Testing the allegiance bias hypothesis: a meta-analysis

This meta-analysis investigated whether the association between researcher allegiance (RA) and the relative effect of two psychotherapies can be explained through the methodological weaknesses of the treatment comparisons. Seventy-nine comparisons of psychotherapies for depression or posttraumatic stress disorder (PTSD) were included. Methodological quality (MQ) was investigated as both a moderator and a mediator of the RA-outcome association. MQ included balanced nonspecific factors, balanced specific factors, conceptual quality, patients-per-therapist ratio, randomization to conditions and outcome assessment. The RA-outcome association was stronger when the MQ was low, suggesting a buffering effect of MQ. In addition, differences in the conceptual quality of treatments mediated the effect of RA on outcome. The results support the view that RA acts as a bias in treatment comparisons.

Transpecific microsatellites for hard pines M. Shepherd, M. Cross, T. Maguire, M. Dieters, C. Williams, R. Henry

Microsatellites are difficult to recover from large plant genomes so cross-specific utilisation is an important source of markers. Fifty micro satellites were tested for cross-specific amplification and polymorphism to two New World hard pine species, slash pine (Pinus elliottii var. elliottii) and Caribbean pine (R caribaea var. hondurensis). Twenty-nine (58%) markers amplified in both hard pine species, and 23 of these 29 were polymorphic. Soft pine (subgenus Strobus) microsatellite markers did amplify, but none were polymorphic. Pinus elliottii var. elliottii and R caribaea var. hondurensis showed mutational changes in the flanking regions and the repeat motif that were informative for Pinus spp. phylogenetic relationships. Most allele length variation could be attributed to variability in repeat unit number. There was no evidence for ascertainment bias.

How accurate is the current picture of human genetic variation?

Our understanding of the distribution of worldwide human genomic diversity has greatly increased over recent years thanks to the availability of large data sets derived from short tandem repeats (STRs), insertion deletion polymorphisms (indels) and single nucleotide polymorphisms (SNPs). A concern, however, is that the current picture of worldwide human genomic diversity may be inaccurate because of biases in the selection process of genetic markers (so-called 'ascertainment bias'). To evaluate this problem, we first compared the distribution of genomic diversity between these three types of genetic markers in the populations from the HGDP-CEPH panel for evidence of bias or incongruities. In a second step, using a very relaxed set of criteria to prevent the intrusion of bias, we developed a new set of unbiased STR markers and compared the results against those from available panels. Contrarily to recent claims, our results show that the STR markers suffer from no discernible bias, and can thus be used as a baseline reference for human genetic diversity and population differentiation. The bias on SNPs is moderate compared to that on the set of indels analysed, which we recommend should be avoided for work describing the distribution of human genetic diversity or making inference on human settlement history.

An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structure

There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genotnes. Several statistical methods have been proposed to study the genetic structure using AFLP's but they assume Hardy-Weinberg equilibrium and do not estimate the inbreeding coefficient, F-IS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific F-IS and F-ST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.uif-grenoble.fi-/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias.

Primed and prejudice: the Kurantha-Bothata study

O sistema de peer review é uma ferramenta fundamental nas publicações científicas, cujo objetivo é selecionar os estudos que contribuem para o avanço do conhecimento. No entanto, questionamentos tem surgido acerca de vieses no sistema de peer review. Um exemplo é o estudo "Lost science in the third world" (Gibbs, 1995), que afirma existirem sérios vieses em relação à origem dos pesquisadores. Ainda que haja evidências para suportar esse argumento, nosso conhecimento acerca de vieses no sistema de peer review ainda é limitado, já que poucos estudos controlados podem ser encontrados na literatura. No presente trabalho, foi realizado um exeprimento no qual os sujeitos deveriam avaliar um artigo sem qualquer identificação de autoria, exceto por uma nota de rodapé onde constava o nome da instituição fictícia que financiou a pesquisa. Sob uma condição, o nome da agência financiadora é associado com o continente africano, enquanto na outra condição, o nome da agência é associado ao continente europeu. Os resultados dão indícios de que possa haver um viés relacionado às origens do autor.

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Strategies for single nucleotide polymorphism (SNP) genotyping to enhance genotype imputation in Gyr (Bos indicus) dairy cattle: Comparison of commercially available SNP chips

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evolution of signal form

Visual signals, used for communication both within and between species, vary immensely in the forms that they take. How is it that all this splendour has evolved in nature? Since it is the receiver’s preferences that cause selective pressures on signals, elucidating the mechanism behind the response of the signal receiver is vital to gain a closer understanding of the evolutionary process. In my thesis I have therefore investigated how receivers, represented by chickens, Gallus gallus domesticus, respond to different stimuli displayed on a peck-sensitive computer screen. According to the receiver bias hypothesis, animals and humans often express biases when responding to certain stimuli. These biases develop as by-products of how the recognition mechanism categorises and discriminates between stimuli. Since biases are generated from general stimulus processing mechanisms, they occur irrespective of species and type of signal, and it is often possible to predict the direction and intensity of the biases. One of the results from the experiments in my thesis demonstrates that similar experience in different species may generate similar biases. By giving chickens at least some of the experience of human faces as humans presumably have, the chickens subsequently expressed preferences for the same faces as a group of human subjects. Another kind of experience generated a bias for symmetry. This bias developed in the context of training chickens to recognise two mirror images of an asymmetrical stimulus. Untrained chickens and chickens trained on only one of the mirror images expressed no symmetry preferences. The bias produced by the training regime was for a specific symmetrical stimulus which had a strong resemblance to the familiar asymmetrical exemplar, rather than a general preference for symmetry. A further kind of experience, training chickens to respond to some stimuli but not to others, generated a receiver bias for exaggerated stimuli, whereas chickens trained on reversed stimuli developed a bias for less exaggerated stimuli. To investigate the potential of this bias to drive the evolution of signals towards exaggerated forms, a simplified evolutionary process was mimicked. The stimuli variants rejected by the chickens were eliminated, whereas the selected forms were kept and evolved prior to the subsequent display. As a result, signals evolved into exaggerated forms in all tested stimulus dimensions: length, intensity and area, despite the inclusion of a cost to the sender for using increasingly exaggerated signals. The bias was especially strong and persistent for stimuli varying along the intensity dimension where it remained despite extensive training. All the results in my thesis may be predicted by the receiver bias hypothesis. This implies that biases, developed due to stimuli experience, may be significant mechanisms driving the evolution of signal form.

Is the allegiance effect an epiphenomenon of true efficacy differences between treatments? a meta-analysis

Many meta-analyses of comparative outcome studies found a substantial association of researcher allegiance (RA) and relative treatment effects. Therefore, RA is regarded as a biasing factor in comparative outcome research (RA bias hypothesis). However, the RA bias hypothesis has been criticized as causality might be reversed. That is, RA might be a reflection of true efficacy differences between treatments (true efficacy hypothesis). Consequently, the RA-outcome association would not be indicative of bias but an epiphenomenon of true efficacy differences. This meta-analysis tested the validity of the true efficacy hypothesis. This was done by controlling the RA-outcome association for true efficacy differences by restricting analysis to direct comparisons of treatments with equivalent efficacy. We included direct comparisons of different versions of trauma-focused therapy (TFT) in the treatment of posttraumatic stress disorder (PTSD). RA was measured from the research reports. Relative effect sizes for symptoms of PTSD were calculated. Random effects meta-regression was conducted. Twenty-nine comparisons of TFTs from 20 studies were identified. Initial heterogeneity among relative effect sizes was low. RA was a significant predictor of outcome and explained 12% of the variance in outcomes. The true efficacy hypothesis predicted the RA-outcome association to be zero; however, a substantial association was found. Thus, this study does not support the true efficacy hypothesis. Given findings from psychotherapy research and other fields that support a biasing influence of researcher preferences, RA should be regarded as a causal factor and conceptualized as a threat to the validity of conclusions from comparative outcome studies.

Researcher allegiance in psychotherapy outcome research: an overview of reviews

Researcher allegiance (RA) is widely discussed as a risk of bias in psychotherapy outcome research. The relevance attached to RA bias is related to meta-analyses demonstrating an association of RA with treatment effects. However, recent meta-analyses have yielded mixed results. To provide more clarity on the magnitude and robustness of the RA-outcome association this article reports on a meta-meta-analysis summarizing all available meta-analytic estimates of the RA-outcome association. Random-effects methods were used. Primary study overlap was controlled. Thirty meta-analyses were included. The mean RA-outcome association was r=.262 (p=.002, I(2)=28.98%), corresponding to a moderate effect size. The RA-outcome association was robust across several moderating variables including characteristics of treatment, population, and the type of RA assessment. Allegiance towards the RA bias hypothesis moderated the RA-outcome association. The findings of this meta-meta-analysis suggest that the RA-outcome association is substantial and robust. Implications for psychotherapy outcome research are discussed.

Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement

Molecular data are now widely used in epidemiological studies to investigate the transmission, distribution, biology, and diversity of pathogens. Our objective was to establish recommendations to support good scientific reporting of molecular epidemiological studies to encourage authors to consider specific threats to valid inference. The statement Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) builds upon the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) initiative. The STROME-ID statement was developed by a working group of epidemiologists, statisticians, bioinformaticians, virologists, and microbiologists with expertise in control of infection and communicable diseases. The statement focuses on issues relating to the reporting of epidemiological studies of infectious diseases using molecular data that were not addressed by STROBE. STROME-ID addresses terminology, measures of genetic diversity within pathogen populations, laboratory methods, sample collection, use of molecular markers, molecular clocks, timeframe, multiple-strain infections, non-independence of infectious-disease data, missing data, ascertainment bias, consistency between molecular and epidemiological data, and ethical considerations with respect to infectious-disease research. In total, 20 items were added to the 22 item STROBE checklist. When used, the STROME-ID recommendations should advance the quality and transparency of scientific reporting, with clear benefits for evidence reviews and health-policy decision making.

Multivariate genetic analysis of academic skills of the Queensland Core Skills Test and IQ highlight the importance of genetic g

This study examined the genetic and environmental relationships among 5 academic achievement skills of a standardized test of academic achievement, the Queensland Core Skills Test (QCST; Queensland Studies Authority, 2003a). QCST participants included 182 monozygotic pairs and 208 dizygotic pairs (mean 17 years +/- 0.4 standard deviation). IQ data were included in the analysis to correct for ascertainment bias. A genetic general factor explained virtually all genetic variance in the component academic skills scores, and accounted for 32% to 73% of their phenotypic variances. It also explained 56% and 42% of variation in Verbal IQ and Performance IQ respectively, suggesting that this factor is genetic g. Modest specific genetic effects were evident for achievement in mathematical problem solving and written expression. A single common factor adequately explained common environmental effects, which were also modest, and possibly due to assortative mating. The results suggest that general academic ability, derived from genetic influences and to a lesser extent common environmental influences, is the primary source of variation in component skills of the QCST.

Interpreting adverse signals in diabetes drug development programs

Detection and interpretation of adverse signals during preclinical and clinical stages of drug development inform the benefit-risk assessment that determines suitability for use in real-world situations. This review considers some recent signals associated with diabetes therapies, illustrating the difficulties in ascribing causality and evaluating absolute risk, predictability, prevention, and containment. Individual clinical trials are necessarily restricted for patient selection, number, and duration; they can introduce allocation and ascertainment bias and they often rely on biomarkers to estimate long-term clinical outcomes. In diabetes, the risk perspective is inevitably confounded by emergent comorbid conditions and potential interactions that limit therapeutic choice, hence the need for new therapies and better use of existing therapies to address the consequences of protracted glucotoxicity. However, for some therapies, the adverse effects may take several years to emerge, and it is evident that faint initial signals under trial conditions cannot be expected to foretell all eventualities. Thus, as information and experience accumulate with time, it should be accepted that benefit-risk deliberations will be refined, and adjustments to prescribing indications may become appropriate. © 2013 by the American Diabetes Association.