bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between recovering from tempo perturbations and reading measurements
Authors: Wei Yi , Hancock Roeland 
Published: December 2023

AbstractA strong correlation between auditory temporal processing and reading proficiency has been consistently observed across clinical and nonclinical populations, spanning various age groups and languages. Specifically, rhythm sensitivity in both the music and speech domains has been considered to be fundamental for accurately tracking the hierarchical acoustic components in speech, playing a central role in the development of reading skills. However, the empirical validation of this hypothesis has primarily utilized stimuli with an isochronous underlying beat structure, which is limited in its ability to capture the nonlinearity inherent in the perception of timing within the speech and music domains. In our current study, we introduced perturbation stimuli and demonstrated a relationship between sensorimotor synchronization performance and reading measurements in the neurotypical adult population. Specifically, the current study highlighted that sensorimotor synchronization during the post-perturbation time window yields notably superior predictive value across a wide array of reading measurements when compared to the pre-perturbation time window, which, in contrast, did not predict reading measurements. Furthermore, our novel curve fitting analysis effectively captured the nonlinear aspects of participants’ sensorimotor synchronization performance when recovering from tempo perturbation, providing further insight into their auditory temporal processing abilities when responding to timing changes in auditory signals—a phenomenon commonly encountered in both speech and music contexts.
Ivermectin increases striatal cholinergic activity to facilitate dopamine terminal function
Authors: Wadsworth Hillary A. , Warnecke Alicia M.P. , Barlow Joshua C. , Kayden Robinson J. , Steimle Emma , Ronström Joakim , Williams Pacen , Galbraith Christopher , Baldridge Jared , Jakowec Michael W. , Davies Daryl L. , Yorgason Jordan T. 
Published: December 2023

AbstractIvermectin (IVM) is a commonly prescribed antiparasitic treatment with pharmacological effects on invertebrate glutamate ion channels resulting in paralysis and death of invertebrates. However, it can also act as a modulator of some vertebrate ion channels and has shown promise in facilitating L-DOPA treatment in preclinical models of Parkinson’s disease. The pharmacological effects of IVM on dopamine terminal function were tested, focusing on the role of two of IVM’s potential targets: purinergic P2X4 and nicotinic acetylcholine receptors. Ivermectin enhanced electrochemical detection of dorsal striatum dopamine release. Although striatal P2X4 receptors were observed, IVM effects on dopamine release were not blocked by P2X4 receptor inactivation. In contrast, IVM attenuated nicotine effects on dopamine release, and antagonizing nicotinic receptors prevented IVM effects on dopamine release. IVM also enhanced striatal cholinergic interneuron firing. L-DOPA enhances dopamine release by increasing vesicular content. L-DOPA and IVM co-application further enhanced release but resulted in a reduction in the ratio between high and low frequency stimulations, suggesting that IVM is enhancing release largely through changes in terminal excitability and not vesicular content. Thus, IVM is increasing striatal dopamine release through enhanced cholinergic activity on dopamine terminals.
Reduction of low-frequency oscillations in cerebral circulation correlates with pupil dilation during cognition: an fNIRS study
Authors: Moreno-Castillo Mayra , Manjarrez Elias 
Published: December 2023

AbstractNumerous studies have utilized functional near-infrared spectroscopy (fNIRS) to investigate brain hemodynamics during diverse cognitive tasks. However, although these studies have consistently reported increased oxygenation levels in the prefrontal cortex, they have not explored their effects on the amplitude of brain low-frequency oscillations (LFO). Additionally, other reports have shown that pupil dilation occurs during cognitive tasks, which may indicate a correlation between LFO amplitude and pupil dilation. However, no study has demonstrated such a correlation. Our research has two aims: firstly, to analyze the impact of cognitive tasks on the amplitude of LFO using oxyhemoglobin (HbO2) fNIRS signals, and secondly, to assess the relationship between the amplitude of these LFO and pupil diameters during such cognitive tasks. We found that during arithmetic tasks, the brain LFOs recorded on the prefrontal cortex were temporarily reduced while pupil diameter increased. These findings offer new insights into the physiological functions of reactivity of LFO in cerebral circulation. Additionally, combining fNIRS signals to track LFO on the prefrontal cortex with pupil measurement shows the feasibility of developing efficient hybrid brain-computer interfaces of LFO-pupil detection capable of predicting the initiation and ending of cognitive processes.Significant statementInspired by the Berger effect, which demonstrates alpha wave reactivity with eye-opening, our study investigated reactivity in other physiological oscillations related to brain hemodynamics during cognition. Our findings revealed a novel phenomenon: a temporary reduction in the amplitude of low-frequency oscillations (LFOs) of oxyhemoglobin (HbO2) in the brain’s prefrontal cortex, concurrent with increased pupil diameter during arithmetic tasks. This discovery expands our knowledge of LFO in cerebral circulation and creates new avenues for studying fNIRS-LFO reactivity during cognitive tasks in healthy individuals and patients.
iTraNet: A Web-Based Platform for integrated Trans-Omics Network Visualization and Analysis
Authors: Sugimoto Hikaru , Morita Keigo , Li Dongzi , Bai Yunfan , Mattanovich Matthias , Kuroda Shinya 
Published: December 2023

ABSTRACTA major goal in biology is to comprehensively understand molecular interactions within living systems. Visualization and analysis of biological networks play crucial roles in understanding these biochemical processes. Biological networks include diverse types, from gene regulatory networks and protein–protein interactions (PPIs) to metabolic networks. Metabolic networks include substrates, products, and enzymes, which are regulated by allosteric mechanisms and gene expression. Given this complexity, there is a pressing need to investigate trans-omics networks that include these various regulations to understand living systems. However, analyzing various omics layers is laborious due to the diversity of databases and the intricate nature of network analysis. We developed iTraNet, a user-friendly interactive web application that visualizes and analyzes trans-omics networks involving four major types of networks: gene regulatory networks (including transcription factor, microRNA, and mRNA); PPIs; metabolic networks (including enzyme, mRNA, and metabolite); and metabolite exchange networks (including transporter, mRNA, and metabolite). Using iTraNet, we found that in wild-type mice, hub molecules within the network tended to respond to glucose administration, whereas inob/obmice, this tendency disappeared. With its ability to facilitate network visualization and analysis, we anticipate that iTraNet will help researchers gain insights into biological systems. iTraNet is available at (https://transomics.streamlit.app/).GRAPHICAL ABSTRACT
Translating from mice to humans: using preclinical blood-based biomarkers for the prognosis and treatment of traumatic brain injury
Authors: Lisi Ilaria , Moro Federico , Mazzone Edoardo , Marklund Niklas , Pischiutta Francesca , Kobeissy Firas , Mao Xiang , Corrigan Frances , Helmy Adel , Nasrallah Fatima , Pietro Valentina Di , Ngwenya Laura B , Portela Luis , Semple Bridgette , Smith Douglas H. , Wellington Cheryl , Loane David J , Wang Kevin , Zanier Elisa R ,   the InTBIR Fundamental & Translational Working Group
Published: December 2023

AbstractRodent models are important research tools for studying the pathophysiology of traumatic brain injury (TBI) and developing potential new therapeutic interventions for this devastating neurological disorder. However, the failure rate for the translation of drugs from animal testing to human treatments for TBI is 100%, perhaps due, in part, to distinct timescales of pathophysiological processes in rodents versus humans that impedes translational advancements. Incorporating clinically relevant biomarkers in preclinical studies may provide an opportunity to calibrate preclinical models to human TBI biomechanics and pathophysiology. To support this important translational goal, we conducted a systematic literature review of preclinical TBI studies in rodents measuring blood levels of clinically used NfL, t-Tau, p-Tau, UCH-L1, or GFAP, published in PubMed/MEDLINE up to June 13th, 2023. We focused on blood biomarker temporal trajectories and their predictive and pharmacodynamic value and discuss our findings in the context of the latest clinical TBI biomarker data. Out of 369 original studies identified through the literature search, 71 met the inclusion criteria, with a median quality score on the CAMARADES checklist of 5 (interquartile range 4-7). NfL was measured in 17 preclinical studies, GFAP in 41, t-Tau in 17, p-Tau in 7, and UCH-L1 in 19 preclinical studies. Data in rodent models show that all blood biomarkers exhibited injury severity-dependent elevations, with GFAP and UCH-L1 peaking within hours after TBI, NfL peaking within days after TBI and remaining elevated up to 6 months post-injury, whereas t-Tau and p-Tau levels were gradually increased many weeks after TBI. Blood NfL levels emerges as a prognostic indicator of white matter loss after TBI, while both NfL and GFAP hold promise for pharmacodynamic studies of neuroprotective treatments. Therefore, blood-based preclinical biomarker trajectories could serve as important anchor points that may advance translational research in the TBI field. However, further investigation into biomarker levels in the subacute and chronic phases will be needed to more clearly define pathophysiological mechanisms and identify new therapeutic targets for TBI.
Perception of Motion Salience Shapes the Emergence of Collective Motions
Authors: Xiao Yandong , Lei Xiaokang , Zheng Zhicheng , Xiang Yalun , Liu Yang-Yu , Peng Xingguang 
Published: December 2023

ABSTRACTAs one of the most common and spectacular manifestations of coordinated behavior, collective motion is the spontaneous emergence of the ordered movement in a system consisting of many self-propelled agents, e.g., flocks of birds, schools of fish, herds of animals, and human crowds. Despite extensive studies on collective motions, a systems-level understanding of different motion patterns of collective behaviors is still lacking. This further hinders the adoption of bio-inspired mechanisms for applications of swarm robotics. Here, by leveraging three large bird-flocking datasets, we systematically investigate the emergence of different patterns of collective motions:mobbing, circling, andtransit. We find that flocks with higher maneuverable motions (i.e.,mobbingandcircling) prefer to evolve a more nested structure of leader-follower (LF) relations and a clear hierarchy to mitigate the damage of individual freedom to group cohesion. In contrast, flocks with smooth motion (i.e.,transit) do not display this tactful strategy to organize the group. To explain this empirical finding, we propose a measure based on the perception of motion salience (MS) to quantify the trade-off between individual freedom and group cohesion. Moreover, we perform the correlation analysis between LF and MS, finding that individuals with higher MS tend to lead the group with higher maneuverable motions. Those findings prompt us to develop a swarm model with adaptive MS-based (AMS) interactions and confirm that AMS interactions are responsible for the emergence of nested and hierarchical LF relations in the flocks with highly maneuverable motions. Finally, we implement AMS interactions in swarm robotics that consists of ∼102miniature mobile robots. The swarm experiments of collective following and collective evacuation demonstrate that AMS interactions not only empower the swarm to promptly respond to the transient perturbation but also strengthen the self-organization of collective motions in terms of temporal cognition.
Dynamic Causal Modelling Highlights the Importance of Decreased Self-Inhibition of the Sensorimotor Cortex in Motor Fatigability
Authors: Heimhofer Caroline , Bächinger Marc , Lehner Rea , Frässle Stefan , Balsters Joshua Henk , Wenderoth Nicole 
Published: December 2023

AbstractMotor fatigability emerges when challenging motor tasks must be maintained over an extended period of time. It is a frequently observed phenomenon in everyday life which affects patients as well as healthy individuals. Motor fatigability can be measured using simple tasks like finger tapping at maximum speed for 30s. This typically results in a rapid decrease of tapping frequency, a phenomenon called motor slowing. In a previous study (Bächinger et al. 2019), we showed that motor slowing goes hand in hand with a gradual increase of activation in the primary sensorimotor cortex (SM1), supplementary motor area (SMA), and dorsal premotor cortex (PMd). Previous electrophysiological measurements further suggested that the increase in SM1 activity might reflect a breakdown of inhibition and, particularly, a breakdown of surround inhibition which might have led to heightened coactivation of antagonistic muscles. It is unclear what drives the activity increase in SM1 caused by motor slowing and whether motor fatigability affects the dynamic interactions between SM1 and upstream motor areas like SMA and PMd. Here, we performed dynamic causal modelling to answer this question. Our main findings revealed that motor slowing was associated with a significant reduction in SM1 self-inhibition which is in line with previous electrophysiological results. Additionally, the model revealed a significant decrease in the driving input to premotor areas suggesting that structures other than cortical motor areas might cause motor fatigability.
Continuous estimation of reaching space in superficial layers of the motor cortex
Authors: Galiñanes Gregorio Luis , Huber Daniel 
Published: December 2023

ABSTRACTMotor cortex plays a key role in controlling voluntary arm movements towards spatial targets. The cortical representation of spatial information has been extensively studied and was found to range from combinations of muscle synergies to cognitive maps of locations in space. How such abstract representations of target space evolve during a behavior, how they integrate with other behavioral features and what role they play in movement control is less clear. Here we addressed these questions by recording the activity of layer 2/3 (L2/3) neurons in the motor cortex using two-photon calcium imaging in head-restrained mice, while they reached for water droplets presented at different spatial locations around their snout. Our results reveal that a majority (>80%) of L2/3 neurons with task-related activity are target-space selective and their activity is contingent on a single target position in an ego-centric reference frame. This spatial framework is preferentially organized along three cardinal directions (Center, Left and Right). Surprisingly, the coding of target space is not limited to the activity during movement planning or execution, but is also predominant during preceding and subsequent phases of the task, and even persists beyond water consumption. More importantly, target specificity is independent of the movement kinematics and is immediately updated when the target is moved to a new position. Our findings suggest that, rather than descending motor commands, the ensemble of L2/3 neurons in the motor cortex conjointly encode internal (behavioral) and external (spatial) aspects of the task, playing a role in higher-order representations related to estimation processes of the ongoing actions.
Mild blast TBI raises gamma connectivity, EEG power, and reduces GABA interneuron density
Authors: May Hazel G , Tsikonofilos Konstantinos , Donat Cornelius K , Sastre Magdalena , Kozlov Andriy S , Sharp David J , Bruyns-Haylett Michael 
Published: December 2023

AbstractAt least one traumatic brain injury (TBI) will be experienced by approximately 50-60 million of the world’s population in their lifetime and is the biggest cause of death and disability in those under 40. Mild traumatic brain injury (mTBI) can induce subtle changes but have long-lasting effects that may be difficult to detect through conventional neurological assessment, including standard clinical imaging techniques. These changes can lead to an increased risk of future neurodegeneration and emphasises the need to use more sensitive diagnostic tools such as EEG in order to identify injury and opportunities for therapeutic intervention.In this study, we investigated electrophysiological and histopathological changes in a rat model of mild blast-induced TBI. We used a 32-channel EEG electrode array to detect global and local changes in neural activity and functional connectivity in acute (3 to 4-hours) as well as chronic phases (1 and 3-months) post-injury. GABAergic inhibitory interneurons, crucial for maintaining an excitatory/inhibitory balance, were quantified using immunohistochemistry.Mild blast-induced TBI had minimal effects on resting power and connectivity at the acute timepoint but resulted in resting-state global power increases at all frequencies as well as a relative power increase in slow-wave frequencies in the chronic phase post-injury. Functional connectivity increases in the gamma frequency along with increases in power in the chronic phase pointed towards an alteration in the excitatory/inhibitory balance. Indeed, electrophysiological changes were associated with reduced density of GABAergic interneurons at 7-days, 1-month, and 3months post-injury, with a decrease in somatostatin-positive cell density in the 5th layer of all cortical regions of interest, and a parvalbumin decrease in the 5thlayer of the primary auditory cortex. In contrast, the total number of neurons, measured by NeuN did not change significantly, thus demonstrating a biased impact on inhibitory interneuron populations.Our work demonstrates that the techniques and metrics of injury assessment employed in this study are sensitive enough to reflect the subtle changes present in mTBI and therefore hold potential clinical relevance. By using non-invasive EEG assessments and histopathology, we were able to reveal direct correlates and potential sources of the abnormalities caused by mild blast-induced TBI.
Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments
Authors: Lang Stuart , Fletcher Daniel A. , Petit Alain-Pierre , Luise Nicola , Fyfe Paul , Zuccotto Fabio , Porter David , Hope Anthony , Bellany Fiona , Kerr Catrina , Mackenzie Claire J. , Wyatt Paul G. , Gray David W. 
Published: December 2023

AbstractIdentification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to theN-terminal domain (NTD) of HIV-CA at a site close to the interface with theC-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds37and38, which have19F-pK values of 5.3 and 5.4 respectively.Abstract Figure
Factors influencingAgrobacterium-mediated genetic transformation efficiency in wheat
Authors: Karthikeyan Thiyagarajan , Miguel Noguera Luis , Pacheco Mario , Govindan Velu , Vikram Prashant 
Published: December 2023

AbstractAssessment of the efficiency ofAgrobacterium tumefaciensmediated transformation in four bread wheat varieties was focused and upon optimization of experiments done to obtain tangible results. The four varieties namely Fielder, Navojoa, Baj and Kachu/saul were transformed with optimized protocols, subsequently randomly selected from selection medium amalgamated with phosphinothricin (Glufosinate). Initially the variety Fielder was proceeded with 36 different concentrations of synthetic auxins 2,4-D and Picloram as 36 treatments. The treatment 30 (48 μg of 2,4-D and 64 μg of Picloram) has shown higher efficiency and is comparable in terms of the three traits studied. Additionally, antioxidants and growth regulators were adjusted to obtain better result towards reasonable transformation frequency. Based on the optimization for the variety Fielder, additional varieties were also tested and selected against the selectable marker PPT. Selected genotypes were subjected forgusAorBargene PCR amplification. The result revealed the frequency of transgenesis with the range of 60-70% with the varieties studied, however the whole experiment needs further repetitions for confirmatory result. Transgenic genotypes of the Fielder variety showed moderate to strongGUSexpression in leaves, anthers, seeds, seed coats, roots compare to non-transgenic control plant tissues. PPT leaf painting assay showed the lack of necrosis on painted area of leaves in transgenic genotypes compared to the non-transgenic ones.
Knockout ofHsp70genes significantly affects locomotion speed and gene expression in leg skeletal muscles ofDrosophila melanogaster
Authors: Makhnovskii Pavel A. , Kukushkina Inna V. , Kurochkina Nadia S. , Popov Daniil V. 
Published: December 2023

AbstractThe functions of theHsp70genes were studied using a line ofD. melanogasterwith knockout of six these genes out of thirteen. Namely, effect of knockout ofHsp70genes on negative geotaxis climbing (locomotor) speed and the ability to adapt to climbing training (0.5-1.5 h/day, 7 days/week, 19 days) were examined. Seven- and 23-day-oldHsp70−flies demonstrated a comparable reduction (2-fold) in locomotor speed and widespread changes in leg skeletal muscle transcriptome (RNA-seq), compared tow1118flies. To identify the functions of genes related to decreased locomotor speed the overlapped differentially expressed genes at both time points were analyzed: the up-regulated genes encoded extracellular proteins, regulators of drug metabolism and antioxidant response, while down-regulated genes encoded regulators of carbohydrate metabolism and transmembrane proteins. Additionally, inHsp70−flies, activation of transcription factors related to disruption of the fibril structure and heat shock response (Hsf) were predicted, using the position weight matrix approach. In the control flies, adaptation to chronic exercise training was associated mainly with gene response to a single exercise bout, while the predicted transcription factors were related to stress/immune (Hsf, NF-kB, etc.) and early gene response. In contrast,Hsp70−flies demonstrated no adaptation to training, as well as significantly impaired gene response to a single exercise bout. In conclusion, the knockout ofHsp70genes not only reduced physical performance, but also disrupted adaptation to chronic physical training, which is associated with changes in leg skeletal muscle transcriptome and impaired gene response to a single exercise bout.New & NoteworthyKnockout of sixHsp70genes inD. melanogasterreduced locomotion (climbing) speed that is associated with genotype-specific differences in leg skeletal muscle gene expression.Disrupted adaptation ofHsp70−flies to chronic exercise training is associated with impaired gene response to a single exercise bout.