bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient beta activity and connectivity during sustained motor behaviour
Authors: Echeverria-Altuna Irene , Quinn Andrew J. , Zokaei Nahid , Woolrich Mark W. , Nobre Anna C. , van Ede Freek 
Published: March 2021

AbstractNeural oscillations are thought to play a central role in orchestrating activity states between distant neural populations. In humans, long-range neural connectivity has been particularly well characterised for 13-30 Hz beta activity which becomes phase coupled between the motor cortex and the contralateral muscle during isometric contraction. Based on this and related observations, beta activity and connectivity have been linked to sustaining stable cognitive and motor states – or the ‘status quo’ – in the brain. Recently, however, beta activity has been shown to be short-lived, as opposed to sustained – though so far this has been reported for regional beta activity in tasks without sustained motor demands. Here, we measured magnetoencephalography (MEG) and electromyography (EMG) in 18 human participants performing an isometric-contraction (gripping) task designed to yield sustained behavioural output. If cortico-muscular beta connectivity is directly responsible for sustaining a stable motor state, then beta activity should be (or become) sustained in this context. In contrast, we found that beta activity and connectivity with the downstream muscle were transient, even when participants engaged in sustained gripping. Moreover, we found that sustained motor requirements did not prolong beta-event duration in comparison to rest. These findings suggest that long-range neural synchronisation may entail short ‘bursts’ of frequency-specific connectivity, even when task demands – and behaviour – are sustained.HighlightsTrial-average 13-30 Hz beta activity and connectivity with the muscle appear sustained during stable motor behaviourSingle-trial beta activity and connectivity are short-lived, even when motor behaviour is sustainedSustained task demands do not prolong beta-event duration in comparison to resting state
Cooperative Stabilization of Close-Contact Zones Leads to Sensitivity and Selectivity in T-Cell Recognition
Authors: Różycki Bartosz , Weikl Thomas R. 
Published: March 2021

AbstractT cells are sensitive to 1 to 10 foreign-peptide-MHC complexes among a vast majority of self-peptide-MHC complexes, and discriminate selectively between peptide-MHC complexes that differ not much in their binding affinity to T-cell receptors (TCRs). Quantitative models that aim to explain this sensitivity and selectivity largely focus on single TCR/peptide-MHC complexes, but T cell adhesion involves a multitude of different complexes. In this article, we demonstrate in a three-dimensional computational model of T-cell adhesion that the cooperative stabilization of close-contact zones is sensitive to 1 to 3 foreign-peptide-MHC complexes and occurs at a rather sharp threshold affinity of these complexes, which implies selectivity. In these close-contact zones with lateral extensions of hundred to several hundred nanometers, few TCR/foreign-peptide-MHC complexes and many TCR/self-peptide-MHC complexes are segregated from LFA-1/ICAM-1 complexes that form at larger membrane separations. Previous high-resolution microscopy experiments indicate that the sensitivity and selectivity in the formation of closed-contact zones reported here is relevant for T-cell recognition, because the stabilization of close-contact zones by foreign, agonist peptide-MHC complexes precedes T-cell signaling and activation in the experiments.
Protection against neonatal respiratory viral infection via maternal treatment during pregnancy with the benign immune training agent OM-85
Authors: Lauzon-Joset Jean-Francois , Mincham Kyle T , Scott Naomi M , Khandan Yasmine , Stumbles Philip A , Holt Patrick G , Strickland Deborah H 
Published: March 2021

AbstractObjectivesIncomplete maturation of immune regulatory functions at birth are antecedent to the heightened risk for severe respiratory infections during infancy. Our forerunner animal model studies demonstrated that maternal treatment with the benign microbial-derived immune modulating agent OM-85 during pregnancy promotes accelerated maturation of immune regulatory networks in the developing fetal bone marrow. Here, we aimed to establish proof-of-concept that this would enhance resilience to severe early life respiratory viral infection during the neonatal period.MethodsPregnant BALB/c mice were treated orally with OM-85 during gestation and their offspring infected intranasally with a mouse-adapted rhinovirus (vMC0) at postnatal day 2. We then assessed clinical course, lung viral titres and lung immune parameters to determine whether offspring from OM-85 treated mothers demonstrate enhanced immune protection against neonatal vMC0infection.ResultsOffspring from OM-85 treated mothers display enhanced capacity to clear an otherwise lethal respiratory viral infection during the neonatal period, with a concomitant reduction in the exaggerated nature of the ensuing immune response. These treatment effects were associated with accelerated postnatal myeloid cell seeding of neonatal lungs and enhanced expression of microbial sensing receptors in lung tissues, coupled in particular with enhanced capacity to rapidly expand and maintain networks of lung dendritic cells expressing function-associated markers crucial for maintenance of local immune homeostasis in the face of pathogen challenge.ConclusionMaternal OM-85 treatment may represent a novel therapeutic strategy to reduce the burden, and potential long-term sequlae, of severe neonatal respiratory viral infection by accelerating development of innate immune competence.
Slow rTMS to the left DLPFC enhances verbal memory formation
Authors: van der Plas Mircea , Braun Verena , Stauch Benjamin Johannes , Hanslmayr Simon 
Published: March 2021

AbstractEncoding of episodic memories relies on stimulus-specific information processing and involves the left prefrontal cortex. We here present an incidental finding from a simultaneous EEG-TMS experiment as well as a replication of this unexpected effect. Our results reveal that stimulating the left dorsolateral prefrontal cortex (DLPFC) with slow repetitive transcranial magnetic stimulation (rTMS) leads to enhanced word memory performance. 40 healthy human participants engaged in a list learning paradigm. Half of the subjects (N=20) received 1 Hz rTMS to the left DLPFC while the other half (N=20) received 1 Hz rTMS to the vertex and served as a control group. Subjects receiving left DLPFC stimulation demonstrated enhanced memory performance compared to the control group. This effect was replicated in a double-blind within-subjects experiment where 24 participants received 1 Hz rTMS to the left DLPFC and vertex. In this second experiment, DLPFC stimulation also induced better memory performance compared to vertex stimulation. In addition to these behavioural effects, we found that 1 Hz rTMS to DLPFC induced stronger beta power modulation in posterior areas, a state which is known to be beneficial for memory encoding. Further analysis indicated, that beta modulations did not have an oscillatory origin. Instead, the observed beta modulations were a result of a spectral tilt, suggesting inhibition of these parietal regions. These results show that applying 1 Hz rTMS to DLPFC, an area involved in episodic memory formation, improves memory performance via modulating neural activity in parietal regions.
Multiple targets of balancing selection inLeishmania donovanicomplex parasites
Authors: Grace Cooper Alastair , Forrester Sarah , Silva Vladimir Costa , Aare Aleksander , Kilford Hannah , Chew Yen Peng , James Sally , Costa Dorcas L. , Mottram Jeremy C. , Costa Carlos C. H. N. , Jeffares Daniel C. 
Published: March 2021

AbstractTheLeishmania donovanispecies complex are the causative agents of visceral leishmaniasis, which cause 20-40,000 fatalities a year. Here, we conduct a screen for balancing selection in this species complex. We used 387 publicly-availableL. donovaniandL. infantumgenomes, and sequence 93 isolates ofL. infantumfrom Brazil to describe the global diversity of this species complex. We identify five genetically-distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We find that signals of balancing selection are generally not shared between populations, consistent with transient adaptive events, rather than long-term balancing selection. We then apply multiple diversity metrics to identify candidate genes with robust signatures of balancing selection, identifying a curated set of 19 genes with robust signatures. These include zeta toxin, nodulin-like and flagellum attachment proteins. This study highlights the extent of genetic divergence betweenL. donovani complexparasites and provides genes for further study.
A pan-ontology view of machine-derived knowledge representations and feedback mechanisms for curation
Authors: Konopka Tomasz , Smedley Damian 
Published: March 2021

AbstractBiomedical ontologies are established tools that organize knowledge in specialized research areas. They can also be used to train machine-learning models. However, it is unclear to what extent representations of ontology concepts learned by machine-learning models capture the relationships intended by ontology curators. It is also unclear whether the representations can provide insights to improve the curation process. Here, we investigate ontologies from across the spectrum of biological research and assess the concordance of formal ontology hierarchies with representations based on plain-text definitions. By comparing the internal properties of each ontology, we describe general patterns across the pan-ontology landscape and pinpoint areas with discrepancies in individual domains. We suggest specific mechanisms through which machine-learning approaches can lead to clarifications of ontology definitions. Synchronizing patterns in machine-derived representations with those intended by the ontology curators will likely streamline the use of ontologies in downstream applications.
Spatio-temporal modelling for the evaluation of an altered Indian saline Ramsar site and its drivers for ecosystem management and restoration
Authors: Naik Rajashree , Sharma L.K. 
Published: March 2021

AbstractSaline wetlands are keystone ecosystems in arid and semi-arid landscapes that are currently under severe threat. This study conducted spatio-temporal modelling of the largest saline Ramsar site of India, in Sambhar wetland from 1963-2059. One CORONA aerial photograph of 1963 and Landsat images of 1972, 1981, 1992, 2009, and 2019 were acquired and classified under 8 classes as Aravalli, barren land, saline soil, salt crust, saltpans, waterbody, settlement, and vegetation for spatial modelling integrated with bird census, soil-water parameters, GPS locations, and photographs. Past decadal area statistics state reduction of waterbody from 30.7 to 3.4% at constant rate (4.23%) to saline soil. Saline soil increased from 12.4 to 21.7% and saline soil converted to barren land from 45.4 to 49.6%; saltpans from 7.4 to 14% and settlement from increased 0.1 to 1.3% till 2019. Future predictions hint at a net increase of 20% by wetland, vegetation by 30%, settlement by 40%, saltpan by 10%, barren land by 5%, and net loss of 20%, each by Aravalli and salt crust. The biggest loss of 120% was seen by saline soil converted to barren land. Notably, 40% of the current wetland will be lost by 2059. Additionally, soil-water parameters result state a loss of saline character of wetland ecosystem; subsequently bird statistics indicate a shift in migratory birds disturbing the wetland food web. India has been losing a critical habitat of migratory birds, halophytes, and halophiles, along with livelihood. This study looks to bridge the missing link from local to global wetland ecological disconnect, providing thereby lake management and restoration strategies.
Panakeia - A universal tool for bacterial pangenome analysis
Authors: Beier Sina , Thomson Nicholas R. 
Published: March 2021

AbstractWe present Panakeia, a tool which strives to be easy to use and providing a detailed view of the pangenome structure which can efficiently be utilised for discovery, or further in-depth analysis, of features of interest. It analyses synteny and multiple structural patterns of the pangenome, giving insights into the biological diversity and evolution of the studied taxon. Panakeia hence provides both broad and detailed information on the structure of a pangenome, for diverse and highly clonal populations of bacteria. Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years. This enables comparison of strains from different ecological niches and can be used to define the functional potential in a bacterial population. It gives us a much better view of microbial genomics than can be gained from singular genomes which after all are just single representatives of a much more varied population.Previously published pangenome tools often reduce the information to a presence/absence matrix of unconnected genes or generate massive hard to interpret output graphs. However, Panakeia includes synteny and structural information and presents it in a way that can readily be used for further analysis. Panakeia can be downloaded athttps://github.com/BioSina/Panakeia.
Human stem cell-based retina-on-chip as new translational model for validation of AAV retinal gene therapy vectors
Authors: Achberger Kevin , Cipriano Madalena , Düchs Matthias , Schön Christian , Michelfelder Stefan , Stierstorfer Birgit , Lamla Thorsten , Kauschke Stefan G. , Chuchuy Johanna , Roosz Julia , Mesch Lena , Cora Virginia , Pars Selin , Pashkovskaia Natalia , Corti Serena , Kleger Alexander , Kreuz Sebastian , Maier Udo , Liebau Stefan , Loskill Peter 
Published: March 2021

SummaryGene therapies using adeno-associated viruses (AAVs) are amongst the most promising strategies to treat or even cure hereditary and acquired retinal diseases. However, the development of new efficient AAV vectors is slow and costly, largely because of the lack of suitable non-clinical models. By faithfully recreating structure and function of human tissues, human induced pluripotent stem cell (iPSC)-derived retinal organoids could become an essential part of the test cascade addressing translational aspects. Organ-on-Chip (OoC) technology further provides the capability to recapitulate microphysiological tissue environments as well as a precise control over structural and temporal parameters. By employing our recently developed Retina-on-chip that merges organoid and OoC-technology, we analyzed the efficacy, kinetics and cell tropism of seven first and second generation AAV vectors. The presented data demonstrate the potential of iPSC-based OoC models as the next generation of screening platforms for future gene therapeutic studies.
Optimal BR signalling is required for adequate cell wall orientation in the Arabidopsis root meristem
Authors: Li Zhenni , Sela Ayala , Fridman Yulia , Höfte Herman , Savaldi-Goldstein Sigal , Wolf Sebastian 
Published: March 2021

AbstractThe plant steroid hormones brassinosteroids (BRs) regulate growth in part through altering the properties of the cell wall, the extracellular matrix of plant cells. Conversely, cell wall signalling connects the state of cell wall homeostasis to the BR receptor complex and modulates BR activity. Here we report that both pectin-triggered cell wall signalling and impaired BR signalling result in altered cell wall orientation in the Arabidopsis root meristem. BR-induced defects in the orientation of newly placed walls are associated with aberrant localization of the cortical division zone but with normal specification of its positioning. Tissue- specific perturbations of BR signalling revealed that the cellular malfunction is unrelated to previously described whole organ growth defects. Thus, tissue type separates the pleiotropic effects of cell wall/BR signals and highlights their importance during cell wall placement.
Intracellular Oxidative Stress Levels are Significantly Associated with the Green Autofluorescence Intensity of Buthionine Sulfoximine-Treated B16-F10 Cells
Authors: Tang Wanzhi , Ying Weihai 
Published: March 2021

AbstractSince oxidative stress is a critical common pathological factor of numerous diseases, it is critical to find biomarkers for non-invasive evaluations of the levels of oxidative stress in the body. Our previous studies have indicated that epidermal green autofluorescence (AF) is a novel biomarker of this type: The oxidative stress inducer buthionine sulfoximine (BSO) can dose-dependently increase the epidermal green AF of mice, with BSO doses being significantly associated with the AF intensity. However, it is necessary to use skin cell cultures to investigate the mechanisms underlying the relationships between BSO and the green AF intensity. In our current study we found that BSO concentration-dependently increased the green AF intensity of B16-F10 cells a skin cell line, with BSO concentrations being significantly associated with the AF intensity. BSO also concentration-dependently increased the intracellular DCF signals an index of ROS levels. The green AF intensity of the cells was also significantly associated with the intracellular ROS levels. Moreover, we found that the green AF intensity was significantly associated with the cell death induced by BSO. Collectively, our study has provided first evidence indicating that the green AF intensity of skin cells is significantly associated with both intracellular ROS levels and cell death of the skin cells exposed to oxidative stress, which has indicated that green AF is a novel biomarker for both oxidative stress and cell death.
Multitaper Estimates of Phase-Amplitude Coupling
Authors: Lepage Kyle Q. , Fleming Cavan N. , Witcher Mark , Vijayan Sujith 
Published: March 2021

AbstractPhase-amplitude coupling (PAC) is the association of the amplitude of a high-frequency oscillation with the phase of a low-frequency oscillation. In neuroscience, this relationship provides a mechanism by which neural activity might be coordinated between distant regions. The dangers and pitfalls of assessing phase-amplitude coupling with existing statistical measures have been well-documented. The limitations of these measures include: (i) response to non-oscillatory, high-frequency, broad-band activity, (ii) response to high-frequency components of the low-frequency oscillation, (iii) adhoc selection of analysis frequency-intervals, and (iv) reliance upon data shuffling to assess statistical significance. In this work, a multitaper phase-amplitude coupling estimator is proposed that addresses issues (i)-(iv) above. Specifically, issue (i) is addressed by replacing the analytic signal envelope estimator computed using the Hilbert transform with a multitaper estimator that down-weights non-sinusoidal activity using a classical, multitaper super-resolution technique. Issue (ii) is addressed by replacing coherence between the low-frequency and high-frequency components in a standard PAC estimator with multitaper partial coherence, while issue (iii) is addressed with a physical argument regarding meaningful neural oscillation. Finally, asymptotic statistical assessment of the multitaper estimator is introduced to address issue (iv).
Leveraging joint mechanics simplifies the neural control of movement
Authors: Ludvig Daniel , Whitmore Mariah W. , Perreault Eric J. 
Published: March 2021

ABSTRACTBehaviors we perform every day, such as manipulating an object or walking, require precise control of interaction forces between our bodies and the environment. These forces are generated by active muscle contractions, specified by the nervous system, and by joint mechanics, determined by the intrinsic properties of the musculoskeletal system. Depending on behavioral goals, joint mechanics might simplify or complicate control of movement by the nervous system. However, whether humans can exploit joint mechanics to simplify neural control remains unclear. Here we evaluated if leveraging joint mechanics can simplify neural control by comparing performance in three tasks that required subjects to generate specified torques about the ankle during imposed sinusoidal movements; only one task required torques that could be generated by leveraging the intrinsic mechanics of the joint. We developed a novel approach that used continuous estimates of impedance, a quantitative description of joint mechanics, and measures of muscle activity to determine the mechanical and neural contributions to the net ankle torque generated in each motor task. We found that the torque resulting from changes in neural control was reduced when ankle impedance was consistent with the task being performed, resulting in a task that required less muscular effort. Subjects perceived this task to be easier than those that were not consistent with the impedance of the ankle and were able to perform it with the highest level of consistency. These results demonstrate that leveraging the mechanical properties of a joint can simplify task completion and improve performance.KEY POINTSInteracting with our environment requires production of interaction forces, which are generated by muscle contractions, specified by the nervous system, and by joint mechanics, determined by the intrinsic properties of the musculoskeletal system.We assessed whether leveraging joint mechanics can simplify neural control by having subjects complete 3 tasks, only one of which could be accomplished by leveraging joint mechanics.We found that subjects reduced their muscular effort, perceived the task to be easier and completed the task more consistently when the mechanics of the ankle were consistent with the task.These results highlight the importance of considering limb mechanics when interpreting measures of neural control related to movement and may benefit the design of mechanical interfaces that optimize human performance.
On the capacity of putative plant odorant-binding proteins to bind volatile plant isoprenoids
Authors: Giordano Deborah , Facchiano Angelo , D’Auria Sabato , Loreto Francesco 
Published: March 2021

AbstractPlants use odors not only to recruit other organisms for symbioses, but to ‘talk’ to each other. Volatile organic compounds (VOCs) from “emitting” plants inform the “receiving” (listening) plants of impending stresses or simply of their presence. However, the receptors that allow receivers to perceive the volatile cue are elusive. Most likely, plants (as animals) have odorant bind proteins (OBPs), and in fact few OBPs are known to bind “stress-induced” plant VOCs. We investigated whether OBPs may bind volatile constitutive and stress-induced isoprenoids, the most emitted plant VOCs, with well-established roles in plant communication. First, we performed a data base search that generated a list of candidate plant OBPs. Second, we investigatedin silicothe ability of the identified candidate plant OBPs to bind VOCs by molecular simulation experiments. Our results show that monoterpenes can bind the same OBPs that were described to bind other stress-induced VOCs. Whereas, the constitutive hemiterpene isoprene does not bind any investigated OBP and may not have an info-chemical role. We conclude that, as for animal, plant OBPs may bind different VOCs. Despite being generalist and not specialized, plant OBPs may play an important role in allowing plants to eavesdrop messages sent by neighboring plants.