bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian two-stage modeling of longitudinal and time-to-event data with an integrated fractional Brownian motion covariance structure
Authors: Palipana Anushka , Song Seongho , Gupta Nishant , Szczesniak Rhonda 
Published: March 2024

ABSTRACTIt is difficult to characterize complex variations of biological processes, often longitudinally measured using biomarkers that yield noisy data. While joint modeling with a longitudinal submodel for the biomarker measurements and a survival submodel for assessing the hazard of events can alleviate measurement error issues, the continuous longitudinal submodel often uses random intercepts and slopes to estimate both between- and within-patient heterogeneity in biomarker trajectories. To overcome longitudinal submodel challenges, we replace random slopes with scaled integrated fractional Brownian motion (IFBM). As a more generalized version of integrated Brownian motion, IFBM reasonably depicts noisily measured biological processes. From this longitudinal IFBM model, we derive novel target functions to monitor the risk of rapid disease progression as real-time predictive probabilities. Predicted biomarker values from the IFBM submodel are used as inputs in a Cox submodel to estimate event hazard. This two-stage approach to fit the submodels is performed via Bayesian posterior computation and inference. We use the proposed approach to predict dynamic lung disease progression and mortality in women with a rare disease called lymphangioleiomyomatosis who were followed in a national patient registry. We compare our approach to those using integrated Ornstein-Uhlenbeck or conventional random intercepts-and-slopes terms for the longitudinal submodel. In the comparative analysis, the IFBM model consistently demonstrated superior predictive performance.
Accounting for network noise in graph-guided Bayesian modeling of structured high-dimensional data
Authors: Li Wenrui , Chang Changgee , Kundu Suprateek , Long Qi 
Published: March 2024

Abstract
There is a growing body of literature on knowledge-guided statistical learning methods for analysis of structured high-dimensional data (such as genomic and transcriptomic data) that can incorporate knowledge of underlying networks derived from functional genomics and functional proteomics. These methods have been shown to improve variable selection and prediction accuracy and yield more interpretable results. However, these methods typically use graphs extracted from existing databases or rely on subject matter expertise, which are known to be incomplete and may contain false edges. To address this gap, we propose a graph-guided Bayesian modeling framework to account for network noise in regression models involving structured high-dimensional predictors. Specifically, we use 2 sources of network information, including the noisy graph extracted from existing databases and the estimated graph from observed predictors in the dataset at hand, to inform the model for the true underlying network via a latent scale modeling framework. This model is coupled with the Bayesian regression model with structured high-dimensional predictors involving an adaptive structured shrinkage prior. We develop an efficient Markov chain Monte Carlo algorithm for posterior sampling. We demonstrate the advantages of our method over existing methods in simulations, and through analyses of a genomics dataset and another proteomics dataset for Alzheimer’s disease.
Peri-ictal activation of dorsomedial dorsal raphe serotonin neurons reduces mortality associated with maximal electroshock seizures
Authors: Petrucci Alexandra N , Jones Allysa R , Kreitlow Benjamin L , Buchanan Gordon F 
Published: March 2024

Abstract
Over one-third of patients with epilepsy will develop refractory epilepsy and continue to experience seizures despite medical treatment. These patients are at the greatest risk for sudden unexpected death in epilepsy. The precise mechanisms underlying sudden unexpected death in epilepsy are unknown, but cardiorespiratory dysfunction and arousal impairment have been implicated. Substantial circumstantial evidence suggests serotonin is relevant to sudden unexpected death in epilepsy as it modulates sleep/wake regulation, breathing and arousal. The dorsal raphe nucleus is a major serotonergic center and a component of the ascending arousal system. Seizures disrupt the firing of dorsal raphe neurons, which may contribute to reduced responsiveness. However, the relevance of the dorsal raphe nucleus and its subnuclei to sudden unexpected death in epilepsy remains unclear. The dorsomedial dorsal raphe may be a salient target due to its role in stress and its connections with structures implicated in sudden unexpected death in epilepsy. We hypothesized that optogenetic activation of dorsomedial dorsal raphe serotonin neurons in TPH2-ChR2-YFP (n = 26) mice and wild-type (n = 27) littermates before induction of a maximal electroshock seizure would reduce mortality. In this study, pre-seizure activation of dorsal raphe nucleus serotonin neurons reduced mortality in TPH2-ChR2-YFP mice with implants aimed at the dorsomedial dorsal raphe. These results implicate the dorsomedial dorsal raphe in this novel circuit influencing seizure-induced mortality. It is our hope that these results and future experiments will define circuit mechanisms that could ultimately reduce sudden unexpected death in epilepsy.
Parkinson’s disease impairs cortical sensori-motor decision-making cascades
Authors: Tomassini Alessandro , Cope Thomas E , Zhang Jiaxiang , Rowe James B 
Published: March 2024

Abstract
The transformation from perception to action requires a set of neuronal decisions about the nature of the percept, identification and selection of response options and execution of the appropriate motor response. The unfolding of such decisions is mediated by distributed representations of the decision variables—evidence and intentions—that are represented through oscillatory activity across the cortex. Here we combine magneto-electroencephalography and linear ballistic accumulator models of decision-making to reveal the impact of Parkinson’s disease during the selection and execution of action. We used a visuomotor task in which we independently manipulated uncertainty in sensory and action domains. A generative accumulator model was optimized to single-trial neurophysiological correlates of human behaviour, mapping the cortical oscillatory signatures of decision-making, and relating these to separate processes accumulating sensory evidence and selecting a motor action. We confirmed the role of widespread beta oscillatory activity in shaping the feed-forward cascade of evidence accumulation from resolution of sensory inputs to selection of appropriate responses. By contrasting the spatiotemporal dynamics of evidence accumulation in age-matched healthy controls and people with Parkinson’s disease, we identified disruption of the beta-mediated cascade of evidence accumulation as the hallmark of atypical decision-making in Parkinson’s disease. In frontal cortical regions, there was inefficient processing and transfer of perceptual information. Our findings emphasize the intimate connection between abnormal visuomotor function and pathological oscillatory activity in neurodegenerative disease. We propose that disruption of the oscillatory mechanisms governing fast and precise information exchanges between the sensory and motor systems contributes to behavioural changes in people with Parkinson’s disease.
Hierarchical functional differences between gyri and sulci at different scales
Authors: Zhao Lin , Dai Haixing , Wu Zihao , Jiang Xi , Zhu Dajiang , Zhang Tuo , Liu Tianming 
Published: March 2024

Abstract
Gyri and sulci are 2 fundamental cortical folding patterns of the human brain. Recent studies have suggested that gyri and sulci may play different functional roles given their structural and functional heterogeneity. However, our understanding of the functional differences between gyri and sulci remains limited due to several factors. Firstly, previous studies have typically focused on either the spatial or temporal domain, neglecting the inherently spatiotemporal nature of brain functions. Secondly, analyses have often been restricted to either local or global scales, leaving the question of hierarchical functional differences unresolved. Lastly, there has been a lack of appropriate analytical tools for interpreting the hierarchical spatiotemporal features that could provide insights into these differences. To overcome these limitations, in this paper, we proposed a novel hierarchical interpretable autoencoder (HIAE) to explore the hierarchical functional difference between gyri and sulci. Central to our approach is its capability to extract hierarchical features via a deep convolutional autoencoder and then to map these features into an embedding vector using a carefully designed feature interpreter. This process transforms the features into interpretable spatiotemporal patterns, which are pivotal in investigating the functional disparities between gyri and sulci. We evaluate the proposed framework on Human Connectome Project task functional magnetic resonance imaging dataset. The experiments demonstrate that the HIAE model can effectively extract and interpret hierarchical spatiotemporal features that are neuroscientifically meaningful. The analyses based on the interpreted features suggest that gyri are more globally activated, whereas sulci are more locally activated, demonstrating a distinct transition in activation patterns as the scale shifts from local to global. Overall, our study provides novel insights into the brain’s anatomy–function relationship.
Enhancement of weak signals by dynamic stochastic resonance in dark-field microscopy imaging
Authors: Zhang Bo , Xu Yue , Ma Yun Peng , Liu Hui , Li Yuan Fang , Huang Cheng Zhi 
Published: March 2024

Abstract
Enhancing weak signal acquisition is pivotal for bolstering analysis and detection capabilities. Herein, a dynamic stochastic resonance (DSR) algorithm for weak signal amplification that was identified to significantly improve the imaging visibility of dark-field microscopy nanoparticles under low illumination conditions is presented. When further combined with composite filed microscopy, DSR displays signal amplification much more effectively, showing high promise for detection purposes.
Association Between Social Vulnerability and Streptococcus pneumoniae Antimicrobial Resistance in US Adults
Authors: Mohanty Salini , Ye Gang , Sheets Charles , Cossrow Nicole , Yu Kalvin C , White Meghan , Klinker Kenneth P , Gupta Vikas 
Published: March 2024

Abstract

Background
Growing evidence indicates antimicrobial resistance disproportionately affects individuals living in socially vulnerable areas. This study evaluated the association between the CDC/ATSDR Social Vulnerability Index (SVI) and Streptococcus pneumoniae (SP) antimicrobial resistance (AMR) in the United States.

Methods
Adult patients ≥18 years with 30-day nonduplicate SP isolates from ambulatory/hospital settings from January 2011 to December 2022 with zip codes of residence were evaluated across 177 facilities in the BD Insights Research Database. Isolates were identified as SP AMR if they were non-susceptible to ≥1 antibiotic class (macrolide, tetracycline, extended-spectrum cephalosporins, or penicillin). Associations between SP AMR and SVI score (overall and themes) were evaluated using generalized estimating equations with repeated measurements within county to account for within-cluster correlations.

Results
Of 8008 unique SP isolates from 574 US counties across 39 states, the overall proportion of AMR was 49.9%. A significant association between socioeconomic status (SES) theme and SP AMR was detected with higher SES theme SVI score (indicating greater social vulnerability) associated with greater risk of AMR. On average, a decile increase of SES, indicating greater vulnerability, was associated with a 1.28% increased risk of AMR (95% confidence interval [CI], .61%, 1.95%; P = .0002). A decile increase of household characteristic score was associated with a 0.81% increased risk in SP AMR (95% CI, .13%, 1.49%; P = .0197). There was no association between racial/ethnic minority status, housing type and transportation theme, or overall SVI score and SP AMR.

Conclusions
SES and household characteristics were the SVI themes most associated with SP AMR.
Type 1 Human Immunodeficiency Virus (HIV-1) Incidence, Adherence, and Drug Resistance in Individuals Taking Daily Emtricitabine/Tenofovir Disoproxil Fumarate for HIV-1 Pre-exposure Prophylaxis: Pooled Analysis From 72 Global Studies
Authors: Landovitz Raphael J , Tao Li , Yang Juan , de Boer Melanie , Carter Christoph , Das Moupali , Baeten Jared M , Liu Albert , Hoover Karen W , Celum Connie , Grinsztejn Beatriz , Morris Sheldon , Wheeler Darrell P , Mayer Kenneth H , Golub Sarit A , Bekker Linda-Gail , Diabaté Souleymane , Hoornenborg Elske , Myers Janet , Leech Ashley A , McCormack Sheena , Chan Philip A , Sweat Michael , Matthews Lynn T , Grant Robert ,   the Global F/TDF PrEP Study Team, Beyrer Chris , Brown Joelle , Clark Jesse , Colson Paul , Eakle Robyn , Farley Jason , Flash Charlene A , Gallardo Jorge , Gottlieb Geoffrey , Grangeiro Alexandre , Heffron Renee , Hosek Sybil , Hull Mark , Idoko John , Inwani Irene , Koenig Helen , Kurth Ann , Lee Shui-shan , Mayer Kenneth , Mboup Souleymane , Meyer Jaimie , Mills Anthony , Mujugira Andrew , Pala Pietro , Phoenix John , Piatt Janice , Russell Darren , Sanders Eduard , Scott Rachel , Sevelius Jae , Shang Hong , Siegel Marc , Swaminathan Shobha , Tamayo Vivian , Tan Darrell , Taylor Allan , Vuylsteke Bea 
Published: March 2024

Abstract

Background
Oral pre-exposure prophylaxis (PrEP) with emtricitabine/tenofovir disoproxil fumarate (F/TDF) has high efficacy against HIV-1 acquisition. Seventy-two prospective studies of daily oral F/TDF PrEP were conducted to evaluate HIV-1 incidence, drug resistance, adherence, and bone and renal safety in diverse settings.

Methods
HIV-1 incidence was calculated from incident HIV-1 diagnoses after PrEP initiation and within 60 days of discontinuation. Tenofovir concentrations in dried blood spots (DBS), drug resistance, and bone/renal safety indicators were evaluated in a subset of studies.

Results
Among 17 274 participants, there were 101 cases with new HIV-1 diagnosis (.77 per 100 person-years; 95% confidence interval [CI]: .63–.94). In 78 cases with resistance data, 18 (23%) had M184I or V, 1 (1.3%) had K65R, and 3 (3.8%) had both mutations. In 54 cases with tenofovir concentration data from DBS, 45 (83.3%), 2 (3.7%), 6 (11.1%), and 1 (1.9%) had average adherence of &lt;2, 2−3, 4−6, and ≥7 doses/wk, respectively, and the corresponding incidence was 3.9 (95% CI: 2.9–5.3), .24 (.060–.95), .27 (.12–.60), and .054 (.008–.38) per 100 person-years. Adherence was low in younger participants, Hispanic/Latinx and Black participants, cisgender women, and transgender women. Bone and renal adverse event incidence rates were 0.69 and 11.8 per 100 person-years, respectively, consistent with previous reports.

Conclusions
Leveraging the largest pooled analysis of global PrEP studies to date, we demonstrate that F/TDF is safe and highly effective, even with less than daily dosing, in diverse clinical settings, geographies, populations, and routes of HIV-1 exposure.
Narrativity and literariness in receptions of Josephus’s teknophagia story
Authors: Binyam Yonatan 
Published: March 2024

Abstract
In this article, I present an analysis of the narrative discourses and literary elements found in the teknophagia story that originates with Josephus’s Bellum Judaicum and trace the development of those motifs in subsequent Latin, Hebrew, Arabic, and Ethiopic versions of the story. I first outline the reception history of Josephus within medieval Coptic and Ethiopic literary traditions, by way of the Hebrew Sefer Yosippon and one of its Latin sources, the De Excidio Hierosolymitano. I then illustrate how the literariness of the various authors who reworked the teknophagia story influences a reading of the narrative discourses of each text. In doing so, I emphasize the unique iteration of the account of the cannibalistic mother that appears in the Christian-Arabic and Ethiopic histories, showing how this version of the story develops out of not only earlier stylistic changes, but also from the literary elements introduced into the story by the redactor of the Arabic reworking of the Hebrew Yosippon.
The interpreter’s role and deaf students’ autonomy in mainstream classrooms
Authors: Prinzi Lisa M 
Published: March 2024

Abstract
This article explores the interpreter's role and approaches to working with deaf students as seen from deaf individuals' and interpreters' perspectives. A group of 41 formerly mainstreamed deaf individuals and interpreters offered insights into how the interpreter's role in mainstream classrooms influences deaf student autonomy and participation. This research illustrates the significance of autonomy for mainstreamed deaf students and suggests a correlation between the interpreter’s role and deaf students’ perceived autonomy in the classroom. In addition, the findings suggest that deaf students do not always know what an interpreter is supposed to do in K-12 classrooms. This study also finds that educational team members do not always explicitly communicate their roles and responsibilities to deaf students, leading to confusion that impacts their autonomy and overall experience. Finally, this research finds that deaf students are not trained with the ability to negotiate and renegotiate the interpreter’s role. This article concludes with considerations and recommendations for deaf education and interpreter education communities.
Motor adaptation in deaf and hearing native signers
Authors: Stroh Anna-Lena , Overvliet Krista E , Zierul Björn , Rösler Frank , Röder Brigitte 
Published: March 2024

Abstract
Previous studies have suggested that deafness could lead to deficits in motor skills and other body-related abilities. However, the literature regarding motor skills in deaf adults is scarce and existing studies often included participants with heterogeneous language backgrounds and deafness etiologies, thus making it difficult to delineate the effects of deafness. In this study, we investigated motor learning in deaf native signers and hearing nonsigners. To isolate the effects of deafness and those of acquiring a signed language, we additionally tested a group of hearing native signers. Two well-established paradigms of motor learning were employed, in which participants had to adapt their hand movements to a rotation of the visual feedback (Experiment 1) or to the introduction of a force field (Experiment 2). Proprioceptive estimates were assessed before and after adaptation. Like hearing nonsigners, deaf and hearing signers showed robust adaptation in both motor adaptation paradigms. No significant differences in motor adaptation and memory were observed between deaf signers and hearing nonsigners, as well as between hearing signers and hearing nonsigners. Moreover, no discernible group differences in proprioceptive accuracy were observed. These findings challenge the prevalent notion that deafness leads to deficits in motor skills and other body-related abilities.
Deceptive Features on Platforms
Authors: Johnen Johannes , Somogyi Robert 
Published: March 2024

Abstract
Many products sold on online platforms have additional features like fees for services, shipping, luggage, upgrades, and so on. We study when a two-sided platform shrouds additional features towards potentially naive buyers. We explore a novel mechanism according to which platforms shroud to manipulate network externalities between buyers and sellers. Exploring this mechanism, we argue the advent of online marketplaces led to less transparent markets. First, platforms have stronger incentives to shroud seller fees than sellers themselves. Second, platforms shroud their own fees less if they earn more revenue from sellers; so when sellers on the platform compete more fiercely, platforms—somewhat perversely—shroud more. We connect these results to many applications and the current debate on regulating online platforms.
Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana
Authors: Poikela Noora , Laetsch Dominik R , Hoikkala Ville , Lohse Konrad , Kankare Maaria 
Published: March 2024

Abstract
Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.
Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations
Authors: Matheson Joseph , Masel Joanna 
Published: March 2024

Abstract
Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. In agreement with previous analytical approximations, in our simulations of a human-like genome with a realistically high genome-wide deleterious mutation rate, the effects of unlinked background selection exceed those of linked background selection. Background selection reduces neutral genetic diversity by a factor that is independent of census population size. Outside of genic regions, the strength of background selection increases with the mean selection coefficient, contradicting the linked theory but in agreement with the unlinked theory. Neutral diversity within genic regions is fairly independent of the strength of selection. Deleterious genetic load among haploid individuals is underdispersed, indicating nonindependent evolution of deleterious mutations. Empirical evidence for underdispersion was previously interpreted as evidence for global epistasis, but we recover it from a non-epistatic model.