Towards Next Generation Neural Interfaces: Optimizing Power, Bandwidth and Data Quality

In this paper, we review the state-of-the-art in neural interface recording architectures. Through this we identify schemes which show the trade-off between data information quality (lossiness), computation (i.e. power and area requirements) and the number of channels. These trade-offs are then extended by considering the front-end amplifier bandwidth to also be a variable. We therefore explore the possibility of band-limiting the spectral content of recorded neural signals (to save power) and investigate the effect this has on subsequent processing (spike detection accuracy). We identify the spike detection method most robust to such signals, optimize the threshold levels and modify this to exploit such a strategy.Accepted versio

Sources of water-soluble Brown Carbon at a South-Eastern European Site

Atmospheric brown carbon (BrC) is a highly uncertain, but potentially important contributor to light absorption in the atmosphere. Laboratory and field studies have shown that BrC can be produced from multiple sources, including primary emissions from fossil fuel combustion and biomass burning (BB), as well as secondary formation through a number of reaction pathways. It is currently thought that the dominant source of atmospheric BrC is primary emissions from BB, but relatively few studies demonstrate this in environments with complex source profiles. A field campaign was conducted during a month-long wintertime period in 2020 on the campus of the University of Peloponnese in the southwest of Patras, Greece which represents an urban site. During this time, ambient filter samples (a total of 35 filters) were collected from which the water-soluble BrC was determined using a semi-automated system similar to Hecobian et al. (2010), where absorption was measured over a 1 m path length. To measure the BrC, a UV-Vis Spectrophotometer was coupled to a Liquid Waveguide Capillary Cell and the light absorption intensity was recorded at 365 and 700 nm. The latter was used as a reference wavelength. We found that the average BrC absorption in Patras at a wavelength of 365 nm was 8.5 ± 3.9 Mm-1 suggesting that there was significant BrC in the organic aerosol during this period. Attribution of sources of BrC was done using simultaneous chemical composition data observations (primarily organic carbon, black carbon, and nitrate) combined with Positive Matrix Factorization analysis. This analysis showed that in addition to the important role of biomass burning (a contribution of about 20%) and other combustion emissions (also close to 20%), oxidized organic aerosol (approximately 40%) is also a significant contributor to BrC in the study area. Reference Hecobian, A., Zhang, X., Zheng, M., Frank, N., Edgerton, E.S., Weber, R.J., 2010. Water-soluble organic aerosol material and the light-absorption characteristics of aqueous extracts measured over the Southeastern United States. Atmos. Chem. Phys. 10, 5965–5977. https://doi.org/10.5194/acp-10-5965-201

Oxidative Potential of Atmospheric Particles at an Eastern Mediterranean Site

Aerosol oxidative potential (OP; the inherent ability of ambient particles to generate reactive oxygen species in vivo) may be linked to the health effects of population exposure to aerosol and is a metric of their toxicity. The goal of this work was to quantify the water-soluble OP of particles in an urban area in Patras, Greece and to investigate its links with source emissions or components of this particulate matter (PM). A field campaign was conducted during a monthlong wintertime period in 2020 (January 10 to February 13) on the campus of the University of Peloponnese in the southwest of Patras. During this time, ambient filter samples (a total of 35 filters) were collected. To measure the water-soluble OP we used a semiautomated system similar to Fang et al. (2015) based on the dithiothreitol (DTT) assay. The accuracy of our system was validated by measuring the DTT activity of 11 phenanthrequinone (PQN) solutions on both our system and the identical semi-automated validated system at the National Observatory of Athens (NOA). These two sets of analysed DTT activities (current vs. NOA system) were significantly correlated (R2=0.99) with a slope of 1.15 ± 0.04 and an intercept close to zero. We found that the average water-soluble OP in Patras was 1.5 ± 0.3 nmol min-1 m-3, ranging from 0.7 to 2 nmol min-1 m-3. The OP measured in Patras during the campaign is higher than reported values from similar wintertime studies in other urban areas such as Athens (Paraskevopoulou et al., 2019). The average watersoluble OP during a summer study for Patras was significantly lower and equal to 0.18 ± 0.02 nmol min-1 m- 3. Taking into account the average PM1 mass concentrations for these two periods (summer: 6 μg m-3 and winter: 23 μg m-3) it is clear that the increase in OP was two times the increase in PM mass making the wintertime aerosol more toxic. Additionally, the water-soluble brown carbon (BrC) was determined using an offline semi-automated system, where absorption was measured over a 1 m path length. The average BrC absorption in Patras at a wavelength of 365 nm was 8.6 ± 3.9 Mm-1 suggesting that there was significant BrC in the organic aerosol during this period. The coefficients of determination, R2, in Table 1 are used as a metric of the potential relationships between the various carbonaceous aerosol components and the DTT activity. The results suggest that the OP is not dominated by a single source or component, but that there are multiple components contributing to it during the study period. Interestingly, the highest correlation coefficient (R2 = 0.46) was found between the OP and Brown Carbon. This is consistent with recently published results for an urban site in Atlanta where the oxidative potential measured with the DTT method also had stronger correlations with BrC during the winter (Gao et al., 2020)

Single synapse glutamate imaging reveals multiple levels of release mode regulation in mammalian synapses

Mammalian central synapses exhibit vast heterogeneity in signaling strength. In order to understand the extent of this diversity, how it is achieved, and its functional implications, characterization of a large number of individual synapses is required. Using glutamate imaging, we characterized the evoked release probability and spontaneous release frequency of over 24,000 individual synapses. We found striking variability and no correlation between action potential-evoked and spontaneous synaptic release strength, suggesting distinct regulatory mechanisms. Subpixel localization of individual evoked and spontaneous release events reveals tight spatial regulation of evoked release and enhanced spontaneous release outside of evoked release region. Using on-stage post hoc immune-labeling of vesicle-associated proteins, Ca(2+)-sensing proteins, and soluble presynaptic proteins we were able to show that distinct molecular ensembles are associated with evoked and spontaneous modes of synaptic release

Sources and processes that control the submicron organic aerosol composition in an urban Mediterranean environment (Athens): a high temporal-resolution chemical composition measurement study

Submicron aerosol chemical composition was studied during a year-long period (26 July 2016–31 July 2017) and two wintertime intensive campaigns (18 December 2013–21 February 2014 and 23 December 2015–17 February 2016), at a central site in Athens, Greece, using an Aerosol Chemical Speciation Monitor (ACSM). Concurrent measurements included a particle-into-liquid sampler (PILS-IC), a scanning mobility particle sizer (SMPS), an AE-33 Aethalometer, and ion chromatography analysis on 24 or 12&thinsp;h filter samples. The aim of the study was to characterize the seasonal variability of the main submicron aerosol constituents and decipher the sources of organic aerosol (OA). Organics were found to contribute almost half of the submicron mass, with 30&thinsp;min resolution concentrations during wintertime reaching up to 200&thinsp;µg&thinsp;m−3. During winter (all three campaigns combined), primary sources contributed about 33&thinsp;% of the organic fraction, and comprised biomass burning (10&thinsp;%), fossil fuel combustion (13&thinsp;%), and cooking (10&thinsp;%), while the remaining 67&thinsp;% was attributed to secondary aerosol. The semi-volatile component of the oxidized organic aerosol (SV-OOA; 22&thinsp;%) was found to be clearly linked to combustion sources, in particular biomass burning; part of the very oxidized, low-volatility component (LV-OOA; 44&thinsp;%) could also be attributed to the oxidation of emissions from these primary combustion sources. These results, based on the combined contribution of biomass burning organic aerosol (BBOA) and SV-OOA, indicate the importance of increased biomass burning in the urban environment of Athens as a result of the economic recession. During summer, when concentrations of fine aerosols are considerably lower, more than 80&thinsp;% of the organic fraction is attributed to secondary aerosol (SV-OOA 31&thinsp;% and LV-OOA 53&thinsp;%). In contrast to winter, SV-OOA appears to result from a well-mixed type of aerosol that is linked to fast photochemical processes and the oxidation of primary traffic and biogenic emissions. Finally, LV-OOA presents a more regional character in summer, owing to the oxidation of OA over the period of a few days.</p

Evaluation of the CO2 Storage Capacity in Sandstone Formations from the Southeast Mesohellenic trough (Greece)

This study investigates the capability of the Southeast Mesohellenic Trough (SE MHT) sandstone formations to serve as a potential reservoir for CO2 storage in response to the emerging climate change issues by promoting environmentally friendly mineral sequestration applications. Sandstone samples, for the first time, were evaluated for their petrographic characteristics, mineral chemistry, geochemical properties, as well as their petrophysical and gas adsorption properties through tests. The sandstones were tested and classified into distinct groups. The most promising site to be considered for pilot CO2 storage testing is the Pentalofos Formation locality since its sandstones display specific mineral phases with the proper modal composition to conceivably react with injected CO2, leading to the development of newly formed and stable secondary mineral phases. The gas adsorption results are also more encouraging for sandstones from this sedimentary formation. All the measured UCS (uniaxial compressive strength), Ei (bending stiffness), and ν (Poisson’s ratio) results are above those dictated by international standards to perform CO2 storage practices safely. Furthermore, the specified targeted locality from the Pentalofos Formation holds the geological advantage of being overlaid by an impermeable cap-rock formation, making it suitable for deploying CO2 mineralization practices. The demarcated area could permanently store a calculated amount of ~50 × 105 tons of CO2 within the geological reservoir by reacting with the specified mineral phases, as specified through the proposed petrographic PrP index (potential reactive phases)

Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes.

Background: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study, we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients and in combination with bioinformatics analysis to evaluate the utility of selected differentially expressed miRNAs in the serum as potential OA biomarkers. Methods: Serum samples were collected from 12 primary OA patients, and 12 healthy individuals were screened using the Agilent Human miRNA Microarray platform interrogating 2549 miRNAs. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative real-time PCR (qRT-PCR) in all serum and in articular cartilage samples from OA patients (n = 12) and healthy individuals (n = 7). Bioinformatics analysis was used to investigate the involved pathways and target genes for the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to controls. Two hundred and five miRNAs (73.5%) were upregulated and 74 (26.5%) downregulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC) > 0.8 and p < 0.05. Bioinformatics analysis in the 77 miRNAs revealed that their target genes were involved in multiple signaling pathways associated with OA, among which FoxO, mTOR, Wnt, pI3K/akt, TGF-β signaling pathways, ECM-receptor interaction, and fatty acid biosynthesis. qRT-PCR validation in seven selected out of the 77 miRNAs revealed 3 significantly downregulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p, and hsa-miR-140-3p) in the serum of OA patients, which were in silico predicted to be enriched in pathways involved in metabolic processes. Target-gene analysis of hsa-miR-140-3p, hsa-miR-33b-3p, and hsa-miR-671-3p revealed that InsR and IGFR1 were common targets of all three miRNAs, highlighting their involvement in regulation of metabolic processes that contribute to OA pathology. Hsa-miR-140-3p and hsa-miR-671-3p expression levels were consistently downregulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A serum miRNA signature was established for the first time using high density resolution miR-arrays in OA patients. We identified a three-miRNA signature, hsa-miR-140-3p, hsa-miR-671-3p, and hsa-miR-33b-3p, in the serum of OA patients, predicted to regulate metabolic processes, which could serve as a potential biomarker for the evaluation of OA risk and progression.Peer reviewedFinal Published versio

Mammalian deltavirus without hepadnavirus coinfection in the neotropical rodent Proechimys semispinosus.

Hepatitis delta virus (HDV) is a human hepatitis-causing RNA virus, unrelated to any other taxonomic group of RNA viruses. Its occurrence as a satellite virus of hepatitis B virus (HBV) is a singular case in animal virology for which no consensus evolutionary explanation exists. Here we present a mammalian deltavirus that does not occur in humans, identified in the neotropical rodent species Proechimys semispinosus The rodent deltavirus is highly distinct, showing a common ancestor with a recently described deltavirus in snakes. Reverse genetics based on a tandem minus-strand complementary DNA genome copy under the control of a cytomegalovirus (CMV) promoter confirms autonomous genome replication in transfected cells, with initiation of replication from the upstream genome copy. In contrast to HDV, a large delta antigen is not expressed and the farnesylation motif critical for HBV interaction is absent from a genome region that might correspond to a hypothetical rodent large delta antigen. Correspondingly, there is no evidence for coinfection with an HBV-related hepadnavirus based on virus detection and serology in any deltavirus-positive animal. No other coinfecting viruses were detected by RNA sequencing studies of 120 wild-caught animals that could serve as a potential helper virus. The presence of virus in blood and pronounced detection in reproductively active males suggest horizontal transmission linked to competitive behavior. Our study establishes a nonhuman, mammalian deltavirus that occurs as a horizontally transmitted infection, is potentially cleared by immune response, is not focused in the liver, and possibly does not require helper virus coinfection

PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures

Motivation: MicroRNAs (miRNAs) are short single-stranded non-coding molecules that usually function as negative regulators to silence or suppress gene expression. Due to interested in the dynamic nature of the miRNA and reduced microarray and sequencing costs, a growing number of researchers are now measuring high-dimensional miRNAs expression data using repeated or multiple measures in which each individual has more than one sample collected and measured over time. However, the commonly used site-by-site multiple testing may impair the value of repeated or multiple measures data by ignoring the inherent dependent structure, which lead to problems including underpowered results after multiple comparison correction using false discovery rate (FDR) estimation and less biologically meaningful results. Hence, new methods are needed to tackle these issues. Results: We propose a penalized regression model incorporating grid search method (PGS), for analyzing association study of high-dimensional microRNA expression data with repeated measures. The development of this analytical framework was motivated by a real-world miRNA dataset. Comparisons between PGS and the site-by-site testing revealed that PGS provided smaller phenotype prediction errors and higher enrichment of phenotype-related biological pathways than the site-by-site testing. Simulation study showed that PGS provided more accurate estimates and higher sensitivity than site-by-site testing with comparable specificities. Availability: R source code for PGS algorithm, implementation example, and simulation study are available for download at https://github.com/feizhe/PGS

Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases

Background: Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we sought to examine the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. // Methods: Sera were collected from JIA (n=118), JDM (n=49) and JSLE (n=30) patients, and from healthy control (n=54) children and adolescents, prior to the coronavirus disease-19 (COVID-19) pandemic. We employed sensitive flow cytometry-based assays to determine titres of antibodies that reacted with the spike and nucleoprotein of HCoV-OC43 and cross-reacted with the spike and nucleoprotein of SARS-CoV-2, and compared with respective titres in sera from patients with multisystem inflammatory syndrome in children and adolescents (MIS-C). // Findings: Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients maintained comparable or stronger humoral responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. // Conclusions: Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies