Knowing when to stop: Aberrant precision and evidence accumulation in schizophrenia

Predictive coding and active inference formulations of the dysconnection hypothesis suggest that subjects with schizophrenia (SZ) hold unduly precise prior beliefs to compensate for a failure of sensory attenuation. This implies that SZ subjects should both initiate responses prematurely during evidence-accumulation tasks and fail to inhibit their responses at long stop-signal delays. SZ and healthy control subjects were asked to report the timing of billiards-ball collisions and were occasionally required to withhold their responses. SZ subjects showed larger temporal estimation errors, which were associated with premature responses and decreased response inhibition. To account for these effects, we used hierarchical (Bayesian) drift-diffusion models (HDDM) and model selection procedures to adjudicate among four hypotheses. HDDM revealed that the precision of prior beliefs (i.e., starting point) rather than increased sensory precision (i.e., drift rate) drove premature responses and impaired response inhibition in patients with SZ. From the perspective of active inference, we suggest that premature predictions in SZ are responses that, heuristically, are traded off against accuracy to ensure action execution. On the basis of previous work, we suggest that the right insular cortex might mediate this trade-off

Modeling electricity loads in California: a continuous-time approach

In this paper we address the issue of modeling electricity loads and prices with diffusion processes. More specifically, we study models which belong to the class of generalized Ornstein-Uhlenbeck processes. After comparing properties of simulated paths with those of deseasonalized data from the California power market and performing out-of-sample forecasts we conclude that, despite certain advantages, the analyzed continuous-time processes are not adequate models of electricity load and price dynamics.Comment: To be published in Physica A (2001): Proceedings of the NATO ARW on Application of Physics in Economic Modelling, Prague, Feb. 8-10, 200

Everyday cosmopolitanism in representations of Europe among young Romanians in Britain

The paper presents an analysis of everyday cosmopolitanism in constructions of Europe among young Romanian nationals living in Britain. Adopting a social representations approach, cosmopolitanism is understood as a cultural symbolic resource that is part of everyday knowledge. Through a discursively-oriented analysis of focus group data, we explore the ways in which notions of cosmopolitanism intersect with images of Europeanness in the accounts of participants. We show that, for our participants, representations of Europe are anchored in an Orientalist schema of West-vs.-East, whereby the West is seen as epitomising European values of modernity and progress, while the East is seen as backward and traditional. Our findings further show that representations of cosmopolitanism reinforce this East/West dichotomy, within a discourse of ‘Occidental cosmopolitanism’. The paper concludes with a critical discussion of the diverse and complex ideological foundations of these constructions of European cosmopolitanism and their implications

Mapping the meaning of "difference' in Europe: A social topography of prejudice

This paper draws on original empirical research to investigate popular understandings of prejudice in two national contexts: Poland and the United Kingdom. The paper demonstrates how common-sense meanings of prejudice are inflected by the specific histories and geographies of each place: framed in terms of ‘distance’ (Poland) and ‘proximity’ (United Kingdom), respectively. Yet, by treating these national contexts as nodes and linking them analytically the paper also exposes a connectedness in these definitions which brings into relief the common processes that produce prejudice. The paper then explores how inter-linkages between the United Kingdom and Poland within the wider context of the European Union are producing – and circulating through the emerging international currency of ‘political correctness’ – a common critique of equality legislation and a belief that popular concerns about the way national contexts are perceived to be changing as a consequence of super mobility and super diversity are being silenced. This raises a real risk that in the context of European austerity and associated levels of socioeconomic insecurity, negative attitudes and conservative values may begin to be represented as popular normative standards which transcend national contexts to justify harsher political responses towards minorities. As such, the paper concludes by making a case for prejudice reduction strategies to receive much greater priority in both national and European contexts

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection

Background: Emerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remain comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone.Results: We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats.Conclusions: The neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1400 genomes with host and pathogenicity metadata supports training of machine-learning models and sequence comparison, not limited to the pathogen detection task

Relative Abundance of Transcripts (RATs):Identifying differential isoform abundance from RNA-seq [version 1; referees: 1 approved, 2 approved with reservations]

The biological importance of changes in RNA expression is reflected by the wide variety of tools available to characterise these changes from RNA-seq data. Several tools exist for detecting differential transcript isoform usage (DTU) from aligned or assembled RNA-seq data, but few exist for DTU detection from alignment-free RNA-seq quantifications. We present the RATs, an R package that identifies DTU transcriptome-wide directly from transcript abundance estimates. RATs is unique in applying bootstrapping to estimate the reliability of detected DTU events and shows good performance at all replication levels (median false positive fraction < 0.05). We compare RATs to two existing DTU tools, DRIM-Seq & SUPPA2, using two publicly available simulated RNA-seq datasets and a published human RNA-seq dataset, in which 248 genes have been previously identified as displaying significant DTU. RATs with default threshold values on the simulated Human data has a sensitivity of 0.55, a Matthews correlation coefficient of 0.71 and a false discovery rate (FDR) of 0.04, outperforming both other tools. Applying the same thresholds for SUPPA2 results in a higher sensitivity (0.61) but poorer FDR performance (0.33). RATs and DRIM-seq use different methods for measuring DTU effect-sizes complicating the comparison of results between these tools, however, for a likelihood-ratio threshold of 30, DRIM-Seq has similar FDR performance to RATs (0.06), but worse sensitivity (0.47). These differences persist for the simulated drosophila dataset. On the published human RNA-seq dataset the greatest agreement between the tools tested is 53%, observed between RATs and SUPPA2. The bootstrapping quality filter in RATs is responsible for removing the majority of DTU events called by SUPPA2 that are not reported by RATs. All methods, including the previously published qRT-PCR of three of the 248 detected DTU events, were found to be sensitive to annotation differences between Ensembl v60 and v87

Cell cycle regulation of embryonic stem cells and mouse embryonic fibroblasts lacking functional Pax7

The transcription factor Pax7 plays a key role during embryonic myogenesis and in adult organisms in that it sustains the proper function of satellite cells, which serve as adult skeletal muscle stem cells. Recently we have shown that lack of Pax7 does not prevent the myogenic differentiation of pluripotent stem cells. In the current work we show that the absence of functional Pax7 in differentiating embryonic stem cells modulates cell cycle facilitating their proliferation. Surprisingly, deregulation of Pax7 function also positively impacts at the proliferation of mouse embryonic fibroblasts. Such phenotypes seem to be executed by modulating the expression of positive cell cycle regulators, such as cyclin E

Evidence of environmental niche separation between threatened mobulid rays in Aotearoa New Zealand: Insights from species distribution modelling

\ua9 2024 The Author(s). Journal of Biogeography published by John Wiley &amp; Sons Ltd.Aim: Mobulid rays are a group of threatened batoid fishes susceptible to population decline from targeted fisheries and accidental capture. Spatial distributions of mobulid rays remain poorly known. Prior studies found commonalities between favourable environments and prey among various mobulid species, yet most were conducted in tropical waters. To explore the habitat use and distribution of mobulid rays in a temperate environment we model the habitat suitability of two mobulid rays (Mobula mobular and Mobula birostris) in Aotearoa New Zealand using fisheries and citizen science occurrence data spanning almost two decades. Location: Northeastern coast of Aotearoa, New Zealand. Methods: Boosted Regression Tree models were used to predict the annual habitat suitability and favourable environmental conditions of the two species based on available sightings records in conjunction with high resolution (1 km2) environmental data. Results: The sympatric study species had contrasting habitat requirements. We found a separation in their spatial distribution defined by the 200 m isobath – the onshore extent for M. birostris and the offshore extent for M. mobular. While there were only subtle variations in relative habitat suitability for M. mobular over the study period, M. birostris exhibited greater interannual variability. Despite differing interannual patterns, spatial separation, as a function of environmental properties, persisted regardless of the year. Main Conclusions: Our results suggest that associations between mobulid species may differ from tropical regions due to regional adaptations to prey availability or local environmental conditions unique to colder and more productive temperate waters. Our findings highlight the importance of multi-species surveys and the inclusion of temporal variability in support of separate species-specific management plans to account for differing stressors impacting each species

Cyanobacteria microflora in a limestone spring (Troniny spring, Central Poland)

The paper reports a study of cyanobacterial diversity in a cold-water limestone limnocrene in Central Poland. Samples were collected from 1998 to 2000 and in June 2012. The morphology, population characteristics and species composition of the cyanobacteria assemblages were investigated, and the frequency of taxa was recorded. The large number of taxa identified (30) reflects the microhabitat heterogeneity of this spring. Some species considered epiphytes grew on limestone rocks. The occurrence of the majority of the most frequent taxa was related to the physicochemical characteristics of the spring, but none of them can be considered obligatory crenobionts characteristic of limestone springs. The studied spring is a unique ecosystem with an interesting cyanobacteria microflora whose occurrence is attributable to the spring’s water chemistry, low temperature and variety of microhabitats

SUPPA2:fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Supplementary methods. (PDF 315 kb