bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motor cortical dynamics are shaped by multiple distinct subspaces during naturalistic behavior
Authors: Perich Matthew G. , Conti Sara , Badi Marion , Bogaard Andrew , Barra Beatrice , Rajan Kanaka , Bloch Jocelyne , Courtine Gregoire , Micera Silvestro , Capogrosso Marco , Milekovic Tomislav 
Published: August 2020

ABSTRACTBehavior relies on continuous influx of sensory information about the body. In primates, motor cortex must integrate somatic feedback to accurately reach and manipulate objects. Yet, prior work demonstrates that motor cortex is well-described with deterministic, rather than input-driven, dynamics. Deterministic dynamics facilitate robust movement generation, but flexible motor output requires rapid responses to unexpected inputs. Here, we resolved this paradox by simultaneously recording neural population activity in motor and somatosensory cortex from four monkeys performing a naturalistic object interaction behavior resulting in occasional errors. Motor cortex was strikingly input-driven surrounding behavioral error correction. Intriguingly, input-driven dynamics were isolated to a subspace of the population activity that putatively captured somatosensory feedback. Using electrical stimulation of ascending somatosensory tracts, we causally verified that this feedback subspace captured peripheral inputs to cortex. Our results demonstrate that cortical activity is compartmentalized within distinct subspaces, enabling flexible integration of salient inputs for robust behavior.
Deep Learning Based Segmentation of Brain Tissue from Diffusion MRI
Authors: Zhang Fan , Breger Anna , Kevin Cho Kang Ik , Ning Lipeng , Westin Carl-Fredrik , O’Donnell Lauren J. , Pasternak Ofer 
Published: August 2020

AbstractSegmentation of brain tissue types from diffusion MRI (dMRI) is an important task, required for quantification of brain microstructure and for improving tractography. Current dMRI segmentation is mostly based on anatomical MRI (e.g., T1- and T2-weighted) segmentation that is registered to the dMRI space. However, such inter-modality registration is challenging due to more image distortions and lower image resolution in the dMRI data as compared with the anatomical MRI data. In this study, we present a deep learning method that learns tissue segmentation from high-quality imaging datasets from the Human Connectome Project (HCP), where registration of anatomical data to dMRI is more precise. The method is then able to predict a tissue segmentation directly from new dMRI data, including data collected with a different acquisition protocol, without requiring anatomical data and inter-modality registration. We train a convolutional neural network (CNN) to learn a tissue segmentation model using a novel augmented target loss function designed to improve accuracy in regions of tissue boundary. To further improve accuracy, our method adds diffusion kurtosis imaging (DKI) parameters that characterize non-Gaussian water molecule diffusion to the conventional diffusion tensor imaging parameters. The DKI parameters are calculated from the recently proposed mean-kurtosis-curve method that corrects implausible DKI parameter values and provides additional features that discriminate between tissue types. We demonstrate high tissue segmentation accuracy on HCP data, and also when applying the HCP-trained model on dMRI data from a clinical acquisition with lower resolution and fewer gradient directions.
Sexual dimorphism of synaptonemal complex length among populations of threespine stickleback fish
Authors: Madison Barquiesha S. , Nath Shivangi , Flanagan Mary K. , Dorsey Brittany A. , White Michael A. 
Published: August 2020

AbstractCrossover frequencies often differ substantially between sexes (i.e. heterochiasmy). Although this phenomenon is widespread throughout taxa, the mechanisms that lead to heterochiasmy remain unclear. One pattern that has emerged is that the overall length of the synaptonemal complex likely has a direct influence on the total number of crossovers in each sex. However, this has only been investigated in a handful of species. The threespine stickleback fish (Gasterosteus aculeatus) is an excellent species to explore whether synaptonemal complex length is associated with differences in the total number of crossovers, as females have much longer linkage maps than males. We used an immunocytological approach to quantify synaptonemal complex length in late pachytene female and male meiocytes in two different populations of threespine stickleback fish. Overall, the freshwater population had shorter synaptonemal complex lengths than the marine population. In both populations we observed sexual dimorphism, with females possessing longer axes. Our results support a model where chromosome axis length determines overall crossover frequency and establish the threespine stickleback as a useful species to explore the mechanistic basis of heterochiasmy as well as the genetic basis underlying variation in synaptonemal complex length.
Optically pumped magnetometers disclose magnetic field components of the muscular action potential
Authors: Broser Philip J. , Middelmann Thomas , Sometti Davide , Braun Christoph 
Published: August 2020

ABSTRACTAimTo track the magnetic field generated by the propagating muscle action potential (MAP).MethodIn this prospective, proof of principle study, the magnetic activity of the intrinsic foot muscle after electric stimulation of the tibial nerve was measured using optically pumped magnetometers (OPMs). A classical biophysical electric dipole model of the propagating MAP was implemented to model the source of the data.ResultsThe signal profile generated by the activity of the intrinsic foot muscles was measured by four OPM devices. Three devices were located above the same muscle to compare the direction and the strength of the magnetic signal while propagating along the muscle.InterpretationOPM devices allow for a new, non-invasive way to study MAP patterns. Since magnetic fields are less altered by the tissue surrounding the dipole source compared to electric activity, a precise analysis of the spatial characteristics and temporal dynamics of the MAP is possible. The classic electric dipole model explains major but not all aspects of the magnetic field. The field has longitudinal components generated by intrinsic structures of the muscle fibre. By understanding these magnetic components, new methods could be developed to analyse the muscular signal transduction pathway in greater detail.What this paper adds- Technological concepts to record and analyse the small magnetic fields generated by electric muscular activity- Model to link the signals measured by the OPM sensors to the underlying physiology- Insights into the propagation of muscle action potential and the sequential control of motor activity
Genetics of resistance to common root rot (spot blotch),Fusariumcrown rot, and sharp eyespot in wheat
Authors: Su Jun , Zhao Jiaojie , Zhao Shuqing , Li Mengyu , Pang Shuyong , Chen Shisheng , Chen Feng , Zhen Wenchao , Kang Zhensheng , Wang Xiaodong 
Published: August 2020

AbstractDue to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch),Fusariumcrown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot,Fusariumcrown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.
Failure of vergence size constancy challenges our understanding of visual scale
Authors: Linton Paul 
Published: August 2020

AbstractThe closer an object is, the more the eyes have to rotate to fixate on it. This degree of eye rotation (or vergence) is thought to play an essential role in size constancy, the process of perceiving an object as having a constant physical size despite changes in distance. But vergence size constancy has never been tested divorced from confounding cues such as changes in the retinal image. We control for these confounding cues and find no evidence of vergence size constancy. This has three important implications. First, we need a new explanation for binocular vision’s contribution to visual scale. Second, the vergence modulation of neurons in V1 can no longer be responsible for size constancy. Third, given the role attributed to vergence in multisensory integration, multisensory integration appears to be more reliant on cognitive factors than previous thought.
Nucleotide usage biases distort inferences of the species tree
Authors: Borges Rui , Boussau Bastien , Szöllősi Gergely J. , Kosiol Carolin 
Published: August 2020

AbstractDespite the importance of natural selection in species’ evolutionary history, phylogenetic methods that take into account population-level processes typically ignore selection. The assumption of neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to compromise phylogenetic inferences significantly. However, genome-wide processes like GC-bias and some variation segregating at the coding regions are known to evolve in the nearly neutral range. As we are now using genome-wide data to estimate species trees, it is natural to ask whether weak but pervasive selection is likely to blur species tree inferences. We developed a polymorphism-aware phylogenetic model tailored for measuring signatures of nucleotide usage biases to test the impact of selection in the species tree. Our analyses indicate that while the inferred relationships among species are not significantly compromised, the genetic distances are systematically underestimated in a node-height dependent manner: i.e., the deeper nodes tend to be more underestimated than the shallow ones. Such biases have implications for molecular dating. We dated the evolutionary history of 30 worldwide fruit fly populations, and we found signatures of GC-bias considerably affecting the estimated divergence times (up to 23%) in the neutral model. Our findings call for the need to account for selection when quantifying divergence or dating species evolution.Significance statementAlthough little is known about the impact of natural selection on species tree estimation, expectations are that it occurs at a minority of loci in eukaryotic genomes and is thus unlikely to affect the divergence process. However, growing evidence suggests that a large amount of the genomic variation evolves under weak but pervasive selection (e.g., fixation biases created by GC-bias gene conversion). We tested the impact of unaccounted-for nearly neutral selection on species tree estimation and found that the estimated branch lengths are systematically biased. Our results highlight the need for selection-aware models in species tree estimation and molecular dating.
Multiscale integration of environmental stimuli in plant tropism produces complex behaviors
Authors: Moulton Derek E. , Oliveri Hadrien , Goriely Alain 
Published: August 2020

Plant tropism refers to the directed movement of an organ or organism in response to external stimuli. Typically, these stimuli induce hormone transport that triggers cell growth or deformation. In turn, these local cellular changes create mechanical forces on the plant tissue that are balanced by an overall deformation of the organ, hence changing its orientation with respect to the stimuli. This complex feedback mechanism takes place in a three-dimensional growing plant with varying stimuli depending on the environment. We model this multiscale process in filamentary organs for an arbitrary stimulus by linking explicitly hormone transport to local tissue deformation leading to the generation of mechanical forces and the deformation of the organ in three dimensions. We show, as examples, that the gravitropic, phototropic, nutational, and thigmotropic dynamic responses can be easily captured by this framework. Further, the integration of evolving stimuli and/or multiple contradictory stimuli can lead to complex behavior such as sun following, canopy escape, and plant twining.Significance StatementTo survive and to thrive, plants rely on their ability to sense multiple environmental signals, such as gravity or light, and respond to them by growing and changing their shape. To do so, the signals must be transduced down to the cellular level to create the physical deformations leading to shape changes. We propose a multiscale theory of tropism that takes multiple stimuli and transforms them into auxin transport that drives tissue-level growth and remodeling, thus modifying the plant shape and position with respect to the stimuli. This feedback loop can be dynamically updated to understand the response to individual stimuli or the complex behavior generated by multiple stimuli such as canopy escape or pole wrapping for climbing plants.
Covert attention increases the gain of stimulus-evoked population codes
Authors: Foster Joshua J. , Thyer William , Wennberg Janna W. , Awh Edward 
Published: August 2020

AbstractCovert spatial attention has a variety of effects on the responses of individual neurons. However, relatively little is known about the net effect of these changes on sensory population codes, even though perception ultimately depends on population activity. Here, we measured the electroencephalogram (EEG) in human observers (male and female), and isolated stimulus-evoked activity that was phase-locked to the onset of attended and ignored visual stimuli. Using an encoding model, we reconstructed spatially selective population tuning functions from the pattern of stimulus-evoked activity across the scalp. Our EEG-based approach allowed us to measure very early visually evoked responses occurring ~100 ms after stimulus onset. In Experiment 1, we found that covert attention increased the amplitude of spatially tuned population responses at this early stage of sensory processing. In Experiment 2, we parametrically varied stimulus contrast to test how this effect scaled with stimulus contrast. We found that the effect of attention on the amplitude of spatially tuned responses increased with stimulus contrast, and was well-described by an increase in response gain (i.e., a multiplicative scaling of the population response). Together, our results show that attention increases the gain of spatial population codes during the first wave of visual processing.Significance StatementWe know relatively little about how attention improves population codes, even though perception is thought to critically depend on population activity. In this study, we used an encoding-model approach to test how attention modulates the spatial tuning of stimulus-evoked population responses measured with EEG. We found that attention multiplicatively scales the amplitude of spatially tuned population responses. Furthermore, this effect was present within 100 ms of stimulus onset. Thus, our results show that attention improves spatial population codes by increasing their gain at this early stage of processing.
Reinforcement Learning approaches to hippocampus-dependent flexible spatial navigation
Authors: Tessereau Charline , O’Dea Reuben , Coombes Stephen , Bast Tobias 
Published: August 2020

AbstractHumans and non-human animals show great flexibility in spatial navigation, including the ability to return to specific locations based on as few as one single experience. To study spatial navigation in the laboratory, watermaze tasks, in which rats have to find a hidden platform in a pool of cloudy water surrounded by spatial cues, have long been used. Analogous tasks have been developed for human participants using virtual environments. Spatial learning in the watermaze is facilitated by the hippocampus. In particular, rapid, one-trial, allocentric place learning, as measured in the Delayed-Matching-to-Place (DMP) variant of the watermaze task, which requires rodents to learn repeatedly new locations in a familiar environment, is hippocampal dependent. In this article, we review some computational principles, embedded within a Reinforcement Learning (RL) framework, that utilise hippocampal spatial representations for navigation in watermaze tasks. We consider which key elements underlie their efficacy, and discuss their limitations in accounting for hippocampus-dependent navigation, both in terms of behavioural performance (i.e., how well do they reproduce behavioural measures of rapid place learning) and neurobiological realism (i.e., how well do they map to neurobiological substrates involved in rapid place learning). We discuss how an actor-critic architecture, enabling simultaneous assessment of the value of the current location and of the optimal direction to follow, can reproduce one-trial place learning performance as shown on watermaze and virtual DMP tasks by rats and humans, respectively, if complemented with map-like place representations. The contribution of actor-critic mechanisms to DMP performance is consistent with neurobiological findings implicating the striatum and hippocampo-striatal interaction in DMP performance, given that the striatum has been associated with actor-critic mechanisms. Moreover, we illustrate that hierarchical computations embedded within an actor-critic architecture may help to account for aspects of flexible spatial navigation. The hierarchical RL approach separates trajectory control via a temporal-difference error from goal selection via a goal prediction error and may account for flexible, trial-specific, navigation to familiar goal locations, as required in some arm-maze place memory tasks, although it does not capture one-trial learning of new goal locations, as observed in open field, including watermaze and virtual, DMP tasks. Future models of one-shot learning of new goal locations, as observed on DMP tasks, should incorporate hippocampal plasticity mechanisms that integrate new goal information with allocentric place representation, as such mechanisms are supported by substantial empirical evidence.
Trophic niche of the invasive gregarious speciesCrepidula fornicata, in relation to ontogenic changes
Authors: Androuin Thibault , Dubois Stanislas F. , Hubas Cédric , Lefebvre Gwendoline , Le Grand Fabienne , Schaal Gauthier , Carlier Antoine 
Published: August 2020

AbstractThe slipper limpetCrepidula fornicatais a common and widespread invasive gregarious species along the European coast. Among its life-history traits, well documented ontogenic changes in behavior (i.e., motile male to sessile female) suggests a potential shift in feeding strategy across its life stages. Considering the ecological significance of this species in colonized areas, understanding how conspecifics share the trophic resource is crucial. Using fatty acids (FA) and stable isotopes (SI) as complementary trophic markers, we conducted a field survey between late winter and spring to investigate the trophic niche of three ontogenic stages ofC. fornicatathat bear different sexual (male/female) and motility (motile/sessile) traits. Potential trophic sources were characterized by their pigment, FA and SI compositions and discriminated well over the study period. We showed that the biofilm coveringC. fornicatashells harbored a higher biomass of primary producers (i.e., chlorophytes and diatoms) than the surrounding sediment surface. Over the study period, we observed a covariation between the three ontogenic stages for both FA and SI compositions which suggest that the trophic niche ofC. fornicatadoes not change significantly across its benthic life. During periods of low food availability, slipper limpets displayed an opportunistic suspension-feeding behaviour, relying on both fresh and detrital organic matter, likely coming from superficial sedimentary organic matter. During high food availability (i.e., spring phytoplankton bloom), all ontogenic stages largely benefited from this fresh supply of organic matter (pelagic diatoms in this case). However, the three ontogenic stages showed consistent differences in FA composition, and to a lesser extent in SI composition. These differences persist over time, as they originate more likely from ontogenic physiological changes (e.g., differential growth rates, metabolic rate or gametogenesis) rather than diet discrepancies.
It’s not just poverty: unregulated global market and bad governance explain unceasing deforestation in Western Madagascar
Authors: Vieilledent Ghislain , Nourtier Marie , Grinand Clovis , Pedrono Miguel , Clausen Alison , Rabetrano Tsiky , Rakotoarijaona Jean-Roger , Rakotoarivelo Bruno , Rakotomalala Fety A. , Rakotomalala Linjanantenaina , Razafimpahanana Andriamandimbisoa , Ralison José M. , Achard Frédéric 
Published: August 2020

AbstractMadagascar is recognized both for its unparalleled biodiversity and the high level of threat suffered by this biodiversity, associated in particular with anthropogenic deforestation. Despite sustained efforts to fight poverty and curb deforestation, forest cover in Madagascar is rapidly decreasing. To try to explain why it is so difficult to stop deforestation in Madagascar, we analysed the recent deforestation process in Western Madagascar through satellite image analysis and field surveys. We show that deforestation has increased from less than 0.9%/yr on 2000–2010 to more than 2%/yr on 2010–2017. We identified two major causes of deforestation, which were not associated with subsistence agriculture: slash-and-burn agriculture for the cultivation of cash crops (maize and peanut), and uncontrolled fires to create open pasture. Maize production is mainly at the destination of the domestic market and is used in particular for livestock feeding. Peanut production has boomed since 2013 and more than half of it is now exported towards asiatic countries. The money earned by farmers is principally invested into zebu herd acquisition. Trade of agricultural commodities benefits several intermediaries, some of whom have political responsibilities thus creating conflicts of interest. On the other hand, agents from institutions in charge of the management of the protected areas have no means to enforce laws against deforestation. In the absence of an efficient strategy to stop deforestation, we predicted that 38-93% of the forest present in 2000 will have disappeared in 2050. Forest loss, apart from biodiversity loss and climate-change global issues, will be at the expense of local population. In order to stop deforestation, international aid should be used to improve local governance to enforce environmental laws and pressure should be put on trading companies to buy certified agricultural commodities that are not derived from deforestation.