Miracle-dz/UniFAR-FTUs huggingface dataset:
You are what you eat—ecological niche and microhabitat influence venom activity and composition in aquatic bugs

True water bugs (Nepomorpha) are mostly predacious insects that live in aquatic habitats. They use their piercing–sucking mouthparts to inject venomous saliva that facilitates the capture and extra-oral digestion of prey animals, but their venom can also be deployed for defence. In Central Europe, nepomorph species representing different families coexist in the same habitat. However, their feeding ecology, including venom composition and deployment, has not been investigated in detail. We used an integrated proteotranscriptomic and bioactivity-based approach to test whether venom composition and activity differ between four water bug species sharing the same habitat but occupying different ecological niches. We found considerable species-dependent differences in the composition of digestive enzymes and venom components that probably evolved as adaptations to particular food sources, foraging strategies and/or microhabitats. The venom of Corixa punctata differed substantially from that of the three strictly predatory species (Ilyocoris cimicoides, Notonecta glauca and Nepa cinerea), and the abundance of herbivory-associated proteins confirms a mostly plant-based diet. Our findings reveal independent adaptations of the digestive and defensive enzyme repertoires accompanied by the evolution of distinct feeding strategies in aquatic bugs.
Explorando sistemas hamiltonianos: estudo analítico

A double pendulum submitted to external torques is employed to introduce some basic fundamentals of dynamical systems theory to physics undergraduate courses, soon after the student takes the analytical mechanics discipline. This system is a good example for the introduction of such techniques. Hamilton's equations of motion indicate the existence of stationary solutions (equilibrium points) in the phase space of the model. The identification of the nature of these points allows the description of the system dynamics around their linear neighborhood. Moreover, qualitative results obtained in the linear neighborhood of a fixed point are not changed by the introduction of non-vanishing constant external torques. This work emphasizes the analysis of the linear neighborhood of the equilibrium points.
Photomechanical bending mechanics of polydomain azobenzene liquid crystal polymer network films

Glassy, polydomain azobenzene liquid crystal polymer networks (azo-LCNs) have been synthesized, characterized, and modeled to understand composition dependence on large amplitude, bidirectional bending, and twisting deformation upon irradiation with linearly polarized blue-green (440–514 nm) light. These materials exhibit interesting properties for adaptive structure applications in which the shape of the photoresponsive material can be rapidly reconfigured with light. The basis for the photomechanical output observed in these materials is absorption of actinic light by azobenzene, which upon photoisomerization dictates an internal stress within the local polymer network. The photoinduced evolution of the underlying liquid crystal microstructure is manifested as macroscopic deformation of the glassy polymer film. Accordingly, this work examines the polarization-controlled bidirectional bending of highly concentrated azo-LCN materials and correlates the macroscopic output (observed as bending) to measured .
Further results on stability of asynchronous discrete-time linear systems

Focuses on the stability problem of discrete-time asynchronous linear systems, which can be viewed as linear systems with time-varying delays. Within this context, a stronger version of the necessity part of the classical Chazan-Miranker theorem is proved and new results for special classes of system matrices are also presented.
Observability conditions of induction motors at low frequencies

The paper studies the observability conditions for the induction motor. We first review the sufficient condition derived by from the classical geometrical analysis, then we present some particular case where these conditions turn out to be also necessary. The purpose of the paper is to clarify observability problems found in particular when the machine is operating at low frequencies without angular velocity sensor. The observability analysis also clarifies the fact that the observability problems are physically due to low frequency operation conditions, rather than to low rotational speed operation (even if these two cases coincide in absence of torque load).
Within-subject predictors of speech recognition in cochlear implants: A null result

This study examines the predictive relations among a variety of measures of electrode function in multichannel cochlear implant users and that stimulation site’s ability to transmit speech information. A within-subject design was used in which the relative ability of individual channels to transmit speech information was estimated by the correlational method for speech recognition. Individual electrode function measures included behavioral dynamic range, slope of the electrically evoked compound action potential (EAP) input/output function, and EAP recovery from forward masking. No consistent relations were found between any of these measures and the measures of speech transmission.
Throughput properties of a queueing network with distributed dynamic routing and flow control

A queueing network with arbitrary topology, state dependent routing and flow control is considered. Customers may enter the network at any queue and they are routed through it until they reach certain queues from which they may leave the system. The routing is based on local state information. The service rate of a server is controlled based on local state information as well. A distributed policy for routing and service rate control is identified that achieves maximum throughput. The policy can be implemented without knowledge of the arrival and service rates. The importance of flow control is demonstrated by showing that, in certain networks, if the servers cannot be forced to idle, then no maximum throughput policy exists when the arrival rates are not known. Also a model for exchange of state information among neighboring nodes is presented and the network is studied when the routing is based on delayed state information. A distributed policy is shown to achieve maximum throughput in the case of delayed state information. Finally, some implications for deterministic flow networks are discussed.
Broadband echo spectra from euphausiids and copepods

A seven‐octave‐bandwidth echo sounding system [J. Acoust. Soc. Am. 105, 994 (1999)] was used to observe diverse zooplankton along the coast of western Norway during the period 28 April–9 May 1999. Echo spectra were obtained from freshly caught, swimming specimens of the euphausiid Meganyctiphanes norvegica and copepod Calanus finmarchicus ex situ in a tank mounted on the stern deck of R/V Johan Hjort. Echo spectra were also obtained from scatterers in situ at 15‐m depth in the same sea areas where the experimental animals were caught. Pulse compression was used to reduce the risk of analyzing overlapping echoes. All echo spectra were absolute, as the system was calibrated by the standard‐target method using a 10‐mm‐diameter sphere of tungsten carbide with 6% cobalt binder. Comparison of echo spectra over the nominal bandwidth 1600–2600 kHz supports the claim of acoustic classification. Additional evidence is provided by reference to modeling computations [J. Acoust. Soc. Am. 105, 1050 (1999); 105, 1111 (1.
Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis

Deciphering the mechanism of secondary cell wall/SCW formation in plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although transcriptional regulation is essential for SCW formation, little is known about the implication of post-transcriptional mechanisms in this process. Here we report that two bonafide RNA-binding proteins homologous to the animal translational regulator Musashi, MSIL2 and MSIL4, function redundantly to control SCW formation in Arabidopsis. MSIL2/4 interactomes are similar and enriched in proteins involved in mRNA binding and translational regulation. MSIL2/4 mutations alter SCW formation in the fibers, leading to a reduction in lignin deposition, and an increase of 4-O-glucuronoxylan methylation. In accordance, quantitative proteomics of stems reveal an overaccumulation of glucuronoxylan biosynthetic machinery, including GXM3, in the msil2/4 mutant stem. We showed that MSIL4 immunoprecipitates GXM mRNAs, suggesting a novel aspect of SCW regulation, linking post-transcriptional control to the regulation of SCW biosynthesis genes.
Neuron cilia constrain glial regulators to microdomains around distal neurons

Each glia interacts with multiple neurons, but the fundamental logic of whether it interacts with all equally remains unclear. We find that a single sense-organ glia modulates different contacting neurons distinctly. To do so, it partitions regulatory cues into molecular microdomains at specific neuron contact-sites, at its delimited apical membrane. For one glial cue, K/Cl transporter KCC-3, microdomain-localization occurs through a two-step, neuron-dependent process. First, KCC-3 shuttles to glial apical membranes. Second, some contacting neuron cilia repel it, rendering it microdomain-localized around one distal neuron-ending. KCC-3 localization tracks animal aging, and while apical localization is sufficient for contacting neuron function, microdomain-restriction is required for distal neuron properties. Finally, we find the glia regulates its microdomains largely independently. Together, this uncovers that glia modulate cross-modal sensor processing by compartmentalizing regulatory cues into microdomains. Glia across species contact multiple neurons and localize disease-relevant cues like KCC-3. Thus, analogous compartmentalization may broadly drive how glia regulate information processing across neural circuits.
High-level cognition is supported by information-rich but compressible brain activity patterns

Brain activity patterns are highly flexible and often complex, but also highly structured. Here we examined how fundamental properties of brain activity patterns relate to ongoing cognitive processes. To this end, we applied dimensionality reduction algorithms and pattern classifiers to functional neuroimaging data collected as participants listened to a story, temporally scrambled versions of the story, or underwent a resting state scanning session. These experimental conditions were intended to require different depths of processing and inspire different levels of cognitive engagement. We considered two primary aspects of the data. First, we treated the maximum achievable decoding accuracy across participants as an indicator of the “informativeness” of the recorded patterns. Second, we treated the number of features (components) required to achieve a threshold decoding accuracy as a proxy for the “compressibility” of the neural patterns (where fewer components indicate greater compression). Overall, we found that the peak decoding accuracy (achievable without restricting the numbers of features) was highest in the intact (unscrambled) story listening condition. However, the number of features required to achieve comparable classification accuracy was also lowest in the intact story listening condition. Taken together, our work suggests that our brain networks flexibly reconfigure according to ongoing task demands, and that the activity patterns associated with higher-order cognition and high engagement are both more informative and more compressible than the activity patterns associated with lower-order tasks and lower levels of engagement. Significance Statement How our brains respond to ongoing experiences depends on what we are doing and thinking about, among other factors. To study how brain activity reflects ongoing cognition, we examined two fundamental aspects of brain activity under different cognitive circumstances: informativeness and compressibility. Informativeness refers to the extent to which brain patterns are both temporally specific and consistent across different people. Compressibility refers to how robust the informativeness of brain patterns is to dimensionality reduction. Brain activity evoked by higher-level cognitive tasks are both more informative and more compressible than activity evoked by lower-level tasks. Our findings suggest that our brains flexibly reconfigure themselves to optimize different aspects of how they function according to ongoing cognitive demands.
Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming

Below-ground carbon transformations represent a natural climate change mitigation solution, but newly-acquired traits adaptive to climate stress may alter microbial climate feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment at the Harvard Forest Long-term Ecological Research (LTER) site where, for over three decades, soils are continuously heated 5 °C above ambient temperatures. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect trait-based adaptations related to growth and carbon utilization. From our culture collection of soil bacteria isolated from experimental heated and control plots, we sequenced genomes representing taxa dominant in soil communities and sensitive to warming, including independent lineages of Alphaproteobacteria, Actinobacteria, and Betaproteobacteria. We investigated differences in genomic attributes and patterns of functional gene content to identify genetic signatures of adaptation. Comparative pangenomics revealed differently abundant gene clusters with functional annotations related to carbon and nitrogen metabolism. We also observed differences in global codon usage bias between heated and control genomes, suggesting potential adaptive traits related to growth or growth efficiency. This effect was more varied for organisms with fewer 16S rrn operons, suggesting that these organisms experience different selective pressures on growth efficiency. Together, these data illustrate the emergence of lineage-specific traits as well as common ecological-evolutionary microbial responses to climate change.
Pten, Pi3K and PtdIns(3,4,5)P3 dynamics modulate pulsatile actin branching in Drosophila retina morphogenesis

Epithelial remodeling of the Drosophila retina depends on the pulsatile contraction and expansion of apical contacts between the cells that form its hexagonal lattice. Phosphoinositide PI(3,4,5)P3 (PIP3) accumulates around tricellular adherens junctions (tAJs) during contact expansion and dissipates during contraction, but with unknown function. Here we found that manipulations of Pten or Pi3K that either decreased or increased PIP3 resulted in shortened contacts and a disordered lattice, indicating a requirement for PIP3 dynamics and turnover. These phenotypes are caused by a loss of protrusive branched actin, resulting from impaired activity of the Rac1 Rho GTPase and the WAVE regulatory complex (WRC). We additionally found that during contact expansion, Pi3K moves into tAJs to promote the cyclical increase of PIP3 in a spatially and temporally precise manner. Thus, dynamic regulation of PIP3 by Pten and Pi3K controls the protrusive phase of junctional remodeling, which is essential for planar epithelial morphogenesis. Graphical Abstract: Control of contact length by Pi3K, Pten and PIP3. Pi3K regulates the transition from contraction to expansion through its tension-dependent localization to tAJs and modulation of its lipid phosphatase activity. Pten localizes uniformly to regulate PIP3 turnover and attenuate PIP3 production. (A) Tension shortens contacts, concentrates Pi3K at four spots at a distance from tAJs, and inhibits Pi3K’s lipid phosphatase function. (B) High tension ultimately disassembles contractile networks allowing Pi3K to flow toward tAJs, produce PIP3 and activate the WRC to promote actin branching and contact expansion. (C) High protrusion in expanded contacts disperses the WRC and disassembles the branched actin network. (D) Branched actin disassembly allows the assembly and contraction of an actomyosin network, which increases tension and contracts the contact leading to the flow of Pi3K away from tAJs and inhibition of its lipid phosphatase function, thus completing the cycle.
Scaling models of visual working memory to natural images

Over the last few decades, psychologists have developed precise quantitative models of human recall performance in visual working memory (VWM) tasks. However, these models are tailored to a particular class of artificial stimulus displays and simple feature reports from participants (e.g., the color or orientation of a simple object). Our work has two aims. The first is to build models that explain people’s memory errors in continuous report tasks with natural images. Here, we use image generation algorithms to generate continuously varying response alternatives that differ from the stimulus image in natural and complex ways, in order to capture the richness of people’s stored representations. The second aim is to determine whether models that do a good job of explaining memory errors with natural images also explain errors in the more heavily studied domain of artificial displays with simple items. We find that: (i) features taken from state-of-the-art deep encoders predict trial-level difficulty in natural images better than several reasonable baselines; and (ii) the same visual encoders can reproduce set-size effects and response bias curves in the artificial stimulus domains of orientation and color. Moving forward, our approach offers a scalable way to build a more generalized understanding of VWM representations by combining recent advances in both AI and cognitive modeling.
Goal-Oriented Mesh Adaptivity for Fluid-Structure Interaction with Application to Heart-Valve Settings

We apply a ﬂuid-structure interaction method to simulate prototypical dynamics of the aortic heart-valve. Our method of choice is based on a monolithic coupling scheme for ﬂuid-structure interactions in which the ﬂuid equations are rewritten in the ‘arbitrary Lagrangian Eulerian’ (ALE) framework. To prevent the backﬂow of structure waves because of their hyperbolic nature, a damped structure equation is solved on an artiﬁcial layer that is used to prolongate the computational domain. The increased computational cost in the presence of the artiﬁcial layer is resolved by using local mesh adaption. In particular, heuristic mesh reﬁnement techniques are compared to rigorous goal-oriented mesh adaption with the dual weighted residual (DWR) method. A version of this method is developed for stationary settings. For the nonstationary test cases the indicators are obtained by a heuristic error estimator, which has a good performance for the measurement of wall stresses. The results for prototypical problems demonstrate that heart-valve dynamics can be treated with our proposed concepts and that the DWR method performs best with respect to a certain target functional.
Hidden from plain sight: Novel Chlamydiota diversity emerging from screening genomic and metagenomic data

Chlamydiota are an ancient and hyperdiverse Phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae genomes from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 genomes respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names ‘Candidatus Sacchlamydia’ (Family Rhabdochlamydiaceae) and ‘Candidatus Amphrikania’ (Family Simkaniaceae), as well as a third new clade of environmental MAGs ‘Candidatus Acheromydia’ (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, we observe great predicted diversity in Parachlamydiales metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade. Graphical Abstract
Space-to-Space Power Beaming Enabling High Performance Rapid Geocentric Orbit Transfer

The use of electric propulsion is more prevalent than ever, with industry pursuing all electric orbit transfers. Electric propulsion provides high mass utilization through efficient propellant transfer. However, the transfer times become detrimental as the delta V transitions from near-impulsive to low-thrust. Increasing power and therefore thrust has diminishing returns as the increasing mass of the power system limits the potential acceleration of the spacecraft. By using space-to-space power beaming, the power system can be decoupled from the spacecraft and allow significantly higher spacecraft alpha (W/kg) and therefore enable significantly higher accelerations while maintaining high performance. This project assesses the efficacy of space-to-space power beaming to enable rapid orbit transfer while maintaining high mass utilization. Concept assessment requires integrated techniques for low-thrust orbit transfer steering laws, efficient large-scale rectenna systems, and satellite constellation configuration optimization. This project includes the development of an integrated tool with implementation of IPOPT, Q-Law, and power-beaming models. The results highlight the viability of the concept, limits and paths to infusion, and comparison to state-of-the-art capabilities. The results indicate the viability of power beaming for what may be the only approach for achieving the desired transit times with high specific impulse.