TY - JOUR A1 - Kline, Rachel A. A1 - Lößlein, Lena A1 - Kurian, Dominic A1 - Aguilar Martí, Judit A1 - Eaton, Samantha L. A1 - Court, Felipe A. A1 - Gillingwater, Thomas H. A1 - Wishart, Thomas M. T1 - An optimized comparative proteomic approach as a tool in neurodegenerative disease research JF - Cells N2 - Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability. KW - proteomics KW - systems biology KW - experimental design KW - neurodegeneration KW - pathway analysis KW - data filtering Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-285912 SN - 2073-4409 VL - 11 IS - 17 ER - TY - JOUR A1 - Muth, Felicitas V. A1 - Wirth, Robert A1 - Kunde, Winfried T1 - Temporal binding past the Libet clock: testing design factors for an auditory timer JF - Behavior Research Methods N2 - Voluntary actions and causally linked sensory stimuli are perceived to be shifted towards each other in time. This so-called temporal binding is commonly assessed in paradigms using the Libet Clock. In such experiments, participants have to estimate the timing of actions performed or ensuing sensory stimuli (usually tones) by means of a rotating clock hand presented on a screen. The aforementioned task setup is however ill-suited for many conceivable setups, especially when they involve visual effects. To address this shortcoming, the line of research presented here establishes an alternative measure for temporal binding by using a sequence of timed sounds. This method uses an auditory timer, a sequence of letters presented during task execution, which serve as anchors for temporal judgments. In four experiments, we manipulated four design factors of this auditory timer, namely interval length, interval filling, sequence predictability, and sequence length, to determine the most effective and economic method for measuring temporal binding with an auditory timer. KW - temporal binding KW - auditory timer KW - experimental design KW - measures KW - intentional binding Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-234922 VL - 53 IS - 3 ER - TY - JOUR A1 - Wirth, Robert A1 - Foerster, Anna A1 - Kunde, Wilfried A1 - Pfister, Roland T1 - Design choices: Empirical recommendations for designing two-dimensional finger-tracking experiments JF - Behavior Research Methods N2 - The continuous tracking of mouse or finger movements has become an increasingly popular research method for investigating cognitive and motivational processes such as decision-making, action-planning, and executive functions. In the present paper, we evaluate and discuss how apparently trivial design choices of researchers may impact participants’ behavior and, consequently, a study’s results. We first provide a thorough comparison of mouse- and finger-tracking setups on the basis of a Simon task. We then vary a comprehensive set of design factors, including spatial layout, movement extent, time of stimulus onset, size of the target areas, and hit detection in a finger-tracking variant of this task. We explore the impact of these variations on a broad spectrum of movement parameters that are typically used to describe movement trajectories. Based on our findings, we suggest several recommendations for best practice that avoid some of the pitfalls of the methodology. Keeping these recommendations in mind will allow for informed decisions when planning and conducting future tracking experiments. KW - movement tracking KW - experimental design KW - Simon task KW - measures Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235569 VL - 52 ER - TY - JOUR A1 - Kirsch, Wladimir A1 - Ullrich, Benjamin A1 - Kunde, Wilfried T1 - Are Effects of Action on Perception Real? Evidence from Transformed Movements JF - PLoS ONE N2 - It has been argued that several reported non-visual influences on perception cannot be truly perceptual. If they were, they should affect the perception of target objects and reference objects used to express perceptual judgments, and thus cancel each other out. This reasoning presumes that non-visual manipulations impact target objects and comparison objects equally. In the present study we show that equalizing a body-related manipulation between target objects and reference objects essentially abolishes the impact of that manipulation so as it should do when that manipulation actually altered perception. Moreover, the manipulation has an impact on judgements when applied to only the target object but not to the reference object, and that impact reverses when only applied to the reference object but not to the target object. A perceptual explanation predicts this reversal, whereas explanations in terms of post-perceptual response biases or demand effects do not. Altogether these results suggest that body-related influences on perception cannot as a whole be attributed to extra-perceptual factors. KW - vision KW - preprocessing KW - analysis of variance KW - sensory perception KW - hands KW - fingers KW - experimental design KW - perception Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-178574 VL - 11 IS - 12 ER - TY - JOUR A1 - Halder, Sebastian A1 - Hammer, Eva Maria A1 - Kleih, Sonja Claudia A1 - Bogdan, Martin A1 - Rosenstiel, Wolfgang A1 - Birbaumer, Niels A1 - Kübler, Andrea T1 - Prediction of Auditory and Visual P300 Brain-Computer Interface Aptitude JF - PLoS ONE N2 - Objective Brain-computer interfaces (BCIs) provide a non-muscular communication channel for patients with late-stage motoneuron disease (e.g., amyotrophic lateral sclerosis (ALS)) or otherwise motor impaired people and are also used for motor rehabilitation in chronic stroke. Differences in the ability to use a BCI vary from person to person and from session to session. A reliable predictor of aptitude would allow for the selection of suitable BCI paradigms. For this reason, we investigated whether P300 BCI aptitude could be predicted from a short experiment with a standard auditory oddball. Methods Forty healthy participants performed an electroencephalography (EEG) based visual and auditory P300-BCI spelling task in a single session. In addition, prior to each session an auditory oddball was presented. Features extracted from the auditory oddball were analyzed with respect to predictive power for BCI aptitude. Results Correlation between auditory oddball response and P300 BCI accuracy revealed a strong relationship between accuracy and N2 amplitude and the amplitude of a late ERP component between 400 and 600 ms. Interestingly, the P3 amplitude of the auditory oddball response was not correlated with accuracy. Conclusions Event-related potentials recorded during a standard auditory oddball session moderately predict aptitude in an audiory and highly in a visual P300 BCI. The predictor will allow for faster paradigm selection. Significance Our method will reduce strain on patients because unsuccessful training may be avoided, provided the results can be generalized to the patient population. KW - experimental design KW - acoustic signals KW - amyotrophic lateral sclerosis KW - man-computer interface KW - electroencephalography KW - event-related potentials KW - physical properties KW - vision Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130327 VL - 8 IS - 2 ER -