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Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
(2021)
Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm-Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.
Actin droplet machine
(2019)
The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers.
Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits.
The rock material pentlandite with the composition Fe4.5Ni4.5S8 was synthesized via high temperature synthesis from the elements. The structure and composition of the material was characterized via powder X-ray diffraction (PXRD), Mössbauer spectroscopy (MB), scanning electron microscopy (SEM), differential scanning calorimetry (DSC) and energy dispersive X-ray spectroscopy (EDX). Two preparation methods of pentlandite bulk electrodes are presented. In the first approach a piece of synthetic pentlandite rock is directly contacted via a wire ferrule. The second approach utilizes pentlandite pellets, pressed from finely ground powder, which is immobilized in a Teflon casing. Both electrodes, whilst being prepared by an additive-free method, reveal high durability during electrocatalytic conversions in comparison to common drop-coating methods. We herein showcase the striking performance of such electrodes to accomplish the hydrogen evolution reaction (HER) and present a standardized method to evaluate the electrocatalytic performance by electrochemical and gas chromatographic methods. Furthermore, we report stability tests via potentiostatic methods at an overpotential of 0.6 V to explore the material limitations of the electrodes during electrolysis under industrial relevant conditions.
The Sound of Success: Investigating Cognitive and Behavioral Effects of Motivational Music in Sports
(2017)
Listening to music before, during, or after sports is a common phenomenon, yet its functions and effects on performance, cognition, and behavior remain to be investigated. Listening to music before, during, or after sports is a common phenomenon, yet its functions and effects on performance, cognition, and behavior remain to be investigated. In this study we present a novel approach to the role of music in sports and exercise that focuses on the notion of musical self-enhancement (Elvers, 2016). We derived the following hypotheses from this framework: listening to motivational music will (i) enhance self-evaluative cognition, (ii) improve performance in a ball game, and (iii) evoke greater risk-taking behavior. To evaluate the hypotheses, we conducted a between-groups experiment (N = 150) testing the effectiveness of both an experimenter playlist and a participant-selected playlist in comparison to a no-music control condition. All participants performed a ball-throwing task developed by Decharms and Davé (1965), consisting of two parts: First, participants threw the ball from fixed distances into a funnel basket. During this task, performance was measured. In the second part, the participants themselves chose distances from the basket, which allowed their risk-taking behavior to be assessed. The results indicate that listening to motivational music led to greater risk taking but did not improve ball-throwing performance. This effect was more pronounced in male participants and among those who listened to their own playlists. Furthermore, self-selected music enhanced state self-esteem in participants who were performing well but not in those who were performing poorly. We also discuss further implications for the notion of musical self-enhancement. // Listening to music before, during, or after sports is a common phenomenon, yet its functions and effects on performance, cognition, and behavior remain to be investigated. In this study we present a novel approach to the role of music in sports and exercise that focuses on the notion of musical self-enhancement (Elvers, 2016). We derived the following hypotheses from this framework: listening to motivational music will (i) enhance self-evaluative cognition, (ii) improve performance in a ball game, and (iii) evoke greater risk-taking behavior. To evaluate the hypotheses, we conducted a between-groups experiment (N = 150) testing the effectiveness of both an experimenter playlist and a participant-selected playlist in comparison to a no-music control condition. All participants performed a ball-throwing task developed by Decharms and Davé (1965), consisting of two parts: First, participants threw the ball from fixed distances into a funnel basket. During this task, performance was measured. In the second part, the participants themselves chose distances from the basket, which allowed their risk-taking behavior to be assessed. The results indicate that listening to motivational music led to greater risk taking but did not improve ball-throwing performance. This effect was more pronounced in male participants and among those who listened to their own playlists. Furthermore, self-selected music enhanced state self-esteem in participants who were performing well but not in those who were performing poorly. We also discuss further implications for the notion of musical self-enhancement.
Music listening has become a highly individualized activity with smartphones and music streaming services providing listeners with absolute freedom to listen to any kind of music in any situation. Until now, little has been written about the processes underlying the selection of music in daily life. The present study aimed to disentangle some of the complex processes among the listener, situation, and functions of music listening involved in music selection. Utilizing the experience sampling method, data were collected from 119 participants using a smartphone application. For 10 consecutive days, participants received 14 prompts using stratified-random sampling throughout the day and reported on their music-listening behavior. Statistical learning procedures on multilevel regression models and multilevel structural equation modeling were used to determine the most important predictors and analyze mediation processes between person, situation, functions of listening, and music selection. Results revealed that the features of music selected in daily life were predominantly determined by situational characteristics, whereas consistent individual differences were of minor importance. Functions of music listening were found to act as a mediator between characteristics of the situation and music-selection behavior. We further observed several significant random effects, which indicated that individuals differed in how situational variables affected their music selection behavior. Our findings suggest a need to shift the focus of music-listening research from individual differences to situational influences, including potential person-situation interactions.