Miracle-dz/UniFAR-FTUs huggingface dataset:
Aerothermoacoustic Response of Shape Memory Alloy Hybrid Composite Panels

theacousticexcitationisconsideredtobeawhite-Gaussianrandompressurewithzeromeananduniformmagnitude over the panel surface. Nonlinear temperature-dependence of material properties is considered in the formulation. The dynamic nonlinear equations of motion are transformed to modal coordinates to reduce the computational efforts. The Newton–Raphson iteration method is employed to obtain the dynamic response at each time step of the Newmark numerical integration scheme. Finally, the nonlinear response of a shape memory alloy hybrid composite panel is presented, illustrating the effect of shape memory alloy fiber embeddings, aerodynamic pressure, sound pressure level, and temperature rise on the panel response.
Metabolomic characterization of behaviorally manipulated ants with multiomic data integration

9 Parasitically manipulated Camponotus floridanus ants show multiple diseased behaviors and a 10 fatal summiting phenotype when infected by Ophiocordyceps camponoti-floridani fungi. Altered host 11 behavior as a response to and driven by parasites occur in a broad swath of taxa. In many cases, such as 12 this interaction, the underlying mechanisms have not yet been clearly characterized. The drastic 13 phenotypic changes observed could in some cases reflect large physiological changes within cells, 14 spanning different molecular levels from nucleic acids to metabolites. Here, we link existing genomic and 15 transcriptomic data to a new metabolomic dataset we produced to hypothesize on the mechanisms of 16 manipulated “zombie ants” from a multiomic perspective. Multiple lines of evidence point toward 17 dysregulation of neurotransmitters and neuronal signaling. We propose that these processes are altered 18 during infection and manipulation based on: neurotransmitter synthesis and receptor gene expression, 19 altered metabolite abundances, with plausible behavioral ties to known effects of these neurotransmitters 20 in ants and other insects, and possible suppression of a connected immunity pathway. We additionally 21 report signals for fungal metabolic activity during manipulation and early evidence for alterations of host 22 processes related to detoxification, anti-stress protectants, and insect hormone metabolism.
A generative model of memory construction and consolidation

Episodic memories are (re)constructed, combining unique features with familiar schemas, share neural substrates with imagination, and show schema-based distortions that increase with consolidation. Here we present a computational model in which hippocampal replay (from an autoassociative network) trains generative models (variational autoencoders) in neo-cortex to (re)create sensory experiences via latent variable representations in entorhinal, medial prefrontal, and anterolateral temporal cortices. Simulations show effects of memory age and hippocampal lesions in agreement with previous models, but also provide mechanisms for se-mantic memory, imagination, episodic future thinking, relational inference, and schema-based distortions including boundary extension. The model explains how unique sensory and predict-able conceptual or schematic elements of memories are stored and reconstructed by efficiently combining both hippocampal and neocortical systems, optimising the use of limited hippocam-pal storage for new and unusual information. Overall, we believe hippocampal replay training neocortical generative models provides a comprehensive account of memory construction, ima-gination and consolidation.
On entropy consistency of large time step schemes II: approximate Riemann solvers

It is shown that for scalar conservation laws with a convex flux function any sequence of approximate solutions, constructed by large time step schemes using approximate Riemann solvers as a building block, gives the unique entropy solution in the limit of decreasing mesh size if the Courant number is less than 1. When the curvature of the flux function is nearly constant the above results may be extended to Courant numbers slightly larger than 1.
Evidence of phylosymbiosis in Formica ants

Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes. To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing. We reveal that Formica species and clades harbour highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e. phylosymbiosis, in that related hosts harbour more similar microbial communities. Our analysis also revealed significant correlations between microbe co-occurrences, which suggests that synergistic and antagonistic interactions may contribute to the phylosymbiotic signal. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localisation within the host.
Lévy Processes and Path Integral Methods with Applications in the Energy Markets

The objective of this thesis was to explore methods for valuation of derivatives in energy markets. One aim was to determine whether the Normal inverse Gaussian distributions would be better suited for modelling energy prices than normal distributions. Another aim was to develop working implementations of Path Integral methods for valuing derivatives, based on some one-factor model of the underlying spot price. Energy prices are known to display properties like mean-reversion, periodicity, volatility clustering and extreme jumps. Periodicity and trend are modelled as a deterministic function of time, while mean-reversion effects are modelled with auto-regressive dynamics. It is established that the Normal inverse Gaussian distributions are superior to the normal distributions for modelling the residuals of an auto-regressive energy price model. Volatility clustering and spike behaviour are not reproduced with the models considered here. After calibrating a model to fit real energy data, valuation of derivatives is achieved by propagating probability densities forward in time, applying the Path Integral methodology. It is shown how this can be implemented for European options and barrier options, under the assumptions of a deterministic mean function, mean-reversion dynamics and Normal inverse Gaussian distributed residuals. The Path Integral methods developed compares favourably to Monte Carlo simulations in terms of execution time. The derivative values obtained by Path Integrals are sometimes outside of the Monte Carlo confidence intervals, and the relative error may thus be too large for practical applications. Improvements of the implementations, with a view to minimizing errors, can be subject to further research.
Fine scale sampling reveals spatial heterogeneity of rhizosphere microbiome in young Brachypodium plants

For a deeper and comprehensive understanding of the diversity, composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary across distinct parts of the root giving rise to spatially distinct microbial niches. To address this, we analyzed microbial community from two spatially distinct zones of the primary root (the tip vs. the base) in Brachypodium distachyon, grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a stronger rhizosphere effect in the root base vs. bulk soil compared to the root tips vs. bulk soil, resulting in an enrichment of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, few OTUs belonging to less characterized lineages such as Verrucomicrobia and Acidobacteria. While the microbial community distributions are similar across growth containers, the EcoFAB displayed higher replicate reproducibility. Genome-resolved and bulk metagenomics revealed that genes associated with transcriptional regulation, transport of nutrients and catabolic enzymes indicating active metabolism, biofilm formation and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to the root tips, implying the presence of easily available, labile carbon and nutrients in the rhizosphere relative to bulk soil. Such insights into the relationships between root structure, exudation and microbial communities are critical for developing understanding of plant-microbe interactions.
Transcranial focused ultrasound-mediated neurochemical and functional connectivity changes in deep cortical regions in humans

Low-intensity transcranial ultrasound stimulation (TUS) is an emerging non-invasive technique for focally modulating human brain function. The mechanisms and neurochemical substrates underlying TUS neuromodulation in humans and how these relate to excitation and inhibition are still poorly understood. In 24 healthy controls, we separately stimulated two deep cortical regions and investigated the effects of theta-burst TUS, a protocol shown to increase corticospinal excitability, on the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and functional connectivity. We show for the first time in humans that theta-burst TUS selectively reduces GABA levels in the posterior cingulate, but not the dorsal anterior cingulate cortex. Functional connectivity increased following TUS in both regions. Our findings suggest that TUS changes overall excitability by reducing GABAergic inhibition, that changes in TUS-mediated neuroplasticity last at least 50 minutes after stimulation, and that these effects may be state-dependent – a mechanism increasingly recognized to influence the brain’s response to neuromodulation.
Wolbachia is a nutritional symbiont in Drosophila melanogaster

The intracellular bacterium Wolbachia is a common symbiont of many arthropods and nematodes, well studied for its impacts on host reproductive biology. However, its broad success as a vertically transmitted infection cannot be attributed to manipulations of host reproduction alone. Using the Drosophila melanogaster model and their natively associated Wolbachia strain “wMel”, we show that Wolbachia infection supports fly development and buffers against nutritional stress. Wolbachia infection across several fly genotypes and a range of nutrient conditions resulted in reduced pupal mortality, increased adult emergence, and larger size. We determined that the exogenous supplementation of pyrimidines rescued these phenotypes in the Wolbachia-free, flies suggesting that Wolbachia plays a role in providing this metabolite that is normally limiting for fly growth. Additionally, Wolbachia was sensitive to host pyrimidine metabolism: Wolbachia titers increased upon transgenic knockdown of the Drosophila de novo pyrimidine synthesis pathway but not knockdown of the de novo purine synthesis pathway. We propose that Wolbachia acts as a nutritional symbiont to supplement fly development and enhance host fitness. SIGNIFICANCE STATEMENT Wolbachia is a bacterial symbiont of arthropods and nematodes, well described for its manipulations of arthropod reproduction. However, many have theorized there must be more to this symbiosis, even in well-studied Wolbachia-host relationships such with Drosophila. Reproductive impacts alone cannot explain the success and ubiquity of this bacterium. Here, we use Drosophila melanogaster and their native Wolbachia infections to show that Wolbachia supports fly development and significantly buffers flies against nutritional stress. Additionally, we show that this advantage is likely mediated by pyrimidines. These developmental advantages might help explain the ubiquity of Wolbachia infections.
The scheduling of adolescence with Netrin-1 and UNC5C

Dopamine axons are the only axons known to grow during adolescence. Here, using rodent models, we examined how two proteins, Netrin-1 and its receptor, UNC5C, guide dopamine axons towards the prefrontal cortex and shape behaviour. We demonstrate in mice (Mus musculus) that dopamine axons reach the cortex through a transient gradient of Netrin-1 expressing cells – disrupting this gradient reroutes axons away from their target. Using a seasonal model (Siberian hamsters; Phodopus sungorus) we find that mesocortical dopamine development can be regulated by a natural environmental cue (daylength) in a sexually dimorphic manner – delayed in males, but advanced in females. The timings of dopamine axon growth and UNC5C expression are always phase-locked. Adolescence is an ill-defined, transitional period; we pinpoint neurodevelopmental markers underlying this period.
PPAR-γ is a promising therapeutic target for memory deficits induced by early alcohol exposure

Background Patients diagnosed with fetal alcohol spectrum disorder (FASD) show persistent cognitive disabilities, including memory deficits. However, the neurobiological substrates of these deficits remain unclear. Here, we studied the participation of the expanded endocannabinoid system (ECS), which is known to be affected by alcohol in other life periods, and it is involved in memory impairments of neurodevelopmental disorders. Methods C57BL/6 female mice were exposed to a time-limited access to either water or alcohol to model prenatal and lactation alcohol exposure (PLAE). The expanded ECS was analyzed in the prefrontal cortex and the hippocampus of the offspring at post-partum day (PD) 25 and 70. Then, memory performance was tested after the repeated administration (from PD25 to PD34) of: i) URB597, to increase N-acylethanolamines (NAEs), and GW9662, a peroxisome proliferator-activated receptor gamma (PPAR-γ) antagonist; ii) pioglitazone, a PPAR-γ agonist. Finally, we used a viral approach to upregulate astrocytic PPAR-γ in the hippocampus to restore memory deficits. Results We report that PLAE causes a hippocampal reduction of NAEs and PPAR-γ at PD25. Moreover, URB597 suppresses PLAE-induced memory deficits through PPAR-γ, since its effects are prevented by GW9662. Direct PPAR-γ activation, using pioglitazone, also ameliorates memory impairments. Lastly, we demonstrate that the upregulation of PPAR-γ in hippocampal astrocytes is sufficient to rescue PLAE-induced memory deficits. Conclusion Our data reveal a bidirectional link between memory deficits and expanded ECS alterations in the context of early alcohol exposure. Furthermore, we proved that PPAR-γ in hippocampal astrocytes represents a specific therapeutic target for memory deficits in FASD.
Microbial methane cycling in a landfill on a decadal time scale

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase 69% by the year 2050, there is a pressing need to better understand the biogeochemical processes that control microbial methane cycling in landfills. In this study, we had the rare opportunity to characterize the microbial community responsible for methane cycling in landfill waste covering a 39-year timeframe. We coupled long term geochemical analyses to whole-community DNA (i.e., metagenomic) sequencing and identified key features that shape methane cycling communities over the course of a landfill’s lifecycle. Anaerobic methanogenic microbes are more abundant, diverse, and metabolically versatile in newer waste, fueling rapid methane production early in a landfill’s lifecycle. Aerobic methanotrophs were repeatedly found in leachate where low levels of oxygen were present and exhibited adaptations that aid survival under steep redox gradients in landfills. The potential for anaerobic methane oxidation, which has historically been overlooked despite anoxic habitats dominating landfills, was prevalent in a 26-year-old landfill cell which was in a state of slow methanogenesis. Finally, we identified the metabolic potential for methane oxidation in lineages that are widespread in aquatic and terrestrial habitats, whose capacity to metabolize methane remains poorly characterized. Ultimately, this work expands the diversity of methane cycling guilds in landfills and outlines how these communities can curb methane emissions from municipal solid waste. Significance Microbes are major contributors to methane emissions from solid waste however the temporal dynamics of methane cycling communities in landfills remain poorly understood. We addressed this gap by using whole-community DNA (i.e., metagenomic) approaches to characterize microbial methane cycling in waste covering a 39-year timeframe. We show that methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. We highlight that methane oxidation in the absence of oxygen is overlooked in landfill biogeochemical models and that novel lineages can potentially contribute to methane sinks across a broad range of habitats. These findings can strengthen predictive models for methane cycling in landfills and inform sustainable waste management strategies to curb methane emissions from solid waste.
On Finding K Nearest Neighbors in the Plane

Abstract : The nearest neighbor problem arises in several applications such as density estimation, pattern classification and information retrieval. The problem is to find, among a set of points (or feature vectors), the one which is most similar or closest to a given test point according to some dissimilarity or distance measure. One straightforward way of solving it is to compute the 'distances' between each point of the set and the test point and then search for the point P with minimum distance. The k-nearest neighbor problem to be considered here is a variant of the classical nearest neighbor problem.
The gender gap in university enrolment: evidence from subjective expectations

ABSTRACT In most OECD countries, more women than men enrol in undergraduate degrees. I analyse this gap in enrolment using the elicited subjective beliefs of a sample of 240 17–18-year-olds living in England. I use these beliefs to estimate a discrete choice model. The results from this model can explain the majority of the gender gap in enrolment. Gender differences in preferences over future outcomes rather than differences in subjective beliefs account for most of the gap. An important difference between men and women is women value feeling independent whereas men do not.
Investigation of charge carrier injection in silicon nitride/silicon junctions

Contactless measurements of the conductance of silicon wafers with silicon nitride top layers are presented. The deposition of silicon nitride layers leads to an increase of the conductance, both for p‐Si and n‐Si. This is attributed to the increase of the number of electrons in the Si wafer, in an inversion layer in p‐Si, and in an accumulation layer in n‐Si. Comparison of the increase of the conductance with the fixed charge density in the nitride layer points to a strongly reduced electron mobility in these layers. It is shown that the change of the conductance increases with growing thickness of the nitride layer up to a thickness of 20 nm, whereafter a constant value is attained.
Title: Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius

: Phylogenetic trees are routinely built from huge and yet incomplete multi-locus datasets 10 often leading to multiple equally scoring trees under many common criteria. As typical tree inference software output only a single tree, identifying all trees with identical score challenges phylogenomics. Here, we introduce Gentrius – an efficient algorithm that tackles this problem. We showed on simulated and biological datasets that Gentrius generates millions of trees within seconds. Depending on the distribution of missing data across species and loci and the inferred 15 phylogeny, the number of equally good trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data. One-Sentence
Auroral electrojet activity index AE and its universal time variations.

An index, denoted by AE, is derived as a measure of global electrojet activity. The basic data used are 2.5-minute readings of the H trace in the standard magnetograms from seven auroral-zone observatories. The readings are referenced to a level determined for each observatory from quiet intervals. All the data from the seven observatories are then plotted against UT, and two envelopes are drawn to embrace all the points. The index AE at any epoch is defined by the distance (or separation) between the upper and lower envelopes at that epoch. When viewed as functions of UT the upper and lower envelopes themselves show development and decay of positive and negative variations. It is found that a positive excursion usually accompanies a negative (larger) variation, confirming the well known feature of polar disturbance. The AE index for a 6-day period, February 10–15, 1958, shows that polar disturbances statistically repeat with a time interval of about 4 hours, and that the average duration of their most active phase is a little more than 1 hour. It is pointed out that the average repetition time of 4 hours is comparable with that of the electron flux enhancements observed by Anderson et al. in the magnetosphere tail. It is suggested that polar disturbances are directly related to Anderson's ‘electron islands’ in the magnetosphere tail.
A note on two upwind strategies for RBF‐based grid‐free schemes to solve steady convection–diffusion equations

In this paper, two radial basis function (RBF)‐based local grid‐free upwind schemes have been discussed for convection–diffusion equations. The schemes have been validated over some convection–diffusion problems with sharp boundary layers. It is found that one of the upwind schemes realizes the boundary layers more accurately than the rest. Comparisons with the analytical solutions demonstrate that the local RBF grid‐free upwind schemes based on the exact velocity direction are stable and produce accurate results on domains discretized even with scattered distribution of nodal points. Copyright © 2009 John Wiley & Sons, Ltd.
Dynamics of thermally activated reversal in nonuniformly magnetized single particles

The dynamics of thermally activated reversal in elongated ferromagnetic particles is studied. A micromagnetic model is used which accounts for thermal fluctuations through the addition of a stochastic fluctuation field. Results are given approximating a particle of 5:1 aspect ratio, with exchange length equal to particle radius, which is typical of current particulate media. Fast relaxation of the magnetization is observed. Thermal effective volumes inferred from our results can be significantly less than particle volumes.