Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of Maximum Friction Coefficient Using Recurrent Artificial Neural Networks

Knowledge of vehicle dynamics and in particular the maximum friction coefficient is required for the optimization of advanced driver assistance systems and the implementation of autonomous driving. Since the maximum friction coefficient cannot be measured directly, estimating this coefficient based on available sensors is a field of interest. In particular, model-based approaches based on Kalman filter derivates are used. However, their accuracy is limited by the accuracy of the physical model. Due to the real-time capability required, more detailed modeling is not possible. In addition, system identification and a robust filter design are needed. As a result, data-based approaches are gaining popularity in vehicle dynamics, which are also suitable for estimating the maximum friction coefficient. In this paper, maximum friction coefficient estimation is presented using recurrent artificial neural networks (RANN) based on vehicle sensors. In order to avoid incorrect estimations during low vehicle excitation, an excitation monitoring approach is introduced. Typical longitudinal and lateral driving maneuvers on different road surfaces simulated in IPG CarMaker with a Dacia Duster are used for training, validation and testing of the RANN. Finally, the data-based approach shows improved results compared to the model-based approach of a sensitivity-based unscented Kalman filter (sUKF) from previous works.
Searching for an interstellar medium association for HESS J1534 − 571

The Galactic supernova remnant HESS J1534-571 (also known as G323.7-1.0) has a shell-like morphology in TeV gamma-ray emission and is a key object in the study of cosmic ray origin. Little is known about its distance and local environment. We examine Mopra $^{12}$CO/$^{13}$CO(1-0) data, Australian Telescope Compact Array HI, and Parkes HI data towards HESS J1534-571. We trace molecular clouds in at least five velocity ranges, including clumpy interstellar medium structures near a dip in HI emission at a kinematic velocity consistent with the Scutum-Crux arm at ~3.5 kpc. This feature may be a cavity blown-out by the progenitor star, a scenario that suggests HESS J1534-571 resulted from a core-collapse event. By employing parametrisations fitted to a sample of supernova remnants of known distance, we find that the radio continuum brightness of HESS J1534-571 is consistent with the ~3.5 kpc kinematic distance of the Scutum-Crux arm HI dip. Modelling of the supernova evolution suggests an ~8-24 kyr age for HESS J1534-571 at this distance.
DARC: A Visual Analytics System for Multivariate Applicant Data Aggregation, Reasoning and Comparison

People often make decisions based on their comprehensive understanding of various materials, judgement of reasons, and comparison among choices. For instance, when hiring committees review multivariate applicant data, they need to consider and compare different aspects of the applicants’ materials. However, the amount and complexity of multivariate data increase the difficulty to analyze the data, extract the most salient information, and then rapidly form opinions based on the extracted information. Thus, a fast and comprehensive understanding of multivariate data sets is a pressing need in many fields, such as business and education. In this work, we had in-depth interviews with stakeholders and characterized user requirements involved in data-driven decision making in reviewing school applications. Based on these requirements, we propose DARC, a visual analytics system for facilitating decision making on multivariate applicant data. Through the system, users are supported to gain insights of the multivariate data, picture an overview of all data cases, and retrieve original data in a quick and intuitive manner. The effectiveness of DARC is validated through observational user evaluations and interviews.
Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins

The combination of thermal proteome profiling and pulsed SILAC labelling shows that mitochondrial dysfunction imprints a characteristic pattern on the abundance and thermal stability of the proteome. Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.
Chromosome-scale genome assemblies of five different Brassica oleracea morphotypes provide insights in intraspecific diversification

Brassica oleracea is an economically important vegetable and fodder crop species that includes many morphotypes exhibiting enormous phenotypic variations. Previously, a pan-genome study based on short reads mapping approach has shown extensive structural variations between B. oleracea morphotypes. Here, to capture more complete genome sequences of B. oleracea, we report new chromosome-scale genome assemblies for five different morphotypes, namely broccoli, cauliflower, kale, kohlrabi and white cabbage, which were created by combining long-read sequencing data and Bionano DLS optical maps. The five assemblies are the most continuous and complete B. oleracea genomes to date (contig N50 > 10 Mb). Comparative analysis revealed both highly syntenic relationships and extensive structural variants among the five genomes. Dispensable and specific gene clusters accounted for ~38.19% of total gene clusters based on a pan-genome analysis including our five newly assembled genomes and four previously reported genomes. Using the pan-genome of B. oleracea and B. rapa, we revealed their different evolutionary dynamics of LTR-RTs. Furthermore, we inferred the ancestral genome of B. oleracea and the common ancestral genome of B. oleracea and B. rapa via a pan-genome approach. We observed faster WGT-derived gene loss in B. rapa than in B. oleracea before intraspecific diversification. We also revealed continuing gene loss bias during intraspecific diversification of the two species and a strong bias towards losing only one copy among the three paralogous genes. This study provides valuable genomic resources for B. oleracea improvement and insights towards understanding genome evolution during the intraspecific diversification of B. oleracea and B. rapa.
Equalizing epigenetically imprinted centromeres in early mammalian embryos

The CENP-A histone variant epigenetically defines centromeres, where its levels and locations are precisely maintained through mitotic cell divisions. However, differences in centromere CENP-A propagation in soma versus female/male germline remains poorly understood. Here, we generated CenpamScarlet mice and followed CENP-A dynamics in gametes, zygotes, and embryos. We found that, unlike somatic cells, progenitor female and male germ cells carry high centromeric CENP-A levels that decrease upon terminal differentiation. The reduction in CENP-A is differentially regulated between sexes, resulting in a ten-fold higher level in oocytes compared to sperm. In the zygote, the parent-of-origin CENP-A asymmetry is equalized prior to initial S-phase by redistribution of nuclear CENP-A from maternal to paternal chromosomes. Redistribution of CENP-A requires both CDK1/2 and PLK1 centromeric machinery. These experiments provide direct evidence for resetting of epigenetically imprinted centromeres in early pronuclear stage embryos and imply a mechanism to sense the non-equivalency of parental chromosomes. Highlights Increased CENP-A density at centromeres is a conserved property of germline stem cells while CENP-A reduction is coincident with germ cell differentiation Paternal and maternal CENP-A containing nucleosomes are intergenerationally inherited CENP-A density at centromeres differs between male and female mature gametes Upon fertilization, maternal nuclear CENP-A is redistributed to equalize with parental CENP-A CENP-C and MIS18BP1 are asymmetrically enriched in the parental pronuclei in accordance with CENP-A asymmetry. Licensing for centromere equalization begins before zygotic DNA replication
Intuitive interpretation of heterochromatin and euchromatin through rapid Hi-C analysis

Hi-C is a technique that provides contact frequencies between pairs of loci on chromosomes. The conventional classification of heterochromatin and euchromatin based on Hi-C data is performed by principal component analysis; however, it requires long computational times and does not provide insight into the difference in contact frequencies between heterochromatin and euchromatin. Here, we propose a simple, intuitive and rapid method named the scaled contact number (SCN), which allows the contact frequencies to be visually interpreted and heterochromatin and euchromatin to be classified based on Hi-C results in a few minutes for long chromosomes at 1-kb resolution. The robustness of SCN was validated by confirming that SCN with reduced reads gives almost the same results as the original SCN. Overall, the approach described herein thus considerably decreases the time and computing power required to analyze Hi-C and further provides mechanistic insight indicating that euchromatin has more contacts than heterochromatin.
Cone beam cover method: An approach to performing backprojection in Katsevich's exact algorithm for spiral cone beam CT

The conventional implementation of Katsevich's inversion formula involves the computation of PI segment. This is done by solving a nonlinear equation with a numerical algorithm such as Newton's method. In this study, we develop an implementation of Katsevich's inversion formula without computing PI segment. Our implementation involves a new concept, cone beam cover, which is closely related to PI segment and Tam-Danielsson window. Unlike the implementation based on PI segment, the algorithm complexity of our implementation can be estimated with several important imaging parameters. This result may be instructive for practical applications to choose scanning parameters and reduce the algorithm complexity. The proposed implementation is validated with satisfactory numerical experiments.
Tocilizumab treatment leads to early resolution of lymphopenia and myeloid dysregulation in patients hospitalized with COVID-19

High interleukin (IL)-6 levels are associated with more severe clinical manifestations in patients hospitalized with COVID-19, but the complex role of IL-6 in antiviral and inflammatory processes has made it difficult to decipher its involvement in the disease. IL-6 receptor blockade by tocilizumab (anti-IL6R; Actemra) is used globally for the treatment of severe COVID-19, yet a molecular understanding of the therapeutic benefit remains unclear. We characterized the immune profile and identified cellular and molecular pathways directly modified by tocilizumab in peripheral blood samples collected from patients enrolled in the COVACTA study, a phase 3, randomized, double-blind, placebo-controlled trial that assessed the efficacy and safety of tocilizumab in hospitalized patients with severe COVID-19 pneumonia. We identified factors predicting disease severity and clinical outcomes, including markers of inflammation, lymphopenia, myeloid dysregulation, and organ injury. Proteomic analysis confirmed a pharmacodynamic effect for tocilizumab in addition to identifying novel pharmacodynamic biomarkers. Transcriptomic analysis revealed that tocilizumab treatment leads to faster resolution of lymphopenia and myeloid dysregulation associated with severe COVID-19, indicating greater anti-inflammatory activity relative to standard of care and potentially leading to faster recovery in patients hospitalized with COVID-19. One sentence summary Interleukin-6 receptor blockade with tocilizumab accelerated resolution of myeloid dysfunction and lymphopenia in patients hospitalized with COVID-19
Two new species of Crocus series Scardici from the Western Balkans

Crocus series Scardici has only two members, C. scardicus and C. pelistericus distributed at higher elevations in the Balkan Peninsula. In the course of our research, we discovered two new species growing on alpine meadows and pastures in the serpentine massifs in Albania and limestones in North Macedonia, respectively. The morphology and phylogenetic analyses (two nuclear single-copy markers, nrITS, two chloroplast markers) place the new species within series Scardici. Both new species are closely related to C. scardicus, but morphologically and ecologically clearly differentiated. We also measured genome sizes for all series Scardici species and report here the largest genomes found up to now in crocuses. The impact of different habitat types and isolation on separate mountain ranges in this alpine group of plants is discussed, too.
Game bird carcasses are less persistent than raptor carcasses, but can predict raptor persistence dynamics

Researchers conduct post-construction fatality monitoring (PCFM) to determine a wind energy facility’s direct impacts on wildlife. Results of PCFM can be used to evaluate compliance with permitted take, potentially triggering adaptive management measures or offsetting mitigation; reducing uncertainty in fatality rates benefits wind companies, wildlife agencies, and other stakeholders. As part of PCFM, investigators conduct carcass persistence trials to account for imperfect detection during carcass surveys. In most PCFM studies, pen-raised game birds and other non-raptor surrogates have been used to estimate persistence of all large birds, including raptors. However, there is a growing body of evidence showing carcass persistence varies by bird type; raptor fatality estimates based on game bird carcass persistence may therefore be biased high. We conducted raptor and game bird carcass persistence field trials for 1 year at 6 wind energy facilities. Raptor carcass persistence varied by habitat and season, whereas the best-supported game bird model only included habitat. Raptor persistence probabilities were higher than corresponding game bird persistence probabilities for 13 of the 16 habitat and season combinations. Analysis of a curated large bird persistence meta-dataset showed that raptor carcass persistence varied by season, habitat, and region. The probability of persisting through a 30-day search interval ranged from 0.44 to 0.99 for raptors and from 0.16 to 0.79 for game birds. Raptor persistence was significantly higher than game bird persistence for 95% of the sampled strata. We used these carcass persistence estimates to develop linear mixed-effects models that predict raptor persistence probabilities based on estimated game bird persistence probabilities. Our scaling model provides an important statistical method to address gaps in raptor persistence data at sites in a broad range of landscape contexts in the continental United States and should be used to inform fatality estimation when site-specific raptor persistence data are limited or absent.
The influence of familiarity on the neural coding of face sex

In behaviour, humans have been shown to represent the sex of faces categorically when the faces are familiar to them. This leads to them judging faces crossing the category boundary (i.e. from male to female) as more different than faces that are within the same category. In this study, we investigated how faces of different sexes are encoded in the brain, and how familiarity changes the neural coding of sex. We recorded participants’ brain activity using fMRI while they viewed both familiar and unfamiliar faces that were morphed in their sex characteristics (i.e. between male and female). Participants viewed pairs of faces that were either identical, or differed in their sex morph level, with or without a categorical change in perceived sex (i.e. crossing the perceived male/female category boundary). This allowed us to disentangle physical and categorical neural coding of face sex, and to investigate if neural coding of face categories was enhanced by face familiarity. Our results show that the sex of familiar, but not unfamiliar, faces was encoded categorically in the medial prefrontal and orbitofrontal cortex as well as in the right intraparietal sulcus. In contrast, the fusiform face area showed a sensitivity to the physical changes in the sex of faces that was unaffected by face familiarity. The occipital face area showed its highest responses to faces towards the ends of the sex morph continuum (i.e. the most male or most female faces), and these responses were also unaffected by face familiarity. These results suggest that there is a dissociation between the brain regions encoding physical and categorical representations of face sex, with occipital and fusiform face regions encoding physical face sex properties and frontal and parietal regions encoding high-level categorical face sex representations that are linked to face identity.
Long-Range Hopping Conductivity in Proteins

Single molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1V. In the conventional fast transport scenario where the free energy barrier is zero, the hopping rate is determined by the reorganization energy of approximately 0.8 eV, which sets the time scale of a single hopping event to at least 1μs. Furthermore, the Fermi energies of metal electrodes used in experiments are far-removed from the equilibrium redox states of the aromatic residues of the protein, which should additionally slow down the electron transfer. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transfer. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the nonergodic sampling of molecular configurations by the protein results in reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ~ 0.2 eV, which is small enough to enable long-range hopping. Using the MD values of the reorganization energies we calculate a current decay with distance that is in agreement with experiment. Significance Electron transfer is fundamental to biology, facilitating a range of metabolic processes and efficient energy conversion. Conventionally, electron transfer through proteins is thought to occur via a chain of metal or organic co-factors connecting one side of the protein to another. Recent experiments, however, show that proteins lacking any co-factors can nonetheless transport electrons with high efficiency if properly connected to metal electrodes. This study provides a theoretical model of such cofactor-less transfer, showing that transient occupation of non-equilibrium states of the protein’s aromatic residues reduces the barrier to electron hopping, facilitating long range and rapid transport. Our results widen the pool of proteins potentially involved in biological electron transport and provide theoretical underpinning to design of protein molecular electronics.
Species Richness and Speciation Rates for all Terrestrial Animals Emerge from a Synthesis of Ecological Theories

The total number of species on earth and the rate at which new species are created are fundamental questions for ecology, evolution and conservation. These questions have typically been approached separately, despite their obvious interconnection. In this manuscript we approach both questions in conjunction, for all terrestrial animals, which enables a more holistic integration and generates novel emergent predictions. To do this, we combine two previously unconnected bodies of theory: general ecosystem modelling and individual based ecological neutral theory. General ecosystem models provide us with estimated numbers of individual organisms, separated by functional group and body size. Neutral theory, applied within a guild of functionally similar individuals, connects species richness, speciation rate and number of individual organisms. In combination, for terrestrial endotherms where species numbers are known, they provide us with estimates for speciation rates as a function of body size and diet class. Extrapolating the same rates to guilds of ectotherms enables us to estimate the species richness of those groups, including species yet to be described. We find that speciation rates per species per million years decrease with increasing body size. Rates are also higher for carnivores compared to omnivores or herbivores of the same body size. Our estimate for the total number of terrestrial species of animals is in the range 1.03 − 2.92 million species, a value consistent with estimates from previous studies, despite having used a fundamentally new approach. Perhaps what is most remarkable about these results is that they have been obtained using only limited data from larger endotherms and their speciation rates, with the rest of the predictive process being based on mechanistic theory. This work illustrates the potential of a new approach to classic eco-evolutionary questions, while also adding weight to existing predictions. As we now face an era of dramatic biological change, new methods will be needed to mechanistically model global biodiversity at the species and individual organism level. This will be a huge challenge but the combination of general ecosystem models and neutral theory that we introduce here could be the only way to tractably achieve it.