Biology subjects

Williams, K. A.

Publications and source records attributed to Williams, K. A..

10 recordsLinked to original sources

bioRxiv2026

Overwinter roost activity patterns in response to environmental conditions along a rural-urban gradient

1. Organisms rely on environmental cues, such as moonlight illumination and weather, to modulate nocturnal behaviors that reduce predation risk and conserve energy during demanding periods. Urbanization can alter the reliability of cues, potentially impairing organisms' ability to respond appropriately with consequences in increasingly urbanized landscapes. 2. We leveraged the Motus Wildlife Tracking System to identify roost initiation, roost departure and nocturnal restlessness of dark-eyed juncos (Junco hyemalis) overwintering along an urban to rural gradient to determine if activity patterns are affected by weather, moonlight illumination, and urbanization. 3. Nocturnal behavior of overwintering juncos varied with environmental factors, including moonlight illumination and temperature. However, the strength of these responses differed among sites, suggesting that natural cues of moonlight illumination were masked in urban areas, where individuals were more responsive to temperature. 4. Our results suggest that urbanization weakens birds' responsiveness to natural light cues, likely because artificial lighting reduces the visibility of moonlight; representing a key mechanism by which human-altered landscapes can disrupt nocturnal ecology in birds.

animal behavior and cognition↗

bioRxiv2026

roostR: An R package to examine diel activity patterns from Motus radio telemetry data

1. Monitoring the diel activity patterns of free-living animals is a methodological challenge. Signal strength fluctuations from Very High Frequency (VHF) radio transmitters deployed within the Motus Wildlife Tracking System can be used as a proxy for activity. However, analytical tools to extract behavioral metrics that quantify activity patterns from these data are needed. 2. We developed roostR, an open-source R package that converts Motus detection data into quantitative behavioral metrics, including roost initiation and departure, roost duration, observation time, and restlessness. The package uses a sequential pipeline built around signal volatility and rolling medians to detect transitions between active and inactive states. Default parameter values were tuned using data from 55 dark-eyed juncos (Junco hyemalis) overwintering in southeastern Ohio. 3. We provide an example from a dark-eyed junco over a 58-day period. roostR estimated roost onset on 48 nights and departure on 56 mornings, with higher rolling median signal differences during the day than at night, consistent with a diurnal animal, and variable restlessness periods each night. We also used the package to estimate roost behavior of an American tree sparrow (Spizelloides arborea) over 43-nights. 4. roostR enables researchers to extract individual activity data from Motus datasets. Because all thresholds are user-adjustable, the pipeline is adaptable across species, tag specifications, and ecological contexts, enabling researchers to test hypotheses about how environmental factors influence diel activity patterns.

animal behavior and cognition↗

bioRxiv2026

Accounting for recurrent mutation in the frequency spectrum of rare alleles

As whole-genome and whole-exome datasets increase in size, they uncover alleles at lower and lower frequencies in the population. Samples of rare alleles often include recurrent mutations, where derived alleles are identical by state and not by descent. As a result, the site frequency spectrum (SFS) becomes challenging to analyze because it is strongly dependent on the mutation rate. To overcome this hurdle, we define the single mutation frequency spectrum (SMFS), which is the frequency spectrum of alleles descendant from a single mutational event. For rare alleles, the SFS with recurrent mutation is then a weighted sum of the convolutions of the SMFS with itself. This simple, yet powerful, model decouples recurrent mutation from the population genetic processes giving rise to the SMFS, such as genetic drift and selection. We show how both forward-in-time and backward-in-time models with recurrent mutations can be recast in terms of the SMFS. We then develop a method for combinatorial hierarchic estimation of the SMFS (which we name CHES). We apply this simple, yet robust, method to a human exome sequencing dataset to show that the SMFS with recurrent mutation can account for SFS differences between low and high mutation rate sites. The inferred SMFS shows an approximate scaling law with allele frequencies inconsistent with both a constant population size and an exponentially growing population model. Lastly, we use our model to compare the expected and observed proportions of missense and stop-gain mutations in the human exome, using this disparity to infer the strength of selection on these classes of mutations. Our combined results show how the SMFS can explain the dependency of the SFS on the mutation rate and how it reflects human demographic and evolutionary history.

genetics↗

bioRxiv2024

Semantic integration demands modulate large-scale network interactions in the brain

The ability to integrate semantic information into the context of a sentence is essential for human communication. Several studies have shown that the predictability of a final keyword based on the sentence context influences semantic integration on the behavioral, neurophysiological, and neural level. However, the architecture of the underlying network interactions for semantic integration across the lifespan remains unclear. In this study, 32 healthy participants (30-75 years) performed an auditory cloze probability task during functional magnetic resonance imaging (fMRI), requiring lexical decisions on the sentences final words. Semantic integration demands were implicitly modulated by presenting sentences with expected, unexpected, anomalous, or pseudoword endings. To elucidate network interactions supporting semantic integration, we combined univariate task-based fMRI analyses with seed-based connectivity and between-network connectivity analyses. Behavioral data revealed typical semantic integration effects, with increased integration demands being associated with longer response latencies and reduced accuracy. Univariate results demonstrated increased left frontal and temporal brain activity for sentences with higher integration demands. Between-network interactions highlighted the role of task-positive and default mode networks for sentence processing with increased semantic integration demands. Furthermore, increasing integration demands led to a higher number of behaviorally relevant network interactions, suggesting that the increased between-network coupling becomes more relevant for successful task performance as integration demands increase. Our findings elucidate the complex network interactions underlying semantic integration across the aging continuum. Stronger interactions between various task-positive and default mode networks correlated with more efficient processing of sentences with increased semantic integration demands. These results may inform future studies with healthy old and clinical populations.

neuroscience↗

bioRxiv2024

Strategies for Mitigating Impacts to Aerofauna from Offshore Wind Energy Development: Available Evidence and Data Gaps

A diversity of approaches exist for mitigating (e.g., avoiding, minimizing, or compensating for) the effects of offshore wind energy (OSW) development on birds and bats, but little is known about the effectiveness of many of these approaches. To address this knowledge gap, we reviewed the scientific and gray literature to evaluate the evidence base for potential bird- and bat-related mitigation approaches for OSW, including studies from other industries where relevant (e.g., terrestrial wind energy, offshore oil and gas industry). Of a total of 219 mitigation approaches, most focused on minimization, with far fewer addressing avoidance or compensation. Sixty-five percent had no evidence of testing. Of the 76 mitigation approaches that were field tested or implemented, we found evidence of effectiveness for only 40 approaches, of which only 10 were specific to the OSW sector. Consequently, a majority of all the mitigation approaches for birds (82%) and bats (89%) lacked any evidence of effectiveness. For birds, minimization approaches related to lighting reduction were the most tested and effective methods for reducing maladaptive attraction and collisions. For bats, minimization approaches involving adjustments to turbine operations (e.g., curtailment of turbine blades) were most tested and effective methods for reducing collisions. Given the limited evidence of effectiveness for most mitigation approaches, assuming their success systematically underestimating project-level and cumulative impacts, underscoring the need to prioritize avoidance, consistent with the mitigation hierarchy, and rigorously test mitigation approaches for birds and bats in offshore environments. RESUMEIl existe une diversite dapproches pour attenuer (e.g. eviter, minimiser ou compenser) les effets du developpement de l lEnergie Eolienne Extracotiere (EEE) sur les oiseaux et les chauves-souris, mais lefficacite de nombreuses de ces approches est encore peu connue. Pour combler ces lacunes, nous avons passe en revue la litterature scientifique et la litterature grise afin devaluer les donnees probantes concernant les mesures dattenuation potentielle pour lEEE et les oiseaux et les chauves-souris,, inclus des etudes dautres industries lorsque cela etait pertinent (e.g., lenergie eolienne terrestre, lindustrie petroliere et gaziere extracotiere). Sur un total de 219 approches dattenuation pertinentes pour lEEE, la plupart des approches se concentraient sur la minimisation, avec beaucoup moins dapproches portant sur levitement ou la compensation. Soixante-et-un pourcent des approches proposees ne semblent pas avoir ete testees. Parmi les 76 approches dattenuation qui ont ete testees sur le terrain ou mises en uvre, nous avons trouve des preuves de leur efficacite pour seulement 40 approches, dont seulement 10 etaient specifiques ale secteur de lEEE. Par consequent, la majorite des approches dattenuation pour les oiseaux (82 %) et les chauves-souris (89%) ne disposaient daucune preuve defficacite. Chez les oiseaux, les approches de minimisation liees a la reduction de leclairage etaient les methodes les plus couramment testees et les plus efficaces pour reduire lattraction et les collisions. Chez les chauves-souris, les approches de minimisation impliquant la modification du fonctionnement des turbines (e.g., reduction de la vitesse de rotation ou mise en drapeau des helices) etaient les methodes les plus couramment testees et les plus efficaces pour reduire les collisions. Compte tenu des preuves limitees de lefficacite de la plupart des approches dattenuation, le fait de presumer de leur succes conduit a une sous-estimation systematique des impacts a lechelle des projets et des impacts cumulatifs, ce qui souligne la necessite de privilegier levitement, conformement a la hierarchie dattenuation, et de tester rigoureusement les mesures dattenuation pour les oiseaux et les chauves-souris en milieux offshore. IMPLICATIONS FOR MANAGERSO_LIBased on our literature review of potential mitigation approaches for birds and bats in relation to offshore wind development, most approaches remain untested or lack evidence of effectiveness (bats - 89%, birds - 82%). C_LIO_LIMost minimization approaches have primarily been tested in the terrestrial context, leaving important questions regarding the transferability of these results to the offshore environment. C_LIO_LIGiven the limited evidence of effectiveness for most mitigation approaches, assuming their success systematically underestimates project-level and cumulative impacts, underscoring the need to prioritize avoidance and rigorously test mitigation approaches for birds and bats in offshore environments. C_LI

ecology↗

bioRxiv2024

A Flexible Framework for Assessing the Cumulative Effects of Offshore Wind Energy Activities and Other Pressures on Aerofauna

The offshore wind energy (OSW) industry is pivotal for renewable energy transition and climate resiliency. However, OSW activities may negatively affect aerofauna, contributing to CE from human activities and natural processes. Cumulative effects assessments (CEA) are vital for informed planning and management of OSW activities during regional assessment, site selection, and site evaluation. To reduce impacts on aerofauna, OSW developments should be sited in areas that avoid or minimize cumulative effects (CE). This study presents a cohesive and flexible framework for assessing the CE from OSW activities, other human activities, and natural processes on aerofauna to support decision-making during the initial OSW planning phases. The framework uses a species-based approach, applicable to various receptors, and adapts to available information on ecology, socioeconomics, and pressures. The analytical strategy uses a CE metric to indicate the presence or magnitude of effects from all pressures on receptors. Spatially explicit optimization methods identify OSW site configurations that minimize a CE metric. The framework accommodates alternative pressure scenarios that include foreseeable future human activities and natural processes and can explore the sensitivity of the result to uncertain parameters. Given sufficient spatial information on receptor density, pressure magnitude, and cause-effect pathways, the spatial optimization algorithm can find solutions that minimize population-level impacts from CE. If this ideal standard cannot be achieved due to information gaps, alternative metrics may be used to inform the immediate decision-making process.

ecology↗

bioRxiv2023

Identification of State Markers in Anorexia Nervosa: Replication and Extension of Inflammation Associated Biomarkers Using Multiplex Profiling in Anorexia Nervosa and Atypical Anorexia Nervosa

Proteomics provides an opportunity for detection and monitoring of anorexia nervosa (AN) and its related variant, atypical-AN (atyp-AN). However, research to date has been limited by the small number of proteins explored, exclusive focus on adults with AN, and lack of replication across studies. This study performed Olink Proseek Multiplex profiling of 92 proteins involved in inflammation among females with AN and atyp-AN (N = 64), all < 90% of expected body weight, and age-matched healthy controls (HC; N=44). After correction for multiple testing, nine proteins differed significantly in the AN/atyp-AN group relative to HC group (lower levels: CXCL1, HGF, IL-18R1, TNFSF14, TRANCE; higher levels: CCL23, Flt3L, LIF-R, MMP-1). The expression levels of three proteins (lower IL-18R1, TRANCE; higher LIF-R) were uniquely disrupted in females with AN. No unique expression levels emerged for atyp-AN. Across the whole sample, twenty-one proteins correlated positively with BMI (ADA, AXIN1, CD5, CD244, CD40, CD6, CXCL1, FGF-21, HGF, IL-10RB, IL-12B, IL18, IL-18R1, IL6, LAP TGF-beta-1, SIRT2, STAMBP, TNFRSF9, TNFSF14, TRAIL, TRANCE) and six (CCL11, CCL23, FGF-19, IL8, LIF-R, OPG) were negatively correlated with BMI. Overall, our results replicate the prior study demonstrating a dysregulated inflammatory status in AN, and extend these results to atyp-AN (AN/atyp-AN all < 90% of expected body weight). Of the 27 proteins correlated with BMI, 18 were replicated from a prior study using similar methods, highlighting the promise of inflammatory protein expression levels as biomarkers of disease monitoring. Additional studies of individuals across the entire weight spectrum are needed to understand the role of inflammation in atyp-AN.

immunology↗

bioRxiv2022

Age-related reorganization of functional network architecture for language processing

Semantic memory is a fundamental human ability which is central to communication. Although it is usually well preserved in healthy aging, memory problems in verbal communication due to slowed access and retrieval processes are a common complaint with increasing age. So far, the neural bases of this paradox remain poorly understood. The current neuroimaging study investigated age differences in the functional network architecture during semantic word retrieval in young and older adults. Using group spatial independent component analysis, we defined functional networks for verbal semantic fluency. Combining task-based functional connectivity, graph theory and cognitive measures of fluid and crystallized intelligence, our findings show age-accompanied large-scale network reorganization even when older adults have intact word retrieval abilities. In particular, functional networks of older adults were characterized by reduced decoupling between systems, reduced segregation and efficiency, and a larger number of hub regions relative to young adults. Exploring the predictive utility of these age-related changes in network topology revealed high, albeit less efficient, performance for older adults whose brain graphs showed stronger dedifferentiation and reduced distinctiveness. Our results extend theoretical accounts on neurocognitive aging by revealing the compensational potential of the commonly reported pattern of network dedifferentiation when older adults can rely on their prior knowledge for successful task processing. However, we also demonstrate the limitations of such compensatory reorganization processes and demonstrate that a youth-like network architecture in terms of balanced integration and segregation is associated with more economical processing. Significance StatementCognitive aging is associated with widespread neural reorganization processes in the human brain. However, the behavioral impact of such reorganization is not well understood. Here, we used taskbased fMRI to demonstrate a large-scale reorganization of brain networks in older adults even when their semantic abilities are intact. In particular, functional networks of older adults were characterized by increased coupling between different systems, reduced segregation and efficiency, and a larger number of hub regions relative to young adults. Associating these changes with behavior revealed high, albeit less efficient, performance for networks in older adults showing stronger dedifferentiation and reduced distinctiveness. Our results highlight the compensatory potential of network reconfiguration with age, but also reveal the limitations of such reorganization processes.

neuroscience↗

bioRxiv2021

The role of the angular gyrus in semantic cognition - A synthesis of five functional neuroimaging studies

Semantic knowledge is central to human cognition. The angular gyrus (AG) is widely considered a key brain region for semantic cognition. However, the role of the AG in semantic processing is controversial. Key controversies concern response polarity (activation vs. deactivation) and its relation to task difficulty, lateralization (left vs. right AG), and functional-anatomical subdivision (PGa vs. PGp subregions). Here, we combined the fMRI data of five studies on semantic processing (n = 172) and analyzed the response profiles from the same anatomical regions-of-interest for left and right PGa and PGp. We found that the AG was consistently deactivated during non-semantic conditions, whereas response polarity during semantic conditions was inconsistent. However, the AG consistently showed relative response differences between semantic and non-semantic conditions, and between different semantic conditions. A combined analysis across all studies revealed that AG responses could be best explained by separable effects of task difficulty and semantic processing demand. Task difficulty effects were stronger in PGa than PGp, regardless of hemisphere. Semantic effects were stronger in left than right AG, regardless of subregion. These results suggest that the AG is engaged in both domain-general task-difficulty-related processes and domain-specific semantic processes. In semantic processing, we propose that left AG acts as a "multimodal convergence zone" that binds different semantic features associated with the same concept, enabling efficient access to task-relevant features.

neuroscience↗

bioRxiv2021

Examining the effectiveness of blanket curtailment strategies in reducing bat fatalities at terrestrial wind farms in North America

Blanket curtailment of turbine operations during low wind conditions has become an accepted operational minimization tactic to reduce bat mortality at terrestrial wind facilities. Site-specific studies have demonstrated that operational curtailment effectively reduces impacts, but the exact nature of the relationship between increased cut-in speed and fatality reduction in bats remains unclear. To evaluate the efficacy of differing blanket curtailment regimes in reducing bat fatality, we examined data from turbine curtailment experiments in the United States and Canada in a meta-analysis framework. We tested multiple statistical models to explore possible linear and non-linear relationships between turbine cut-in speed and bat fatality reduction while controlling for control cut-in speed. Because the overall sample size for this meta-analysis was small (n = 36 control-treatment studies from 16 field sites from the American Wind Wildlife Information Center and a recent review), we conducted a power analysis to assess the number of control-impact curtailment studies that would be needed to understand the relationship between fatality rate and change in cut-in speed under different fatality reduction scenarios. We also identified the characteristics of individual field studies that may influence their power to detect fatality reduction due to curtailment. Using a response ratio approach, we found any curtailment strategy reduced fatality rates by 56% for studies included in this analysis (p < 0.001). However, we did not find strong evidence for linear (p =0 0.07) or non-linear (p > 0.11) associations between increasing cut-in speeds and fatality reduction. The power analyses showed that the power to detect effects in the meta-analysis was low if fatality reductions were less than 50%. Synthesizing across all analyses, we need more well-designed curtailment studies to determine the effect of increasing curtailment speed and the effect size is likely of a magnitude that we had limited power to detect.

ecology↗