bluuebunny/crossref_metadata_2025_split huggingface dataset:
Video gaming, but not reliance on GPS, is associated with spatial navigation performance
Authors: Yavuz Emre , He Chuanxiuyue , Goodroe Sarah , Ganstrom Chris , Coutrot Antoine , Hornberger Michael , Hegarty Mary , Spiers Hugo J. 
Published: August 2023

AbstractRecent evidence suggests that greater reliance on GPS-assisted devices is associated with poorer navigation ability. Contrastingly, studies have shown that video gaming can enhance navigation ability. While gender differences in navigation ability in favour of men are well-reported, it remains unclear if the effects of reliance on GPS and video gaming on navigation performance are influenced by gender. We investigated whether gender would influence the effect of gaming experience and reliance on GPS on navigation ability using the mobile app Sea Hero Quest, which has been shown to predict real-world wayfinding performance. Alongside navigation performance assessment we asked a series of self-report questions relating to reliance on GPS, navigation strategies and gaming experience with a group of US-based participants (n = 822, 280 men, 542 women, mean age = 26.3 years, range = 18-52 years). A multivariate linear regression model found no significant association between reliance on GPS and navigation performance for either gender. There was a significant association between weekly hours of video gaming and navigation performance which was not moderated by gender. After accounting for video game experience, gender was no longer significantly associated with navigation performance. These findings have implications for which daily activities may enhance or disrupt specific cognitive abilities. Future studies applying an interventional design and real-world navigation testing would be useful to determine whether video games playing increases navigation skill, or whether those who are good at navigating tend to play more video games.
A multi-channel TMS system enabling accurate stimulus orientation control during concurrent ultra-high-field MRI for preclinical applications
Authors: Souza Victor H. , Sinisalo Heikki , Korhonen Juuso T. , Paasonen Jaakko , Nyrhinen Mikko , Nieminen Jaakko O. , Koponen Maria , Kettunen Mikko , Gröhn Olli , Ilmoniemi Risto J. 
Published: August 2023

AbstractMonitoring cortical responses to neuromodulation protocols on preclinical models can elucidate fundamental mechanisms of brain function. Concurrent brain stimulation and imaging is challenging, usually compromising spatiotemporal resolution, accuracy, and versatility. Here we report a non-invasive brain stimulation system with electronic control of neuromodulation parameters in a 9.4-T magnetic resonance imaging (MRI) environment. In the imaging scanner, transcranial magnetic stimulation is delivered with a set of two coils and the MRI signals are recorded with a radiofrequency coil. The coil set provides millisecond-scale electronic control of the stimulus orientation with 1° resolution. Without physically rotating the coils, we evoked orientation-specific muscle responses after cortical stimulation on an anesthetized rat. We show that the stimulation pulses do not affect the anatomical imaging quality, and imaging signals are disrupted only if recorded before 10 ms after pulse delivery. Concurrent electronically targeted brain stimulation and neuroimaging sets the stage for the causal investigation of whole-brain network functions, endorsing more efficient treatment protocols.
Comparative Analysis of Cameras and Software Tools for Skeleton Tracking
Authors: Aharony Naama , Meshurer Amir , Krakovski Maya , Parmet Yisrael , Melzer Itshak , Edan Yael 
Published: August 2023

AbstractBackgroundSkeleton tracking is a valuable tool for monitoring user performance and has been performed with different sensors and software tools. It enables to quantify 3D motion accurately. We present a comparative analysis of cameras and software tools utilized in skeleton tracking. We describe an experimental design and analysis methods with four steps. Specifically, we conducted an analysis comparing two ZED-2i cameras with a RealSense camera using commercial skeleton tracking algorithms.MethodsThe comparative analysis methodology describes the experimental design and analysis methods for comparing kinematic data from both upper and lower extremities. An experiment to evaluate the performance of three different cameras (RealSense, ZED2mm, and ZED4mm) and three skeleton tracking algorithms (PyZED, Nuitrack, and MediaPipe) was performed with 16 participants. The participants were required to walk along a 6-meter-long path while moving their hands up and down horizontally. Ground truth was measured by a Vicon 3D motion analysis system. Two groups of features corresponding to the upper and lower extremities were derived from the raw data and compared using two methods. In the first method, the RMSE values were compared to the data from the Vicon system. The RMSE results were also combined using two grading techniques with different feature importance weights to determine the camera with the lowest RMSE. In the second method, a linear mix model with a Wald statistical test was applied.ResultsThe ZED-2i cameras outperformed the RealSense camera across upper- and lower-extremity features and different weights. The ZED2mm camera showed better average median grading, lower standard deviation, and superior performance in the model analysis.ConclusionThe comparative analysis methodology provides a systematic method to compare software tools and cameras for skeleton tracking. The ranking enables to prioritize different features. Skeleton tracking with the ZED cameras yielded better performances for both upper and lower extremities features.
Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles
Authors: Jan Maxime , Jimenez Sonia , Hor Charlotte N. , Dijk Derk-Jan , Skeldon Anne C. , Franken Paul 
Published: August 2023

AbstractTranscriptome studies aim at gaining insight into the molecular pathways underlying biological processes. Analyses of gene-expression dynamics in research on circadian rhythms and sleep homeostasis describe these two processes independently, using separate models such as sinusoidal oscillations and exponential saturating functions. Rhythmically expressed genes are, however, influenced by both processes. We therefore implemented a driven, damped harmonic oscillator model which can accommodate both types of dynamics by varying the degree of damping. This makes it possible to estimate the contribution of circadian and sleep-wake driven influences on the expression of a gene within the framework of a single model. We applied the model to cortex, liver, and blood data obtained in mice and humans. The model reliably captured a wide range of rhythmic dynamics under various experimental conditions, including the long-term amplitude reduction of cortical clock-gene rhythms observed after sleep deprivation. Cortical gene expression was generally influenced more by sleep-wake driven than circadian factors, while the opposite was observed in liver and blood. Importantly, the model suggested that sleep-wake state can alter gene expression with a delayed, long-lasting response not previously considered. Our model further predicted that, perhaps paradoxically, the gain in sleep time after sleep deprivation, delayed re-establishing baseline expression rhythms of intrinsically oscillatory transcripts indicating that similar to insufficient sleep, also excess sleep can impact rhythmic gene expression. Because of the tissue- and gene-specific responses, sleep deprivation led to a profound intra- and inter-tissue desynchronization which in the cortex lasted well beyond phenotypic sleep-wake recovery. The results demonstrate that analyzing rhythmic gene expression must take the complex interactions between circadian and sleep-wake influences into account. The model is a versatile tool with a low number of free parameters to fit and predict gene expression under a variety of conditions relevant to society.
Pleistocene glaciation advances the younger temporal dimension of species diversification in a major biodiversity hotspot
Authors: Rana Santosh Kumar , Rana Hum Kala , Landis Jacob B. , Kuang Tianhui , Chen Juntong , Wang Hengchang , Deng Tao , Davis Charles C. , Sun Hang 
Published: August 2023

SummaryThe expansive Himalayan-Hengduan Mountains (HM) and Qinghai-Tibet Plateau (QTP) form a biodiversity hotspot imperiled by global change. The species diversity, resulting from myriad factors led to plant diversification from 10 million years ago till now. However, despite understanding speciation timing better, a lack of in-depth population-level studies and a dearth of organismal sampling among closely related species and populations leaves an incomplete view of diversification trends and biotic influences.We delve into the complex factors influencing diversification through genomic and eco-morphological analysis within theStellera chamaejasmeL. complex, known for its significant floral diversity.Our results uncover four cryptic species, indicating a more recent and younger diversification period (∼2.67–0.9 Mya), driven by Pleistocene glaciation and a complex set of interacting biotic factors. These factors prompted allopatric speciation and advocated cyclical warming–cooling episodes along latitudinal and altitudinal gradients throughout the Pleistocene.The study emphasizes the existence of cryptic species within these mountains, broadening our understanding of species diversification to more recent than previously recognized. This novel perspective may reshape evolutionary paradigms in plant science. Additionally, it also brings to light concerns over future warming’s possible impacts on alpine species distribution and speciation, underlining the urgency for increased conservation efforts.
A multigenerational Turing model reproduces transgressive petal spot phenotypes in hybridMimulus
Authors: Simmons Emily S. G. , Cooley Arielle M. , Puzey Joshua R. , Conradi Smith Gregory D. 
Published: August 2023

AbstractThe origin of phenotypic novelty is a perennial question of genetics and evolution. To date, few studies of biological pattern formation specifically address multi-generational aspects of inheritance and phenotypic novelty. For quantitative traits influenced by many segregating alleles, offspring phenotypes are often intermediate to parental values. In other cases, offspring phenotypes can be transgressive to parental values. For example, in the model organismMimulus(monkeyflower), the offspring of parents with solid-colored petals exhibit novel spotted petal phenotypes. These patterns are controlled by an activator-inhibitor gene regulatory network with a small number of loci. Here we develop and analyze a model of hybridization and pattern formation that accounts for inheritance in diploid gene regulatory networks composed of either homozygous or heterozygous alleles. We find that the resulting model of multi-generational Turing-type pattern formation can reproduce the transgressive petal phenotypes observed inMimulus. The model gives insight into how non-patterned parent phenotypes can yield phenotypically transgressive, patterned offspring, aiding in the development of empirically testable hypotheses.
Amyloidosis and ageing have differential effects on microglial Ca2+activity in the mouse brain
Authors: Izquierdo Pablo , Jolivet Renaud B. , Attwell David , Madry Christian 
Published: August 2023

ABSTRACTIn microglia, changes in intracellular calcium concentration ([Ca2+]i) may regulate process motility, inflammasome activation, and phagocytosis. However, while neurons and astrocytes exhibit frequent spontaneous Ca2+activity, microglial Ca2+signals are much rarer and poorly understood. Here, we studied [Ca2+]ichanges of microglia in acute brain slices using Fluo-4–loaded cells and mice expressing GCaMP5g in microglia. Spontaneous Ca2+transients occurred ∼5 times more frequently in individual microglial processes than in their somata. We assessed whether microglial Ca2+responses change in Alzheimer’s disease (AD) usingAppNL-G-Fknock-in mice. Proximity to Aβ plaques strongly affected microglial Ca2+activity. Although spontaneous Ca2+transients were unaffected in microglial processes, they were 5-fold more frequent in microglial somata near Aβ plaques than in wild-type microglia. Microglia away from Aβ plaques in AD mice showed intermediate properties for morphology and Ca2+responses, partly resembling those of wild-type microglia. By contrast, somatic Ca2+responses evoked by tissue damage were less intense in microglia near Aβ plaques than in wild-type microglia, suggesting different mechanisms underlying spontaneous vs. damage-evoked Ca2+signals. Finally, as similar processes occur in neurodegeneration and old age, we studied whether ageing affected microglial [Ca2+]i. Somatic damage-evoked Ca2+responses were greatly reduced in microglia from old mice, as in the AD mice. In contrast to AD, however, old age did not alter the occurrence of spontaneous Ca2+signals in microglial somata but reduced the rate of events in processes. Thus, we demonstrate distinct compartmentalised Ca2+activity in microglia from healthy, aged and AD-like brains.
Plug-and-play protein biosensors using aptamer-regulated in vitro transcription
Authors: Lee Heonjoon , Xie Tian , Yu Xinjie , Schaffter Samuel W. , Schulman Rebecca 
Published: August 2023

AbstractMolecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors or digital protein biosensors with detection ranges that can be tuned over two orders of magnitude. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors suitable for diverse research and diagnostic applications.One sentence summaryWe develop a modular platform for biosensing across a wide dynamic range using aptamer-regulated transcription to detect different proteins and molecular circuits to process the RNA transcript outputs.
Interareal synaptic inputs underlying whisking-related activity in the primary somatosensory barrel cortex
Authors: Kawatani Masahiro , Horio Kayo , Ohkuma Mahito , Li Wan-Ru , Yamashita Takayuki 
Published: August 2023

AbstractBody movements, especially orofacial movements, are known to influence brain-wide neuronal activity. In the sensory cortex, thalamocortical bottom-up inputs and motor-sensory top-down inputs are thought to affect the dynamics of membrane potentials (Vm) of neurons and change their processing of sensory information during movements. However, direct perturbation of the axons projecting to the sensory cortex from other remote areas during movements has remained unassessed, and therefore the interareal circuits generating motor-related signals in sensory cortices are still unclear. Using a Gi-coupled opsin, eOPN3, we here inhibited interareal signals incoming to the whisker primary somatosensory cortex (wS1) of awake behaving mice and tested their effects on whisking-related changes in neuronal activities in wS1. Spontaneous whisking in air induced the changes in spike rates of a fraction of wS1 neurons which were accompanied by depolarization and substantial reduction of slow-wave oscillatory fluctuations of Vm. Despite an extensive innervation, inhibition of inputs from the whisker primary motor cortex (wM1) to wS1 did not alter the spike rates and Vmdynamics of wS1 neurons during whisking. In contrast, inhibition of axons from the whisker-related thalamus (wTLM) and the whisker secondary somatosensory cortex (wS2) to wS1 largely attenuated the whisking-related supra- and sub-threshold Vmdynamics of wS1 neurons. Our findings thus suggest that sensorimotor integration in wS1 during spontaneous whisking is mediated by direct synaptic inputs from wTLM and wS2 rather than from wM1.Significance statementThe traditional viewpoint underscores the importance of motor-sensory projections in shaping movement-induced neuronal activity within sensory cortices. However, this study challenges such established views. We reveal that the synaptic inputs from the whisker primary motor cortex do not alter the dynamics of neuronal activity in the whisker primary somatosensory cortex (wS1) during spontaneous whisker movements. Furthermore, we make a novel observation that inhibiting inputs from the whisker secondary somatosensory cortex (wS2) substantially curtails movement-related activities in wS1. These findings provoke a reconsideration of the role of motor-sensory projections in sensorimotor integration and bring to light a new function for wS2-to-wS1 projections.
Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis
Authors: Kodali Mahesh , Antone Jerry , Alsop Eric , Jayakumar Rojashree , Parikh Khushi , Sanchez-Molina Paula , Ajami Bahareh , Arnold Steven , Jensen Kendall , Das Sudeshna , Weinberg Marc S. 
Published: August 2023

AbstractCerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approaches to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
Gaze tracking of large-billed crows (Corvus macrorhynchos) in a motion-capture system
Authors: Itahara Akihiro , Kano Fumihiro 
Published: August 2023

ABSTRACTThe visually guided behaviors of corvids (Corvidae) are often examined in previous studies because they provide important clues about their perception, attention, and cognition. However, the details regarding how they orient their heads toward the visual targets (or how they use their visual fields when attending to the visual targets) remain largely unclear. This study used a newly established motion capture system to examine the visual field use of large-billed crows (Corvus macrorhynchos). Study 1 employed an established ophthalmoscopic reflex technique to identify the visual field configuration, including the binocular width and optic axes, as well as the degree of eye movement. Study 2 used the motion capture system to track the head movements of freely moving crows and examined how they oriented their reconstructed visual fields toward attention-getting objects. When visual targets were moving, the crows used their binocular visual fields, particularly around the projection of the beak-tip. When the visual targets stopped moving, crows frequently used non-binocular visual fields, particularly around the regions where their optic axes were found in Study 1 (close to their visual axes). On such occasions, the crows slightly preferred the right eye. Overall, the visual field use of crows is clearly predictable. Thus, while the untracked eye movements could introduce some level of uncertainty (typically within 15 degrees), we demonstrated the feasibility of inferring a crow’s attentional focus by 3D tracking of their heads. Our system represents a promising initial step towards establishing gaze tracking methods for studying corvid behavior and cognition.
Measuring and monitoring skill learning in closed-loop myoelectric hand prostheses using speed-accuracy tradeoffs
Authors: Mamidanna Pranav , Gholinezhad Shima , Farina Dario , Dideriksen Jakob Lund , Dosen Strahinja 
Published: August 2023

AbstractObjectiveClosed-loop myoelectric prostheses, which combine supplementary sensory feedback and electromyography (EMG) based control, hold the potential to narrow the divide between natural and bionic hands. The use of these devices, however, requires dedicated training. Therefore, it is crucial to develop methods that quantify how users acquire skilled control over their prostheses to effectively monitor skill progression and inform the development of interfaces that optimize this process.ApproachBuilding on theories of skill learning in human motor control, we measured speed-accuracy tradeoff functions (SAFs) to comprehensively characterize learning-induced changes in skill – as opposed to merely tracking changes in task success across training – facilitated by a closed-loop interface that combined proportional control and EMG feedback. Sixteen able-bodied and one amputee participated in a 3-day experiment where they were instructed to perform the box-and-blocks task using a timed force-matching paradigm at four specified speeds to reach two target force levels, such that the SAF could be determined.Main resultsWe found that the participants’ accuracy increased in a similar way across all speeds we tested. Consequently, the shape of the SAF remained similar across days, at both force levels. Further, we observed that EMG feedback enabled participants to improve their motor execution in terms of reduced trial-by-trial variability, a hallmark of skilled behavior. We then fit a power law model of the SAF, and demonstrated how the model parameters could be used to identify and monitor changes in skill.SignificanceWe comprehensively characterized how an EMG feedback interface enabled skill acquisition, both at the level of task performance and movement execution. More generally, we believe that the proposed methods are effective for measuring and monitoring user skill progression in closed-loop prosthesis control.