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College of Sciences

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School of Biological Sciences

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School of Chemistry and Biochemistry

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School of Earth and Atmospheric Sciences

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School of Mathematics

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School of Physics

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Publication Search Results

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Interlaboratory Comparison of a Complex Targeted Assay: Improving Consistency and Reliability in Metabolomics Analyses

(Georgia Institute of Technology, 2023-12-07) Phillips, Emily R.

Ideal isotope-labeled internal standards for analysis via targeted metabolomics approaches are presented for negative and positive ion modes for both hydrophilic interaction liquid chromatography (HILIC) and reverse phase liquid chromatography (RPLC) chromatography coupled to mass spectrometry. These best performing analytes (BPA) were deduced after experimentation from a collaborative research project involving six top metabolomics research laboratories in the country. These results are detailed in this work, supported by observed behaviors of included chemical classes and chromatographic behaviors, and align with the group hypothesis and expectations
Directability Through AI Customization: The Effect of Choice on Trust and Acceptance in Highly Automated Vehicles

(Georgia Institute of Technology, 2023-12-05) Scott-Sharoni, Sidney Tammie

People feel apprehensive about using or relying on highly automated vehicles (American Automotive Association, 2019). One method of assuaging fears involves providing explanations for the system’s behaviors using a Human-Machine Interface (HMI). However, understanding the amount of information for optimal human-automation interaction can prove difficult due to differences in individuals’ preferences, experiences, and needs. An underexplored method that may account for these discrepancies involves providing users with choices or customization. The Coactive Design Approach suggests that including directability, or the power to influence a system’s actions, may improve how users interact with systems (Johnson et al., 2014). The following study investigated how customization affordances and modified vehicle aspect of a Level 4 automated vehicle affected trust and acceptance. One hundred twenty participants experienced one highly automated simulator drive, during which they engaged in a visually demanding game. A MANOVA assessed the interaction of and main effects of customization availability and modified vehicle aspect on trust and acceptance. While participants who customized had higher average trust and acceptance in the automated vehicle than participants who did not customize, only the main effect of vehicle aspect significantly impacted the multivariate dimension of trust and acceptance in the automated vehicle. That is, modifications to the vehicle impacted users regardless of whether they chose the modification. The game score and subjective trust did significantly correlate to a small, positive extent, indicating that higher trust in a system may improve non-driving related task performance. Future research should continue to investigate the role of choice in the interaction between individuals and highly automated systems to understand the psychological impacts of directability.
Memory Self-Modification as a Function of Confidence during Reconsolidation

(Georgia Institute of Technology, 2023-07-31) Yaun, Jeffrey W.

Students are often surprised to find that the grade they receive on an exam does not comport with the confidence they felt about their answers. What use, then, is confidence if it does not necessarily indicate accuracy? Better understanding of this question may not lie in approaching from a perspective of accuracy, but in the consistency of recall. Does confidence influence what is recalled, and does the act of recall itself provide enough of an opportunity to change what is recalled? What does this indicate about reconsolidation, the proposed process of reactivating and updating memory? This study examined these questions by providing participants with a pair of videos and a set of questions about their content, along with confidence judgements about their answers. After 4-day gap periods, participants twice recorded free-recall sessions about one of the two videos, then answered the original questions again. Results indicated that initial confidence is a strong predictor of subsequent recall and the consistency of recall, but failed to be a predictor for accuracy of recall. The predicted interaction of recall with confidence to predict consistency also failed to be statistically significant. Confidence may therefore play a greater role in the consistency of recall than in objective accuracy. The lack of a recall effect on accuracy or consistency may also indicate a more gradual process for changes in memory traces than predicted by reconsolidation theory.
Experiments to optimize the ribose-seq protocol

(Georgia Institute of Technology, 2023-07-31) Bahl, Smriti

Ribonucleoside monophosphates (rNMPs), the units of RNA, are the most abundant non-standard nucleotides found in genomic DNA. They can be incorporated by DNA polymerases during DNA replication and repair, by hydroxyl radicals during oxidative stress or during incomplete maturation of Okazaki fragments. rNMPs have profound consequences on genome stability, DNA structure, function, and various cellular processes. To better understand these effects, the Storici lab developed the ribose-seq protocol which is a systematic technique for capturing and analyzing rNMPs in genomic DNA. The aim of this study is to optimize the ribose-seq protocol by enhancing the efficiency and accuracy of rNMP detection while minimizing the required amount of starting DNA, thereby enabling easier acquisition also for possible clinical applications. We systematically investigated three key steps of the protocol: (1) adaptor ligation, (2) self-ligation using Arabidopsis thaliana tRNA ligase (AtRNL), and (3) degradation of linear single-stranded DNA (ssDNA) using exonuclease. Through rigorous experimentation and analysis, we observed that modifying the adaptor ligation conditions resulted in approximately a 30% increase in ligation efficiency of the adaptor to the fragmented DNA. The use of AtRNL with an extended incubation period at lower temperature enabled improved circularization of DNA containing the rNMPs, resulting in more abundant ribose-seq library product. Furthermore, novel exonucleases were evaluated as potential replacements for T5 exonuclease in order to effectively eliminate the remaining linear ssDNA following AtRNL self-ligation and protect the circular ssDNA structures containing rNMPs from exonuclease-mediated degradation. To validate the findings of this project, ribose-seq libraries were constructed using Saccharomyces cerevisiae DNA, demonstrating the potential to reduce the starting DNA amount by up to 50%. These findings present a significant advancement in the ribose-seq methodology, enabling researchers to investigate ribonucleotide-mediated genomic processes with enhanced sensitivity and reduced resource requirements.
Mechanisms of Coherence and Incoherence Between GWAS and Single-Cell eQTL Effects in Crohn's Disease

(Georgia Institute of Technology, 2023-05-02) Collins, Jared Blake

The integration of expression quantitative trait loci with GWAS data has proven invaluable in the exploration of mechanisms through which genetic variants influence complex traits. However, it has also highlighted instances of incoherence in which the eQTL effects of GWAS risk variants seemingly contradict observed case and control expression. Patterns of incoherence may indicate variants associated with disease via protection, but due to the highly heterogenous nature of varying cell-types, may also indicate cell-type specific associations with disease that are convoluted by bulk RNA sequencing. Here, we conduct exploratory analysis integrating sceQTL and GWAS data associated with Crohn’s Disease to assess patterns of coherence and incoherence, using both bulk RNA-seq and predicted single-cell gene expression for case-control expression. We show that integration of GWAS summary statistics with single-cell eQTL data is a promising approach for uncovering cell type specific patterns of coherence and incoherence, and may suggest functional mechanisms underlying these associations.
Changes of community structure of seagrass-associated elasmobranchs and teleosts in Florida’s “Big Bend” ecosystem

(Georgia Institute of Technology, 2023-05-02) Rackley, Piper M.

Sharks play a significant ecological role as predatory species in the world’s oceans. While they have been around for millions of years, they face many threats today, such as fishing and habitat destruction (via pollution and coastal development), that diminish their populations, and some species are on the verge of extinction. Over the past four decades, ocean water temperatures have risen significantly and have severely altered marine ecosystems. Florida’s “Big Bend” ecosystem is a diverse seagrass ecosystem and is characterized by the gradient of freshwater influence that enters the system from major rivers in its northern region. This study took place from 2009 to 2021 and covered four sections of the “Big Bend” that varied in abiotic factors, such as salinity, water clarity, temperature, etc. We hypothesize that the abundance and distribution of these elasmobranch and large teleost species are associated with differences in abiotic factors between our sampling sites. Specifically, salinities and water temperature will play a significant role in the habitat usage of these organisms, and we expect there to be significant impacts of these factors that indicate habitat preferences amongst these species.
Conceptualization and Assessment of the Home Workspace: A Person-Centered Approach

(Georgia Institute of Technology, 2023-04-13) Egan, Jennifer

The prevalence of working from home (WFH) as an alternative work arrangement has gradually increased as a result of pivotal technological, societal, and global developments from the 1990s (Felstead & Henseke, 2017). WFH is not a novel phenomenon, but relatively little attention has been given to the impact of how the spatial environment of the home workspace affects an individual’s work experience (Stephenson et al., 2020). Given that remote work is unlikely to recede to pre-Covid-19 pandemic levels (Bana et al., 2020), organizational psychologists should consider the impact of home workspace environments on worker-related outcomes. This study builds upon boundary theory (Ashforth et al., 2000) and architectural perspectives by using person-centered, sensory based (i.e., visual, auditory, olfactory) measures of the home environment. 199 administrative staff participants were administered a survey that measured connections between objective aspects of the home environment (e.g., workspace size), sensory inputs from the home domain, psychological outcomes, and respondent intentions to WFH in the future. Ultimately, objective and self-situated aspects of the home environment positively related to the sensory inputs. Auditory and visual inputs positively related to general stress and home-work boundary violations. Specifically, auditory inputs from the home environment predicted general stress, while visual inputs predicted a more general assessment of home-work boundary violations. Finally, home-work boundary violations were positively related to a worker’s intention to work from home in the future. Implications for theory, remote workers, organizational leaders, and designers, are discussed.
3D-printed stand, timing interface, and coil localization tools for concurrent TMS-fMRI experiments

(Georgia Institute of Technology, 2023-04-03) Goldstein, Samuel

Concurrent TMS-fMRI involves administrating TMS while subjects are inside an MRI scanner and allows the study of the effects of neurostimulation on simultaneous brain activity. Despite its high promise, the technique has proven challenging to implement for at least three reasons. First, it is difficult to position and stabilize the TMS coil inside the MRI scanner in a way that precisely targets a pre-specified brain region. Second, standard task-presentation software suffers from imprecise timing, which can lead to TMS causing large image artifacts. Third, it is difficult to verify the exact TMS coil position during scanning. In this paper, we describe solutions to all three of these challenges. First, we develop a 3D-printed TMS stand that is fully adjustable and can reach most areas of the scalp. The stand is compatible with various MR coils and features an adjustable mirror holder. Second, we create an interface that can precisely time the TMS pulses with respect to the fMRI image acquisition with a variance of under 1 ms. Third, we develop software for precisely determining the TMS coil position inside the MRI scanner and computing the location of maximal stimulation. All three tools are either free or inexpensive. We provide detailed instructions for building and implementing these tools to facilitate an efficient and reliable concurrent TMS-fMRI setup.
Faculty Time Allocation i-deals and Work-family Balance

(Georgia Institute of Technology, 2023-03-27) Storey, Rebecca Anne

Poor work-family is balance is one reason that faculty exit their careers in academia. A possible remedy to this issue can be found in the work design literature. Faculty can take active roles in shaping their employment arrangements to meet their needs by negotiating time allocation idiosyncratic deals (i-deals). Time allocation i-deals are personalized work arrangements negotiated between a faculty member and their chair in which they negotiate time allocated across research, teaching, and service demands. Using three waves of archival data collected from faculty in the United States, the present study used needs-supplies (N-S) fit theory to explore whether poor work-family balance prompts faculty to negotiate a time allocation i-deal, and if greater work-family balance is an outcome of these arrangements. Two individual differences, role centrality and decision authority, were also tested as moderators in the relationship between work-family balance and subsequent i-deal use. Altogether, the within-person hypothesized relationships were not significant. However, at the between-person level, time allocation i-deals were positively associated with work-family balance. These findings suggest that faculty who have greater time allocation customization enjoy greater work-family balance, but work-family balance is not maintained over time by continually altering levels of time allocation customization via i-deals.
Are Prosaccades Always Automatic?: Validating the Antisaccade Task as a Measure of Controlled Attention

(Georgia Institute of Technology, 2023-02-10) Mashburn, Cody Anthony

Recently, mainstream cognitive psychology has become aware of difficulties in measuring individual differences in the ability to direct attention in a goal-direct manner. Such difficulties may suggest that attention control is not a measurable general cognitive ability but may instead be highly task-specific. Accuracy rates from the antisaccade task are a notable exception to the measurement difficulties often seen in other tasks, but the measure’s construct validity has been questioned. Some researchers have argued that antisaccade accuracy is a function of individual differences in general processing speed (e.g., Rey-Mermet et al., 2019). The present study evaluated this position in a combined differential-experimental study. I assessed whether the adaptive procedures adopted by previous studies in non-attention-demanding tasks increased attention control demands, leading to inaccurate estimates of criterion-related validity. I compared two versions of the prosaccade task (a non-attention-demanding variant of the antisaccade task), a non-adaptive version and an adaptive version which adjusted the presentation duration of a target stimulus on a trial-by-trial basis. I also attempted to eliminate the relationship between antisaccade accuracy and working memory capacity/fluid intelligence by accounting for speed measures from both prosaccade tasks. Mean pupil size was larger in the pre-target period of the adaptive prosaccade task than in the non-adaptive prosaccade task, suggesting the adaptive procedure made the task more effortful. Crucially, however, no matter how I attempted to control for processing speed, I could not eliminate the relationship between antisaccade accuracy and cognitive abilities, implying that antisaccade accuracy is not merely a proxy measure for general speed.