial including 1,693 patients with suspected PE, the all-cause death or readmission rates during the 3-month follow-up of patients with confirmed PE were analyzed. PE probability group was prospectively assessed by the revised Geneva score (RGS). Similar analyses were made with the a posteriori-calculated simplified Geneva score (SGS). RESULTS PE was confirmed in 357 patients and 21 (5.9%) died during the 3-month follow-up. The mortality rate differed significantly with the initial RGS group, as with the SGS group. For the RGS, the mortality increased from 0% (95% Confidence Interval: [0-5.4%]) in the low-probability group to 14.3% (95% CI: [6.3-28.2%]) in the high-probability group, and for the SGS, from 0% (95% CI: [0-5.4%] to 17.9% (95% CI: [7.4-36%]). Readmission occurred in 58 out of the 352 patients with complete information on readmission (16.5%). No significant change of readmission rate was found among the RGS or SGS groups. CONCLUSIONS Returning to the initial PE probability evaluation may help clinicians predict 3-month mortality in patients with confirmed PE. (ClinicalTrials.gov: NCT00117169).

Economic efficiency analysis of different strategies to control post-weaning multi-systemic wasting syndrome and porcine circovirus type 2 subclinical infection in 3-weekly batch system farms.

The study assessed the economic efficiency of different strategies for the control of post-weaning multi-systemic wasting syndrome (PMWS) and porcine circovirus type 2 subclinical infection (PCV2SI), which have a major economic impact on the pig farming industry worldwide. The control strategies investigated consisted on the combination of up to 5 different control measures. The control measures considered were: (1) PCV2 vaccination of piglets (vac); (2) ensuring age adjusted diet for growers (diets); (3) reduction of stocking density (stock); (4) improvement of biosecurity measures (bios); and (5) total depopulation and repopulation of the farm for the elimination of other major pathogens (DPRP). A model was developed to simulate 5 years production of a pig farm with a 3-weekly batch system and with 100 sows. A PMWS/PCV2SI disease and economic model, based on PMWS severity scores, was linked to the production model in order to assess disease losses. This PMWS severity scores depends on the combination post-weaning mortality, PMWS morbidity in younger pigs and proportion of PCV2 infected pigs observed on farms. The economic analysis investigated eleven different farm scenarios, depending on the number of risk factors present before the intervention. For each strategy, an investment appraisal assessed the extra costs and benefits of reducing a given PMWS severity score to the average score of a slightly affected farm. The net present value obtained for each strategy was then multiplied by the corresponding probability of success to obtain an expected value. A stochastic simulation was performed to account for uncertainty and variability. For moderately affected farms PCV2 vaccination alone was the most cost-efficient strategy, but for highly affected farms it was either PCV2 vaccination alone or in combination with biosecurity measures, with the marginal profitability between 'vac' and 'vac+bios' being small. Other strategies such as 'diets', 'vac+diets' and 'bios+diets' were frequently identified as the second or third best strategy. The mean expected values of the best strategy for a moderately and a highly affected farm were £14,739 and £57,648 after 5 years, respectively. This is the first study to compare economic efficiency of control strategies for PMWS and PCV2SI. The results demonstrate the economic value of PCV2 vaccination, and highlight that on highly affected farms biosecurity measures are required to achieve optimal profitability. The model developed has potential as a farm-level decision support tool for the control of this economically important syndrome.