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Open Access
Molecular basis of product recognition during PIP5K-mediated production of PI(4,5)P2 with positive feedback
(Journal of Biological Chemistry, 2024-08-03) Duewell, Benjamin R.; Faris, Katherine A.; Hansen, Scott D.
The ability for cells to localize and activate peripheral membrane-binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyzes the phosphorylation of PI(4)P to generate most of the PI(4,5)P2 lipids found in eukaryotic plasma membranes. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. Here, we examine how two motifs contribute to PI(4,5)P2 recognition to control membrane association and catalysis of PIP5K. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PI(4,5)P2 lipids. After correctly orienting on the membrane, PIP5K transitions to binding PI(4,5)P2 lipids near the active site through a motif previously referred to as the substrate or PIP-binding motif (PIPBM). The PIPBM has broad specificity for anionic lipids and serves a role in regulating membrane association in vitro and in vivo. Overall, our data supports a two-step membrane-binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2 production.
Open Access
Breathing-Based Meditation for Improving COPD Burden: A Mixed Single- Case and Qualitative Approach
(LISDEN Publishing Inc., 2023-12-19) Lin, Ting-fen; Linville, Deanna; Nese, Rhonda N. T.; Seeley, John; Shune, Samantha
Chronic obstructive pulmonary disease (COPD) impacts the physiological and psychoemotional aspects of life. COPD-related secondary sequelae also synergistically interact with each other. For example, dyspnea affects the severity of breath, body functions, and the mind (e.g., anxiety, panic, fear). Such negative psycho-emotional states can further negatively impact the breath and the body (e.g., increased dyspnea). Given the breadth of the impact of COPD on multiple facets of health and well-being, it is essential to investigate comprehensive approaches to managing COPD, simultaneously addressing the mind, body, and breath. Sudarshan Kriya Yoga (SKY), a breathwork meditation program, has previously yielded a wide range of physiological and psycho-emotional benefits but has not been explored in individuals with COPD. Using single-case multiple-baseline and qualitative phenomenology methodologies, this study investigated 1) the relation between dyspnea and SKY and 2) the feasibility and general perceived effectiveness of SKY among individuals with COPD. Nine individuals with varying severities of COPD participated. Data collection included ratings of perceived dyspnea (work of breathing, shortness of breath, dyspnea-related distress, dyspnea-related anxiety) and semi-structured in-depth interviews. Results suggest that SKY is feasible and acceptable for individuals with COPD. Additionally, the results demonstrate proof of concept that SKY can help alleviate aspects of the COPD disease burden related to the mind, body, and breath as well as reduce the cyclical effect of the disease sequelae. Larger-scale trials are warranted, but this study is the first to support SKY as a viable complementary and integrative health approach for individuals with COPD.
Open Access
Selecting the Number and Labels of Topics in Topic Modeling: A Tutorial
(Sage Journals, 2023-05-25) Weston, Sara J.; Shryock, Ian; Light, Ryan; Fisher, Phillip A.
Topic modeling is a type of text analysis that identifies clusters of co-occurring words, or latent topics. A challenging step of topic modeling is determining the number of topics to extract. This tutorial describes tools researchers can use to identify the number and labels of topics in topic modeling. First, we outline the procedure for narrowing down a large range of models to a select number of candidate models. This procedure involves comparing the large set on fit metrics, including exclusivity, residuals, variational lower bound, and semantic coherence. Next, we describe the comparison of a small number of models using project goals as a guide and information about topic representative and solution congruence. Finally, we describe tools for labeling topics, including frequent and exclusive words, key examples, and correlations among topics.
Open Access
Parent Gender Affects the Influence of Parent Emotional Eating and Feeding Practices on Child Emotional Eating
(Frontiers in Psychology, 2021-09-10) Trevino, Shaina D.; Kelly, Nichole R.; Budd, Elizabeth L.; Giuliani, Nicole R.
Extant research supports a direct association between parent’s own emotional eating and their child’s emotional eating, and demonstrates correlations among parent emotional eating, feeding practices, and child emotional eating. However, the majority of this work focuses on the separate influences of these factors. The current study aims to add to the literature by simultaneously examining the indirect effects of three major parental feeding practices (i.e., emotion regulation, instrumental, and restrictive feeding) in the association between parent emotional eating and child emotional eating, and exploring how these indirect effects vary based on parent gender. Parents (86 fathers, 324 mothers) of an elementary school-age child (M = 8.35, SD = 2.29, range = 5–13) completed an online survey through Qualtrics Panels. Results suggested that restrictive feeding partially accounted for the association between parent and child emotional eating in the combined sample of mothers and fathers. Exploratory analyses revealed that the indirect effects of parental feeding practices in the association between parent emotional eating and child emotional eating varied based on parent gender. Among mothers, restrictive feeding was the only feeding practice that partially accounted for the association between maternal and child emotional eating, whereas all three feeding practices fully accounted for the association between father and child emotional eating. As the bulk of the literature on parent emotional eating and feeding has solely focused on mothers, these findings offer insight into how feeding practices may differentially function in the relation between parent emotional eating and child emotional eating for mothers versus fathers.
Open Access
Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation
(Oxford Academic, 2023-06-05) Short, Aidan W.; Streisfeld, Matthew A.
The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared only among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated evolution of phenotypic traits between lineages.
Open Access
Examination of current U.S. female firefighting personal protective equipment (PPE) sizing and fitting process challenges: an opportunity to improve safety
(SpringerOpen, 2022-11-25) Sokolowski, Susan L.; Griffin, Linsey; Wu, Yingying; McKinney, Ellen; Morris, Kristen; Bettencourt, Chrissy
Between 2010 and 2014, the National Fire Protection Association (NFPA) estimated that female firefighters experienced 1260 injuries on the fireground each year. Previous research attributed some of these injuries to ill-fitting fire personal protective equipment (PPE). Therefore, in this mixed-method paper, the authors explored the relationship between fire PPE and injuries, and how they related to sizing and fit. To achieve this aim, data were collected from manufacturer-provided web communications regarding sizing and fit, user surveys (n = 74), and 1:1 interviews (n = 31) with U.S. female firefighters. The data considered how the size and fit standards established by the NFPA and how leading fire PPE manufacturers’ interpretation of standards impacted fit for female firefighters. Interview and survey data pinpointed experiences with the PPE sizing processes that led to poor fit. The data also identified previously undocumented knowledge gaps between NFPA size standards, commercialized products, and processes used by manufacturers and firehouses to fit female practitioners. The study discovered several opportunities to improve the size and fitting process women experienced when acquiring new turnout gear. With effective fire industry partnerships and future research, women can experience fewer injuries, improved comfort, and work performance with their PPE while establishing equality with their male counterparts.
Open Access
The numeric understanding measures: Developing and validating adaptive and nonadaptive numeracy scales
(Cambridge University Press, 2023-06-28) Silverstein, Michael C.; Bjälkebring, Pär; Shoots-Reinhard, Brittany; Peters, Ellen
Numeracy—the ability to understand and use numeric information—is linked to good decision-making. Several problems exist with current numeracy measures, however. Depending on the participant sample, some existing measures are too easy or too hard; also, established measures often contain items well-known to participants. The current article aimed to develop new numeric understanding measures (NUMs) including a 1-item (1-NUM), 4-item (4-NUM), and 4-item adaptive measure (A-NUM). In a calibration study, 2 participant samples (n = 226 and 264 from Amazon’s Mechanical Turk [MTurk]) each responded to half of 84 novel numeracy items.We calibrated items using 2-parameter logistic item response theory (IRT) models. Based on item parameters, we developed the 3 new numeracy measures. In a subsequent validation study, 600 MTurk participants completed the new numeracy measures, the adaptive Berlin Numeracy Test, and the Weller Rasch-Based Numeracy Test, in randomized order. To establish predictive and convergent validities, participants also completed judgment and decision tasks, Raven’s progressive matrices, a vocabulary test, and demographics. Confirmatory factor analyses suggested that the 1-NUM, 4-NUM, and A-NUM load onto the same factor as existing measures. The NUM scales also showed similar association patterns to subjective numeracy and cognitive ability measures as established measures. Finally, they effectively predicted classic numeracy effects. In fact, based on power analyses, the A-NUM and 4-NUM appeared to confer more power to detect effects than existing measures. Thus, using IRT, we developed 3 brief numeracy measures, using novel items and without sacrificing construct scope. The measures can be downloaded as Qualtrics files (https://osf.io/pcegz/).
Open Access
Creating the Qur’an: A Historical-Critical Study
(University of California Press, 2022) Shoemaker, Stephen J.
Creating the Qur’an presents the first systematic historical-critical study of the Qur’an’s origins, drawing on methods and perspectives commonly used to study other scriptural traditions. Demonstrating in detail that the Islamic tradition relates not a single attested account of the holy text’s formation, Stephen J. Shoemaker shows how the Qur’an preserves a surprisingly diverse array of memories regarding the text’s early history and its canonization. To this he adds perspectives from radiocarbon dating of manuscripts, the linguistic history of Arabic, the social and cultural history of late ancient Arabia, and the limitations of human memory and oral transmission, as well as various peculiarities of the Qur’anic text itself. Considering all the relevant data to present the most comprehensive and convincing examination of the origin and evolution of the Qur’an available, Shoemaker concludes that the canonical text of the Qur’an was most likely produced only around the turn of the eighth century.
Open Access
Measuring Hispanics/Latinxs: Racial Heterogeneity and Its Consequences for Modeling Social Outcomes in U.S. Population Samples
(Sage Journals, 2023-05-23) Shiao, Jiannbin Lee
Quantitative sociologists have recognized the challenges of studying Latinx Americans, given their unique racial heterogeneity and unique measurement in surveys through dedicated Latinx-ethnicity questions. Using the National Longitudinal Study of Adolescent to Adult Health, the author examines who identifies as Hispanic/Latinx when the option is a permitted response on a combined race/ethnicity question. The study reveals that national origin, connection to Latinx communities, racial appearance, and consistency in prior ethnic identification as Latinx affect the likelihood of racial identification as Latinx. These associations have heterogeneous consequences for modeling social outcomes in samples with both Latinx and non-Latinx respondents. Latinx Americans divide on skin tone in models of education and health, but they divide on national origin in models of interracial dating. This suggests that researchers should operationalize Latinxs using measures recognizing a modal group of Latinx-only identifiers while capturing heterogeneity by skin tone and national origin across the broader ever-Latinx population.
Open Access
Intimations of a New Paradigm for Lexical Studies in Psychology
(Frontiers in Psychology, 2022-07-01) Saucier, Gerard
Several consecutive productive decades of research on basic dimensions of personality have given a firmer footing to the discipline due, in part, to contributions of lexical studies of personality. These studies helped establish more consensus as to structure—a set of a few dimensions worth measuring—which has enabled knowledge to accumulate within something of a standard assessment paradigm. Admittedly, these dimensions are quite broad, and if one wishes to characterize their content quite accurately, he or she must often resort to compound labels (e.g., honesty/humility, intellect/imagination). The factors they refer to are, basically, collages of more fine-grained components; the composition of the collages varies somewhat from one measure to another, and one language to another. There are, however, cracks in the paradigm. The “few dimensions” most widely regarded as measurement worthy—the Big Five—embody a good degree of ethnocentric bias, deriving from origin in Western samples and studies in and of Germanic-language-family contexts. These dimensions often replicate only partially or weakly. And, although these have good evidence for comparative predictive validity (in competition with SES and IQ; Roberts et al., 2007), the magnitude of prediction is not overwhelming. Better prediction is likely to come from more comprehensive models (Paunonen and Ashton, 2001; Mõttus et al., 2017). In lexical studies, five factors account for only a narrow slice—about a quarter—of the variance that stimuli based on the personality vocabulary can afford (e.g., Saucier and Iurino, 2020). Personality data are not 75% noise! Structures with far more than five factors (accounting for closer to half the variance) have recently been found to be replicable to a good degree (Saucier and Iurino, 2020).
Open Access
Investigating Fractal Analysis as a Diagnostic Tool That Probes the Connectivity of Hippocampal Neurons
(Frontiers in Physiology, 2022-06-23) Rowland, Conor; Harland, Julian H.; Smith, Julian H.; Moslehi, Saba; Dalrymple-Alford, John; Taylor, Richard P.
Many of nature’s fractal objects benefit from the favorable functionality that results from their pattern repetition at multiple scales. Our recent research focused on the importance of fractal scaling in establishing connectivity between neurons. Fractal dimension DA of the neuron arbors was shown to relate to the optimization of competing functional constraints—the ability of dendrites to connect to other neurons versus the costs associated with building the dendrites. Here, we consider whether pathological states of neurons might affect this fractal optimization and if changes in DA might therefore be used as a diagnostic tool in parallel with traditional measures like Sholl analyses. We use confocal microscopy to obtain images of CA1 pyramidal neurons in the coronal plane of the dorsal rat hippocampus and construct 3-dimensional models of the dendritic arbors using Neurolucida software. We examine six rodent groups which vary in brain condition (whether they had lesions in the anterior thalamic nuclei, ATN) and experience (their housing environment and experience in a spatial task). Previously, we showed ATN lesions reduced spine density in hippocampal CA1 neurons, whereas enriched housing increased spine density in both ATN lesion and sham rats. Here, we investigate whether ATN lesions and experience also effect the complexity and connectivity of CA1 dendritic arbors. We show that sham rats exposed to enriched housing and spatial memory training exhibited higher complexity (as measured by DA) and connectivity compared to other groups. When we categorize the rodent groups into those with or without lesions, we find that both categories achieve an optimal balance of connectivity with respect to material cost. However, the DA value used to achieve this optimization does not change between these two categories, suggesting any morphological differences induced by the lesions are too small to influence the optimization process. Accordingly, we highlight considerations associated with applying our technique to publicly accessible repositories of neuron images with a broader range of pathological conditions.
Open Access
Neuron arbor geometry is sensitive to the limited-range fractal properties of their dendrites
(Frontiers in Network Physiology, 2023-01-25) Rowland, Conor; Smith, Julian H.; Moslehi, Saba; Harland, Bruce; Dalrymple-Alford, John; Taylor, Richard P.
Fractal geometry is a well-known model for capturing the multi-scaled complexity of many natural objects. By analyzing three-dimensional images of pyramidal neurons in the rat hippocampus CA1 region, we examine how the individual dendrites within the neuron arbor relate to the fractal properties of the arbor as a whole. We find that the dendrites reveal unexpectedly mild fractal characteristics quantified by a low fractal dimension. This is confirmed by comparing two fractal methods—a traditional “coastline” method and a novel method that examines the dendrites’ tortuosity across multiple scales. This comparison also allows the dendrites’ fractal geometry to be related to more traditional measures of their complexity. In contrast, the arbor’s fractal characteristics are quantified by a much higher fractal dimension. Employing distorted neuron models that modify the dendritic patterns, deviations from natural dendrite behavior are found to induce large systematic changes in the arbor’s structure and its connectivity within a neural network. We discuss how this sensitivity to dendrite fractality impacts neuron functionality in terms of balancing neuron connectivity with its operating costs. We also consider implications for applications focusing on deviations from natural behavior, including pathological conditions and investigations of neuron interactions with artificial surfaces in human implants.
Open Access
Aesthetics and Psychological Effects of Fractal Based Design
(Frontiers in Psychology, 2021-08-17) Robles, Kelly E.; Roberts, Michelle; Viengkham, Catherine; Smith, Julian H.; Rowland, Conor; Moslehi, Saba; Stadlober, Sabrina; Lesjak, Anastasija; Lesjak, Martin; Taylor, Richard P.; Spehar, Branka; Sereno, Margaret
Highly prevalent in nature, fractal patterns possess self-similar components that repeat at varying size scales. The perceptual experience of human-made environments can be impacted with inclusion of these natural patterns. Previous work has demonstrated consistent trends in preference for and complexity estimates of fractal patterns. However, limited information has been gathered on the impact of other visual judgments. Here we examine the aesthetic and perceptual experience of fractal ‘global-forest’ designs already installed in humanmade spaces and demonstrate how fractal pattern components are associated with positive psychological experiences that can be utilized to promote occupant wellbeing. These designs are composite fractal patterns consisting of individual fractal ‘tree-seeds’ which combine to create a ‘global fractal forest.’ The local ‘tree-seed’ patterns, global configuration of tree-seed locations, and overall resulting ‘global-forest’ patterns have fractal qualities. These designs span multiple mediums yet are all intended to lower occupant stress without detracting from the function and overall design of the space. In this series of studies, we first establish divergent relationships between various visual attributes, with pattern complexity, preference, and engagement ratings increasing with fractal complexity compared to ratings of refreshment and relaxation which stay the same or decrease with complexity. Subsequently, we determine that the local constituent fractal (‘treeseed’) patterns contribute to the perception of the overall fractal design, and address how to balance aesthetic and psychological effects (such as individual experiences of perceived engagement and relaxation) in fractal design installations. This set of studies demonstrates that fractal preference is driven by a balance between increased arousal (desire for engagement and complexity) and decreased tension (desire for relaxation or refreshment). Installations of these composite mid-high complexity ‘globalforest’ patterns consisting of ‘tree-seed’ components balance these contrasting needs, and can serve as a practical implementation of biophilic patterns in human-made environments to promote occupant wellbeing.
Open Access
Introduced annuals mediate climate-driven community change in Mediterranean prairies of the Pacific Northwest, USA
(Wiley, 2021-11-01) Reed, Paul B.; Pfeifer-Meister, Laurel E.; Roy, Bitty A.; Johnson, Bart R.; Bailes, Graham T.; Nelson, Aaron A.; Bridgham, Scott D.
Aim: How climate change will alter plant functional group composition is a critical question given the well-recognized effects of plant functional groups on ecosystem services. While climate can have direct effects on different functional groups, indirect effects mediated through changes in biotic interactions have the potential to amplify or counteract direct climatic effects. As a result, identifying the underlying causes for climate effects on plant communities is important to conservation and restoration initiatives. Location: Western Pacific Northwest (Oregon and Washington), USA. Methods: Utilizing a 3-year experiment in three prairie sites across a 520-km latitudinal climate gradient, we manipulated temperature and precipitation and recorded plant cover at the peak of each growing season. We used structural equation models to examine how abiotic drivers (i.e. temperature, moisture and soil nitrogen) controlled functional group cover, and how these groups in turn determined overall plant diversity. Results: Warming increased the cover of introduced annual species, causing subsequent declines in other functional groups and diversity. While we found direct effects of temperature and moisture on extant vegetation (i.e. native annuals, native perennials and introduced perennials), these effects were typically amplified by introduced annuals. Competition for moisture and light or space, rather than nitrogen, were critical mechanisms of community change in this seasonally water-limited Mediterranean-climate system. Diversity declines were driven by reductions in native annual cover and increasing dominance by introduced annuals. Main conclusions: A shift towards increasing introduced annual dominance in this system may be akin to that previously experienced in California grasslands, resulting in the “Californication” of Pacific Northwest prairies. Such a phenomenon may challenge local land managers in their efforts to maintain species-rich and functionally diverse prairie ecosystems in the future.
Open Access
Navigating the intersection of 3D printing, software regulation and quality control for point‑of‑care manufacturing of personalized anatomical models
(BMC, 2023-04-07) Paxton, Naomi C.
3D printing technology has become increasingly popular in healthcare settings, with applications of 3D printed anatomical models ranging from diagnostics and surgical planning to patient education. However, as the use of 3D printed anatomical models becomes more widespread, there is a growing need for regulation and quality control to ensure their accuracy and safety. This literature review examines the current state of 3D printing in hospitals and FDA regulation process for software intended for use in producing 3D printed models and provides for the first time a comprehensive list of approved software platforms alongside the 3D printers that have been validated with each for producing 3D printed anatomical models. The process for verification and validation of these 3D printed products, as well as the potential for inaccuracy in these models, is discussed, including methods for testing accuracy, limits, and standards for accuracy testing. This article emphasizes the importance of regulation and quality control in the use of 3D printing technology in healthcare, the need for clear guidelines and standards for both the software and the printed products to ensure the safety and accuracy of 3D printed anatomical models, and the opportunity to expand the library of regulated 3D printers.
Open Access
Non-singular and singular flat bands in tunable phononic metamaterials
(APS, 2023-04-18) Karki, Pragalv; Paulose, Jayson
Dispersionless flat bands can be classified into two types: (1) non-singular flat bands whose eigenmodes are completely characterized by compact localized states, and (2) singular flat bands that have a discontinuity in their Bloch eigenfunctions at a band touching point with an adjacent dispersive band, thereby requiring additional extended states to span their eigenmode space. In this study, we design and numerically demonstrate two-dimensional thin-plate phononic metamaterials in which tunable flat bands of both kinds can be achieved. Non-singular flat bands are achieved by fine tuning the ratio of the global tension and the bending stiffness in triangular and honeycomb lattices of plate resonators. A singular flat band arises in a kagome lattice due to the underlying lattice geometry, which can be made degenerate with two additional flat bands by tuning the plate tension. A discrete model of the continuum thin-plate system reveals the interplay of geometric and mechanical factors in determining the existence of flat bands of both types. The singular nature of the kagome lattice flat band is established via a metric called the Hilbert-Schmidt distance calculated between a pair of eigenstates infinitesimally close to the quadratic band touching point.We also simulate a phononic manifestation of a robust boundary mode arising from the singular flat band and protected by real-space topology in a finite system. Our theoretical and computational study establishes a framework for exploring flat-band physics in a tunable classical system, and for designing phononic metamaterials with potentially useful sound manipulation capabilities.
Open Access
Comparison of fractal and grid electrodes for studying the effects of spatial confinement on dissociated retinal neuronal and glial behavior
(Nature, 2022-10-20) Moslehi, Saba; Rowland, Conor; Smith, Julian H.; Griffiths, Willem; Watterson, William J.; Niell, Cristopher M.; Alemán, Benjamín J.; Perez, Maria-Thereza; Taylor, Richard P.
Understanding the impact of the geometry and material composition of electrodes on the survival and behavior of retinal cells is of importance for both fundamental cell studies and neuromodulation applications. We investigate how dissociated retinal cells from C57BL/6J mice interact with electrodes made of vertically-aligned carbon nanotubes grown on silicon dioxide substrates. We compare electrodes with different degrees of spatial confinement, specifically fractal and grid electrodes featuring connected and disconnected gaps between the electrodes, respectively. For both electrodes, we find that neuron processes predominantly accumulate on the electrode rather than the gap surfaces and that this behavior is strongest for the grid electrodes. However, the ‘closed’ character of the grid electrode gaps inhibits glia from covering the gap surfaces. This lack of glial coverage for the grids is expected to have long-term detrimental effects on neuronal survival and electrical activity. In contrast, the interconnected gaps within the fractal electrodes promote glial coverage. We describe the differing cell responses to the two electrodes and hypothesize that there is an optimal geometry that maximizes the positive response of both neurons and glia when interacting with electrodes.
Open Access
Temporary establishment of bacteria from indoor plant leaves and soil on human skin
(BMC, 2022-12-22) Mhuireach, Gwynne A.; Fahimipour, Ashkaan K.; Vandegrift, Roo; Muscarella, Mario E.; Hickey, Roxana; Bateman, Ashley C.; Van Den Wymelenberg, Kevin G.; Bohannan, Brendan J. M.
Background: Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing. Results: Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their preperturbed state, although some abundant soil taxa resisted removal through washing. Conclusions: This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.
Open Access
The lifetime of charged dust in the atmosphere
(Oxford Academic, 2022-10-14) Harper, Joshua Méndez; Harvey, Dana; Huang, Tianshu; McGrath, Jake, III; Meer, David; Burton, Justin C.
Wind-blown dust plays a critical role in numerous geophysical and biological systems, yet current models fail to explain the transport of coarse-mode particles (>5μm) to great distances from their sources. For particles larger than a few microns, electrostatic effects have been invoked to account for longer-than-predicted atmospheric residence times. Although much effort has focused on elucidating the charging processes, comparatively little effort has been expended understanding the stability of charge on particles once electrified. Overall, electrostatic-driven transport requires that charge remain present on particles for days to weeks. Here,we present a set of experiments designed to explore the longevity of electrostatic charge on levitated airborne particles after a single charging event. Using an acoustic levitator,we measured the charge on particles of different material compositions suspended in atmospheric conditions for long periods of time. In dry environments, the total charge on particles decayed in over 1week. The decay timescale decreased to days in humid environments. These results were independent of particle material and charge polarity. However, exposure to UV radiation could both increase and decrease the decay time depending on polarity. Our work suggests that the rate of charge decay on airborne particles is solely determined by ion capture from the air. Furthermore, using a one-dimensional sedimentation model, we predict that atmospheric dust of order 10μm will experience the largest change in residence time due to electrostatic forces.
Open Access
Degeneracies and symmetry breaking in pseudo-Hermitian matrices
(APS, 2023-04-18) Melkani, Abhijeet
Real eigenvalues of pseudo-Hermitian matrices, such as real matrices and PT −symmetric matrices, frequently split into complex conjugate pairs. This is accompanied by the breaking of certain symmetries of the eigenvectors and, typically, also a drastic change in the behavior of the system. In this paper, we classify the eigenspace of pseudo-Hermitian matrices and show that such symmetry breaking occurs if and only if eigenvalues of opposite kinds collide on the real axis of the complex eigenvalue plane. This enables a classification of the disconnected regions in parameter space where all eigenvalues are real—which correspond, physically, to the stable phases of the system. These disconnected regions are surrounded by exceptional surfaces, which comprise all the real-valued exceptional points of pseudo-Hermitian matrices. The exceptional surfaces, together with the diabolic points created by their intersections, comprise all points of pseudo-Hermiticity breaking. In particular, this clarifies that the degeneracy involved in symmetry breaking is not necessarily an exceptional point. We also discuss how our study relates to conserved quantities and derive the conditions for when degeneracies caused by external symmetries are susceptible to thresholdless pseudo-Hermiticity breaking. We illustrate our results with examples from photonics, condensed matter physics, and mechanics.