bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillations and aperiodic activity: Evidence for dynamic changes in both during memory encoding
Authors: Preston Michael , Schaworonkow Natalie , Voytek Bradley 
Published: October 2022

AbstractElectrical recordings of human brain activity via electroencephalography (EEG) show prominent, rhythmic voltage fluctuations. These periodic oscillations have been linked to nearly every cognitive and perceptual process, as well numerous disease states. Recent methodological and theoretical advances, however, have given rise to evidence for a functional role for non-oscillatory, aperiodic neural activity. Physiologically, this aperiodic activity has been linked to the relative contributions of neuronal excitatory and inhibitory signaling. Most importantly, however, traditional data analysis methods often conflate oscillations and aperiodic activity, masking the potentially separate roles these processes play in perception, cognition, and disease. Here we present a reanalysis of intracranial human EEG recordings from Fellner et al., 2019, using new methods for separately parameterizing oscillations and aperiodic activity in a time-resolved manner. We find that human memory encoding is not related to just oscillations or aperiodic activity, but rather that both processes are rapidly co-modulated during memory encoding. These results provide strong evidence for event-related dynamics of aperiodic and oscillatory activity in human memory, paving the way for future investigations into the unique functional roles of these two independent, but linked, processes in human cognition.
FANGORN: A quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences
Authors: Walsh Calum J. , Srinivas Meghana , van Sinderen Douwe , Cotter Paul D. , Kenny John G. 
Published: October 2022

ABSTRACTSequence comparison of 16S rRNA PCR amplicons is an established approach to taxonomically identify bacterial isolates and profile complex microbial communities. One potential application of recent advances in long-read sequencing technologies is to sequence entire rRNA operons and capture significantly more phylogenetic information than sequencing of the 16S rRNA (or regions thereof) alone, with the potential to increase the proportion of amplicons that can be reliably classified to lower taxonomic ranks. Here we describe FANGORN (Full-length Amplicons for the Next Generation Of rRNa analysis), a publicly available database of quality-checked 16S-ITS-23S rRNA operons, accompanied by multiple taxonomic classifications. FANGORN will aid researchers in analysis of their data and act as a standardised database to allow comparison of results between studies.
Scalable early detection of grapevine virus infection with airborne imaging spectroscopy
Authors: Romero Galvan Fernando E. , Pavlick Ryan , Trolley Graham , Aggarwal Somil , Sousa Daniel , Starr Charles , Forrestel Elisabeth , Bolton Stephanie , del Mar Alsina Maria , Dokoozlian Nick , Gold Kaitlin M. 
Published: October 2022

AbstractViral diseases, including Grapevine Leafroll-associated Virus Complex 3 (GLRaV-3), cause $3 billion in damages and losses to the United States wine and grape industry annually. GLRaV-3 has a well-studied, year-long latent period in which vines are infectious but do not yet display visible symptoms, making it an ideal model pathosystem to evaluate the scalability of symptomatic and asymptomatic imaging spectroscopy-based disease detection. Plant disease causes physiological and chemical changes to occur locally and systemically throughout a plant, which imaging spectroscopy can detect both directly and indirectly. Reliable and scalable disease detection during the latent period would greatly reduce management costs, as current detection methods are entirely ground-based, labor-intensive, and expensive. Here, we use data collected in September 2020 by the NASA Airborne Visible/Infrared Imaging Spectrometer Next Generation (AVIRIS-NG) to detect GLRaV-3 in Cabernet Sauvignon grapevines in Lodi, CA. During September 2020 and 2021, industry collaborators scouted 317 acres of Vitis vinifera winegrapes for visible disease symptoms, and collected a subset for confirmation molecular testing at a commercial facility. Grapevines identified as visibly diseased in 2021 were assumed to have been latently infected (asymptomatic) during the September 2020 AVIRIS-NG data collection. We combined random forest with synthetic minority oversampling technique (SMOTE) to train multiple spectral models able to distinguish between non-infected (NI) and GLRaV-3-infected grapevines. We observed clear spectral differences that allowed for differentiation between NI and GLRaV-3 infected vines both pre- and post-symptomatically at 1m through 5m resolution. Our two best performing models had 87% accuracy (0.73 Kappa) distinguishing between NI and asymptomatic (aSy), and 85% accuracy (0.71 Kappa) distinguishing between NI and (aSy + symptomatic [Sy]) respectively. We hypothesize these spectral differences are linked to changes in overall plant physiology induced by disease, as visible foliar symptoms were restricted to the lower canopy.HighlightsAirborne imaging spectroscopy allows for scalable early-detection models of grapevine leafroll-associated virus complex 3 (GLRaV-3).Random Forest based models trained with scouting ground data and imaging spectroscopy are accurate up to 5 meter but perform best at 3 meter spatial resolution.GLRaV-3 detection via imaging spectroscopy will not replace existing field scouting strategies or molecular testing but supplement by allowing for more strategic resource deployment to improve the overall financial, environmental, and societal sustainability of winegrape production.
Serotonergic Modulation of Spinal Circuitry Restores Motor Function after Chronic Spinal Cord Injury
Authors: Walvekar Sarita , Robinson Robert B. , Chadwick Hailey M. , Burch Rebecca M. , Ding Hanzhang , Perlmutter Steve I. , Moorjani Samira 
Published: October 2022

AbstractElectrical stimulation of the nervous system has been employed to enhance the recovery of motor function produced by use-dependent rehabilitation, which is the current gold standard of treatment, following spinal cord injury. However, the therapeutic effects almost always rely on the sustained activation of muscles or neurons, making the benefits largely contingent on continued delivery of stimulation. In the present study, we describe a neuromodulatory intervention that combined intraspinal delivery of serotonergic agonists with use-dependent rehabilitation to restore motor function after a chronic moderate-to-severe cervical contusion in rats that produces impairments in upper-limb movements and dexterity. We show that targeted delivery of quipazine, a broad-spectrum serotonergic agonist, caudal to the lesion increased the effectiveness of physical rehabilitation, leading to substantially improved motor-recovery outcomes in severely-injured, but not moderately-injured, animals. Delivery of quipazine significantly augmented recovery of skilled reach and grasp movements after a severe injury, but moderately-injured animals received no additional benefit from quipazine over physical rehabilitation alone. This difference was perhaps due to a greater loss of serotonin after a severe injury and a resulting environment in which exogenously-applied serotonin can improve circuit function. Our experiments highlight an important role for serotonin in restoration of motor function that is dependent on the severity of the spinal cord injury. They also allude to a potential role for residual serotonin as a biomarker of injury severity. Remarkably, quipazine-mediated behavioral improvements persisted for weeks after termination of neuromodulator delivery, signaling repair of severely-damaged adult spinal circuitry that drives lasting motor recovery.Significance StatementWe describe a neuromodulatory intervention that combined intraspinal delivery of serotonergic agonists with use-dependent physical rehabilitation, which is the current standard of treatment, to promote motor recovery after a chronic moderate-to-severe spinal-contusion injury. Our results show that targeted delivery of serotonergic agonists caudal to the lesion increased the effectiveness of use-dependent rehabilitation, leading to substantially improved motor-recovery outcomes in severely-injured, but not moderately-injured, animals. Notably, therapeutic gains persisted for weeks after termination of neuromodulator delivery—a finding that is both unique and clinically relevant—signaling plasticity induction and repair in chronically-damaged adult spinal circuitry. Our experiments provide important insights into serotonergic modulation of spinal circuitry and highlight a potential role for residual serotonin as a neurochemical biomarker of injury severity.
Wavelet-based Approach for Diagnosing Attention Deficit Hyperactivity Disorder (ADHD)
Authors: Vimalajeewa Dixon , McDonald Ethan , Bruce Scott Alan , Vidakovic Brani 
Published: October 2022

AbstractAttention deficit hyperactivity disorder (ADHD) is a common cognitive disorder affecting children. ADHD can interfere with educational, social, and emotional development, so early detection is essential for obtaining proper care. Standard ADHD diagnostic protocols rely heavily on subjective assessments of perceived behavior. An objective diagnostic measure would be a welcome development and potentially aid in accurately and efficiently diagnosing ADHD. Analysis of pupillary dynamics has been proposed as a promising alternative method of detecting affected individuals effectively. This study proposes a method based on the self-similarity of pupillary dynamics and assesses its strength as a potential diagnostic biomarker. Localized discriminatory features are developed in the wavelet domain and selected via a rolling window method to build classifiers. The application on a task-based pupil diameter time series dataset of children aged 10-12 years shows that the proposed method achieves greater than 78% accuracy in detecting ADHD. Comparing with a recent approach that constructs features in the original data domain, the proposed wavelet-based classifier achieves more accurate ADHD classification with fewer features. The findings suggest that the proposed diagnostic procedure involving interpretable wavelet-based self-similarity features of pupil diameter data can potentially aid in improving the efficacy of ADHD diagnosis.
Distinct Heterogeneity in the Naive T cell Compartments of Children and Adults
Authors: Gustafson Claire E. , Thomson Zachary , He Ziyuan , Swanson Elliott , Henderson Katherine , Pebworth Mark-Phillip , Okada Lauren Y. , Heubeck Alexander T. , Roll Charles R. , Hernandez Veronica , Weiss Morgan , Genge Palak C. , Reading Julian , Giles Josephine R. , Manne Sasikanth , Dougherty Jeanette , Jasen CJ , Greenplate Allison R. , Becker Lynne A. , Graybuck Lucas T. , Vasaikar Suhas V. , Szeto Gregory L. , Savage Adam K. , Speake Cate , Buckner Jane H. , Li Xiao-jun , Torgerson Troy R. , Wherry E. John , Bumol Thomas F. , Vella Laura A. , Henrickson Sarah E. , Skene Peter J. 
Published: October 2022

Abstract:The naive T cell compartment undergoes multiple changes across age that associate with altered susceptibility to infection and autoimmunity. In addition to the acquisition of naive-like memory T cell subsets, mouse studies describe substantial molecular reprogramming of the naive compartment in adults compared with adolescents. However, these alterations are not well delineated in human aging. Using a new trimodal single cell technology (TEA-seq), we discovered that the composition and transcriptional and epigenetic programming of the naive T cell compartment in children (11-13 yrs) is distinct from that of older adults (55-65 yrs). Naive CD4 T cells, previously considered relatively resistant to aging, exhibited far more pronounced molecular reprogramming than naive CD8 T cells, in which alterations are preferentially driven by shifts in naive-like memory subsets. These data reveal the complex nature of the naive T cell compartment that may contribute to differential immune responses across the spectrum of human age.One Sentence Summary:The naive CD8 and CD4 T cell compartments in humans are heterogeneous and impacted differently with age, in which naive CD8 T cell subsets dramatically shift in composition and true naive CD4 T cells display significant molecular re-programming.
Surgical procedure for implantation of Opto-Array in nonhuman primates
Authors: Azadi Reza , Bohn Simon , Eldridge Mark A. G. , Afraz Arash 
Published: October 2022

AbstractOptogenetics allows precise temporal control of neuronal activity in the brain. Engineered viral vectors are routinely used to transduce neurons with light-sensitive opsins. However, reliable virus injection and light delivery in animals with large brains, such as nonhuman primates, has proven challenging. The Opto-Array is a novel yet simple device that is used to deliver light to extended regions of surface cortex for high-throughput behavioral optogenetics in large brains. Here we present protocols for surgical delivery of virus and implantation of the Opto-Array in two separate surgeries in a rhesus monkey’s inferior temporal cortex. As a proof of concept, we measured the behavioral performance of an animal detecting cortical optogenetic stimulations with different illumination power and duration using the Opto-Array. The animal was able to detect the optogenetic stimulation for all tested illumination powers and durations. A regression analysis also showed both power and duration of illumination significantly modulate the detectability of the optogenetic stimulation. The outcome of this approach is superior to the standard practice of injecting and recording through a chamber for large areas of surface cortex. Moreover, the chronic nature of the Opto-Array allows perturbation of neuronal activity of the same site across multiple sessions because it is highly stable, thus data can be pooled over months. The detailed surgical method presented here makes it possible to use optogenetics to modulate neuronal activity across large regions of surface cortex in the nonhuman primate brain.
Cortical Contributions to Medial Frontal β-Bursts during Executive Control
Authors: Errington Steven P. , Westerberg Jacob A. , Woodman Geoffrey F. , Schall Jeffrey D. 
Published: October 2022

ABSTRACTEEG β-bursts observed over the medial frontal cortex are claimed to mediate response inhibition despite their infrequent occurrence. The weak association with stopping behavior is supposed to be a by-product of the low signal-to-noise ratio of EEG recordings. We tested the premise that β-bursts are more common within the cerebral cortex and more directly associated with response inhibition. We sampled simultaneously EEG and intracortical local field potentials (LFP) within the medial frontal cortex (MFC) of two macaque monkeys performing a response inhibition task. Intracortical β-bursts were just as infrequent as those in EEG and did not parallel the likelihood of canceling a planned response. Cortical β-bursts were more prevalent in upper layers but were not synchronized across a cortical column or with EEG β-bursts. These findings contradict claims for a causal contribution of β-bursts during response inhibition, provide important constraints for biophysical and cortical circuit models, and invite further considerations of β-burst function in cognitive control.
Circular RNAs arising from synaptic host genes are modulated by SFPQ RNA-binding protein and increased during human neuronal differentiation
Authors: Watts Michelle , Oksanen Marika , Lejerkrans Sanna , Mastropasqua Francesca , Gorospe Myriam , Tammimies Kristiina 
Published: October 2022

AbstractBackgroundCircular RNAs (circRNAs) are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored.ResultsUsing total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes.ConclusionsOur study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.
Structural changes in perineuronal nets and their perforating GABAergic synapses precede motor coordination recovery post stroke
Authors: Dzyubenko Egor , Willig Katrin I. , Yin Dongpei , Sardari Maryam , Tokmak Erdin , Labus Patrick , Schmermund Ben , Hermann Dirk M. 
Published: October 2022

SummaryStroke remains one of the leading causes of long-term disability worldwide, and the development of effective restorative therapies is hindered by an incomplete understanding of intrinsic brain recovery mechanisms. Here we explored how perineuronal nets (PNNs), the facet-like extracellular matrix layers surrounding fast-spiking interneurons, contribute to neurological recovery after focal cerebral ischemia in mice with and without induced stroke tolerance. Due to the insufficient resolution of conventional microscopy methods, the contribution of structural changes in PNNs to post stroke brain plasticity remained unknown. Using superresolution stimulated emission depletion (STED) and structured illumination (SR-SIM) microscopy, we revealed that PNN facets become larger and less dense in the post-acute stroke phase. These morphological alterations in PNNs are transient and correlate with the increased surface of contact between activated microglia and PNN-coated neurons. The transient loosening of PNNs after stroke allows for dynamic reorganization of GABAergic axonal terminals on inhibitory interneurons in the motor cortical layer 5. The coherent remodeling of PNNs and their perforating inhibitory synapses precedes the recovery of motor coordination after stroke and depends on the severity of the ischemic injury. Our data suggest a novel mechanism of motor cortical plasticity after stroke, and we propose that prolonging PNN loosening during the post-acute period can extend the opening neuroplasticity window into the chronic stroke phase.HighlightsPNNs are degraded partially and transiently post-strokeTransient attenuation of PNNs correlates with GABAergic synapse remodelingTransient attenuation of PNNs precedes functional recovery post strokeActivated microglia preferentially contact PNN-coated neurons post strokeGraphical Abstract
Uncovering footprints of natural selection through time-frequency analysis of genomic summary statistics
Authors: Arnab Sandipan Paul , Amin Md Ruhul , DeGiorgio Michael 
Published: October 2022

AbstractNatural selection leaves a spatial pattern along the genome, with a distortion in the haplotype distribution near the selected locus that becomes less prominent with increasing distance from the locus. Evaluating the spatial signal of a population-genetic summary statistic across the genome allows for patterns of natural selection to be distinguished from neutrality. Different summary statistics highlight diverse components of genetic variation and, therefore, considering the genomic spatial distribution of multiple summary statistics is expected to aid in uncovering subtle signatures of selection. In recent years, numerous methods have been devised that jointly consider genomic spatial distributions across summary statistics, utilizing both classical machine learning and contemporary deep learning architectures. However, better predictions may be attainable by improving the way in which features used as input to machine learning algorithms are extracted from these summary statistics. To achieve this goal, we apply three time-frequency analysis approaches (wavelet transform, multitaper spectral analysis, and S-transform) to summary statistic arrays. Each analysis method converts a one-dimensional summary statistic arrays to a two-dimensional image of spectral density or visual representation of time-frequency analysis, permitting the simultaneous assessment of temporal and spectral information. We use these images as input to convolutional neural networks and consider combining models across different time-frequency representation approaches through the ensemble stacking technique. Application of our modeling framework to data simulated from neutral and selective sweep scenarios reveals that it achieves almost perfect accuracy and power across a diverse set of evolutionary settings, including population size changes and test sets for which sweep strength, softness, and timing parameters were drawn from a wide range. Moreover, a scan of whole-genome sequencing of central European humans recapitulated previous well-established sweep candidates, as well as predicts novel cancer associated genes as sweeps with high support. Given that this modeling framework is also robust to missing data, we believe that it will represent a welcome addition to the population-genomic toolkit for learning about adaptive processes from genomic data.
Plant functional types and tissue stoichiometry explain nutrient transfer in common arbuscular mycorrhizal networks of temperate grasslands
Authors: Dawson Hilary Rose , Shek Katherine L. , Maxwell Toby M. , Reed Paul B. , Bomfim Barbara , Bridgham Scott D. , Bohannan Brendan J. M. , Silva Lucas C.R. 
Published: October 2022

AbstractPlants and mycorrhizal fungi form mutualistic relationships that affect how resources flow between organisms and within ecosystems. Common mycorrhizal networks (CMNs) could facilitate preferential transfer of carbon and limiting nutrients, but this remains difficult to predict. Do CMNs favor fungal resource acquisition at the expense of plant resource demands (a fungi-centric view), or are they passive channels through which plants regulate resource fluxes (a plant-centric view)? We used stable isotope tracers (13CO2and15NH3), plant traits, and mycorrhizal DNA to quantify above- and belowground carbon and nitrogen transfer between 18 plant species along a 520-km latitudinal gradient in the Pacific Northwest, USA. Plant functional type and tissue stoichiometry were the most important predictors of interspecific resource transfer. Of “donor” plants, 98% were13C-enriched, but we detected transfer in only 2% of “receiver” plants. However, all donors were15N-enriched and we detected transfer in 81% of receivers. Nitrogen was preferentially transferred to annuals (0.26 ± 0.50 mg N per g leaf mass) compared to perennials (0.13 ± 0.30 mg N per g leaf mass). This corresponded with tissue stoichiometry differences. Our findings suggest that plants and fungi that are located closer together in space and with stronger demand for resources over time are more likely to receive larger amounts of those limiting resources.