Cognitive Reactivity,Implicit Associations,and the Incidence of Depression: A Two-Year Prospective Study

Background

Cognitive reactivity to sad mood is a vulnerability marker of depression. Implicit self-depressed associations are related to depression status and reduced remission probability. It is unknown whether these cognitive vulnerabilities precede the first onset of depression.

Aim

To test the predictive value of cognitive reactivity and implicit self-depressed associations for the incidence of depressive disorders.

Methods

Prospective cohort study of 834 never-depressed individuals, followed over a two-year period. The predictive value of cognitive reactivity and implicit self-depressed associations for the onset of depressive disorders was assessed using binomial logistic regression. The multivariate model corrected for baseline levels of subclinical depressive symptoms, neuroticism, for the presence of a history of anxiety disorders, for family history of depressive or anxiety disorders, and for the incidence of negative life events.

Results

As single predictors, both cognitive reactivity and implicit self-depressed associations were significantly associated with depression incidence. In the multivariate model, cognitive reactivity was significantly associated with depression incidence, together with baseline depressive symptoms and the number of negative life events, whereas implicit self-depressed associations were not.

Conclusion

Cognitive reactivity to sad mood is associated with the incidence of depressive disorders, also when various other depression-related variables are controlled for. Implicit self-depressed associations predicted depression incidence in a bivariate test, but not when controlling for other predictors.     

Predators Reduce Extinction Risk in Noisy Metapopulations

Background

Spatial structure across fragmented landscapes can enhance regional population persistence by promoting local “rescue effects.” In small, vulnerable populations, where chance or random events between individuals may have disproportionately large effects on species interactions, such local processes are particularly important. However, existing theory often only describes the dynamics of metapopulations at regional scales, neglecting the role of multispecies population dynamics within habitat patches.

Findings

By coupling analysis across spatial scales we quantified the interaction between local scale population regulation, regional dispersal and noise processes in the dynamics of experimental host-parasitoid metapopulations. We find that increasing community complexity increases negative correlation between local population dynamics. A potential mechanism underpinning this finding was explored using a simple population dynamic model.

Conclusions

Our results suggest a paradox: parasitism, whilst clearly damaging to hosts at the individual level, reduces extinction risk at the population level.     

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms

Background

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly.

Methods/Findings

We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition.

Conclusions

A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the “ingredients” (species) in ecological communities but their “recipes” as well.     

Are the Healthy Behaviors of US High-Deductible Health Plan Enrollees Driven by People Who Chose These Plans? Smoking as a Case Study

Purpose

To determine whether negative associations between enrollment in a high-deductible health plan (HDHP) and one exemplar unhealthy behavior – daily smoking – are found only among people who chose these plans.

Design

Cross-sectional analysis of nationally-representative data.

Setting

United States from 2007 to 2008.

Subjects

6,941 privately insured non-elderly adult participants in the 2007 Health Tracking Household Survey.

Measures

Self-reported smoking status.

Analysis

We classified subjects as HDHP or traditional health plan enrollees with employer-sponsored insurance (ESI) and no choice of plans, ESI with a choice of plans, or coverage through the non-group market. We used multivariate logistic regression to measure associations between HDHP enrollment and daily smoking within each of the 3 coverage source groups while controlling for potential confounders.

Results

HDHP enrollment was associated with lower odds of smoking among individuals with ESI and a choice of plans (AOR 0.55, 95% CI 0.33–0.90) and those with non-group coverage (AOR 0.64, 95% CI 0.34–1.22), though the latter association was not statistically significant. HDHP enrollment was not associated with lower odds of smoking among individuals with ESI and no choice of plans (AOR 1.04, 95% CI 0.69–1.56).

Conclusions

HDHP enrollment is associated with lower odds of smoking only among individuals who chose to enroll in an HDHP. Lower rates of unhealthy behaviors among HDHP enrollees may be a reflection of individuals who choose these plans.     

Reaction Time and Incident Cancer: 25 Years of Follow-Up of Study Members in the UK Health and Lifestyle Survey

Objectives

To investigate the association of reaction time with cancer incidence.

Methods

6900 individuals aged 18 to 94 years who participated in the UK Health and Lifestyle Survey in 1984/1985 and were followed for a cancer registration for 25 years.

Results

Disease surveillance gave rise to 1015 cancer events from all sites. In general, there was essentially no clear pattern of association for either simple or choice reaction time with cancer of all sites combined, nor specific malignancies. However, selected associations were found for lung cancer, colorectal cancer and skin cancer.

Conclusions

In the present study, reaction time and its components were not generally related to cancer risk.     

A novel recursive algorithm for the calculation of the detailed identity coefficients

Background

A recursive algorithm to calculate the fifteen detailed coefficients of identity is introduced. Previous recursive procedures based on the generalized coefficients of kinship provided the detailed coefficients of identity under the assumption that the two individuals were not an ancestor of each other.

Findings

By using gametic relationships to include three, four or two pairs of gametes, we can obtain these coefficients for any pair of individuals. We have developed a novel linear transformation that allows for the calculation of pairwise detailed identity coefficients for any pedigree given the gametic relationships. We illustrate the procedure using the well-known pedigree of Julio and Mencha, which contains 20 Jicaque Indians of Honduras, to calculate their detailed coefficients.

Conclusions

The proposed algorithm can be used to calculate the detailed identity coefficients of two or more individuals with any pedigree relationship.     

Host lifestyle affects human microbiota on daily timescales

Background

Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities.

Results

Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically similar species. Still, even during periods of overall community stability, the dynamics of select microbial taxa could be associated with specific host behaviors. Most prominently, changes in host fiber intake positively correlated with next-day abundance changes among 15% of gut microbiota members.

Conclusions

Our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.

Electronic supplementary material

The online version of this article (doi:10.1186/gb-2014-15-7-r89) contains supplementary material, which is available to authorized users.     

Does Sex-Selective Predation Stabilize or Destabilize Predator-Prey Dynamics?

Background

Little is known about the impact of prey sexual dimorphism on predator-prey dynamics and the impact of sex-selective harvesting and trophy hunting on long-term stability of exploited populations.

Methodology and Principal Findings

We review the quantitative evidence for sex-selective predation and study its long-term consequences using several simple predator-prey models. These models can be also interpreted in terms of feedback between harvesting effort and population size of the harvested species under open-access exploitation. Among the 81 predator-prey pairs found in the literature, male bias in predation is 2.3 times as common as female bias. We show that long-term effects of sex-selective predation depend on the interplay of predation bias and prey mating system. Predation on the ‘less limiting’ prey sex can yield a stable predator-prey equilibrium, while predation on the other sex usually destabilizes the dynamics and promotes population collapses. For prey mating systems that we consider, males are less limiting except for polyandry and polyandrogyny, and male-biased predation alone on such prey can stabilize otherwise unstable dynamics. On the contrary, our results suggest that female-biased predation on polygynous, polygynandrous or monogamous prey requires other stabilizing mechanisms to persist.

Conclusions and Significance

Our modelling results suggest that the observed skew towards male-biased predation might reflect, in addition to sexual selection, the evolutionary history of predator-prey interactions. More focus on these phenomena can yield additional and interesting insights as to which mechanisms maintain the persistence of predator-prey pairs over ecological and evolutionary timescales. Our results can also have implications for long-term sustainability of harvesting and trophy hunting of sexually dimorphic species.     

Bigger Helpers in the Ant Cataglyphis bombycina: Increased Worker Polymorphism or Novel Soldier Caste?

Introduction

The mechanisms by which development favors or constrains the evolution of new phenotypes are incompletely understood. Polyphenic species may benefit from developmental plasticity not only regarding ecological advantages, but also potential for evolutionary diversification. For instance, the repeated evolution of novel castes in ants may have been facilitated by the existence of alternative queen and worker castes and their respective developmental programs.

Material and Methods

Cataglyphis bombycina is exceptional in its genus because winged queens and size-polymorphic workers occur together with bigger individuals having saber-shaped mandibles. We measured seven body parts in more than 150 individuals to perform a morphometric analysis and assess the developmental origin of this novel phenotype.

Results

Adults with saber-shaped mandibles differ from both workers and queens regarding the size of most body parts. Their relative growth rates are identical to workers for some pairs of body parts, and identical to queens for other pairs of body parts; critical sizes differ in all cases.

Conclusions

Big individuals are a third caste, i.e. soldiers, not major workers. Novel traits such as elongated mandibles are combined with a mix of queen and worker growth rates. We also reveal the existence of a dimorphism in the queen caste (microgynes and macrogynes). We discuss how novel phenotypes can evolve more readily in the context of an existing polyphenism. Both morphological traits and growth rules from existing queen and worker castes can be recombined, hence mosaic phenotypes are more likely to be viable. In C. bombycina, such a mosaic phenotype appears to function both for defense (saber-shaped mandibles) and fat storage (big abdomen). Recycling of developmental programs may have contributed to the morphological diversity and ecological success of ants.     

Phylogenetic analysis of local-scale tree soil associations in a lowland moist tropical forest

Background

Local plant-soil associations are commonly studied at the species-level, while associations at the level of nodes within a phylogeny have been less well explored. Understanding associations within a phylogenetic context, however, can improve our ability to make predictions across systems and can advance our understanding of the role of evolutionary history in structuring communities.

Methodology/Principal Findings

Here we quantified evolutionary signal in plant-soil associations using a DNA sequence-based community phylogeny and several soil variables (e.g., extractable phosphorus, aluminum and manganese, pH, and slope as a proxy for soil water). We used published plant distributional data from the 50-ha plot on Barro Colorado Island (BCI), Republic of Panamá. Our results suggest some groups of closely related species do share similar soil associations. Most notably, the node shared by Myrtaceae and Vochysiaceae was associated with high levels of aluminum, a potentially toxic element. The node shared by Apocynaceae was associated with high extractable phosphorus, a nutrient that could be limiting on a taxon specific level. The node shared by the large group of Laurales and Magnoliales was associated with both low extractable phosphorus and with steeper slope. Despite significant node-specific associations, this study detected little to no phylogeny-wide signal. We consider the majority of the ‘traits’ (i.e., soil variables) evaluated to fall within the category of ecological traits. We suggest that, given this category of traits, phylogeny-wide signal might not be expected while node-specific signals can still indicate phylogenetic structure with respect to the variable of interest.

Conclusions

Within the BCI forest dynamics plot, distributions of some plant taxa are associated with local-scale differences in soil variables when evaluated at individual nodes within the phylogenetic tree, but they are not detectable by phylogeny-wide signal. Trends highlighted in this analysis suggest how plant-soil associations may drive plant distributions and diversity at the local-scale.     

MOSBIE: a tool for comparison and analysis of rule-based biochemical models

Background

Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presents significant challenges that range from identifying structural similarities and differences between models to understanding how these differences affect system dynamics.

Results

We present the development and features of an interactive model exploration system, MOSBIE, which provides utilities for identifying similarities and differences between models within a family. Models are clustered using a custom similarity metric, and a visual interface is provided that allows a researcher to interactively compare the structures of pairs of models as well as view simulation results.

Conclusions

We illustrate the usefulness of MOSBIE via two case studies in the cell signaling domain. We also present feedback provided by domain experts and discuss the benefits, as well as the limitations, of the approach.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-316) contains supplementary material, which is available to authorized users.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

Quantifying the Role of Adverse Events in the Mortality Difference between First and Second-Generation Antipsychotics in Older Adults: Systematic Review and Meta-Synthesis

Background

Observational studies have reported higher mortality among older adults treated with first-generation antipsychotics (FGAs) versus second-generation antipsychotics (SGAs). A few studies examined risk for medical events, including stroke, ventricular arrhythmia, venous thromboembolism, myocardial infarction, pneumonia, and hip fracture.

Objectives

1) Review robust epidemiologic evidence comparing mortality and medical event risk between FGAs and SGAs in older adults; 2) Quantify how much these medical events explain the observed mortality difference between FGAs and SGAs.

Data sources

Pubmed and Science Citation Index.

Study eligibility criteria, participants, and interventions

Studies of antipsychotic users that: 1) evaluated mortality or medical events specified above; 2) restricted to populations with a mean age of 65 years or older 3) compared FGAs to SGAs, or both to a non-user group; (4) employed a “new user” design; (5) adjusted for confounders assessed prior to antipsychotic initiation; (6) and did not require survival after antipsychotic initiation. A separate search was performed for mortality estimates associated with the specified medical events.

Study appraisal and synthesis methods

For each medical event, we used a non-parametric model to estimate lower and upper bounds for the proportion of the mortality difference—comparing FGAs to SGAs—mediated by their difference in risk for the medical event.

Results

We provide a brief, updated summary of the included studies and the biological plausibility of these mechanisms. Of the 1122 unique citations retrieved, we reviewed 20 observational cohort studies that reported 28 associations. We identified hip fracture, stroke, myocardial infarction, and ventricular arrhythmias as potential intermediaries on the causal pathway from antipsychotic type to death. However, these events did not appear to explain the entire mortality difference.

Conclusions

The current literature suggests that hip fracture, stroke, myocardial infarction, and ventricular arrhythmias partially explain the mortality difference between SGAs and FGAs.     

Time-ordered networks reveal limitations to information flow in ant colonies

Background

An important function of many complex networks is to inhibit or promote the transmission of disease, resources, or information between individuals. However, little is known about how the temporal dynamics of individual-level interactions affect these networks and constrain their function. Ant colonies are a model comparative system for understanding general principles linking individual-level interactions to network-level functions because interactions among individuals enable integration of multiple sources of information to collectively make decisions, and allocate tasks and resources.

Methodology/Findings

Here we show how the temporal and spatial dynamics of such individual interactions provide upper bounds to rates of colony-level information flow in the ant Temnothorax rugatulus. We develop a general framework for analyzing dynamic networks and a mathematical model that predicts how information flow scales with individual mobility and group size.

Conclusions/Significance

Using thousands of time-stamped interactions between uniquely marked ants in four colonies of a range of sizes, we demonstrate that observed maximum rates of information flow are always slower than predicted, and are constrained by regulation of individual mobility and contact rate. By accounting for the ordering and timing of interactions, we can resolve important difficulties with network sampling frequency and duration, enabling a broader understanding of interaction network functioning across systems and scales.     

‘When Birds of a Feather Flock Together’: Synesthetic Correspondences Modulate Audiovisual Integration in Non-Synesthetes

Background

Synesthesia is a condition in which the stimulation of one sense elicits an additional experience, often in a different (i.e., unstimulated) sense. Although only a small proportion of the population is synesthetic, there is growing evidence to suggest that neurocognitively-normal individuals also experience some form of synesthetic association between the stimuli presented to different sensory modalities (i.e., between auditory pitch and visual size, where lower frequency tones are associated with large objects and higher frequency tones with small objects). While previous research has highlighted crossmodal interactions between synesthetically corresponding dimensions, the possible role of synesthetic associations in multisensory integration has not been considered previously.

Methodology

Here we investigate the effects of synesthetic associations by presenting pairs of asynchronous or spatially discrepant visual and auditory stimuli that were either synesthetically matched or mismatched. In a series of three psychophysical experiments, participants reported the relative temporal order of presentation or the relative spatial locations of the two stimuli.

Principal Findings

The reliability of non-synesthetic participants'' estimates of both audiovisual temporal asynchrony and spatial discrepancy were lower for pairs of synesthetically matched as compared to synesthetically mismatched audiovisual stimuli.

Conclusions

Recent studies of multisensory integration have shown that the reduced reliability of perceptual estimates regarding intersensory conflicts constitutes the marker of a stronger coupling between the unisensory signals. Our results therefore indicate a stronger coupling of synesthetically matched vs. mismatched stimuli and provide the first psychophysical evidence that synesthetic congruency can promote multisensory integration. Synesthetic crossmodal correspondences therefore appear to play a crucial (if unacknowledged) role in the multisensory integration of auditory and visual information.     

Temperament clusters in a normal population: implications for health and disease

Background

The object of this study was to identify temperament patterns in the Finnish population, and to determine the relationship between these profiles and life habits, socioeconomic status, and health.

Methods/Principal Findings

A cluster analysis of the Temperament and Character Inventory subscales was performed on 3,761 individuals from the Northern Finland Birth Cohort 1966 and replicated on 2,097 individuals from the Cardiovascular Risk in Young Finns study. Clusters were formed using the k-means method and their relationship with 115 variables from the areas of life habits, socioeconomic status and health was examined.

Results

Four clusters were identified for both genders. Individuals from Cluster I are characterized by high persistence, low extravagance and disorderliness. They have healthy life habits, and lowest scores in most of the measures for psychiatric disorders. Cluster II individuals are characterized by low harm avoidance and high novelty seeking. They report the best physical capacity and highest level of income, but also high rate of divorce, smoking, and alcohol consumption. Individuals from Cluster III are not characterized by any extreme characteristic. Individuals from Cluster IV are characterized by high levels of harm avoidance, low levels of exploratory excitability and attachment, and score the lowest in most measures of health and well-being.

Conclusions

This study shows that the temperament subscales do not distribute randomly but have an endogenous structure, and that these patterns have strong associations to health, life events, and well-being.     

Temporal variability is a personalized feature of the human microbiome

Background

It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over 3 months.

Results

We found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were more stable in composition than individuals with less diverse communities.

Conclusions

Longitudinal sampling of a relatively large number of individuals allowed us to observe high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status. Furthermore, our findings show that, not only is the composition of an individual’s microbiome highly personalized, but their degree of temporal variability is also a personalized feature.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0531-y) contains supplementary material, which is available to authorized users.     

A differential network approach to exploring differences between biological states: an application to prediabetes

Background

Variations in the pattern of molecular associations are observed during disease development. The comprehensive analysis of molecular association patterns and their changes in relation to different physiological conditions can yield insight into the biological basis of disease-specific phenotype variation.

Methodology

Here, we introduce a formal statistical method for the differential analysis of molecular associations via network representation. We illustrate our approach with extensive data on lipoprotein subclasses measured by NMR spectroscopy in 4,406 individuals with normal fasting glucose, and 531 subjects with impaired fasting glucose (prediabetes). We estimate the pair-wise association between measures using shrinkage estimates of partial correlations and build the differential network based on this measure of association. We explore the topological properties of the inferred network to gain insight into important metabolic differences between individuals with normal fasting glucose and prediabetes.

Conclusions/Significance

Differential networks provide new insights characterizing differences in biological states. Based on conventional statistical methods, few differences in concentration levels of lipoprotein subclasses were found between individuals with normal fasting glucose and individuals with prediabetes. By performing the differential analysis of networks, several characteristic changes in lipoprotein metabolism known to be related to diabetic dyslipidemias were identified. The results demonstrate the applicability of the new approach to identify key molecular changes inaccessible to standard approaches.