Scoring of sperm chromosomal abnormalities by manual and automated approaches: qualitative and quantitative comparisons.
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ABSTRACT:
SUBMITTER: Tempest HG
PROVIDER: S-EPMC3739098 | biostudies-other | 2010 Mar
REPOSITORIES: biostudies-other
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Project description:Disentangling the separate and synergistic effects of chemicals poses methodological challenges for accurate exposure assessment and for investigating epidemiologically how chemicals affect reproduction. We investigated combined exposures to ubiquitous contemporary use pesticides, specifically organophosphates (OP) and pyrethroids (PYR), and their association with germ cell abnormalities among adult men. Fluorescence in situ hybridization was used to determine disomy in sperm nuclei and urine was analyzed for concentrations of PYR metabolites (3-phenoxybenzoic acid; 3PBA) and OP dialkyl phosphate (DAP) metabolites. Incidence rate ratios using Poisson models were estimated for each disomy type by exposure quartile of DAP metabolites and 3PBA, controlling for confounders. The shape of the associations between PYRs, OPs and disomy were frequently nonmonotonic. There were consistent interactions between OP and PYR metabolite concentrations and the risk for sperm abnormalities. Taking both chemicals into account simultaneously resulted in quantitatively different associations than what was reported previously for OPs and PYRs separately, demonstrating the importance of modeling multiple concentrations simultaneously. Methods investigating interactions using Poisson models are needed to better quantify chemical interactions and their effects on count-based health outcomes, the importance of which was shown here for germ cell abnormalities.
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Project description:New chest compression detection technology allows for the recording and graphical depiction of clinical cardiopulmonary resuscitation (CPR) chest compressions. The authors sought to determine the inter-rater reliability of chest compression pattern classifications by human raters. Agreement with automated chest compression classification was also evaluated by computer analysis.This was an analysis of chest compression patterns from cardiac arrest patients enrolled in the ongoing Resuscitation Outcomes Consortium (ROC) Continuous Chest Compressions Trial. Thirty CPR process files from patients in the trial were selected. Using written guidelines, research coordinators from each of eight participating ROC sites classified each chest compression pattern as 30:2 chest compressions, continuous chest compressions (CCC), or indeterminate. A computer algorithm for automated chest compression classification was also developed for each case. Inter-rater agreement between manual classifications was tested using Fleiss's kappa. The criterion standard was defined as the classification assigned by the majority of manual raters. Agreement between the automated classification and the criterion standard manual classifications was also tested.The majority of the eight raters classified 12 chest compression patterns as 30:2, 12 as CCC, and six as indeterminate. Inter-rater agreement between manual classifications of chest compression patterns was ? = 0.62 (95% confidence interval [CI] = 0.49 to 0.74). The automated computer algorithm classified chest compression patterns as 30:2 (n = 15), CCC (n = 12), and indeterminate (n = 3). Agreement between automated and criterion standard manual classifications was ? = 0.84 (95% CI = 0.59 to 0.95).In this study, good inter-rater agreement in the manual classification of CPR chest compression patterns was observed. Automated classification showed strong agreement with human ratings. These observations support the consistency of manual CPR pattern classification as well as the use of automated approaches to chest compression pattern analysis.
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Project description:Objective:To compare the accuracy of cephalometric analyses made with fully automated tracings, computerized tracing, and app-aided tracings with equivalent hand-traced measurements, and to evaluate the tracing time for each cephalometric analysis method. Methods:Pre-treatment lateral cephalometric radiographs of 40 patients were randomly selected. Eight angular and 4 linear parameters were measured by 1 operator using 3 methods: computerized tracing with software Dolphin Imaging 13.01(Dolphin Imaging and Management Solutions, Chatsworth, Calif, USA), app-aided tracing using the CephNinja 3.51 app (Cyncronus LLC, WA, USA), and web-based fully automated tracing with CephX (ORCA Dental AI, Las Vegas, NV). Correction of CephX landmarks was also made. Manual tracings were performed by 3 operators. Remeasurement of 15 radiographs was carried out to determine the intra-examiner and inter-examiner (manual tracings) correlation coefficient (ICC). Inter-group comparisons were made with one-way analysis of variance. The Tukey test was used for post hoc testing. Results:Overall, greater variability was found with CephX compared with the other methods. Differences in GoGn-SN (°), I-NA (°), I-NB (°), I-NA (mm), and I-NB (mm) were statistically (p<0.05) and clinically significant using CephX, whereas CephNinja and Dolphin were comparable to manual tracings. Correction of CephX landmarks gave similar results to CephNinja and Dolphin. All the ICCs exceeded 0.85, except for I-NA (°), I-NB (°), and I-NB (mm), which were traced with CephX. The shortest analyzing time was obtained with CephX. Conclusion:Fully automatic analysis with CephX needs to be more reliable. However, CephX analysis with manual correction is promising for use in clinical practice because it is comparable to CephNinja and Dolphin, and the analyzing time is significantly shorter.
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Project description:PurposeTo determine the agreement between the manual scoring of home sleep apnea tests (HSATs) by international sleep technologists and automated scoring systems.MethodsFifteen HSATs, previously recorded using a type 3 monitor, were saved in European Data Format. The studies were scored by nine experienced technologists from the sleep centers of the Sleep Apnea Global Interdisciplinary Consortium (SAGIC) using the locally available software. Each study was scored separately by human scorers using the nasal pressure (NP), flow derived from the NP signal (transformed NP), or respiratory inductive plethysmography (RIP) flow. The same procedure was followed using two automated scoring systems: Remlogic (RLG) and Noxturnal (NOX).ResultsThe intra-class correlation coefficients (ICCs) of the apnea-hypopnea index (AHI) scoring using the NP, transformed NP, and RIP flow were 0.96 [95% CI 0.93-0.99], 0.98 [0.96-0.99], and 0.97 [0.95-0.99], respectively. Using the NP signal, the mean differences in AHI between the average of the manual scoring and the automated systems were - 0.9 ± 3.1/h (AHIRLG vs AHIMANUAL) and - 1.3 ± 2.6/h (AHINOX vs AHIMANUAL). Using the transformed NP, the mean differences in AHI were - 1.9 ± 3.3/h (AHIRLG vs AHIMANUAL) and 1.6 ± 3.0/h (AHINOX vs AHIMANUAL). Using the RIP flow, the mean differences in AHI were - 2.7 ± 4.5/h (AHIRLG vs AHIMANUAL) and 2.3 ± 3.4/h (AHINOX vs AHIMANUAL).ConclusionsThere is very strong agreement in the scoring of the AHI for HSATs between the automated systems and experienced international technologists. Automated scoring of HSATs using commercially available software may be useful to standardize scoring in future endeavors involving international sleep centers.
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Project description:This study aimed to evaluate the reliability of in vivo confocal microscopic neuroanalysis by beginners using manual and automated modules. Images of sub-basal corneal nerve plexus (SCNP) from 108 images of 18 healthy participants were analyzed by 7 beginner observers using manual (CCMetrics, [CCM]) and automated (ACCMetrics, [ACCM]) module. SCNP parameters analyzed included corneal nerve fiber density (NFD), corneal nerve branch density (NBD), corneal nerve fiber length (NFL), and tortuosity coefficient (TC). The intra-observer repeatability, inter-observer reliability, inter-module agreement, and left-right eye symmetry level of SCNP parameters were examined. All observers showed good intra-observer repeatability using CCM (intraclass correlation coefficient [ICC] > 0.60 for all), except when measuring TC. Two observers demonstrated especially excellent repeatability in analyzing NFD, NBD, and NFL using manual mode, indicating the quality of interpretation may still be observer-dependent. Among all SCNP parameters, NFL had the best inter-observer reliability (Spearman's rank-sum correlation coefficient [SpCC] and ICC > 0.85 for the 3 original observers) and left-right symmetry level (SpCC and ICC > 0.60). In the additional analysis of inter-observer reliability using results by all 7 observers, only NFL showed good inter-observer reliability (ICC = 0.79). Compared with CCM measurements, values of ACCM measurements were significantly lower, implying a poor inter-module agreement. Our result suggested that performance of quantitative corneal neuroanalysis by beginners maybe acceptable, with NFL being the most reliable parameter, and automated method cannot fully replace manual work.
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Project description:Transmitted de novo structural chromosomal abnormalities, the majority of which are paternally derived, can lead to abnormal reproductive outcomes as well as genetic diseases in offspring. We developed and validated a new multicolor FISH procedure (sperm ACM, which utilizes DNA probes specific for the alpha [1cen], classical, [1q12], and midi [1p36.3] satellites of chromosome 1) which utilizes DNA probes specific for three regions of chromosome 1 to detect human sperm that carry numerical abnormalities plus two categories of structural aberrations: (1) duplications and deletions of 1pter and 1cen, and (2) chromosomal breaks within the 1cen-1q12 region. In healthy men, the average frequencies of sperm with duplications and deletions were (a) 4.5 +/- 0.5 and 4.1 +/- 1.3 per 10(4) involving 1pter and (b) 0.9 +/- 0.4 and 0.8 +/- 0.3 per 10(4) involving 1cen, respectively. The frequency of sperm exhibiting breaks within the 1cen-1q12 region was 14.1 +/- 1.2 per 10(4). Structural aberrations accounted for 71% of the abnormalities detected by sperm ACM, which was significantly higher than numerical abnormalities (P=2x10-8). Our findings also suggest that, for healthy men, (a) sperm carrying postmeiotic chromosomal breaks appear to be more prevalent than those carrying products of premeiotic or meiotic breakage or rearrangements, (b) the high frequency of chromosome breaks measured after "fertilization" by the hamster-egg cytogenetic method already appear to be present and detectable within human sperm by FISH, and (c) there are nonrandom and donor-specific distributions of breakpoint locations within 1q12 in sperm. FISH facilitates the analysis of much larger numbers of sperm than was possible when the hamster-egg method was used. Therefore, FISH-based procedures for simultaneously detecting chromosomal breaks, rearrangements, and numerical abnormalities in sperm may have widespread applications in human genetics, genetic toxicology, and reproductive medicine.
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Project description:Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis, and trichomoniasis. Approximately 10% of vaginal swabs are negative but designated "altered flora" by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections. Vaginal swabs were collected from 93 women (mean age, 23.53 years; range, 18 to 42 years) in a cross-sectional study. Microscopy results for BV and Candida were compared to those from two molecular approaches: (i) a comprehensive quantitative PCR (qPCR) assay, including testing for aerobic vaginitis (AV), Candida, sexually transmitted infections (STI), and BV (Applied Biosystems) with an accompanying BV interpretive algorithm (Coriell Life Sciences), and (ii) microbiome profiling of the 16S rRNA gene (Illumina). Microscopy plus BV Nugent score had 76% overall agreement with the qPCR plus BV interpretive algorithm method (24 positive, 47 negative). OF the nine samples designated altered flora by Nugent, five were categorized BV positive and four were BV negative by the qPCR method. Although BV negative, 3/4 of the latter samples had positive AV targets with one also was STI positive. Microscopic identification of Candida versus that by qPCR had 94% agreement (9 positive, 78 negative). The comprehensive qPCR assay revealed alternative etiologies summarized as 38% BV, 10% AV, 5% Candida, 2% STI, 10% mixed infection (positive targets in multiple panels), and 35% negative for all targets. 16S microbiome analysis confirmed the bacterial qPCR results and identified differentiating patterns between AV, BV, and Lactobacillus-dominated vaginal microbiomes.
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Project description:BackgroundCross-mapping establishes equivalence between terms from different terminology systems, which is useful for interoperability, updated terminological versions, and reuse of terms. Due to the number of terms to be mapped, this work can be extensive, tedious, and thorough, and it is susceptible to errors; this can be minimized by automated processes, which use computational tools.ObjectiveThe aim of this study was to compare the results of manual and automated term mapping processes.MethodsIn this descriptive, quantitative study, we used the results of two mapping processes as an empirical basis: manual, which used 2638 terms of nurses' records from a university hospital in southern Brazil and the International Classification for Nursing Practice (ICNP); and automated, which used the same university hospital terms and the primitive terms of the ICNP through MappICNP, an algorithm based on rules of natural language processing. The two processes were compared via equality and exclusivity assessments of new terms of the automated process and of candidate terms.ResultsThe automated process mapped 569/2638 (21.56%) of the source bank's terms as identical, and the manual process mapped 650/2638 (24.63%) as identical. Regarding new terms, the automated process mapped 1031/2638 (39.08%) of the source bank's terms as new, while the manual process mapped 1251 (47.42%). In particular, manual mapping identified 101/2638 (3.82%) terms as identical and 429 (16.26%) as new, whereas the automated process identified 20 (0.75%) terms as identical and 209 (7.92%) as new. Of the 209 terms mapped as new by the automated process, it was possible to establish an equivalence with ICNP terms in 48 (23.0%) cases. An analysis of the candidate terms offered by the automated process to the 429 new terms mapped exclusively by the manual process resulted in 100 (23.3%) candidates that had a semantic relationship with the source term.ConclusionsThe automated and manual processes map identical and new terms in similar ways and can be considered complementary. Direct identification of identical terms and the offering of candidate terms through the automated process facilitate and enhance the results of the mapping; confirmation of the precision of the automated mapping requires further analysis by researchers.
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