julilili42/papers huggingface dataset:
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
2022-03-10

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. Results: We present the System Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the cooperative development of the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyze qualitative models. Conclusion: SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.
The smooth cyclotron line in Her X-1 as seen with NuSTAR
2022-03-10

Her X-1, one of the brightest and best studied X-ray binaries, shows a cyclotron resonant scattering feature (CRSF) near 37 keV. This makes it an ideal target for detailed study with the Nuclear Spectroscopic Telescope Array (NuSTAR), taking advantage of its excellent hard X-ray spectral resolution. We observed Her X-1 three times, coordinated with Suzaku, during one of the high flux intervals of its 35d super-orbital period. This paper focuses on the shape and evolution of the hard X-ray spectrum. The broad-band spectra can be fitted with a powerlaw with a high-energy cutoff, an iron line, and a CRSF. We find that the CRSF has a very smooth and symmetric shape, in all observations and at all pulse-phases. We compare the residuals of a line with a Gaussian optical depth profile to a Lorentzian optical depth profile and find no significant differences, strongly constraining the very smooth shape of the line. Even though the line energy changes dramatically with pulse phase, we find that its smooth shape does not. Additionally, our data show that the continuum is only changing marginally between the three observations. These changes can be explained with varying amounts of Thomson scattering in the hot corona of the accretion disk. The average, luminosity-corrected CRSF energy is lower than in past observations and follows a secular decline. The excellent data quality of NuSTAR provides the best constraint on the CRSF energy to date.
Mean curvature flow with surgery of mean convex surfaces in $\\mathbb{R}^3$
2022-03-10

We define a notion of mean curvature flow with surgery for two-dimensional surfaces in with positive mean curvature. Our construction relies on the earlier work of Huisken and Sinestrari in the higher dimensional case. One of the main ingredients in the proof is a new estimate for the inscribed radius established by the first author.
Fighting network space: it is time for an SQL-type language to filter phylogenetic networks
2022-03-10

The search space of rooted phylogenetic trees is vast and a major research focus of recent decades has been the development of algorithms to effectively navigate this space. However this space is tiny when compared with the space of rooted phylogenetic networks, and navigating this enlarged space remains a poorly understood problem. This, and the difficulty of biologically interpreting such networks, obstructs adoption of networks as tools for modelling reticulation. Here, we argue that the superimposition of biologically motivated constraints, via an SQL-style language, can both stimulate use of network software by biologists and potentially significantly prune the search space.
Excursions of excited random walks on integers
2022-03-10

Several phase transitions for excited random walks on the integers are known to be characterized by a certain drift parameter delta. For recurrence/transience the critical threshold is |delta|=1, for ballisticity it is |delta|=2 and for diffusivity |delta|=4. In this paper we establish a phase transition at |delta|=3. We show that the expected return time of the walker to the starting point, conditioned on return, is finite iff |delta|&gt;3. This result follows from an explicit description of the tail behaviour of the return time as a function of delta, which is achieved by diffusion approximation of related branching processes by squared Bessel processes.
Optimal rigidity estimates for nearly umbilical surfaces in arbitrary codimension
2022-03-10

In [dLMu05], DeLellis and Müller proved a quantitative version of Codazzi's theorem, namely for a smooth embedded surface with area normalized to , it was shown that , and building on this, closeness of to a round sphere in was established, when is small. This was supplemented in [dLMu06] by giving a conformal parametrization with small conformal factor in , again when is small. In this article, we extend these results to arbitrary codimension. In contrast to [dLMu05], our argument is not based on the equation of Mainardi-Codazzi, but instead uses the monotonicity formula for varifolds.
Explicit Riemannian manifolds with unexpectedly behaving center of mass
2022-03-10

The (relativistic) center of mass of an asymptotically flat Riemannian manifold is often defined by certain surface integral expressions evaluated along a foliation of the manifold near infinity, e. g. by Arnowitt, Deser, and Misner (ADM). There are also what we call 'abstract' definitions of the center of mass in terms of a foliation near infinity itself, going back to the constant mean curvature (CMC-) foliation studied by Huisken and Yau; these give rise to surface integral expressions when equipped with suitable systems of coordinates. We discuss subtle asymptotic convergence issues regarding the ADM- and the coordinate expressions related to the CMC-center of mass. In particular, we give explicit examples demonstrating that both can diverge -- in a setting where Einstein's equation is satisfied. We also give explicit examples of the same asymptotic order of decay with prescribed mass and center of mass. We illustrate both phenomena by providing analogous examples in Newtonian gravity. Our examples conflict with some results in the literature.
Two-Page Book Embeddings of 4-Planar Graphs
2022-03-10

Back in the Eighties, Heath showed that every 3-planar graph is subhamiltonian and asked whether this result can be extended to a class of graphs of degree greater than three. In this paper we affirmatively answer this question for the class of 4-planar graphs. Our contribution consists of two algorithms: The first one is limited to triconnected graphs, but runs in linear time and uses existing methods for computing hamiltonian cycles in planar graphs. The second one, which solves the general case of the problem, is a quadratic-time algorithm based on the book-embedding viewpoint of the problem.
A note on the short-time quantum propagator
2022-03-10

In the Feynman formalism of quantum mechanics one encounters a postulate, namely, that the propagator in an infinitesimal time-interval is the classical wave function. This postulate, which was later studied thoroughly by Holland, was recently highlighted by using the improved Makri-Miller propagator. The present note, whose conclusion is in agreement with that recent achievement, demonstrates that the Heisenberg picture of quantum mechanics invariably includes the Feynman postulate and is able to yield a proof for it. In other words, by starting out from the Heisenberg picture, it is proved that when terms of second-order in time can be neglected, the dynamics of a system is classical.
Smooth Orthogonal Drawings of Planar Graphs
2022-03-10

In \\emph{smooth orthogonal layouts} of planar graphs, every edge is an alternating sequence of axis-aligned segments and circular arcs with common axis-aligned tangents. In this paper, we study the problem of finding smooth orthogonal layouts of low \\emph{edge complexity}, that is, with few segments per edge. We say that a graph has \\emph{smooth complexity} k---for short, an SC_k-layout---if it admits a smooth orthogonal drawing of edge complexity at most . Our main result is that every 4-planar graph has an SC_2-layout. While our drawings may have super-polynomial area, we show that, for 3-planar graphs, cubic area suffices. Further, we show that every biconnected 4-outerplane graph admits an SC_1-layout. On the negative side, we demonstrate an infinite family of biconnected 4-planar graphs that requires exponential area for an SC_1-layout. Finally, we present an infinite family of biconnected 4-planar graphs that does not admit an SC_1-layout.
A note on multi-time equations in quantum mechanics
2022-03-10

The main aim of this note is to show that the formalism of multi-time equations in quantum mechanics meant to represent a manifestly Lorentz-invariant theory suffers from at least three imperfections: (1) It does not cover those physical systems for which the Schrödinger picture of quantum mechanics does not exist. (2) The integrabiliy condition which has been proposed in the formalism does not imply as necessary that for every partial Hamiltonian there exists a Schrödinger equation. (3) The formalism does not generally allow for interactions even in a non-relativistic multi-particle quantum system.
't Hooft loop and the phases of SU(2) LGT
2022-03-10

We analyze the vacuum structure of SU(2) lattice gauge theories in D=2,3,4, concentrating on the stability of 't Hooft loops. High precision calculations have been performed in D=3; similar results hold also for D=4 and D=2. We discuss the impact of our findings on the continuum limit of Yang-Mills theories.
Point Configurations and Translations
2022-03-10

The spaces of point configurations on the projective line up to the action of and its maximal torus are canonically compactified by the Grothdieck-Knudsen and Losev-Manin moduli spaces and respectively. We examine the configuration space up to the action of the maximal unipotent group and define an analogous compactification. For this we first assign a canonical quotient to the action of a unipotent group on a projective variety. Moreover, we show that similar to and this quotient arises in a sequence of blow-ups from a product of projective spaces.
Algorithms and Bounds for Drawing Non-planar Graphs with Crossing-free Subgraphs
2022-03-10

We initiate the study of the following problem: Given a non-planar graph G and a planar subgraph S of G, does there exist a straight-line drawing Γ of G in the plane such that the edges of S are not crossed in Γ by any edge of G? We give positive and negative results for different kinds of connected spanning subgraphs S of G. Moreover, in order to enlarge the subset of instances that admit a solution, we consider the possibility of bending the edges of G not in S; in this setting we discuss different trade-offs between the number of bends and the required drawing area.
Long-term analysis of numerical integrators for oscillatory Hamiltonian systems under minimal non-resonance conditions
2022-03-10

For trigonometric and modified trigonometric integrators applied to oscillatory Hamiltonian differential equations with one or several constant high frequencies, near-conservation of the total and oscillatory energies are shown over time scales that cover arbitrary negative powers of the step size. This requires non-resonance conditions between the step size and the frequencies, but in contrast to previous results the results do not require any non-resonance conditions among the frequencies. The proof uses modulated Fourier expansions with appropriately modified frequencies.
Autocatalytic Sets and Biological Specificity
2022-03-10

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from within that system. RAF (reflexively autocatalytic and food-generated) theory provides a formal way to study such processes. Beginning with Kauffman's notion of "collectively autocatalytic sets", this theory has been further developed over the last decade with the discovery of efficient algorithms and new mathematical analysis. In this paper, we study how the behaviour of a simple binary polymer model can be extended to models where the pattern of catalysis more precisely reflects the ligation and cleavage reactions involved. We find that certain properties of these models are similar to, and can be accurately predicted from, the simple binary polymer model; however, other properties lead to slightly different estimates. We also establish a number of new results concerning the structure of RAFs in these systems.
Strong Effect of Weak Charging in Suspensions of Anisotropic Colloids
2022-03-10

Suspensions of hard colloidal particles frequently serve as model systems in studies on fundamental aspects of phase transitions. But often colloidal particles that are considered as ``hard'' are in fact weakly charged. If the colloids are spherical, weak charging has a only a weak effect on the structural properties of the suspension, which can be easily corrected for. However, this does not hold for anisotropic particles. We introduce a model for the interaction potential between charged ellipsoids of revolution (spheroids) based on the Derjaguin approximation of Debye--Hückel Theory and present a computer simulation study on aspects of the system's structural properties and phase behaviour. In line with previous experimental observations, we find that even a weak surface charge has a strong impact on the correlation functions. A likewise strong impact is seen on the phase behaviour, in particular, we find stable cubatic order in suspensions of oblate ellipsoids.
Genetic information, physical interpreters and thermodynamics; the material-informatic basis of biosemiosis
2022-03-10

The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of construction. In reality, any biochemical machine for which a DNA codescript is efficacious is itself produced through the mechanical interpretation of an identical or very similar codescript. In these terms the origin of life can be described as a bootstrap process involving the simultaneous accumulation of genetic information and the generation of a machine that interprets it as instructions for its own construction. This problem is discussed within the theoretical frameworks of thermodynamics, informatics and self-reproducing automata, paying special attention to the physico-chemical origin of genetic coding and the conditions, both thermodynamic and informatic, which a system must fulfil in order for it to sustain semiosis. The origin of life is equated with biosemiosis
Capillary attraction induced collapse of colloidal monolayers at fluid interfaces
2022-03-10

We investigate the evolution of a system of colloidal particles, trapped at a fluid interface and interacting via capillary attraction, as function of the range of the capillary interaction and temperature. We address the collapse of an initially homogeneous particle distribution and of a radially symmetric (disk--shaped) distribution of finite size, both theoretically by using a perturbative approach inspired by cosmological models and numerically by means of Brownian dynamics (BD) and dynamical density functional theory (DDFT). The results are summarized in a "dynamical phase diagram", describing a smooth crossover from collective (gravitational-like) collapse to local (spinodal-like) clustering. In this crossover region, the evolution exhibits a peculiar shock wave behavior at the outer rim of the contracting, disk-shaped distribution.
Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
2022-03-11

Abstract Activation of plant pattern-triggered immunity (PTI) relies on the recognition of microbe-derived structures, termed patterns, through plant-encoded surface-resident pattern recognition receptors (PRRs). We show that proteobacterial translation initiation factor 1 (IF1) triggers PTI in Arabidopsis thaliana and related Brassicaceae species. Unlike for most other immunogenic patterns, IF1 elicitor activity cannot be assigned to a small peptide epitope, suggesting that tertiary fold features are required for IF1 receptor activation. We have deployed natural variation in IF1 sensitivity to identify Arabidopsis leucine-rich repeat (LRR) receptor-like protein 32 (RLP32) as IF1 receptor using a restriction site-associated DNA sequencing approach. RLP32 confers IF1 sensitivity to rlp32 mutants, IF1-insensitive Arabidopsis accessions and IF1-insensitive Nicotiana benthamiana , binds IF1 specifically and forms complexes with LRR receptor kinases SOBIR1 and BAK1 to mediate signaling. Similar to other PRRs, RLP32 confers resistance to Pseudomonas syringae , highlighting an unexpectedly complex array of bacterial pattern sensors within a single plant species.
An oomycete NLP cytolysin forms transient small pores in lipid membranes
2022-03-11

Microbial plant pathogens secrete a range of effector proteins that damage host plants and consequently constrain global food production. Necrosis and ethylene-inducing peptide 1–like proteins (NLPs) are produced by numerous phytopathogenic microbes that cause important crop diseases. Many NLPs are cytolytic, causing cell death and tissue necrosis by disrupting the plant plasma membrane. Here, we reveal the unique molecular mechanism underlying the membrane damage induced by the cytotoxic model NLP. This membrane disruption is a multistep process that includes electrostatic-driven, plant-specific lipid recognition, shallow membrane binding, protein aggregation, and transient pore formation. The NLP-induced damage is not caused by membrane reorganization or large-scale defects but by small membrane ruptures. This distinct mechanism of lipid membrane disruption is highly adapted to effectively damage plant cells.
Exploring the Structure and Interrelations of Time-Stable Psychological Resilience, Psychological Vulnerability, and Social Cohesion
2022-03-11

The current study explores the relationship between three constructs of high relevance in the context of adversities which have, however, not yet been systematically linked on the level of psychological dispositions: psychological vulnerability, psychological resilience, and social cohesion. Based on previous theoretical and empirical frameworks, a collection of trait questionnaires was assessed in a Berlin sample of 3,522 subjects between 18 and 65 years of age. Using a confirmatory factor analytical approach, we found no support for a simple three-factor structure. Results from exploratory structural analyses suggest that instead of psychological resilience and psychological vulnerability constituting two separate factors, respective indicators load on one bipolar latent factor. Interestingly, some psychological resilience indicators contributed to an additional specific latent factor, which may be interpreted as adaptive capacities, that is, abilities to adapt to changes or adjust to consequences of adversities. Furthermore, instead of evidence for one single social cohesion factor on the psychological level, indicators of perceived social support and loneliness formed another specific factor of social belonging, while indicators of prosocial competencies were found to form yet another distinct factor, which was positively associated to the other social factors, adaptive capacities and social belonging. Our results suggest that social cohesion is composed of different independent psychological components, such as trust, social belonging, and social skills. Furthermore, our findings highlight the importance of social capacities and belonging for psychological resilience and suggest that decreasing loneliness and increasing social skills should therefore represent a valuable intervention strategy to foster adaptive capacities.
Activated Platelets Upregulate β2 Integrin Mac-1 (CD11b/CD18) on Dendritic Cells, Which Mediates Heterotypic Cell–Cell Interaction
2022-03-11

Abstract Recent evidence suggests interaction of platelets with dendritic cells (DCs), while the molecular mechanisms mediating this heterotypic cell cross-talk are largely unknown. We evaluated the role of integrin Mac-1 (αMβ2, CD11b/CD18) on DCs as a counterreceptor for platelet glycoprotein (GP) Ibα. In a dynamic coincubation model, we observed interaction of human platelets with monocyte-derived DCs, but also that platelet activation induced a sharp increase in heterotypic cell binding. Inhibition of CD11b or GPIbα led to significant reduction of DC adhesion to platelets in vitro independent of GPIIbIIIa, which we confirmed using platelets from Glanzmann thrombasthenia patients and transgenic mouse lines on C57BL/6 background (GPIbα−/−, IL4R-GPIbα-tg, and muMac1 mice). In vivo, inhibition or genetic deletion of CD11b and GPIbα induced a significant reduction of platelet-mediated DC adhesion to the injured arterial wall. Interestingly, only intravascular antiCD11b inhibited DC recruitment, suggesting a dynamic DC–platelet interaction. Indeed, we could show that activated platelets induced CD11b upregulation on Mg2+-preactivated DCs, which was related to protein kinase B (Akt) and dependent on P-selectin and P-selectin glycoprotein ligand 1. Importantly, specific pharmacological targeting of the GPIbα–Mac-1 interaction site blocked DC–platelet interaction in vitro and in vivo. These results demonstrate that cross-talk of platelets with DCs is mediated by GPIbα and Mac-1, which is upregulated on DCs by activated platelets in a P-selectin glycoprotein ligand 1–dependent manner.
Real-Time Control of a Multi-Degree-of-Freedom Mirror Myoelectric Interface During Functional Task Training
2022-03-11

Motor learning mediated by motor training has in the past been explored for rehabilitation. Myoelectric interfaces together with exoskeletons allow patients to receive real-time feedback about their muscle activity. However, the number of degrees of freedom that can be simultaneously controlled is limited, which hinders the training of functional tasks and the effectiveness of the rehabilitation therapy. The objective of this study was to develop a myoelectric interface that would allow multi-degree-of-freedom control of an exoskeleton involving arm, wrist and hand joints, with an eye toward rehabilitation. We tested the effectiveness of a myoelectric decoder trained with data from one upper limb and mirrored to control a multi-degree-of-freedom exoskeleton with the opposite upper limb (i.e., mirror myoelectric interface) in 10 healthy participants. We demonstrated successful simultaneous control of multiple upper-limb joints by all participants. We showed evidence that subjects learned the mirror myoelectric model within the span of a five-session experiment, as reflected by a significant decrease in the time to execute trials and in the number of failed trials. These results are the necessary precursor to evaluating if a decoder trained with EMG from the healthy limb could foster learning of natural EMG patterns and lead to motor rehabilitation in stroke patients.