bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purification, characterization and influence on membrane properties of the plant-specific sphingolipids GIPC
Authors: Cassim Adiilah Mamode , Navon Yotam , Gao Yu , Decossas Marion , Fouillen Laetitia , Grélard Axelle , Nagano Minoru , Lambert Olivier , Bahammou Delphine , Van Delft Pierre , Maneta-Peyret Lilly , Simon-Plas Françoise , Heux Laurent , Fragneto Giovanna , Mortimer Jenny C. , Deleu Magali , Lins Laurence , Mongrand Sébastien 
Published: October 2020

AbstractThe plant plasma membrane (PM) is an essential barrier between the cell and the external environment. The PM is crucial for signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols and phospholipids. The most abundant sphingolipids in the plant PM are the Glycosyl Inositol Phosphoryl Ceramides (GIPCs), representing up to 40% of total sphingolipids, assumed to be almost exclusively in the outer leaflet of the PM. In this study, we investigated the structure of GIPCs and their role in membrane organization. Since GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of different long chain bases and fatty acids. The glycan head groups of the different GIPC series from monocots and dicots were analysed by GC-MS showing different sugar moieties. Multiple biophysics tools namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state2H-NMR and molecular modelling were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the phytosterols species and regulate the gel-to-fluid phase transition during temperature variations.
Intrusive Experiences In Post-Traumatic Stress Disorder: Treatment Response Induces Changes In The Effective Connectivity of The Anterior Insula
Authors: Leroy Arnaud , Very Etienne , Birmes Philippe , Szaffarczyk Sébastien , Lopes Renaud , Outteryck Olivier , Faure Cécile , Duhem Stéphane , Grandgenèvre Pierre , Warembourg Frédérique , Vaiva Guillaume , Jardri Renaud 
Published: October 2020

ABSTRACTBackgroundOne of the core features of posttraumatic stress disorder (PTSD) is reexperiencing the trauma. The anterior insula (AI) was proposed to play a crucial role in these intrusive experiences. However, the dynamic function of the AI in reexperiencing trauma, as well as its putative modulation by effective therapy, still need to be specified.MethodsThirty PTSD patients were enrolled and exposed to traumatic memory reactivation therapy. Resting-state fMRI scans were acquired before and after treatment. To explore AI directed influences over the rest of the brain, we referred to a mixed-model using pre/post Granger causality analysis seeded on the AI as a within-subject factor and treatment response as a between-subject factor. To further identify correlates of reexperiencing trauma, we investigated how intrusive severity affected: (i) causality maps and (ii) the spatial stability of other intrinsic brain networks.ResultsWe observed dynamic changes in AI effective connectivity in PTSD patients. Many within- and between-network causal paths were found to be less influenced by the AI after effective therapy. Insular influences were found positively correlated with flashback severity, while reexperiencing was linked with a strongerdefault mode network(DMN) and more unstablecentral executive network(CEN) connectivity.ConclusionWe showed that directed changes in AI signaling to the DMN and CEN at rest may underlie the degree of intrusive symptoms in PTSD. A positive response to treatment further induced changes in network-to-network anticorrelated patterns. Such findings may guide targeted neuromodulation strategies in PTSD patients not suitably improved by conventional treatment.
Axon Diameter Measurements using Diffusion MRI are Infeasible
Authors: Paquette Michael , Eichner Cornelius , Knösche Thomas R. , Anwander Alfred 
Published: October 2020

AbstractThe feasibility of non-invasive axonal diameter quantification with diffusion MRI is a strongly debated topic due to the neuroscientific potential of such information and its relevance for the axonal signal transmission speed. It has been shown that under ideal conditions, the minimal diameter producing detectable signal decay is bigger than most human axons in the brain, even using the strongest currently available MRI systems. We show that resolving the simplest situations including multiple diameters is unfeasible even with diameters much bigger than the diameter limit. Additionally, the recently proposed effective diameter resulting from fitting a single value over a distribution is almost exclusively influenced by the biggest axons. We show how impractical this metric is for comparing different distributions. Overall, axon diameters currently cannot be quantified by diffusion MRI in any relevant way.
Acute treatment with TrkB agonist LM22A-4 confers neuroprotection and preserves myelin integrity in a mouse model of pediatric traumatic brain injury
Authors: Fletcher Jessica L. , Dill Larissa K. , Wood Rhiannon J. , Wang Sharon , Robertson Kate , Murray Simon S. , Zamani Akram , Semple Bridgette D. 
Published: October 2020

ABSTRACTYoung children have a high risk of sustaining a traumatic brain injury (TBI), which can have debilitating life-long consequences. Importantly, the young brain shows particular vulnerability to injury, likely attributed to ongoing maturation of the myelinating nervous system at the time of insult. Here, we examined the effect of acute treatment with partial tropomyosin receptor kinase B (TrkB) agonist, LM22A-4, on the pathological and neurobehavioral outcomes after pediatric TBI, with the hypothesis that targeting TrkB would minimize tissue damage and support functional recovery. We focused on myelinated tracts— the corpus callosum and external capsules—based on recent evidence that TrkB activation potentiates oligodendrocyte remyelination. Male mice at postnatal day 21 received an experimental TBI or sham surgery. Acutely post-injury, extensive cell death, a robust glial response and disruption of compact myelin were evident in the injured brain. TBI or sham mice then received intranasal saline vehicle or LM22A-4 for 14 days. Behavior testing was performed from 4 weeks post-injury, and brains were collected at 5 weeks for histology. TBI mice showed hyperactivity, reduced anxiety-like behavior, and social memory impairments. LM22A-4 ameliorated the abnormal anxiolytic phenotype but had no effect on social memory deficits. Use of spectral confocal reflectance microscopy detected persistent myelin fragmentation in the external capsule of TBI mice at 5 weeks post-injury, which was accompanied by regionally distinct deficits in oligodendrocyte progenitor cells and postmitotic oligodendrocytes, as well as chronic reactive gliosis and atrophy of the corpus callosum and injured external capsule. LM22A-4 treatment ameliorated myelin deficits in the perilesional external capsule, as well as tissue volume loss and the extent of reactive gliosis. However, there was no effect of this TrkB agonist on oligodendroglial populations detected at 5 weeks post-injury. Collectively, our results demonstrate that targeting TrkB immediately after TBI during early life confers neuroprotection and preserves myelin integrity, and this was associated with some improved neurobehavioral outcomes as the pediatric injured brain matures.
The cardiac TRPA1 channel drives calcium-mediated mechano-arrhythmogenesis
Authors: Cameron Breanne A. , Stoyek Matthew R. , Bak Jessi J. , Connolly Michael S. , DeLong Emma A. , Greiner Joachim , Peyronnet Rémi , Kohl Peter , Quinn T Alexander 
Published: October 2020

SUMMARY PARAGRAPHMaintenance of cardiac function involves a regulatory loop in which electrical excitation causes the heart to contract through excitation-contraction coupling (ECC),1and the mechanical state of the heart directly affects its electrical activity through mechano-electric coupling (MEC).2However, in pathological states such as acute ischaemia that alter early or late electro-mechanical coordination (i.e., disturbances in ECC or repolarisation-relaxation coupling, RRC), MEC may contribute to the initiation and / or sustenance of arrhythmias (mechano-arrhythmogenesis).3The molecular identity of specific factor(s) underlying mechano-arrhythmogenesis in acute ischaemia, however, remain undefined.4By rapid stretch of rabbit single left ventricular cardiomyocytes, we show that upon ATP-sensitive potassium channel-induced alterations of RRC, overall vulnerability to mechano-arrhythmogenesis is increased, with mechano-sensitive5–11transient receptor potential kinase ankyrin 1 (TRPA1) channels12acting as the molecular driver through a Ca2+-mediated mechanism. Specifically, TRPA1 activation drives stretch-induced excitation and creates a substrate for self-sustained arrhythmias, which are maintained by increased cytosolic free Ca2+concentration ([Ca2+]i) and spontaneous [Ca2+]ioscillations. This TRPA1-dependent mechano-arrhythmogenesis involves microtubules, and can be prevented by block of TRPA1 or buffering of [Ca2+]i. Thus, in cardiac pathologies with disturbed RRC dynamics and / or augmented TRPA1 activity, TRPA1 may represent an anti-arrhythmic target with untapped therapeutic potential.13–17
Cross species multi-omics reveals cell wall sequestration and elevated global transcription as mechanisms of boron tolerance in plants
Authors: Wang Guannan , DiTusa Sandra Feuer , Oh Dong-Ha , Herrmann Achim D. , Mendoza-Cozatl David G. , O’Neill Malcolm A. , Smith Aaron P. , Dassanayake Maheshi 
Published: October 2020

AbstractBoron toxicity is a worldwide problem for crop production, yet we have only a limited understanding of the genetic responses and adaptive mechanisms to this environmental stress in plants. Here we identified responses to excess boron in boron stress-sensitiveArabidopsis thalianaand its boron stress-tolerant extremophyte relativeSchrenkiella parvulausing comparative genomics, transcriptomics, metabolomics, and ionomics. S. parvulamaintains a lower level of total boron and free boric acid in its roots and shoots and sustains growth for longer durations thanA. thalianawhen grown with excess boron.S. parvulalikely excludes boron more efficiently thanA. thaliana, which we propose is partly driven by BOR5, a boron transporter that we functionally characterized in the current study. Both species allocate significant transcriptomic and metabolomic resources to enable their cell walls to serve as a partial sink for excess boron, particularly discernable inA. thalianashoots. We provide evidence that theS. parvulatranscriptome is pre-adapted to boron toxicity, exhibiting substantial overlap with the boron-stressed transcriptome ofA. thaliana. Our transcriptomic and metabolomics data also suggest that RNA metabolism is a primary target of boron toxicity. Cytoplasmic boric acid likely forms complexes with ribose and ribose-containing compounds critical to RNA and other primary metabolic functions. A model depicting some of the cellular responses that enable a plant to grow in the presence of normally toxic levels of boron is presented.
Parallelized calculation of permutation tests
Authors: Ekvall Markus , Höhle Michael , Käll Lukas 
Published: October 2020

AbstractMotivationPermutation tests offer a straight forward framework to assess the significance of differences in sample statistics. A significant advantage of permutation tests are the relatively few assumptions about the distribution of the test statistic are needed, as they rely on the assumption of exchangeability of the group labels. They have great value, as they allow a sensitivity analysis to determine the extent to which the assumed broad sample distribution of the test statistic applies. However, in this situation, permutation tests are rarely applied because the running time of naive implementations is too slow and grows exponentially with the sample size. Nevertheless, continued development in the 1980s introduced dynamic programming algorithms that compute exact permutation tests in polynomial time. Albeit this significant running time reduction, the exact test has not yet become one of the predominant statistical tests for medium sample size. Here, we propose a computational parallelization of one such dynamic programming-based permutation test, the Green algorithm, which makes the permutation test more attractive.ResultsParallelization of the Green algorithm was found possible by nontrivial rearrangement of the structure of the algorithm. A speed-up – by orders of magnitude – is achievable by executing the parallelized algorithm on a GPU. We demonstrate that the execution time essentially becomes a non-issue for sample sizes, even as high as hundreds of samples. This improvement makes our method an attractive alternative to, e.g., the widely used asymptotic Mann-Whitney U-test.AvailabilityIn Python 3 code from the GitHub repositoryhttps://github.com/statisticalbiotechnology/parallelPermutationTestunder an Apache 2.0 license.Contactlukask@kth.seSupplementary informationSupplementary data are available atBioinformaticsonline.
Aberrant ventral dentate gyrus structure and function in individuals susceptible to post-traumatic stress disorder
Authors: Dirven Bart C.J. , van der Geugten Dewi , van Bodegom Miranda , Madder Leonie , van Agen Laura , Homberg Judith R. , Kozicz Tamas , Henckens Marloes J.A.G. 
Published: October 2020

ABSTRACTPost-traumatic stress disorder (PTSD) is a psychiatric disorder vulnerable individuals can develop following a traumatic event, whereas others are resilient. Enhanced insight into the mechanistic underpinnings contributing to these inter-individual differences in PTSD susceptibility is key to improved treatment and prevention. Aberrant function of the hippocampal dentate gyrus (DG) may contribute to its psychopathology, with the dorsal DG potentially encoding trauma memory generalization and the ventral DG anxiety. Using a mouse model, we investigated the association between deviant DG structure and function and susceptibility to develop PTSD-like symptoms following trauma. Mice were exposed to a traumatic event (unpredictable, inescapable foot shocks) and tested for PTSD symptomatology following recovery. In three independent experiments, DG neuronal morphology, synaptic protein gene expression and neuronal activity during trauma encoding and recall were assessed. Behaviorally, PTSD-like animals displayed some increased anxiety-like behavior already prior to trauma, increased novelty-induced freezing, but no clear differences in remote trauma memory recall. Comparison of the ventral DG of PTSD-like vs resilient mice revealed lower spine density, reduced expression of the postsynaptic protein homer 1b/c gene, a larger population of neurons active during trauma encoding and a greater presence of somatostatin neurons to be associated with PTSD susceptibility. In contrast, the dorsal DG of PTSD-like animals did not differ in terms of spine density or gene expression, but displayed more active neurons during trauma encoding and a lower amount of somatostatin neurons. These data propose a critical role for -mainly the ventral-DG in establishing symptomatology addressed in this PTSD model.
Reward Value Is More Important Than Physical Saliency During Bumblebee Visual Search For Multiple Rewarding Targets
Authors: Nityananda Vivek , Chittka Lars 
Published: October 2020

AbstractSeveral animals, including bees, use visual search to distinguish targets of interest and ignore distractors. While bee flower choice is well studied, we know relatively little about how they choose between multiple rewarding flowers in complex floral environments. Two important factors that could influence bee visual search for multiple flowers are the physical saliency (colour contrast against the background) of flowers and the reward value associated with them. We here investigated how these two different factors contribute to bee visual search. We trained bees to independently recognize two rewarding colours that in different experiments differed in either physical saliency, reward value or both. We then measured their choices and attention to these colours in the presence of distractors in a test without reinforcement. We found that bees preferred more salient or higher rewarding flowers and ignored distractors. When the high-reward flowers were less salient than the low-reward flowers, bees were nonetheless equally likely to choose high-reward flowers. Bees were more also more likely to attend to these high-reward flowers, with higher inspection times around them and faster search times when choosing them. When flowers differed in reward, we also found an effect of the training order with low-reward targets being more likely to be chosen if they had been encountered during the more immediate training session prior to the test. Our results parallel recent findings from humans demonstrating that reward value can attract attention even when targets are less salient and irrelevant to the current task.
Spatial relations trigger visual binding of people
Authors: Adibpour Parvaneh , Hochmann Jean-Rémy , Papeo Liuba 
Published: October 2020

AbstractTo navigate the social world, humans must represent social entities, and the relationships between those entities, starting with spatial relationships. Recent research suggests that two bodies are processed with particularly high efficiency in visual perception, when they are in a spatial positioning that cues interaction, i.e. close and face-to-face. Socially relevant spatial relations such as facingness may facilitate visual perception by triggering grouping of bodies into a new integrated percept, which would make the stimuli more visible and easier to process. We used electroencephalography and a frequency-tagging paradigm to measure a neural correlate of grouping (or visual binding), while female and male participants saw images of two bodies face-to-face or back-to-back. The two bodies in a dyad flickered at frequency F1 and F2, respectively, and appeared together at a third frequency Fd (dyad frequency). This stimulation should elicit a periodic neural response for each body at F1 and F2, and a third response at Fd, which would be larger for face-to-face (vs.back-to-back) bodies, if those stimuli yield additional integrative processing. Results showed that responses at F1 and F2 were higher for upright than for inverted bodies, demonstrating that our paradigm could capture neural activity associated with viewing bodies. Crucially, the response to dyads at Fd was larger for face-to-face (vs.back-to-back) dyads, suggesting integration mediated by grouping. We propose that spatial relations that recur in social interaction (i.e., facingness) promote binding of multiple bodies into a new representation. This mechanism can explain how the visual system contributes to integrating and transforming the representation of disconnected body-shapes into structured representations of social events.
Flash properties of Gaussia Luciferase are the result of covalent inhibition after a limited number of cycles
Authors: Dijkema Fenne Marjolein , Nordentoft Matilde Knapkøien , Didriksen Anders Krøll , Corneliussen Anders Sværke , Willemoës Martin , Winther Jakob R. 
Published: October 2020

AbstractLuciferases are widely used as reporters for gene expression and for sensitive detection systems. While luciferases from firefly andRenillahave long been used for analysis of intracellular expression, the luciferase (GLuc) from the marine copepodGaussia princeps, has gained popularity, primarily because it is secreted and displays a very high light intensity. Firefly luciferase is characterized by kinetic behavior which is consistent with conventional steady-state Michaelis-Menten kinetics (termed “glow” kinetics). GLuc, conversely, displays what has been termed “flash” kinetics which signify a burst in light emission followed by a rapid decay. As the mechanistic background for this behavior is poorly characterized, we decided to decipher the mechanism in more detail. We show that decay in light signal is not due to depletion of substrate, but rather is caused by the irreversible inactivation of the enzyme. Inactivation takes place after between 10 and 200 reaction cycles, depending on substrate concentration. We found that the rate of inactivation is described by the sum of two exponentials with associated rate constants. The dominant of these of these increases linearly with substrate concentration while the minor is substrate-concentration independent. In terms of rate of initial luminescence reaction, this increases with the substrate concentration to the power of 1.53 and shows no signs of saturation up to 10 μM coelenterazine. Finally, we found that the inactivated form of the enzyme has a larger apparent size in both size exclusion chromatography and SDS-PAGE analysis and shows a fluorescence peak at 410 nm when excited at 333 nm. These findings indicate that the “flash” kinetics inGaussialuciferase are caused by an irreversible covalent binding to a derivative of the substrate during the reaction.
The underlying mechanisms of improved balance after one and ten sessions of balance training in older adults
Authors: Alizadehsaravi Leila , Koster Ruud A.J. , Muijres Wouter , Maas Huub , Bruijn Sjoerd M. , van Dieën Jaap H. 
Published: October 2020

AbstractTraining improves balance control in older adults, but the time course and neural mechanisms underlying these improvements are unclear. We studied balance robustness and performance, H-reflex gains, paired reflex depression, and co-contraction duration in ankle muscles after one and ten training sessions in 22 older adults (+65yrs). Mediolateral balance robustness, time to balance loss in unipedal standing on a platform with decreasing rotational stiffness, improved (33%) after one session, with no further improvement after ten sessions. Balance performance, absolute mediolateral center of mass velocity, improved (18.75%) after one session in perturbed unipedal standing and (18.18%) after ten sessions in unperturbed unipedal standing. Co-contraction duration of soleus/tibialis anterior increased (16%) after ten sessions. H-reflex gain and paired reflex depression excitability did not change. H-reflex gains were lower, and soleus/tibialis anterior co-contraction duration was higher in participants with more robust balance after ten sessions, and co-contraction duration was higher in participants with better balance performance at several time-points. Changes in robustness and performance were uncorrelated with changes in co-contraction duration, H-reflex gain, or paired reflex depression. In older adults, balance robustness improved over a single session, while performance improved gradually over multiple sessions. Changes in co-contraction and excitability of ankle muscles were not exclusive causes of improved balance.HighlightsBalance robustness and balance performance in perturbed unipedal standing was improved after one balance training session, with no further improvement after ten sessions.Balance performance in unperturbed unipedal standing was improved after ten sessionsH-reflex and paired reflex depression did not change after training in unipedal or bipedal standing.Co-contraction duration of antagonistic ankle muscles increased after ten sessions in perturbed and unperturbed unipedal standing.Changes in co-contraction duration and excitability of ankle muscles were not exclusive causes of improved balance.