This method paper presents a template solution for text mining of scientific literature using the R tm package. Literature to be analyzed can be collected manually or automatically using the code provided with this paper. Once the literature is collected, the three steps for conducting text mining can be performed as outlined below:• loading and cleaning of text from articles,• processing, statistical analysis, and clustering, and• presentation of results using generalized and tailor-made visualizations.The text mining steps can be applied to a single, multiple, or time series groups of documents.References are provided to three published peer reviewed articles that use the presented text mining methodology. The main advantages of our method are: (1) Its suitability for both research and educational purposes, (2) Compliance with the Findable Accessible Interoperable and Reproducible (FAIR) principles, and (3) code and example data are made available on GitHub under the open-source Apache V2 license.
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BACKGROUND AND PURPOSE: The MyotonPRO is a portable device that measures muscle tone and biomechanical muscle properties objectively. MyotonPRO has already proven to be effective in measuring muscle properties in healthy and diseased populations. However, to the best of our knowledge, it has never been tested in individuals suffering from paratonia, a form of hypertonia frequently accompanying dementia. The aims of the present study were to (1) compare muscle tone, elasticity, and stiffness between 3 different subpopulations of young and old healthy adults and individuals with paratonia, and (2) investigate the intra- and interrater reproducibility of MyotonPRO measurements of the biceps brachii (BB) muscle in each subpopulation.METHODS: MyotonPRO measurements of muscle tone, elasticity, and dynamic stiffness were carried out by 2 investigators on 2 different days over the BB muscles of 54 participants (18 healthy young adults, 20 healthy older adults, and 16 older individuals with paratonia). Muscle properties were compared between subpopulations using ANOVA/Welch and post hoc tests. Reliability (intraclass correlation coefficient) and agreement parameters (standard error of measurement and the minimal detectable change) were calculated.RESULTS: Statistically significant differences between subpopulations were found in all parameters, except for stiffness between healthy elderly and individuals with paratonia. In the healthy subpopulations, (a) intrarater reliability was very high and intrarater agreement was good between 2 consecutive series, (b) between days intrarater reliability was low to high and intrarater agreement was variable, (c) interrater reliability was high to very high and interrater agreement was good. In individuals with paratonia, (a) intrarater reliability was moderate to high and agreement was variable between series, (b) between days intrarater reliability was poor to moderate and agreement was poor, (c) interrater reliability ranged from low to high with poor agreement.CONCLUSIONS: MyotonPRO measurements of the BB muscle showed good reproducibility in both healthy subpopulations, particularly for measurements performed within the same day. In individuals with paratonia, reliability and agreement were substantially lower. MyotonPRO can be used in clinical assessment and research. However, in individuals with paratonia, careful interpretation of results is required. Research in a larger sample of persons with paratonia at different stages of disease severity is recommended.
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PURPOSE: To examine the reproducibility of the institutional version of the Dutch Activity Card Sort (ACS-NL) and the possible presence of gender bias.METHODS: Older rehabilitation inpatients (N = 52) were included. Intra- and inter-rater agreement for the ACS-NL total and subscale scores was examined by intraclass correlations (ICC), and agreement of individual items by the κ coefficient (k). Gender bias was examined by the proportion of men and women selecting an ACS item.RESULTS: ICC for inter-rater agreement of the ACS total score ranged between 0.78 and 0.87, ICC for intra-rater agreement ranged between 0.79 and 0.89. Median inter-rater κ for ACS-NL items was 0.72 (interquartile scores; 0.62-0.80). The inter-rater agreement (k = 0.43) and intra-rater agreement (k = 0.39) for the five most important activities was lower. Twenty ACS activities favoured men and seven activities favoured women. As a result, men scored systematically higher on the ACS-NL than women. Logistic regression analysis correcting for activity engagement level confirmed our findings.CONCLUSIONS: The reproducibility of the ACS-NL was high. The ACS-NL institutional version score may be biased in favour of men.
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BACKGROUND: Near-infrared spectroscopy (NIRS) measurements of oxygenation reflect O2 delivery and utilization in exercising muscle and may improve detection of a critical exercise threshold.PURPOSE: First, to detect an oxygenation breakpoint (Δ[O2HbMb-HHbMb]-BP) and compare this breakpoint to ventilatory thresholds during a maximal incremental test across sexes and training status. Second, to assess reproducibility of NIRS signals and exercise thresholds and investigate confounding effects of adipose tissue thickness on NIRS measurements.METHODS: Forty subjects (10 trained male cyclists, 10 trained female cyclists, 11 endurance trained males and 9 recreationally trained males) performed maximal incremental cycling exercise to determine Δ[O2HbMb-HHbMb]-BP and ventilatory thresholds (VT1 and VT2). Muscle haemoglobin and myoglobin O2 oxygenation ([HHbMb], [O2HbMb], SmO2) was determined in m. vastus lateralis. Δ[O2HbMb-HHbMb]-BP was determined by double linear regression. Trained cyclists performed the maximal incremental test twice to assess reproducibility. Adipose tissue thickness (ATT) was determined by skinfold measurements.RESULTS: Δ[O2HbMb-HHbMb]-BP was not different from VT1, but only moderately related (r = 0.58-0.63, p<0.001). VT1 was different across sexes and training status, whereas Δ[O2HbMb-HHbMb]-BP differed only across sexes. Reproducibility was high for SmO2 (ICC = 0.69-0.97), Δ[O2HbMb-HHbMb]-BP (ICC = 0.80-0.88) and ventilatory thresholds (ICC = 0.96-0.99). SmO2 at peak exercise and at occlusion were strongly related to adipose tissue thickness (r2 = 0.81, p<0.001; r2 = 0.79, p<0.001). Moreover, ATT was related to asymmetric changes in Δ[HHbMb] and Δ[O2HbMb] during incremental exercise (r = -0.64, p<0.001) and during occlusion (r = -0.50, p<0.05).CONCLUSION: Although the oxygenation threshold is reproducible and potentially a suitable exercise threshold, VT1 discriminates better across sexes and training status during maximal stepwise incremental exercise. Continuous-wave NIRS measurements are reproducible, but strongly affected by adipose tissue thickness.
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Objective Primary to provide an overview of diagnostic accuracy for clinical tests for common elbow (sport) injuries, secondary accompanied by reproducible instructions to perform these tests. Design A systematic literature review according to the PRISMA statement. Data sources A comprehensive literature search was performed in MEDLINE via PubMed and EMBASE. Eligibility criteria We included studies reporting diagnostic accuracy and a description on the performance for elbow tests, targeting the following conditions: distal biceps rupture, triceps rupture, posteromedial impingement, medial collateral ligament (MCL) insufficiency, posterolateral rotatory instability (PLRI), lateral epicondylitis and medial epicondylitis. After identifying the articles, the methodological quality was assessed using the QUADAS-2 checklist. Results Our primary literature search yielded 1144 hits. After assessment 10 articles were included: six for distal biceps rupture, one for MCL insufficiency, two for PLRI and one for lateral epicondylitis. No articles were selected for triceps rupture, posteromedial impingement and medial epicondylitis. Quality assessment showed high or unclear risk of bias in nine studies. We described 24 test procedures of which 14 tests contained data on diagnostic accuracy. Conclusions Numerous clinical tests for the elbow were described in literature, seldom accompanied with data on diagnostic accuracy. None of the described tests can provide adequate certainty to rule in or rule out a disease based on sufficient diagnostic accuracy.
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During crime scene investigations, numerous traces are secured and may be used as evidence for the evaluation of source and/or activity level propositions. The rapid chemical analysis of a biological trace enables the identification of body fluids and can provide significant donor profiling information, including age, sex, drug abuse, and lifestyle. Such information can be used to provide new leads, exclude from, or restrict the list of possible suspects during the investigative phase. This paper reviews the state-of-the-art labelling techniques to identify the most suitable visual enhancer to be implemented in a lateral flow immunoassay setup for the purpose of trace identification and/or donor profiling. Upon comparison, and with reference to the strengths and limitations of each label, the simplistic one-step analysis of noncompetitive lateral flow immunoassay (LFA) together with the implementation of carbon nanoparticles (CNPs) as visual enhancers is proposed for a sensitive, accurate, and reproducible in situ trace analysis. This approach is versatile and stable over different environmental conditions and external stimuli. The findings of the present comparative analysis may have important implications for future forensic practice. The selection of an appropriate enhancer is crucial for a well-designed LFA that can be implemented at the crime scene for a time- and cost-efficient investigation.
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Background. Recent research has shown that the Fitkids Treadmill Test (FTT) is a valid and reproducible exercise test for the assessment of aerobic exercise capacity in children and adolescents who are healthy. Objective. The study objective was to provide sex- and age-related normative values for FTT performance in children and adolescents who were healthy, developing typically, and 6 to 18 years of age. Design. This was a cross-sectional, observational study. Methods. Three hundred fifty-six children and adolescents who were healthy (174 boys and 182 girls; mean age12.9 years, SD3.7) performed the FTT to their maximal effort to assess time to exhaustion (TTE). The least-mean-square method was used to generate sex- and age-related centile charts (P3, P10, P25, P50, P75, P90, and P97) for TTE on the FTT. Results. In boys, the reference curve (P50) showed an almost linear increase in TTE with age, from 8.8 minutes at 6 years of age to 16.1 minutes at 18 years of age. In girls, the P50 values for TTE increased from 8.8 minutes at 6 years of age to 12.5 minutes at 18 years of age, with a plateau in TTE starting at approximately 10 years of age. Limitations. Youth who were not white were underrepresented in this study. Conclusions. This study describes sex- and age-related normative values for FTT performance in children and adolescents who were healthy, developing typically, and 6 to 18 years of age. These age- and sex-related normative values will increase the usefulness of the FTT in clinical practice.
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The massive die-off of the herbivorous sea urchin Diadema antillarum in 1983 and 1984 resulted in phase shifts on Caribbean coral reefs, where macroalgae replaced coral as the most dominant benthic group. Since then, D. antillarum recovery has been slow to non-existent on most reefs. Studying settlement rates can provide insight into the mechanisms constraining the recovery of D. antillarum, while efficient settlement collectors can be used to identify locations with high settlement rates and to collect settlers for restoration practices. The aim of this study was to compare pre and post die-off settlement rates and to determine possible settlement peaks in the Eastern Caribbean island of St. Eustatius. Additionally, we aimed to determine the effectiveness and reproducibility of five different settlement collectors for D. antillarum. D. antillarum settlement around St. Eustatius was highest in May, June and August and low during the rest of the study. Before the die-off, settlement recorded for Curaçao was high throughout the year and was characterized by multiple settlement peaks. Even though peak settlement rates in this study were in the same order of magnitude as in Curaçao before the die-off, overall yearly settlement rates around St. Eustatius were still lower. As no juvenile or adult D. antillarum were observed on the reefs around the settlement collectors, it is likely that other factors are hindering the recovery of the island's D. antillarum populations. Of all five materials tested, bio ball collectors were the most effective and reproducible method to monitor D. antillarum settlement. Panels yielded the least numbers of settlers, which can partly be explained by their position close to the seabed. Settler collection was higher in mid-water layers compared to close to the bottom and maximized when strings of bio balls were used instead of clumps. We recommend research into the feasibility of aiding D. antillarum recovery by providing suitable settlement substrate during the peak of the settlement season and adequate shelter to increase post-settlement survival of settlers. The bio ball collectors could serve as a suitable settlement substrate for this new approach of assisted natural recovery.
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Background There currently is no field test available for measuring maximal exercise capacity in people with stroke. Objective To determine the feasibility, reproducibility and validity of the Shuttle Test (ST) to measure exercise capacity in people with stroke. Design Longitudinal study design. Setting Rehabilitation department, day care centres from a nursing home and private practices specialized in neuro rehabilitation. Subjects People with subacute or chronic stroke. Interventions A standardized protocol was used to determine feasibility, reproducibility and validity of the 10-meter Shuttle Test (10mST). Main measures Number of shuttles completed, 1stVentilatory Threshold (1stVT). Results The associations of the number of shuttles completed and cardiopulmonary capacity as measured with a portable gas analyser were r > 0.7, confirming good convergent validity in subacute and chronic people with stroke. Criterion validity, however, indicates it is not a valid test for measuring maximal cardiopulmonary capacity (VO2max). Only 60% of participants were able to reach the 1stVT. Higher cardiopulmonary capacity and a higher total score of the lower extremity Motricity Index contributed significantly to a higher number of shuttles walked (p = 0.001). Conclusions The Shuttle Test may be a safe and useful exercise test for people after stroke, but may not be appropriate for use with people who walk slower than 2 km/h or 0.56 m/s.
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