Action Selection in Everyday Activities: The Opportunistic Planning Model.

While action selection strategies in well-defined domains have received considerable attention, little is yet known about how people choose what to do next in ill-defined tasks. In this contribution, we shed light on this issue by considering everyday tasks, which in many cases have a multitude of possible solutions (e.g.

Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data.

Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational procedures like digital genomic footprinting on chromatin accessibility assays such as ATACseq can be used to identify bound TFs in a genome-wide scale. This method utilizes short regions of low accessibility signals due to steric hindrance of DNA bound proteins, called footprints (FPs), which are combined with motif databases for TF identification.

A Smart Model of Imaginal Perspective Taking.

The ability to judge spatial relations from perspectives that differ from one's current body orientation and location is important for many everyday activities. Despite considerable research on imaginal perspective taking, however, detailed computational accounts of the processes involved in this ability are missing. In this contribution, I introduce Smart (Spatial Memory Access by Reference Frame SelecTion) as a computational cognitive model of imaginal perspective taking processes.

PAMPAS: A PsychoAcoustical Method for the Perceptual Analysis of multidimensional Sonification.

The sonification of data to communicate information to a user is a relatively new approach that established itself around the 1990s. To date, many researchers have designed their individual sonification from scratch. There are no standards in sonification design and evaluation.

TF-COMB - Discovering grammar of transcription factor binding sites.

Cooperativity between transcription factors is important to regulate target gene expression. In particular, the binding grammar of TFs in relation to each other, as well as in the context of other genomic elements, is crucial for TF functionality. However, tools to easily uncover co-occurrence between DNA-binding proteins, and investigate the regulatory modules of TFs, are limited.

The development of visuospatial abilities and their impact on laparoscopic skill acquisition: a clinical longitudinal study.

Objectives: To investigate how visuospatial abilities develop and influence intraoperative laparoscopic performance during surgical residency training programmes.

Background: Laparoscopic surgery is a challenging technique to acquire and master. Visuospatial ability is an important attribute but most prior research have predominantly explored the influence of visuospatial abilities in lab-based settings and/or among inexperienced surgeons.

Everyday Activities.

The ease with which humans usually perform everyday activities masks their inherit complexity. Tasks such as setting a table prior to a meal or preparing a hot beverage require the coordination of several cognitive abilities. At the same time, many everyday activities are simple enough to afford investigation in controlled lab settings.

Alignment in spatial memory: Encoding of reference frames or of relations?

A common assumption about spatial memory is that it is organized along one or more reference directions such that access to memory is easier along directions aligned with the reference direction(s). This assumption rests to no small part on frequently replicated alignment effects arising in judgment of relative direction. In this contribution, we report an experiment designed to investigate a possible alternative explanation of alignment effects.

ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation.

While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting.

Does direction matter? Linguistic asymmetries reflected in visual attention.

Language and vision interact in non-trivial ways. Linguistically, spatial utterances are often asymmetrical as they relate more stable objects (reference objects) to less stable objects (located objects). Researchers have claimed that such linguistic asymmetry should also be reflected in the allocation of visual attention when people process a depicted spatial relation described by spatial language.

WIlsON: Web-based Interactive Omics VisualizatioN.

Motivation: High throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects of the understanding of biological systems, both generating extensive need for customized and dynamic visualization.

Results: Here we describe WIlsON, an interactive workbench for analysis and visualization of multi-omics data.

Spatial cognition in minimally invasive surgery: a systematic review.

Background: Spatial cognition is known to play an important role in minimally invasive surgery (MIS), as it was found to enable faster surgical skill acquisition, reduce surgical time and errors made and significantly improve surgical performance. No prior research attempted to summarize the available literature, to indicate the level of importance of the individual spatial abilities and how they impact surgical performance and skill acquisition in MIS.

Methods: Psychological and medical databases were systematically searched to identify studies directly exploring spatial cognition in MIS learning and performance outcomes.

Inter-process relations in spatial language: Feedback and graded compatibility.

Mapping spatial expressions such as "behind the cup" to a spatial region requires two processes that have been largely explored independently: reference frame selection and spatial term assignment (Logan & Sadler, 1996). Reference frame selection carves a space into regions. Spatial term assignment evaluates these regions by determining the acceptability of the term for the given configuration.

Computationally constructing a repository of compound remote associates test items in American English with comRAT-G.

The Remote Associates Test (RAT) has been used to measure creativity, however few repositories or standardizations of test items exist, like the normative data on 144 items provided by Bowden and Jung-Beeman. comRAT is a computational solver which has been used to solve the compound RAT in linguistic and visual forms, showing correlation to human performance over the normative data provided by Bowden and Jung-Beeman. This paper describes using a variant of comRAT, comRAT-G, to generate and construct a repository of compound RAT items for use in the cognitive psychology and cognitive modeling community.

Mechanisms of Reference Frame Selection in Spatial Term Use: Computational and Empirical Studies.

Previous studies have shown that multiple reference frames are available and compete for selection during the use of spatial terms such as "above." However, the mechanisms that underlie the selection process are poorly understood. In the current paper we present two experiments and a comparison of three computational models of selection to shed further light on the nature of reference frame selection.

Modeling mental spatial reasoning about cardinal directions.

This article presents research into human mental spatial reasoning with orientation knowledge. In particular, we look at reasoning problems about cardinal directions that possess multiple valid solutions (i.e.

Determinants of attentional modulation near the hands.

A series of visual search experiments conducted by Abrams et al. (2008) indicates that disengagement of visual attention is slowed when the array of objects that are to be searched are close to the hands (hands on the monitor) than if they are not close to the hands (hands in the lap). These experiments establish the impact one's hands can have on visual attentional processing.

Just the tip of the iceberg: the bicoded map is but one instantiation of scalable spatial representation structures.

Although the bicoded map constitutes an interesting candidate representation, proposing it as the predominant representation for three-dimensional space is too restrictive. We present and argue for scalable spatial representation structures as a more comprehensive alternative account that includes the bicoded map as a special case.

Indicators of early and late processing reveal the importance of within-trial-time for theories of associative learning.

In four human learning experiments (Pavlovian skin conductance, causal learning, speeded classification task), we evaluated several associative learning theories that assume either an elemental (modified unique cue model and Harris' model) or a configural (Pearce's configural theory and an extension of it) form of stimulus processing. The experiments used two modified patterning problems (A/B/C+, AB/BC/AC+ vs. ABC-; A+, BC+ vs.

Differences between Spatial and Visual Mental Representations.

This article investigates the relationship between visual mental representations and spatial mental representations in human visuo-spatial processing. By comparing two common theories of visuo-spatial processing - mental model theory and the theory of mental imagery - we identified two open questions: (1) which representations are modality-specific, and (2) what is the role of the two representations in reasoning. Two experiments examining eye movements and preferences for under-specified problems were conducted to investigate these questions.

[Stress incontinence after prostatectomy in treatment reality: results from a rehabilitation clinic].

Background: In the current discussion on the operative therapy of prostate cancer, not only"if" but also"how" play a major role. Both questions are closely related as, e.g.

Casimir: an architecture for mental spatial knowledge processing.

Mental spatial knowledge processing often uses spatio-analogical or quasipictorial representation structures such as spatial mental models or mental images. The cognitive architecture Casimir is designed to provide a framework for computationally modeling human spatial knowledge processing relying on these kinds of representation formats. In this article, we present an overview of Casimir and its components.

ALTSim: a MATLAB simulator for current associative learning theories.

ALTSim is a MATLAB-based simulator of several associative learning models, including Pearce's configural model, the extended configural model, the Rescorla-Wagner model, the unique cue hypothesis, the modified unique cue hypothesis, the replaced elements model, and Harris's elemental model. It allows for specifying all relevant parameters, as well as exact stimulus sequences by graphical user interfaces. It is an easy-to-use tool that facilitates evaluating and comparing the featured associative learning models.

HMS: a MATLAB simulator of the Harris model of associative learning.

Harris (2006) recently proposed a new elemental model of the processes involved in associative learning. Although Harris explicated all relevant mathematical and conceptual details of the model in his article, implementing a computer simulation of his model requires considerable programming expertise and work. We therefore present the Harris model simulator (HMS), a MATLAB simulator of Harris's model.