bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal variabilities provide additional category-related information in object category decoding: a systematic comparison of informative EEG features
Authors: Karimi-Rouzbahani Hamid , Shahmohammadi Mozhgan , Vahab Ehsan , Setayeshi Saeed , Carlson Thomas 
Published: September 2020

AbstractHow does the human brain encode visual object categories? Our understanding of this has advanced substantially with the development of multivariate decoding analyses. However, conventional electroencephalography (EEG) decoding predominantly use the “mean” neural activation within the analysis window to extract category information. Such temporal averaging overlooks the within-trial neural variability which is suggested to provide an additional channel for the encoding of information about the complexity and uncertainty of the sensory input. The richness of temporal variabilities, however, has not been systematically compared with the conventional “mean” activity. Here we compare the information content of 31 variability-sensitive features against the “mean” of activity, using three independent highly-varied datasets. In whole-trial decoding, the classical event-related potential (ERP) components of “P2a” and “P2b” provided information comparable to those provided by “Original Magnitude Data (OMD)” and “Wavelet Coefficients (WC)”, the two most informative variability-sensitive features. In time-resolved decoding, the “OMD” and “WC” outperformed all the other features (including “mean”), which were sensitive to limited and specific aspects of temporal variabilities, such as their phase or frequency. The information was more pronounced in Theta frequency band, previously suggested to support feed-forward visual processing. We concluded that the brain might encode the information in multiple aspects of neural variabilities simultaneously e.g. phase, amplitude and frequency rather than “mean” per se. In our active categorization dataset, we found that more effective decoding of the neural codes corresponds to better prediction of behavioral performance. Therefore, the incorporation of temporal variabilities in time-resolved decoding can provide additional category information and improved prediction of behavior.
A mesh microelectrode array for non-invasive electrophysiology within neural organoids
Authors: McDonald Matthew , Sebinger David , Brauns Lisa , Gonzalez-Cano Laura , Menuchin-Lasowski Yotam , Mierzejewski Michael , Psathaki Olympia-Ekaterini , Stumpf Angelika , Wickham Jenny , Rauen Thomas , Schöler Hans , Jones Peter D. 
Published: September 2020

AbstractOrganoids are emergingin vitromodels of human physiology. Neural models require the evaluation of functional activity of single cells and networks, which is best measured by microelectrode arrays. The characteristics of organoids clash with existingin vitroorin vivomicroelectrode arrays. With inspiration from implantable mesh electronics and growth of organoids on polymer scaffolds, we fabricated suspended hammock-like mesh microelectrode arrays for neural organoids. We have demonstrated the growth of organoids enveloping these meshes and the culture of organoids on meshes for up to one year. Furthermore, we present proof-of-principle recordings of spontaneous electrical activity across the volume of an organoid. Our concept enables a new class of microelectrode arrays forin vitromodels of three-dimensional electrically active tissue.
Submesoscale dynamics directly shape bacterioplankton community structure in space and time
Authors: Fadeev Eduard , Wietz Matthias , von Appen Wilken-Jon , Nöthig Eva-Maria , Engel Anja , Grosse Julia , Graeve Martin , Boetius Antje 
Published: September 2020

AbstractSubmesoscale eddies and fronts are recognized as important components of oceanic mixing and energy fluxes. These submesoscale phenomena occur in the surface ocean for a period of a few days on scales between several hundred meters and a few tens of kilometers. Remote sensing and modeling suggest that they may influence marine ecosystem dynamics, but their limited temporal and spatial scales make them challenging for observation and in situ sampling. Here, the study of a submesoscale filament in summerly Arctic waters (depth 0 - 400 m) revealed enhanced vertical mixing of Polar and Atlantic water masses, resulting in a ca. 4 km wide and ca. 50 km long filament with distinct physical and biogeochemical conditions. Compared to the surrounding waters the filament was characterized by a distinct phytoplankton bloom dominated by diatoms and two-fold higher bacterioplankton cell densities. High-throughput 16S rRNA gene sequencing of both bacterioplankton communities revealed 3-4 orders of magnitude higher sequence abundance ofSynechococcusinside the filament, as well as tenfold higher sequence abundance of taxonomic groups typically found during summertime in aging phytoplankton blooms (e.g.,Flavobacteriales). In contrast, the surrounding waters contained severalfold higher sequence abundance of winterly taxonomic groups that are also associated with polar water masses (e.g., SAR202 clade). Altogether, our results show that physical submesoscale processes in the ocean can shape distinct biogeochemical conditions and microbial communities within a few kilometers. Furthermore, our results underline the importance of such submesoscale features for our understanding of surface ocean diversity and biogeochemical processes.
Robust spatial ventriloquism effect and aftereffect under memory interference
Authors: Park Hame , Kayser Christoph 
Published: September 2020

ABSTRACTOur brain adapts to discrepancies in the sensory inputs. One example is provided by the ventriloquism effect, experienced when the sight and sound of an object are displaced. Here the discrepant multisensory stimuli not only result in a biased localization of the sound, but also recalibrate the perception of subsequent unisensory acoustic information in the so-called ventriloquism aftereffect. This aftereffect has been linked to memory-related processes based on its parallels to general sequential effects in perceptual decision making experiments and insights obtained in neuroimaging studies. For example, we have recently implied memory-related medial parietal regions in the trial-by-trial ventriloquism aftereffect. Here, we tested the hypothesis that the ventriloquism aftereffect is indeed susceptible to manipulations interfering with working memory. Across three experiments we systematically manipulated the temporal delays between stimuli and response for either the ventriloquism or the aftereffect trials, or added a sensory-motor masking trial in between. Our data reveal no significant impact of either of these manipulations on the aftereffect, suggesting that the recalibration reflected by the ventriloquism aftereffect is surprisingly resilient to manipulations interfering with memory-related processes.
Comparative analysis of human brain organoids of brainstem and midbrain at single-cell resolution
Authors: Kinugawa Kaoru , Luginbühl Joachim , Matsui Takeshi K. , Eura Nobuyuki , Sakaguchi Yoshihiko M. , Shin Jay W , Sugie Kazuma , Schwamborn Jens C. , Mori Eiichiro 
Published: September 2020

ABSTRACTHuman brain organoids provide us the means to investigate human brain development and neurological diseases, and single-cell RNA-sequencing (scRNA-seq) technologies allow us to identify homologous cell types and the molecular heterogeneity between individual cells. Previously established human brain organoids of brainstem (hBSOs) and midbrain (hMBOs) were analyzed by scRNA-seq, but the difference in cellular composition between these organoids remains unclear. Here, we integrated and compared the single-cell transcriptome of hBSOs and hMBOs. Our analysis demonstrated that the hBSOs and hMBOs contain some unique cell types, including inflammatory and mesenchymal cells. Further comparison of the hBSOs and hMBOs with publicly available scRNA-seq dataset of human fetal midbrain (hMB) showed high similarity in their neuronal components. These results provide new insights into human brain organoid technologies.
Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease
Authors: Caetano Ana J. , Yianni Val , Volponi Ana A. , Booth Veronica , D’Agostino Eleanor M. , Sharpe Paul T. 
Published: September 2020

AbstractHuman oral soft tissues provide the first barrier of defence against chronic inflammatory disease and hold a remarkable scarless wounding phenotype. Tissue homeostasis requires coordinated actions of epithelial, mesenchymal and immune cells. However, the extent of heterogeneity within the human oral mucosa and how tissue cell types are affected during the course of disease progression is unknown. Using single cell transcriptome profiling we reveal a striking remodelling of the epithelial and mesenchymal niches with a decrease in functional populations that are linked to the aetiology of the disease. Analysis of ligand-receptor interaction pairs identify potential intercellular hubs driving the inflammatory component of the disease. Our work establishes a reference map of the human oral mucosa in health and disease, and a framework for the development of new therapeutic strategies.
Gaze Behaviour Reveals Flexible Encoding of Competing Reach Goals Under Conditions of Target Uncertainty
Authors: de Brouwer Anouk J. , Carter Michael J. , Smail Lauren C. , Wolpert Daniel M. , Gallivan Jason P. , Flanagan J. Randall 
Published: September 2020

AbstractIn daily tasks, we are often confronted with competing potential targets and must select one to act on. It has been suggested that, prior to target selection, the human brain encodes the motor goals of multiple, potential targets. However, this view remains controversial and it has been argued that only a single motor goal is encoded, or that motor goals are only specified after target selection. To investigate this issue, we measured participants’ gaze behaviour while viewing two potential reach targets, one of which was cued after a preview period. We applied visuomotor rotations to dissociate each visual target location from its corresponding motor goal location; i.e., the location participants needed to aim their hand toward to bring the rotated cursor to the target. During the preview period, participants most often fixated both motor goals but also frequently fixated one, or neither, motor goal location. Further gaze analysis revealed that on trials in which both motor goals were fixated, both locations were held in memory simultaneously. These findings show that, at the level of single trials, the brain most often encodes multiple motor goals prior to target selection, but may also encode either one or no motor goals. This result may help reconcile a key debate concerning the specification of motor goals in cases of target uncertainty.
Microglia-neuron communication at nodes of Ranvier depends on neuronal activity through potassium release and contributes to myelin repair
Authors: Ronzano R. , Roux T. , Thetiot M. , Aigrot M.S. , Richard L. , Lejeune F.X. , Mazuir E. , Vallat J.M. , Lubetzki C. , Desmazières A. 
Published: September 2020

AbstractMicroglia, the resident immune cells of the central nervous system, are key players in healthy brain homeostasis and plasticity. In neurological diseases, such as Multiple Sclerosis, activated microglia either promote tissue damage or favor neuroprotection and myelin regeneration. The mechanisms for microglia-neuron communication remain largely unkown. Here, we identify nodes of Ranvier as a direct and stable site of interaction between microglia and axons, in both mouse and human tissue. Using dynamic imaging, we highlight the preferential interaction of microglial processes with nodes of Ranvier along myelinated fibers. We show that microglianode interaction is modulated by neuronal activity and associated potassium release, with THIK-1 ensuring their microglial read-out. Disrupting axonal K+flux following demyelination polarizes microglia towards a pro-inflammatory phenotype and decreases remyelination rate. Taken together, these findings identify the node of Ranvier as a major site for microglia-neuron communication, participating in the pro-remyelinating effect of microglia after myelin injury.
Defining Substrate Requirements for Cleavage of Farnesylated Prelamin A by the Integral Membrane Zinc Metalloprotease ZMPSTE24
Authors: Wood Kaitlin M. , Spear Eric D. , Mossberg Otto W. , Odinammadu Kamsi O. , Xu Wenxin , Michaelis Susan 
Published: September 2020

AbstractThe integral membrane zinc metalloprotease ZMPSTE24 plays a key role in the proteolytic processing of farnesylated prelamin A, the precursor of the nuclear scaffold protein lamin A. Failure of this processing step results in the accumulation of permanently farnesylated forms of prelamin A which cause the premature aging disease Hutchinson-Gilford Progeria Syndrome (HGPS), as well as related progeroid disorders, and may also play a role in physiological aging. ZMPSTE24 is an intriguing and unusual protease because its active site is located inside of a closed intramembrane chamber formed by seven transmembrane spans with side portals in the chamber permitting substrate entry. The specific features of prelamin A that make it the sole known substrate for ZMPSTE24 in mammalian cells are not well-defined. At the outset of this work it was known that farnesylation is essential for prelamin A cleavagein vivoand that the C-terminal region of prelamin A (41 amino acids) is sufficient for recognition and processing. Here we investigated additional features of prelamin A that are required for cleavage by ZMPSTE24 using a well-established humanized yeast system. We analyzed the 14-residue C-terminal region of prelamin A that lies between the ZMPSTE24 cleavage site and the farnesylated cysteine, as well 23-residue region N-terminal to the cleavage site, by generating a series of alanine substitutions, alanine additions, and deletions in prelamin A. Surprisingly, we found that there is considerable flexibility in specific requirements for the length and composition of these regions. We discuss how this flexibility can be reconciled with ZMPSTE24’s selectivity for prelamin A.
Replicability, repeatability, and long-term reproducibility of cerebellar morphometry
Authors: Sörös Peter , Wölk Louise , Bantel Carsten , Bräuer Anja , Klawonn Frank , Witt Karsten 
Published: September 2020

AbstractTo identify robust and reproducible methods of cerebellar morphometry that can be used in future large-scale structural MRI studies, we investigated the replicability, repeatability, and longterm reproducibility of three fully-automated software tools: FreeSurfer, CERES, and ACAPULCO. Replicability was defined as computational replicability, determined by comparing two analyses of the same high-resolution MRI data set performed with identical analysis software and computer hardware. Repeatability was determined by comparing the analyses of two MRI scans of the same participant taken during two independent MRI sessions on the same day for the Kirby-21 study. Long-term reproducibility was assessed by analyzing two MRI scans of the same participant in the longitudinal OASIS-2 study. We determined percent difference, the image intraclass correlation coefficient, the coefficient of variation, and the intraclass correlation coefficient between two analyses. Our results show that CERES and ACAPULCO use stochastic algorithms that result in surprisingly high differences between identical analyses for ACAPULCO and small differences for CERES. Changes between two consecutive scans from the Kirby-21 study were less than ±5% in most cases for FreeSurfer and CERES (i.e., demonstrating high repeatability). As expected, long-term reproducibility was lower than repeatability for all software tools. In summary, CERES is an accurate, as demonstrated before, and reproducible tool for fully-automated segmentation and parcellation of the cerebellum. We conclude with recommendations for the assessment of replicability, repeatability, and longterm reproducibility in future studies on cerebellar structure.
Inhibition of HIF-1α accumulation in prostate cancer cells is initiated during early stages of mammalian orthoreovirus infection
Authors: Bussiere Luke D. , Miller Cathy L. 
Published: September 2020

ABSTRACTMammalian orthoreovirus (MRV) is a safe and effective cancer killing virus that has completed Phase I-III clinical trials against numerous cancer types. While many patients experience benefit from MRV therapy, pre-defined set points necessary for FDA approval have not been reached. Therefore, additional research into MRV biology and the effect of viral therapy on different tumor genetic subtypes and microenvironments is necessary to identify tumors most amenable to MRV virotherapy. In this work we analyzed the stage of viral infection necessary to inhibit HIF-1α, an aggressive cancer activator induced by hypoxia. We ruled out a number of viral proteins and the virus genome as being necessary and determined that a step parallel with virus core movement across the endosomal membrane was required for this inhibition. Altogether, this work clarifies the mechanisms of MRV-induced HIF-1α inhibition and provides biological relevance for using MRV to inhibit the devastating effects of tumor hypoxia.
Evolution of bone cortical compactness in slow arboreal mammals
Authors: Alfieri F. , Nyakatura J.A. , Amson E. 
Published: September 2020

AbstractLifestyle convergences and related phenotypes are a major topic in evolutionary biology. Low bone cortical compactness (CC), shared by the two genera of ‘tree sloths’, has been linked to their convergently evolved slow arboreal ecology. The proposed relationship of low CC with ‘tree sloths’ lifestyle suggests a potential convergent acquisition of this trait in other slow arboreal mammals. ‘Tree sloths’, ‘Lorisidae’, Palaeopropithecidae,Megaladapisand koalas were included in a phylogenetically informed CC analysis of the humerus and femur, as well as closely related but ecologically distinct taxa. We found that ‘tree sloths’ are unparalleled by any analysed clade, in featuring an extremely low CC. A tendency for low CC was however found in palaeopropithecids (especiallyPalaeopropithecus) andMegaladapis. On the other hand, low CC was not found in ‘Lorisidae’. Koalas, although deviating from the compact structure generally observed in mammals, are not clearly distinct from their sister taxon (wombats) and show humeral CC that is higher than femoral CC. Multiple factors seem to influence CC, preventing the recognition of a simple relationship between slow arborealism and low CC. Highly compact cortical bone in extinct sloths confirms that low CC in ‘tree sloths’ likely represents a recent convergence.
A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt
Authors: Tóth Adrienn Gréta , Csabai István , Maróti Gergely , Jerzsele Ákos , Dubecz Attila , Patai Árpád V. , Nagy Sára Ágnes , Makrai László , Bányai Krisztián , Szita Géza , Solymosi Norbert 
Published: September 2020

ABSTRACTAntimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The protection of bacteria against antimicrobials based on antimicrobial resistance genes (ARGs) developed in evolution. One of the essential clinical questions is the origin of ARGs of pathogen bacteria. Since the bacteria can share genetic components by horizontal gene transfer (HGT), all even non-pathogen bacteria may provide ARG to any pathogens when they became close physically. The bacteria of the human gut may make contact with bacteria entered into the body by food. The fermented food contains bacteria in high amount by its nature. Here we studied the diversity of ARG content by a unified metagenomic approach in various kefir and yoghurt products, in grain and isolated bacterial strains. We found numerous ARGs of commonly used fermenting bacteria with diversity characteristics in kefir and yoghurt samples. Even with the strictest filter restrictions we identified ARGs undermining the efficacy of aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, diaminopyrimidine, elfamycin, fluoroquinolone, fosfomycin, glycylcycline, lincosamides, macrolide, monobactam, nitrofuran, nitroimidazole, penam, penem, peptide, phenicol, rifamycin, tetracycline and triclosan. In the case of genelmrD, we detected genetic environment providing mobility of this ARG. Our findings support that theory during the fermentation process the food ARG content can grow by the bacteria multiplication. Results presented suggest that starting culture strains of fermented food should be monitored and selected to decrease the ARG amount intake by nutrition.
Influence of On-Off dynamics and selective attention on the spatial pattern of correlated variability in neocortex
Authors: Shi Yan-Liang , Steinmetz Nicholas A. , Moore Tirin , Boahen Kwabena , Engel Tatiana A. 
Published: September 2020

ABSTRACTCorrelated activity fluctuations in neocortex influence sensory responses and behavior. Neural correlations reflect anatomical connectivity and change dynamically with cognitive states, such as attention. Yet, how anatomical connectivity and cognitive states define the population structure of correlations is not known. We measured correlations in single cortical columns and found that the magnitude of correlations, their attentional modulation and dependence on lateral distance are predicted by On-Off dynamics, synchronous fluctuations in population activity across cortical layers. We developed a network model, in which spatial connectivity correlates the On-Off dynamics across nearby columns. We show that attentional inputs modulate the spatial extent of On-Off dynamics, resulting in spatially non-uniform changes in correlations. We confirm this prediction in our columnar recordings by showing that attentional modulation of correlations depends on lateral distance. Our results reveal how heterogeneous spatial patterns of correlations arise from the connectivity and network dynamics during attention.
Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients
Authors: Miller-Vedam Lakshmi E. , Bräuning Bastian , Popova Katerina D. , Oakdale Nicole T. Schirle , Bonnar Jessica L. , Prabu Jesuraj Rajan , Boydston Elizabeth A. , Sevillano Natalia , Shurtleff Matthew J. , Stroud Robert M. , Craik Charles S. , Schulman Brenda A. , Frost Adam , Weissman Jonathan S. 
Published: September 2020

AbstractMembrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies revealed at least two separable EMC activities, as an insertase regulating tail-anchored protein levels and as a polytopic membrane protein holdase chaperone. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a novel, non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC’s multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.