Automated Coding of Job Descriptions From a General Population Study: Overview of Existing Tools, Their Application and Comparison

OBJECTIVES: Automatic job coding tools were developed to reduce the laborious task of manually assigning job codes based on free-text job descriptions in census and survey data sources, including large occupational health studies. The objective of this study is to provide a case study of comparative performance of job coding and JEM (Job-Exposure Matrix)-assigned exposures agreement using existing coding tools. METHODS: We compared three automatic job coding tools [AUTONOC, CASCOT (Computer-Assisted Structured Coding Tool), and LabourR], which were selected based on availability, coding of English free-text into coding systems closely related to the 1988 version of the International Standard Classification of Occupations (ISCO-88), and capability to perform batch coding. We used manually coded job histories from the AsiaLymph case-control study that were translated into English prior to auto-coding to assess their performance. We applied two general population JEMs to assess agreement at exposure level. Percent agreement and PABAK (Prevalence-Adjusted Bias-Adjusted Kappa) were used to compare the agreement of results from manual coders and automatic coding tools. RESULTS: The coding per cent agreement among the three tools ranged from 17.7 to 26.0% for exact matches at the most detailed 4-digit ISCO-88 level. The agreement was better at a more general level of job coding (e.g. 43.8-58.1% in 1-digit ISCO-88), and in exposure assignments (median values of PABAK coefficient ranging 0.69-0.78 across 12 JEM-assigned exposures). Based on our testing data, CASCOT was found to outperform others in terms of better agreement in both job coding (26% 4-digit agreement) and exposure assignment (median kappa 0.61). CONCLUSIONS: In this study, we observed that agreement on job coding was generally low for the three tools but noted a higher degree of agreement in assigned exposures. The results indicate the need for study-specific evaluations prior to their automatic use in general population studies, as well as improvements in the evaluated automatic coding tools

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Estimating national-level exposure to antineoplastic agents in the workplace: CAREX Canada findings

Objectives: Occupational exposure to antineoplastic agents occurs in various environments and is associated with increased cancer risk and adverse reproductive outcomes. National-level information describing the location and extent of occupational exposure to antineoplastic agents is unavailable in Canada and most other countries. CAREX Canada aimed to estimate the prevalence and relative levels of occupational exposures to antineoplastic agents across work setting, occupation, and sex. Methods: 'Exposure' was defined as any potential for worker contact with antineoplastic agents. Baseline numbers of licensed workers were obtained from their respective professional bodies. For unlicensed workers, Census data or data extrapolated from human resources reports (e.g., staffing ratios) were used. Prevalence was estimated by combining population estimates with exposure proportions from peer-reviewed and grey literature. Exposure levels (classified as low, moderate, and high) by occupation and work setting were estimated qualitatively by combining estimates of contact frequency and exposure control practices. Results: Approximately 75 000 Canadians (0.42% of the total workforce) are estimated as occupationally exposed to antineoplastic agents; over 75% are female. The largest occupational group exposed to antineoplastic agents is community pharmacy workers, with 30 200 exposed. By work setting, 39 000 workers (52% of all exposed) are located in non-hospital settings; the remaining 48% are exposed in hospitals. The majority (75%) of workers are in the moderate exposure category. Conclusions: These estimates of the prevalence and location of occupational exposures to antineoplastic agents could be used to identify high-risk groups, estimate disease burden, and target new research and prevention activities. The limited secondary data available for developing these estimates highlights the need for increased quantitative measurement and documentation of antineoplastic agent contamination and exposure, particularly in work environments where use is emerging

Use and Reliability of Exposure Assessment Methods in Occupational Case-Control Studies in the General Population: Past, Present, and Future

Introduction: Retrospective occupational exposure assessment has been challenging in case-control studies in the general population. We aimed to review (i) trends of different assessment methods used in the last 40 years and (ii) evidence of reliability for various assessment methods. Methods: Two separate literature reviews were conducted. We first reviewed all general population cancer case-control studies published from 1975 to 2016 to summarize the exposure assessment approach used. For the second review, we systematically reviewed evidence of reliability for all methods observed in the first review. Results: Among the 299 studies included in the first review, the most frequently used assessment methods were self-report/assessment (n = 143 studies), case-by-case expert assessment (n = 139), and job-exposure matrices (JEMs; n = 82). Usage trends for these methods remained relatively stable throughout the last four decades. Other approaches, such as the application of algorithms linking questionnaire responses to expert-assigned exposure estimates and modelling of exposure with historical measurement data, appeared in 21 studies that were published after 2000. The second review retrieved 34 comparison studies examining methodological reliability. Overall, we observed slightly higher median kappa agreement between exposure estimates from different expert assessors (~0.6) than between expert estimates and exposure estimates from self-reports (~0.5) or JEMs (~0.4). However, reported reliability measures were highly variable for different methods and agents. Limited evidence also indicates newer methods, such as assessment using algorithms and measurement-calibrated quantitative JEMs, may be as reliable as traditional methods. Conclusion: The majority of current research assesses exposures in the population with similar methods as studies did decades ago. Though there is evidence for the development of newer approaches, more concerted effort is needed to better adopt exposure assessment methods with more transparency, reliability, and efficiency

Use and Reliability of Exposure Assessment Methods in Occupational Case-Control Studies in the General Population: Past, Present, and Future

Introduction: Retrospective occupational exposure assessment has been challenging in case-control studies in the general population. We aimed to review (i) trends of different assessment methods used in the last 40 years and (ii) evidence of reliability for various assessment methods. Methods: Two separate literature reviews were conducted. We first reviewed all general population cancer case-control studies published from 1975 to 2016 to summarize the exposure assessment approach used. For the second review, we systematically reviewed evidence of reliability for all methods observed in the first review. Results: Among the 299 studies included in the first review, the most frequently used assessment methods were self-report/assessment (n = 143 studies), case-by-case expert assessment (n = 139), and job-exposure matrices (JEMs; n = 82). Usage trends for these methods remained relatively stable throughout the last four decades. Other approaches, such as the application of algorithms linking questionnaire responses to expert-assigned exposure estimates and modelling of exposure with historical measurement data, appeared in 21 studies that were published after 2000. The second review retrieved 34 comparison studies examining methodological reliability. Overall, we observed slightly higher median kappa agreement between exposure estimates from different expert assessors (~0.6) than between expert estimates and exposure estimates from self-reports (~0.5) or JEMs (~0.4). However, reported reliability measures were highly variable for different methods and agents. Limited evidence also indicates newer methods, such as assessment using algorithms and measurement-calibrated quantitative JEMs, may be as reliable as traditional methods. Conclusion: The majority of current research assesses exposures in the population with similar methods as studies did decades ago. Though there is evidence for the development of newer approaches, more concerted effort is needed to better adopt exposure assessment methods with more transparency, reliability, and efficiency

Wind Loading on Scaled Down Fractal Tree Models of Major Urban Tree Species in Singapore

10.3390/f11080803Forests118803-80

Wind Loading on Scaled Down Fractal Tree Models of Major Urban Tree Species in Singapore

Estimation of the aerodynamic load on trees is essential for urban tree management to mitigate the risk of tree failure. To assess that in a cost-effective way, scaled down tree models and numerical simulations were utilized. Scaled down tree models reduce the cost of experimental studies and allow the studies to be conducted in a controlled environment, namely in a wind or water tunnel, but the major challenge is to construct a tree model that resembles the real tree. We constructed 3D-printed scaled down fractal tree models of major urban tree species in Singapore using procedural modelling, based on species-specific growth processes and field statistical data gathered through laser scanning of real trees. The tree crowns were modelled to match the optical porosity of real trees. We developed a methodology to model the tree crowns using porous volumes filled with randomized tetrahedral elements. The wind loads acting on the tree models were then measured in the wind tunnel and the velocity profiles from selected models were captured using particle image velocimetry (PIV). The data was then used for the validation of Large Eddy Simulations (LES), in which the trees were modelled via a discretized momentum sink with 10–20 elements in width, height, and depth, respectively. It is observed that the velocity profiles and drag of the simulations and the wind tunnel tests are in reasonable agreement. We hence established a clear relationship between the measured bulk drag on the tree models in the wind tunnel, and the local drag coefficients of the discretized elements in the simulations. Analysis on the bulk drag coefficient also shows that the effect of complex crown shape could be more dominant compared to the frontal optical porosity

Evaluation of Automatically Assigned Job-Specific Interview Modules

OBJECTIVE: In community-based epidemiological studies, job- and industry-specific 'modules' are often used to systematically obtain details about the subject's work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the correct module. We evaluated, in the context of a case-control study of lymphoid neoplasms in Asia ('AsiaLymph'), the performance of an algorithm that provided automatic, real-time module assignment during a computer-assisted personal interview. METHODS: AsiaLymph's occupational component began with a lifetime occupational history questionnaire with free-text responses and three solvent exposure screening questions. To assign each job to one of 23 study-specific modules, an algorithm automatically searched the free-text responses to the questions 'job title' and 'product made or services provided by employer' using a list of module-specific keywords, comprising over 5800 keywords in English, Traditional and Simplified Chinese. Hierarchical decision rules were used when the keyword match triggered multiple modules. If no keyword match was identified, a generic solvent module was assigned if the subject responded 'yes' to any of the three solvent screening questions. If these question responses were all 'no', a work location module was assigned, which redirected the subject to the farming, teaching, health professional, solvent, or industry solvent modules or ended the questions for that job, depending on the location response. We conducted a reliability assessment that compared the algorithm-assigned modules to consensus module assignments made by two industrial hygienists for a subset of 1251 (of 11409) jobs selected using a stratified random selection procedure using module-specific strata. Discordant assignments between the algorithm and consensus assignments (483 jobs) were qualitatively reviewed by the hygienists to evaluate the potential information lost from missed questions with using the algorithm-assigned module (none, low, medium, high). RESULTS: The most frequently assigned modules were the work location (33%), solvent (20%), farming and food industry (19%), and dry cleaning and textile industry (6.4%) modules. In the reliability subset, the algorithm assignment had an exact match to the expert consensus-assigned module for 722 (57.7%) of the 1251 jobs. Overall, adjusted for the proportion of jobs in each stratum, we estimated that 86% of the algorithm-assigned modules would result in no information loss, 2% would have low information loss, and 12% would have medium to high information loss. Medium to high information loss occurred for <10% of the jobs assigned the generic solvent module and for 21, 32, and 31% of the jobs assigned the work location module with location responses of 'someplace else', 'factory', and 'don't know', respectively. Other work location responses had ≤8% with medium to high information loss because of redirections to other modules. Medium to high information loss occurred more frequently when a job description matched with multiple keywords pointing to different modules (29-69%, depending on the triggered assignment rule). CONCLUSIONS: These evaluations demonstrated that automatically assigned modules can reliably reproduce an expert's module assignment without the direct involvement of an industrial hygienist or interviewer. The feasibility of adapting this framework to other studies will be language- and exposure-specific

Evaluation of Automatically Assigned Job-Specific Interview Modules

OBJECTIVE: In community-based epidemiological studies, job- and industry-specific 'modules' are often used to systematically obtain details about the subject's work tasks. The module assignment is often made by the interviewer, who may have insufficient occupational hygiene knowledge to assign the correct module. We evaluated, in the context of a case-control study of lymphoid neoplasms in Asia ('AsiaLymph'), the performance of an algorithm that provided automatic, real-time module assignment during a computer-assisted personal interview. METHODS: AsiaLymph's occupational component began with a lifetime occupational history questionnaire with free-text responses and three solvent exposure screening questions. To assign each job to one of 23 study-specific modules, an algorithm automatically searched the free-text responses to the questions 'job title' and 'product made or services provided by employer' using a list of module-specific keywords, comprising over 5800 keywords in English, Traditional and Simplified Chinese. Hierarchical decision rules were used when the keyword match triggered multiple modules. If no keyword match was identified, a generic solvent module was assigned if the subject responded 'yes' to any of the three solvent screening questions. If these question responses were all 'no', a work location module was assigned, which redirected the subject to the farming, teaching, health professional, solvent, or industry solvent modules or ended the questions for that job, depending on the location response. We conducted a reliability assessment that compared the algorithm-assigned modules to consensus module assignments made by two industrial hygienists for a subset of 1251 (of 11409) jobs selected using a stratified random selection procedure using module-specific strata. Discordant assignments between the algorithm and consensus assignments (483 jobs) were qualitatively reviewed by the hygienists to evaluate the potential information lost from missed questions with using the algorithm-assigned module (none, low, medium, high). RESULTS: The most frequently assigned modules were the work location (33%), solvent (20%), farming and food industry (19%), and dry cleaning and textile industry (6.4%) modules. In the reliability subset, the algorithm assignment had an exact match to the expert consensus-assigned module for 722 (57.7%) of the 1251 jobs. Overall, adjusted for the proportion of jobs in each stratum, we estimated that 86% of the algorithm-assigned modules would result in no information loss, 2% would have low information loss, and 12% would have medium to high information loss. Medium to high information loss occurred for <10% of the jobs assigned the generic solvent module and for 21, 32, and 31% of the jobs assigned the work location module with location responses of 'someplace else', 'factory', and 'don't know', respectively. Other work location responses had ≤8% with medium to high information loss because of redirections to other modules. Medium to high information loss occurred more frequently when a job description matched with multiple keywords pointing to different modules (29-69%, depending on the triggered assignment rule). CONCLUSIONS: These evaluations demonstrated that automatically assigned modules can reliably reproduce an expert's module assignment without the direct involvement of an industrial hygienist or interviewer. The feasibility of adapting this framework to other studies will be language- and exposure-specific