julilili42/papers huggingface dataset:
CubeSat attitude determination with decomposed Kalman filters
2023-02-01

Abstract CubeSats are the cost-effective entry to space research and applications. As mission requirements increase to carry out more complex tasks, the constraints on the satellite challenge how attitude estimation and control systems are designed. Limited energy, sensors, and computational capacity require compromises. In this paper, we propose a Kalman filter architecture to reduce the computational cost of attitude estimation, leveraging the conditional independence structure of its physical model. Our method decomposes attitude dynamics and kinematics, leading to a linear attitude quaternion and a nonlinear angular velocity filter. As accommodating all vector measurements would require a nonlinear filter, we propose the virtual sensor paradigm that transforms the nonlinear observation model into a linear one, without relying on approximations. Our numerical experiments showcase superior error dynamics and robustness to epistemic uncertainty compared to a nonlinear quaternionic filter, and we also investigate performance against star tracker measurement frequency and sensitivity to the angle between Sun and Earth magnetic field measurements.
Power-to-Gas: neuer Rückenwind für ein altes Modellsystem
2023-02-01

Abstract Methanothermobacter has been pivotal in elucidating the biochemistry of hydrogenotrophic methanogenesis. These microbes generate cellular energy to grow by producing methane from hydrogen and carbon dioxide. Recently, this physiological trait was adopted for biotechnology in power-to-gas processes to store renewable electric energy in form of methane in the natural gas grid. We established a genetic system and a genome-scale metabolic model for Methanothermobacter (Microbe of the Year 2021) to support further technology advancement and implementation for large-scale production of renewable methane.
Discovering Exceptional Development of Commitment in Interdisciplinary Study Programs
2023-02-01

Abstract. In psychology and the social sciences, it is often of interest how complex structural relations among variables are moderated by profiles or combinations of persons’ attributes. Some state-of-the-art methods, such as latent class analysis, are well-suited for this purpose. However, they can lead to methodological problems (e.g., convergence issues) or interpretative difficulties (e.g., due to nondistinctive profiles). For these cases, two other approaches combining structural equation modeling with machine learning have been proposed, namely structural equation model (SEM) trees and SubgroupSEM. These approaches allow for exploration of how parameters of a SEM differ depending on combinations of a person's attributes. This can be useful for generating hypotheses for future research. In this paper, we provide an empirical illustration of SubgroupSEM using an example from research on the development of commitment in interdisciplinary study programs in German higher education and identify combinations of vocational interests related to exceptional development.
Thinking the contemporary: beyond distinctiveness in the literary humanities
2023-02-01

This article seeks to recalibrate current debates about the value of the humanities by shifting their focus away from notions of the ‘distinctiveness’ of the humanities. Rather than defining the humanities by demarcating their disciplinary boundaries, it suggests that it might be more productive to see them as nodes of networks of intellectual and social practices. The article considers teaching as such a networked intellectual and social practice, before theorising such perspectives via Foucault’s and Badiou’s notion of the ‘contemporary’. The article concludes by turning its attention back to the practice of teaching, approached via the ‘abolition of the English Department’ proclaimed by Ngũgĩ, Owuor Anyumba and lo Liong in Nairobi in 1969.
Mapping specific habitat requirements as a base for conservation measures for two strongly endangered burnet moth species in Southern France: Zygaena brizae and Zygaena cynarae (Lepidoptera, Zygaenidae)
2023-02-01

Abstract Zygaena species are sensitive indicators of ecological changes and habitat destruction. Here, field results on the ecology of two highly endangered species, Zygaena brizae and Zygaena cynarae, from optimal habitats near Col d'Araud in Hautes-Alpes, France are reported. Both species have faced severe population decline in the last decades in Southwest France, probably due to habitat deterioration. During May and June 2022, larvae, imagines and egg batches were mapped in carefully characterized habitat patches. In total, 713 imagines, 67 larvae and 20 egg batches of Zygaena cynarae (which was the most common burnet moth in the area in 2022) and 23 imagines, 84 larvae, 2 pupae and 18 egg batches of Zygaena brizae were observed. While Zygaena brizae occurs both on mesophile and on semi-dry slopes (only north-and west-facing), supported by increasing numbers of the larval food plant (Cirsium tuberosum), larval habitats of Zygaena cynarae are characterized by the common occurrence of the larval food plant (Peucedanum cervaria) and by (optimally) 10-30% tree cover. Most colonized patches are south-facing and flat; open habitat patches with many larval food plants are not inhabited. All inhabited patches are extensively grazed by sheep, goats, cattle or horses-the specifics do not seem to matter. Details of grazing schedule, sunshine duration, slope exposure and other habitat parameters are reported and evaluated to support conservation measures of these burnet moth species. Implications for insect conservation: Our results provide robust data about the specific habitat requirements of these two strongly endangered burnet moth species.
Towards Learned Emulation of Interannual Water Isotopologue Variations in General Circulation Models
2023-02-01

Simulating abundances of stable water isotopologues, i.e. molecules differing in their isotopic composition, within climate models allows for comparisons with proxy data and, thus, for testing hypotheses about past climate and validating climate models under varying climatic conditions. However, many models are run without explicitly simulating water isotopologues. We investigate the possibility to replace the explicit physics-based simulation of oxygen isotopic composition in precipitation using machine learning methods. These methods estimate isotopic composition at each time step for given fields of surface temperature and precipitation amount. We implement convolutional neural networks (CNNs) based on the successful UNet architecture and test whether a spherical network architecture outperforms the naive approach of treating Earth's latitude-longitude grid as a flat image. Conducting a case study on a last millennium run with the iHadCM3 climate model, we find that roughly 40\\% of the temporal variance in the isotopic composition is explained by the emulations on interannual and monthly timescale, with spatially varying emulation quality. A modified version of the standard UNet architecture for flat images yields results that are equally good as the predictions by the spherical CNN. We test generalization to last millennium runs of other climate models and find that while the tested deep learning methods yield the best results on iHadCM3 data, the performance drops when predicting on other models and is comparable to simple pixel-wise linear regression. An extended choice of predictor variables and improving the robustness of learned climate--oxygen isotope relationships should be explored in future work.
The impact of Syk-inhibition on 5B9 monoclonal HIT antibody-mediated procoagulant platelet formation
2023-02-01

Introduction Heparin-induced thrombocytopenia (HIT) is a prothrombotic disease caused by immunoglobulin G (IgG) antibodies (Abs) that recognize complexes of heparin and platelet (PLT) factor 4 (PF4). Formation of anti-PF4/heparin HIT IgG immune complexes can be recognized by PLT immune receptor Fc-gamma-RIIA which results in immunoreceptor tyrosine-based activation motif (ITAM) mediated activating signal downstream with a pivotal role of the enzyme spleen tyrosine kinase (Syk). While it is well recognized that HIT Abs induce PLT activation, the potential contribution of different Ab-induced PLT subpopulations to the prothrombotic condition in HIT remains elusive. 5B9 is a chimeric monoclonal HIT-antibody that resembles the pathogenesis of HIT. This study aims to characterize 5B9 HIT Ab-induced Fc-gamma-RIIA mediated PLT subpopulations and to investigate the therapeutic potential of different Syk inhibitors on 5B9 Ab-induced PLT alterations.
Pharmacological targeting of ACKR3/CXCR7 enhances anticoagulant acylcarnitine levels in platelets and modulates thrombotic response to lipids
2023-02-01

Introduction Pharmacological targeting of chemokine receptor CXCR7 restricts generation of atherothrombotic, while favoring anti-thrombotic lipids that impose platelet inhibition ex vivo in coronary artery disease (CAD) patients with an atherogenic platelet lipidome. CXCR7 ligation induces the platelet inhibitory cAMP dependent signaling cascade in coordination with the prostacyclin receptor. Current investigation explores the impact of the non-canonical CXCR7 in modulating platelet thrombotic response and procoagulant potential.
An NlpC/P60 protein catalyzes a key step in peptidoglycan recycling at the intersection of energy recovery, cell division and immune evasion in the intracellular pathogen Chlamydia trachomatis
2023-02-02

The obligate intracellular Chlamydiaceae do not need to resist osmotic challenges and thus lost their cell wall in the course of evolution. Nevertheless, these pathogens maintain a rudimentary peptidoglycan machinery for cell division. They build a transient peptidoglycan ring, which is remodeled during the process of cell division and degraded afterwards. Uncontrolled degradation of peptidoglycan poses risks to the chlamydial cell, as essential building blocks might get lost or trigger host immune response upon release into the host cell. Here, we provide evidence that a primordial enzyme class prevents energy intensive de novo synthesis and uncontrolled release of immunogenic peptidoglycan subunits in Chlamydia trachomatis . Our data indicate that the homolog of a Bacillus NlpC/P60 protein is widely conserved among Chlamydiales . We show that the enzyme is tailored to hydrolyze peptidoglycan-derived peptides, does not interfere with peptidoglycan precursor biosynthesis, and is targeted by cysteine protease inhibitors in vitro and in cell culture. The peptidase plays a key role in the underexplored process of chlamydial peptidoglycan recycling. Our study suggests that chlamydiae orchestrate a closed-loop system of peptidoglycan ring biosynthesis, remodeling, and recycling to support cell division and maintain long-term residence inside the host. Operating at the intersection of energy recovery, cell division and immune evasion, the peptidoglycan recycling NlpC/P60 peptidase could be a promising target for the development of drugs that combine features of classical antibiotics and anti-virulence drugs.
Extra-viral DNA in adeno-associated viral vector preparations induces TLR9-dependent innate immune responses in human plasmacytoid dendritic cells
2023-02-02

Abstract Adeno-associated viral (AAV) vector suspensions produced in either human derived HEK cells or in Spodoptera frugiperda ( Sf9 ) insect cells differ in terms of residual host cell components as well as species-specific post-translational modifications displayed on the AAV capsid proteins. Here we analysed the impact of these differences on the immunogenic properties of the vector. We stimulated human plasmacytoid dendritic cells with various lots of HEK cell-produced and Sf9 cell-produced AAV-CMV-eGFP vectors derived from different manufacturers. We found that AAV8-CMV-eGFP as well as AAV2-CMV-eGFP vectors induced lot-specific but not production platform-specific or manufacturer-specific inflammatory cytokine responses. These could be reduced or abolished by blocking toll-like receptor 9 signalling or by enzymatically reducing DNA in the vector lots using DNase. Successful HEK cell transduction by DNase-treated AAV lots and DNA analyses demonstrated that DNase did not affect the integrity of the vector but degraded extra-viral DNA. We conclude that both HEK- and Sf9 -cell derived AAV preparations can contain immunogenic extra-viral DNA components which can trigger lot-specific inflammatory immune responses. This suggests that improved strategies to remove extra-viral DNA impurities may be instrumental in reducing the immunogenic properties of AAV vector preparations.
The grapevine LysM receptor-like kinase VvLYK5-1 recognizes chitin oligomers through its association with VvLYK1-1
2023-02-02

The establishment of defense reactions to protect plants against pathogens requires the recognition of invasion patterns (IPs), mainly detected by plasma membrane-bound pattern recognition receptors (PRRs). Some IPs, also termed elicitors, are used in several biocontrol products that are gradually being developed to reduce the use of chemicals in agriculture. Chitin, the major component of fungal cell walls, as well as its deacetylated derivative, chitosan, are two elicitors known to activate plant defense responses. However, recognition of chitooligosaccharides (COS) in Vitis vinifera is still poorly understood, hampering the improvement and generalization of protection tools for this important crop. In contrast, COS perception in the model plant Arabidopsis thaliana is well described and mainly relies on a tripartite complex formed by the cell surface lysin motif receptor-like kinases (LysM-RLKs) AtLYK1/CERK1, AtLYK4 and AtLYK5, the latter having the strongest affinity for COS. In grapevine, COS perception has for the moment only been demonstrated to rely on two PRRs VvLYK1-1 and VvLYK1-2. Here, we investigated additional players by overexpressing in Arabidopsis the two putative AtLYK5 orthologs from grapevine, VvLYK5-1 and VvLYK5-2 . Expression of VvLYK5-1 in the atlyk4/5 double mutant background restored COS sensitivity, such as chitin-induced MAPK activation, defense gene expression, callose deposition and conferred non-host resistance to grapevine downy mildew ( Erysiphe necator) . Protein-protein interaction studies conducted in planta revealed a chitin oligomer-triggered interaction between VvLYK5-1 and VvLYK1-1. Interestingly, our results also indicate that VvLYK5-1 mediates the perception of chitin but not chitosan oligomers showing a part of its specificity.
Delineation of Soil Management Zone Maps at the Regional Scale Using Machine Learning
2023-02-02

Applying fertilizers to soil in a site-specific way that maximizes yields and minimizes environmental damage is an important goal. Developing soil management zones (MZs) is a suitable method for achieving sustainable agricultural production. Thus, this work aims to investigate MZs delineated based on the different soil properties using machine learning methods. To achieve these, 202 soil samples were collected at the agricultural land of pomegranate, pistachio, and saffron. A “random forest” model was applied to map soil properties based on environmental covariates. The predicted “Lin’s concordance correlation coefficient” values in validation soil properties varied from 0.65 to 0.79. The maps indicated low amounts of soil organic carbon, available potassium, available phosphate, and total nitrogen in most of the region. Furthermore, the study identified four different MZs according to relationships between soil properties and environmental covariates. Generally, the ranking of zones in terms of soil fertility was MZ4 &gt; MZ1 &gt; MZ3 &gt; MZ2 based on the investigated soil properties and the soil quality (SQ) map. The five grades of SQ (i.e., very high, high, moderate, low, and very low) indicated that there was heterogeneous SQ in each MZ in the study area. There were 1.65 ha identified in MZ4 with very low SQ. This result is important in determining the amount of fertilizer to add to the soil in the different areas. It confirms the need for more specific regional management of agriculture lands in this region.
In vitro to in vivo acetaminophen hepatotoxicity extrapolation using classical schemes, pharmacodynamic models and a multiscale spatial-temporal liver twin
2023-02-02

In vitro to in vivo extrapolation represents a critical challenge in toxicology. In this paper we explore extrapolation strategies for acetaminophen (APAP) based on mechanistic models, comparing classical (CL) homogeneous compartment pharmacodynamic (PD) models and a spatial-temporal (ST), multiscale digital twin model resolving liver microarchitecture at cellular resolution. The models integrate consensus detoxification reactions in each individual hepatocyte. We study the consequences of the two model types on the extrapolation and show in which cases these models perform better than the classical extrapolation strategy that is based either on the maximal drug concentration (Cmax) or the area under the pharmacokinetic curve (AUC) of the drug blood concentration. We find that an CL-model based on a well-mixed blood compartment is sufficient to correctly predict the in vivo toxicity from in vitro data. However, the ST-model that integrates more experimental information requires a change of at least one parameter to obtain the same prediction, indicating that spatial compartmentalization may indeed be an important factor.
Association Between Hospital-Documented Atrial Fibrillation and Central Retinal Artery Occlusion
2023-02-02

Background: Carotid stenosis is thought to be the primary risk factor for central retinal artery occlusion (CRAO); however, it is not known whether atrial fibrillation (AF)—a cardiac arrhythmia that underlies over 25% of cerebral ischemic strokes—predisposes patients to CRAO. Methods: A retrospective, observational, cohort study was performed using data from the State Inpatient Databases and State Emergency Department Databases from New York (2006–2015), California (2003–2011), and Florida (2005–2015) to determine the association between AF and CRAO. The primary exposure was hospital-documented AF. The primary end point was hospital-documented CRAO, defined as having an International Classification of Diseases, Ninth Revision, Clinical Modification , code 362.31 in the primary diagnosis position. Cause-specific hazard models were used to model CRAO-free survival among patients according to hospital-documented AF status. Results: Of 39 834 885 patients included in the study, 2 723 842 (median age, 72.7 years; 48.5% women) had AF documented during the exposure window. The median follow-up duration was 6 years and 1 month. Patients with AF were older, more likely to be of non-Hispanic White race/ethnicity, and had a higher burden of cardiovascular comorbidities compared with patients without AF. The cumulative incidence of CRAO determined prospectively after exclusions was 8.69 per 100 000 at risk in those with AF and 2.39 per 100 000 at risk in those without AF over the study period. Before adjustment, AF was associated with higher risk of CRAO (hazard ratio, 2.55 [95% CI, 2.15–3.03]). However, after adjustment for demographics, state, and cardiovascular comorbidities, there was an inverse association between AF and risk of CRAO (adjusted hazard ratio, 0.72 [95% CI, 0.60–0.87]). These findings were robust in our prespecified sensitivity analyses. By contrast, positive control outcomes of embolic and ischemic stroke showed an expected strong relationship between AF and risk of stroke. Conclusions: We found an inverse association between AF and CRAO in a large, representative study of hospitalized patients; however, this cohort did not ascertain AF or CRAO occurring outside of hospital or emergency department settings.
Ecosystem changes through the Permian–Triassic and Triassic–Jurassic critical intervals: Evidence from sedimentology, palaeontology and geochemistry
2023-02-02

ABSTRACT The Permian–Triassic and Triassic–Jurassic critical intervals are among the most significant ecological upheavals in the Phanerozoic. Both evolutionary junctures are characterized by environmental deterioration associated with a marked biodiversity decline. In this study, Permian–Triassic and Triassic–Jurassic boundary sections from South China and the Northern Calcareous Alps were investigated. In order to reconstruct the interplay between biotic and abiotic processes, a multifaceted approach that included optical microscopy, X‐ray diffraction, Raman spectroscopy, stable carbon isotopes and lipid biomarkers was employed. The lower parts of these two sections are similar as both consist of limestone with abundant fossils of eukaryotic organisms. However, the Permian–Triassic record is dominated by dasyclad green algae and fusulinid foraminifera, while the Triassic–Jurassic record is typified by corals and coralline sponges. Moving upward, both sections consist mainly of micrite and marl. Concerning the Permian–Triassic section, it transits to volcanic ash intercalated by a distinct limestone bed with abundant calcispheres (tentatively attributed to ancestors of dinoflagellates). The Triassic–Jurassic section does not provide direct evidence for volcanic activity, but also becomes rich in calcisphere‐type cysts towards the top. Additionally, the section preserves abundant 4‐methyl sterenes (diagnostic for dinoflagellates) and C 37–39 n ‐alkanes (indicative for haptophytes). Hence, both critical intervals were associated with marked blooms of (ancestral) dinoflagellates and haptophytes (for example, coccolithophorids). These blooms were followed by ecological lag‐phases, as indicated by low carbonate contents and scarce fossils which only increased further up the sections. For both critical intervals, it is commonly assumed that the formation of voluminous volcanic provinces (Siberian Traps and Central Atlantic Magmatic Province, respectively), as well as associated processes (for example, burning of organic‐rich sediments such as coal), resulted in ecological devastation. However, results suggest that volcanism also had a positive effect on certain planktonic primary producers such as dinoflagellates and haptophytes, perhaps by delivering essential nutrients.
Ultra-low-dose CT is feasible for torsion measurement of the lower limb in patients with metal implants
2023-02-02

Objectives: Patients who need torsion measurement of the lower limb often have metal implants hindering e.g. MRI. A new ultra-low-dose (ULD-)CT protocol might be feasible for torsion measurement at cost of relatively low radiation exposure. Methods: We retrospectively included all patients with clinically indicated torsion measurement in the period July 2019 to June 2021 and metal implants in the scanning field. The ULD-CT protocol comprised automated tube current time product and automated tube voltage with reference settings of 100kV/20mAs (hip), 80kV/20mAs (knee) and 80kV/10mAs (ankle). Femoral neck anteversion, tibial, intra-articular knee and overall leg torsion measurements were performed by two radiologists independently. Diagnostic confidence regarding the delineation of the relevant cortical bone was rated on a 5-point Likert scale (1 = non-diagnostic, 5 = excellent). Results: 102 consecutive patients could be included (BMI 27.38 ± 5.85) with 154 metal implants. Median total dose length product of the ULD-CT-torsion measurement was 16.5mGycm [11-39]. Both readers showed high agreement with a maximum torsional difference of 4.1°. Diagnostic confidence was rated best (5/5) in 92.2% (reader 1) and 93.1% (reader 2) with a worst rating of 3/5. Conclusion: The new ULD-CT protocol is feasible for torsion measurement of the lower limb – even in patients with metal implants. Advances in knowledge: Metal implants are not an obstacle for ULD-CT torsion measurements of the lower limb.