A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies

The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was approximately 80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.

Systematic review of the psychological consequences of false-positive screening mammograms

- Background In the UK, women aged 50–73 years are invited for screening by mammography every 3 years. In 2009–10, more than 2.24 million women in this age group in England were invited to take part in the programme, of whom 73% attended a screening clinic. Of these, 64,104 women were recalled for assessment. Of those recalled, 81% did not have breast cancer; these women are described as having a false-positive mammogram. - Objective The aim of this systematic review was to identify the psychological impact on women of false-positive screening mammograms and any evidence for the effectiveness of interventions designed to reduce this impact. We were also looking for evidence of effects in subgroups of women. - Data sources MEDLINE, MEDLINE In-Process & Other Non-Indexed Citations, EMBASE, Health Management Information Consortium, Cochrane Central Register for Controlled Trials, Cochrane Database of Systematic Reviews, Centre for Reviews and Dissemination (CRD) Database of Abstracts of Reviews of Effects, CRD Health Technology Assessment (HTA), Cochrane Methodology, Web of Science, Science Citation Index, Social Sciences Citation Index, Conference Proceedings Citation Index-Science, Conference Proceeding Citation Index-Social Science and Humanities, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, Sociological Abstracts, the International Bibliography of the Social Sciences, the British Library's Electronic Table of Contents and others. Initial searches were carried out between 8 October 2010 and 25 January 2011. Update searches were carried out on 26 October 2011 and 23 March 2012. - Review methods Based on the inclusion criteria, titles and abstracts were screened independently by two reviewers. Retrieved papers were reviewed and selected using the same independent process. Data were extracted by one reviewer and checked by another. Each included study was assessed for risk of bias. - Results Eleven studies were found from 4423 titles and abstracts. Studies that used disease-specific measures found a negative psychological impact lasting up to 3 years. Distress increased with the level of invasiveness of the assessment procedure. Studies using instruments designed to detect clinical levels of morbidity did not find this effect. Women with false-positive mammograms were less likely to return for the next round of screening [relative risk (RR) 0.97; 95% confidence interval (CI) 0.96 to 0.98] than those with normal mammograms, were more likely to have interval cancer [odds ratio (OR) 3.19 (95% CI 2.34 to 4.35)] and were more likely to have cancer detected at the next screening round [OR 2.15 (95% CI 1.55 to 2.98)]. - Limitations This study was limited to UK research and by the robustness of the included studies, which frequently failed to report quality indicators, for example failure to consider the risk of bias or confounding, or failure to report participants' demographic characteristics. - Conclusions We conclude that the experience of having a false-positive screening mammogram can cause breast cancer-specific psychological distress that may endure for up to 3 years, and reduce the likelihood that women will return for their next round of mammography screening. These results should be treated cautiously owing to inherent weakness of observational designs and weaknesses in reporting. Future research should include a qualitative interview study and observational studies that compare generic and disease-specific measures, collect demographic data and include women from different social and ethnic groups.

Psychological consequences of false-positive screening mammograms in the UK

- Objectives To identify the psychological effects of false-positive screening mammograms in the UK. - Methods Systematic review of all controlled studies and qualitative studies of women with a false-positive screening mammogram. The control group participants had normal mammograms. All psychological outcomes including returning for routine screening were permitted. All studies had a narrative synthesis. - Results The searches returned seven includable studies (7/4423). Heterogeneity was such that meta-analysis was not possible. Studies using disease-specific measures found that, compared to normal results, there could be enduring psychological distress that lasted up to 3 years; the level of distress was related to the degree of invasiveness of the assessment. At 3 years the relative risks were, further mammography, 1.28 (95% CI 0.82 to 2.00), fine needle aspiration 1.80 (95% CI 1.17 to 2.77), biopsy 2.07 (95% CI 1.22 to 3.52) and early recall 1.82 (95% CI 1.22 to 2.72). Studies that used generic measures of anxiety and depression found no such impact up to 3 months after screening. Evidence suggests that women with false-positive mammograms have an increased likelihood of failing to reattend for routine screening, relative risk 0.97 (95% CI 0.96 to 0.98) compared with women with normal mammograms. - Conclusions Having a false-positive screening mammogram can cause breast cancer-specific distress for up to 3 years. The degree of distress is related to the invasiveness of the assessment. Women with false-positive mammograms are less likely to return for routine assessment than those with normal ones.

Constituting religion after Williams: The false dichotomy of theocracy and secularism

The Williams case is a relevant segue to consider the broader issue of constitutional relations between church and state in Australia. This paper argues that the dichotomous approach of theocracy as opposed to secularism is false and actually undermines the proper operation of s 116. A theocracy would contravene s 116 as an establishment of religion, but secularism also amounts to a conflict with s 116 as prohibiting the free exercise of religion. The necessary alternative is to find a middle ground compatible with s 116, one which will not establish any single state religion but will allow the contribution of different religious perspectives in the process of policy-making. This paper briefly considers how such an approach may be implemented.

False Error Study of On-line Soft Error Detection Mechanisms

With technology scaling, vulnerability to soft errors in random logic is increasing. There is a need for on-line error detection and protection for logic gates even at sea level. The error checker is the key element for an on-line detection mechanism. We compare three different checkers for error detection from the point of view of area, power and false error detection rates. We find that the double sampling checker (used in Razor), is the simplest and most area and power efficient, but suffers from very high false detection rates of 1.15 times the actual error rates. We also find that the alternate approaches of triple sampling and integrate and sample method (I&S) can be designed to have zero false detection rates, but at an increased area, power and implementation complexity. The triple sampling method has about 1.74 times the area and twice the power as compared to the Double Sampling method and also needs a complex clock generation scheme. The I&S method needs about 16% more power with 0.58 times the area as double sampling, but comes with more stringent implementation constraints as it requires detection of small voltage swings.

Maximum Margin Classifiers with Specified False Positive and False Negative Error Rates

This paper addresses the problem of maximum margin classification given the moments of class conditional densities and the false positive and false negative error rates. Using Chebyshev inequalities, the problem can be posed as a second order cone programming problem. The dual of the formulation leads to a geometric optimization problem, that of computing the distance between two ellipsoids, which is solved by an iterative algorithm. The formulation is extended to non-linear classifiers using kernel methods. The resultant classifiers are applied to the case of classification of unbalanced datasets with asymmetric costs for misclassification. Experimental results on benchmark datasets show the efficacy of the proposed method.

Sex ratio of the false trevaly Lactarius lactarius (Bloch and Schneider)

The sex ratio in Lactarius lactarius at different months and years was studied. Sex ratio data show that males outnumber females in all months except in October. The insignificant difference in the number of individuals of both the sexes during spawning months (January, March, October and November) indicated that males and females congregate during the spawning season. Among the larger specimens, males constituted the minority.

The fecundity of the false trevally, Lactarius lactarius (Bloch and Schneider) along the Karwar coast

A clear knowledge of the reproductive potential or fecundity of a fish is quite an essential pre-requisite for the proper management and conservation of the resources. The fecundity studies are also undertaken to determine the index of diversity dependent factor affecting the population size (Simpson, 1951). Qasim & Qayyam (1963) have detailed the various pathways by which an understanding of fecundity could be used for fishery biological work. The ability of egg production varies within the individual limits such as length, somatic weight, gonadal weight, volume of fish etc.

Eliminating False Matches for the Projective Registration of Free-Form Surfaces with Small Translational Motions

Liu, Yonghuai. Eliminating False Matches for the Projective Registration of Free-Form Surfaces with Small Translational Motions. IEEE Transactions on Systems, Man and Cybernetics, Part B: Cybernetics, vol. 35, no. 3, pp. 607-624, 2005.

Detecting False Identity through Behavioural Patterns

T. Boongoen and Q. Shen. 'Detecting False Identity through Behavioural Patterns', In Proceedings of International Crime Science Conference, British Library, London UK, 2008. Publisher's online version forthcoming.;The full text is currently unavailable in CADAIR pending approval by the publisher. Sponsorship: UK EPSRC grant EP/D057086

Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates.

MOTIVATION: Technological advances that allow routine identification of high-dimensional risk factors have led to high demand for statistical techniques that enable full utilization of these rich sources of information for genetics studies. Variable selection for censored outcome data as well as control of false discoveries (i.e. inclusion of irrelevant variables) in the presence of high-dimensional predictors present serious challenges. This article develops a computationally feasible method based on boosting and stability selection. Specifically, we modified the component-wise gradient boosting to improve the computational feasibility and introduced random permutation in stability selection for controlling false discoveries. RESULTS: We have proposed a high-dimensional variable selection method by incorporating stability selection to control false discovery. Comparisons between the proposed method and the commonly used univariate and Lasso approaches for variable selection reveal that the proposed method yields fewer false discoveries. The proposed method is applied to study the associations of 2339 common single-nucleotide polymorphisms (SNPs) with overall survival among cutaneous melanoma (CM) patients. The results have confirmed that BRCA2 pathway SNPs are likely to be associated with overall survival, as reported by previous literature. Moreover, we have identified several new Fanconi anemia (FA) pathway SNPs that are likely to modulate survival of CM patients. AVAILABILITY AND IMPLEMENTATION: The related source code and documents are freely available at https://sites.google.com/site/bestumich/issues. CONTACT: yili@umich.edu.

Adult personality inconsistency and problems with parents: uncovering the roots of the false self

Research has established that individuals who tend to vary their personality depending on who they are with, show a variety of signs of psychological maladjustment in comparison to those who do not; they show more negative affect (Baird, Le and Lucas, 2006), lower life satisfaction (Suh, 2002), lower self-esteem (Sheldon et al., 1997), lower role-satisfaction (Donahue et al., 1993), higher rates of depression (Lutz and Ross, 2003), more anxiety (Diehl, Hastings and Stanton, 2001) and poorer physical health (Cross, Gore and Morris, 2003). It has also been shown that personality variability is positively related to the experience of inauthenticity and falsity (Sheldon et al., 1997). Donahue, Roberts, Robins and John (1993) found that personality inconsistency of this type is related to tension within the family. Psychoanalytic theory has also linked the operation of an adult false self to experiences with parents, particularly in early life (Winnicott, 1960). It was hypothesized that personality variability and the adult experience of falsity in social situations would be related to an emotionally unstable relationship with parents. The method to test this comprised a questionnaire-based survey given to a non-clinical population. The final sample comprised 305, with 193 women and 112 men, aged from 19 to 55. The first questionnaire asked participants to rate personality traits, including emotional stability, in three social contexts - with parents, with friends and with work colleagues. The second part involved 3 questions; participants were asked to select in which of the aforementioned three social contexts they felt “most themselves”; in which they were “most authentic” and in which they “put on a front”. It was found, consistent with predictions, that an index of overall personality variability calculated from the personality questionnaire correlated strongly with emotional instability around parents (r = 0.46, p<0.001), while not correlating with emotional instability in either of the other two contexts measured. This suggests a specific link between a person’s relationship with their parents and their overall personality integration. Furthermore, it was found that participants who cited one of the three social contexts (parents, friends, work colleagues) as being one in which they were “more themselves” or “more authentic” had significantly higher ratings of emotional instability with parents than those participants who found that they were equally authentic across settings (F = 9.8, p<0.005). The results suggest a clear link between a person’s relationships with their parents and their adult personality integration. An explanation is that individuals who experience an anxious or ambiguous attachment with their parents in childhood may fear rejection or abandonment in later life, and so habitually adapt their personality to fit in to social contexts as adults, in order to be accepted by others and to minimize the possibility of social rejection. These individuals meanwhile retain an emotionally unstable relationship with their parents in adulthood. This interpretation is speculative but is open to empirical testing. Clinicians should be aware that attachment problems with parents may underlie poor personality integration in adulthood.