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To detect modest associations of dietary intake with disease risk, observational studies need to be large and control for moderate measurement errors. The reproducibility of dietary intakes of macronutrients, food groups and dietary patterns (vegetarian and Mediterranean) was assessed in adults in the UK Biobank study on up to five occasions using a web-based 24-h dietary assessment (n 211 050), and using short FFQ recorded at baseline (n 502 655) and after 4 years (n 20 346). When the means of two 24-h assessments were used, the intra-class correlation coefficients (ICC) for macronutrients varied from 0·63 for alcohol to 0·36 for polyunsaturated fat. The ICC for food groups also varied from 0·68 for fruit to 0·18 for fish. The ICC for the FFQ varied from 0·66 for meat and fruit to 0·48 for bread and cereals. The reproducibility was higher for vegetarian status (κ > 0·80) than for the Mediterranean dietary pattern (ICC = 0·45). Overall, the reproducibility of pairs of 24-h dietary assessments and single FFQ used in the UK Biobank were comparable with results of previous prospective studies using conventional methods. Analyses of diet–disease relationships need to correct for both measurement error and within-person variability in dietary intake in order to reliably assess any such associations with disease in the UK Biobank.
The value of new archaeological knowledge is strongly determined by how credible it is, and a key measure of scientific credibility is how replicable new results are. However, few archaeologists learn the skills necessary to conduct replication as part of their training. This means there is a gap between the ideals of archaeological science and the skills we teach future researchers. Here we argue for replications as a core type of class assignment in archaeology courses to close this gap and establish a culture of replication and reproducibility. We review replication assignments in other fields and describe how to implement a replication assignment suitable for many types of archaeology programs. We describe our experience with replication in an upper-level undergraduate class on stone artifact analysis. Replication assignments can help archaeology programs give students the skills that enable transparent and reproducible research.
The present study aimed to evaluate the validity and reproducibility of a thirteen-item FFQ regarding identification of dietary conditions in a rural population in China.
A reproducibility study repeated the first FFQ (FFQ1) approximately 4 weeks later (FFQ2). A validity study evaluated the mean of three consecutive 24 h diet recalls as the reference measure.
Residents of a rural area in Henan Province, which is located in the central region of China.
A total of 295 individuals participated in the reproducibility study. In addition, 123 people agreed to participate in the validity study. Spearman’s correlation coefficients between the two FFQ ranged from 0·06 (vegetables) to 0·58 (eggs). Spearman’s correlation coefficients between the two methods of collection ranged from 0·01 for cereal to 0·49 for staple foods. The mean of the intraclass correlation coefficients of the two FFQ (FFQ1 v. FFQ2) was 0·19. Bland–Altman analysis indicated good agreement for most food groups across the range of intake for the two studies.
The study demonstrated that our FFQ design could be used as a representative tool to conduct a dietary evaluation of a rural population.
An in-house self-held respiration monitoring device (SHRMD) was developed for providing deep inspiration breath hold (DIBH) radiotherapy. The use of SHRMD is evaluated in terms of reproducibility, stability and heart dose reduction.
Methods and materials:
Sixteen patients receiving radiotherapy of left breast cancer were planned for treatment with both a free breathing (FB) scan and a DIBH scan. Both FB and DIBH plans were generated for comparison of the heart, left anterior descending (LAD) artery and lung dose. All patients received their treatments with DIBH using SHRMD. Megavoltage cine images were acquired during treatments for evaluating the reproducibility and stability of treatment position using SHRMD.
Compared with FB plans, the maximum dose to the heart by DIBH technique with SHRMD was reduced by 29·9 ± 15·6%; and the maximum dose of the LAD artery was reduced by 41·6 ± 18·3%. The inter-fractional overall mean error was 0·01 cm and the intra-fractional overall mean error was 0·04 cm.
This study demonstrated the potential benefits of using the SHRMD for DIBH to reduce the heart and LAD dose. The patients were able to perform stable and reproducible DIBHs.
Evaluation of Cr, Mn, Fe, Zn and Se in humans is challenged by the potentially high within-individual variability of these elements in biological specimens, which are poorly characterised. This study aimed to evaluate their within-day, between-day and between-month variability in spot samples, first-morning voids and 24-h collections. A total of 529 spot urine samples (including eighty-eight first-morning voids and 24-h collections) were collected from eleven Chinese adult men on days 0, 1, 2, 3, 4, 30, 60 and 90 and analysed for these five elements using inductively coupled plasma-MS. Intraclass correlation coefficients (ICC) were utilised to characterise the reproducibility, and their sensitivity and specificity were analysed to assess how well a single measurement classified individuals’ 3-month average exposures. Serial measurements of Zn in spot samples exhibited fair to good reproducibility (creatinine-adjusted ICC = 0·47) over five consecutive days, which became poor when the samples were gathered months apart (creatinine-adjusted ICC = 0·33). The reproducibility of Cr, Mn, Fe and Se in spot samples was poor over periods ranging from days to months (creatinine-adjusted ICC = 0·01–0·12). Two spot samples were sufficient for classifying 60 % of the men who truly had the highest (top 33 %) 3-month average Zn concentrations; for Cr, Mn, Fe and Se, however, at least three specimens were required to achieve similar sensitivities. In conclusion, urinary Cr, Mn, Fe, Zn and Se concentrations showed a strong within-individual variability, and a single measurement is not enough to efficiently characterise individuals’ long-term exposures.
When relating glycaemic index (GI) and glycaemic load (GL) to health outcomes, many prospective cohort studies assess the nutritional exposure only once in time, that is, at the start of the study, presuming a stability in nutritional consumption during the course of the study. The aim of this study is to investigate the reproducibility of GI and GL. This is a prospective cohort study in which 562 middle-aged Belgian adults noted all foods and drinks consumed during 3 d in 2002 and 2012. GI and GL were calculated after reference tables. The Pearson correlation coefficients between 2002 and 2012 were 0·27 for GI and 0·41 for GL. For GI, 33 % of the participants remained in the same quintile between 2002 and 2012, whereas 31 % moved to a non-adjacent quintile. For GL, this was 34 and 28 %, respectively. The lowest and the highest quintiles of GI were the most stable, with 40 and 44 % of the participants staying in the same quintile. This was only 22 % for the fourth quintile. The same tendency was present for GL – that is, the most extreme quintiles were the most stable. This study shows 10-year correlation coefficients for GI and GL below 0·50. Multiple nutritional assessments and limiting the analysis to the extreme quintiles of GI and GL will limit a possible misclassification in the prospective cohort studies owing to the low reproducibility.
UK Biobank is an open access prospective cohort of 500 000 men and women. Information on the frequency of consumption of main foods was collected at recruitment with a touchscreen questionnaire; prior to examining the associations between diet and disease, it is essential to evaluate the performance of the dietary touchscreen questionnaire. The objectives of the present paper are to: describe the repeatability of the touchscreen questionnaire in participants (n 20 348) who repeated the assessment centre visit approximately 4 years after recruitment, and compare the dietary touchscreen variables with mean intakes from participants (n 140 080) who completed at least one of the four web-based 24-h dietary assessments post-recruitment. For fish and meat items, 90 % or more of participants reported the same or adjacent category of intake at the repeat assessment visit; for vegetables and fruit, and for a derived partial fibre score (in fifths), 70 % or more of participants were classified into the same or adjacent category of intake (κweighted > 0·50 for all). Participants were also categorised based on their responses to the dietary touchscreen questionnaire at recruitment, and within each category the group mean intake of the same food group or nutrient from participants who had completed at least one web-based 24-h dietary assessment was calculated. The comparison showed that the dietary touchscreen variables, available on the full cohort, reliably rank participants according to intakes of the main food groups.
While junior clinical researchers at academic medical institutions across the US often desire to be actively engaged in randomized-clinical trials, they often lack adequate resources and research capacity to design and implement them. This insufficiency hinders their ability to generate a rigorous randomization scheme to minimize selection bias and yield comparable groups. Moreover, there are limited online user-friendly randomization tools. Thus, we developed a free robust randomization app (RRApp). RRApp incorporates 6 major randomization techniques: simple randomization, stratified randomization, block randomization, permuted block randomization, stratified block randomization, and stratified permuted block randomization. The design phase has been completed, including robust server scripts and a straightforward user-interface using the “shiny” package in R. Randomization schemes generated in RRApp can be input directly into the Research Electronic Data Capture (REDCap) system. RRApp has been evaluated by biostatisticians and junior clinical faculty at the Icahn School of Medicine at Mount Sinai. Constructive feedback regarding the quality and functionality of RRApp was also provided by attendees of the 2016 Association for Clinical and Translational Statisticians Annual Meeting. RRApp aims to educate early stage clinical trialists about the importance of randomization, while simultaneously assisting them, in a user-friendly fashion, to generate reproducible randomization schemes.
Credibility and trustworthiness are the bedrock upon which any science is built. The strength of these foundations has been increasingly questioned across the sciences as instances of research misconduct and mounting concerns over the prevalence of detrimental research practices have been identified. Consequently, the purpose of this article is to encourage our scientific community to positively and proactively engage in efforts that foster a healthy and robust industrial and organizational (I-O) psychology. We begin by advancing six defining principles that we believe reflect the values of robust science and offer criteria for evaluating proposed efforts to change scientific practices. Recognizing that the contemporary scientific enterprise is a complex and diverse network of actors and institutions, we then conclude by identifying 12 stakeholders who play important roles in achieving a culture of robust science in I-O psychology and offer recommendations for actions we can take as members of these groups to strengthen our science.
First promulgated in 1959, the 3Rs of Replacement, Reduction and Refinement have evolved as fundamental principles underlying the use of animals and alternatives in science throughout the modern world. This review describes a contemporary approach to delivering the 3Rs through acknowledging the contribution of new technologies and emphasising that applying the 3Rs can be beneficial to good science as well as to animal welfare. This science-led approach moves the concept of the 3Rs out of an ethical silo where they were often considered by scientists to be an inconvenient obligation. On the contrary, relevant examples demonstrate the opportunity to practise better science using 3Rs technologies which deliver faster, more reproducible and more cost-effective results. Indeed, methods harnessing Replacement approaches may permit discoveries which are simply not feasible using animals and frequently are more flexible and agile since compliance with regulatory oversight requirements is simplified. Although the necessity for rigorous oversight is well recognised, it is important that the associated bureaucracy is not allowed to become prohibitive, causing scientists to avoid pursuing justifiable and important research involving animals. Public support for research is conditional – animals should not suffer unnecessarily and sufficient potential benefit should accrue from the research. However, society also actively seeks pioneering medical and scientific advances which can only be achieved through research. Therefore, a balance must be struck between safeguarding animal welfare whilst enabling high-quality science. It is this balance which promotes and sustains public confidence that animal based research is acceptable and being appropriately managed.
Many philosophers of science and methodologists have argued that the ability to repeat studies and obtain similar results is an essential component of science. A finding is elevated from single observation to scientific evidence when the procedures that were used to obtain it can be reproduced and the finding itself can be replicated. Recent replication attempts show that some high profile results – most notably in psychology, but in many other disciplines as well – cannot be replicated consistently. These replication attempts have generated a considerable amount of controversy, and the issue of whether direct replications have value has, in particular, proven to be contentious. However, much of this discussion has occurred in published commentaries and social media outlets, resulting in a fragmented discourse. To address the need for an integrative summary, we review various types of replication studies and then discuss the most commonly voiced concerns about direct replication. We provide detailed responses to these concerns and consider different statistical ways to evaluate replications. We conclude there are no theoretical or statistical obstacles to making direct replication a routine aspect of psychological science.
Currently, many scientific fields such as psychology or biomedicine face a methodological crisis concerning the reproducibility, replicability, and validity of their research. In neuroimaging, similar methodological concerns have taken hold of the field, and researchers are working frantically toward finding solutions for the methodological problems specific to neuroimaging. This article examines some ethical and legal implications of this methodological crisis in neuroimaging. With respect to ethical challenges, the article discusses the impact of flawed methods in neuroimaging research in cognitive and clinical neuroscience, particularly with respect to faulty brain-based models of human cognition, behavior, and personality. Specifically examined is whether such faulty models, when they are applied to neurological or psychiatric diseases, could put patients at risk, and whether this places special obligations on researchers using neuroimaging. In the legal domain, the actual use of neuroimaging as evidence in United States courtrooms is surveyed, followed by an examination of ways that the methodological problems may create challenges for the criminal justice system. Finally, the article reviews and promotes some promising ideas and initiatives from within the neuroimaging community for addressing the methodological problems.
To develop and evaluate a Nutrition Transition-FFQ (NT-FFQ) to measure nutrition transition among adolescents in South India.
We developed an interviewer-administered NT-FFQ comprising a 125-item semi-quantitative FFQ and a twenty-seven-item eating behaviour survey. The reproducibility and validity of the NT-FFQ were assessed using Spearman correlations, intra-class correlation coefficients (ICC), and levels of agreement using Bland–Altman and cross-classification over 2 months (NT-FFQ1 and NT-FFQ2). Validity of foods was evaluated against three 24-h dietary recalls (24-HR). Face validity of eating behaviours was evaluated through semi-structured cognitive interviews. The reproducibility of eating behaviours was assessed using weighted kappa (κw) and cross-classification analyses.
A representative sample of 198 adolescents aged 14–18 years.
Reproducibility of NT-FFQ: Spearman correlations ranged from 0·33 (pulses) to 0·80 (red meat) and ICC from 0·05 (fruits) to 1·00 (tea). On average, concordance (agreement) was 60 % and discordance was 7 % for food groups. For eating behaviours, κw ranged from 0·24 (eating snacks while watching television) to 0·67 (eating lunch at home) with a mean of 0·40. Validity of NT-FFQ: Spearman correlations ranged from 0·11 (fried traditional foods) to 0·70 (tea) and ICC ranged from 0·02 (healthy global foods) to 1·00 (grains). The concordance and discordance were 48 % and 8 %, respectively. Bland–Altman plots showed acceptable agreement between NT-FFQ2 and 24-HR. The eating behaviours had acceptable face validity.
The NT-FFQ has good reproducibility and acceptable validity for food intake and eating behaviours. The NT-FFQ can quantify the nutrition transition among Indian adolescents.
The aim of this study was to test the reproducibility and validity of a self-administered FFQ for the Trace Element Study of Korean Adults in the Yeungnam area (SELEN). Study subjects were recruited from the SELEN cohort selected from rural and urban areas in Yeungnam, Korea. A semi-quantitative FFQ with 146 items was developed considering the dietary characteristics of cohorts in the study area. In a validation study, seventeen men and forty-eight women aged 38–62 years completed 3-d dietary records (DR) and two FFQ over a 3-month period. The validity was examined with the FFQ and DR, and the reproducibility was estimated using partial correlation coefficients, the Bland–Altman method and cross-classification. There were no significant differences between the mean intakes of selected nutrients as estimated from FFQ1, FFQ2 and DR. The median correlation coefficients for all nutrients were 0·47 and 0·56 in the reproducibility and validity tests, respectively. Bland–Altman’s index and cross-classification showed acceptable agreement between FFQ1 and FFQ2 and between FFQ2 and DR. Ultimately, 78 % of the subjects were classified into the same and adjacent quartiles for most nutrients. In addition, the weighted κ value indicated that the two methods agreed fairly. In conclusion, this newly developed FFQ was a suitable dietary assessment method for the SELEN cohort study.
The objective of the present study was to assess the reproducibility of data-driven dietary patterns in different samples extracted from similar populations. Dietary patterns were extracted by applying principal component analyses to the dietary information collected from a sample of 3550 women recruited from seven screening centres belonging to the Spanish breast cancer (BC) screening network (Determinants of Mammographic Density in Spain (DDM-Spain) study). The resulting patterns were compared with three dietary patterns obtained from a previous Spanish case–control study on female BC (Epidemiological study of the Spanish group for breast cancer research (GEICAM: grupo Español de investigación en cáncer de mama)) using the dietary intake data of 973 healthy participants. The level of agreement between patterns was determined using both the congruence coefficient (CC) between the pattern loadings (considering patterns with a CC≥0·85 as fairly similar) and the linear correlation between patterns scores (considering as fairly similar those patterns with a statistically significant correlation). The conclusions reached with both methods were compared. This is the first study exploring the reproducibility of data-driven patterns from two studies and the first using the CC to determine pattern similarity. We were able to reproduce the EpiGEICAM Western pattern in the DDM-Spain sample (CC=0·90). However, the reproducibility of the Prudent (CC=0·76) and Mediterranean (CC=0·77) patterns was not as good. The linear correlation between pattern scores was statistically significant in all cases, highlighting its arbitrariness for determining pattern similarity. We conclude that the reproducibility of widely prevalent dietary patterns is better than the reproducibility of more population-specific patterns. More methodological studies are needed to establish an objective measurement and threshold to determine pattern similarity.
We investigated the validity and reproducibility of the FFQ used in the Dutch European Investigation of Cancer and Nutrition cohort, in order to rank subjects according to intakes of fatty acid classes and individual fatty acids. In total, 121 men and women (23–72 years) filled out three FFQ at 6-month intervals between 1991 and 1992. As a reference method, they filled out twelve monthly 24-h dietary recalls (24HDR) during the same year. Intra-class correlation coefficients for the FFQ showed moderate to good reproducibility across all fatty acids (classes and individual) in men (0·56–0·81) and women (0·57–0·83). In men, Spearman’s correlation coefficients (rs) for the FFQ compared with the 24HDR indicated moderate to good relative validity (rs=0·45–0·71) for all fatty acids, except for arachidonic acid and marine PUFA (rs<0·40). In women, relative validity was moderate to good for MUFA and trans-fatty acids (TFA) and the majority of SFA (rs=0·40–0·66), was fair for the short-chain SFA and lauric acid (rs=0·30–0·33) and was fair to moderate for PUFA (rs=0·22–0·47). Bland–Altman plots showed good agreement between the FFQ and 24HDR, and proportional bias for fatty acids with very low intakes. In conclusion, the FFQ showed good reproducibility for subject ranking based on intakes of fatty acids (classes and individual). The relative validity measures indicated that the FFQ is an adequate tool to rank subjects according to intakes of high-abundant fatty acids, but less for low-abundant fatty acids.
The strongly coloured Cu-triethylenetetramine complex (Cu-Trien) provides a fast and easy way to measure the cation exchange capacity of clay samples, but the reliability of this method has been questioned in recent publications. This work identifies several reasons for the poor reliability, thus improving both the precision and accuracy of the CEC method. Pure Trien is shown here to intercalate as does the Cu-Trien complex. Hence, the purity of Trien and also the Cu/Trien ratio require special attention. Using cold Cu-Trien solutions produces systematic deviations in CEC determinations caused by errors in the pipetted volumes. The present study demonstrates, for the first time, that the Cu-Trien complex protonates and changes its effective charge beyond 2+. Based on titration experiments at three different temperatures, a correction function is derived for calculating the total charge of the Cu-Trien complex as a function of pH. Accounting for these pH-corrected charges indicates that Cu-Trien may well be insensitive to edge charges on smectite. Finally, it is shown here that the ratio of sample mass to the initial amount of Cu-Trien is critical because excess adsorption of Cu-Trien in addition to CEC sensu strictu was observed.
Increased vitamin D fortification of dairy products has increased the supply of vitamin D-containing products with different vitamin D contents on the market in Finland. The authors developed a ninety-eight-item FFQ with eight food groups and with a question on supplementation to assess dietary and supplemental vitamin D and Ca intakes in Finnish women (60ºN). The FFQ was validated in subgroups with different habitual vitamin D supplement use (0–57·5 µg/d) against the biomarker serum 25-hydroxyvitamin D (S-25(OH)D) and against 3-d food records (FR) (n 29–67). Median total vitamin D intake among participants was 9·4 (range 1·6–30·5) µg/d. Spearman’s correlations for vitamin D and Ca ranged from 0·28 (P 0·146, FFQ v. S-25(OH)D, persons not using supplements) to 0·75 (P<0·001, FFQ v. FR, supplement use included). The correlations between the FFQ and S-25(OH)D concentrations improved within increasing supplement intake. The Bland–Altman analysis showed wide limits of agreement between FFQ and FR: for vitamin D between −7·8 and 8·8 µg/d and for Ca between −938 and 934 mg/d, with mean differences being 0·5 µg/d and 2 mg/d, respectively. The triads method was used to calculate the validity coefficients of the FFQ for vitamin D, resulting in a mean of 1·00 (95 % CI 0·59, 1·00) and a range from 0·33 to 1·00. The perceived variation in the estimates could have been avoided with a longer FR period and larger number of participants. The results are comparable with earlier studies, and the FFQ provides a reasonable estimation of vitamin D and Ca intakes.
Cryptosporidium parvum is the major cause of livestock and zoonotically-acquired human cryptosporidiosis. The ability to track sources of contamination and routes of transmission by further differentiation of isolates would assist risk assessment and outbreak investigations. Multiple-locus variable-number of tandem-repeats (VNTR) analysis provides a means for rapid characterization by fragment sizing and estimation of copy numbers, but structured, harmonized development has been lacking for Cryptosporidium spp. To investigate potential for application in C. parvum surveillance and outbreak investigations, we studied nine commonly used VNTR loci (MSA, MSD, MSF, MM5, MM18, MM19, MS9-Mallon, GP60 and TP14) for chromosome distribution, repeat unit length and heterogeneity, and flanking region proximity and conservation. To investigate performance in vitro, we compared these loci in 14 C. parvum samples by capillary electrophoresis in three laboratories. We found that many loci did not contain simple repeat units but were more complex, hindering calculations of repeat unit copy number for standardized reporting nomenclature. However, sequenced reference DNA enabled reproducible fragment sizing and inter-laboratory allele assignation based on size normalized to that of the sequenced fragments by both single round and nested polymerase chain reactions. Additional Cryptosporidium loci need to be identified and validated for robust inter-laboratory surveillance and outbreak investigations.
FFQ are widely used in large-scale studies to assess dietary intake. To aid interpretation of diet–disease associations assessment of validity must be performed. Reproducibility is one aspect of validity focusing on the stability of repeated assessment with the same method which may also reveal problems in instrument design or participant instructions. The aim of the present study was to evaluate the reproducibility of a web-based FFQ targeting Danish adolescents within the Danish National Birth Cohort (DNBC). Data for the present study were obtained from a prospective design nested within the DNBC. Adolescents aged 13 to 15 years old (n 48, 60 % girls) completed the FFQ twice 4 weeks apart. The proportion of adolescents consistently classified into the same tertile according to amount of food intake ranged from 45 % (fish) to 77 % (vegetables), whereas classification into opposite tertiles ranged from 0 % (fruit, oils and dressing) to 15 % (beverages). Overall, no significant differences were observed in intake of food groups or nutrients between the two completions of the FFQ. Mean crude Spearman correlation for all food groups was 0·56 and mean intra-class correlation for all food groups was 0·61. In conclusion, the reproducibility of the FFQ for Danish adolescents was acceptable. The study revealed that adolescents aged 13–15 years seemed capable of recalling consistently overall dietary habits and had some difficulties estimating the frequency of consumption of regularly consumed food items.