Miracle-dz/UniFAR-FTUs huggingface dataset:
The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile

The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesized that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. In this study, we describe the role of the C. difficile lipoprotein CD1687 during DCA-induced biofilm formation. We showed that the expression of CD1687 , which is part of an operon within the CD1685-CD1689 gene cluster, is controlled by multiple transcription starting sites and some are induced in response to DCA. Only CD1687 is required for biofilm formation and the overexpression of CD1687 is sufficient to induce biofilm formation. Using RNAseq analysis, we showed that CD1687 affects the expression of transporters and metabolic pathways and we identified several potential binding partners by pull-down assay, including transport-associated extracellular proteins. We then demonstrated that CD1687 is surface exposed in C. difficile , and that this localization is required for DCA-induced biofilm formation. Given this localization and the fact that C. difficile forms eDNA-rich biofilms, we confirmed that CD1687 binds DNA in a non-specific manner. We thus hypothesize that CD1687 is a component of the downstream response to DCA leading to biofilm formation by promoting interaction between the cells and the biofilm matrix by binding eDNA.
Magnetization dynamics driven by the combined action of ac magnetic field and dc spin-polarized current

The spin-polarized current flowing through a ferromagnet can apply a torque able to drive magnetization reversal or to excite persistent dynamical states of magnetization. In the present work we simulate the dynamic behavior of nanomagnets in nanopillar spin valve structures due to the combined action of ac magnetic fields and dc spin-polarized current. The simulations are performed using a micromagnetic model which includes the effect of the spin-polarized current. We also discuss possible experimental realizations of the ac-field-assisted current-induced switching. Two particular cases of the ac-field polarization are studied: circular and linear. We find that in both cases ac field accelerates the switching process.
Properties of a Latent Trait Reliability Coefficient

This article takes as its point of departure a coefficient for gauging the reliability of composites based on a fitting of a logit model with normal prior to dichotomous items pertaining to social attitudes (abortion) and/or life feelings (alienation). The effect of item locations on that coefficient relative to that of item slopes is analyzed by means of simulated data. The sampling variation to which that coefficient is subject is investigated by Monte Carlo methods and by sampling theory; procedures for taking that variation into account are presented and illustrated. Discussion includes remarks on the following topics: sample size, sample design, missing responses, number of response categories, time-dependent reliability, group differences in reliability, random versus fixed effects.
A Numerical Method for Bubble Motion with Phase Change

A numerical method for computing the motion of bubbles undergoing liquid? vapor phase change is presented. The method is based on a level set technique for capturing the phase interface, which is modified to include the effect of phase change at the interface as well as to achieve mass conservation during the whole calculation procedure. The modified level set method is applied for numerical simulation of bubble rise and growth in a stationary liquid. The numerical results are found to compare well with the data reported in the literature and the analytical solutions.
A FAIR Problem-Solving Lifecycle Architecture

Research infrastructures are intended to provide access to scientific data and resources needed for problem-solving. Approaches to support interoperability and reuse of heterogeneous resources in such infrastructures need investigation. Researchers tend to integrate and reuse existing resources but do not spend much effort to publish the resources created during solving scientific problems to make them reusable in communities. As the result, further users of these results have to spend their time and effort on integrating resources to reuse them. We propose an architecture of research infrastructures that are initially based on the lifecycle of problem-solving in research communities providing interoperability and reuse of the sources and previous research results. In this architecture, most of the data maintenance tasks are moved from the data integration stage to the data publishing stage, and data are manipulated following the domain specifications accepted by communities. This makes providing the interoperability and reuse of resources in the infrastructure more competent and easy and avoids repeated integration.
Hybrid methods for interactive shape manipulation

1 Notations 2 1 Introduction 3 2 Context-Aware Skeletal Shape Deformation 8 2.1 Background 8 2.2 Outline and contributions 11 2.3 Shape deformation framework 12 2.3.1 User setup and notations 12 2.3.2 Basic skeletal surface deformation 13 2.3.3 Using context: example shapes 16 2.4 Compact representation of examples 19 2.5 Implementation issues 21 2.6 Experimental results 22 2.6. 1 The video 24 2.6. 2 Complexity 24 2.7 Discussion and future work 26 3 Complex Barycentric Coordinates with Applications to Planar Shape Deformation 29 3.1 Previous work 29 3.2 Complex barycentric coordinates 32 3.2.1 Definitions 32 3.2.2 Continuous Cauchy coordinates 36 3.2.3 Discrete Cauchy-Green coordinates 37 3.2.4 Complex three-point coordinates 40 T ec hn io n C om pu te r Sc ie nc e D ep ar tm en t P h. D . T he si s P H D -2 01 012 2 01 0 3.3 Cauchy-type coordinates and shape deformation 43 3.3.1 Szegö coordinates 44 3.3.2 Point-to-point Cauchy coordinates 48 3.4 Experimental Results 51 3.4.1 Szegö vs. Cauchy-Green 52 3.4.2 Point to point Cauchy-Green vs. MLS 54 3.5 Conclusions and Discussion 57 4 Controllable Conformal Maps for Shape Deformation and Interpolation 59 4.1 Previous Work 60 4.2 Contributions 61 4.3 Conformal Shape Deformation 61 4.3.1 Shape Representation 63 4.3.2 Shape Reconstruction 64 4.3.3 Shape Interpolation 66 4.4 Cauchy Coordinates 67 4.4.1 Regular Cauchy Coordinates 68 4.4.2 Generalized Cauchy Coordinates 70 4.5 Dirichlet Problems and Hilbert Transforms 72 4.5. 1 The Dirichlet Problem 74 4.5. 2 The Hilbert Transform 75 4.6 The Antiderivative 76 4.7 Deformation by Angle Prescription 77 4.7. 1 Rotational Handles 77 4.7. 2 Cage-Based 77 4.8 Implementation Details 78 4.9 Computing Harmonic Coordinates 81 4.10 The Riemann mapping 82 T ec hn io n C om pu te r Sc ie nc e D ep ar tm en t P h. D . T he si s P H D -2 01 012 2 01 0 4.11 Discussion 83 5 Conclusions and Discussion 87 Appendix A 89 Appendix B 100 Appendix C 101 Appendix D 102 Appendix E 103 Appendix F 104 Appendix G 106 Bibliography 108 T ec hn io n C om pu te r Sc ie nc e D ep ar tm en t P h. D . T he si s P H D -2 01 012 2 01 0
Ultrafast all‐optical switching in semiconductor nonlinear directional couplers at half the band gap

Efficient ultrafast all‐optical switching in nonlinear directional couplers made of AlGaAs and AlGaAs/GaAs quantum wells near half the band gap is reported. The switching is limited by multiphoton absorption which is dominated by three‐photon absorption in this spectral range. The three‐photon absorption in the quantum well nonlinear directional coupler is stronger than that of bulk AlGaAs. Autocorrelations of the output pulses in the bar and cross states confirm pulse breakup through nonlinear coupling, and illustrate the effects of multiphoton absorption. All sets of experimental data are fitted well by a theoretical model.
Trivariate functions in solid modeling, medical imaging and computer graphics

Over the past decade, volume graphics has been recognized as an important field of research. Most early research in volume graphics was focused on the problem of rendering of volumetric models. Only recently, volume modeling had been suggested. Volume modeling encompass the tools, data representations and algorithms that are needed to describe and manipulate the inner parts of a model, as well as its outer shell. Volume modeling can applied in wide range of fields such as material sciences, medical imaging, the movie-making industry, etc. As with surface-based geometric modeling, volume modeling seeks to supply the designer with a set of robust, fast and predictable manipulation tools for designing volumetric models. Several alternative representations can be used to model volumetric data. The most common is that of voxels. This representation is well understood and more suitable for volume rendering. However, for modeling purposes, voxels are probably not the best of choices mainly due to their bulkiness. For example, even a moderatesize CT scan may contain 256 × 256 × 256 scalars with a 16 bit-per-voxel resolution. Such a model requires more than 128 MByte of storage and even with today’s powerful computers, interaction with models as large as this can become cumbersome and slow. Moreover, since our aim is to develop tools for volumetric modeling, we should consider the state-of-the-art in surface-based modeling. In computer aided geometric design (CAGD), tensor product B-spline functions are, perhaps, the most commonly used surface representations. Therefore, we consider their extension into three-dimensional parametric space as a data representation for volume modeling. This thesis focuses on tools and algorithms for modeling with trivariate tensor product B-spline functions. These functions are used to solve several geometric modeling and computer graphics problems. We present diverse and novel applications 1 T ec hn io n C om pu te r S ci en ce D ep ar tm en t P h. D . T he si s P H D -2 00 605 20 06
Tests of Significance Following R. A. Fisher1

1 Specification 2 Procedure 3 Interpretation (i) Probability (ii) The Level of Significance P (iii) Fisher's Logic (iv) The Logic for Inexact Tests (v) Fisher on Support (vi) The Logic for Repetition (vii) The Critical Level a (viii) Fisher's Dualism 4 Conditionality 5 On 'Repeated Sampling from the Same Population' 6 Seidenfeld's Argument 7 Samples Alike in all 'Relevant' Respects 8 The 'Random' Sample
Dielectric breakdown and Poole–Frenkel field saturation in silicon oxynitride thin films

Dielectric breakdown is studied in silicon oxynitride thin films varying in composition from SiN1.33 to SiO0.60N0. 93. The films are observed to exhibit Poole–Frenkel emission as the dominant charge transport mechanism, with a compositionally dependent ionization potential ranging from 1.22 to 1.51 eV. The barrier lowering energy at the point of dielectric breakdown is independently determined to be likewise compositionally dependent, with the energies correlated to within ∼2kT of the ionization potential. Field saturation-induced trap ionization is discussed as a means to negate carrier scattering from bulk traps as an impediment to impact ionization and dielectric breakdown.
THE THEORY OF THE POLARIZATION OF CORONAL FORBIDDEN LINES

A brief review, presented in simplified terms, is given for the theory of the origin of coronal emission-line polarization. A classical view of the scattering problem in terms of harmonic oscillators is first presented where the influence of the magnetic field is demonstrated. The Van Vleck depolarization phenomena is described in these terms. Next, a more precise physical picture of the emission-line polarization is established through a discussion of the Zeeman effect in scattering. Sample results are discussed for three-dimensional coronal emission4ine models based upon the solution of the statistical equilibrium equations for magnetic sublevels of the Fe xiv ion. Finally, comments are directed toward the determination of magnetic fields based upon emission-line polarization observations where both medeling and deconvolution procedures are mentioned. Key words: corona - polarization - magnetic fields - forbidden lines
Machine Learning Project-2: Finding meaning in autogenerated text

Understanding the intent of spoken utterances can be a difficult task, not only for humans on occasions, but even more so for computers. In this project we aim at doing to later by implementing a pipeline that combines automatic speech recognition (ASR) and natural language processing (NLP) with the concepts that where introduced during the course. Utilizing different ASR and NLP techniques we where able to construct suitable feature spaces from labeled audio files that could be used to train classifiers and identify the intent of the user. Using a TF-IDF embedding with the Wave2vec ASR and logistic regression resulted in a correct intent classification with ∼ 87% accuracy.
Human Blood Extracellular Vesicles Activate Transcription of NF-kB-Dependent Genes in A549 Lung Adenocarcinoma Cells

Extracellular vesicles (EVs) produced by various cell types are heterogeneous in size and composition. Changes in the RNA sets of EVs in biological fluids are considered the basis for the development of new approaches to minimally invasive diagnostics and the therapy of human diseases. In this study, EVs were obtained from the blood of healthy donors by centrifugation, followed by ultracentrifugation. It was shown that EVs consist of several populations including small exosome-like vesicles and larger microvesicle-like particles. The composition of EVs’ RNAs was determined. A549 lung adenocarcinoma cells were incubated with EV and the NGS analysis of differentially expressed genes was performed. During the incubation of A549 cells with EVs, the levels of mRNA encoding components for the NF-kB signaling pathway increased, as well as the expression of genes controlled by the NF-kB transcription factor. Overall, our results suggest that components of EVs trigger the NF-kB signaling cascade in A549 cells, leading to the transcription of genes including cytokines, adhesion molecules, cell cycle regulators, and cell survival factors. Our data provide insight into the interaction between blood EVs and human cells and can be used for designing new tools for the diagnosis and treatment of human diseases.
Detecting novelty in USPTO patent applications with neural networks

—Despite providing a publicly accessible definition of novelty, the United State’s Patents and Trademarks Oﬀice (USPTO) receives tens of thousands of non-compliant utility applications every year. This paper provides information regarding the non-linear correlations between a patent application’s data and its novelty, and describes a model which predicts whether a patent will be approved.
CAR Triggered Release of Type-1 Interferon Limits CAR T-Cell Activities by an Artificial Negative Autocrine Loop

The advent of chimeric antigen receptor (CAR) T cells expedited the field of cancer immunotherapy enabling durable remissions in patients with refractory hematological malignancies. T cells redirected for universal cytokine-mediated killing (TRUCKs), commonly referred to as “fourth generation” CAR T-cells, are designed to release engineered payloads upon CAR-induced T-cell activation. Building on the TRUCK technology, we aimed to generate CAR T-cells with a CAR-inducible artificial, self-limiting autocrine loop. To this end, we engineered CAR T-cells with CAR triggered secretion of type-1 interferons (IFNs). At baseline, IFNα and IFNβ CAR T-cells showed similar capacities in cytotoxicity and cytokine secretion compared to conventional CAR T-cells. However, under “stress” conditions of repetitive rounds of antigen stimulation using BxPC-3 pancreas carcinoma cells as targets, anti-tumor activity faded in later rounds while being fully active in destructing carcinoma cells during first rounds of stimulation. Mechanistically, the decline in activity was primarily based on type-1 IFN augmented CAR T-cell apoptosis, which was far less the case for CAR T-cells without IFN release. Such autocrine self-limiting loops can be used for applications where transient CAR T-cell activity and persistence upon target recognition is desired to avoid lasting toxicities.
Linear Matrix Inequality and its Application in Control Theory

As a result of linear matrix inequality (LMI) and its good nature of mathematics as well as the breakthrough of solution method, many control problems can be transformed into a standard LMI problem to solve. Linear matrix inequality has received widely attention and applications in control system analysis and design. This paper introduces some of the basic content of LMI, such as the general description, the relevant algorithms and software. The controller will be designed using LMI such that the closed-loop system is asymptotically stable, and simulation will be given using Matlab. Finally, the population model will be given and analyzed.
The Dripping Handrail Model: Transient Chaos in Accretion Systems

We define and study a simple dynamical model for accretion systems, the "dripping handrail" (DHR). The time evolution of this spatially extended system is a mixture of periodic and apparently random (but actually deterministic) behavior. The nature of this mixture depends on the values of its physical parameters - the accretion rate, diffusion coefficient, and density threshold. The aperiodic component is a special kind of deterministic chaos called transient chaos. The model can simultaneously exhibit both the quasiperiodic oscillations (QPO) and very low frequency noise (VLFN) that characterize the power spectra of fluctuations of several classes of accretion systems in astronomy. For this reason, our model may be relevant to many such astrophysical systems, including binary stars with accretion onto a compact object - white dwarf, neutron star, or black hole - as well as active galactic nuclei. We describe the systematics of the DHR's temporal behavior, by exploring its physical parameter space using several diagnostics: power spectra, wavelet "scalegrams," and Lyapunov exponents. In addition, we note that for large accretion rates the DHR has periodic modes; the effective pulse shapes for these modes - evaluated by folding the time series at the known period - bear a resemblance to the similarly- determined shapes for some x-ray pulsars. The pulsing observed in some of these systems may be such periodic-mode accretion, and not due to pure rotation as in the standard pulsar model.
Laplacian smoothing and Delaunay triangulations

SUMMARY In contrast to most triangulation algorithms which implicitly assume that triangulation point locations are fixed, 'Laplacian' smoothing focuses on moving point locations to improve triangulation. Laplacian smoothing is attractive for its simplicity but it does require an existing triangulation. In this paper the effect of Laplacian smoothing on Delaunay triangulations is explored. It will become clear that constraining Laplacian smoothing to maintain a Delaunay triangulation measurably improves Laplacian smoothing. An early reference to the use of Laplacian smoothing is to be found in a papel by Buell and Bush. ' They surveyed the use of Laplace's equation to generate two-dimensional meshes, and described an equipotential method2 which extends finite differences of Laplace's equation on rectangular grids to differences on triangular grids. On triangular grids, the weighted difference equations
Epitaxial graphene on single domain 3C-SiC(100) thin films grown on off-axis Si(100)

The current process of growing graphene by thermal decomposition of 3C-SiC(100) on silicon is technologically attractive. Here, we study epitaxial graphene on single domain 3C-SiC films on off-axis Si(100). The structural and electronic properties of such graphene layers are explored by atomic force microscopy, x-ray photoelectron spectroscopy, and Raman spectroscopy. Using low energy electron diffraction, we show that graphene exhibits single planar domains. Near-edge x-ray absorption fine structure is used to characterize the sample, which confirms that the graphene layers present sp2 hybridization and are homogeneously parallel to the substrate surface.
Linear-Light Shading with Linearly Transformed Cosines

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Linear-Light Shading with Linearly Transformed Cosines Eric Heitz, Stephen Hill
A null space control of two wheels driven mobile manipulator using passivity theory

This paper describes a control strategy of null space motion of a two wheels driven mobile manipulator. Recently, robot is utilized in various industrial fields and it is preferable for the robot manipulator to have multiple degrees of freedom motion. Several studies of kinematics for null space motion have been proposed. However stability analysis of null space motion is not enough. Furthermore, these approaches apply to stable systems, but they do not apply unstable systems. Then, in this research, base of manipulator equips with two wheels driven mobile robot. This robot is called two wheels driven mobile manipulator, which becomes unstable system. In the proposed approach, a control design of null space uses passivity based stabilizing. A proposed controller is decided so that closed-loop system of robot dynamics satisfies passivity. This is passivity based control. Then, control strategy is that stabilizing of the robot system applies to work space observer based approach and null space control while keeping end-effector position. The validity of the proposed approach is verified by simulations and experiments of two wheels driven mobile manipulator.
Spectral-domain dyadic Green’s function in layered chiral media

A spectral-domain dyadic Green’s function formulation defining the fields in a multilayer chiral medium resulting from the arbitrary distribution of sources is presented. The constitutive parameters and the chirality of each layer are assumed to be different. The fields are obtained in terms of electric- and magnetic-type dyadic Green’s functions. The singular behavior of these dyadic Green’s functions in the source region is taken into account by extracting the delta function singularities. The fields in any layer are obtained in terms of the appropriately defined global reflection and transmission matrices.