julilili42/papers huggingface dataset:
Two Pathways Compete in the Mn(II)-Catalyzed Oxidation of Aminotrismethylene Phosphonate (ATMP)
2022-03-16

Mn(II)-catalyzed oxidation by molecular oxygen is considered a relevant process for the environmental fate of aminopolyphosphonate chelating agents such as aminotrismethylene phosphonate (ATMP). However, the potential roles of Mn(III)ATMP-species in the underlying transformation mechanisms are not fully understood. We combined kinetic studies, compound-specific stable carbon isotope analysis, and equilibrium speciation modeling to shed light on the significance of such Mn-ATMP species for the overall ATMP oxidation by molecular oxygen. The fraction of ATMP complexed with Mn(II) inversely correlated with both (i) the Mn(II)-normalized transformation rate constants of ATMP and (ii) the observed carbon isotope enrichment factors (ε<sub>c</sub>-values). These findings provide evidence for two parallel ATMP transformation pathways exhibiting distinctly different reaction kinetics and carbon isotope fractionation: (i) oxidation of ATMP present in Mn(III)ATMP complexes (ε<sub>c</sub> ≈ -10 ‰) and (ii) oxidation of free ATMP by such Mn(III)ATMP species (ε<sub>c</sub> ≈ -1 ‰) in a catalytic cycle. The higher reaction rate of the latter pathway implies that aminopolyphosphonates can be trapped in catalytic Mn-complexes before being transformed and suggests that Mn(III)ATMP might be a potent oxidant also for other reducible solutes in aqueous environments.
The impact of 3D printed models on spatial orientation in echocardiography teaching
2022-03-16

Abstract Purpose During our transthoracic echocardiography (TTE) courses, medical students showed difficulty in spatial orientation. We implemented the use of 3D printed cardiac models of standard TTE views PLAX, PSAX, and A4C and assessed their efficacy in TTE-teaching. Methods One hundred fifty-three participants were split into two groups. A pre-test-retest of anatomy, 2D -, and 3D orientation was conducted. The intervention group ( n = 77) was taught using 3D models; the control group ( n = 76) without. Both were comparable with respect to baseline parameters. Besides test-scores, a Likert scale recorded experiences, difficulties, and evaluation of teaching instruments. Results From the 153 students evaluated, 123 improved, 20 did worse, and ten achieved the same result after the course. The median overall pre-test score was 29 of 41 points, and the retest score was 35 ( p &lt; 0.001). However, the intervention group taught with the 3D models, scored significantly better overall ( p = 0.016), and in 2D-thinking ( p = 0.002) and visual thinking ( p = 0.006) subtests. A backward multivariate linear regression model revealed that the 3D models are a strong individual predictor of an excellent visual thinking score. In addition, our study showed that students with difficulty in visual thinking benefited considerably from the 3D models. Conclusion Students taught using the 3D models significantly improved when compared with conventional teaching. Students regarded the provided models as most helpful in their learning process. We advocate the implementation of 3D-printed heart models featuring the standard views for teaching echocardiography. These findings may be transferable to other evidence based medical and surgical teaching interventions.
A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing
2022-03-16

<ns4:p>Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.</ns4:p>
The Activation of GPR27 Increases Cytosolic L-Lactate in 3T3 Embryonic Cells and Astrocytes
2022-03-16

G-protein-coupled receptors (GPCRs) represent a family with over 800 members in humans, and one-third of these are targets for approved drugs. A large number of GPCRs have unknown physiologic roles. Here, we investigated GPR27, an orphan GPCR belonging to the family of super conserved receptor expressed in the brain, with unknown functions. Cytosolic levels of L-lactate ([lactate]i), the end product of aerobic glycolysis, were measured with the Laconic fluorescence resonance energy transfer nanosensor. In single 3T3 wild-type (WT) embryonic cells, the application of 8535 (1 μM), a surrogate agonist known to activate GPR27, resulted in an increase in [lactate]i. Similarly, an increase was recorded in primary rat astrocytes, a type of neuroglial cell abundant in the brain, which contain glycogen and express enzymes of aerobic glycolysis. In CRISPR-Cas9 GPR27 knocked out 3T3 cells, the 8535-induced increase in [lactate]i was reduced compared with WT controls. Transfection of the GPR27-carrying plasmid into the 3T3KOGPR27 cells rescued the 8535-induced increase in [lactate]i. These results indicate that stimulation of GPR27 enhances aerobic glycolysis and L-lactate production in 3T3 cells and astrocytes. Interestingly, in the absence of GPR27 in 3T3 cells, resting [lactate]i was increased in comparison with controls, further supporting the view that GPR27 regulates L-lactate homeostasis.
Geometric Invariant Theory via Cox Rings
2022-03-16

We consider actions of reductive groups on a varieties with finitely generated Cox ring, e.g., the classical case of a diagonal action on a product of projective spaces. Given such an action, we construct via combinatorial data in the Cox ring all maximal open subsets such that the quotient is quasiprojective or embeddable into a toric variety. As applications, we obtain an explicit description of the chamber structure of the linearized ample cone and several Gelfand-MacPherson type correspondences relating quotients of reductive groups to quotients of torus actions. Moreover, our approach provides information on the geometry of many of the resulting quotient spaces.
Changes in Envelope Structure and Cell–Cell Communication during Akinete Differentiation and Germination in Filamentous Cyanobacterium Trichormus variabilis ATCC 29413
2022-03-16

Planktonic freshwater filamentous cyanobacterium Trichormus variabilis ATCC 29413 (previously known as Anabaena variabilis) can differentiate heterocysts and akinetes to survive under different stress conditions. Whilst heterocysts enable diazotrophic growth, akinetes are spore-like resting cells that make the survival of the species possible under adverse growth conditions. Under suitable environmental conditions, they germinate to produce new vegetative filaments. Several morphological and physiological changes occur during akinete formation and germination. Here, using scanning electron microscopy (SEM), we found that the mature akinetes had a wrinkled envelope, and the surface of the envelope smoothened as the cell size increased during germination. Thereupon, the akinete envelope ruptured to release the short emerging filament. Focused ion beam–scanning electron microscopy (FIB/SEM) tomography of immature akinetes revealed the presence of cytoplasmic granules, presumably consisting of cyanophycin or glycogen. In addition, the akinete envelope architecture of different layers, the exopolysaccharide and glycolipid layers, could be visualized. We found that this multilayered envelope helped to withstand osmotic stress and to maintain the structural integrity. Furthermore, by fluorescence recovery after photobleaching (FRAP) measurements, using the fluorescent tracer calcein, we found that intercellular communication decreased during akinete formation as compared with the vegetative cells. In contrast, freshly germinating filaments restored cell communication.
Remorin proteins serves as membrane topology scaffolds in plants
2022-03-16

Abstract Organization of membrane topologies in plants has so far been mainly attributed to the cell wall and the cytoskeleton. Taking rhizobial infections of legume root cells, where plasma membranes undergo dynamic and large-scale topology changes, as an initial model, we challenged this paradigm and tested whether additional scaffolds such as plant-specific remorins that accumulate on highly curved and often wall-less plasma membrane domains, control local membrane dynamics. Indeed, loss-of-function mutants of the remorin protein SYMREM1 failed to develop stabilized membrane tubes as found in colonized cells in wild-type plants, but released empty membrane spheres instead. Expression of this and other remorins in wall-less protoplasts allowed engineering different membrane topologies ranging from membrane blebs to long membrane tubes. Reciprocally, mechanically induced membrane indentations were equally stabilized by SYMREM1. This function is likely supported by remorin oligomerization into antiparallel dimers and the formation of higher order membrane scaffolding structures. Taken together we describe an evolutionary confined mechanism that allows the stabilization of large-scale membrane conformations and curvatures in plants. One-sentence summary The remorin SYMREM1 evolved as structural membrane scaffold that stabilizes membrane tubulation and curvature during symbiotic intracellular infections.
Individualized Gaussian Process-based Prediction of Memory Performance and Biomarker Status in Ageing and Alzheimer’s disease
2022-03-16

Abstract Neuroimaging markers based on Magnetic Resonance Imaging (MRI) combined with various other measures (such as informative covariates, vascular risks, brain activity, neuropsychological test etc.,) might provide useful predictions of clinical outcomes during progression towards Alzheimer’s disease (AD). The Bayesian approach aims to provide a trade-off by employing relevant features combinations to build decision support systems in clinical settings where uncertainties are relevant. We tested the approach in the MRI data across 959 subjects, aged 59-89 years and 453 subjects with available neuropsychological test scores and CSF biomarker status (amyloid-beta ( Aβ )42/40 &amp; and phosphorylated tau (pTau)) from a large sample multi-centric observational cohort (DELCODE). In order to explore the beneficial combinations of information from different sources, we presented a MRI-based predictive modelling of memory performance and CSF biomarker status (positive or negative) in the healthy ageing group as well as subjects at risk of Alzheimer’s disease using a Gaussian process multikernel framework. Furthermore, we systematically evaluated predictive combinations of input feature sets and their model variations, i.e. (A) combinations of brain tissue classes and feature type (modulated vs. unmodulated), choices of filter size of smoothing (ranging from 0 to 15 mm full width at half maximum), and image resolution (1mm, 2mm, 4mm and 8mm); (B) incorporating demography and covariates (C) the impact of the size of the training data set (i.e., number of subjects); (D) the influence of reducing the dimensions of data and (E) choice of kernel types. Finally, the approach was tested to reveal individual cognitive scores at follow-up (up to 4 years) using the baseline features. The highest accuracy for memory performance prediction was obtained for a combination of neuroimaging markers, demographics, genetic information (ApoE4) and CSF-biomarkers explaining 57% of outcome variance in out of sample predictions. The best accuracy for Aβ 42 / 40 status classification was achieved for combination demographics, ApoE4 and memory score while usage of structural MRI improved the classification of individual patient’s pTau status.
Engineering the speedup of quantum tunneling in Josephson systems via\\n dissipation
2022-03-16

We theoretically investigate the escape rate occurring via quantum tunneling\\nin a system affected by tailored dissipation. Specifically, we study the\\nenvironmental assisted quantum tunneling of the superconducting phase in a\\ncurrent-biased Josephson junction. We consider Ohmic resistors inducing\\ndissipation both in the phase and in the charge of the quantum circuit. We find\\nthat the charge dissipation leads to an enhancement of the quantum escape rate.\\nThis effect appears already in the low Ohmic regime and also occurs in the\\npresence of phase dissipation that favors localization. Inserting realistic\\ncircuit parameters, we address the question of its experimental observability\\nand discuss suitable parameter spaces for the observation of the enhanced rate.\\n
On the Formation and Dynamical Evolution of Planets in Binaries
2022-03-16

Among the extrasolar planetary systems about 30 are located in a stellar binary orbiting one of the stars, preferably the more massive primary. The dynamical influence of the second companion alters firstly the orbital elements of the forming protoplanet directly and secondly the structure of the disk from which the planet formed which in turn will modify the planet's evolution. We present detailed analysis of these effects and present new hydrodynamical simulations of the evolution of protoplanets embedded in circumstellar disks in the presence of a companion star, and compare our results to the system Cep. To analyse the early formation of planetary embryos, we follow the evolution of a swarm of planetesimals embedded in a circumstellar disk. Finally, we study the evolution of planets embedded in circumbinary disks.
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense
2022-03-16

This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of Thlaspi arvense, investigating the genetic and environmental drivers of epigenetic variation. 207 lines from across Europe were grown in common environment and scored for genetic and DNA methylation variation by Whole Genome Sequencing and Whole Genome Bisulfite Sequencing respectively. This repository includes (1) average methylation values for all lines and the respective processed (transformed and/or corrected for coverage) values used for Genome Wide Association Studies (GWAS). (2) GWAS results (filtered for -log(p)&gt;1) for all processed average methylation values are available with the .gwas extention and can be easily opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/). (3) Variance Decomposition Analysis results of Differentially Methylated regions called using scripts available at https://github.com/Dario-Galanti/popDMRs_refine_VCA.
Spectral Analysis of Central Stars of Planetary Nebulae
2022-03-16

Spectral analysis by means of NLTE model atmospheres has presently arrived at a high level of sophistication. High-resolution spectra of central stars of planetary nebulae can be reproduced in detail from the infrared to the X-ray wavelength range. In the case of LSV +4621, the exciting star of Sh 2-216, we demonstrate the state-of-the-art in the determination of photospheric properties like, e.g., effective temperature, surface gravity, and abundances of elements from hydrogen to nickel. From such detailed model atmospheres, we can reliably predict the ionizing spectrum of a central star which is a necessary input for the precise analysis of its ambient nebula. NLTE model-atmosphere spectra, however, are not only accessible for specialists. In the framework of the German Astrophysical Virtual Observatory (GAVO), we provide pre-calculated grids of tables with synthetic spectra of hot, compact stars as well as a tool to calculate individual model-atmosphere spectra in order to make the use of synthetic stellar spectra as easy as the use of blackbody flux distributions had been in the last century.
Discrete Quantum Gravity: II. Simplicial complexes, irreps of SL(2,C), and a Lorentz invariant weight in a state sum model
2022-03-16

In part I of [1] we have developed the tensor and spin representation of SO(4) in order to apply it to the simplicial decomposition of the Barrett-Crane model. We attach to each face of a triangle the spherical function constructed from the Dolginov-Biedenharn function. In part II we apply the same technique to the Lorentz invariant state sum model. We need three new ingredients: the classification of the edges and the corresponding subspaces that arises in the simplicial decomposition, the irreps of SL(2,C) and its isomorphism to the bivectors appearing in the 4-simplices, the need of a zonal spherical function from the intertwining condition of the tensor product for the simple representations attached to the faces of the simplicial decomposition.
Embedding operators into strongly continuous semigroups
2022-03-16

We study linear operators on Banach spaces for which there exists a -semigroup such that . We present a necessary condition in terms of the spectral value 0 and give classes of examples where this can or cannot be achieved.
Microscopic Theory of Superconductor-Constriction-Superconductor Josephson Junctions in a Magnetic Field
2022-03-16

Self-consistent solutions of microscopic Eilenberger theory are presented for a two-dimensional model of a superconducting channel with a geometric constriction. Magnetic fields, external ones as well as those caused by the supercurrents, are included and the relevant equations are solved numerically without further assumptions. Results concerning the influence of temperature, geometric parameters, of and of external magnetic fields on the Andreev bound states in the weak link and on the current-phase relation are presented. We find that the Andreev bound states within the junction obtain peculiar substructure when a finite supercurrent flows. As long as the London penetration depth is comparable to or bigger than the extension of the constriction, the Josephson effect is independent of . Furthermore, the weak link is very insensitive to external magnetic fields. Features restricted to a self-consistent calculation are discussed.
Lattice polytopes of degree 2
2022-03-16

A theorem of Scott gives an upper bound for the normalized volume of lattice polygons with exactly interior lattice points. We will show that the same bound is true for the normalized volume of lattice polytopes of degree 2 even in higher dimensions. In particular, there is only a finite number of quadratic polynomials with fixed leading coefficient being the -polynomial of a lattice polytope.
The zero-one law for planar random walks in i.i.d. random environments revisited
2022-03-16

In this note we present a simplified proof of the zero-one law by Merkl and Zerner (2001) for directional transience of random walks in i.i.d. random environments (RWRE) on the square lattice. Also, we indicate how to construct a two-dimensional counterexample in a non-uniformly elliptic and stationary environment which has better ergodic properties than the example given by Merkl and Zerner.
Category theorems for stable semigroups
2022-03-16

Inspired by the classical category theorems of Halmos and Rohlin for the discrete measure preserving transformations, we prove analogous results in the abstract setting of unitary and isometric C_0-semigroups on a separable Hilbert space. More presicely, we show that the set of all weakly stable unitary groups (isometric semigroups) is of first category, while the set of all almost weakly stable unitary groups (isometric semigroups) is residual for an appropriate topology.
First-person visualizations of the special and general theory of relativity
2022-03-16

Visualizations that adopt a first-person point of view allow observation and, in the case of interactive simulations, experimentation with relativistic scenes. This paper gives examples of three types of first-person visualizations: watching objects that move at nearly the speed of light, being a high-speed observer looking at a static environment and having a look-around near a compact object. I illustrate and explain the main aspects of the visual observations, outline their use in teaching relativity and report on teaching experiences. For teaching purposes, our visualization work is available on the web site http://www.spacetimetravel.org and its German counterpart http://www.tempolimit-lichtgeschwindigkeit.de . This paper assumes some basic knowledge about relativity on the part of the reader. It addresses instructors of physics at the undergraduate and advanced secondary school level as well as their students.
Discrete Quantum Gravity: I. Zonal spherical functions of the representationsof the SO(4,R) group with respect to the SU(2) subgroup and their application to the Barrett-Crane model
2022-03-16

Starting from the defining transformations of complex matrices for the group, we construct the fundamental representation and the tensor and spinor representations of the group . Given the commutation relations for the corresponding algebra, the unitary representations of the group in terms of the generalized Euler angles are constructed. The crucial step for the Barrett-Crane model in Quantum Gravity is the description of the amplitude for the quantum 4-simplex that is used in the state sum partition function. We obtain the zonal spherical functions for the construction of the SO(4,R) invariant weight and associate them to the triangular faces of the 4-simplices.
UV and FUV spectroscopy of the hybrid PG 1159-type central star NGC 7094
2022-03-16

Previous studies aiming at the iron-abundance determination in three PG 1159 stars (K 1-16, PG 1159-035, NGC 7094) and a [WC]-PG 1159 transition star (Abell 78) have revealed that no object shows any iron line in the UV spectrum. The stars are iron-deficient by at least 1 dex, typically. A possible explanation is that iron nuclei were transformed by neutron captures into heavier elements (s-process), however, the extent of the iron-destruction would be much stronger than predicted by AGB star models. But if n-captures are the right explanation, then we should observe an enrichment of trans-iron elements. In this paper we report on our search for a possible nickel overabundance in one of the four Fe deficient PG 1159 stars, namely the central star NGC 7094. We are unable to identify any nickel line in HST and FUSE spectra and conclude that Ni is not overabundant. It is conceivable that iron was transformed into even heavier elements, but their identification suffers from the lack of atomic data.