A survey of experimental stimulus presentation code sharing in major areas of psychology.

Computer code plays a vital role in modern science, from the conception and design of experiments through to final data analyses. Open sharing of code has been widely discussed as being advantageous to the scientific process, allowing experiments to be more easily replicated, helping with error detection, and reducing wasted effort and resources. In the case of psychology, the code used to present stimuli is a fundamental component of many experiments. It is not known, however, the degree to which researchers are sharing this type of code. To estimate this, we conducted a survey of 400 psychology papers published between 2016 and 2021, identifying those working with the open-source tools Psychtoolbox and PsychoPy that openly share stimulus presentation code. For those that did, we established if it would run following download and also appraised the code's usability in terms of style and documentation. It was found that only 8.4% of papers shared stimulus code, compared to 17.9% sharing analysis code and 31.7% sharing data. Of shared code, 70% ran directly or after minor corrections. For code that did not run, the main error was missing dependencies (66.7%). The usability of the code was moderate, with low levels of code annotation and minimal documentation provided. These results suggest that stimulus presentation code sharing lags behind other forms of code and data sharing, potentially due to less emphasis on such code in open-science discussions and in journal policies. The results also highlight a need for improved documentation to maximize code utility.

No Frequency-Specific Effect of Transcranial Random Noise Stimulation on Resting EEG.

BACKGROUND: Transcranial random noise stimulation (tRNS) is a form of noninvasive transcranial electrical stimulation that applies alternating current in various randomized frequencies to the cortex, thereby improving cognitive functioning in multiple domains. However, the precise mechanism of tRNS, as well as its impact on human electroencephalography (EEG), remains unclear. This is partly because most studies have used tRNS in conjunction with a cognitive task, making it difficult to tease apart whether the observed changes in EEG are a result of tRNS, the cognitive task, or their interaction. METHODS: Forty-nine healthy individuals participated in this study and were randomly assigned to active tRNS (n = 24) and sham (n = 25) groups. tRNS was delivered for 20 minutes over Fp1/Fp2 and Oz. Resting-state EEG data were collected before and after either tRNS or sham stimulation. RESULTS: Cluster-based permutation tests using FieldTrip revealed no frequency-specific effect of tRNS on resting-state EEG data across four frequency bands (theta, alpha, beta, gamma). CONCLUSIONS: These observations suggest that tRNS itself does not target or alter specific EEG frequencies. Rather, tRNS most likely interacts with the cognitive task/activity at hand to produce an observable difference in post-tRNS EEG. Positive tRNS-EEG findings from previous studies are also likely to have resulted from the interactive and cognitive activity-dependent nature of tRNS.

Driving Frequency Modulates Correlations Between Executive Functions and Driving Performance: A Driving Simulator Study.

Driving a car requires a complex combination of various cognitive functions (e.g., visual perception, motor control, decision making, and others), and deficits in any of these processes may compromise driving safety. Amongst these, executive functions such as inhibitory control, task switching, and decision-making are important, as they enable drivers to process information from their surroundings and respond appropriately to changing road conditions. Although previous research has focused on laboratory measures of individual executive functions, it remains unclear whether performance on such laboratory tests readily translates to actual on-the-road driving performance, especially since drivers' skill levels can vary widely, based on their driving frequency. To this end, we divided 30 participants into two categories based on their driving frequency (i.e., daily commuter vs. weekend only drivers), and we used three well-known executive functioning tasks (the stop signal task, Iowa gambling task or IGT, and a task-switching test) to see whether scores on these tasks predicted such driving performances and behaviors such as braking time, lane-keeping, speed limit violations, and inter-vehicle distance (e.g., in a driving simulator). Participants went through a follow-lead-car scenario in the driving simulator for 20 minutes and then completed the three executive tasks. We found that stop signal reaction time (SSRT) best predicted driving performance, and remained predictive against driver distraction, as well as variabilities in driving frequency. The IGT predicted speed limit violations in high-frequency drivers, whereas task-switching cost predicted lane keeping performance in low-frequency drivers. Together, these results highlight the importance of driving frequency when considering correlates between executive functions and driving performance and behavior. They also imply that executive tasks better predict driving performance in low-frequency (or inexperienced) drivers, while driver temperament (i.e., impulsiveness as indicated by IGT) better predicted driving performance in high-frequency (or experienced) drivers.

The hidden arrow in the FedEx logo: Do we really unconsciously "see" it?

The FedEx logo makes clever use of figure-ground ambiguity to create an "invisible" arrow in the background space between "E" and "x". Most designers believe the hidden arrow can convey an unconscious impression of speed and precision about the FedEx brand, which may influence subsequent behavior. To test this assumption, we designed similar images with hidden arrows to serve as endogenous (but camouflaged) directional cues in a Posner's orienting task, where a cueing effect would suggest subliminal processing of the hidden arrow. Overall, we observed no cue congruency effect, unless the arrow is explicitly highlighted (Experiment 4). However, there was a general effect of prior knowledge: when people were under pressure to suppress background information, those who knew about the arrow could do so faster in all congruence conditions (i.e., neutral, congruent, incongruent), although they fail to report seeing the arrow during the experiment. This was true in participants from North America who had heard of the FedEx arrow before (Experiment 1 & 3), and also in our Taiwanese sample who were just informed of such design (Experiment 2). These results can be well explained by the Biased Competition Model in figure-ground research, and together suggest: (1) people do not unconsciously perceive the FedEx arrow, at least not enough to exhibit a cueing effect in attention, but (2) knowing about the arrow can fundamentally change the way we visually process these negative-space logos in the future, making people react faster to images with negative space regardless of the hidden content.

Effect of Non-canonical Spatial Symmetry on Subitizing.

Subitizing refers to ability of people to accurately and effortlessly enumerate a small number of items, with a capacity around four elements. Previous research showed that "canonical" organizations, such as familiar layouts on a dice, can readily improve subitizing performance of people. However, almost all canonical shapes found in the world are also highly symmetrical; therefore, it is unclear whether previously reported facilitative effect of canonical organization is really due to canonicality, or simply driven by spatial symmetry. Here, we investigated the possible effect of symmetry on subitizing by using symmetrical, yet non-canonical, shape structures. These symmetrical layouts were compared with highly controlled random patterns (Experiment 1), as well as fully random and canonical patterns (Experiment 2). Our results showed that symmetry facilitates subitizing performance, but only at set size of 6, suggesting that the effect is insufficient to improve performance of people in the lower or upper range. This was also true, although weaker, in reaction time (RT), error distance measures, and Weber Fractions. On the other hand, canonical layouts produced faster and more accurate subitizing performances across multiple set sizes. We conclude that, although previous findings mixed symmetry in their canonical shapes, their findings on shape canonicality cannot be explained by symmetry alone. We also propose that our symmetrical and canonical results are best explained by the "groupitizing" and pattern recognition accounts, respectively.

Altered EEG Signal Complexity Induced by Hand Proximity: A Multiscale Entropy Approach.

Visual short-term memory (VSTM) is an important cognitive function that acts as a temporary storage for visual information. Previous studies have shown that VSTM capacity can be modulated by the location of one's hands, where hand proximity enhances neural processing and memory of nearby visual stimuli. The present study used traditional event-related potentials (ERP) along with multiscale entropy (MSE) analysis to shed light on the neural mechanism(s) behind such near-hand effect. Participants' electroencephalogram (EEG) data were recorded as they performed a VSTM task with their hands either proximal or distal to the display. ERP analysis showed altered memory processing in the 400-700 ms time window during memory retrieval period. Importantly, MSE analysis also showed significant EEG difference between hand proximal and distal conditions between scales 10 to 20, and such difference is clustered around the right parietal cortex - a region that is involved in VSTM processing and bimodal hand-eye integration. The implications of higher MSE time scale in the parietal cortex are discussed in the context of signal complexity and its possible relation to cognitive processing. To our knowledge, this study provides the first investigation using MSE to characterize the temporal characteristics and signal complexity behind the effect of hand proximity.

Variation of picture angles and its effect on the Concealed Information Test.

BACKGROUND: The reaction time-based Concealed Information Test (RT-CIT) is a memory paradigm used to detect crime-related knowledge. However, this would also imply that the RT-CIT would be vulnerable to factors that are known to compromise object recognition or memory integrity. From this perspective, one key issue is whether "guilty" memory can be detected if the crime-related images are photographed at different angles from what the perpetrator saw, which is almost always the case in the field. To investigate this, here we manipulated the deviation angles, from 0° to 330° in 11 steps, between the study and test phases to assess how the RT-CIT holds up against angular rotations. RESULTS: We observed a robust RT-CIT effect at all deviation angles for both deep-encoders (Experiment 1) and shallow-encoders (Experiment 2). The RT-CIT was effective within the first 250 or so trials for both encoding groups, with smaller probe-irrelevant differences beyond that. CONCLUSIONS: With appropriate encoding and memory strength, RT-CIT images do not necessarily have to match the exact angle of the perpetrator's perspective at the time of the crime. Unnatural angles such as 90° and 270° or unconventional rotational axes may require caution. Trial number under 250 trials show maximal Probe-Irrelevant difference, but more trials may add power to improve detection accuracy.

Anodal and Cathodal tDCS Over the Right Frontal Eye Fields Impacts Spatial Probability Processing Differently in Pro- and Anti-saccades.

Learning regularities that exist in the environment can help the visual system achieve optimal efficiency while reducing computational burden. Using a pro- and anti-saccade task, studies have shown that probabilistic information regarding spatial locations can be a strong modulator of frontal eye fields (FEF) activities and consequently alter saccadic behavior. One recent study has also shown that FEF activities can be modulated by transcranial direct current stimulation, where anodal tDCS facilitated prosaccades but cathodal tDCS prolonged antisaccades. These studies together suggest that location probability and tDCS can both alter FEF activities and oculomotor performance, yet how these two modulators interact with each other remains unclear. In this study, we applied anodal or cathodal tDCS over right FEF, and participants performed an interleaved pro- and anti-saccade task. Location probability was manipulated in prosaccade trials but not antisaccade trials. We observed that anodal tDCS over rFEF facilitated prosaccdes toward low-probability locations but not to high-probability locations; whereas cathodal tDCS facilitated antisaccades away from the high-probability location (i.e., same location as the low-probability locations in prosaccades). These observed effects were specific to rFEF as tDCS over the SEF in a separate control experiment did not yield similar patterns. These effects were also more pronounced in low-performers who had slower saccade reaction time. Together, we conclude that (1) the overlapping spatial endpoint between prosaccades (i.e., toward low-probability location) and antisaccades (i.e., away from high-probability location) possibly suggest an endpoint-selective mechanism within right FEF, (2) anodal tDCS and location probability cannot be combined to produce a bigger facilitative effect, and (3) anodal rFEF tDCS works best on low-performers who had slower saccade reaction time. These observations are consistent with the homeostasis account of tDCS effect and FEF functioning.

Electrophysiological markers of working memory usage as an index for truth-based lies.

People prefer to lie using altered truthful events from memory, perhaps because doing so can increase their credibility while reducing cognitive and working memory (WM) load. One possible way to counter such deceptive behavior is to track WM usage, since fabricating coherent lies or managing between truth and lies is likely to involve heavy WM load. In this study, participants memorized a list of words in the study session and used these old words to provide deceptive answers when cued later, in the testing session. Our behavioral results showed that people needed more time to make a deceptive response during the execution stage, and this prolonged deceptive reaction time (RT) was negatively correlated with each participant's WM capacity. Event-related potential findings showed a more negative-going frontal amplitude between the lie and truth conditions during the preparation stage, suggesting that WM preparatory processes can be detected long before a deceptive response is verbalized. Furthermore, we observed a larger positive frontal-central amplitude during the execution stage, which was negatively correlated with participants' lie-truth RT differences, suggesting that participants' efficiency in producing deceptive responses can be readily traced electrophysiologically. Together, these findings suggest that WM capacity and preparation are crucial to efficient lying and that their related electrophysiological signatures can potentially be used to uncover deceptive behaviors.

The relationship between the development of response inhibition and intelligence in preschool children.

Building on the theoretical framework that intellectual behavior relies on one's ability to process both task-relevant and task-irrelevant information, this study aimed to empirically investigate the association of response inhibition with intelligence in preschool children's development. In a sample of 152 typically developing children aged between 3.6 and 6.6 years, we found evidence that suggests that inhibitory control is linked to age-related differences in intelligence. Stop-signal inhibition improved at a rate similar to the age-related changes in Verbal IQ. Components of variance analyses revealed that stop-signal reaction time predicted a larger proportion of the age-related variance in children's verbal intelligence than non-age-related variance. Results are discussed with respect to possible explanations for this intriguing relationship between response inhibition and the verbal aspects of intelligence.

Frontal midline theta as a neurophysiological correlate for deficits of attentional orienting in children with developmental coordination disorder.

Children with developmental coordination disorder (DCD) have been demonstrated to show attentional orienting deficits. The neural mechanism, however, has thus far remained elusive. Here, we measure oscillations in the EEG associated with attentional orienting to address this issue. The EEG was recorded from DCD children and typical developing (TD) controls during an eye-gaze cueing paradigm. DCD group responded more slowly than TD group across all conditions. Additionally, TD group showed higher frontal midline theta activities in both valid and invalid conditions relative to a neutral condition, with such an effect absent in the DCD group. Theta oscillations might reflect attentional processing in relation to the cues being performed in TD group, with the lessened modulation of theta in DCD group possibly reflecting a deficit in attentional orienting. Possible explanations for the DCD-TD differences in theta oscillation and attentional orienting are discussed.

Pch2 prevents Mec1/Tel1-mediated Hop1 phosphorylation occurring independently of Red1 in budding yeast meiosis.

A prominent feature of meiosis in most sexually reproducing organisms is interhomolog recombination whereby a significant fraction of the programmed meiotic double-strand breaks are repaired using intact homologous non-sister chromatids rather than sister chromatids. Budding yeast DNA damage checkpoint kinases Mec1 and Tel1 act together with the axial element protein Red1 to promote interhomolog recombination by phosphorylating another axial element protein Hop1. Mec1 and Tel1 also phosphorylate γH2A and the synaptonemal complex protein Zip1 independently of Red1 to facilitate premeiotic DNA replication and to destabilize homology-independent centromere pairing, respectively. It has been unclear why Hop1 phosphorylation is Red1-dependent. Here, we report that the pachytene checkpoint protein 2 (Pch2) specifically prevents Red1-independent Hop1 phosphorylation. Our findings reveal a new function for Pch2 in linking two axial element proteins Red1 and Hop1 thus coordinating their effects in meiotic recombination and the checkpoint network.

The neural development of response inhibition in 5- and 6-year-old preschoolers: an ERP and EEG study.

Many studies have used event-related potential and neural oscillations to probe the underlying neural mechanisms of inhibitory control in adults, but little has been done in typically developing preschoolers. In this study we tested healthy preschool children between the ages of 5 and 6, and observed better response inhibition in 6-year-olds compared to 5-year-olds. Importantly, this age-related difference could not be explained by the N2 component from event-related potential, but was reflected in an increase in right frontal beta power from electroencephalogram. These results suggest that frontal beta power during the preschool period may reflect neural development of inhibitory control.

Tying SUMO modifications to dynamic behaviors of chromosomes during meiotic prophase of Saccharomyces cerevisiae.

In budding yeast Saccharomyces cerevisiae, centromeres and telomeres are tethered to the nuclear envelope during premeiotic interphase. Immediately after cells enter meiotic prophase, chromosomes undergo global reorganization, including bouquet formation (telomere clustering), non-homologous centromere coupling, homologous pairing, and assembly/disassembly of synaptonemal complexes. These chromosome dynamics have been implicated in promoting pairing, synapsis, crossover DNA recombination and segregation between homologous chromosomes. This review discusses recent studies related to the role of small ubiquitin-like modifier (SUMO) modification in controlling the overall budding yeast chromosome dynamics during meiotic prophase.

SUMO modifications control assembly of synaptonemal complex and polycomplex in meiosis of Saccharomyces cerevisiae.

The synaptonemal complex (SC) is a proteinaceous complex that apparently mediates synapsis between homologous chromosomes during meiotic prophase. In Saccharomyces cerevisiae, the Zip1 protein is the integral component of the SC. In the absence of a DNA double-strand break or the SC initiation protein Zip3, Zip1 proteins aggregate to form a polycomplex (PC). In addition, Zip1 is also responsible for DSB-independent nonhomologous centromere coupling at early meiotic prophase. We report here that Zip3 is a SUMO (small ubiquitin-related modifier) E3 ligase and that Zip1 is a binding protein for SUMO-conjugated products. Our results also suggest that at early meiotic prophase, Zip1 interacts with Zip3-independent Smt3 conjugates (e.g., Top2) to promote nonhomologous centromere coupling. At and after mid-prophase, the Zip1 protein begins to associate with Zip3-dependent Smt3 conjugates (e.g., Red1) along meiotic chromosomes in the wild-type cell to form SCs and with Smt3 polymeric chains in the zip3 mutant to form PCs.

Molecular visualization of the yeast Dmc1 protein ring and Dmc1-ssDNA nucleoprotein complex.

Saccharomyces cerevisiae Dmc1, a meiosis-specific homologue of RecA, catalyzes homologous pairing and strand exchange during meiotic DNA recombination. The purified budding yeast Dmc1 (ScDmc1) protein exhibits much weaker recombinase activity in vitro as compared to that of the Escherichia coli RecA protein. Using atomic force microscopy (AFM) with carbon nanotube tips, we found ScDmc1 forms rings with an external diameter of 18 nm and a central cavity of 4 nm. In the presence of single-stranded DNA (ssDNA), the majority of the ScDmc1 protein (90%) bound DNA as protein rings; only a small faction (10%) was able to form filamentous structure. In contrast, nearly all RecA proteins form fine helical nucleoprotein filaments with ssDNA under identical conditions. RecA-mediated recombinase activity is initiated through the nucleation of RecA onto ssDNA to form helical nucleoprotein filaments. Our results support the notion that ScDmc1 becomes catalytically active only when it forms a helical nucleoprotein filament with ssDNA.

Solution structure of gamma-bungarotoxin: the functional significance of amino acid residues flanking the RGD motif in integrin binding.

Gamma-bungarotoxin, a snake venom protein isolated from Bungarus multicinctus, contains 68 amino acids, including 10 cysteine residues and a TAVRGDGP sequence at positions 30-37. The solution structure of gamma-bungarotoxin has been determined by nuclear magnetic resonance (NMR) spectroscopy. The structure is similar to that of the short-chain neurotoxins that contain three loops extending from a disulfide-bridged core. The tripeptide Arg-Gly-Asp (RGD) sequence is located at the apex of the flexible loop and is similar to that of other RGD-containing proteins. However, gamma-bungarotoxin only inhibits platelet aggregations with an IC50 of 34 microM. To understand its weak activity in inhibiting platelet aggregation, we mutated the RGD loop sequences of rhodostomin, a potent platelet aggregation inhibitor, from RIPRGDMP to TAVRGDGP, resulting in a 196-fold decrease in activity. In addition, the average Calpha-to-Calpha distance between R33 and G36 of gamma-bungarotoxin is 6.02 A, i.e., shorter than that of other RGD-containing proteins that range from 6.55 to 7.46 A. These results suggested that the amino acid residues flanking the RGD motif might control the width of the RGD loop. This structural difference may be responsible for its decrease in platelet aggregation inhibition compared with other RGD-containing proteins.

Heterodimeric complexes of Hop2 and Mnd1 function with Dmc1 to promote meiotic homolog juxtaposition and strand assimilation.

Saccharomyces cerevisiae Hop2 and Mnd1 are abundant meiosisspecific chromosomal proteins, and mutations in the corresponding genes lead to defects in meiotic recombination and in homologous chromosome interactions during mid-prophase. Analysis of various double mutants suggests that HOP2, MND1, and DMC1 act in the same genetic pathway for the establishment of close juxtaposition between homologous meiotic chromosomes. Biochemical studies indicate that Hop2 and Mnd1 proteins form a stable heterodimer with a higher affinity for double-stranded than single-stranded DNA, and that this heterodimer stimulates the strand assimilation activity of Dmc1 in vitro. Together, the genetic and biochemical results suggest that Hop2, Mnd1, and Dmc1 are functionally interdependent during meiotic DNA recombination.