nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through ``multi-omics'' data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential gene expression analyses. The pipeline provides a quick and efficient way to obtain a matrix of read counts that can be used black with tools such as DESeq2 and edgeR for differential expression analysis. Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research.

A multi-representation approach to the contextual interference effect: effects of sequence length and practice

The present study investigated the long-term benefit of Random-Practice (RP) over Blocked-Practice (BP) within the contextual interference (CI) effect for motor learning. We addressed the extent to which motor sequence length and practice amount factors moderate the CI effect given that previous reports, often in applied research, have reported no long-term advantage from RP. Based on predictions arising from the Cognitive framework of Sequential Motor Behavior (C-SMB) and using the Discrete Sequence Production (DSP) task, two experiments were conducted to compare limited and extended practice amounts of 4- and 7-key sequences under RP and BP schedules. Twenty-four-hour delayed retention performance confirmed the C-SMB prediction that the CI-effect occurs only with short sequences that receive little practice. The benefit of RP with limited practice was associated with overnight motor memory consolidation. Further testing with single-stimulus as well as novel and unstructured (i.e., random) sequences indicated that limited practice under RP schedules enhances both reaction and chunking modes of sequence execution with the latter mode benefitting from the development of implicit and explicit forms of sequence representation. In the case of 7-key sequences, extended practice with RP and BP schedules provided for equivalent development of sequence representations. Higher explicit awareness of sequence structures was associated with faster completion of practiced but also of novel and unstructured sequences.

Nanopore sequencing in non-human forensic genetics

The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories.

Cognitive and Motor Learning in Internally-Guided Motor Skills

Several canonical experimental paradigms (e.g., serial reaction time task, discrete sequence production task, m × n task) have been proposed to study the typical behavioral phenomenon and the nature of learning in sequential keypress tasks. A characteristic feature of most paradigms is that they are representative of externally-specified sequencing—motor tasks where the environment or task paradigm extrinsically provides the sequence of stimuli, i.e., the responses are stimulus-driven. Previous studies utilizing such canonical paradigms have largely overlooked the learning behaviors in a more realistic class of motor tasks that involve internally-guided sequencing—where the sequence of motor actions is self-generated or internally-specified. In this work, we use the grid-navigation task as an instance of internally-guided sequencing to investigate the nature of learning in such paradigms. The participants performed Grid-Sailing Task (GST), which required navigating (by executing sequential keypresses) a 5 × 5 grid from start to goal (SG) position while using a particular key-mapping (KM) among the three cursor-movement directions and the three keyboard buttons. The participants performed two behavioral experiments—Single-SG and Mixed-SG condition. The Single-SG condition required performing GST on a single SG position repeatedly, whereas the Mixed-SG condition involved performing GST using the same KM on two novel SG positions presented in a random, inter-mixed manner. In the Single-SG condition, we show that motor learning contributes to the sequence-specific learning in GST with the repeated execution of the same trajectories. In the Mixed-SG condition, since the participants utilize the previously learned KM, we anticipate a transfer of learning from the Single-SG condition. The acquisition and transfer of a KM-specific internal model facilitates efficient trajectory planning on novel SG conditions. The acquisition of such a KM-specific internal model amounts to trajectory-independent cognitive learning in GST. We show that cognitive learning contributes to the learning in GST by showing transfer-related performance improvements in the Mixed-SG condition. In sum, we show the role of cognitive and motor learning processes in internally-guided sequencing and further make a case for using GST-like grid-navigation paradigms in investigating internally guided skill learning.

Examining the Relationship between Production, Trade and Consumption Using Hierarchical Analysis Methods

Reproduction is a continuous process of production, distribution and consumption of products in the hierarchy of economic space. Simultaneously, local production depends on both domestic demand and wholesale promotion of products to international markets. The study determines the influence of the wholesale, defining the distribution and trade stages, on the shipping volume, characterising the production stage. The research aims to correlate territorial hierarchy (country → region → municipality) with the reproduction sequence (production → distribution/trade → consumption). Additionally, it attempts to decompose the observed variation of the shipping volume in accordance with the hierarchy of economic space using the hierarchical linear modelling (HLM). The differences between municipalities are analysed in the context of two territorial levels: municipal (population income, determining consumption) and regional (wholesale trade, characterising the distribution) ones. The research examined the data for 2017 on 331 municipalities of 7 constituent entities of the Russian Federation. The study results show that hierarchical analysis methods can be used to analyse the relationship between production, distribution and consumption. In the considered territory, the shipping volume was mostly influenced by domestic consumption and to a much lesser extent wholesale trade. The application of hierarchical analysis methods enhances the analysis of reproduction. Moreover, it allows the government to create favourable conditions for implementing the programmesof infrastructure development and assessing supply capabilities of trade and production enterprises

Motor Chunking in Internally Guided Sequencing

Motor skill learning involves the acquisition of sequential motor movements with practice. Studies have shown that we learn to execute these sequences efficiently by chaining several elementary actions in sub-sequences called motor chunks. Several experimental paradigms, such as serial reaction task, discrete sequence production, and m × n task, have investigated motor chunking in externally specified sequencing where the environment or task paradigm provides the sequence of stimuli, i.e., the responses are stimulus driven. In this study, we examine motor chunking in a class of more realistic motor tasks that involve internally guided sequencing where the sequence of motor actions is self-generated or internally specified. We employ a grid-navigation task as an exemplar of internally guided sequencing to investigate practice-driven performance improvements due to motor chunking. The participants performed the grid-sailing task (GST) (Fermin et al., 2010), which required navigating (by executing sequential keypresses) a 10 × 10 grid from start to goal position while using a particular type of key mapping between the three cursor movement directions and the three keyboard buttons. We provide empirical evidence for motor chunking in grid-navigation tasks by showing the emergence of subject-specific, unique temporal patterns in response times. Our findings show spontaneous chunking without pre-specified or externally guided structures while replicating the earlier results with a less constrained, internally guided sequencing paradigm.

Brain Inspired Sequences Production by Spiking Neural Networks With Reward-Modulated STDP

Understanding and producing embedded sequences according to supra-regular grammars in language has always been considered a high-level cognitive function of human beings, named “syntax barrier” between humans and animals. However, some neurologists recently showed that macaques could be trained to produce embedded sequences involving supra-regular grammars through a well-designed experiment paradigm. Via comparing macaques and preschool children's experimental results, they claimed that human uniqueness might only lie in the speed and learning strategy resulting from the chunking mechanism. Inspired by their research, we proposed a Brain-inspired Sequence Production Spiking Neural Network (SP-SNN) to model the same production process, followed by memory and learning mechanisms of the multi-brain region cooperation. After experimental verification, we demonstrated that SP-SNN could also handle embedded sequence production tasks, striding over the “syntax barrier.” SP-SNN used Population-Coding and STDP mechanism to realize working memory, Reward-Modulated STDP mechanism for acquiring supra-regular grammars. Therefore, SP-SNN needs to simultaneously coordinate short-term plasticity (STP) and long-term plasticity (LTP) mechanisms. Besides, we found that the chunking mechanism indeed makes a difference in improving our model's robustness. As far as we know, our work is the first one toward the “syntax barrier” in the SNN field, providing the computational foundation for further study of related underlying animals' neural mechanisms in the future.

Discrepancy between repetition suppression and pattern analysis provides new insights into the role of M1 and parietal areas in sequence learning

How does the brain change during skill learning? We previously conducted a longitudinal fMRI motor sequence learning study and, using multivariate techniques, found learning-related changes in premotor and parietal areas, but not in the primary motor cortex (M1) (1). However, a study using repetition suppression (RS) had previously suggested that M1 represents learned sequences. Here we replicate this discrepancy in a single experiment, allowing us to investigate the differences between RS and multivariate pattern analysis in detail. We found that the RS effect in M1 and parietal areas reflect fundamentally different processes. M1’s activity represents the starting finger of the sequence, an effect that vanishes with repetition. In contrast, activity patterns in parietal areas exhibit sequence dependency, which persists with repetition. These findings demonstrate that combining RS and pattern analysis can provide novel functional insights, here specifically into the relative contribution of cortical motor areas to sequence production.

Beneficial effects of cerebellar tDCS on motor learning are associated with altered putamen-cerebellar connectivity: a simultaneous tDCS-fMRI study

Non-invasive transcranial stimulation of cerebellum and primary motor cortex (M1) has been shown to enhance motor learning. However, the mechanisms by which stimulation improves learning remain largely unknown. Here, we sought to shed light on the neural correlates of transcranial direct current stimulation (tDCS) during motor learning by simultaneously recording functional magnetic resonance imaging (fMRI). We found that right cerebellar tDCS, but not left M1 tDCS, led to enhanced sequence learning in the serial reaction time task. Performance was also improved following cerebellar tDCS compared to sham in a sequence production task, reflecting superior training effects persisting into the post-training period. These behavioral effects were accompanied by increased learning-specific activity in right M1, left cerebellum lobule VI, left inferior frontal gyrus and right inferior parietal lobule during cerebellar tDCS compared to sham. Despite the lack of group-level changes comparing left M1 tDCS to sham, activity increase in right M1, supplementary motor area, and bilateral superior frontal cortex, under M1 tDCS, was associated with better sequence performance. This suggests that lack of group effects in M1 tDCS relate to inter-individual variability in learning-related activation patterns. We further investigated how tDCS modulates effective connectivity in the cortico-striato-cerebellar learning network. Using dynamic causal modelling, we found altered connectivity patterns during both M1 and cerebellar tDCS when compared to sham. Specifically, during cerebellar tDCS, negative modulation of a connection from putamen to cerebellum was decreased for sequence learning only, effectively leading to decreased inhibition of the cerebellum. These results show specific effects of cerebellar tDCS on functional activity and connectivity in the motor learning network and may facilitate the optimization of motor rehabilitation involving cerebellar non-invasive stimulation.

Competitive state of actions during planning predicts sequence execution accuracy

SummaryHumans can learn and retrieve novel skilled movement sequences from memory, yet the content and structure of sequence planning are not well understood. Previous computational and neurophysiological work suggests that actions in a sequence are planned as parallel graded activations and selected for output through competition (competitive queuing; CQ). However, the relevance of CQ during planning to sequence fluency and accuracy, as opposed to sequence timing, is unclear. To resolve this question, we assessed the competitive state of constituent actions behaviourally during sequence preparation. In three separate multi-session experiments, 55 healthy participants were trained to retrieve and produce 4-finger sequences with particular timing from long-term memory. In addition to sequence production, we evaluated reaction time (RT) and error rate increase to constituent action probes at several points during the preparation period. Our results demonstrate that longer preparation time produces a steeper CQ activation and selection gradient between adjacent sequence elements, whilst no effect was found for sequence speed or temporal structure. Further, participants with a steeper CQ gradient tended to produce correct sequences faster and with a higher temporal accuracy. In a computational model, we hypothesize that the CQ gradient during planning is driven by the width of acquired positional tuning of each sequential item, independently of timing. Our results suggest that competitive activation during sequence planning is established gradually during sequence planning and predicts sequence fluency and accuracy, rather than the speed or temporal structure of the motor sequence.HighlightsPre-ordering of actions during sequence planning can be assessed behaviourallyCompetitive gradient reflects sequence preparedness and skill, but not speed or timingGradient is retrieved rapidly and revealed during automatic action selectionPositional tuning of actions boosts the competitive gradient during planning