A flexible framework for sparse simultaneous component based data integration

<p>Abstract</p> <p>1 Background</p> <p>High throughput data are complex and methods that reveal structure underlying the data are most useful. Principal component analysis, frequently implemented as a singular value decomposition, is a popular technique in this respect. Nowadays often the challenge is to reveal structure in several sources of information (e.g., transcriptomics, proteomics) that are available for the same biological entities under study. Simultaneous component methods are most promising in this respect. However, the interpretation of the principal and simultaneous components is often daunting because contributions of each of the biomolecules (transcripts, proteins) have to be taken into account.</p> <p>2 Results</p> <p>We propose a sparse simultaneous component method that makes many of the parameters redundant by shrinking them to zero. It includes principal component analysis, sparse principal component analysis, and ordinary simultaneous component analysis as special cases. Several penalties can be tuned that account in different ways for the block structure present in the integrated data. This yields known sparse approaches as the lasso, the ridge penalty, the elastic net, the group lasso, sparse group lasso, and elitist lasso. In addition, the algorithmic results can be easily transposed to the context of regression. Metabolomics data obtained with two measurement platforms for the same set of <it>Escherichia coli </it>samples are used to illustrate the proposed methodology and the properties of different penalties with respect to sparseness across and within data blocks.</p> <p>3 Conclusion</p> <p>Sparse simultaneous component analysis is a useful method for data integration: First, simultaneous analyses of multiple blocks offer advantages over sequential and separate analyses and second, interpretation of the results is highly facilitated by their sparseness. The approach offered is flexible and allows to take the block structure in different ways into account. As such, structures can be found that are exclusively tied to one data platform (group lasso approach) as well as structures that involve all data platforms (Elitist lasso approach).</p> <p>4 Availability</p> <p>The additional file contains a MATLAB implementation of the sparse simultaneous component method.</p

Assessing the Effects of a Real-Life Contact Intervention on Prejudice Toward LGBT People

Prejudice against sexual and gender minorities (e.g., LGBT people) is quite prevalent and is harmful. We examined an existing-and often-used-contact intervention in pre-existing groups in an educational setting and assessed its effectiveness in reducing different forms of LGBT negativity. We focused particularly on modern LGBT negativity: a relatively subtle form of prejudice, involving ambivalence, denial, and/or the belief that there is too much attention for LGBT prejudice. We used a mixed design in which condition (experimental vs. control group) was the between-participants factor, which was randomized at the group level, and time (pretest vs. posttest vs. follow-up) was the within-participants factor (N = 117). Interventions were video recorded and the behavior of LGBT educators and participants was coded. Participants responded positively to the intervention, especially to the LGBT educator's "coming-out story." Exploratory analysis of the video data indicated that the perceived effectiveness of the intervention was higher in groups where participants were more engaged, although caution is necessary in interpreting this finding. The most important measure indicated that modern LGBT negativity decreased in the intervention groups directly after the intervention, but returned to baseline levels one week later. However, in the control condition, modern LGBT negativity had increased over time. Taken together, this suggests that an actual reduction in modern LGBT negativity was short-lived (i.e., the intervention effect disappeared within 7 days)

Can liberal democracy help us to survive the environmental crisis?

Objective A cancer diagnosis during pregnancy may be considered as an emotional challengefor pregnant women and their partners. We aimed to identify women and partners at risk for highlevels of distress based on their coping profile.Methods Sixty‐one pregnant women diagnosed with cancer and their partners filled out theCognitive Emotion Regulation Questionnaire (CERQ) and the newly constructed Cancer andPregnancy Questionnaire (CPQ). K‐means cluster analysis was performed on the CERQ scales.Scores on the CPQ were compared between the women and their partners and between theCERQ‐clusters.Results Comparison of women and partners on the CPQ did not reveal significant differenceson distress about the child’s health, the cancer disease, and the pregnancy or on information sat-isfaction (P = .16, P = .44, P = .50, and P = .47, respectively). However, women were more inclinedto maintain the pregnancy than their partners (P = .011). Three clusters were retrieved based onthe CERQ scales, characterized by positive coping, internalizing coping, and blaming. Women andpartners using internalizing strategies had significantly higher scores on concerns about thechild’s health (P = .039), the disease and treatment (P (P = .009) compared with positive and blaming strategies. No cluster differences were foundfor information satisfaction (P = .71) and tendency to maintain the pregnancy (P = .35).Conclusion Women and partners using internalizing coping strategies deal with the highestlevels of distress and may benefit from additional psychosocial support.</div

Assessing the Effects of a Real-Life Contact Intervention on Prejudice Toward LGBT People

Prejudice against sexual and gender minorities (e.g., LGBT people) is quite prevalent and is harmful. We examined an existing-and often-used-contact intervention in pre-existing groups in an educational setting and assessed its effectiveness in reducing different forms of LGBT negativity. We focused particularly on modern LGBT negativity: a relatively subtle form of prejudice, involving ambivalence, denial, and/or the belief that there is too much attention for LGBT prejudice. We used a mixed design in which condition (experimental vs. control group) was the between-participants factor, which was randomized at the group level, and time (pretest vs. posttest vs. follow-up) was the within-participants factor (N = 117). Interventions were video recorded and the behavior of LGBT educators and participants was coded. Participants responded positively to the intervention, especially to the LGBT educator's "coming-out story." Exploratory analysis of the video data indicated that the perceived effectiveness of the intervention was higher in groups where participants were more engaged, although caution is necessary in interpreting this finding. The most important measure indicated that modern LGBT negativity decreased in the intervention groups directly after the intervention, but returned to baseline levels one week later. However, in the control condition, modern LGBT negativity had increased over time. Taken together, this suggests that an actual reduction in modern LGBT negativity was short-lived (i.e., the intervention effect disappeared within 7 days)

Performing DISCO-SCA to search for distinctive and common information in linked data

Behavioral researchers often obtain information about the same set of entities from different sources. A main challenge in the analysis of such data is to reveal, on the one hand, the mechanisms underlying all of the data blocks under study and, on the other hand, the mechanisms underlying a single data block or a few such blocks only (i.e., common and distinctive mechanisms, respectively). A method called DISCO-SCA has been proposed by which such mechanisms can be found. The goal of this article is to make the DISCO-SCA method more accessible, in particular for applied researchers. To this end, first we will illustrate the different steps in a DISCO-SCA analysis, with data stemming from the domain of psychiatric diagnosis. Second, we will present in this article the DISCO-SCA graphical user interface (GUI). The main benefits of the DISCO-SCA GUI are that it is easy to use, strongly facilitates the choice of model selection parameters (such as the number of mechanisms and their status as being common or distinctive), and is freely available. Keywords: Common and distinctive, Simultaneous component analysis, Rotation, Linked data, Graphical user interfac