bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neonatal sensitivity to vocal emotions: A developmental change at 37 weeks of gestational age
Authors: Hou Xinlin , Zhang Peng , Mo Licheng , Peng Cheng , Zhang Dandan 
Published: January 2024

AbstractEmotional responsiveness in neonates, particularly their ability to discern vocal emotions, plays an evolutionarily adaptive role in human communication and adaptive behaviors. The developmental trajectory of emotional sensitivity in neonates is crucial for understanding the foundations of early social-emotional functioning. However, the precise onset of this sensitivity and its relationship with gestational age (GA) remain subjects of investigation. In a study involving 120 healthy neonates categorized into six groups based on their GA (ranging from 35 and 40 weeks), we explored their emotional responses to vocal stimuli. These stimuli encompassed disyllables with happy and neutral prosodies, alongside acoustically matched nonvocal control sounds. The assessments occurred during natural sleep states using the odd-ball paradigm and event-related potentials. The results reveal a distinct developmental change at 37 weeks GA, marking the point at which neonates exhibit heightened perceptual acuity for emotional vocal expressions. This newfound ability is substantiated by the presence of the mismatch response, akin to an initial form of adult mismatch negativity, elicited in response to positive emotional vocal prosody. Notably, this perceptual shift’s specificity becomes evident when no such discrimination is observed in acoustically matched control sounds. Neonates born before 37 weeks GA do not display this level of discrimination ability. This developmental change has important implications for our understanding of early social-emotional development, highlighting the role of gestational age in shaping early perceptual abilities. Moreover, while these findings introduce the potential for a valuable screening tool for conditions like autism, characterized by atypical social-emotional functions, it is important to note that the current data are not yet robust enough to fully support this application. This study makes a substantial contribution to the broader field of developmental neuroscience and holds promise for future research on early intervention in neurodevelopmental disorders.Significance statementThis study illuminates a key developmental change, pinpointing the emergence of heightened emotional perceptual acuity at 37 weeks of gestational age. Employing rigorous methods, we reveal that neonates at this stage exhibit remarkable discrimination abilities for emotional vocal prosody, a vital turning point in early social-emotional functioning. These findings emphasize the pivotal role of gestational age in shaping neonatal perception and provides a potential pathway for early screening of neurodevelopmental disorders, particularly autism. This insight holds profound implications for understanding the foundations of early social-emotional development in humans, offering a potential tool for early intervention in neurodevelopmental disorders, thereby enhancing child health and well-being.
Comprehensive benchmark of differential transcript usage analysis for static and dynamic conditions
Authors: Lio Chit Tong , Düz Tolga , Hoffmann Markus , Willruth Lina-Liv , Baumbach Jan , List Markus , Tsoy Olga 
Published: January 2024

AbstractRNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential transcript usage (DTU) analysis. The choice of the right analysis tool is non-trivial and depends on experimental factors such as the availability of single- or paired-end and bulk or single-cell data. To help users select the most promising tool for their task, we performed a comprehensive benchmark of DTU detection tools. We cover a wide array of experimental settings, using simulated bulk and single-cell RNA-seq data as well as real transcriptomics datasets, including time-series data. Our results suggest that DEXSeq, edgeR, and LimmaDS are better choices for paired-end data, while DSGseq and DEXSeq can be used for single-end data. In single-cell simulation settings, we showed that satuRn performs better than DTUrtle. In addition, we showed that Spycone is optimal for time series DTU/IS analysis based on the evidence provided using GO terms enrichment analysis.
Intestinal helminth infection impairs vaccine-induced T cell responses and protection against SARS-CoV-2
Authors: Desai Pritesh , Karl Courtney E. , Ying Baoling , Liang Chieh-Yu , Garcia-Salum Tamara , Santana Ana Carolina , Caten Felipe Ten , Urban Joseph F. , Elbashir Sayda M. , Edwards Darin K. , Ribeiro Susan P. , Thackray Larissa B. , Sekaly Rafick P. , Diamond Michael S. 
Published: January 2024

SUMMARYAlthough vaccines have reduced COVID-19 disease burden, their efficacy in helminth infection endemic areas is not well characterized. We evaluated the impact of infection byHeligmosomoides polygyrus bakeri(Hpb), a murine intestinal hookworm, on the efficacy of an mRNA vaccine targeting the Wuhan-1 spike protein of SARS-CoV-2. Although immunization generated similar B cell responses in Hpb-infected and uninfected mice, polyfunctional CD4+and CD8+T cell responses were markedly reduced in Hpb-infected mice. Hpb-infected and mRNA vaccinated mice were protected against the ancestral SARS-CoV-2 strain WA1/2020, but control of lung infection was diminished against an Omicron variant compared to animals immunized without Hpb infection. Helminth mediated suppression of spike-specific CD8+T cell responses occurred independently of STAT6 signaling, whereas blockade of IL-10 rescued vaccine-induced CD8+T cell responses. In mice, intestinal helminth infection impairs vaccine induced T cell responses via an IL-10 pathway and compromises protection against antigenically shifted SARS-CoV-2 variants.
Timing of Regadenoson-induced Peak Hyperemia and the Effects on Coronary Flow Reserve
Authors: Kattapuram Nathan , Shadman Shahrad , Morgan Eric E. , Benton Charles , Awojoodu Stacian , Kim Dong-Yun , Ramos Joao , Barac Ana , Bandettini W. Patricia , Kellman Peter , Weissman Gaby , Carlsson Marcus 
Published: January 2024

AbstractBackgroundRegadenoson is used to induce hyperemia in cardiac imaging, facilitating diagnosis of ischemia and assessment of coronary flow reserve (CFR). While the regadenoson package insert recommends administration of radionuclide tracer 10-20 seconds after injection, peak hyperemia has been observed at approximately 100 seconds after injection in healthy volunteers undergoing cardiovascular magnetic resonance imaging (CMR). It is unclear when peak hyperemia occurs in a patient population.ObjectivesThe goal of this study was to determine time to peak hyperemia after regadenoson injection in healthy volunteers and patients, and whether the recommended image timing in the package insert underestimates CFR.MethodsHealthy volunteers (n=15) and patients (n=25) underwent stress CMR, including phase-contrast imaging of the coronary sinus at rest and multiple timepoints after 0.4 mg regadenoson injection. Coronary sinus flow (ml/min) was divided by resting values to yield CFR. Smoothed, time-resolved curves for CFR were generated with pointwise 95% confidence intervals.ResultsCFR between 60 and 120 seconds was significantly higher than CFR at 30 seconds after regadenoson injection (p < 0.05) as shown by non-overlapping 95% confidence intervals for both healthy volunteers (30 s, [2.8, 3.4]; 60 s, [3.8, 4.4]; 90 s, [4.1, 4.7]; 120 s, [3.6, 4.3]) and patients (30 s, [2.1, 2.5]; 60 s, [2.6, 3.1]; 90 s, [2.7, 3.2]; 120 s, [2.5, 3.1]).ConclusionImaging at 90 seconds following regadenoson injection is the optimal approach to capture peak hyperemia. Imaging at 30 seconds, which is more aligned with the package insert recommendation, would yield an underestimate of CFR and confound assessment of microvascular dysfunction.
Pathways linking physical and mental health: The role of brain structure and environment
Authors: Tian Ye Ella , Cole James H , Bullmore Edward T , Zalesky Andrew 
Published: January 2024

AbstractDepression and anxiety are prevalent in people with a chronic physical illness. Increasing evidence suggests that co-occurring physical and mental illness is associated with shared biological pathways. However, little is known about the brain’s role in mediating links between physical and mental health. Using multimodal brain imaging and organ-specific physiological markers from the UK Biobank, we establish prospective associations between the baseline health of seven body organs and mental health outcomes at 4-14 years follow-up, focussing on depression and anxiety. We reveal multiple pathways, mediated by the brain, through which poor organ health may lead to poor mental health. We identify several lifestyle factors that influence mental health through their selective impact on the physiology of specific organ systems and brain structure. Our work reveals the interplay between brain, body and lifestyle and their collective influence on mental health. Pathways elucidated here may inform behavioral interventions to mitigate or prevent the synergistic co-occurrence of physical and mental disorders.
Functional connectivity of stimulus-evoked brain responses to natural speech in post-stroke aphasia
Authors: Mehraram Ramtin , Clercq Pieter De , Kries Jill , Vandermosten Maaike , Francart Tom 
Published: January 2024

AbstractOne out of three stroke-patients develop language processing impairment known as aphasia. The need for ecological validity of the existing diagnostic tools motivates research on biomarkers, such as stimulus-evoked brain responses. With the aim of enhancing the physiological interpretation of the latter, we used EEG to investigate how functional brain network patterns associated with the neural response to natural speech are affected in persons with post-stroke chronic aphasia.EEG was recorded from 24 healthy controls and 40 persons with aphasia while they listened to a story. Stimulus-evoked brain responses at all scalp regions were measured as neural envelope tracking in the delta (0.5-4 Hz), theta (4-8 Hz) and low-gamma bands (30-49 Hz) using mutual information. Functional connectivity between neural-tracking signals was measured, and the Network-Based Statistics toolbox was used to: 1) assess the added value of the neural tracking vs EEG time series, 2) test between-group differences and 3) investigate any association with language performance in aphasia. Graph theory was also used to investigate topological alterations in aphasia.Functional connectivity was higher when assessed from neural tracking compared to EEG time series. Persons with aphasia showed weaker low-gamma-band left-hemispheric connectivity, and graph theory-based results showed a greater network segregation and higher region-specific node strength. Aphasia also exhibited a correlation between delta-band connectivity within the left pre-frontal region and language performance.We demonstrated the added value of neural tracking when investigating functional brain networks associated with natural speech processing in post-stroke aphasia. Its higher sensitivity to language-related brain circuits favours its use as informative biomarker for the assessment of aphasia.
Nitrous oxide respiration in acidophilic methanotrophs
Authors: Awala Samuel Imisi , Gwak Joo-Han , Kim Yongman , Jung Man-Young , Dunfield Peter. F. , Wagner Michael , Rhee Sung-Keun 
Published: January 2024

AbstractMethanotrophic bacteria mitigate methane (CH4) emissions from natural environments. Although aerobic methanotrophs are considered strict aerobes, they are often highly abundant in extremely hypoxic and even anoxic environments. Despite the presence of denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we revealed that two acidophilic methanotrophs encoding N2O reductase (clade I and type II nosZ, respectively):Methylocella tundraeT4 andMethylacidiphilum caldifontisIT6, respired N2O and grew anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. However, NO3−and NO2−could be reduced during methanol oxidation inMethylocella tundraeT4 andMethylocella silvestrisBL2 without significantly increasing cell biomass. The lack of growth on methanol + NO3−or NO2−was likely due to the production of toxic reactive nitrogen species and C1 metabolites. However, the oxidation of pyruvate, a C3 electron donor, combined with NO3−or NO2−reduction resulted in anaerobic growth ofMethylocella tundraeT4 andMethylocella silvestrisBL2. In the extreme acidophile,Methylacidiphilum caldifontisIT6, N2O respiration supported cell growth at an extremely acidic pH of 2.0. InMethylocella tundraeT4, simultaneous consumption of N2O and CH4was observed in suboxic conditions, both in microrespirometry and growth experiments, indicating the robustness of its N2O reductase activity in the presence of O2. Furthermore, CH4oxidation per O2reduced in O2-limiting conditions increased when N2O was added, indicating that cells of T4 can direct more O2towards methane monooxygenase when respiring N2O as a terminal electron acceptor. Upregulation ofnosZand distinct repertories of methanol dehydrogenase-encoding genes (XoxF- and MxaFI-type) inMethylocella tundraeT4 cells grown anaerobically on methanol with N2O as the sole electron acceptor indicated adaptation mechanisms to anoxia. Our findings demonstrate that some methanotrophs can respire N2O independently or in tandem with O2, significantly expanding their potential ecological niche and paving the way for enhanced growth and survival in dynamic environments. This metabolic capability has application potential for simultaneously mitigating the emissions of the key greenhouse gases, CO2, CH4,and N2O, from natural and engineered environments.
Automating the Human Connectome Project’s Temporal ICA Pipeline
Authors: Yang Chunhui , Coalson Timothy S. , Smith Stephen M. , Elam Jennifer S. , Van Essen David C. , Glasser Matthew F. 
Published: January 2024

AbstractFunctional magnetic resonance imaging (fMRI) data are dominated by noise and artifacts, with only a small fraction of the variance relating to neural activity. Temporal independent component analysis (tICA) is a recently developed method that enables selective denoising of fMRI artifacts related to physiology such as respiration. However, an automated and easy to use pipeline for tICA has not previously been available; instead, two manual steps have been necessary: 1) setting the group spatial ICA dimensionality after MELODIC’s Incremental Group-PCA (MIGP) and 2) labeling tICA components as artifacts versus signals. Moreover, guidance has been lacking as to how many subjects and timepoints are needed to adequately re-estimate the temporal ICA decomposition and what alternatives are available for smaller groups or even individual subjects. Here, we introduce a nine-step fully automated tICA pipeline which removes global artifacts from fMRI dense timeseries after sICA+FIX cleaning and MSMAll alignment driven by functionally relevant areal features. Additionally, we have developed an automated “reclean” Pipeline for improved spatial ICA (sICA) artifact removal. Two major automated components of the pipeline are 1) an automatic group spatial ICA (sICA) dimensionality selection for MIGP data enabled by fitting multiple Wishart distributions; 2) a hierarchical classifier to distinguish group tICA signal components from artifactual components, equipped with a combination of handcrafted features from domain expert knowledge and latent features obtained via self-supervised learning on spatial maps. We demonstrate that the dimensionality estimated for the MIGP data from HCP Young Adult 3T and 7T datasets is comparable to previous manual tICA estimates, and that the group sICA decomposition is highly reproducible. We also show that the tICA classifier achieved over 0.98 Precision-Recall Area Under Curve (PR-AUC) and that the correctly classified components account for over 95% of the tICA-represented variance on multiple held-out evaluation datasets including the HCP-Young Adult, HCP-Aging and HCP-Development datasets under various settings. Our automated tICA pipeline is now available as part of the HCP pipelines, providing a powerful and user-friendly tool for the neuroimaging community.
Impact of Unc-51 Like Kinase 4 (ULK4) on the Reactivity of the Extended Reward System in Response to Conditioned Stimuli
Authors: Treutlein Jens , Löhlein Simone , Einenkel Karolin E. , Diekhof Esther K. , Gruber Oliver 
Published: January 2024

AbstractObjectivesULK4is an established candidate gene for mental disorders and antipsychotic treatment response and codes for a serine/threonine kinase that regulates the neural stem cell pool and controls cortex development. We investigated the effects of functional genetic variation at theULK4locus on the human extended dopaminergic reward system using functional magnetic resonance imaging (fMRI) during performance of a well-established reward paradigm.Methods234 study participants with functional neuroimaging (fMRI) data of the extended reward system and withULK4genotype data were included in this study. Effects of genetic variation in theULK4gene on reward system functioning were determined using the Desire-Reason-Dilemma (DRD) paradigm which allows to assess brain activation in response to conditioned reward stimuli (Diekhof et al. 2010).ResultsAmong common missense variants of theULK4gene, variant prioritization revealed strongest functional signatures for variant rs17215589, coding for amino acid exchange Ala715Thr. For rs17215589 minor allele carriers, we detected increased activation responses to conditioned reward stimuli in the ventral tegmental area, the nucleus accumbens and several cortical brain regions of the extended reward system.ConclusionsOur findings provide further evidence in humans that genetic variation inULK4may increase the vulnerability to mental disorders by modulating the function of the extended reward system. Future studies are needed to confirm the functional modulation of the extended reward system by ULK4 and to specify the role of this mechanism in the pathogenesis of psychiatric disorders.
Exploration of the EEG response to periodic thermal and vibrotactile stimuli
Authors: Courtin Arthur S. , Mouraux André 
Published: January 2024

AbstractUnder certain conditions, a stimulus applied at a given frequency will lead to a periodic variation of neural activity at the same frequency. Taking advantage of this periodicity, it is possible to tag this response in the EEG frequency spectrum. Frequency tagging of sustained periodic noxious heat stimuli led to the recording of phase-locked and non-phase-locked responses whose functional significance remains unclear.This study aimed at assessing whether such responses can also be recorded during the repetitive presentation of brief innocuous cold, noxious heat and vibrotactile stimuli. Comparison between the responses obtained with different stimulation modalities should inform us on the nature of the neural processes underlying these responses (modality aspecific, somatosensory, thermosensory, nociceptive). Comparison between upper and lower limb stimulation should inform us on the somatotopic organization of these responses and, therefore, on their potential sources.Based on our results, on one hand, trains of brief innocuous cold, noxious heat and vibrations can elicit phase-locked and non-phase-locked responses which appear highly similar to those evoked by sustained periodic noxious heat stimuli when frequency tagged. On the other hand, when analysed in the time domain or using time-frequency decomposition, these responses appeared highly similar to those that can be recorded following isolated brief noxious heat or tactile stimuli. These responses consisted in phase-locked activity corresponding to the vertex potential, thought to reflect modality non-specific attentional processes, and in an alpha-to-beta ERD originating in the S1/M1 area contralateral to the stimulated hand, probably reflecting non-specific somatosensory activity.
ARViS: A bleed-free multi-site automated injection robot for accurate, fast, and dense delivery of virus to mouse and marmoset brains
Authors: Nomura Shinosuke , Terada Shin-Ichiro , Ebina Teppei , Uemura Masato , Masamizu Yoshito , Ohki Kenichi , Matsuzaki Masanori 
Published: January 2024

SummaryGenetically encoded fluorescent sensors continue to be developed and improved. If they could be expressed across multiple cortical areas in non-human primates, it would be possible to measure a variety of spatiotemporal dynamics of primate-specific cortical activity. Here, we develop an Automated Robotic Virus injection System (ARViS) for broad expression of a biosensor. ARViS consists of two technologies: image recognition of vasculature structures on the cortical surface to determine multiple injection sites without hitting them, and robotic control of micropipette insertion perpendicular to the cortical surface with 50-μm precision. In mouse cortex, ARViS sequentially injected virus solution into 100 sites over a duration of 100-minutes with a bleeding probability of only 0.1% per site. Furthermore, ARViS successfully achieved 266-site injections over the frontoparietal cortex of a common marmoset. We demonstrate one-photon and two-photon calcium imaging in the marmoset frontoparietal cortex, illustrating the effective expression of biosensors delivered by ARViS.
GABAB- GluK1 kainate receptor interplay modulates amygdala excitability and behavioral response to chronic stress
Authors: Ryazantseva Maria , Liiwand Maj , Lauri Sari E. 
Published: January 2024

AbstractAmygdala hyperexcitability is a hallmark for stress-induced anxiety disorders. Stress-associated changes in both principal neurons and interneurons contribute to the increased excitability, but how exactly these mechanisms perturb function of behaviorally relevant circuits in the amygdala remains unclear. Here, we show that GluK1 subunit-containing kainate receptors in parvalbumin (PV) interneurons maintain high GABA release and control excitability of lateral amygdala (LA) principal neurons via tonic GABAB-receptor-mediated inhibition. Downregulation of GluK1 expression in PV interneurons after chronic restraint stress (CRS) releases the tonic inhibition and increases excitability of LA principal neurons. Stress-induced LA hyperexcitability facilitates glutamatergic transmission selectively to central amygdala PKCδ-expressing neurons, implicated in fear generalization. Consistent with significance in anxiogenesis, absence of GluK1- GABABregulation confers resilience against CRS-induced LA hyperexcitability and anxiety-like behavior. Our data reveal a unique novel mechanism involving an interplay between glutamatergic and GABAergic systems in the regulation of amygdala excitability in response to chronic stress.