Oscillatory architecture of memory circuits

The coordinated activity between remote brain regions underlies cognition and memory function. Although neuronal oscillations have been proposed as a mechanistic substrate for the coordination of information transfer and memory consolidation during sleep, little is known about the mechanisms that support the widespread synchronization of brain regions and the relationship of neuronal dynamics with other bodily rhythms, such as breathing. During exploratory behavior, the hippocampus and the prefrontal cortex are organized by theta oscillations, known to support memory encoding and retrieval, while during sleep the same structures are dominated by slow oscillations that are believed to underlie the consolidation of recent experiences. The expression of conditioned fear and extinction memories relies on the coordinated activity between the mPFC and the basolateral amygdala (BLA), a neuronal structure encoding associative fear memories. However, to date, the mechanisms allowing this long-range network synchronization of neuronal activity between the mPFC and BLA during fear behavior remain virtually unknown. Using a combination of extracellular recordings and open- and closed-loop optogenetic manipulations, we investigated the oscillatory and coding mechanisms mediating the organization and coupling of the limbic circuit in the awake and asleep brain, as well as during memory encoding and retrieval. We found that freezing, a behavioral expression of fear, is tightly associated with an internally generated brain state that manifests in sustained 4Hz oscillatory dynamics in prefrontal-amygdala circuits. 4Hz oscillations accurately predict the onset and termination of the freezing state. These oscillations synchronize prefrontal-amygdala circuits and entrain neuronal activity to dynamically regulate the development of neuronal ensembles. This enables the precise timing of information transfer between the two structures and the expression of fear responses. Optogenetic induction of prefrontal 4Hz oscillations promotes freezing behavior and the formation of long-lasting fear memory, while closed-loop phase specific manipulations bidirectionally modulate fear expression. Our results unravel a physiological signature of fear memory and identify a novel internally generated brain state, characterized by 4Hz oscillations. This oscillation enables the temporal coordination and information transfer in the prefrontal-amygdala circuit via a phase-specific coding mechanism, facilitating the encoding and expression of fear memory. In the search for the origin of this oscillation, we focused our attention on breathing, the most fundamental and ubiquitous rhythmic activity in life. Using large-scale extracellular recordings from a number of structures, including the medial prefrontal cortex, hippocampus, thalamus, amygdala and nucleus accumbens in mice we identified and characterized the entrainment by breathing of a host of network dynamics across the limbic circuit. We established that fear-related 4Hz oscillations are a state-specific manifestation of this cortical entrainment by the respiratory rhythm. We characterized the translaminar and transregional profile of this entrainment and demonstrated a causal role of breathing in synchronizing neuronal activity and network dynamics between these structures in a variety of behavioral scenarios in the awake and sleep state. We further revealed a dual mechanism of respiratory entrainment, in the form of an intracerebral corollary discharge that acts jointly with an olfactory reafference to coordinate limbic network dynamics, such as hippocampal ripples and cortical UP and DOWN states, involved in memory consolidation. Respiration provides a perennial stream of rhythmic input to the brain. In addition to its role as the condicio sine qua non for life, here we provide evidence that breathing rhythm acts as a global pacemaker for the brain, providing a reference signal that enables the integration of exteroceptive and interoceptive inputs with the internally generated dynamics of the hippocampus and the neocortex. Our results highlight breathing, a perennial rhythmic input to the brain, as an oscillatory scaffold for the functional coordination of the limbic circuit, enabling the segregation and integration of information flow across neuronal networks

Breathing coordinates cortico-hippocampal dynamics in mice during offline states

Network dynamics have been proposed as a mechanistic substrate for the information transfer across cortical and hippocampal circuits. However, little is known about the mechanisms that synchronize and coordinate these processes across widespread brain regions during offline states. Here we address the hypothesis that breathing acts as an oscillatory pacemaker, persistently coupling distributed brain circuit dynamics. Using large-scale recordings from a number of cortical and subcortical brain regions in behaving mice, we uncover the presence of an intracerebral respiratory corollary discharge, that modulates neural activity across these circuits. During offline states, the respiratory modulation underlies the coupling of hippocampal sharp-wave ripples and cortical DOWN/UP state transitions, which mediates systems memory consolidation. These results highlight breathing, a perennial brain rhythm, as an oscillatory scaffold for the functional coordination of the limbic circuit that~supports the segregation and integration of information flow across neuronal networks during offline states

CORONAVIRUS (COVID-19) VACCINATION: OPINIONS AND ATTITUDES OF SOCIAL WORKERS. A GREEK NATIONAL SURVEY

There is a general belief that vaccines constitute the most effective form of limiting the spread of diseases and protecting public health. Yet, as highly effective tools as vaccines may be, studies reveal that the rates of support and acceptance of vaccinations during the COVID-19 pandemic from public health personnel in Western countries indicate hesitancy among them. As professional Social Workers are part of the public health personnel who are priority groups for many vaccinations, the present study focused on their opinions and attitudes towards vaccination and their role in motivating their beneficiaries. The purpose of this quantitative Greek National Survey among 771 Social Workers, members of the Association of Social Workers of Greece (ASGLE), who are professionally active in Greece, was to understand and analyze their attitudes towards the available vaccines against COVID-19 and compulsory vaccination. Through the online self-completion questionnaire, which was used for the collection of data, the survey also aimed to evaluate the Social Workers’ knowledge and sources from which they received information about Covid-19, their motivational sources, their views on compulsory vaccination of health professionals and their views on motivating their beneficiaries with regards to vaccination.  Article visualizations

Extending the YAGO Knowledge Graph with Geospatial Knowledge

Η βάση γνώσης YAGO είναι μία από τις μεγαλύτερες βάσεις γνώσεις, που διαθέτουν τα δε- δομένα τους ως ανοιχτά διασυνδεδεμένα δεδομένα. Χωρική πληροφορία, δηλαδή η ανα- παράσταση της τοποθεσίας οντοτήτων με ένα σημείο, προστέθηκε στη δεύτερη έκδοση του YAGO. Σε αυτή τη δουλειά έχουμε ως σκοπό να επεκτείνουμε το γράφο γνώσης του YAGO με ποιοτική γεωχωρική πληροφορία (πολύγωνα και ευθείες), η οποία προέρχεται από πολλαπλές πηγές. Μελετήσαμε δεδομένα τα οποία διανέμονται όχι μόνο από έργα που βασίζονται στον πληθοπορισμό αλλά και από επίσημες πηγές διαφόρων κρατών. Εί- ναι σημαντικό να μην προσθέσουμε στο γράφο γνώσης πληροφορία που ήδη υπάρχει σε αυτόν και γι’ αυτό το λόγο ψάχνουμε συσχετίσεις μεταξύ των οντοτήτων του YAGO και εκείνων που ανήκουν στα σύνολα δεδομένων που εξετάσαμε. Τα αποτελέσματα δείχνουν πως η μεθοδολογία μας παρήγαγε συσχετίσεις με πολύ μεγάλη ακρίβεια. Στο τέλος της εργασίας αυτής παρουσιάζουμε τον επεκταμένο γράφο γνώσης.YAGO is one of the largest knowledge bases that provide their data as Linked Open Data. Spatial information, in the form of points, was introduced in YAGO2, the second version of YAGO. In this work we present an extension of YAGO with qualitative geospatial inform- ation (i.e., polygons and lines), which was extracted from multiple sources. We studied datasets that are provided from crowdsourced projects as well as from official sources of several countries. It is important to point out that we do not introduce duplicate information in the knowledge graph of YAGO, by creating entities that already exist. Hence, at first, we try to match entities of YAGO with the entities of the data sources that we used. Our results show that our methodology produced matches with very high precision. This work is concluded with a demonstration of the extended knowledge graph

Deciphering the molecular mechanism of water boiling at heterogeneous interfaces

Water boiling control evolution of natural geothermal systems is widely exploited in industrial processes due to the unique non-linear thermophysical behavior. Even though the properties of water both in the liquid and gas state have been extensively studied experimentally and by numerical simulations, there is still a fundamental knowledge gap in understanding the mechanism of the heterogeneous nucleate boiling controlling evaporation and condensation. In this study, the molecular mechanism of bubble nucleation at the hydrophilic and hydrophobic solid–water interface was determined by performing unbiased molecular dynamics simulations using the transition path sampling scheme. Analyzing the liquid to vapor transition path, the initiation of small void cavities (vapor bubbles nuclei) and their subsequent merging mechanism, leading to successively growing vacuum domains (vapor phase), has been elucidated. The molecular mechanism and the boiling nucleation sites’ location are strongly dependent on the solid surface hydrophobicity and hydrophilicity. Then simulations reveal the impact of the surface functionality on the adsorbed thin water molecules film structuring and the location of high probability nucleation sites. Our findings provide molecular-scale insights into the computational aided design of new novel materials for more efficient heat removal and rationalizing the damage mechanisms

Diffusion and Gas Flow Dynamics in Partially Saturated Smectites.

Clays and clay rocks are considered good natural and engineered barriers for deep geological disposal of nuclear waste worldwide. Metal corrosion and organic waste degradation in underground repositories generate significant amounts of gas that should be able to migrate through the multibarrier system to avoid potential pressure buildup, which could be compromising the integrity of the barriers and host rocks. The gas is expected to accumulate in larger pores and eventually form an interconnected network. Under such conditions, the migration of gas molecules takes place both in pore water films and gas-filled macropores. Therefore, mass fluxes depend on the distribution of gas molecules between the water-rich and gas-rich phases and their mobility in both compartments. Classical molecular dynamics (MD) simulations were employed to investigate the mobilities of He, H2, CO2, Ar, and CH4 in a Na-montmorillonite mesopore as a function of the degree of saturation, as well as evaluate the hydrodynamic behavior of the pore fluid in partially saturated clays. The diffusivity of the gas molecules was determined by observing the asymptotic behavior of the mean square displacement in the gas-rich phase and at the gas-water interface. The partition coefficient and Gibbs free energy were analyzed to investigate the transfer of gas molecules between the gas-rich and water-rich phases by observing the molecular trajectories as they cross the vapor-liquid interface. The results revealed that the diffusion coefficient in the gas phase increased with increasing gas-filled pore width and converged asymptotically toward the diffusion coefficient in the bulk state. It could be shown that the diffusion coefficient of gas molecules dissolved in the water films remained constant as long as the interacting water surface was in the bulk-liquid-like phase. This behavior changes in very thin water films. It was observed that the partitioning coefficient of gas molecules at the solid-liquid interface is nearly the same as that in the bulk-liquid-like phase. Partitioning is observed to be strongly dependent on the temperature and gas molecular weights. In the second part of the study, nonequilibrium molecular dynamics (NEMD) simulations were performed to investigate the mobility of gases in pressure-driven decoupled gas-phase dynamics (DGPD) and coupled gas and water phase dynamics (CGWPD) in a partially saturated Na-montmorillonite slit mesopore. The dynamic viscosity of the gas phase was calculated from NEMD simulations and indicated that the viscosity of the gas phase was almost the same in both methods (DGPD and CGWPD). The average slip length for gas molecules at the gas-water interface was also calculated, revealing that the slip-free boundary condition assumed in continuum models is generally invalid for microfluidics and that a slip boundary condition exists at the microscale for specific surface interactions. Finally, a Bosanquet-type equation was developed to predict the diffusion coefficient and dynamic viscosity of gas as a function of the average pore width, gas mean-free path, geometric factor, and thickness of the adsorbed water film

GeoTriples: Transforming geospatial data into RDF graphs using R2RML and RML mappings

A lot of geospatial data has become available at no charge in many countries recently. Geospatial data that is currently made available by government agencies usually do not follow the linked data paradigm. In the few cases where government agencies do follow the linked data paradigm (e.g., Ordnance Survey in the United Kingdom), specialized scripts have been used for transforming geospatial data into RDF. In this paper we present the open source tool GeoTriples which generates and processes extended R2RML and RML mappings that transform geospatial data from many input formats into RDF. GeoTriples allows the transformation of geospatial data stored in raw files (shapefiles, CSV, KML, XML, GML and GeoJSON) and spatially-enabled RDBMS (PostGIS and MonetDB) into RDF graphs using well-known vocabularies like GeoSPARQL and stSPARQL, but without being tightly coupled to a specific vocabulary. GeoTriples has been developed in European projects LEO and Melodies and has been used to transform many geospatial data sources into linked data. We study the performance of GeoTriples experimentally using large publicly available geospatial datasets, and show that GeoTriples is very efficient and scalable especially when its mapping processor is implemented using Apache Hadoop

Water-Ecosystems-Food nexus security achievement in the context of climate change: the case study of an agricultural Mediterranean Basin, Greece

Natural resources conservation is considered indispensable for a sustainable future. A thorough managerial analysis of the current and future conservation and availability to meet future demands is both necessary and challenging. As water of adequate quantity and good quality is required for a favourable condition of natural ecosystems and for agricultural production, a comprehensive analysis which would consider hydrological, environmental and agricultural dimensions is needed to properly address their interactions and potential impacts. This study presents a Water-Ecosystems-Food (WEF) nexus methodological flamework aiming at identification and mitigation of critical challenges. The framework is tested in a highly productive water basin in north Greece, the Kokkinorema River Bain, which is also characterised by intense agriculture practices. The presented methodological approach was developed in the context of a natural resources sustainability scheme adapted by the national funded AgroClim project. The selection and prioritisation of the most efficient measures, including Nature-based Solutions, would be driven by a Decision Support System (DSS) tool which will feed upon ecological, social, economic and legislative information. The proposed DSS will also incorporate future climate scenarios to evaluate and address expected future water scarcity, ecosystems degradation and reduced agricultural productivity issues. The proposed methodology for addressing nexus challenges could be transferred to any other natural resources-stressed water basin with similar characteristics

STAMINA: Bioinformatics Platform for Monitoring and Mitigating Pandemic Outbreaks

This paper presents the components and integrated outcome of a system that aims to achieve early detection, monitoring and mitigation of pandemic outbreaks. The architecture of the platform aims at providing a number of pandemic-response-related services, on a modular basis, that allows for the easy customization of the platform to address user’s needs per case. This customization is achieved through its ability to deploy only the necessary, loosely coupled services and tools for each case, and by providing a common authentication, data storage and data exchange infrastructure. This way, the platform can provide the necessary services without the burden of additional services that are not of use in the current deployment (e.g., predictive models for pathogens that are not endemic to the deployment area). All the decisions taken for the communication and integration of the tools that compose the platform adhere to this basic principle. The tools presented here as well as their integration is part of the project STAMINA

Re-thinking the Etiological Framework of Neurodegeneration

Neurodegenerative diseases are among the leading causes of disability and death worldwide. The disease-related socioeconomic burden is expected to increase with the steadily increasing life expectancy. In spite of decades of clinical and basic research, most strategies designed to manage degenerative brain diseases are palliative. This is not surprising as neurodegeneration progresses "silently" for decades before symptoms are noticed. Importantly, conceptual models with heuristic value used to study neurodegeneration have been constructed retrospectively, based on signs and symptoms already present in affected patients;a circumstance that may confound causes and consequences. Hence, innovative, paradigm-shifting views of the etiology of these diseases are necessary to enable their timely prevention and treatment. Here, we outline four alternative views, not mutually exclusive, on different etiological paths toward neurodegeneration. First, we propose neurodegeneration as being a secondary outcome of a primary cardiovascular cause with vascular pathology disrupting the vital homeostatic interactions between the vasculature and the brain, resulting in cognitive impairment, dementia, and cerebrovascular events such as stroke. Second, we suggest that the persistence of senescent cells in neuronal circuits may favor, together with systemic metabolic diseases, neurodegeneration to occur. Third, we argue that neurodegeneration may start in response to altered body and brain trophic interactions established via the hardwire that connects peripheral targets with central neuronal structures or by means of extracellular vesicle (E\-mediated communication. Lastly, we elaborate on how lifespan body dysbiosis may be linked to the origin of neurodegeneration. We highlight the existence of bacterial products that modulate the gut-brain axis causing neuroinflammation and neuronal dysfunction. As a concluding section, we end by recommending research avenues to investigate these etiological paths in the future. We think that this requires an integrated, interdisciplinary conceptual research approach based on the investigation of the multimodal aspects of physiology and pathophysiology. It involves utilizing proper conceptual models, experimental animal units, and identifying currently unused opportunities derived from human data. Overall, the proposed etiological paths and experimental recommendations will be important guidelines for future cross-discipline research to overcome the translational roadblock and to develop causative treatments for neurodegenerative diseases