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PubMed2002

Context-specific Bayesian clustering for gene expression data.

The recent growth in genomic data and measurements of genome-wide expression patterns allows us to apply computational tools to examine gene regulation by transcription factors. In this work, we present a class of mathematical models that help in understanding the connections between transcription factors and functional classes of genes based on genetic and genomic data. Such a model represents the joint distribution of transcription factor binding sites and of expression levels of a gene in a unified probabilistic model. Learning a combined probability model of binding sites and expression patterns enables us to improve the clustering of the genes based on the discovery of putative binding sites and to detect which binding sites and experiments best characterize a cluster. To learn such models from data, we introduce a new search method that rapidly learns a model according to a Bayesian score. We evaluate our method on synthetic data as well as on real life data and analyze the biological insights it provides. Finally, we demonstrate the applicability of the method to other data analysis problems in gene expression data.

Bayes Theorem↗
PubMed2005

Concurrent administration of coenzyme Q10 and alpha-tocopherol improves learning in aged mice.

The main purpose of this study was to determine whether supplemental intake of coenzyme Q10 (CoQ) (ubiquinone-10) or alpha-tocopherol, either alone or together, could improve brain function of aged mice, as reflected in their cognitive or psychomotor performance. Separate groups of aged mice (24 months) were administered either CoQ (123 mg/kg/day), or alpha-tocopherol acetate (200 mg/kg/day), or both, or the vehicle (soybean oil) via gavage for a period of 14 weeks. Three weeks following the initiation of these treatments, mice were given a battery of age-sensitive behavioral tests for the assessment of learning, recent memory, and psychomotor function. In a test that required the mice to rapidly identify and remember the correct arm of a T-maze, and to respond preemptively in order to avoid an electric shock, the intake of alpha-tocopherol plus CoQ resulted in more rapid learning compared to the control group. Learning was not significantly improved in the mice receiving CoQ or alpha-tocopherol alone. None of the treatments resulted in a significant improvement of psychomotor performance in the old mice. In a separate study, treatment with higher doses of CoQ alone (250 or 500 mg/kg/day) for 14 weeks failed to produce effects comparable to those of the combination of alpha-tocopherol and CoQ. The apparent interaction of CoQ and alpha-tocopherol treatments is consistent with the previous suggestion, based on biochemical studies, that coenzyme Q and alpha-tocopherol act in concert. Overall, the findings suggest that concurrent supplementation of alpha-tocopherol with CoQ is more likely to be effective as a potential treatment for age-related learning deficits than supplementation with CoQ or alpha-tocopherol alone.

Aging↗
PubMedDate not supplied

Sensitivity to word order cues by normal and language/learning disabled adults.

UNLABELLED: Sixteen adults with language/learning disabilities (L/LD) and 16 adults who lacked a personal or familial history of L/LD participated in a study designed to test sensitivity to word order cues that signaled grammatical versus ungrammatical word strings belonging to an artificial grammar. In an exposure phase, participants heard word strings constructed of novel CVC words for a period of 5 min. In a test phase, participants were asked to judge new sentences as either obeying or violating the rules of the grammar they heard. L/LD participants performed significantly below the comparison group on this task. The results suggest that this skill, which emerges early in life for normal children, is problematic for adults with L/LD. LEARNING OUTCOMES: The reader will become familiar with a paradigm that allows assessment of rapid learning of word order rules and how this learning differs for normal and language/learning disabled adults.

Adolescent↗
PubMed1995

Why there are complementary learning systems in the hippocampus and neocortex: insights from the successes and failures of connectionist models of learning and memory.

Damage to the hippocampal system disrupts recent memory but leaves remote memory intact. The account presented here suggests that memories are first stored via synaptic changes in the hippocampal system, that these changes support reinstatement of recent memories in the neocortex, that neocortical synapses change a little on each reinstatement, and that remote memory is based on accumulated neocortical changes. Models that learn via changes to connections help explain this organization. These models discover the structure in ensembles of items if learning of each item is gradual and interleaved with learning about other items. This suggests that the neocortex learns slowly to discover the structure in ensembles of experiences. The hippocampal system permits rapid learning of new items without disrupting this structure, and reinstatement of new memories interleaves them with others to integrate them into structured neocortical memory systems.

Amnesia, Retrograde↗
PubMed2002

Learning to see the trees before the forest: reversible deactivation of the superior colliculus during learning of local and global visual features.

Previous studies have established that deactivation of the superior colliculus severely retards the normally rapid learning of pattern discriminations in the mature cat. The purpose of this study was to test the hypothesis that the midbrain plays an important role in the learning of simple pattern discriminations and that the contribution of this pathway is to the perception of global, rather than local, features of a figure. To answer this question, pattern discrimination learning was studied in three intact cats and in three experimental cats during bilateral reversible deactivation of the superficial layers of the superior colliculus (SC). The animals concurrently learned to discriminate three pairs of compound visual patterns composed of small (local element) Ts or 7s. Congruent and incongruent stimulus pairs were large (global) Ts vs. 7s comprising the same or different local elements, respectively. The random stimulus pair consisted of randomly scattered local elements (Ts vs. 7s). The animals were trained to respond to the large Ts in the congruent and incongruent pairs and the small Ts in the random pair. In the normal cats, learning of the random pair was much slower than the learning of the congruent and incongruent pairs. This finding demonstrated the theory of global precedence, because the animals learned the global features of the congruent and incongruent pairs much more quickly than the local features of the random pair. In contrast, during bilateral deactivation of the superficial layers of the SC, the learning of the incongruent pair was significantly retarded and took longer to learn than the random pair. Congruent and random pair learning rates were unchanged. The specific deficit in learning the incongruent pair indicates that the learning of global, but not local, elements of the visual pattern is impaired during deactivation of the SC. The unimpaired use of local features permitted the animals to learn the congruent and random pairs at normal rates. Therefore, deactivation of the superficial layers of the SC during pattern discrimination learning reverses the precedence for global visual features that is typical of normal learning.

Animals↗
PubMed2004

Levels of abstraction in orangutan (Pongo abelii) categorization.

Levels of abstraction have rarely been manipulated in studies of natural concept formation in nonhumans. Isolated examples have indicated that animals, relative to humans, may learn concepts at varying levels of abstraction with differential ease. The ability of 6 orangutans (Pongo abelii) of various ages to make natural concept discriminations at 3 levels of abstraction was therefore investigated. The orangutans were rewarded for selecting photos of orangutans instead of humans and other primates (concrete level), primates instead of other animals (intermediate level), and animals instead of nonanimals (abstract level) in a 2-choice touch screen procedure. The results suggest that, like a gorilla (Gorilla gorilla gorilla) tested previously (Vonk & MacDonald, 2002), orangutans can learn concepts at each level of abstraction, and unlike other nonhumans, most of these subjects rapidly learned the intermediate level discrimination.

Animals↗
PubMed2004

Dynamic analysis of learning in behavioral experiments.

Understanding how an animal's ability to learn relates to neural activity or is altered by lesions, different attentional states, pharmacological interventions, or genetic manipulations are central questions in neuroscience. Although learning is a dynamic process, current analyses do not use dynamic estimation methods, require many trials across many animals to establish the occurrence of learning, and provide no consensus as how best to identify when learning has occurred. We develop a state-space model paradigm to characterize learning as the probability of a correct response as a function of trial number (learning curve). We compute the learning curve and its confidence intervals using a state-space smoothing algorithm and define the learning trial as the first trial on which there is reasonable certainty (>0.95) that a subject performs better than chance for the balance of the experiment. For a range of simulated learning experiments, the smoothing algorithm estimated learning curves with smaller mean integrated squared error and identified the learning trials with greater reliability than commonly used methods. The smoothing algorithm tracked easily the rapid learning of a monkey during a single session of an association learning experiment and identified learning 2 to 4 d earlier than accepted criteria for a rat in a 47 d procedural learning experiment. Our state-space paradigm estimates learning curves for single animals, gives a precise definition of learning, and suggests a coherent statistical framework for the design and analysis of learning experiments that could reduce the number of animals and trials per animal that these studies require.

Algorithms↗
PubMed2004

Dopamine D2 receptors mediate two-odor discrimination and reversal learning in C57BL/6 mice.

BACKGROUND: Dopamine modulation of neuronal signaling in the frontal cortex, midbrain, and striatum is essential for processing and integrating diverse external sensory stimuli and attaching salience to environmental cues that signal causal relationships, thereby guiding goal-directed, adaptable behaviors. At the cellular level, dopamine signaling is mediated through D1-like or D2-like receptors. Although a role for D1-like receptors in a variety of goal-directed behaviors has been identified, an explicit involvement of D2 receptors has not been clearly established. To determine whether dopamine D2 receptor-mediated signaling contributes to associative and reversal learning, we compared C57Bl/6J mice that completely lack functional dopamine D2 receptors to wild-type mice with respect to their ability to attach appropriate salience to external stimuli (stimulus discrimination) and disengage from inappropriate behavioral strategies when reinforcement contingencies change (e.g. reversal learning). RESULTS: Mildly food-deprived female wild-type and dopamine D2 receptor deficient mice rapidly learned to retrieve and consume visible food reinforcers from a small plastic dish. Furthermore, both genotypes readily learned to dig through the same dish filled with sterile sand in order to locate a buried food pellet. However, the dopamine D2 receptor deficient mice required significantly more trials than wild-type mice to discriminate between two dishes, each filled with a different scented sand, and to associate one of the two odors with the presence of a reinforcer (food). In addition, the dopamine D2 receptor deficient mice repeatedly fail to alter their response patterns during reversal trials where the reinforcement rules were inverted. CONCLUSIONS: Inbred C57Bl/6J mice that develop in the complete absence of functional dopamine D2 receptors are capable of olfaction but display an impaired ability to acquire odor-driven reinforcement contingencies. Furthermore, the ability of dopamine D2 receptor deficient mice to adjust their responding to a previously reinforced stimulus when unexpected outcomes are encountered is significantly impaired. These findings suggest that signaling mediated by the dopamine D2 receptor is important for regulating associative and reversal learning and may have implications for the treatment of human attention disorders.

Animals↗
PubMed1996

Complex Visual Learning by Rats

Rats' learning about visual patterns was studied in a computerized Y-maze where wide-angle stimuli were viewed from a distance. Many patterns were available; some were spatially complex and others were more homogeneous figures. Experiment 1 used a discrimination paradigm in which a single S+ could be paired with any one of 15 different S-s. Hooded rats learned successively six such discrimination problems. Their learning rate improved across the series, and comparison with controls suggested that the learning-set did not merely reflect simple habituation. Experiments 2 and 3 employed Dark Agouti rats, again learning many discrimination problems. Each problem comprised a constant stimulus which was paired with stimuli which varied in trial-unique fashion. The version in which the constant stimulus was nonrewarded (S-) and the varying stimuli rewarded was performed better than the converse, constant S+ and varying nonrewarded, reflecting rats' preference for relatively unfamiliar stimuli. In the constant S- task, rats showed substantial within-problem learning when three novel problems were given per day for 20 trials each. Rats are capable of rapid learning about complex visual displays if we engage their natural dispositions to use vision for distal stimuli and to approach relatively unfamiliar cues.

Journal Article↗
PubMed2006

fMRI investigation of cortical and subcortical networks in the learning of abstract and effector-specific representations of motor sequences.

A visuo-motor sequence can be learned as a series of visuo-spatial cues or as a sequence of effector movements. Earlier imaging studies have revealed that a network of brain areas is activated in the course of motor sequence learning. However, these studies do not address the question of the type of representation being established at various stages of visuo-motor sequence learning. In an earlier behavioral study, we demonstrated that acquisition of visuo-spatial sequence representation enables rapid learning in the early stage and progressive establishment of somato-motor representation helps speedier execution by the late stage. We conducted functional magnetic resonance imaging (fMRI) experiments wherein subjects learned and practiced the same sequence alternately in normal and rotated settings. In one rotated setting (visual), subjects learned a new motor sequence in response to an identical sequence of visual cues as in normal. In another rotated setting (motor), the display sequence was altered as compared to normal, but the same sequence of effector movements was used to perform the sequence. Comparison of different rotated settings revealed analogous transitions both in the cortical and subcortical sites during visuo-motor sequence learning-a transition of activity from parietal to parietal-premotor and then to premotor cortex and a concomitant shift was observed from anterior putamen to a combined activity in both anterior and posterior putamen and finally to posterior putamen. These results suggest a putative role for engagement of different cortical and subcortical networks at various stages of learning in supporting distinct sequence representations.

Adult↗
PubMed2001

Disrupting basolateral amygdala function impairs unconditioned freezing and avoidance in rats.

Lesions of the lateral/basolateral amygdala nuclei (BLC) disrupt freezing behaviour in response to explicit or contextual cues (conditioned stimuli--CS) paired previously with footshock (unconditioned stimulus). This deficit in expression of defensive behaviour in response to conditioned stimuli is often interpreted as inability of lesioned rats to learn CS-US associations. However, findings of several studies indicate that BLC-lesioned rats can rapidly learn CS-US associations. Such findings suggest that lesioned rats can learn CS-US associations but are impaired in the expression of freezing behaviour. In the present study we report that both temporary inactivation (lidocaine) and permanent excitotoxic (NMDA) lesions of the BLC impair the unconditioned freezing and avoidance behaviours of rats in response to a novel fear-eliciting stimulus, a ball of cat hair. These findings suggest that the BLC influences the expression of freezing and avoidance behaviours, and/or that it potentiates rats' experience of fear. Along with prior evidence of spared memory for aversive learning after BLC lesions, these findings suggest that disrupted freezing to conditioned cues in BLC-lesioned rats does not necessarily reflect inability to form CS-US associations.

Amygdala↗
PubMedDate not supplied

Learning by selection in the trion model of cortical organization.

The basic issue of whether mammalian learning in cortex proceeds via a selection principle, as stressed by Edelman, versus an instructional one is of major importance. We present here a realization of selection learning in the trion model, which is based on the Mountcastle columnar organizational principle of cortex. We suggest that mammalian cortex starts out with an a priori connectivity between minicolumns that is highly structured in time and in space, competing between excitation and inhibition. This provides a "naive" repertoire of spatial-temporal firing patterns that stimuli and internal processing map onto. These patterns can be learned with small modifications to the connectivity strengths determined by a Hebbian learning rule. As various patterns are learned, the repertoire changes somewhat in order to respond properly to various stimuli, but the majority of all possible stimuli still map onto spatial-temporal firing patterns of the original repertoire. In order to show that the example presented here is showing true selectivity and is not an artifact of more stimuli evolving into the learned pattern, we develop a selectivity measure. We suggest that some form of instructional learning (in which connectivities are finely tuned) is present for difficult tasks requiring many trials, whereas very rapid learning involves selectional learning. Both types of learning must be considered to understand behavior.

Animals↗
PubMed2005

Neurobiology of infant attachment.

A strong attachment to the caregiver is critical for survival in altricial species, including humans. While some behavioral aspects of attachment have been characterized, its neurobiology has only recently received attention. Using a mammalian imprinting model, we are assessing the neural circuitry that enables infant rats to attach quickly to a caregiver, thus enhancing survival in the nest. Specifically, the hyper-functioning noradrenergic locus coeruleus (LC) enables pups to learn rapid, robust preference for the caregiver. Conversely, a hypo-functional amygdala appears to prevent the infant from learning aversions to the caregiver. Adult LC and amygdala functional emergence correlates with sensitive period termination. This study suggests the neonatal brain is not an immature version of the adult brain but is uniquely designed to optimize attachment to the caregiver. Although human attachment may not rely on identical circuitry, the work reviewed here suggests a new conceptual framework in which to explore human attachments, particularly attachments to abusive caregivers.

Age Factors↗
PubMed1999

Spatial learning of an escape task by young corn snakes, Elaphe guttata guttata.

Spatial learning is critical to most animals for many behaviours necessary to survival. In vertebrates, most studies on spatial learning and memory have been conducted in mammalian and avian species with few studies on reptiles. We examined spatial learning in the corn snake, Elaphe guttata guttata by training 17 young snakes to find the one open shelter in an eight-hole arena, where the entrance was not visible from the arena surface. Over a 16-trial, 4-day training period, snakes showed (1) a significant decrease in the mean latency to the goal, (2) a significant decrease in the mean total distance travelled, (3) a significant increase in the percentage of the total distance travelled in the quadrant containing the goal, and (4) a significant increase in movement in the goal quadrant above chance. Although no differences were found in the number of errors made over the training period, snakes made fewer errors on all days than expected by chance. This study shows that snakes can learn rapidly a spatial-escape task that is relevant behaviourally and suggests that entering a shelter reinforces this learning. Mechanisms of orientation for the task described are discussed. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed2006

Different roles for amygdala central nucleus and substantia innominata in the surprise-induced enhancement of learning.

Within most modern learning theories, the discrepancy between expected and obtained outcomes ("prediction error" or "surprise") is a critical determinant of the acquisition of learned associations. The results of studies from many laboratories show that the surprising omission of an expected event may enhance attention to stimuli that remain present, such that subsequent learning about those stimuli is enhanced. A series of reports from our laboratories demonstrated that these surprise-induced enhancements of stimulus associability depend on circuitry that includes the amygdala central nucleus (CeA), the cholinergic neurons in the sublenticular substantia innominata/nucleus basalis magnocellularis (SI/nBM), as well as certain cortical projections of these latter neurons. In this study, we found very different roles for CeA and SI/nBM in surprise-induced enhancements of stimulus associability. In four experiments that used transient inactivation techniques, we found that surprise-induced enhancement of subsequent learning about a stimulus depended on intact CeA function at the time of surprise but not when more rapid learning was subsequently expressed. In contrast, normal SI/nBM function was critical to the expression of enhanced learning but was not necessary when surprise was induced. These data suggest that these two components of the so-called "extended amygdala" serve distinct roles in the encoding and retrieval of information used in modulating attention to stimuli in associative learning. Additional circuitry linking these brain regions may also be important in the maintenance of that information.

Amygdala↗
PubMed1988

Practice effect of volunteers in repeated psychometric testing. How to handle this intervening variable in clinical pharmacology studies?

Performance in psychometric tests may show a practice effect with repeated testing. Ideally, a plateau of efficiency should be reached prior to first drug intake. In order to assess the period of familiarization in a multiple choice reaction task (MCRT) 17 healthy subjects practiced the test up to 36 times in the drug free run-in period of 2 trials. A tentative "inclusion criterion" was used in 7 subjects to decide whether their learning phase could be regarded as being finished. Seven to 20 training sessions were required for a first rapid learning phase. There were remarkable differences in the absolute performance of the subjects and in the time course of their practice effect. However, the time course of the learning phase was not dependent on the absolute performance level. By means of the tentative "inclusion criterion" it was possible to reject a subject with a low but highly variable performance. However, it was not stringent enough to indicate the final plateau of efficiency. More "drug free" data concerning the practice effect should be published to enable the users of psychometric tests to make a reasonable selection according to their needs and to help them design their trials properly.

Adult↗
PubMed2003

Role of the hippocampal system in associative learning beyond the spatial domain.

Expert opinion remains divided on the issue of whether the hippocampal system functions exclusively in spatial information processing, e.g. in navigation or in understanding spatial relations, or whether it plays a more general role in higher brain function. Previous work on monkeys and rats has tended to support the former view, whereas observations in the clinic point to the latter, including functions as diverse as declarative knowledge, episodic memory, word learning, and understanding relations among objects. One influential theory posits a general role for the hippocampal system in associative learning, with emphasis on associations learned rapidly and recently. The results presented here are consistent with this theory, along with previous clinical and theoretical studies indicating that the hippocampal system is necessary for associative learning even if no component of the association relies on spatial information. In the study reported here, rhesus monkeys learned a series of conditional stimulus-response associations involving complex visual stimuli presented on a video monitor. Each stimulus instructed one of three responses: tapping the stimulus with the hand, steady hand contact with the stimulus for a brief period of time, or steady contact for a longer time. Fornix transection impaired the learning of these associations, even though both the stimuli and the responses were nonspatially differentiated, and this deficit persisted for at least 2 years. This finding indicates that the hippocampal system plays an important role in associative learning regardless of the relevance of spatial information to any aspect of the association. Fornix-transected monkeys were impaired in learning new stimulus-response associations even when the stimuli were highly familiar. Thus, the deficit was one of associating each stimulus with a response, as opposed to problems in distinguishing the stimuli from each other. In contrast to these effects, fornix transection did not impair performance when familiar stimuli instructed a response according to an already-learned association, which shows that the deficit was one of learning new associations rather than one of retention or retrieval of previously learned ones. Taken together, these results show that fornix transection causes a long-lasting impairment in associative learning outside of the spatial domain, in a manner consistent with theories of hippocampal-system function that stress a general role in the rapid acquisition of associative knowledge.

Animals↗
PubMed1986

Reversal and nonreversal shifts under amphetamine.

Rats were trained in a Y maze on a two-choice simultaneous brightness discrimination with light as S+ and dark as S- (position irrelevant). Half of the animals were then switched to reversal, where the reinforcement contingencies of the original training were reversed, and the other half were switched to nonreversal, in which they learned a simultaneous right-left discrimination. Nonreversal was acquired faster than reversal in saline injected animals. The administration of 1 mg/kg d-amphetamine did not affect the acquisition of the initial brightness discrimination and of nonreversal. In contrast, the drug facilitated dramatically reversal learning. The results indicate that amphetamine enhances the attention to, or the associability of, the discriminative stimuli, leading to rapid learning to these stimuli under changed contingencies of reinforcement.

Animals↗