Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias

<div><p>The activity of neural populations in the brains of humans and animals can exhibit vastly different spatial patterns when faced with different tasks or environmental stimuli. The degrees of similarity between these neural activity patterns in response to different events are used to characterize the representational structure of cognitive states in a neural population. The dominant methods of investigating this similarity structure first estimate neural activity patterns from noisy neural imaging data using linear regression, and then examine the similarity between the estimated patterns. Here, we show that this approach introduces spurious bias structure in the resulting similarity matrix, in particular when applied to fMRI data. This problem is especially severe when the signal-to-noise ratio is low and in cases where experimental conditions cannot be fully randomized in a task. We propose Bayesian Representational Similarity Analysis (BRSA), an alternative method for computing representational similarity, in which we treat the covariance structure of neural activity patterns as a hyper-parameter in a generative model of the neural data. By marginalizing over the unknown activity patterns, we can directly estimate this covariance structure from imaging data. This method offers significant reductions in bias and allows estimation of neural representational similarity with previously unattained levels of precision at low signal-to-noise ratio, without losing the possibility of deriving an interpretable distance measure from the estimated similarity. The method is closely related to Pattern Component Model (PCM), but instead of modeling the estimated neural patterns as in PCM, BRSA models the imaging data directly and is suited for analyzing data in which the order of task conditions is not fully counterbalanced. The probabilistic framework allows for jointly analyzing data from a group of participants. The method can also simultaneously estimate a signal-to-noise ratio map that shows where the learned representational structure is supported more strongly. Both this map and the learned covariance matrix can be used as a structured prior for maximum <i>a posteriori</i> estimation of neural activity patterns, which can be further used for fMRI decoding. Our method therefore paves the way towards a more unified and principled analysis of neural representations underlying fMRI signals. We make our tool freely available in Brain Imaging Analysis Kit (BrainIAK).</p></div

A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulation for F2 in Ar

Laser pulse induced photodissociation of molecules in rare gas solids is investigated by representative quantum wavepackets or classical trajectories which are directed towards, or away from cage exits, yielding dominant photodissociation into different neighbouring cages. The directionality is determined by a sequence of reflections inside the relief provided by the slopes of the potential energy surface of the excited system, which in turn depend on the initial preparation of the matrix isolated system, e.g. by laser pulses with different frequencies or by vibrational pre-excitation of the cage atoms. This reflection principle is demonstrated for a simple, two-dimensional model of F2 in Ar

Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ultrashort Laser Pulses

The electronic excitation induced by ultrashort laser pulses and the subsequent photodissociation dynamics of molecular fluorine in an argon matrix are studied. The interactions of photofragments and host atoms are modeled using a Diatomics-In-Molecule Hamiltonian. Two types of methods are compared: Quantum-classical simulations where the nuclei are treated classically, with surface-hopping algorithms to describe either radiative or non-radiative transitions between different electronic states. Fully quantum-mechanical simulations, but for a model system of reduced dimensionality, in which the two most essential degrees of freedom are considered. Some of the main results are: The sequential energy transfer events from the photoexcited F2 into the lattice modes are such that the ``reduced dimensionality'' model is valid for the first 200 fs. This, in turn, allows us to use the quantum results to investigate the details of the excitation process with short laser pulses. Thus, it also serves as a reference for the quantum-classical ``surface hopping'' model of the excitation process. Moreover, it supports the validity of a laser pulse control strategy developed on the basis of the ``reduced dimensionality'' model. Both in the quantum and quantum-classical simulations, the separation of the F atoms following photodissociation does not exceed 20 bohr. The cage exit mechanisms appear qualitatively similar in the two sets of simulations but quantum effects are quantitatively important. Nonlinear effects are important in determining the photoexcitation yield. In summary, this paper demonstrates that quantum-classical simulations combined with reduced dimensionality quantum calculations can be a powerful approach to the analysis and control of the dynamics of complex systems

Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16?

竹食サル類の苦味感覚の進化を解明 --竹が先か苦味が先か--. 京都大学プレスリリース. 2021-04-16.Bitter taste facilitates the detection of potentially harmful substances and is perceived via bitter taste receptors (TAS2Rs) expressed on the tongue and oral cavity in vertebrates. In primates, TAS2R16 specifically recognizes β-glucosides, which are important in cyanogenic plants' use of cyanide as a feeding deterrent. In this study, we performed cell-based functional assays for investigating the sensitivity of TAS2R16 to β-glucosides in three species of bamboo lemurs (Prolemur simus, Hapalemur aureus and H. griseus), which primarily consume high-cyanide bamboo. TAS2R16 receptors from bamboo lemurs had lower sensitivity to β-glucosides, including cyanogenic glucosides, than that of the closely related ring-tailed lemur (Lemur catta). Ancestral reconstructions of TAS2R16 for the bamboo-lemur last common ancestor (LCA) and that of the Hapalemur LCA showed an intermediate sensitivity to β-glucosides between that of the ring-tailed lemurs and bamboo lemurs. Mutagenetic analyses revealed that P. simus and H. griseus had separate species-specific substitutions that led to reduced sensitivity. These results indicate that low sensitivity to β-glucosides at the cellular level-a potentially adaptive trait for feeding on cyanogenic bamboo-evolved independently after the Prolemur-Hapalemur split in each species

Prolonged dopamine signalling in striatum signals proximity and value of distant rewards

Predictions about future rewarding events have a powerful influence on behaviour. The phasic spike activity of dopamine-containing neurons, and corresponding dopamine transients in the striatum, are thought to underlie these predictions, encoding positive and negative reward prediction errors. However, many behaviours are directed towards distant goals, for which transient signals may fail to provide sustained drive. Here we report an extended mode of reward-predictive dopamine signalling in the striatum that emerged as rats moved towards distant goals. These dopamine signals, which were detected with fast-scan cyclic voltammetry (FSCV), gradually increased or—in rare instances—decreased as the animals navigated mazes to reach remote rewards, rather than having phasic or steady tonic profiles. These dopamine increases (ramps) scaled flexibly with both the distance and size of the rewards. During learning, these dopamine signals showed spatial preferences for goals in different locations and readily changed in magnitude to reflect changing values of the distant rewards. Such prolonged dopamine signalling could provide sustained motivational drive, a control mechanism that may be important for normal behaviour and that can be impaired in a range of neurologic and neuropsychiatric disorders.National Institutes of Health (U.S.) (Grant R01 MH060379)National Parkinson Foundation (U.S.)Cure Huntington’s Disease Initiative, Inc. (Grant A-5552)Stanley H. and Sheila G. Sydney Fun

Dietary Salt Levels Affect Salt Preference and Learning in Larval Drosophila

Drosophila larvae change from exhibiting attraction to aversion as the concentration of salt in a substrate is increased. However, some aversive concentrations appear to act as positive reinforcers, increasing attraction to an odour with which they have been paired. We test whether this surprising dissociation between the unconditioned and conditioned response depends on the larvae's experience of salt concentration in their food. We find that although the point at which a NaCl concentration becomes aversive shifts with different rearing experience, the dissociation remains evident. Testing larvae using a substrate 0.025M above the NaCl concentration on which the larvae were reared consistently results in aversive choice behaviour but appetitive reinforcement effects

Task Attention Facilitates Learning of Task-Irrelevant Stimuli

Attention plays a fundamental role in visual learning and memory. One highly established principle of visual attention is that the harder a central task is, the more attentional resources are used to perform the task and the smaller amount of attention is allocated to peripheral processing because of limited attention capacity. Here we show that this principle holds true in a dual-task setting but not in a paradigm of task-irrelevant perceptual learning. In Experiment 1, eight participants were asked to identify either bright or dim number targets at the screen center and to remember concurrently presented scene backgrounds. Their recognition performances for scenes paired with dim/hard targets were worse than those for scenes paired with bright/easy targets. In Experiment 2, eight participants were asked to identify either bright or dim letter targets at the screen center while a task-irrelevant coherent motion was concurrently presented in the background. After five days of training on letter identification, participants improved their motion sensitivity to the direction paired with hard/dim targets improved but not to the direction paired with easy/bright targets. Taken together, these results suggest that task-irrelevant stimuli are not subject to the attentional control mechanisms that task-relevant stimuli abide

Association between hMLH1 hypermethylation and JC virus (JCV) infection in human colorectal cancer (CRC)

Incorporation of viral DNA may interfere with the normal sequence of human DNA bases on the genetic level or cause secondary epigenetic changes such as gene promoter methylation or histone acetylation. Colorectal cancer (CRC) is the second leading cause of cancer mortality in the USA. Chromosomal instability (CIN) was established as the key mechanism in cancer development. Later, it was found that CRC results not only from the progressive accumulation of genetic alterations but also from epigenetic changes. JC virus (JCV) is a candidate etiologic factor in sporadic CRC. It may act by stabilizing β-catenin, facilitating its entrance to the cell nucleus, initialing proliferation and cancer development. Diploid CRC cell lines transfected with JCV-containing plasmids developed CIN. This result provides direct experimental evidence for the ability of JCV T-Ag to induce CIN in the genome of colonic epithelial cells. The association of CRC hMLH1 methylation and tumor positivity for JCV was recently documented. JC virus T-Ag DNA sequences were found in 77% of CRCs and are associated with promoter methylation of multiple genes. hMLH1 was methylated in 25 out of 80 CRC patients positive for T-Ag (31%) in comparison with only one out of 11 T-Ag negative cases (9%). Thus, JCV can mediate both CIN and aberrant methylation in CRC. Like other viruses, chronic infection with JCV may induce CRC by different mechanisms which should be further investigated. Thus, gene promoter methylation induced by JCV may be an important process in CRC and the polyp-carcinoma sequence

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase specificities toward their substrates and for designing substrate-like peptidic inhibitors. We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding. We focus on positions P−2 and P−5, commonly occupied by Arginine (Arg) in substrates of basophilic Ser/Thr kinases. The method accurately identified all the P−2/P−5 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide arrays. The predicted Arg-binding positions and their associated pockets were analyzed in terms of shape, physicochemical properties, amino acid composition, and in-silico mutagenesis, providing structural rationalization for previously unexplained trends in kinase preferences toward Arg moieties. This methodology sheds light on several kinases that were described in the literature as having non-trivial preferences for Arg, and provides some surprising departures from the prevailing views regarding residues that determine kinase specificity toward Arg. In particular, we found that the preference for a P−5 Arg is not necessarily governed by the 170/230 acidic pair, as was previously assumed, but by several different pairs of acidic residues, selected from positions 133, 169, and 230 (PKA numbering). The acidic residue at position 230 serves as a pivotal element in recognizing Arg from both the P−2 and P−5 positions

Altered Risk-Based Decision Making following Adolescent Alcohol Use Results from an Imbalance in Reinforcement Learning in Rats

Alcohol use during adolescence has profound and enduring consequences on decision-making under risk. However, the fundamental psychological processes underlying these changes are unknown. Here, we show that alcohol use produces over-fast learning for better-than-expected, but not worse-than-expected, outcomes without altering subjective reward valuation. We constructed a simple reinforcement learning model to simulate altered decision making using behavioral parameters extracted from rats with a history of adolescent alcohol use. Remarkably, the learning imbalance alone was sufficient to simulate the divergence in choice behavior observed between these groups of animals. These findings identify a selective alteration in reinforcement learning following adolescent alcohol use that can account for a robust change in risk-based decision making persisting into later life