Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling

A well-established notion in cognitive neuroscience proposes that multiple brain systems contribute to choice behaviour. These include: (1) a model-free system that uses values cached from the outcome history of alternative actions, and (2) a model-based system that considers action outcomes and the transition structure of the environment. The widespread use of this distinction, across a range of applications, renders it important to index their distinct influences with high reliability. Here we consider the two-stage task, widely considered as a gold standard measure for the contribution of model-based and model-free systems to human choice. We tested the internal/temporal stability of measures from this task, including those estimated via an established computational model, as well as an extended model using drift-diffusion. Drift-diffusion modeling suggested that both choice in the first stage, and RTs in the second stage, are directly affected by a model-based/free trade-off parameter. Both parameter recovery and the stability of model-based estimates were poor but improved substantially when both choice and RT were used (compared to choice only), and when more trials (than conventionally used in research practice) were included in our analysis. The findings have implications for interpretation of past and future studies based on the use of the two-stage task, as well as for characterising the contribution of model-based processes to choice behaviour

Increased decision thresholds trigger extended information gathering across the compulsivity spectrum

Indecisiveness and doubt are cognitive phenotypes of compulsive disorders, including obsessive-compulsive disorder. Little is known regarding the cognitive mechanisms that drive these behaviours across a compulsivity spectrum. Here, we used a sequential information gathering task to study indecisiveness in subjects with high and low obsessive-compulsive scores. These subjects were selected from a large population-representative database, and matched for intellectual and psychiatric factors. We show that high compulsive subjects sampled more information and performed better when sampling was cost-free. When sampling was costly, both groups adapted flexibly to reduce their information gathering. Computational modelling revealed that increased information gathering behaviour could be explained by higher decision thresholds that, in turn, were driven by a delayed emergence of impatience or urgency. Our findings show that indecisiveness generalises to a compulsivity spectrum beyond frank clinical disorder, and this behaviour can be explained within a decision-theoretic framework as arising from an augmented decision threshold associated with an attenuated urgency signal

Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms

Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo

We dissect the transcriptional regulatory relationships coordinating the dynamic expression patterns of two signaling genes, wnt8 and delta, which are central to specification of the sea urchin embryo endomesoderm. cis-Regulatory analysis shows that transcription of the gene encoding the Notch ligand Delta is activated by the widely expressed Runx transcription factor, but spatially restricted by HesC-mediated repression through a site in the delta 5′UTR. Spatial transcription of the hesC gene, however, is controlled by Blimp1 repression. Blimp1 thus represses the repressor of delta, thereby permitting its transcription. The blimp1 gene is itself linked into a feedback circuit that includes the wnt8 signaling ligand gene, and we showed earlier that this circuit generates an expanding torus of blimp1 and wnt8 expression. The finding that delta expression is also controlled at the cis-regulatory level by the blimp1-wnt8 torus-generating subcircuit now explains the progression of Notch signaling from the mesoderm to the endoderm of the developing embryo. Thus the specific cis-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo

Occupational Animal Contact in Southern and Central Vietnam

Despite the global zoonotic disease burden, the underlying exposures that drive zoonotic disease emergence are not understood. Here, we aimed to assess exposures to potential sources of zoonotic disease and investigate the demographics, attitudes, and behavior of individuals with sustained occupational animal contact in Vietnam. We recruited 581 animal workers (animal-raising farmers, slaughterers, animal health workers, and rat traders) and their families in southern and central Vietnam into a cohort. Cohort members were followed for 3 years and interviewed annually regarding (1) demography and attitudes regarding zoonotic disease, (2) medical history, (3) specific exposures to potential zoonotic infection sources, and (4) socioeconomic status. Interview information over the 3 years was combined and analyzed as cross-sectional data. Of the 297 cohort members interviewed, the majority (79.8%; 237/297) reported raising livestock; almost all (99.6%; 236/237) reported being routinely exposed to domestic animals, and more than a quarter (28.7%; 68/237) were exposed to exotic animals. Overall, 70% (208/297) reported slaughtering exotic animals; almost all (99.5%; 207/208) reported consuming such animals. The consumption of raw blood and meat was common (24.6%; 73/297 and 37%; 110/297, respectively). Over half (58.6%; 174/297) reported recent occupational animal-induced injuries that caused bleeding; the use of personal protective equipment (PPE) was limited. Our work demonstrates that individuals working with animals in Vietnam are exposed to a wide range of species, and there are limited procedures for reducing potential zoonotic disease exposures. We advocate better education, improved animal security, and enforced legislation of PPE for those with occupational animal exposure in Vietnam.Peer reviewe

Credit assignment to state-independent task representations and its relationship with model-based decision making

Model-free learning enables an agent to make better decisions based on prior experience while representing only minimal knowledge about an environment’s structure. It is generally assumed that model-free state representations are based on outcome-relevant features of the environment. Here, we challenge this assumption by providing evidence that a putative model-free system assigns credit to task representations that are irrelevant to an outcome. We examined data from 769 individuals performing a well-described 2-step reward decision task where stimulus identity but not spatial-motor aspects of the task predicted reward. We show that participants assigned value to spatial-motor representations despite it being outcome irrelevant. Strikingly, spatial-motor value associations affected behavior across all outcome-relevant features and stages of the task, consistent with credit assignment to low-level state-independent task representations. Individual difference analyses suggested that the impact of spatial-motor value formation was attenuated for individuals who showed greater deployment of goal-directed (model-based) strategies. Our findings highlight a need for a reconsideration of how model-free representations are formed and regulated according to the structure of the environment

MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes

Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies. Non-long terminal repeat (non-LTR) retrotransposons are a class of MGEs that have been found in most eukaryotic genomes, sometimes in extremely high numbers. In this article, we present a computational tool, MGEScan-non-LTR, for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). Three different states represent two different protein domains and inter-domain linker regions encoded in the non-LTR retrotransposons, and their scores are evaluated by using profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively. In order to classify the non-LTR retrotransposons into one of the 12 previously characterized clades using the same model, we defined separate states for different clades. MGEScan-non-LTR was tested on the genome sequences of four eukaryotic organisms, Drosophila melanogaster, Daphnia pulex, Ciona intestinalis and Strongylocentrotus purpuratus. For the D. melanogaster genome, MGEScan-non-LTR found all known ‘full-length’ elements and simultaneously classified them into the clades CR1, I, Jockey, LOA and R1. Notably, for the D. pulex genome, in which no non-LTR retrotransposon has been annotated, MGEScan-non-LTR found a significantly larger number of elements than did RepeatMasker, using the current version of the RepBase Update library. We also identified novel elements in the other two genomes, which have only been partially studied for non-LTR retrotransposons

Compulsivity and impulsivity traits linked to attenuated developmental frontstriatal myelination trajectories

A transition from adolescence into adulthood corresponds to a period where rapid brain development coincides with an enhanced incidence of psychiatric disorder. The precise developmental brain changes that account for this emergent psychiatric symptomatology remain obscure. Capitalising on a unique longitudinal dataset, that includes in-vivo myelin-sensitive magnetization transfer (MT) MRI, we show that coming of age is characterised by brain-wide growth in MT, within both gray matter and adjacent juxta-cortical white matter. In this healthy population the expression of common developmental traits, namely compulsivity and impulsivity, are tied to a reduced unfolding of these MT trajectories in fronto-striatal regions. This reduction is most marked in dorsomedial and dorsolateral frontal structures for compulsivity, and in lateral and medial frontal areas for impulsivity. The findings highlight a brain developmental linkage for compulsivity and impulsivity is evident in regionally specific reduced unfolding of MT-related myelination.Wellcome Trus

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined