Poor-to-moderate agreement between self and proxy interviews of mobile phone use

In epidemiological studies, cases cannot always be interviewed due to them being too ill or already deceased. Under these circumstances, proxy interviews are often conducted; however, the veridicality of information about mobile phone use gained by proxy interviews has been doubted. The issue is undecided due to the lack of empirical data. We conducted a study of 119 heterosexual couples. Both partners answered two questionnaires about mobile phone use, one about their own use and one about their partner's use. Overall agreement assessed using Cohen's kappa, Passing and Bablok regression, and concordance coefficients between self and proxy data was poor to moderate (e.g., concordance coefficients of 0.55 for duration of use). The only item with good agreement was whether or not a prepaid phone was used (Cohen's kappa 0.78 and 0.63 for male and female estimates, respectively), and to a lesser degree, the onset of mobile phone use (concordance coefficients of 0.66 and 0.61). Poorest agreement was obtained for the side of the head the mobile phone was held during calls (kappa coefficients of 0.20 and 0.24 for female and male estimates, respectively). We conclude that the assessment of mobile phone use by proxy data cannot be relied on except for information about onset of mobile phone use, use of prepaid or contract phones, and, to a lesser degree, duration of daily use. Agreement concerning the important information about side of the head the mobile phone is held during calls was poorest and only slightly better than chance. Bioelectromagnetics 33:561–567, 2012. © 2012 Wiley Periodicals, Inc.     

Computer modelling of kappa carrageenam-mannan interactions

Molecular modelling has been used as a theoretical approach to investigate the kappa carrageenan structure and its interaction with mannan chains. Calculations revealed the existence of six minima for the kappa carrageenan structure in solution. Two of them were very close to the structure found in the solid state. The methodology allowed the calculation of the theoretical counterpart of the structures based on x-ray fibre diffractions studies. In the second step of this study, we have shown that there is the possibility of interactions between kappa carrageenan double helices and mannan chains. This interacting process is allowed by the flexibility of the mannan chains and structural changes of the kappa carrageenan double helices. The calculations suggest that the disaccaride mannan fragment might be required for recognition. The result of our investigation are in good agreement with a model of gel structure based on experimental data. This approach could be applied to simulate and predict other associations in molecular assemblies.     

The augmentation algorithm and molecular phylogenetic trees

Summary The augmentation procedure of G.W. Moore leads to correct estimates of the total number of nucleotide substitutions separating two genes descendent from a common ancestor provided the data base is sufficiently dense. These estimates are in agreement with the true distance values from simulations of known evolutionary pathways. The estimates, on the average, are unbiased: they neither overaugment nor underaugment seriously. The variance of the population of augmented distance values reflects accurately the variance of the population of true distance values and is thus not abnormally large due to procedural defects in the algorithm.The augmented distances are in agreement with stochastic models tested on real data when the latter take proper account of the restricted mutability of codons resulting from natural selection.When the experimental data base is not dense, the augmented distance values and population variance may underestimate both the true distance values and their variance. This has a logical consequence that there exist significant and numerous errors in the ancestral sequences reconstructed by the parsimony principle from such data bases.The restrictions, resulting from natural selection, on the mutability of different nucleotide sites is shown to bear critically on the accuracy of estimates of the total number of nucleotide replacements made by stochastic models.     

Measuring agreement of multivariate discrete survival times using a modified weighted kappa coefficient

Summary .  Assessing agreement is often of interest in clinical studies to evaluate the similarity of measurements produced by different raters or methods on the same subjects. We present a modified weighted kappa coefficient to measure agreement between bivariate discrete survival times. The proposed kappa coefficient accommodates censoring by redistributing the mass of censored observations within the grid where the unobserved events may potentially happen. A generalized modified weighted kappa is proposed for multivariate discrete survival times. We estimate the modified kappa coefficients nonparametrically through a multivariate survival function estimator. The asymptotic properties of the kappa estimators are established and the performance of the estimators are examined through simulation studies of bivariate and trivariate survival times. We illustrate the application of the modified kappa coefficient in the presence of censored observations with data from a prostate cancer study.     

A model for radiofrequency electromagnetic field predictions at outdoor and indoor locations in the context of epidemiological research

We present a geospatial model to predict the radiofrequency electromagnetic field from fixed site transmitters for use in epidemiological exposure assessment. The proposed model extends an existing model toward the prediction of indoor exposure, that is, at the homes of potential study participants. The model is based on accurate operation parameters of all stationary transmitters of mobile communication base stations, and radio broadcast and television transmitters for an extended urban and suburban region in the Basel area (Switzerland). The model was evaluated by calculating Spearman rank correlations and weighted Cohen's kappa (κ) statistics between the model predictions and measurements obtained at street level, in the homes of volunteers, and in front of the windows of these homes. The correlation coefficients of the numerical predictions with street level measurements were 0.64, with indoor measurements 0.66, and with window measurements 0.67. The kappa coefficients were 0.48 (95%‐confidence interval: 0.35–0.61) for street level measurements, 0.44 (95%‐CI: 0.32–0.57) for indoor measurements, and 0.53 (95%‐CI: 0.42–0.65) for window measurements. Although the modeling of shielding effects by walls and roofs requires considerable simplifications of a complex environment, we found a comparable accuracy of the model for indoor and outdoor points. Bioelectromagnetics 31:226–236, 2010. © 2009 Wiley‐Liss, Inc.     

Determination of the solution structure of a platelet-adhesion peptide of von Willebrand factor.

Two-dimensional nuclear magnetic resonance (NMR) spectroscopy in combination with distance geometry (DG) and dynamical simulated annealing (DSA) calculations have been used to determine the tertiary solution structure of a synthetic 29-residue fragment of von Willebrand factor (vWF). This fragment (D514-E542) represents an adhesion site on vWF for its platelet receptor, the glycoprotein Ib-IX complex (GP Ib-IX). The NMR data yielded 109 interproton distance measurements and two chi 1 dihedral angle constraints for use in DG and DSA calculations. Most prominent in the calculated family of solution structures was an amphipathic, right-handed alpha-helix in the C-terminal segment of the peptide. We propose that this highly structured region may be important for the specific molecular interaction of vWF with the GP Ib-IX complex.     

Preliminary Remediation Goals for Terrestrial Wildlife

Remediation of contaminated sites requires information on upper concentration limits of chemicals in environmental media that are protective of ecological receptors. These upper concentration limits can be considered ecological preliminary remediation goals (EcoPRGs). The motivation for developing EcoPRGs was to provide risk managers with a simple tool for evaluating remedial actions that would be protective of the environment. Hazard quotient calculations used to support ecological screening assessments were modified to derive soil EcoPRGs for terrestrial wildlife populations. The primary modification is a population area use factor that is the fraction of a terrestrial animal population potentially affected by the contaminated site. Wildlife assessment population boundaries are based on a receptor's dispersal distance; for mammals dispersal distance is strongly related to the linear dimension (square root) of home range. Assuming that wildlife are unlikely to disperse beyond some distance from their birth or natal site, dispersal distance can be thought of as the radius of the assessment population's boundaries. This general relationship is useful as a simple way to estimate assessment population areas for terrestrial animals and helps fill data gaps for wildlife without direct measurements of dispersal.     

Observation and characterization of the interaction between a single immunoglobulin binding domain of protein L and two equivalents of human kappa light chains

Detailed stopped-flow studies in combination with site-directed mutagenesis, isothermal titration calorimetry data and x-ray crystallographic knowledge have revealed that the biphasic pre-equilibrium fluorescence changes reported for a single Ig-binding domain of protein L from Peptostreptococcus magnus binding to kappa light chain are due to the binding of the kappa light chain at two separate sites on the protein L molecule. Elimination of binding site 2 through the mutation A66W has allowed the K(d) for kappa light chain binding at site 1 to be measured by stopped-flow fluorescence and isothermal titration calorimetry techniques, giving values of 48.0 +/- 8.0 nM and 37.5 +/- 7.3 nM respectively. Conversely, a double mutation Y53F/L57H eliminates binding at site 1 and has allowed the K(d) for binding at site 2 to be determined. Stopped-flow fluorimetry suggests this to be 3.4 +/- 0.8 microM in good agreement with the value of 4.6 +/- 0.8 microM determined by isothermal titration calorimetry. The mutation Y53F reduces the affinity of site 1 to approximately that of site 2.     

Weighted least-squares approach for comparing correlated kappa

In the medical sciences, studies are often designed to assess the agreement between different raters or different instruments. The kappa coefficient is a popular index of agreement for binary and categorical ratings. Here we focus on testing for the equality of two dependent kappa coefficients. We use the weighted least-squares (WLS) approach of Koch et al. (1977, Biometrics 33, 133-158) to take into account the correlation between the estimated kappa statistics. We demonstrate how the SAS PROC CATMOD can be used to test for the equality of dependent Cohen's kappa coefficients and dependent intraclass kappa coefficients with nominal categorical ratings. We also test for the equality of dependent Cohen's kappa and dependent weighted kappa with ordinal ratings. The major advantage of the WLS approach is that it allows the data analyst a way of testing dependent kappa with popular SAS software. The WLS approach can handle any number of categories. Analyses of three biomedical studies are used for illustration.     

Assessing agreement with multiple raters on correlated kappa statistics

In clinical studies, it is often of interest to see the diagnostic agreement among clinicians on certain symptoms. Previous work has focused on the agreement between two clinicians under two different conditions or the agreement among multiple clinicians under one condition. Few have discussed the agreement study with a design where multiple clinicians examine the same group of patients under two different conditions. In this paper, we use the intraclass kappa statistic for assessing nominal scale agreement with such a design. We derive an explicit variance formula for the difference of correlated kappa statistics and conduct hypothesis testing for the equality of kappa statistics. Simulation studies show that the method performs well with realistic sample sizes and may be superior to a method that did not take into account the measurement dependence structure. The practical utility of the method is illustrated on data from an eosinophilic esophagitis (EoE) study.     

基于逻辑斯蒂回归模型的鹭科水鸟栖息地适宜性评价

近年来湿地生态系统遭到不同程度破坏,湿地水鸟及其生存空间日益受到威胁。以香港米埔-后海湾湿地为例,收集2003年1月份与鹭科水鸟密切相关的15个自变量和鹭科水鸟实测数据作为因变量构建逻辑斯蒂回归模型,通过筛选获取9个变量因子,分别为土地利用,NDVI,坡度,降雨,TM4纹理,TM3纹理,道路密度,道路距离,人居密度。经Nagelkerke R2检验模型精度达到0.743,拟合度较高。利用模型结果快速聚类,对栖息地进行适宜性分级,分级结果与同期鹭科水鸟实测数据做拟合,精度达到77.4%。最后采集2009年1月份各变量因子数据对回归方程进行时间尺度检验,与同期实测鹭科水鸟数据拟合精度同样达到75.8%,模型具有较好的通用性。     

Comparison of micrometer‐ and scanning electron microscope‐based measurements of avian eggshell thickness

ABSTRACT The study of avian eggshell structure, including composition, pigmentation, thickness, and strength, has important ecological and economic implications. Previous investigators have used a variety of techniques to derive either direct measures or indirect estimates of eggshell thickness. Assessing the repeatability and method agreement of different techniques is necessary to permit comparison of eggshell thickness values from different studies on various genetic stocks, populations, and species. We recorded and analyzed measurements of eggshell thickness using two methods, micrometers and scanning electron microscopy (SEM), for several Palaeognathae and Neognathae taxa, including nonpasserines and passerines. Applying a tolerance‐interval approach, we found that repeatability of measurements for eggs with thinner shells (<300 μm, all Neognathae taxa) was worse than for eggs with thicker shells (Palaeognathae taxa), but was still statistically and biologically reasonable given that the relative magnitude of intramethod agreements was <11%. Our results support previous predictions that measurements made using a micrometer are comparable to those made using SEM. This finding is particularly important given the relative ease and cost efficiency of the micrometer method. Importantly, these new analyses can be used to validate the use of published data from previous studies of micrometer‐based eggshell thickness for both intra‐ and interspecific comparisons.     

Development of enzyme-linked immunosorbent assays based on recombinant MSP1a and MSP2 of Anaplasma marginale

Indirect enzyme-linked immunosorbent assays (ELISAs) based on recombinant MSP1a and MSP2 from a Brazilian isolate of Anaplasma marginale were developed to detect antibodies against this rickettsia in cattle. The high sensitivities (99% for both tests) and specificities (100% for both tests) were confirmed with sera from cattle positive or negative for A. marginale antibodies, respectively, by immunofluorescent antibody test. By the analysis of 583 sera from cattle of three regions of the state of Pernambuco, Brazil, the agreement between both tests was high, with a kappa index of 0.89. The similar performances of the ELISAs suggest that both tests can be used in epidemiological surveys for detection of antibodies to A. marginale in cattle.     

Intra-Rater and Inter-Rater Reliability of a Medical Record Abstraction Study on Transition of Care after Childhood Cancer

BackgroundThe abstraction of data from medical records is a widespread practice in epidemiological research. However, studies using this means of data collection rarely report reliability. Within the Transition after Childhood Cancer Study (TaCC) which is based on a medical record abstraction, we conducted a second independent abstraction of data with the aim to assess a) intra-rater reliability of one rater at two time points; b) the possible learning effects between these two time points compared to a gold-standard; and c) inter-rater reliability.MethodWithin the TaCC study we conducted a systematic medical record abstraction in the 9 Swiss clinics with pediatric oncology wards. In a second phase we selected a subsample of medical records in 3 clinics to conduct a second independent abstraction. We then assessed intra-rater reliability at two time points, the learning effect over time (comparing each rater at two time-points with a gold-standard) and the inter-rater reliability of a selected number of variables. We calculated percentage agreement and Cohen’s kappa.FindingsFor the assessment of the intra-rater reliability we included 154 records (80 for rater 1; 74 for rater 2). For the inter-rater reliability we could include 70 records. Intra-rater reliability was substantial to excellent (Cohen’s kappa 0-6-0.8) with an observed percentage agreement of 75%-95%. In all variables learning effects were observed. Inter-rater reliability was substantial to excellent (Cohen’s kappa 0.70-0.83) with high agreement ranging from 86% to 100%.ConclusionsOur study showed that data abstracted from medical records are reliable. Investigating intra-rater and inter-rater reliability can give confidence to draw conclusions from the abstracted data and increase data quality by minimizing systematic errors.     

The distance between two functionally significant regions of the 50 S Escherichia coli ribosome: the erythromycin binding site and proteins L7L12

The distance between the erythromycin binding site on the 50 S Escherichia coli ribosome and protein L7 has been measured by singlet-singlet energy transfer. A non-covalently bound erythromycin derivative, fluoroscein isothiocyanate erythromycylamine, was used as the acceptor. This derivative can be completely displaced from ribosomes by erythromycin, suggesting that they have the same binding site. 1,5-Iodoacetylethylenediamine naptholsulfonate-labeled protein L7 served as the fluorescent donor. It was reconstituted with salt/ethanol-washed 50 S cores. This readdition was accompanied by total recovery of elongation factor G-dependent GTPase activity. This suggests that the protein modification does not significantly perturb 50 S function or structure. Energy transfer measurements by both static and lifetime techniques were in good agreement. After consideration of various errors that enter the measurements and calculations, the L7-erythromycin distance is estimated to be 70 ± 10 Å. This long distance is interesting, since both sites may be involved in translocation.The fluorescent derivative of erythromycin was also used to study binding kinetics to the 50 S and 70 S ribosomes. Binding is a simple second-order step and proceeds about 11 times faster on the 70 S particle. Exchange of the fluorescent derivative with excess erythromycin is limited by the dissociation rate, and this is four times faster on the 70 S particle. These results suggest that the erythromycin site is more accessible on the 70 S particle, and may be an indication of conformational changes in the 50 S ribosome upon combination with the 30 S ribosome.     

Comparison of different methods of estimating the mean radiant temperature in outdoor thermal comfort studies

Correlations between outdoor thermal indices and the calculated or measured mean radiant temperature T_mrt are in general of high importance because of the combined effect on human energy balance in outdoor spaces. The most accurate way to determine T_mrt is by means of integral radiation measurements, i.e. measuring the short- and long-wave radiation from six directions using pyranometers and pyrgeometers, an expensive and not always an easily available procedure. Some studies use globe thermometers combined with air temperature and wind speed sensors. An alternative way to determine T_mrt is based on output from the RayMan model from measured data of incoming global radiation and morphological features of the monitoring site in particular sky view factor (SVF) data. The purpose of this paper is to compare different methods to assess the mean radiant temperature T_mrt in terms of differences to a reference condition (T_mrt calculated from field measurements) and to resulting outdoor comfort levels expressed as PET and UTCI values. The T_mrt obtained from field measurements is a combination of air temperature, wind speed and globe temperature data according to the forced ventilation formula of ISO 7726 for data collected in Glasgow, UK. Four different methods were used in the RayMan model for T_mrt calculations: input data consisting exclusively of data measured at urban sites; urban data excluding solar radiation, estimated SVF data and solar radiation data measured at a rural site; urban data excluding solar radiation with SVF data for each site; urban data excluding solar radiation and including solar radiation at the rural site taking no account of SVF information. Results show that all methods overestimate T_mrt when compared to ISO calculations. Correlations were found to be significant for the first method and lower for the other three. Results in terms of comfort (PET, UTCI) suggest that reasonable estimates could be made based on global radiation data measured at the urban site or as a surrogate of missing SR data or globe temperature data recorded at the urban area on global radiation data measured at a rural location.     

Comparison of RFLP and morphological distances between maize Zea mays L. inbred lines. Consequences for germplasm protection purposes

 A total of 145 maize inbred lines, representative of material released in France, were differentiated using RFLP markers and a set of discriminant morphological traits in order to evaluate the use of molecular markers for large-scale germplasm diversity analysis and determination of distinctness. Several criteria are proposed with respect to choice of probes, which should give reliable results for routine studies and have a known single-locus genetic determinism to avoid redundancy. A method is proposed by which to incorporate the data from different restriction enzymes obtained with the same probe. The precision of the estimation of the genetic distance is given. The relationship between molecular and morphological distances appears to be triangular, molecular divergence behaving as a limiting factor for morphological divergence. This suggested a scheme for incorporating molecular markers in studies of distinctness. Received: 20 August 1996 / Accepted: 20 December 1996     

Conformation of [Cd7]-metallothionein-2 from rat liver in aqueous solution determined by nuclear magnetic resonance spectroscopy

The three-dimensional structure of [Cd7]-metallothionein-2 from rat liver was determined in aqueous solution, using nuclear magnetic resonance spectrometry and distance geometry calculations. The experimental data provided proton-proton distance constraints from measurements of nuclear Overhauser effects, constraints on the geometry of the metal-cysteine clusters determined by heteronuclear correlation spectroscopy, and dihedral angle constraints derived from both coupling constants and nuclear Overhauser effects. The structure calculations were performed with the program DISMAN. As in previous studies with rabbit liver metallothionein-2a, the structure calculations were performed separately for the alpha and beta-domains containing the 4 and 3-metal clusters, respectively, since no interdomain constraints were found. For both domains, the global polypeptide fold, the location of polypeptide secondary structure elements, the architecture of the metal-sulfur cluster and the local chirality of the metal co-ordination are very similar to the solution structure of rabbit metallothionein-2a, but show considerable difference relative to the crystal structure of rat metallothionein-2.     

A hyperspectral indicator system for rangeland degradation on the Tibetan Plateau: A case study towards spaceborne monitoring

The Tibetan Plateau suffers from progressive degradation caused by over-grazing due to improper livestock management, global climate change and herbivory from small mammals. Therefore, a robust indicator system for rangeland degradation has to be developed and tested. This paper investigates local patterns of degradation at two sites (Lake Namco and Mt. Kailash) in Xizang province (China) that are covered by vegetation types typical of a large portion of the plateau. The suitability of a two-indicator system is analysed using hyperspectral field measurements, and its transferability to spaceborne data is tested. The indicators are (1) land-cover fractions derived from linear spectral unmixing and (2) chlorophyll content as a proxy for nutrient and water availability calculated using hyperspectral vegetation indices and partial least squares regression. Because cattle remain near settlements overnight in the local semi-nomadic pastoral system, it can be expected that grazing intensity is highest near the settlement and declines with increasing distance. Therefore, we tested the effect of distance on both indicators using a Spearman correlation analysis. The predicted chlorophyll content and land cover fractions of the indicator system were in good agreement with field observations (correlation coefficients between 0.70 and 0.98). High correlations between distance from settlements and land-cover fractions at both study sites demonstrated that the land-cover fraction is a reliable indicator for degradation. A positive correlation between distance from settlements and photosynthetically active vegetation (PV) revealed over-grazing patterns at the first site. Furthermore, the chlorophyll indicator was proven suitable because chlorophyll concentration declined with increasing distance from settlements. This underlines the over-grazing pattern because cattle excrement was the only external source of nutrients in the ecosystem and it was positively correlated with grazing intensity. However, at the second site, we found a significant positive effect of distance on the amount of photosynthetically non-active vegetation; no effect of distance on PV and chlorophyll content was found. Therefore, no evidence of pasture degradation was detected at the second site. Regarding the potential use of satellite data for degradation monitoring, we found that (1) the land-cover indicator derived from multispectral data was more robust than using noise-filtered hyperspectral information and (2) the chlorophyll amount indicator was estimated from simulated EnMAP data with low error rates. Because the proposed two-indicator system can be derived from multi- and hyperspectral satellite data and combines site conditions and local plant cover, it provides a time-saving and robust method to measure pasture degradation across large areas, assuming that respective satellite data are available.