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.

A method of false coincidence removal from measurements of quadruple coincidences between two photoelectrons and two photoions generated in molecular double photoionization

The removal of false coincidences from measurements of coincidences between two photoelectrons and one or two ions formed in molecular double photoionization is described. False coincidences arise by several mechanisms; experimental procedures and mathematical formulae required to remove all the different false coincidence contributions are described. Sample spectra taken of the double photoionization of carbon dioxide are presented to illustrate the method of false coincidence subtraction.

The day after: effects of vocal interactions on territory defence in nightingales

Models on territory acquisition and tenure predict that territorial animals benefit by adjusting territorial defence behaviour to previous challenges they had experienced within the socially complex environment of communication networks.

Plasma cell polyp of the vocal fold

Plasma cell polyps of the vocal fold (plasma cell granulomas) are rare inflammatory polyps of the larynx. They should be included in the clinical and histological differential diagnosis of laryngeal polyps. Histologically they are polyclonal aggregates of plasma cells. It is essential to distinguish them from monoclonal, neoplastic plasma cell proliferations. The treatment of choice is surgical resection, although radiotherapy, laser ablation, antibiotics and steroids have been used successfully. We present a case of plasma cell granuloma presenting as a vocal fold polyp, treated surgically.

False-positive PCR results linked to administration of seasonal influenza vaccine

False-positive PCR results usually occur as a consequence of specimen-to-specimen or amplicon-to-specimen contamination within the laboratory. Evidence of contamination at time of specimen collection linked to influenza vaccine administration in the same location as influenza sampling is described. Clinical, circumstantial and laboratory evidence was gathered for each of five cases of influenza-like illness (ILI) with unusual patterns of PCR reactivity for seasonal H1N1, H3N2, H1N1 (2009) and influenza B viruses. Two 2010 trivalent influenza vaccines and environmental swabs of a hospital influenza vaccination room were also tested for influenza RNA. Sequencing of influenza A matrix (M) gene amplicons from the five cases and vaccines was undertaken. Four 2009 general practitioner (GP) specimens were seasonal H1N1, H3N2 and influenza B PCR positive. One 2010 GP specimen was H1N1 (2009), H3N2 and influenza B positive. PCR of 2010 trivalent vaccines showed high loads of detectable influenza A and B RNA. Sequencing of the five specimens and vaccines showed greatest homology with the M gene sequence of Influenza A/Puerto Rico/8/1934 H1N1 virus (used in generation of influenza vaccine strains). Environmental swabs had detectable influenza A and B RNA. RNA detection studies demonstrated vaccine RNA still detectable for at least 66 days. Administration of influenza vaccines and clinical sampling in the same room resulted in the contamination with vaccine strains of surveillance swabs collected from patients with ILI. Vaccine contamination should therefore be considered, particularly where multiple influenza virus RNA PCR positive signals (e.g. H1N1, H3N2 and influenza B) are detected in the same specimen.