julilili42/papers huggingface dataset:
Bartonella taylorii: A model organism for studying Bartonella infection in vitro and in vivo
2022-03-11

Abstract Bartonella spp. are Gram-negative facultative intracellular pathogens that infect diverse mammals and cause a long-lasting intra-erythrocytic bacteremia in their natural host. These bacteria translocate Bartonella effector proteins (Beps) into host cells via their VirB/VirD4 type 4 secretion system (T4SS) in order to subvert host cellular functions, thereby leading to the downregulation of innate immune responses. Most studies on the functional analysis of the VirB/VirD4 T4SS and the Beps were performed with the major zoonotic pathogen Bartonella henselae for which efficient in vitro infection protocols have been established. However, its natural host, the cat, is unsuitable as an experimental infection model. In vivo studies were mostly confined to rodent models using rodent-specific Bartonella species, while the in vitro infection protocols devised for B. henselae are not transferable for those pathogens. The disparities of in vitro and in vivo studies in different species has hampered progress in our understanding of Bartonella pathogenesis. Here we describe the murine-specific strain B. taylorii IBS296 as a new model organism facilitating the study of bacterial pathogenesis both in vitro in cell cultures and in vivo in laboratory mice. We implemented the split NanoLuc luciferase-based translocation assay to study BepD translocation through the VirB/VirD4 T4SS. We found increased effector-translocation into host cells if the bacteria were grown on tryptic soy agar (TSA) plates and experienced a temperature shift immediately before infection. The improved infectivity in vitro could be correlated to an upregulation of the VirB/VirD4 T4SS. Using our adapted infection protocols, we showed BepD-dependent immunomodulatory phenotypes in vitro. In mice, the implemented growth conditions enabled infection by a massively reduced inoculum without having an impact on the course of the intra-erythrocytic bacteremia. The established model opens new avenues to study the role of the VirB/VirD4 T4SS and the translocated Bep effectors in vitro and in vivo.
On the external branches of coalescents with multiple collisions
2022-03-11

A recursion for the joint moments of the external branch lengths for coalescents with multiple collisions ( -coalescents) is provided. This recursion is used to derive asymptotic results as the sample size tends to infinity for the joint moments of the external branch lengths and for the moments of the total external branch length of the Bolthausen-Sznitman coalescent. These asymptotic results are based on a differential equation approach, which is as well useful to obtain exact solutions for the joint moments of the external branch lengths for the Bolthausen-Sznitman coalescent. The results for example show that the lengths of two randomly chosen external branches are positively correlated for the Bolthausen--Sznitman coalescent, whereas they are negatively correlated for the Kingman coalescent provided that .
Excited random walks: results, methods, open problems
2022-03-12

We consider a class of self-interacting random walks in deterministic or random environments, known as excited random walks or cookie walks, on the d-dimensional integer lattice. The main purpose of this paper is two-fold: to give a survey of known results and some of the methods and to present several new results. The latter include functional limit theorems for transient one-dimensional excited random walks in bounded i.i.d. cookie environments as well as some zero-one laws. Several open problems are stated.
PplT domain proteins – ubiquitous potential prokaryotic phospholipid translocases
2022-03-12

Abstract Flippase proteins exchanging phospholipids between the cytoplasmic membrane leaflets have been identified in Eukaryotes but remained largely unknown in Prokaryotes. Only MprF proteins that synthesize aminoacyl phospholipids in some bacteria have been found to contain a domain that translocates the produced lipids. We show here that this domain, which we named ‘prokaryotic phospholipid translocator’ (PplT), is widespread in Bacteria and Archaea, encoded as a separate protein or fused to different types of enzymes. We also demonstrate that the Escherichia coli PplT protein interacts with many phospholipid-synthetic enzymes and deletion of pplT impaired bacterial growth, which supports its potential role in membrane lipid metabolism. PplT domain proteins may be general prokaryotic lipid flippases with critical roles in cellular homeostasis.
The Be/X-ray binary A0535+26 during its recent 2009/2010 outbursts
2022-03-12

The Be/X-ray binary A0535+26 showed a giant outburst in December 2009 that reached ~5.14 Crab in the 15-50 keV range. Unfortunately, due to Sun constraints it could not be observed by most X-ray satellites. The outburst was preceded by four weaker outbursts associated with the periastron passage of the neutron star. The fourth of them, in August 2009, presented a peculiar double-peaked light curve, with a first peak lasting about 9 days that reached a (15-50 keV) flux of 440 mCrab. The flux then decreased to less than 220 mCrab, and increased again reaching 440 Crab around the periastron. The outburst was monitored with INTEGRAL, RXTE, and Suzaku TOO observations. One orbital period (~111 days) after the 2009 giant outburst, a new and unexpectedly bright outburst took place (~1.4Crab in the 15-50 keV range). It was monitored with TOO obs ervations with INTEGRAL, RXTE, Suzaku, and Swift. First results of the spectral and timing analysis of these observations are presented, with a specific focus on the cyclotron lines present in the system and its variation with the mass accretion rate.
Regular Languages are Church-Rosser Congruential
2022-03-12

This paper proves a long standing conjecture in formal language theory. It shows that all regular languages are Church-Rosser congruential. The class of Church-Rosser congruential languages was introduced by McNaughton, Narendran, and Otto in 1988. A language L is Church-Rosser congruential, if there exists a finite confluent, and length-reducing semi-Thue system S such that L is a finite union of congruence classes modulo S. It was known that there are deterministic linear context-free languages which are not Church-Rosser congruential, but on the other hand it was strongly believed that all regular language are of this form. Actually, this paper proves a more general result.
Approximating Minimum Manhattan Networks in Higher Dimensions
2022-03-12

We study the minimum Manhattan network problem, which is defined as follows. Given a set of points called \\emph{terminals} in , find a minimum-length network such that each pair of terminals is connected by a set of axis-parallel line segments whose total length is equal to the pair's Manhattan (that is, -) distance. The problem is NP-hard in 2D and there is no PTAS for 3D (unless ). Approximation algorithms are known for 2D, but not for 3D. We present, for any fixed dimension and any , an -approximation algorithm. For 3D, we also give a -approximation algorithm for the case that the terminals are contained in the union of parallel planes.
Factorially graded rings and Cox rings
2022-03-12

Cox rings of normal varieties are factorially graded, i.e. homogeneous elements allow a unique decomposition into homogeneous factors. We study this property from an algebraic point of view and give a criterion which in a sense reduces it to factoriality. This will allow us to detect and construct Cox rings in a purely algebraic manner.
Every Formula-Based Logic Program Has a Least Infinite-Valued Model
2022-03-12

Every definite logic program has as its meaning a least Herbrand model with respect to the program-independent ordering "set-inclusion". In the case of normal logic programs there do not exist least models in general. However, according to a recent approach by Rondogiannis and Wadge, who consider infinite-valued models, every normal logic program does have a least model with respect to a program-independent ordering. We show that this approach can be extended to formula-based logic programs (i.e., finite sets of rules of the form A\\leftarrowF where A is an atom and F an arbitrary first-order formula). We construct for a given program P an interpretation M_P and show that it is the least of all models of P. Keywords: Logic programming, semantics of programs, negation-as-failure, infinite-valued logics, set theory
Uniform families of ergodic operator nets
2022-03-12

We study mean ergodicity in amenable operator semigroups and establish the connection to the convergence of strong and weak ergodic nets. We then use these results in order to show the convergence of uniform families of ergodic nets that appear in topological Wiener-Wintner theorems.
Implications of the non-detection of X-ray emission from HD 149427
2022-03-12

HD 149427 is a very enigmatic object. It has been classified either as a planetary nebula or as a D'-type symbiotic star. Its distance is also highly uncertain. Furthermore, HD 149427 is a potential jet source. We report the non-detection of X-ray emission from HD 149427 and explore the implications to its nature. We observed the object with XMM-Newton with an effective exposure time of 33.5 ks. The upper limit for the flux of the X-ray emission in the soft band (&lt;2 keV) is 10^-15 erg/s/cm^2, while in the hard band (&gt;2 keV) it is about 10^-14 erg/s/cm^2. We discuss the implication of our results in light of the possible natures of HD 149427 -- being a planetary nebula or a symbiotic star, close or very distant. The derived upper limits on the mass accretion rate of the white dwarf are untypical for symbiotic stars and may favor the picture of HD 149427 being a young PN. HD 149427 might be a symbiotic star in hibernation -- if a symbiotic star at all. We estimate the possible mass-loss rate and kinetic luminosity of the jet and find no contradiction with our upper limit of soft X-ray emission. Therefore the jet may be still present but it was too faint to be detected via soft X-ray emission.
Computing Cartograms with Optimal Complexity
2022-03-12

In a rectilinear dual of a planar graph vertices are represented by simple rectilinear polygons and edges are represented by side-contact between the corresponding polygons. A rectilinear dual is called a cartogram if the area of each region is equal to a pre-specified weight of the corresponding vertex. The complexity of a cartogram is determined by the maximum number of corners (or sides) required for any polygon. In a series of papers the polygonal complexity of such representations for maximal planar graphs has been reduced from the initial 40 to 34, then to 12 and very recently to the currently best known 10. Here we describe a construction with 8-sided polygons, which is optimal in terms of polygonal complexity as 8-sided polygons are sometimes necessary. Specifically, we show how to compute the combinatorial structure and how to refine the representation into an area-universal rectangular layout in linear time. The exact cartogram can be computed from the area-universal rectangular layout with numerical iteration, or can be approximated with a hill-climbing heuristic. We also describe an alternative construction for Hamiltonian maximal planar graphs, which allows us to directly compute the cartograms in linear time. Moreover, we prove that even for Hamiltonian graphs 8-sided rectilinear polygons are necessary, by constructing a non-trivial lower bound example. The complexity of the cartograms can be reduced to 6 if the Hamiltonian path has the extra property that it is one-legged, as in outer-planar graphs. Thus, we have optimal representations (in terms of both polygonal complexity and running time) for Hamiltonian maximal planar and maximal outer-planar graphs.
Upward Point Set Embeddability for Convex Point Sets is in $P$
2022-03-12

In this paper, we present a polynomial dynamic programming algorithm that tests whether a -vertex directed tree has an upward planar embedding into a convex point-set of size . Further, we extend our approach to the class of outerplanar digraphs. This nontrivial and surprising result implies that any given digraph can be efficiently tested for an upward planar embedding into a given convex point set.
Streaming algorithms for recognizing nearly well-parenthesized expressions
2022-03-12

We study the streaming complexity of the membership problem of 1-turn-Dyck2 and Dyck2 when there are a few errors in the input string. 1-turn-Dyck2 with errors: We prove that there exists a randomized one-pass algorithm that given x checks whether there exists a string x' in 1-turn-Dyck2 such that x is obtained by flipping at most locations of x' using: - O(k log n) space, O(k log n) randomness, and poly(k log n) time per item and with error at most 1/poly(n). - O(k^{1+epsilon} + log n) space for every 0 &lt;= epsilon &lt;= 1, O(log n) randomness, O(polylog(n) + poly(k)) time per item, with error at most 1/8. Here, we also prove that any randomized one-pass algorithm that makes error at most k/n requires at least Omega(k log(n/k)) space to accept strings which are exactly k-away from strings in 1-turn-Dyck2 and to reject strings which are exactly (k+2)-away from strings in 1-turn-Dyck2. Since 1-turn-Dyck2 and the Hamming Distance problem are closely related we also obtain new upper and lower bounds for this problem. Dyck2 with errors: We prove that there exists a randomized one-pass algorithm that given x checks whether there exists a string x' in Dyck2 such that x is obtained from x' by changing (in some restricted manner) at most k positions using: - O(k log n + sqrt(n log n)) space, O(k log n) randomness, poly(k log n) time per element and with error at most 1/poly(n). - O(k^(1+epsilon)+ sqrt(n log n)) space for every 0 &lt;= epsilon &lt;= 1, O(log n) randomness, O(polylog(n) + poly(k)) time per element, with error at most 1/8.
The Open Graph Archive: A Community-Driven Effort
2022-03-12

In order to evaluate, compare, and tune graph algorithms, experiments on well designed benchmark sets have to be performed. Together with the goal of reproducibility of experimental results, this creates a demand for a public archive to gather and store graph instances. Such an archive would ideally allow annotation of instances or sets of graphs with additional information like graph properties and references to the respective experiments and results. Here we examine the requirements, and introduce a new community project with the aim of producing an easily accessible library of graphs. Through successful community involvement, it is expected that the archive will contain a representative selection of both real-world and generated graph instances, covering significant application areas as well as interesting classes of graphs.
Leading order QCD in Coulomb gauge
2022-03-12

Coulomb gauge QCD in the first order formalism can be written in terms of a ghost-free, nonlocal action that ensures total color charge conservation via Gauss' law. Making an Ansatz whereby the nonlocal term (the Coulomb kernel) is replaced by its expectation value, the resulting Dyson-Schwinger equations can be derived. With a leading order truncation, these equations reduce to the gap equations for the static gluon and quark propagators obtained from a quasi-particle approximation to the canonical Hamiltonian approach. Moreover a connection to the heavy quark limit can be established, allowing an intuitive explanation for the charge constraint and infrared divergences.
A quadratic kernel for computing the hybridization number of multiple trees
2022-03-12

It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixed-parameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel.
Magnetic hysteresis effects in superconducting coplanar microwave resonators
2022-03-12

We performed transmission spectroscopy experiments on coplanar half wavelength niobium resonators at a temperature T=4.2 K. We observe not only a strong dependence of the quality factor Q and the resonance frequency f_res on an externally applied magnetic field but also on the magnetic history of our resonators, i.e. on the spatial distribution of trapped Abrikosov vortices in the device. We find these results to be valid for a broad range of frequencies and angles between the resonator plane and the magnetic field direction as well as for resonators with and without antidots near the edges of the center conductor and the ground planes. In a detailed analysis we show, that characteristic features of the experimental data can only be reproduced in calculations, if a highly inhomogeneous rf-current density and a flux density gradient with maxima at the edges of the superconductor is assumed. We furthermore demonstrate, that the hysteretic behaviour of the resonator properties can be used to considerably reduce the vortex induced losses and to fine-tune the resonance frequency by the proper way of cycling to a desired magnetic field.
Magnetized neutron star atmospheres: beyond cold plasma approximation
2022-03-12

All the neutron star (NS) atmosphere models published so far have been calculated in the "cold plasma approximation", which neglects the relativistic effects in the radiative processes, such as cyclotron emission/absorption at harmonics of cyclotron frequency. Here we present new NS atmosphere models which include such effects. We calculate a set of models for effective temperatures T_eff =1-3 MK and magnetic fields B \\sim 10^{10}-10^{11} G, typical for the so-called central compact objects (CCOs) in supernova remnants, for which the electron cyclotron energy E_{c,e} and its first harmonics are in the observable soft X-ray range. Although the relativistic parameters, such as kT_eff /(m_e c^2) and E_{c,e} /(m_e c^2), are very small for CCOs, the relativistic effects substantially change the emergent spectra at the cyclotron resonances, E \\approx sE_{c,e} (s=1, 2,...). Although the cyclotron absorption features can form in a cold plasma due to the quantum oscillations of the free-free opacity, the shape and depth of these features change substantially if the relativistic effects are included. In particular, the features acquire deep Doppler cores, in which the angular distribution of the emergent intensity is quite different from that in the cold plasma approximation. The relative contributions of the Doppler cores to the equivalent widths of the features grow with increasing the quantization parameter b_eff = E_{c,e}/kT_eff and harmonic number s. The total equivalent widths of the features can reach \\sim 150-250 eV; they increase with growing b_eff and are smaller for higher harmonics.
Developing a wearable Augmented Reality for treating phantom limb pain using the Microsoft Hololens 2
2022-03-13

After the amputation of a limb, up to 90% of the patients report a feeling of the missing body part still being present in their perception. This effect is known as phantom limb sensation and ranges from the simple feeling of presence to a specific position, shape or phantom pain. To alleviate this pain, patients engage in mirror therapy during which a mirror is placed in front of the patient's midsection, and the patient, while looking into this mirror, imagines that the amputated limb is in fact the healthy limb reflected in the mirror. However, this method is not without limitations. To address these limitations of conventional Mirror Therapy therapy and take advantage of the inherent potential of commercial technology, we developed an innovative assistive therapy tool based on mixed reality (MR) on the Microsoft Hololens 2. In this way, the patient's residual limb would be augmented by a superimposed virtual arm that is completely independent from the movements of their sound limb and can interact with the environment. Patients should move around freely and perform bi-manual tasks. To achieve this, we developed an MR appliaction that includes controllers for moving the virtual hand via myoelectric sensors (EMG) and inertial units and created and 4 different interaction scenes. We anticipate that this type of immersive MR rehabilitation will have a positive impact on outcomes related to pain scores, hand/arm functionality, range of motion, and motivation to perform therapy, even when no therapist is present.
Poisoning Attacks against Support Vector Machines
2022-03-13

We investigate a family of poisoning attacks against Support Vector Machines (SVM). Such attacks inject specially crafted training data that increases the SVM's test error. Central to the motivation for these attacks is the fact that most learning algorithms assume that their training data comes from a natural or well-behaved distribution. However, this assumption does not generally hold in security-sensitive settings. As we demonstrate, an intelligent adversary can, to some extent, predict the change of the SVM's decision function due to malicious input and use this ability to construct malicious data. The proposed attack uses a gradient ascent strategy in which the gradient is computed based on properties of the SVM's optimal solution. This method can be kernelized and enables the attack to be constructed in the input space even for non-linear kernels. We experimentally demonstrate that our gradient ascent procedure reliably identifies good local maxima of the non-convex validation error surface, which significantly increases the classifier's test error.
On the elusiveness of clusters
2022-03-13

Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one tree embedded in the network contains that cluster. Motivated by parsimony we might wish to construct such a network using as few reticulations as possible, or minimizing the "level" of the network, i.e. the maximum number of reticulations used in any "tangled" region of the network. Although these are NP-hard problems, here we prove that, for every fixed k &gt;= 0, it is polynomial-time solvable to construct a phylogenetic network with level equal to k representing a cluster set, or to determine that no such network exists. However, this algorithm does not lend itself to a practical implementation. We also prove that the comparatively efficient Cass algorithm correctly solves this problem (and also minimizes the reticulation number) when input clusters are obtained from two not necessarily binary gene trees on the same set of taxa but does not always minimize level for general cluster sets. Finally, we describe a new algorithm which generates in polynomial-time all binary phylogenetic networks with exactly r reticulations representing a set of input clusters (for every fixed r &gt;= 0).
Eigenvalues and Stability Properties of Multiplication Operators and Multiplication Semigroups
2022-03-13

We investigate uniform, strong, weak and almost weak stability of multiplication semigroups on Banach space valued -spaces. We show that, under certain conditions, these properties can be characterized by analogous ones of the pointwise semigroups. Using techniques from selector theory, we prove a spectral mapping theorem for the point spectra of the pointwise and global semigroups and apply this as a major tool for determining almost weak stability.