Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Reprodutibilidade de medidas antropométricas estáticas de graduandos de odontologia e de mochos odontológicos

Objective: To evaluate the intraexaminer reproducibility of static anthropometric measurements of undergraduate dental students as well as the characteristics and regulating measurements of the dental stools used by them. Methods: Forty volunteers and 6 types of dental stools were evaluated. For the anthropometric measurements the employed equipments were: an adapted office chair, aflexible measuring tape with two adapted rods, a metallic device with a 90 degree central angle, string, a 35 x 24 cm rectangular wooden board, isolating tape and crepe tape. In order to standardize the position of the adapted office chair and the volunteers' feet, the floor was marked with the isolating and crepe tapes. A string was attached to the waist of each volunteer to mark the area corresponding to the kidney region making it possible to measure the seat-renal region area. The examined anthropometric measurements were height, trunkcephalic heigh, sacral-popliteal distance (OK?), hip width, popliteal height and the seat-renal region height. The evaluated characteristics of the dental stools relative to the seat were depth, horizontal width and minimum/maximum height. The back of the dental stool was evaluated as for the minimum/ maximum height adjustment. The anthropometric and dental stool measurements were obtained by a single examiner at two moments with a 1-week interval between the evaluations. Intra-class correlation coefficient (ρ) was used to estimate the intraexaminer reproducibility. Results: Excellent reproducibility was observed for all anthropometric measurements obtained (ρ=0.99) as well as for all dental stools evaluated (ρ=0.99). Conclusion: The method used to obtain the anthropometric and dental stools measurements was reproducible and can be used reliably.

Facial growth evaluation of complete unilateral cleft lip and palate operated patients: a cleft reference center in Paraíba, Brazil, using the GOSLON yardstick

Objectives: To evaluate the surgical outcomes of patients with complete unilateral cleft lip and palate (CUCLP) operated on by a single surgeon of the cleft reference center of the Lauro Wanderley University Hospital at the Federal University of Paraiba. Methods: Forty-four individuals' dental casts diagnosed with CUCLP, born between 1995 and 2002, mean age of 11 years, were evaluated by three calibrated orthodontic specialists and scored by the Great Ormond Street, London and Oslo (GOSLON) yardstick on two occasions. The scores were compared with those observed in other centers around the world. The Kappa test was applied to evaluate the intra- and inter-examiner agreement. Descriptive statistics was applied for the GOSLON yardsticks core. Results: The mean GOSLON score was 2.75. For the GOSLON yardstick, 43.2 % of the sample presented scores 1 and 2, 31.8 % had score 3, and 25 % were with scores 4 and 5. There was very good intra- and inter-examiner Kappa agreement in the application of the GOSLON yardstick. Conclusions: The data suggest favorable outcomes, with 75 % of cases with no need of orthognathic surgery. The Kappa values confirmed the high reproducibility of the GOSLON yardstick. © 2013 Springer-Verlag Berlin Heidelberg.

Graduação nuclear do carcinoma invasivo de ductos mamários em punção aspirativa por agulha fina: estudo comparativo com grau histológico e avaliação da concordância intra e inter-observador

Pós-graduação em Ginecologia, Obstetrícia e Mastologia - FMB

Reliability of pelvic floor muscle strength assessment in healthy continent women

Background: The aim of this study was to compare pelvic floor muscle (PFM) strength using transvaginal digital palpation in healthy continent women in different age groups, and to compare the inter- and intra-rater reliability of examiners performing anterior and posterior vaginal assessments.Methods: We prospectively studied 150 healthy multiparous women. They were distributed into four different groups, according to age range: G1 (n = 37), 30-40 years-old; G2 (n = 39), 41-50 years-old; G3 (n = 39), 51-60 years-old; and G4 (n = 35), older than 60 years-old. PFM strength was evaluated using transvaginal digital palpation in the anterior and posterior areas, by 3 different examiners, and graded using a 5-point Amaro's scale.Results: There was no statistical difference among the different age ranges, for each grade of PFM strength. There was good intra-rater concordance between anterior and posterior PFM assessment, being 64.7%, 63.3%, and 66.7% for examiners A, B, and C, respectively. The intra-rater concordance level was good for each examiner. However, the inter-rater reliability for two examiners varied from moderate to good.Conclusions: Age has no effect on PFM strength profiles, in multiparous continent women. There is good concordance between anterior and posterior vaginal PFM strength assessments, but only moderate to good inter-rater reliability of the measurements between two examiners.

Evaluation of the agreement by examiners according to classifications of third molars

Objectives. This study recorded and evaluated the intra-and inter-group agreement degree by different examiners for the classification of lower third molars according to both the Winter's and Pell & Gregory's systems. Study Design. An observational and cross-sectional study was realized with forty lower third molars analyzed from twenty digital panoramic radiographs. Four examiner groups (undergraduates, maxillofacial surgeons, oral radiologists and clinical dentists) from Aracaju, Sergipe, Brazil, classified them in relation to angulation, class and position. The variance test (ANOVA) was applied in the examiner findings with significance level of p<0.05 and confidence intervals of 95%. Results. Intra- and inter-group agreement was observed in Winter's classification system among all examiners. Pell & Gregory's classification system showed an average intra-group agreement and a statistical significant difference to position variable in inter-group analysis with greater disagreement to the clinical dentists group (p<0.05). Conclusions. High reproducibility was associated to Winter's classification, whereas the system proposed by Pell & Gregory did not demonstrate appropriate levels of reliability.

Performance of fluorescence-based and conventional methods of occlusal caries detection in primary molars - an in vitro study

International Journal of Paediatric Dentistry 2012; 22: 459466 Aim. This in vitro study aimed to test the performance of fluorescence-based methods in detecting occlusal caries lesions in primary molars compared to conventional methods. Design. Two examiners assessed 113 sites on 77 occlusal surfaces of primary molars using three fluorescence devices: DIAGNOdent (LF), DIAGNOdent pen (LFpen), and fluorescence camera (VistaProof-FC). Visual inspection (ICDAS) and radiographic methods were also evaluated. One examiner repeated the evaluations after one month. As reference standard method, the lesion depth was determined after sectioning and evaluation in stereomicroscope. The area under the ROC curve (Az), sensitivity, specificity, and accuracy of the methods were calculated at enamel (D1) and dentine caries (D3) lesions thresholds. The intra and interexaminer reproducibility were calculated using the intraclass correlation coefficient (ICC) and kappa statistics. Results. At D1, visual inspection presented higher sensitivities (0.970.99) but lower specificities (0.180.25). At D3, all the methods demonstrated similar performance (Az values around 0.90). Visual and radiographic methods showed a slightly higher specificity (values higher than 0.96) than the fluorescence based ones (values around 0.88). In general, all methods presented high reproducibility (ICC higher than 0.79). Conclusions. Although fluorescence-based and conventional methods present similar performance in detecting occlusal caries lesions in primary teeth, visual inspection alone seems to be sufficient to be used in clinical practice.

Three-dimensional Doppler evaluation of single spherical samples from the placenta: intra- and interobserver reliability

Objective To evaluate the intra- and interobserver reliability of assessment of three-dimensional power Doppler (3D-PD) indices from single spherical samples of the placenta. Methods Women with singleton pregnancies at 2440 weeks' gestation were included. Three scans were independently performed by two observers; Observer 1 performed the first and third scan, intercalated by the scan of Observer 2. The observers independently analyzed the 3D-PD datasets that they had previously acquired using four different methods, each using a spherical sample: random sample extending from basal to chorionic plate; random sample with 2 cm3 of volume; directed sample to the region subjectively determined as containing more color Doppler signals extending from basal to chorionic plate; or directed sample with 2 cm3 of volume. The vascularization index (VI), flow index (FI) and vascularization flow index (VFI) were evaluated in each case. The observers were blinded to their own and each other's results. Additional evaluation was performed according to placental location: anterior, posterior and fundal or lateral. Intra- and interobserver reliability was assessed by intraclass correlation coefficients (ICC). Results Ninety-five pregnancies were included in the analysis. All three placental 3D-PD indices showed only weak to moderate reliability (ICC < 0.66 and ICC < 0.48, intra- and interobserver, respectively). The highest values of ICC were observed when using directed spherical samples from basal to chorionic plate. When analyzed by placental location, we found lower ICCs for lateral and fundal placentae compared to anterior and posterior ones. Conclusion Intra- and interobserver reliability of assessment of placental 3D-PD indices from single spherical samples in pregnant women greater than 24 weeks' gestation is poor to moderate, and clinical usefulness of these indices is likely to be limited. Copyright (c) 2012 ISUOG. Published by John Wiley & Sons, Ltd.

Reproducibility and validity of video screen measurements of gait in children with spastic cerebral palsy

PURPOSE: To determine the reproducibility and validity of video screen measurement (VSM) of sagittal plane joint angles during gait. METHODS: 17 children with spastic cerebral palsy walked on a 10m walkway. Videos were recorded and 3d-instrumented gait analysis was performed. Two investigators measured six sagittal joint/segment angles (shank, ankle, knee, hip, pelvis, and trunk) using a custom-made software package. The intra- and interrater reproducibility were expressed by the intraclass correlation coefficient (ICC), standard error of measurements (SEM) and smallest detectable difference (SDD). The agreement between VSM and 3d joint angles was illustrated by Bland-Altman plots and limits of agreement (LoA). RESULTS: Regarding the intrarater reproducibility of VSM, the ICC ranged from 0.99 (shank) to 0.58 (trunk), the SEM from 0.81 degrees (shank) to 5.97 degrees (trunk) and the SDD from 1.80 degrees (shank) to 16.55 degrees (trunk). Regarding the interrater reproducibility, the ICC ranged from 0.99 (shank) to 0.48 (trunk), the SEM from 0.70 degrees (shank) to 6.78 degrees (trunk) and the SDD from 1.95 degrees (shank) to 18.8 degrees (trunk). The LoA between VSM and 3d data ranged from 0.4+/-13.4 degrees (knee extension stance) to 12.0+/-14.6 degrees (ankle dorsiflexion swing). CONCLUSION: When performed by the same observer, VSM mostly allows the detection of relevant changes after an intervention. However, VSM angles differ from 3d-IGA and do not reflect the real sagittal joint position, probably due to the additional movements in the other planes.

Reproducibility and day time bias correction of optoelectronic leg volumetry: a prospective cohort study

Background Leg edema is a common manifestation of various underlying pathologies. Reliable measurement tools are required to quantify edema and monitor therapeutic interventions. Aim of the present work was to investigate the reproducibility of optoelectronic leg volumetry over 3 weeks' time period and to eliminate daytime related within-individual variability. Methods Optoelectronic leg volumetry was performed in 63 hairdressers (mean age 45 ± 16 years, 85.7% female) in standing position twice within a minute for each leg and repeated after 3 weeks. Both lower leg (legBD) and whole limb (limbBF) volumetry were analysed. Reproducibility was expressed as analytical and within-individual coefficients of variance (CVA, CVW), and as intra-class correlation coefficients (ICC). Results A total of 492 leg volume measurements were analysed. Both legBD and limbBF volumetry were highly reproducible with CVA of 0.5% and 0.7%, respectively. Within-individual reproducibility of legBD and limbBF volumetry over a three weeks' period was high (CVW 1.3% for both; ICC 0.99 for both). At both visits, the second measurement revealed a significantly higher volume compared to the first measurement with a mean increase of 7.3 ml ± 14.1 (0.33% ± 0.58%) for legBD and 30.1 ml ± 48.5 ml (0.52% ± 0.79%) for limbBF volume. A significant linear correlation between absolute and relative leg volume differences and the difference of exact day time of measurement between the two study visits was found (P < .001). A therefore determined time-correction formula permitted further improvement of CVW. Conclusions Leg volume changes can be reliably assessed by optoelectronic leg volumetry at a single time point and over a 3 weeks' time period. However, volumetry results are biased by orthostatic and daytime-related volume changes. The bias for day-time related volume changes can be minimized by a time-correction formula.

Non-invasive monitoring of renal oxygenation using BOLD-MRI: a reproducibility study

Blood oxygenation level-dependent (BOLD) MRI was shown to allow non-invasive observation of renal oxygenation in humans. However, clinical applications of this type of functional MRI of the kidney are still limited, most likely because of difficulties in obtaining reproducible and reliable information. The aim of this study was to evaluate the reproducibility and robustness of a BOLD method applied to the kidneys and to identify systematic physiological changes potentially influencing the renal oxygenation of healthy volunteers. To measure the BOLD effect, a modified multi-echo data image combination (MEDIC) sequence was used to acquire 12 T2*-weighted images within a single breath-hold. Three identical measurements were performed on three axial and three coronal slices of right and left kidneys in 18 volunteers. The mean R2* (1/T2*) values determined in medulla and cortex showed no significant differences over three repetitions and low intra-subject coefficients of variation (CV) (3 and 4% in medulla and cortex, respectively). The average R2* values were higher in the medulla (16.15 +/- 0.11) than in the cortex (11.69 +/- 0.18) (P < 0.001). Only a minor influence of slice orientation was observed. Mean R2* values were slightly higher (3%) in the left than in the right kidney (P < 0.001). Differences between volunteers were identified (P < 0.001). Part of these differences was attributable to age-dependent R2* values, since these values increased with age when medulla (P < 0.001, r = 0.67) or cortex (P < 0.020, r = 0.42) were considered. Thus, BOLD measurements in the kidney are highly reproducible and robust. The results allow one to identify the known cortico-medullary gradient of oxygenation evidenced by the gradient of R2* values and suggest that medulla is more hypoxic in older than younger individuals. BOLD-MRI is therefore a useful tool to study sequentially and non-invasively regional oxygenation of human kidneys.

Assessing the intra- and inter-reader reliability of dynamic ultrasound images in power Doppler ultrasonography

OBJECTIVE: To assess the intra-reader and inter-reader reliabilities of interpreting ultrasonography by several experts using video clips. METHOD: 99 video clips of healthy and rheumatic joints were recorded and delivered to 17 physician sonographers in two rounds. The intra-reader and inter-reader reliabilities of interpreting the ultrasound results were calculated using a dichotomous system (normal/abnormal) and a graded semiquantitative scoring system. RESULTS: The video reading method worked well. 70% of the readers could classify at least 70% of the cases correctly as normal or abnormal. The distribution of readers answering correctly was wide. The most difficult joints to assess were the elbow, wrist, metacarpophalangeal (MCP) and knee joints. The intra-reader and inter-reader agreements on interpreting dynamic ultrasound images as normal or abnormal, as well as detecting and scoring a Doppler signal were moderate to good (kappa = 0.52-0.82). CONCLUSIONS: Dynamic image assessment (video clips) can be used as an alternative method in ultrasonography reliability studies. The intra-reader and inter-reader reliabilities of ultrasonography in dynamic image reading are acceptable, but more definitions and training are needed to improve sonographic reproducibility.

Reproducibility of dGEMRIC in assessment of hip joint cartilage: a prospective study

PURPOSE: To investigate the reproducibility of dGEMRIC in the assessment of cartilage health of the adult asymptomatic hip joint. MATERIALS AND METHODS: Fifteen asymptomatic volunteers (mean age, 26.3 years +/- 3.0) were preliminarily studied. Any volunteer that was incidentally diagnosed with damaged cartilage on MRI (n = 5) was excluded. Ten patients that had no evidence of prior cartilage damage (mean age, 26.2 years +/- 3.4) were evaluated further in this study. The reproducibility of dGEMRIC was assessed with two T1(Gd) exams performed 4 weeks apart in these volunteers. The protocol involved an initial standard MRI to confirm healthy cartilage, which was then followed by dGEMRIC. The second scan included only the repeat dGEMRIC. Region of interest (ROI) analyses for T1(Gd)-measurement was performed in seven radial reformats. Statistical analysis included the student's t-test and intra-class correlation (ICC) measurement to assess reproducibility. RESULTS: Overall 70 ROIs were studied. Mean cartilage T1(Gd) values at various loci ranged from 560.9 ms to 684.4 ms at the first set of readings and 551.5 ms to 662.2 ms in the second one. The mean difference per region of interest between the two T1(Gd)-measurements ranged from 21.4 ms (3.7%) to 45.0 ms (6.8%), which was not found to be statistically significant (P = 0.153). There was a high reproducibility detected (ICC range, 0.667-0.915). Intra- and Inter-observer analyses proved a high agreement for T1(Gd) assessment (0.973 and 0.932). CONCLUSION: We found dGEMRIC to be a reliable tool in the assessment of cartilage health status in adult hip joints.

Reproducibility of retinal thickness measurements in healthy subjects using spectralis optical coherence tomography

PURPOSE: To test the reproducibility of retinal thickness measurements in healthy volunteers of a new Frequency-domain optical coherence tomography (OCT) device (Spectralis OCT; Heidelberg Engineering, Heidelberg, Germany). DESIGN: Prospective, observational study. METHODS: Forty-one eyes of 41 healthy subjects were included into the study. Intraobserver reproducibility was tested with 20 x 15 degree raster scans consisting of 37 high-resolution line scans that were repeated three times by one examiner (M.N.M.). Mean retinal thickness was calculated for nine areas corresponding to the Early Treatment Diabetic Retinopathy Study (ETDRS) areas. Coefficients of variation (COV) were calculated. RESULTS: Retinal thickness measurements were highly reproducible for all ETDRS areas. Mean total retinal thickness was 342 +/- 15 microm. Mean foveal thickness was 286 +/- 17 microm. COVs ranged from 0.38% to 0.86%. Lowest COV was found for the temporal outer ETDRS area (area 7; COV, 0.38%). Highest COV was found for the temporal inner ETDRS area (area 3; COV, 0.86%). Mean difference between measurement 1 and 2, measurement 1 and 3, and measurement 2 and 3 for all ETDRS areas was 1.01 microm, 0.98 microm, and 0.99 microm, respectively. CONCLUSION: Spectralis OCT retinal thickness measurements in healthy volunteers showed excellent intraobserver reproducibility with virtually identical results between retinal thickness measurements performed by one operator.

Evaluation of New Cone-beam Computed Tomographic Criteria for Radiographic Healing Evaluation after Apical Surgery: Assessment of Repeatability and Reproducibility.

INTRODUCTION Conventional 2-dimensional radiography uses defined criteria for outcome assessment of apical surgery. However, these radiographic healing criteria are not applicable for 3-dimensional radiography. The present study evaluated the repeatability and reproducibility of new cone-beam computed tomographic (CBCT)-based healing criteria for the judgment of periapical healing 1 year after apical surgery. METHODS CBCT scans taken 1 year after apical surgery (61 roots of 54 teeth in 54 patients, mean age = 54.4 years) were evaluated by 3 blinded and calibrated observers using 4 different indices. Reformatted buccolingual CBCT sections through the longitudinal axis of the treated roots were analyzed. Radiographic healing was assessed at the resection plane (R index), within the apical area (A index), of the cortical plate (C index), and regarding a combined apical-cortical area (B index). All readings were performed twice to calculate the intraobserver agreement (repeatability). Second-time readings were used for analyzing the interobserver agreement (reproducibility). Various statistical tests (Cohen, kappa, Fisher, and Spearman) were performed to measure the intra- and interobserver concurrence, the variability of score ratios, and the correlation of indices. RESULTS For all indices, the rates of identical first- and second-time scores were always higher than 80% (intraobserver Cohen κ values ranging from 0.793 to 0.963). The B index (94.0%) showed the highest intraobserver agreement. Regarding interobserver agreement, the highest rate was found for the B index (72.1%). The Fleiss' κ values for R and B indices exhibited substantial agreement (0.626 and 0.717, respectively), whereas the values for A and C indices showed moderate agreement (0.561 and 0.573, respectively). The Spearman correlation coefficients for R, A, C, and B indices all exhibited a moderate to very strong correlation with the highest correlation found between C and B indices (rs = 0.8069). CONCLUSIONS All indices showed an excellent intraobserver agreement (repeatability). With regard to interobserver agreement (reproducibility), the B index (healing of apical and cortical defects combined) and the R index (healing on the resection plane) showed substantial congruence and thus are to be recommended in future studies when using buccolingual CBCT sections for radiographic outcome assessment of apical surgery.