Visualising and modelling changes in categorical variables in longitudinal studies

Background: Graphical techniques can provide visually compelling insights into complex data patterns. In this paper we present a type of lasagne plot showing changes in categorical variables for participants measured at regular intervals over time and propose statistical models to estimate distributions of marginal and transitional probabilities. Methods. The plot uses stacked bars to show the distribution of categorical variables at each time interval, with different colours to depict different categories and changes in colours showing trajectories of participants over time. The models are based on nominal logistic regression which is appropriate for both ordinal and nominal categorical variables. To illustrate the plots and models we analyse data on smoking status, body mass index (BMI) and physical activity level from a longitudinal study on women's health. To estimate marginal distributions we fit survey wave as an explanatory variable whereas for transitional distributions we fit status of participants (e.g. smoking status) at previous surveys. Results: For the illustrative data the marginal models showed BMI increasing, physical activity decreasing and smoking decreasing linearly over time at the population level. The plots and transition models showed smoking status to be highly predictable for individuals whereas BMI was only moderately predictable and physical activity was virtually unpredictable. Most of the predictive power was obtained from participant status at the previous survey. Predicted probabilities from the models mostly agreed with observed probabilities indicating adequate goodness-of-fit. Conclusions: The proposed form of lasagne plot provides a simple visual aid to show transitions in categorical variables over time in longitudinal studies. The suggested models complement the plot and allow formal testing and estimation of marginal and transitional distributions. These simple tools can provide valuable insights into categorical data on individuals measured at regular intervals over time

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

BACKGROUND: There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. RESULTS: The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC) varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. CONCLUSION: The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are a

A functional polymorphism of the MAOA gene is associated with neural responses to induced anger control

Aggressiveness is highly heritable. Recent experimental work has linked individual differences in a functional polymorphism of the monoamine oxidase-A gene (MAOA) to anger-driven aggression. Other work has implicated the dorsal ACC (dACC) in cognitive-emotional control and the amygdala in emotional arousal. The present imaging genetics study investigated dACC and amygdala reactivity to induced anger control as a function of MAOA genotype. A research assistant asked 38 healthy male undergraduates to control their anger in response to an insult by a rude experimenter. Men with the low-expression allele showed increased dACC and amygdala activation after the insult, but men with the high-expression allele did not. Both dACC and amygdala activation independently mediated the relationship between MAOA genotype and self-reported anger control. Moreover, following the insult, men with the high-functioning allele showed functional decoupling between the amygdala and dACC, but men with the low-functioning allele did not. These results suggest that heightened dACC and amygdala activation and their connectivity are neuroaffective mechanisms underlying anger control in participants with the low-functioning allele of the MAOA gene

Late gadolinium enhancement and adverse outcomes in a contemporary cohort of adult survivors of tetralogy of Fallot

Objective: Myocardial fibrosis has been associated with poorer outcomes in tetralogy of Fallot, however only a handful of studies have assessed its significance in the current era. Our aim was to quantify the amount of late gadolinium enhancement in both the LV and RV in a contemporary cohort of adults with surgically repaired tetralogy of Fallot, and assess the relationship with adverse clinical outcomes. Design: Single centre cohort study Setting: National tertiary referral center Patients: One hundred fourteen patients with surgically repaired tetralogy of Fallot with median age 29.5 years (range 17.5-64.2). Prospective follow-up for mean 2.4 years (SD 1.29). Interventions: Cardiovascular magnetic resonance was performed, and late gadolinium enhancement mass was estimated for the LV using the 5-SD remote myocardium method, and for the RV using a segmental scoring system. Cohort characterization was determined through the use of a computerized database. Outcome measures: Survival analysis from time of scan to first adverse event, defined as an episode of atrial arrhythmia, sustained ventricular arrhythmia, hospitalization with heart failure, or implantable cardioverter-defibrillator insertion. Results: Eleven patients experienced an adverse outcome in the follow-up period, although there were no deaths. LV late gadolinium enhancement was associated with adverse outcomes in a univariate model (P = .027). However, when adjusted for age at scan the significant variables included NYHA class (P = .006), peak oxygen uptake (P = .028), number of prior sternotomies (P = .044), and higher indexed RV and LV end diastolic volumes (P = .002 and P < .001), but not RV or LV late gadolinium enhancement. Conclusions: Formal quantification of late gadolinium enhancement is not currently as helpful in ascertaining prognosis compared to other, more easily assessed parameters in a contemporary cohort of tetralogy of Fallot survivors, however assessment particularly of the LV holds promise for the future

Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus

Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission

Temporal Evolution of Multiday, Epileptic Functional Networks Prior to Seizure Occurrence

Epilepsy is one of the most common neurological disorders, characterized by the occurrence of repeated seizures. Given that epilepsy is considered a network disorder, tools derived from network neuroscience may confer the valuable ability to quantify the properties of epileptic brain networks. In this study, we use well-established brain network metrics (i.e., mean strength, variance of strength, eigenvector centrality, betweenness centrality) to characterize the temporal evolution of epileptic functional networks over several days prior to seizure occurrence. We infer the networks using long-term electroencephalographic recordings from 12 people with epilepsy. We found that brain network metrics are variable across days and show a circadian periodicity. In addition, we found that in 9 out of 12 patients the distribution of the variance of strength in the day (or even two last days) prior to seizure occurrence is significantly different compared to the corresponding distributions on all previous days. Our results suggest that brain network metrics computed fromelectroencephalographic recordings could potentially be used to characterize brain network changes that occur prior to seizures, and ultimately contribute to seizure warning systems

SLC2A9 Is a High-Capacity Urate Transporter in Humans

Serum uric acid levels in humans are influenced by diet, cellular breakdown, and renal elimination, and correlate with blood pressure, metabolic syndrome, diabetes, gout, and cardiovascular disease. Recent genome-wide association scans have found common genetic variants of SLC2A9 to be associated with increased serum urate level and gout. The SLC2A9 gene encodes a facilitative glucose transporter, and it has two splice variants that are highly expressed in the proximal nephron, a key site for urate handling in the kidney. We investigated whether SLC2A9 is a functional urate transporter that contributes to the longstanding association between urate and blood pressure in man

Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations

Hypertension is a complex disease that affects a large proportion of adult population. Although approximately half of the inter-individual variance in blood pressure (BP) level is heritable, identification of genes responsible for its regulation has remained challenging. Genome-wide association study (GWAS) is a novel approach to search for genetic variants contributing to complex diseases. We conducted GWAS for three BP traits [systolic and diastolic blood pressure (SBP and DBP); hypertension (HYP)] in the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) S3 cohort (n = 1644) recruited from general population in Southern Germany. GWAS with 395 912 single nucleotide polymorphisms (SNPs) identified an association between BP traits and a common variant rs11646213 (T/A) upstream of the CDH13 gene at 16q23.3. The initial associations with HYP and DBP were confirmed in two other European population-based cohorts: KORA S4 (Germans) and HYPEST (Estonians). The associations between rs11646213 and three BP traits were replicated in combined analyses (dominant model: DBP, P = 5.55 × 10–5, effect –1.40 mmHg; SBP, P = 0.007, effect –1.56 mmHg; HYP, P = 5.30 × 10−8, OR = 0.67). Carriers of the minor allele A had a decreased risk of hypertension. A non-significant trend for association was also detected with severe family based hypertension in the BRIGHT sample (British). The novel susceptibility locus, CDH13, encodes for an adhesion glycoprotein T-cadherin, a regulator of vascular wall remodeling and angiogenesis. Its function is compatible with the BP biology and may improve the understanding of the pathogenesis of hypertension