bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women and Men Were Proportionally Represented Among Speakers at Major National Neurology Conferences in 2017
Authors: McDermott Mollie , Burke James F. , McCalpin Haley , Shelgikar Anita V. , Gelb Douglas J. , Dunn Abbey , Beimer Nicholas J. , London Zachary N. 
Published: December 2019

AbstractObjectiveTo determine whether speaking roles at five major neurology conferences in 2017 show disproportionate representation by men.MethodsThis study consisted of two cross-sectional analyses. In the first part, we compared speaker characteristics across meetings and by gender using descriptive statistics. In the second part, we linked presenters to the American Medical Association (AMA) Masterfile. For the primary analysis in the second part using linked AMA speaker data, we built models to estimate the influence of gender on speaker roles.Results1493 speakers were identified and included in our cross-sectional analysis. Women made up 28% of presenters from the US and 18% of presenters from other countries. After adjusting for years from medical school graduation and subspecialty, no effect of gender on speaker activity was observed (odds ratio [OR] for women 0.91; 95% confidence interval [CI], 0.77-1.07).ConclusionsFactors aside from national conference speaking activity should be investigated to better understand sex differences in rank at top-ranked academic neurology programs.
Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses
Authors: Lassalle Florent , Beale Mathew A , Bharucha Tehmina , Williams Charlotte A , Williams Rachel J , Cudini Juliana , Goldstein Richard , Haque Tanzina , Depledge Daniel P , Breuer Judith 
Published: December 2019

AbstractHerpes Simplex Virus type 1 (HSV-1) chronically infects over 70% of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. By contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.
Competition between kinesin-1 and myosin-V defineDrosophilaposterior determination
Authors: Lu Wen , Lakonishok Margot , Liu Rong , Billington Neil , Rich Ashley , Glotzer Michael , Sellers James R. , Gelfand Vladimir I. 
Published: December 2019

AbstractLocal accumulation ofoskar (osk) mRNA in theDrosophilaoocyte determines the posterior pole of the future embryo. Two major cytoskeletal components, microtubules and actin filaments, together with a microtubule motor, kinesin-1, and an actin motor, myosin-V, are essential foroskmRNA posterior localization. In this study, we use Staufen, an RNA-binding protein that colocalizes withoskmRNA, as a proxy for posterior determination. We demonstrate that posterior localization ofosk/Staufen is determined by competition between kinesin-1 and myosin-V. While kinesin-1 removesosk/Staufen from the cortex along microtubules, myosin-V anchorsosk/Staufen at the cortex. Myosin-V wins over kinesin-1 at the posterior pole due to low microtubule density at this site, while kinesin-1 wins it at anterior and lateral positions because they have high density of cortically-anchored microtubules. As a result, posterior determinants are removed from the anterior and lateral cortex but retained at the posterior pole. Thus, posterior determination ofDrosophilaoocyte is defined by kinesin-myosin competition, whose outcome is primarily determined by cortical microtubule density.
Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype
Authors: Rougemont Quentin , Dolo Victoria , Oger Adrien , Besnard Anne-Laure , Huteau Dominique , Coutellec Marie-Agnès , Perrier Charles , Launey Sophie , Evanno Guillaume 
Published: December 2019

AbstractUnderstanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) admixture with the closely related anadromousL. fluviatilisecotype having a positive effect onL. planerigenetic diversity. We genotyped 2472 individuals, including 225L. fluviatilis, sampled in 81 sites upstream and downstream from barriers to migration, in 29 West-European rivers. Linear modelling revealed a strong positive relationship between the distance to the source and genetic diversity, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a moderate effect on spatial genetic structure. Accordingly, we found evidence for downstream-directed gene flow, supporting the hypothesis that barriers do not limit dispersal following water flow. DownstreamL. planeripopulations in sympatry withL. fluviatilisdisplayed consistently higher genetic diversity. We conclude that genetic drift and slight downstream gene flow mainly drive the genetic make up of upstreamL. planeripopulations whereas admixture between ecotypes maintains higher levels of genetic diversity inL. planeripopulations sympatric withL. fluviatilis. We discuss the implications of these results for the design of conservation strategies of lamprey, and other freshwater organisms with several ecotypes, in fragmented dendritic river networks.
Golgi outposts locally regulate microtubule orientation in neurons but are not required for the overall polarity of the dendritic cytoskeleton
Authors: Yang Sihui Z. , Wildonger Jill 
Published: December 2019

ABSTRACTMicrotubule-organizing centers (MTOCs) often play a central role in organizing the cellular microtubule networks that underlie cell function. In neurons, microtubules in axons and dendrites have distinct polarities. Dendrite-specific Golgi outposts, in particular multi-compartment outposts, have emerged as regulators of acentrosomal microtubule growth, raising the question of whether outposts contribute to establishing the overall polarity of the dendritic microtubule cytoskeleton. Thecis-Golgi matrix protein GM130 has roles in both the MTOC activity of Golgi and in connecting Golgi compartments to form multi-compartment units. Using a combination of genetic approaches and live imaging in a Drosophila model, we found that GM130 is not essential for the overall polarity of the dendritic microtubule cytoskeleton. However, the mislocalization of multi-compartment Golgi outposts to axons disrupts the uniform orientation of axonal microtubules. This suggests that outposts have the capacity to influence microtubule polarity and, as our data indicate, likely do so independently of microtubule nucleation mediated by the γ-tubulin ring complex (γ-TuRC). Altogether, our results are consistent with the model that multi-compartment Golgi outposts may locally influence microtubule polarity, but that outposts are not necessary for the overall polarity of the dendritic microtubule cytoskeleton.
Why some size illusions affect grip aperture
Authors: Smeets Jeroen B.J. , Kleijn Erik , van der Meijden Marlijn , Brenner Eli 
Published: December 2019

AbstractThere is an extensive literature debating whether perceived size is used to guide grasping. A possible reason for not using judged size is that using judged positions might lead to more precise movements. As this argument does not hold for small objects, and all studies showing an effect of the Ebbinghaus illusion on grasping used small objects, we hypothesized that size information is used for small objects but not for large ones. Using a modified diagonal illusion, we obtained an effect of about 10% on perceptual judgements, without an effect on grasping, irrespective of object size. We therefore reject our precision hypothesis. We discuss the results in the framework of grasping as moving digits to positions on an object. We conclude that the reported disagreement on the effect of illusions is because the Ebbinghaus illusion not only affects size, but –unlike most size illusions– also affects perceived positions.
Trehalose as an alternative to glycerol as a glassing agent for in vivo DNP MRI
Authors: Brender Jeffrey R. , Kishimoto Shun , Eaton Gareth R. , Eaton Sandra S. , Saida Yu , Krishna Murali C. 
Published: December 2019

AbstractIn dynamic nuclear polarization (DNP), the solutions of the hyperpolarizable molecule and the paramagnetic agent need to form a glass when frozen to attain significant levels of polarization in reasonable time periods. Molecules which do not form glasses by themselves are often mixed with excipients to form glasses. While glassing agents are often essential in DNP studies, they have the potential to perturb the metabolic measurements that are being studied. Glycerol, the glassing agent of choice for in vivo DNP studies, is effective at reducing ice crystal formation during freezing but is rapidly metabolized, potentially altering the redox and ATP balance of the system. As a biologically inert alternative to glycerol, we show here that 15–20 wt % trehalose yields a glass that polarizes samples more rapidly than the commonly used 60% wt formulation of glycerol and yields similar polarization levels within clinically relevant timeframes. Trehalose may be an attractive alternative to glycerol for situations where there may be concerns about glycerol’s glucogenic potential and possible alteration of the ATP/ADP and redox balance.
Identifying Brain Network Topology Changes in Task Processes and Psychiatric Disorders
Authors: Rezaeinia Paria , Fairley Kim , Pal Piya , Meyer François G. , Carter R. McKell 
Published: December 2019

ABSTRACTA central goal in neuroscience is to understand how dynamic networks of neural activity produce effective representations of the world. Advances in the theory of graph measures raise the possibility of elucidating network topologies central to the construction of these representations. We leverage a result from the description of lollipop graphs to identify an iconic network topology in functional magnetic resonance imaging data and characterize changes to those networks during task performance and in populations diagnosed with psychiatric disorders. During task performance, we find that task-relevant subnetworks change topology, becoming more integrated by increasing connectivity throughout cortex. Analysis of resting-state connectivity in clinical populations shows a similar pattern of subnetwork topology changes; resting-scans becoming less default-like with more integrated sensory paths. The study of brain network topologies and their relationship to cognitive models of information processing raises new opportunities for understanding brain function and its disorders.AUTHOR SUMMARYOur mental lives are made up of a series of predictions about the world calculated by our brains. The calculations that produce these predictions are a result of how areas in our brain interact. Measures based on graph representations can make it clear what information can be combined and therefore help us better understand the computations the brain is performing. We make use of cutting-edge techniques that overcome a number of previous limitations to identify specific shapes in the functional brain network. These shapes are similar to hierarchical processing streams which play a fundamental role in cognitive neuroscience. The importance of these structures and the technique is highlighted by how they change under different task constraints and in individuals diagnosed with psychiatric disorders.
Use of dual electron probes reveals role of ferritin in erythropoiesis
Authors: Aronova Maria A. , Noh Seung-Jae , Zhang Guofeng , Byrnes Colleen , Meier Emily Riehm , Kim Young C. , Leapman Richard D. 
Published: December 2019

AbstractMuch is known about the finely regulated process of mammalian erythropoiesis that occurs in the bone marrow, whereby erythropoietic stem cells undergo terminal differentiation accompanied by enormous morphological changes to generate highly functional specialized red blood cells. However, a crucial step in erythropoiesis, the labile iron pool and its transport to mitochondria for heme production, is not well understood1. We apply a dual 3D imaging and spectroscopic technique, based on scanned electron probes, to measure distributions of ferritin iron-storage protein in ex vivo human erythropoietic stem cells, and to determine how those distributions change during terminal differentiation. After seven days of differentiation, the cells display a highly specialized architecture of organelles with anchored clustering of mitochondria and massive accumulation of Fe3+ in loaded ferritin cores localized to lysosomal storage depots, providing an iron source for heme production. Macrophages are not present in our ex vivo cultures, so they cannot be the source of the ferritin2. We suggest that lysosomal iron depots are required by developing reticulocytes while terminally differentiating and continuing to produce heme and globin, which assemble and concentrate to fill the cytoplasm after much of the cellular machinery is expelled.
Boldness and exploration vary between shell morphs but not environmental contexts in the snailCepaea nemoralis
Authors: Dahirel Maxime , Gaudu Valentin , Ansart Armelle 
Published: December 2019

AbstractUnderstanding the maintenance of among-individual behavioral variation in populations, and predicting its consequences, are key challenges in behavioral ecology. Studying the association between repeatable behaviors and other traits under selection may shed light on the underlying selective pressures. We used the model snailCepaea nemoralisto examine whether individual behavior is associated with shell morph, a key trait that has been extensively studied in the context of thermal tolerance and predator avoidance, and which is known to be under strict genetic control in this species. We quantified proxies of boldness and exploration in snails of three morphs coming from two habitats with different thermal contexts. We show that both behaviors were repeatable at the among-individual level(within-stateRboldness= 0.22 [95% credible interval: 0.15, 0.29];Rexploration= 0.20 [0.15, 0.25]). Behavior was associated with shell morph, with the darker morph (five-banded) being consistently shyer and slower to explore. There was no evidence that thermal environment of origin influenced behavior. Snails became faster when test temperature increased; we found no evidence morphs differed in their thermal response. Boldness and exploration were correlated among individuals, forming a syndrome (r= 0.28 [0.10, 0.46]). We discuss what these results may tell us about the type of selection exerted by predators. We also detail how our results hint to a genetic link between shell morph and behavior, and the evolutionary implications of such a link. Finally, we discuss how our findings combined with decades of evolutionary research makeC. nemoralisa very valuable model to study the evolution of behavior in response to environmental changes.
The ER cargo receptor SURF4 facilitates efficient erythropoietin secretion
Authors: Lin Zesen , King Richard , Tang Vi , Myers Greggory , Balbin-Cuesta Ginette , Friedman Ann , McGee Beth , Desch Karl , Ozel Ayse Bilge , Siemieniak David , Reddy Pavan , Emmer Brian , Khoriaty Rami 
Published: December 2019

AbstractErythropoietin (EPO), a glycoprotein produced by specialized peritubular fibroblasts in the kidney, is the master regulator of erythropoiesis. EPO is secreted into the plasma in response to tissue hypoxia and stimulates erythroid differentiation and maturation. Though the transcriptional regulation of EPO has been well studied, the molecular determinants of EPO secretion remain unknown. Here, we generated a HEK293T reporter cell line that provides a quantifiable and selectable readout of intracellular EPO levels. Using this cell line, we performed a genome-scale CRISPR screen that identified SURF4 as an important mediator of EPO secretion. TargetingSURF4with multiple independent sgRNAs resulted in intracellular accumulation and extracellular depletion of EPO. Both of these phenotypes were rescued by expression ofSURF4cDNA. Additionally, consistent with a role for SURF4 as an ER cargo receptor of EPO, we found that disruption of SURF4 resulted in accumulation of EPO in the ER compartment, and that SURF4 and EPO physically interact. Furthermore, SURF4 disruption in Hep3B cells also caused a defect in the secretion of endogenous EPO, ruling out an artifact of heterologous overexpression. This work suggests that SURF4 functions as an ER cargo receptor that mediates the efficient secretion of EPO. Our findings also suggest that modulating SURF4 may be an effective treatment for disorders of erythropoeisis that are driven by aberrant EPO levels. Finally, we show that SURF4 overexpression results in increased secretion of EPO, suggesting a new strategy for more efficient production of recombinant EPO.
‘Awake delta’ and theta-rhythmic hippocampal network modes during intermittent locomotor behaviors in the rat
Authors: Schultheiss Nathan W. , Schlecht Maximillian , Jayachandran Maanasa , Brooks Deborah R. , McGlothan Jennifer L. , Guilarte Tomás R. , Allen Timothy A. 
Published: December 2019

AbstractDelta-frequency network activity is commonly associated with sleep or behavioral disengagement accompanied by a dearth of cortical spiking, but delta in awake behaving animals is not well understood. We show that hippocampal (HC) synchronization in the delta frequency band (1-4 Hz) is related to animals’ locomotor behavior using a detailed analysis of simultaneous head- and body-tracking data. In contrast to running-speed modulation of the theta rhythm (6-10 Hz, a critical mechanism in navigation models), we observed that strong delta synchronization occurred when animals were stationary or moving slowly and while theta and fast gamma (55-120 Hz) were weak. We next combined time-frequency decomposition of the local field potential with hierarchical clustering algorithms to categorize momentary estimations of the power spectral density (PSD) into putative modes of HC activity. Delta and theta power measures from these modes were notably orthogonal, and theta and delta coherences between HC recording sites were monotonically related to theta-delta ratios across modes. Next, we focused on bouts of precisely-defined running and stationary behavior. Extraction of delta and theta power density estimates for each instance of these bout types confirmed the orthogonality between frequency bands seen across modes. We found that delta-band and theta-band coherence within HC, and in a small sample, between HC and medial prefrontal cortex (mPFC), mirrored delta and theta components of the PSD. Delta-band synchronization often developed rapidly when animals paused briefly between runs, as well as appearing throughout longer stationary bouts. Taken together, our findings suggest that delta-dominated network modes (and corresponding mPFC-HC couplings) represent functionally-distinct circuit dynamics that are temporally and behaviorally interspersed amongst theta-dominated modes during navigation. As such these modes of mPFC-HC circuit dynamics could play a fundamental role in coordinating encoding and retrieval mechanisms or decision-making processes at a timescale that segments event sequences within behavioral episodes.
Mental state space visualization for interactive modeling of personalized BCI control strategies
Authors: Kuzovkin Ilya , Tretyakov Konstantin , Uusberg Andero , Vicente Raul 
Published: December 2019

AbstractObjectiveNumerous studies in the area of BCI are focused on the search for a better experimental paradigm – a set of mental actions that a user can evoke consistently and a machine can discriminate reliably. Examples of such mental activities are motor imagery, mental computations, etc. We propose a technique that instead allows the user to try different mental actions in the search for the ones that will work best.ApproachThe system is based on a modification of the self-organizing map (SOM) algorithm and enables interactive communication between the user and the learning system through a visualization of user’s mental state space. During the interaction with the system the user converges on the paradigm that is most efficient and intuitive for that particular user.Main resultsResults of the two experiments, one allowing muscular activity, another permitting mental activity only, demonstrate soundness of the proposed method and offer preliminary validation of the performance improvement over the traditional closed-loop feedback approach.SignificanceThe proposed method allows a user to visually explore their mental state space in real time, opening new opportunities for scientific inquiry. The application of this method to the area of brain-computer interfaces enables more efficient search for the mental states that will allow a user to reliably control a BCI system.
FUNCTIONAL NETWORK CONNECTIVITY (FNC)-BASED GENERATIVE ADVERSARIAL NETWORK (GAN) AND ITS APPLICATIONS IN CLASSIFICATION OF MENTAL DISORDERS
Authors: Zhao Jianlong , Zhi Dongmei , Yan Weizheng , Calhoun Vince D. , Sui Jing 
Published: December 2019

ABSTRACTFunctional network connectivity (FNC) obtained from resting-state functional magnetic resonance imaging (fMRI) data have been commonly used to study mental disorders in neuroimaging applications. Likewise, generative adversarial networks (GANs) have performed well in multiple classification benchmark tasks. However, the application of GANs to fMRI is relatively rare. In this work, we proposed an FNC-based GAN for classifying brain disorders from healthy controls (HCs), in which FNC matrices were calculated by correlation of time courses derived from non-artefactual fMRI independent components (ICs). The proposed GAN model consisted of one discriminator (real FNCs) and one generator (fake FNCs), each has four fully-connected layers, and feature matching was implemented between each other to improve classification performance. An average accuracy of 70.1% with 10-fold cross-validation was achieved for classifying 269 major depressive disorder (MDD) patients from 286 HCs, at least 5.9% higher compared to other 6 popular classification approaches (54.5-64.2%). In another application to discriminating between 558 schizophrenia patients and 542 HCs from 7 sites, the proposed GAN model achieved 80.7% accuracy in leave-one-site-out prediction, outperforming support vector machine (SVM) and deep neural net (DNN) by 3-6%. To the best of our knowledge, this is the first attempt to apply GAN model based on fMRI data for mental disorder classification. Such a framework promises wide utility and great potential in neuroimaging biomarker identification.