A simple mechanistic explanation for original antigenic sin and its alleviation by adjuvants.

A large number of published studies have shown that adaptive immunity to a particular antigen, including pathogen-derived, can be boosted by another, cross-reacting antigen while inducing suboptimal immunity to the latter. Although this phenomenon, called original antigenic sin (OAS), was first reported approximately 70 years ago (Francis et al. 1947 Am.

Capturing spiral radial growth of conifers using the superellipse to model tree-ring geometric shape.

Tree-rings are often assumed to approximate a circular shape when estimating forest productivity and carbon dynamics. However, tree rings are rarely, if ever, circular, thereby possibly resulting in under- or over-estimation in forest productivity and carbon sequestration. Given the crucial role played by tree ring data in assessing forest productivity and carbon storage within a context of global change, it is particularly important that mathematical models adequately render cross-sectional area increment derived from tree rings.

DBSproc: An open source process for DBS electrode localization and tractographic analysis.

Deep brain stimulation (DBS) is an effective surgical treatment for movement disorders. Although stimulation sites for movement disorders such as Parkinson's disease are established, the therapeutic mechanisms of DBS remain controversial. Recent research suggests that specific white-matter tract and circuit activation mediates symptom relief.

ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations.

Motivation: Despite numerous successful Genome-wide Association Studies (GWAS), detecting variants that have low disease risk still poses a challenge. GWAS may miss disease genes with weak genetic effects or strong epistatic effects due to the single-marker testing approach commonly used. GWAS may thus generate false negative or inconclusive results, suggesting the need for novel methods to combine effects of single nucleotide polymorphisms within a gene to increase the likelihood of fully characterizing the susceptibility gene.

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

Summary: Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures.

Open Environment for Multimodal Interactive Connectivity Visualization and Analysis.

Brain connectivity investigations are becoming increasingly multimodal and they present challenges for quantitatively characterizing and interactively visualizing data. In this study, we present a new set of network-based software tools for combining functional and anatomical connectivity from magnetic resonance imaging (MRI) data. The computational tools are available as part of Functional and Tractographic Connectivity Analysis Toolbox (FATCAT), a toolbox that interfaces with Analysis of Functional NeuroImages (AFNI) and SUrface MApping (SUMA) for interactive queries and visualization.

An optimal proportion of mixing broad-leaved forest for enhancing the effective productivity of moso bamboo.

Moso bamboos (Phyllostachys edulis) are important forestry plants in southern China, with substantial roles to play in regional economic and ecological systems. Mixing broad-leaved forests and moso bamboos is a common management practice in China, and it is fundamental to elucidate the interactions between broad-leaved trees and moso bamboos for ensuring the sustainable provision of ecosystem services. We examine how the proportion of broad-leaved forest in a mixed managed zone, topology, and soil profile affects the effective productivity of moso bamboos (i.

A hybrid behavioural rule of adaptation and drift explains the emergent architecture of antagonistic networks.

Ecological processes that can realistically account for network architectures are central to our understanding of how species assemble and function in ecosystems. Consumer species are constantly selecting and adjusting which resource species are to be exploited in an antagonistic network. Here we incorporate a hybrid behavioural rule of adaptive interaction switching and random drift into a bipartite network model.

Functional topography of the thalamocortical system in human.

Various studies have indicated that the thalamus is involved in controlling both cortico-cortical information flow and cortical communication with the rest of the brain. Detailed anatomy and functional connectivity patterns of the thalamocortical system are essential to understanding the cortical organization and pathophysiology of a wide range of thalamus-related neurological and neuropsychiatric diseases. The current study used resting-state fMRI to investigate the topography of the human thalamocortical system from a functional perspective.

Joint analysis of BICEP2/keck array and Planck Data.

We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400  deg^{2} patch of sky centered on RA 0 h, Dec. -57.

Does small scale structure significantly affect cosmological dynamics?

The large-scale homogeneity and isotropy of the Universe is generally thought to imply a well-defined background cosmological model. It may not. Smoothing over structure adds in an extra contribution, transferring power from small scales up to large.

Effects of the transmissibility and virulence of pathogens on intraguild predation in fragmented landscapes.

It is well known that pathogenic infection can have a profound effect on the outcome of competition and predation, however the role of pathogenic infection in systems where predators and prey also compete for other resources is yet to be explored (i.e. in systems of intraguild predation).

Effects of agricultural intensification on ability of natural enemies to control aphids.

Agricultural intensification through increasing fertilization input and cropland expansion has caused rapid loss of semi-natural habitats and the subsequent loss of natural enemies of agricultural pests. It is however extremely difficult to disentangle the effects of agricultural intensification on arthropod communities at multiple spatial scales. Based on a two-year study of seventeen 1500 m-radius sites, we analyzed the relative importance of nitrogen input and cropland expansion on cereal aphids and their natural enemies.

Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?

The current increase in Gene Ontology (GO) annotations of proteins in the existing genome databases and their use in different analyses have fostered the improvement of several biomedical and biological applications. To integrate this functional data into different analyses, several protein functional similarity measures based on GO term information content (IC) have been proposed and evaluated, especially in the context of annotation-based measures. In the case of topology-based measures, each approach was set with a specific functional similarity measure depending on its conception and applications for which it was designed.

Fisheries-induced disruptive selection.

Commercial harvesting is recognized to induce adaptive responses of life-history traits in fish populations, in particular by shifting the age and size at maturation through directional selection. In addition to such evolution of a target stock, the corresponding fishery itself may adapt, in terms of fishing policy, technological progress, fleet dynamics, and adaptive harvest. The aim of this study is to assess how the interplay between natural and artificial selection, in the simplest setting in which a fishery and a target stock coevolve, can lead to disruptive selection, which in turn may cause trait diversification.

Anisotropic stress as a signature of nonstandard propagation of gravitational waves.

We make precise the heretofore ambiguous statement that anisotropic stress is a sign of a modification of gravity. We show that in cosmological solutions of very general classes of models extending gravity-all scalar-tensor theories (Horndeski), Einstein-aether models, and bimetric massive gravity-a direct correspondence exists between perfect fluids apparently carrying anisotropic stress and a modification in the propagation of gravitational waves. Since the anisotropic stress can be measured in a model-independent manner, a comparison of the behavior of gravitational waves from cosmological sources with large-scale-structure formation could, in principle, lead to new constraints on the theory of gravity.

Dynamical instability of a Bose-Einstein condensate with higher-order interactions in an optical potential through a variational approach.

We investigate the dynamical instability of Bose-Einstein condensates (BECs) with higher-order interactions immersed in an optical lattice with weak driving harmonic potential. For this, we compute both analytically and numerically a modified Gross-Pitaevskii equation with higher-order nonlinearity and external potentials generated by magnetic and optical fields. Using the time-dependent variational approach, we derive the ordinary differential equations for the time evolution of the amplitude and phase of modulational perturbation.

Zeta diversity as a concept and metric that unifies incidence-based biodiversity patterns.

Patterns in species incidence and compositional turnover are central to understanding what drives biodiversity. Here we propose zeta (ζ) diversity, the number of species shared by multiple assemblages, as a concept and metric that unifies incidence-based diversity measures, patterns, and relationships. Unlike other measures of species compositional turnover, zeta diversity partitioning quantifies the complete set of diversity components for multiple assemblages, comprehensively representing the spatial structure of multispecies distributions.

A DTI-based tractography study of effects on brain structure associated with prenatal alcohol exposure in newborns.

Prenatal alcohol exposure (PAE) is known to have severe, long-term consequences for brain and behavioral development already detectable in infancy and childhood. Resulting features of fetal alcohol spectrum disorders include cognitive and behavioral effects, as well as facial anomalies and growth deficits. Diffusion tensor imaging (DTI) and tractography were used to analyze white matter (WM) development in 11 newborns (age since conception <45 weeks) whose mothers were recruited during pregnancy.

Spatial assortment of mixed propagules explains the acceleration of range expansion.

Range expansion of spreading organisms has been found to follow three types: (i) linear expansion with a constant rate of spread; (ii) bi-phase expansion with a faster linear expansion following a slower linear expansion; and (iii) accelerating expansion with a continuously increasing rate of spread. To date, no overarching formula exists that can be applied to all three types of range expansion. We investigated how propagule pressure, i.

Niche construction on environmental gradients: the formation of fitness valley and stratified genotypic distributions.

The process of niche construction can alter the trajectory of natural selection through organism-environment feedback. As such, the mechanism and impact of niche construction can be better investigated along environmental gradients. Here we investigate how the process of niche construction affects the distribution of genotypes and fitness landscape along an environmental gradient under three selection regimes, namely heterozygote superiority, genetic loci which dictates niche construction ability being either selectively neutral or non-neutral.

The impact of land abandonment on species richness and abundance in the Mediterranean Basin: a meta-analysis.

Land abandonment is common in the Mediterranean Basin, a global biodiversity hotspot, but little is known about its impacts on biodiversity. To upscale existing case-study insights to the Pan-Mediterranean level, we conducted a meta-analysis of the effects of land abandonment on plant and animal species richness and abundance in agroforestry, arable land, pastures, and permanent crops of the Mediterranean Basin. In particular, we investigated (1) which taxonomic groups (arthropods, birds, lichen, vascular plants) are more affected by land abandonment; (2) at which spatial and temporal scales the effect of land abandonment on species richness and abundance is pronounced; (3) whether previous land use and current protected area status affect the magnitude of changes in the number and abundance of species; and (4) how prevailing landforms and climate modify the impacts of land abandonment.

Can topological defects mimic the BICEP2 B-mode signal?

We show that the B-mode polarization signal detected at low multipoles by BICEP2 cannot be entirely due to topological defects. This would be incompatible with the high-multipole B-mode polarization data and also with existing temperature anisotropy data. Adding cosmic strings to a model with tensors, we find that B modes on their own provide a comparable limit on the defects to that already coming from Planck satellite temperature data.

A mathematical model of the unidirectional block caused by the pulmonary veins for anatomically induced atrial reentry.

It is widely believed that the pulmonary veins (PVs) of the left atrium play the central role in the generation of anatomically induced atrial reentry but its mechanism has not been analytically explained. To understand this mechanism, a new analytic approach is proposed by adapting the geometric relative acceleration analysis from spacetime physics based on the hypothesis that a large relative acceleration can translate to a dramatic increase in the curvature of a wavefront and subsequently to conduction failure. By verifying the strong dependency of the propagational direction and the magnitude of anisotropy for conduction failure, this analytic method reveals that a unidirectional block can be generated by asymmetric propagation toward the PVs.