The Gaussian graphical model in cross-sectional and time-series data

We discuss the Gaussian graphical model (GGM; an undirected network of partial correlation coefficients) and detail its utility as an exploratory data analysis tool. The GGM shows which variables predict one-another, allows for sparse modeling of covariance structures, and may highlight potential causal relationships between observed variables. We describe the utility in 3 kinds of psychological datasets: datasets in which consecutive cases are assumed independent (e.g., cross-sectional data), temporally ordered datasets (e.g., n = 1 time series), and a mixture of the 2 (e.g., n > 1 time series). In time-series analysis, the GGM can be used to model the residual structure of a vector-autoregression analysis (VAR), also termed graphical VAR. Two network models can then be obtained: a temporal network and a contemporaneous network. When analyzing data from multiple subjects, a GGM can also be formed on the covariance structure of stationary means---the between-subjects network. We discuss the interpretation of these models and propose estimation methods to obtain these networks, which we implement in the R packages graphicalVAR and mlVAR. The methods are showcased in two empirical examples, and simulation studies on these methods are included in the supplementary materials.Comment: Accepted pending revision in Multivariate Behavioral Researc

Witnessing and re-enacting in Cambodia: reflection on shifting testimonies

Thirty years after the collapse of the Khmer Rouge regime (1975-1979) how do Cambodians cope with the traumatic legacy of Pol Pot's reign of terror? What forms does witnessing take on in post-socialist and transitional Cambodia as senior Khmer Rouge leaders await prosecution at the Cambodian Tribunal? The paper examines aspects of witnessing in today's Cambodia, expressing each in its own way the idea of the 'shifting' of witnessing: the transformation of testimonies due to time passing and contrasted systems of justice through a comparison of testimonies in the trial of the 'Pol Pot/Ieng Sary clique' (1979) and the current Cambodian Tribunal; the complex forms of witnessing emerging from participatory projects developed with Western authors in 'We want (u) to know' (documentary movie made by an international film crew with the inhabitants of the village of Thnol Lok in 2009) and 'Breaking the silence' (theatre play realised by the Dutch dramaturge Annemarie Prins that premiered in Phnom Penh in 2009 and toured Cambodia in the following years); the relationship between documentary and legal forms of witnessing through the example of Vann Nath, a survivor of S-21/Tuol Sleng, the prison where the Khmer Rouge tortured and killed thousands of their fellow countrymen. The paper analyses the difficulty Western organisers of participatory projects experienced in applying the hybrid model of transitional justice to sociocultural contexts of witnessing. Nevertheless it points out their contribution to processes of 'recognition beyond recognition' in which cultural differences in coming to terms with historical trauma are expressed and recorded

Relating ASD symptoms to well-being:Moving across different construct levels

BACKGROUND: Little is known about the specific factors that contribute to the well-being (WB) of individuals with autism spectrum disorder (ASD). A plausible hypothesis is that ASD symptomatology has a direct negative effect on WB. In the current study, the emerging tools of network analysis allow to explore the functional interdependencies between specific symptoms of ASD and domains of WB in a multivariate framework. We illustrate how studying both higher-order (total score) and lower-order (subscale) representations of ASD symptomatology can clarify the interrelations of factors relevant for domains of WB. METHODS: We estimated network structures on three different construct levels for ASD symptomatology, as assessed with the Adult Social Behavior Questionnaire (item, subscale, total score), relating them to daily functioning (DF) and subjective WB in 323 adult individuals with clinically identified ASD (aged 17-70 years). For these networks, we assessed the importance of specific factors in the network structure. RESULTS: When focusing on the highest representation level of ASD symptomatology (i.e. a total score), we found a negative connection between ASD symptom severity and domains of WB. However, zooming in on lower representation levels of ASD symptomatology revealed that this connection was mainly funnelled by ASD symptoms related to insistence on sameness and experiencing reduced contact and that those symptom scales, in turn, impact different domains of WB. CONCLUSIONS: Zooming in across construct levels of ASD symptom severity into subscales of ASD symptoms can provide us with important insights into how specific domains of ASD symptoms relate to specific domains of DF and WB

Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Indexación: Web of Science; PubMedBackground Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6–8 mm berries (B68) phenological stages. Results A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0789-

Bayesian inference for psychology. Part II:Example applications with JASP

Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP (http://www.jasp-stats.org), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder’s BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away

Morphometric and gene expression analyses of stromal expansion during development of the bovine fetal ovary

During ovarian development stroma from the mesonephros penetrates and expands into the ovarian primordium and thus appears to be involved, at least physically, in the formation of ovigerous cords, follicles and surface epithelium. Cortical stromal development during gestation in bovine fetal ovaries (n = 27) was characterised by immunohistochemistry and by mRNA analyses. Stroma was identified by immunostaining of stromal matrix collagen type I and proliferating cells were identified by Ki67 expression. The cortical and medullar volume expanded across gestation, with the rate of cortical expansion slowing over time. During gestation, the proportion of stroma in the cortex and total volume in the cortex significantly increased (P  0.05). The expression levels of 12 genes out of 18 examined, including osteoglycin (OGN) and lumican (LUM), were significantly increased later in development (P < 0.05) and the expression of many genes was positively correlated with other genes and with gestational age. Thus, the rate of cortical stromal expansion peaked in early gestation due to cell proliferation, whilst late in development expression of extracellular matrix genes increased.M.D. Hartanti, A K. Hummitzsch, H.F. Irving-Rodgers, W.M. Bonner, K.J. Copping, R.A. Anderson, I.C. McMillen, V.E.A. Perry and R.J. Rodger

Time to get personal? The impact of researchers choices on the selection of treatment targets using the experience sampling methodology:The impact of researchers choices on the selection of treatment targets using the experience sampling methodology

OBJECTIVE: One of the promises of the experience sampling methodology (ESM) is that a statistical analysis of an individual’s emotions, cognitions and behaviors in everyday-life could be used to identify relevant treatment targets. A requisite for clinical implementation is that outcomes of such person-specific time-series analyses are not wholly contingent on the researcher performing them. METHODS: To evaluate this, we crowdsourced the analysis of one individual patient’s ESM data to 12 prominent research teams, asking them what symptom(s) they would advise the treating clinician to target in subsequent treatment. RESULTS: Variation was evident at different stages of the analysis, from preprocessing steps (e.g., variable selection, clustering, handling of missing data) to the type of statistics and rationale for selecting targets. Most teams did include a type of vector autoregressive model, examining relations between symptoms over time. Although most teams were confident their selected targets would provide useful information to the clinician, not one recommendation was similar: both the number (0–16) and nature of selected targets varied widely. CONCLUSION: This study makes transparent that the selection of treatment targets based on personalized models using ESM data is currently highly conditional on subjective analytical choices and highlights key conceptual and methodological issues that need to be addressed in moving towards clinical implementation

Exploring the psychology of suicidal ideation: A theory driven network analysis

Two leading theories within the field of suicide prevention are the interpersonal psychological theory of suicidal behaviour (IPT) and the integrated motivational-volitional (IMV) model. The IPT posits that suicidal thoughts emerge from high levels of perceived burdensomeness and thwarted belongingness. The IMV model is a multivariate framework that conceptualizes defeat and entrapment as key drivers of suicide ideation. We applied network analysis to cross-sectional data collected as part of the Scottish Wellbeing Study, in which a nationally representative sample of 3508 young adults (18–34 years) completed a battery of psychological measures. Network analysis can help us to understand how the different theoretical components interact and how they relate to suicide ideation. Within a network that included only the core factors from both models, internal entrapment and perceived burdensomeness were most strongly related to suicide ideation. The core constructs defeat, external entrapment and thwarted belonginess were mainly related to other factors than suicide ideation. Within the network of all available psychological factors, 12 of the 20 factors were uniquely related to suicide ideation, with perceived burdensomeness, internal entrapment, depressive symptoms and history of suicide ideation explaining the most variance. None of the factors was isolated, and we identified four larger clusters: mental wellbeing, interpersonal needs, personality, and suicide-related factors. Overall, the results suggest that relationships between suicide ideation and psychological risk factors are complex, with some factors contributing direct risk, and others having indirect impact