Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems.

Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature include the effectively one-dimensional escape characteristic of influenza A and the prolonged coexistence of lineages in influenza B.

Detecting T cell receptors involved in immune responses from single repertoire snapshots.

Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens. Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations. We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders - patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine).

In-Situ Growth of Gadolinium Phthalocyaninato Sandwich Complexes on the Ag(111) Surface.

We report a low-temperature scanning tunneling microscopy investigation of the in-situ growth of gadolinium phthalocyaninato complexes by combined deposition of free-base phthalocyanines and gadolinium atoms on a smooth Ag(111) substrate. A careful control of the stoichiometry allows the expression of a multilevel structurecomposed of irregularly distributed Gd (Pc) complexes, x=2-5, thus paving new avenues for surface-confined columnar growth.

Macroscopic phase resetting-curves determine oscillatory coherence and signal transfer in inter-coupled neural circuits.

Macroscopic oscillations of different brain regions show multiple phase relationships that are persistent across time and have been implicated in routing information. While multiple cellular mechanisms influence the network oscillatory dynamics and structure the macroscopic firing motifs, one of the key questions is to identify the biophysical neuronal and synaptic properties that permit such motifs to arise. A second important issue is how the different neural activity coherence states determine the communication between the neural circuits.

Reduced Fading of Visual Afterimages after Transcranial Magnetic Stimulation over Early Visual Cortex.

In the complete absence of small transients in visual inputs (e.g., by experimentally stabilizing an image on the retina or in everyday life during intent staring), information perceived by the eyes will fade from the perceptual experience.

Receptor crosstalk improves concentration sensing of multiple ligands.

Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway.

Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition.

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-mediated immunity in bacteria allows bacterial populations to protect themselves against pathogens. However, it also exposes them to the dangers of auto-immunity by developing protection that targets its own genome. Using a simple model of the coupled dynamics of phage and bacterial populations, we explore how acquisition rates affect the probability of the bacterial colony going extinct.

Studying the Real-Time Interpretation of Novel Noun and Verb Meanings in Young Children.

Decades of research show that children rely on the linguistic context in which novel words occur to infer their meanings. However, because learning in these studies was assessed after children had heard numerous occurrences of a novel word in informative linguistic contexts, it is impossible to determine how much exposure would be needed for a child to learn from such information. This study investigated the speed with which French 20-month-olds and 3-to-4-year-olds exploit function words to determine the syntactic category of novel words and therefore infer their meanings.

A new counterintuitive training for adult amblyopia.

Objectives: The aim of this study was to investigate whether short-term inverse occlusion, combined with moderate physical exercise, could promote the recovery of visual acuity and stereopsis in a group of adult anisometropic amblyopes.

Methods: Ten adult anisometropic patients underwent six brief (2 h) training sessions over a period of 4 weeks. Each training session consisted in the occlusion of the amblyopic eye combined with physical exercise (intermittent cycling on a stationary bike).

Minimal Circuit Model of Reward Prediction Error Computations and Effects of Nicotinic Modulations.

Dopamine (DA) neurons in the ventral tegmental area (VTA) are thought to encode reward prediction errors (RPE) by comparing actual and expected rewards. In recent years, much work has been done to identify how the brain uses and computes this signal. While several lines of evidence suggest the interplay of the DA and the inhibitory interneurons in the VTA implements the RPE computation, it still remains unclear how the DA neurons learn key quantities, for example the amplitude and the timing of primary rewards during conditioning tasks.

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs.

Motivation: High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level.

Generalized Cross-Frequency Decomposition: A Method for the Extraction of Neuronal Components Coupled at Different Frequencies.

Perceptual, motor and cognitive processes are based on rich interactions between remote regions in the human brain. Such interactions can be carried out through phase synchronization of oscillatory signals. Neuronal synchronization has been primarily studied within the same frequency range, e.

Dynamical ventral tegmental area circuit mechanisms of alcohol-dependent dopamine release.

A large body of data has identified numerous molecular targets through which ethanol (EtOH) acts on brain circuits. Yet how these multiple mechanisms interact to result in dysregulated dopamine (DA) release under the influence of alcohol in vivo remains unclear. In this manuscript, we delineate potential circuit-level mechanisms responsible for EtOH-dependent dysregulation of DA release from the ventral tegmental area (VTA) into its projection areas.

A Simple Model for Low Variability in Neural Spike Trains.

Neural noise sets a limit to information transmission in sensory systems. In several areas, the spiking response (to a repeated stimulus) has shown a higher degree of regularity than predicted by a Poisson process. However, a simple model to explain this low variability is still lacking.

High-frequency forced oscillations in neuronlike elements.

We analyzed a generic relaxation oscillator under moderately strong forcing at a frequency much greater that the natural intrinsic frequency of the oscillator. Additionally, the forcing is of the same sign and, thus, has a nonzero average, matching neuroscience applications. We found that, first, the transition to high-frequency synchronous oscillations occurs mostly through periodic solutions with virtually no chaotic regimes present.

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination.

Despite the extreme diversity of T-cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as "public," have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection.

Macroscopic phase-resetting curves for spiking neural networks.

The study of brain rhythms is an open-ended, and challenging, subject of interest in neuroscience. One of the best tools for the understanding of oscillations at the single neuron level is the phase-resetting curve (PRC). Synchronization in networks of neurons, effects of noise on the rhythms, effects of transient stimuli on the ongoing rhythmic activity, and many other features can be understood by the PRC.

Sensory noise predicts divisive reshaping of receptive fields.

In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals.

Dopamine Neurons Change the Type of Excitability in Response to Stimuli.

The dynamics of neuronal excitability determine the neuron's response to stimuli, its synchronization and resonance properties and, ultimately, the computations it performs in the brain. We investigated the dynamical mechanisms underlying the excitability type of dopamine (DA) neurons, using a conductance-based biophysical model, and its regulation by intrinsic and synaptic currents. Calibrating the model to reproduce low frequency tonic firing results in N-methyl-D-aspartate (NMDA) excitation balanced by γ-Aminobutyric acid (GABA)-mediated inhibition and leads to type I excitable behavior characterized by a continuous decrease in firing frequency in response to hyperpolarizing currents.