bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relationship between Stability of Interpersonal Coordination and Inter-Brain EEG Synchronization during Anti-phase Tapping
Authors: Kurihara Yuto , Takahashi Toru , Osu Rieko 
Published: April 2021

AbstractInter-brain synchronization is enhanced when individuals perform rhythmic interpersonal coordination tasks, such as playing instruments in music ensembles. Experimentally, synchronization has been shown to correlate with the performance of joint tapping tasks. However, it is unclear whether inter-brain synchronization is related to the stability of interpersonal coordination represented as the standard deviation of relative phase (SDRP). In this study, we simultaneously recorded electroencephalograms of two paired individuals during anti-phase tapping in three speed conditions: slow (reference inter-tap interval [ITI]: 0.5 s), fast (reference ITI: 0.25 s), and free (preferred ITI). We calculated the inter-brain synchronization within six regions of interest: frontal, central, left/right temporal, parietal, and occipital regions. We found that synchronization of the central-temporal regions was positively correlated with SDRP in the theta and alpha bands, while synchronization of the frontal-frontal and frontal-central was positively correlated with SDRP in the beta band. These results demonstrate that inter-brain synchronization occurs only when task requirements are high, and that it increases with the instability of the coordination. This may be explained by the stronger mutual prediction required in unstable coordination than that in stable coordination, which increases inter-brain synchronization.
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry
Authors: Song Jian , Yu Changbin 
Published: April 2021

ABSTRACTMotivationThe peptide-centric identification methodologies of data-independent acquisition (DIA) data mainly rely on scores for the mass spectrometric signals of targeted peptides. Among these scores, the coelution scores of peak groups constructed by the chromatograms of peptide fragment ions have a significant influence on the identification. Most of the existing coelution scores are achieved by artificially designing some functions in terms of the shape similarity, retention time shift of peak groups. However, these scores cannot characterize the coelution robustly when the peak group is in the circumstance of interference.ResultsOn the basis that the neural network is more powerful to learn the implicit features of data robustly from a large number of samples, and thus minimizing the influence of data noise, in this work, we propose Alpha-XIC, a neural network-based model to score the coelution. By learning the characteristics of the coelution of peak groups derived from identified peptides, Alpha-XIC is capable of reporting robust coelution scores even for peak groups with interference. With this score appending to initial scores generated by the accompanying identification engine, the ensuing statistical validation tool can update the identification result and recover the misidentified peptides. In our evaluation of the HeLa dataset with gradient lengths ranging from 0.5h to 2h, Alpha-XIC delivered 16.7% ~ 49.1% improvements in the number of identified precursors at 1% FDR. Furthermore, Alpha-XIC was tested on LFQbench, a mixed-species dataset with known ratios, and increased the number of peptides and proteins fell within valid ratios by up to 16.6% and 13.8%, respectively, compared to the initial identification.Availability and ImplementationSource code are available atwww.github.com/YuAirLab/Alpha-XIC.
Connectomic Assessment of Injury Burden and Longitudinal Structural Network Alterations in Moderate-to-severe Traumatic Brain Injury
Authors: Osmanlıoğlu Yusuf , Parker Drew , Alappatt Jacob A. , Gugger James J. , Diaz-Arrastia Ramon R. , Whyte John , Kim Junghoon J. , Verma Ragini 
Published: April 2021

AbstractTraumatic brain injury (TBI) is a major public health problem. Caused by external mechanical forces, a major characteristic of TBI is the shearing of axons across the white matter, which causes structural connectivity disruptions between brain regions. This diffuse injury leads to cognitive deficits, frequently requiring rehabilitation. Heterogeneity is another characteristic of TBI as severity and cognitive sequelae of the disease have a wide variation across patients, posing a big challenge for treatment. Thus, measures assessing network-wide structural connectivity disruptions in TBI are necessary to quantify injury burden of individuals, which would help in achieving personalized treatment, patient monitoring, and rehabilitation planning. Despite TBI being a disconnectivity syndrome, connectomic assessment of structural disconnectivity has been very scarce. In this study, we propose a novel connectomic measure that we call network anomaly score (NAS) to capture the integrity of structural connectivity in TBI patients by leveraging two major characteristics of the disease: diffuseness of axonal injury and heterogeneity of the disease. Over a longitudinal cohort of moderate-to-severe TBI patients, we demonstrate that structural network topology of patients are more heterogeneous and are significantly different than that of healthy controls at 3 months post-injury, where dissimilarity further increases up to 12 months. We also show that NAS captures injury burden as quantified by post-traumatic amnesia and that alterations in the structural brain network is not related to cognitive recovery. Finally we compare NAS to major graph theory measures used in TBI literature and demonstrate the superiority of NAS in characterizing the disease.
iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation
Authors: Garshott Danielle M. , An Heeseon , Sundaramoorthy Elayanambi , Leonard Marilyn , Vicary Alison , Harper J. Wade , Bennett Eric J. 
Published: April 2021

SummarySince multiple ribosomes can engage a single mRNA, nonuniform ribosome progression can result in collisions. Ribosome collisions during translation elongation elicit a multifaceted ribosome-associated quality control (RQC) response. Despite advanced mechanistic understanding of translation initiation, a parallel RQC pathway that acts on collided preinitiation complexes has not been described. Here, we show that blocking progression of scanning or elongating ribosomes past the start codon triggers uS3 and uS5 ribosomal ubiquitylation. We demonstrate that conditions that activate the integrated stress response can also induce preinitiation complex collisions. The ubiquitin ligase, RNF10, and the deubiquitylating enzyme, USP10, are the key regulators of uS3 and uS5 ubiquitylation. Prolonged uS3 and uS5 ubiquitylation results in 40S, but not 60S, ribosomal protein degradation in an autophagy-independent manner. This study identifies a distinct arm in the RQC pathway, initiation RQC (iRQC), that acts on pervasive ribosome collisions during translation initiation to modulate translation activity and capacity.
Patterns of information segregation during working memory and attention revealed by dual-task interference in behavior, pupillometry, and EEG
Authors: Fleming Justin T. , Njoroge J. Michelle , Noyce Abigail L. , Perrahione Tyler K. , Shinn-Cunningham Barbara G. 
Published: April 2021

Project AbstractMaking sense of our environment requires us to extract simultaneous temporal and spatial information from multiple sensory modalities, particularly audition and vision. This sensory information can be stored in working memory (WM) to guide future actions, at which point it must be safeguarded against interference from ongoing sensory processing. Recent fMRI research has uncovered regions in human frontal cortex well-suited to coordinate this interplay between attention and WM for multisensory and multidimensional information. Which of these brain regions are engaged depends on both the sensory modality of the input and the information domain of the task, forming the basis of two complementary networks specialized for auditory/temporal and visual/spatial processing. Motivated by the functional specializations of these networks, we examined whether similarity in sensory modality and information domain modulates neural and perceptual interference between two concurrent tasks. Participants stored temporal or spatial information about auditory or visual stimuli in WM, and on some trials, performed an intervening temporal or spatial auditory task during WM retention. WM recall and auditory perceptual judgments were impaired when the two tasks relied on the same sensory modality and/or information domain. Pupil dilations were also larger in these conditions, indicating increased cognitive effort. Event-related potentials (ERPs) revealed a neural signature of domain-based interference that was masked by behavioral ceiling effects. These results demonstrate that modality and information domain jointly affect how task information is represented in WM, and concomitantly, how tasks engage the complementary auditory-temporal and visual/spatial cognitive control networks.
Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19
Authors: Roy Wong Lok-Yin , Zheng Jian , Wilhelmsen Kevin , Li Kun , Ortiz Miguel E. , Schnicker Nicholas J. , Pezzulo Alejandro A. , Szachowicz Peter J. , Klumpp Klaus , Aswad Fred , Rebo Justin , Narumiya Shuh , Murakami Makoto , Meyerholz David K. , Fortney Kristen , McCray Paul B. , Perlman Stanley 
Published: April 2021

ABSTRACTCoronavirus disease 2019 (COVID-19) is especially severe in aged populations1. Resolution of the COVID-19 pandemic has been advanced by the recent development of SARS-CoV-2 vaccines, but vaccine efficacy is partly compromised by the recent emergence of SARS-CoV-2 variants with enhanced transmissibility2. The emergence of these variants emphasizes the need for further development of anti-SARS-CoV-2 therapies, especially in aged populations. Here, we describe the isolation of a new set of highly virulent mouse-adapted viruses and use them to test a novel therapeutic drug useful in infections of aged animals. Initially, we show that many of the mutations observed in SARS-CoV-2 during mouse adaptation (at positions 417, 484, 501 of the spike protein) also arise in humans in variants of concern (VOC)2. Their appearance during mouse adaptation indicates that immune pressure is not required for their selection. Similar to the human infection, aged mice infected with mouse-adapted SARS-CoV-2 develop more severe disease than young mice. In murine SARS, in which severity is also age-dependent, we showed that elevated levels of an eicosanoid, prostaglandin D2 (PGD2) and of a phospholipase, PLA2G2D, contributed to poor outcomes in aged mice3,4. Using our virulent mouse-adapted SARS-CoV-2, we show that infection of middle-aged mice lacking expression of DP1, a PGD2receptor, or PLA2G2D are protected from severe disease. Further, treatment with a DP1 antagonist, asapiprant, protected aged mice from a lethal infection. DP1 antagonism is one of the first interventions in SARS-CoV-2-infected animals that specifically protects aged animals, and demonstrates that the PLA2G2D-PGD2/DP1 pathway is a useful target for therapeutic interventions. (Words: 254)
Characterization of a fiber-coupled EvenField illumination system for fluorescence microscopy
Authors: Berry Kyla , Taormina Mike , Maltzer Zoe , Turner Kristen , Gorham Melissa , Nguyen Thuc , Serafin Robert , Nicovich Philip R 
Published: April 2021

AbstractFluorescence microscopy benefits from spatially and temporally homogeneous illumination with illumination area matched to the shape and size of the camera sensor. Fiber-coupled illumination schemes have the added benefit of straightforward and robust alignment and ease of installation compared to free-space coupled illumination. Commercial and open-source fiber-coupled, homogenized illumination schemes have recently become available to the public; however, there have been no published comparisons of speckle reduction schemes to date. We characterize three different multimode fibers in combination with two laser speckle reduction devices and compare spatial and temporal profiles to a commercial unit. This work yields a new design, the EvenField Illuminator, which is freely available along for researchers to integrate into their own imaging systems.
Beech tree masting explains the inter-annual variation in the fall and spring peaks ofIxodes ricinusticks with different time lags
Authors: Bregnard Cindy , Rais Olivier , Herrmann Coralie , Kahl Olaf , Brugger Katharina , Voordouw Maarten J. 
Published: April 2021

ABSTRACTBackgroundThe tickIxodes ricinusis an important vector of tick-borne diseases including Lyme borreliosis. In continental Europe, the nymphal stage ofI. ricinusoften has a bimodal phenology with a large spring/early summer peak and a smaller fall peak. While there is consensus about the origin of the spring nymphal peak, there are two alternative hypotheses for the fall nymphal peak, direct development versus delayed diapause. These two hypotheses make different predictions about the time lags of the correlations between the spring peak, the fall peak, and seed production (masting) by deciduous trees.MethodsTo determine which hypothesis is most important for explaining the fall peak, we used data from a long-term surveillance study (15 years) on the density ofI. ricinusnymphal ticks at 4 different elevation sites in an area of Switzerland that is endemic for Lyme borreliosis, and long-term data on the mast of the European beech tree from the literature.ResultsI. ricinusnymphs had a bimodal phenology at the three lower elevation sites, but a unimodal phenology at the top elevation site. At the lower elevation sites, the density of nymphs (DON) in the fall was strongly correlated with the DON in the spring of the following year. The inter-annual variation in the densities ofI. ricinusnymphs in the fall and spring were best explained by a 1-year versus a 2-year time lag with the beech tree masting index. Fall nymphs had higher fat content and are younger than spring nymphs. All of these observations are consistent with the direct development hypothesis for the fall peak ofI. ricinusnymphs at our study site. Our study provides new insight into the complex bimodal phenology of this important disease vector.ConclusionsPublic health officials in Europe should be aware that following a strong mast year, the DON will increase 1 year later in the fall and 2 years later in the spring and summer. Population ecology studies ofI. ricinusshould consider that the spring and fall peak in the same calendar year represent different generations of ticks.
Non-structural carbohydrate concentrations in woody organs, but not leaves, of temperate and tropical tree angiosperms are independent of the ‘fast-slow’ plant economic spectrum
Authors: Ramirez J.A. , Craven D. , Posada J.M. , Reu B. , Sierra C.A. , Hoch G. , Handa I.T. , Messier C. 
Published: April 2021

SummaryBackground and AimsCarbohydrate reserves play a vital role in plant survival during periods of negative carbon balance. Considering active storage of reserves, there is a trade-off between carbon allocation to growth and to reserves and defense. A resulting hypothesis is that allocation to reserves exhibits a coordinated variation with functional traits associated with the ‘fast-slow’ plant economics spectrum.MethodsWe tested the relationship between non-structural carbohydrates (NSC) of tree organs and functional traits using 61 angiosperm tree species from temperate and tropical forests with phylogenetic hierarchical Bayesian models.Key ResultsOur results provide evidence that NSC concentrations in woody organs and plant functional traits are largely decoupled, meaning that species’ resilience is unrelated to their position on the ‘fast-slow’ plant economics spectrum. In contrast, we found that variation between NSC concentrations in leaves and the fast-slow continuum was coordinated, as species with higher leaf NSC had traits values associated with resource conservative species such as lower SLA, lower Amax, and high wood density. We did not detect an influence of leaf habit on the variation of NSC concentrations in tree organs.ConclusionsEfforts to predict the response of ecosystems to global change will need to integrate a suite of plant traits, such as NSC concentrations in woody organs, that are independent of the ‘fast-slow’ spectrum and that capture how species respond to a broad range of global change factors.
Inhibition is the hallmark of CA3 intracellular dynamics around awake ripples
Authors: Kajikawa Koichiro , Hulse Brad K. , Siapas Athanassios G. , Lubenov Evgueniy V. 
Published: April 2021

ABSTRACTHippocampal ripples are transient population bursts that structure cortico-hippocampal communication and play a central role in memory processing. However, the mechanisms controlling ripple initiation in behaving animals remain poorly understood. Here we combine multisite extracellular and whole cell recordings in awake mice to contrast the brain state and ripple modulation of subthreshold dynamics across hippocampal subfields. We find that entorhinal input to DG exhibits UP and DOWN dynamics with ripples occurring exclusively in UP states. While elevated cortical input in UP states generates depolarization in DG and CA1, it produces persistent hyperpolarization in CA3 neurons. Furthermore, growing inhibition is evident in CA3 throughout the course of the ripple buildup, while DG and CA1 neurons exhibit depolarization transients 100 ms before and during ripples. These observations highlight the importance of CA3 inhibition for ripple generation, while pre-ripple responses indicate a long and orchestrated ripple initiation process in the awake state.
Novel neuroanatomical integration and scaling define avian brain shape evolution and development
Authors: Watanabe Akinobu , Balanoff Amy M. , Gignac Paul M. , Eugenia Gold M. , Norell Mark A. 
Published: April 2021

AbstractHow do large and unique brains evolve? Historically, comparative neuroanatomical studies have attributed the evolutionary genesis of highly encephalized brains to deviations along, as well as from, conserved scaling relationships among brain regions. However, the relative contributions of these concerted (integrated) and mosaic (modular) processes as drivers of brain evolution remain unclear, especially in non-mammalian groups. While proportional brain sizes have been the predominant metric used to characterize brain morphology to date, we perform a high-density geometric morphometric analysis on the encephalized brains of crown birds (Neornithes or Aves) compared to their stem taxa—the non-avialan coelurosaurian dinosaurs. When analyzed together with developmental neuroanatomical data of model archosaurs (Gallus,Alligator), crown birds exhibit a distinct allometric relationship that dictates their brain evolution and development. Furthermore, analyses by neuroanatomical regions reveal that the acquisition of this derived shape-to-size scaling relationship occurred in a mosaic pattern, where the ‘avian’-grade optic lobe and cerebellum evolved first among non-avialan dinosaurs, followed by major changes to the evolutionary and developmental dynamics of cerebrum shape after the origin of Avialae.Notably, the brain of crown birds is a more integrated structure than non-avialan archosaurs, implying that diversification of brain morphologies within Neornithes proceeded in a more coordinated manner, perhaps due to spatial constraints and abbreviated growth period. Collectively, these patterns demonstrate a plurality in evolutionary processes that generate encephalized brains in archosaurs and across vertebrates.
Object motion influences feedforward motor responses during mechanical stopping of virtual projectiles: A preliminary study
Authors: Gómez-Granados Ana , Kurtzer Isaac , Gordon Sean , Barany Deborah A. , Singh Tarkeshwar 
Published: April 2021

AbstractAn important window into sensorimotor function is how humans interact and stop moving projectiles, such as stopping a door from closing shut or catching a ball. Previous studies have suggested that humans time the initiation and modulate the amplitude of their muscle activity based on the momentum of the approaching object. However, real-world experiments are constrained by laws of mechanics, which cannot be manipulated experimentally to probe the mechanisms of sensorimotor control and learning. An augmented-reality variant of such tasks allows for experimental manipulation of the relationship between motion and force to obtain novel insights into how the nervous system prepares motor responses to interact with moving stimuli. Existing paradigms for studying interactions with moving projectiles use massless object and are primarily focused on quantifying gaze and hand kinematics. Here, we developed a novel collision paradigm using a robotic manipulandum where participants mechanically stopped a virtual object moving in the horizontal plane. On each block of trials, we varied the virtual object’s momentum by increasing either its speed or mass. Participants stopped the object by applying a force impulse that matched the object momentum. We observed that arm force increased as a function of object momentum linked to changes in virtual mass or speed, mirroring results from studies involving catching free-falling objects. In addition, increasing object speed resulted in later onset of hand force relative to the impending time-to-contact. These findings show that the present paradigm can be used to determine how humans process projectile motion for hand motor control.
Transcriptomic Changes During Stage Progression of Mycosis Fungoides
Authors: Xiao M , Hennessey D , Iyer A , O’Keefe S , Zhang F , Sivanand A , Gniadecki R 
Published: April 2021

AbstractBackgroundMycosis fungoides (MF) is the most common cutaneous T cell lymphoma, which in the early patch/plaque stages runs an indolent course. However, ~25% of MF patients develop skin tumors, a hallmark of progression to the advanced stage and associated with high mortality. The mechanisms involved in stage progression are poorly elucidated.MethodsWe performed whole-transcriptome and whole-exome sequencing of malignant MF cells from skin biopsies obtained by laser-capture microdissection. We compared three types of MF lesions: early-stage plaques (ESP, n=12), and plaques and tumors from patients in late-stage disease (late-stage plaques, LSP, n=10, and tumors, TMR, n=15). Gene Ontology (GO) and KEGG analysis were used to determine pathway changes specific for different lesions which we linked to the recurrent somatic mutations overrepresented in MF tumors.ResultsThe key upregulated pathways during stage progression were those related to cell proliferation and survival (MEK/ERK, Akt-mTOR), Th2/Th9 signaling (IL4, STAT3, STAT5, STAT6), meiomitosis (CT45A1, CT45A3, STAG3, GTSF1, and REC8) and DNA repair (PARP1, MYCN, OGG1). Principal coordinate clustering of the transcriptome revealed extensive gene expression differences between early (ESP) and advanced-stage lesions (LSP and TMR). LSP and TMR showed remarkable similarities at the level of the transcriptome, which we interpreted as evidence of cell percolation between lesions via hematogenous self-seeding.ConclusionStage progression in MF is associated with Th2/Th9 polarization of malignant cells, activation of proliferation, survival, as well as increased genomic instability. Global transcriptomic changes in multiple lesions are probably caused by hematogenous cell percolation between discrete skin lesions.