Quality science from quality measurement: The role of measurement type with respect to replication and effect size magnitude in psychological research

Copyright: © 2018 Kornbrot et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.The quality of psychological studies is currently a major concern. The Many Labs Project (MLP) and the Open-Science-Collaboration (OSC) have collected key data on replicability and statistical effect sizes. We build on this work by investigating the role played by three measurement types: ratings, proportions and unbounded (measures without conceptual upper limits, e.g. time). Both replicability and effect sizes are dependent on the amount of variability due to extraneous factors. We predicted that the role of such extraneous factors might depend on measurement type, and would be greatest for ratings, intermediate for proportions and least for unbounded. Our results support this conjecture. OSC replication rates for unbounded, 43% and proportion 40% combined are reliably higher than those for ratings at 20% (effect size, w = .20). MLP replication rates for the original studies are: pro- portion = .74, ratings = .40 (effect size w = .33). Original effect sizes (Cohen’s d) are highest for: unbounded OSC cognitive = 1.45, OSC social = .90); next for proportions (OSC cogni- tive = 1.01, OSC social = .84, MLP = .82); and lowest for ratings (OSC social = .64, MLP = .31). These findings are of key importance to scientific methodology and design, even if the reasons for their occurrence are still at the level of conjecture.Peer reviewe

Lead and Cadmium Levels and Balance and Vestibular Dysfunction among Adult Participants in the National Health and Nutrition Examination Survey (NHANES) 1999–2004

Background: Few studies have been conducted to identify risk factors for balance and vestibular dysfunction in general populations, but previous studies have reported evidence of adverse effects of lead and cadmium on balance control in high-risk groups

Cross-sectional associations between sleep duration, sedentary time, physical activity, and adiposity indicators among Canadian preschool-aged children using compositional analyses

Abstract Background Sleep duration, sedentary behaviour, and physical activity are three co-dependent behaviours that fall on the movement/non-movement intensity continuum. Compositional data analyses provide an appropriate method for analyzing the association between co-dependent movement behaviour data and health indicators. The objectives of this study were to examine: (1) the combined associations of the composition of time spent in sleep, sedentary behaviour, light-intensity physical activity (LPA), and moderate- to vigorous-intensity physical activity (MVPA) with adiposity indicators; and (2) the association of the time spent in sleep, sedentary behaviour, LPA, or MVPA with adiposity indicators relative to the time spent in the other behaviours in a representative sample of Canadian preschool-aged children. Methods Participants were 552 children aged 3 to 4 years from cycles 2 and 3 of the Canadian Health Measures Survey. Sedentary time, LPA, and MVPA were measured with Actical accelerometers (Philips Respironics, Bend, OR USA), and sleep duration was parental reported. Adiposity indicators included waist circumference (WC) and body mass index (BMI) z-scores based on World Health Organization growth standards. Compositional data analyses were used to examine the cross-sectional associations. Results The composition of movement behaviours was significantly associated with BMI z-scores (p = 0.006) but not with WC (p = 0.718). Further, the time spent in sleep (BMI z-score: γ sleep  = −0.72; p = 0.138; WC: γ sleep  = −1.95; p = 0.285), sedentary behaviour (BMI z-score: γ SB  = 0.19; p = 0.624; WC: γ SB  = 0.87; p = 0.614), LPA (BMI z-score: γ LPA  = 0.62; p = 0.213, WC: γ LPA  = 0.23; p = 0.902), or MVPA (BMI z-score: γ MVPA  = −0.09; p = 0.733, WC: γ MVPA  = 0.08; p = 0.288) relative to the other behaviours was not significantly associated with the adiposity indicators. Conclusions This study is the first to use compositional analyses when examining associations of co-dependent sleep duration, sedentary time, and physical activity behaviours with adiposity indicators in preschool-aged children. The overall composition of movement behaviours appears important for healthy BMI z-scores in preschool-aged children. Future research is needed to determine the optimal movement behaviour composition that should be promoted in this age group

The prevalence of suicidal ideation identified by the Edinburgh Postnatal Depression Scale in postpartum women in primary care: findings from the RESPOND trial

<p>1 Abstract</p> <p>1.1 Background</p> <p>Suicide is a leading cause of perinatal maternal deaths in industrialised countries but there has been little research to investigate prevalence or correlates of postpartum suicidality. The Edinburgh Postnatal Depression Scale is widely used in primary and maternity services to screen for perinatal depressive disorders, and includes a question on suicidal ideation (question 10). We aimed to investigate the prevalence, persistence and correlates of suicidal thoughts in postpartum women in the context of a randomised controlled trial of treatments for postnatal depression.</p> <p>1.2 Methods</p> <p>Women in primary care were sent postal questionnaires at 6 weeks postpartum to screen for postnatal depression before recruitment into an RCT. The Edinburgh Postnatal Depression Scale (EPDS) was used to screen for postnatal depression and in those with high levels of symptoms, a home visit with a standardised psychiatric interview was carried out using the Clinical Interview Schedule-Revised version (CIS-R). Other socio-demographic and clinical variables were measured, including functioning (SF12) and quality of the marital relationship (GRIMS). Women who entered the trial were followed up for 18 weeks.</p> <p>1.3 Results</p> <p>9% of 4,150 women who completed the EPDS question relating to suicidal ideation reported some suicidal ideation (including hardly ever); 4% reported that the thought of harming themselves had occurred to them sometimes or quite often. In women who entered the randomised trial and completed the EPDS question relating to suicidal ideation (n = 253), suicidal ideation was associated with younger age, higher parity and higher levels of depressive symptoms in the multivariate analysis. Endorsement of 'yes, quite often' to question 10 on the EPDS was associated with affirming at least two CIS-R items on suicidality. We found no association between suicidal ideation and SF-12 physical or mental health or the EPDS total score at 18 weeks.</p> <p>1.4 Conclusions</p> <p>Healthcare professionals using the EPDS should be aware of the significant suicidality that is likely to be present in women endorsing 'yes, quite often' to question 10 of the EPDS. However, suicidal ideation does not appear to predict poor outcomes in women being treated for postnatal depression.</p> <p>Trial registration</p> <p>Current Controlled Trials <a href="http://www.controlled-trials.com/ISRCTN16479417">ISRCTN16479417</a>.</p

Open Babel: An open chemical toolbox

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendorneutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license fro

Measuring the health of the Indian elderly: evidence from National Sample Survey data

<p>Abstract</p> <p>Background</p> <p>Comparable health measures across different sets of populations are essential for describing the distribution of health outcomes and assessing the impact of interventions on these outcomes. Self-reported health (SRH) is a commonly used indicator of health in household surveys and has been shown to be predictive of future mortality. However, the susceptibility of SRH to influence by individuals' expectations complicates its interpretation and undermines its usefulness.</p> <p>Methods</p> <p>This paper applies the empirical methodology of Lindeboom and van Doorslaer (2004) to investigate elderly health in India using data from the 52^ndround of the National Sample Survey conducted in 1995-96 that includes both an SRH variable as well as a range of objective indicators of disability and ill health. The empirical testing was conducted on stratified homogeneous groups, based on four factors: gender, education, rural-urban residence, and region.</p> <p>Results</p> <p>We find that region generally has a significant impact on how women perceive their health. Reporting heterogeneity can arise not only from cut-point shifts, but also from differences in health effects by objective health measures. In contrast, we find little evidence of reporting heterogeneity due to differences in gender or educational status within regions. Rural-urban residence does matter in some cases. The findings are robust with different specifications of objective health indicators.</p> <p>Conclusions</p> <p>Our exercise supports the thesis that the region of residence is associated with different cut-points and reporting behavior on health surveys. We believe this is the first paper that applies the Lindeboom-van Doorslaer methodology to data on the elderly in a developing country, showing the feasibility of applying this methodology to data from many existing cross-sectional health surveys.</p

A Measurement of Rb using a Double Tagging Method

The fraction of Z to bbbar events in hadronic Z decays has been measured by the OPAL experiment using the data collected at LEP between 1992 and 1995. The Z to bbbar decays were tagged using displaced secondary vertices, and high momentum electrons and muons. Systematic uncertainties were reduced by measuring the b-tagging efficiency using a double tagging technique. Efficiency correlations between opposite hemispheres of an event are small, and are well understood through comparisons between real and simulated data samples. A value of Rb = 0.2178 +- 0.0011 +- 0.0013 was obtained, where the first error is statistical and the second systematic. The uncertainty on Rc, the fraction of Z to ccbar events in hadronic Z decays, is not included in the errors. The dependence on Rc is Delta(Rb)/Rb = -0.056*Delta(Rc)/Rc where Delta(Rc) is the deviation of Rc from the value 0.172 predicted by the Standard Model. The result for Rb agrees with the value of 0.2155 +- 0.0003 predicted by the Standard Model.Comment: 42 pages, LaTeX, 14 eps figures included, submitted to European Physical Journal

Measurement of the B+ and B-0 lifetimes and search for CP(T) violation using reconstructed secondary vertices

The lifetimes of the B+ and B-0 mesons, and their ratio, have been measured in the OPAL experiment using 2.4 million hadronic Z(0) decays recorded at LEP. Z(0) --> b (b) over bar decays were tagged using displaced secondary vertices and high momentum electrons and muons. The lifetimes were then measured using well-reconstructed charged and neutral secondary vertices selected in this tagged data sample. The results aretau(B+) = 1.643 +/- 0.037 +/- 0.025 pstau(Bo) = 1.523 +/- 0.057 +/- 0.053 pstau(B+)/tau(Bo) = 1.079 +/- 0.064 +/- 0.041,where in each case the first error is statistical and the second systematic.A larger data sample of 3.1 million hadronic Z(o) decays has been used to search for CP and CPT violating effects by comparison of inclusive b and (b) over bar hadron decays, No evidence fur such effects is seen. The CP violation parameter Re(epsilon(B)) is measured to be Re(epsilon(B)) = 0.001 +/- 0.014 +/- 0.003and the fractional difference between b and (b) over bar hadron lifetimes is measured to(Delta tau/tau)(b) = tau(b hadron) - tau((b) over bar hadron)/tau(average) = -0.001 +/- 0.012 +/- 0.008

Colouration and Colour Changes of the Fiddler Crab, Uca capricornis: A Descriptive Study

Colour changes in animals may be triggered by a variety of social and environmental factors and may occur over a matter of seconds or months. Crustaceans, like fiddler crabs (genus Uca), are particularly adept at changing their colour and have been the focus of numerous studies. However, few of these studies have attempted to quantitatively describe the individual variation in colour and pattern or their adaptive significance. This paper quantitatively describes the colour patterns of the fiddler crab Uca capricornis and their ability to change on a socially significant timescale. The most dramatic changes in colour pattern are associated with moulting. These ontogenetic changes result in a general reduction of the colour pattern with increasing size, although females are more colourful and variable than similarly-sized males. Uca capricornis are also capable of rapid colour changes in response to stress, but show no endogenous rhythms associated with the semilunar and tidal cycles commonly reported in other fiddler crabs. The extreme colour polymorphism and the relative stability of the colour patterns in Uca capricornis are consistent with their use in visually mediated mate recognition

Local Enhancement Promotes Cockroach Feeding Aggregations

Communication and learning from each other are part of the success of animal societies. Social insects invest considerable effort into signalling to their nestmates the locations of the most profitable resources in their environment. Growing evidence also indicates that insects glean such information through cues inadvertently provided by their conspecifics. Here, we investigate social information use in the foraging decisions by gregarious cockroaches (Blattella germanica L.). Individual cockroaches given a simultaneous choice in a Y-olfactometer between the odour of feeding conspecifics and the mixed odour of food plus non-feeding conspecifics showed a preference for the arm scented with the odour of feeding conspecifics. Social information (the presence of feeding conspecifics) was produced by cockroaches of all age classes and perceived at short distance in the olfactometer arms, suggesting the use of inadvertently provided cues rather than signals. We discuss the nature of these cues and the role of local enhancement (the selection of a location based on cues associated with the presence of conspecifics) in the formation of feeding aggregations in B. germanica. Similar cue-mediated recruitments could underpin a wide range of collective behaviours in group-living insects