Miracle-dz/UniFAR-FTUs huggingface dataset:
Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines

Postsynaptic mitochondria are critical to the development, plasticity, and maintenance of synaptic inputs. However, their relationship to synaptic structure and functional activity is unknown. We examined a correlative dataset from ferret visual cortex with in vivo two-photon calcium imaging of dendritic spines during visual stimulation and electron microscopy (EM) reconstructions of spine ultrastructure, investigating mitochondrial abundance near functionally- and structurally-characterized spines. Surprisingly, we found no correlation to structural measures of synaptic strength. Instead, we found that mitochondria are positioned near spines with orientation preferences that are dissimilar to the somatic preference. Additionally, we found that mitochondria are positioned near groups of spines with heterogeneous orientation preferences. For a subset of spines with mitochondrion in the head or neck, synapses were larger and exhibited greater selectivity to visual stimuli than those without a mitochondrion. Our data suggest mitochondria are not necessarily positioned to support the energy needs of strong spines, but rather support the structurally and functionally diverse inputs innervating the basal dendrites of cortical neurons.
Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes

The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related non-autonomous retrotransposons, so-called Cassandra. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats (LTRs), advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: 1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and 2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host’s specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra’s origin hypotheses (single or multiple) and Cassandra’s possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.
Multiple embryonic sources converge to form the pectoral girdle skeleton in zebrafish

The morphological transformation of the pectoral/shoulder girdle is fundamental to the water-to-land transition in vertebrate evolution. Although previous studies have resolved the embryonic origins of the tetrapod shoulder girdle, those of the fish pectoral girdle remain uncharacterized, creating a gap in the understanding of girdle transformation mechanisms from fish to modern tetrapods. Here, we identified the embryonic origins of the pectoral girdle of zebrafish (Danio rerio), including the cleithrum as an ancestral pectoral girdle element lost in extant tetrapods. Our combinatorial approach of photoconversion and genetic cell lineage tracing mapped that cleithrum development combines three adjoining embryonic populations: cranial neural crest cells and lateral plate mesoderm-derivatives (trunk lateral plate mesoderm and cardiopharyngeal mesoderm-associated cells). The topographical position of the cleithrum at the head/trunk interface is a shared characteristic among cleithrum-bearing fish, thus its multiple embryonic origins are likely a conserved feature. Moreover, a comparison of the pectoral girdle progenitors between aquatic fish and extant amniotes suggests that cleithrum loss is associated with the disappearance of its unique developmental environment by the insertion of the neck lateral plate mesoderm into the head/trunk interface. Overall, our study establishes an embryological framework for pectoral/shoulder girdle formation and their evolutionary trajectories from their origin in water to diversification on land.
Ectopical expression of bacterial collagen-like protein supports its role as adhesin in host-parasite coevolution

For a profound understanding of the mechanisms of antagonistic coevolution, it is necessary to identify the coevolving genes. The spore-forming bacterium Pasteuria ramosa and its host, the microcrustacean Daphnia, are a well-characterized paradigm for co-evolution, but the underlying genes remain largely unknown. A genome-wide association study identified a polymorphic carboxy-terminal globular domain of Pasteuria collagen-like protein 7 (Pcl7) as a candidate mediating parasite attachment and driving its coevolution with the host. Since P. ramosa cannot currently be genetically manipulated, we used Bacillus thuringiensis as a surrogate parasite to express a fusion protein of a Pcl7 carboxy-terminus from P. ramosa and the amino-terminal domain of a B. thuringiensis collagen-like protein. Mutant B. thuringiensis (Pcl7-Bt) spores but not wild-type B. thuringiensis (WT-Bt) spores, attached to the same site of susceptible hosts as P. ramosa. Furthermore, Pcl7-Bt spores attached readily to host genotypes that were susceptible to the P. ramosa clone that was the origin of the Pcl7 C-terminus, but only slightly to resistant host genotypes. These findings indicated that the fusion protein was properly expressed and folded and demonstrated that indeed the C-terminus of Pcl7 mediates attachment in a host genotype-specific manner. These results provide strong evidence for the involvement of a CLP in the coevolution of Daphnia and P. ramosa and opens new avenues for genetic epidemiological studies of host-parasite interactions. 150-word “Importance” paragraph During host-parasite coevolution, hosts evolve to evade the damaging effect of the parasite, while parasites evolve to maximize their benefits by exploiting the host. The genes underlying this coevolution remain largely unknown. For the prime model-system for coevolutionary research, the crustacean Daphnia and the parasite Pasteuria ramosa, collagen-like proteins (CLPs) in Pasteuria were suggested to play a crucial role for host-parasite interactions. Here we report that transferring part of a CLP coding gene from the unculturable P. ramosa to Bacillus thuringiensis (Bt), confirmed the function of this protein as a genotype-specific adhesin to the host’s cuticle. Our finding highlights the importance of a CLP in host-parasite interactions and will enable us to explore the population genetic dynamics of coevolution in this system.
Static and Dynamic Components of the Redshift

We analyse the possibility that the observed cosmological redshift may be cumulatively due to the expansion of the universe and the tired light phenomenon. Since the source of both the redshifts is the same, they both independently relate to the same proper distance of the light source. Using this approach we have developed a hybrid model combining the Einstein de Sitter model and the tired light model that yields a slightly better fit to Supernovae Ia redshift data using one parameter than the standard ΛCDM model with two parameters. We have shown that the ratio of tired light component to the Einstein de Sitter component of redshift has evolved from 2.5 in the past, corresponding to redshift 1000, to its present value of 1.5. The hybrid model yields Hubble constant H0 =69.11(±0.53)km·s-1 ·Mpc-1 and the deceleration parameter q0 =-0.4. The component of Hubble constant responsible for expansion of the universe is 40% of H0 and for the tired light is 60% of H0. Consequently, the critical density is only 16% of its currently accepted value; a lot less dark matter is needed to make up the critical density. In addition, the best data fit yields the cosmological constant density parameter =0. The tired light effect may thus be considered equivalent to the cosmological constant in the hybrid model.
Genetic variability and vector competence of Aedes aegypti populations from Kisumu and Busia Counties, Western Kenya, for Chikungunya and Zika viruses

Aedes aegypti is the primary vector of several arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), yellow fever virus (YFV), and Zika virus (ZIKV). This vector is widespread globally in tropical and subtropical areas, but also found in temperate areas. Kenya experienced its first chikungunya outbreaks in Lamu County in 2004 and later in Mandera: 2016, and Mombasa: 2017. While there is yet to be a report of Zika outbreaks in Kenya, sero-surveillance studies indicate low-level transmission of this virus in coastal and northern parts of the country. Despite the presence of Ae. aegypti in Kisumu and Busia counties in sufficient densities, and free movement of people between the coast and the two western Kenya counties, no outbreaks of either disease have been reported in these regions. To investigate this phenomenon, we collected Ae. aegypti mosquitoes from county headquarter towns near railway stations connecting the coast and western Kenya and reared them under controlled laboratory conditions. The mosquitoes were then assessed for genetic variability using CO1 genes as well as their efficiency to transmit viruses using Laboratory colonies (F1) of the field mosquitoes challenged with an infectious blood meal containing CHIKV and ZIKV. Genetic analysis revealed the presence of both Ae. aegypti subspecies, (Ae. aegypti aegypti [Aaa] and Ae. aegypti formosus [Aaf]) in the two western Kenya counties, with Aaf being dominant (19:8 for Kisumu samples and 25:6 for Busia samples). Additionally, pairwise comparison revealed minimal genetic differentiation (0.62%) between the study populations, with a high genetic variation (99.38%) observed within each population, indicating significant diversity within individual populations. Ae. aegypti populations from Kisumu and Busia counties exhibited competence for CHIKV, with infection, dissemination, and transmission rates of 55.2%, 85.5%, and 27.1% for Kisumu; and 57.8%, 71.8%, and 25% for Busia populations, respectively. There was no significant difference in vector competence between these two populations. Interestingly, neither population was competent for ZIKV. In conclusion, the data shows that the Ae. aegypti populations in the two cities were homogeneous. This could explain the observed similarity in vector competence for CHIKV and ZIKV. Author Summary Our study investigated the genetic variability and vector competence of Ae. aegypti mosquito populations in Kisumu and Busia Counties to CHIKV and ZIKV; revealing the presence and even distribution of both Aaa and Aaf subspecies. We also found that the Ae. aegypti populations from the two counties were not genetically differentiated. Furthermore, our study revealed that the Ae. aegypti mosquitoes from Kisumu and Busia counties were competent for CHIKV but may be refractory to ZIKV infection. These findings highlight the importance of continued monitoring of Ae. aegypti populations and their potential for arboviral disease transmission in the region.
Selective reactivation of value- and place-dependent information during sharp-wave ripples in the intermediate and dorsal hippocampus

Reactivation of place cells during sharp-wave ripples in the hippocampus is important for memory consolidation. However, whether hippocampal reactivation is affected by the values of events experienced by the animal is largely unknown. Here, we investigated whether place cells in the dorsal (dHP) and intermediate (iHP) hippocampus of rats are differentially reactivated depending on the value associated with a place during the learning of places associated with higher-value rewards in a T-maze. Place cells in the iHP representing the high-value location were reactivated significantly more frequently than those representing the low-value location, characteristics not observed in the dHP. In contrast, the activities of place cells in the dHP coding the routes leading to high-value locations were replayed more than those in the iHP. Our findings suggest that value-based differential reactivation patterns along the septotemporal axis of the hippocampus may play essential roles in optimizing goal-directed spatial learning for maximal reward. Teaser Information carried by sharp-wave ripples differ qualitatively between the dorsal and intermediate hippocampal regions.
Posttraumatic reexperiencing and alcohol use: mediofrontal theta as a neural mechanism for negative reinforcement

Objective Over half of US military veterans with posttraumatic stress disorder (PTSD) use alcohol heavily, potentially to cope with their symptoms. This study investigated the neural underpinnings of PTSD symptoms and heavy drinking in veterans. We focused on brain responses to salient outcomes within predictive coding theory. This framework suggests the brain generates prediction errors (PEs) when outcomes deviate from expectations. Alcohol use might provide negative reinforcement by reducing the salience of negatively-valenced PEs and dampening experiences like loss. Methods We analyzed electroencephalography (EEG) responses to unpredictable gain/loss feedback in veterans of Operations Enduring and Iraqi Freedom. We used time-frequency principal components analysis of event-related potentials to isolate neural responses indicative of PEs, identifying mediofrontal theta linked to losses (feedback-related negativity, FRN) and central delta associated with gains (reward positivity, RewP). Results Intrusive reexperiencing symptoms of PTSD were associated with intensified mediofrontal theta signaling during losses, suggesting heightened negative PE sensitivity. Conversely, increased hazardous alcohol use was associated with reduced theta responses, implying a dampening of these negative PEs. The separate delta-RewP component showed associations with alcohol use but not PTSD symptoms. Conclusions Findings suggest a common neural component of PTSD and hazardous alcohol use involving altered PE processing. We suggest that reexperiencing enhances the intensity of salient negative PEs, while chronic alcohol use may reduce their intensity, thereby providing negative reinforcement by muting emotional disruption from reexperienced trauma. Modifying the mediofrontal theta response could address the intertwined nature of PTSD symptoms and alcohol use, providing new avenues for treatment.
Nonparametric Estimation of Risk-Neutral Distribution via the Empirical Esscher Transform ( Estimação

This paper introduces an empirical version of the Esscher transform for nonparametric option pricing. Traditional parametric methods require the formulation of an explicit risk-neutral model and are operational only for a few probability distributions for the returns of the underlying asset. In our proposal, we make only mild assumptions on the pricing kernel and there is no need for the formulation of the risk-neutral model. First, we simulate sample paths for the returns under the physical measure. Then, based on the empirical Esscher transform, the sample is reweighted, giving rise to a risk-neutralized sample from which derivative prices can be obtained by a weighted sum of the options’ payoffs in each path. We analyze our proposal in experiments with artificial and real data.
A restricted nonlinear large eddy simulation model for high Reynolds number flows

ABSTRACT Recent numerical studies of the restricted nonlinear (RNL) model have demonstrated its ability to reproduce important features of wall turbulence despite a severe reduction in the number of degrees of freedom. In these prior studies, the RNL model included full resolution of the viscous term. In this work, we extend the RNL model to arbitrarily high Reynolds numbers by developing a RNL large eddy simulation (LES) framework along with a method to systematically identify an appropriate streamwise wavenumber support based on spectral properties of wall turbulence. This method leads to a band-limited RNL–LES system which is successful in reproducing some of the most important statistical features captured in previous low to moderate Reynolds number simulations, e.g. the mean velocity and second-order moment profiles. The RNL–LES framework offers a new approach to understanding the connection between coherent structures and the momentum transfer mechanisms of wall turbulence at arbitrarily high Reynolds numbers, where resolution of the viscous terms can become computationally expensive even with the relatively low computational complexity afforded through the dynamical restriction of the RNL model.
Abiotic O2 Levels on Planets around F, G, K, and M Stars: Effects of Lightning-produced Catalysts in Eliminating Oxygen False Positives

Over the last few years, a number of authors have suggested that, under certain circumstances, molecular oxygen (O2) or ozone (O3) generated by abiotic processes may accumulate to detectable concentrations in a habitable terrestrial planet’s atmosphere, producing so-called “false positives” for life. But the models have occasionally disagreed with each other, with some predicting false positives, and some not, for the same apparent set of circumstances. We show here that photochemical false positives derive either from inconsistencies in the treatment of atmospheric and global redox balance or from the treatment (or lack thereof) of lightning. For habitable terrestrial planets with even trace amounts of atmospheric N2, NO produced by lightning catalyzes the recombination of CO and O derived from CO2 photolysis and should be sufficient to eliminate all reported false positives. Molecular oxygen thus remains a useful biosignature gas for Earth-like extrasolar planets, provided that the planet resides within the conventional liquid water habitable zone and has not experienced distinctly non-Earth-like, irrecoverable water loss.
SDSS J183131.63+420220.2: AM CVn star showing ER UMa-type behavior and long standstill

SDSS J183131.63+420220.2 is an AM CVn-type cataclysmic variable. Using Asteroid Terrestrial-impact Last Alert System (ATLAS) and Zwicky Transient Facility (ZTF) data, I found that this object is actually a helium dwarf nova, which experienced a long (~6 yr) standstill (2017 to 2022). The object is currently (in 2023) in ER UMa-type state with supercycles of 20-30 d and large duty cycles exceeding 0.5. This object is the second known star among AM CVn stars having characteristics of ER UMa and Z Cam types. The long duration of the standstill phase is outstanding among helium dwarf novae. These observations indicate that the accretion disk in SDSS J183131.63+420220.2 is very close to thermal stability. I detected a period of 0.01602343(1) d in the ZTF data, which can be the orbital one. Combined with the case of MGAB-V240, the limit of thermal stability of the disks in AM CVn stars appears to be located around the orbital period of 0.0158-0.0160 d.
Light-Weight Vision Transformer with Parallel Local and Global Self-Attention

While transformer architectures have dominated computer vision in recent years, these models cannot easily be deployed on hardware with limited resources for autonomous driving tasks that require real-time-performance. Their computational complexity and memory requirements limits their use, especially for applications with high-resolution inputs. In our work, we redesign the powerful state-of-the-art Vision Transformer PLG-ViT to a much more compact and efficient architecture that is suitable for such tasks. We identify computationally expensive blocks in the original PLG-ViT architecture and propose several redesigns aimed at reducing the number of parameters and floating-point operations. As a result of our redesign, we are able to reduce PLG-ViT in size by a factor of 5, with a moderate drop in performance. We propose two variants, optimized for the best trade-off between parameter count to runtime as well as parameter count to accuracy. With only 5 million parameters, we achieve 79.5% top-1 accuracy on the ImageNet-1K classification benchmark. Our networks demonstrate great performance on general vision benchmarks like COCO instance segmentation. In addition, we conduct a series of experiments, demonstrating the potential of our approach in solving various tasks specifically tailored to the challenges of autonomous driving and transportation.
Obtaining short-fiber orientation model parameters using non-lubricated squeeze flow

Accurate models of fiber orientation dynamics during the processing of polymer-fiber composites are needed for the design work behind important automobile parts. All of the existing models utilize empirical parameters, but a standard method for obtaining them independent of processing does not exist. This study considers non-lubricated squeeze flow through a rectangular channel as a solution. A two-dimensional finite element method simulation of the kinematics and fiber orientation evolution along the centerline of a sample is developed as a first step toward a fully three-dimensional simulation. The model is used to fit to orientation data in a short-fiber-reinforced polymer composite after squeezing. Fiber orientation model parameters obtained in this study do not agree well with those obtained for the same material during startup of simple shear. This is attributed to the vastly different rates at which fibers orient during shearing and extensional flows. A stress model is also used to try to fit to ex.
New constraints on the gamma-ray and high energy neutrino fluxes from the circumstellar interaction of SN 2023ixf

The recent supernova, SN 2023ixf, one of the closest observed type II SNe has revealed the presence of a dense circumstellar material (CSM). Interaction of the SN ejecta with this dense CSM might create high energy protons of PeV energies through shock acceleration. These accelerated protons then colliding with the CSM (inelastic $pp$ collision) can produce secondaries such as high energy gamma-rays and neutrinos. However, no gamma-rays and neutrinos have been detected by Fermi-LAT and IceCube from this event. Fermi-LAT has placed an upper limit on the gamma-ray flux above $100$~MeV to be $2.6 \times 10^{-11}~\rm erg~cm^{-2}~s^{-1}$. On the other hand, IceCube's upper limit on muon neutrino flux is $7.3\times 10^{-2} ~\rm GeV~cm^{-2}$. {\color{black} Taking these limits into account and using the shock-CSM properties derived from multi-wavelength observations, we obtain new upper limits on the gamma-ray ($10^{-11}~\rm erg~cm^{-2}~s^{-1}$) and neutrino ($10^{-3}~\rm GeV~cm^{-2}$) fluxes from SN 2023ixf produced via the $pp$ interaction channel. } While we found the gamma-ray flux to be consistent with Fermi-LAT's upper limit, the neutrino flux is found to be about $2$ orders of magnitude smaller than the IceCube's upper limit. We further analyse the detection prospects of such secondary signals from future SN 2023 like events with upcoming detectors, CTA and IceCube-Gen2 and found to have great discovery potential, if any similar event occurs within $7$ Mpc.