Miracle-dz/UniFAR-FTUs huggingface dataset:
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis

Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal inflammation in RA pathogenesis. Here, we performed paired analysis of human and bacterial transcriptomics in longitudinal blood samples from RA patients. We found that patients with RA and periodontal disease experienced repeated oral bacteremias associated with transcriptional signatures of ISG15+HLADRhi and CD48highS100A2pos monocytes, recently identified in inflamed RA synovia and blood of those with RA flares. The oral bacteria observed transiently in blood were broadly citrullinated in the mouth, and their in situ citrullinated epitopes were targeted by extensively somatically hypermutated ACPAs encoded by RA blood plasmablasts. Together, these results suggest that (i) periodontal disease results in repeated breaches of the oral mucosa that release citrullinated oral bacteria into circulation, which (ii) activate inflammatory monocyte subsets that are observed in inflamed RA synovia and blood of RA patients with flares and (iii) activate ACPA B cells, thereby promoting affinity maturation and epitope spreading to citrullinated human antigens. Description Rheumatoid arthritis autoantibodies target oral bacteria detected in flare-associated bacteremias that activate inflammatory monocytes. Periodontal disease and rheumatoid arthritis The incidence of periodontal disease is high in individuals with rheumatoid arthritis (RA) who also have anti-citrullinated protein antibodies (ACPAs), suggesting a link between these two diseases. Brewer et al. carried out a paired analysis of human and bacterial transcriptomes from blood samples collected longitudinally from RA patients with and without periodontal disease. They identified transcriptional signatures within inflammatory monocyte subsets that correlated with repeated oral bacteremias and clinical arthritis flares in patients with RA and periodontal disease. These oral bacteria were broadly citrullinated, and some of these citrullinated epitopes were the targets of ACPA expressed by RA blood plasmablasts that have undergone affinity maturation. These results confirm that periodontal disease can cause breaches in oral mucosa that release citrullinated bacteria into the blood, which activates inflammatory monocytes and ACPA-specific B cells. —CF
Nonlinear stability of gravitationally unstable, transient, diffusive boundary layers in porous media

Abstract The linear stability of transient diffusive boundary layers in porous media has been studied extensively for its applications to carbon dioxide sequestration. The onset of nonlinear convection, however, remains understudied because the transient base state invalidates the traditional stability methods that are used for autonomous systems. We demonstrate that the onset time of nonlinear convection, $t=t_{\mathit{on}}$, can be determined from an expansion that is two orders of magnitude faster than a direct numerical simulation. Using the expansion, we explore the sensitivity of $t_{\mathit{on}}$ to the initial perturbation magnitude and wavelength, as well as the initial time at which a perturbation is initiated. We find that there is an optimal initial time and wavelength that minimize $t_{\mathit{on}}$, and we obtain analytical relationships for these parameters in terms of aquifer properties and initial perturbation magnitude. This importance of the initial perturbation time and magnitude is often overlooked in previous studies. To investigate perturbation evolution at late-times, $t>t_{\mathit{on}}$, we perform direct numerical simulations that reveal two unique features of transient diffusive boundary layers. First, when a boundary layer is perturbed with a single horizontal Fourier mode, nonlinear mechanisms generate a zero-wavenumber response whose magnitude eventually surpasses that of the fundamental mode. Second, when a boundary layer is simultaneously perturbed with many Fourier modes, the late-time perturbation magnitude is concentrated in the zero-wavenumber mode, and there is no clearly dominant, non-zero, wavenumber. These unique results are further interpreted by comparison with direct numerical simulations of Rayleigh–Bénard convection.
A generalized fast algorithm for n-D discrete cosine transform and its application to motion picture coding

In this paper, a generalized fast computational algorithm for the n-dimensional discrete cosine transform (DCT) of length N=2/sup m/ (m/spl ges/2) is presented. The developed algorithm is proved and its efficiency is evaluated theoretically. The theoretical results show that compared with the conventional method of computing the one-dimensional along n directions, the number of multiplications needed by our algorithm is only 1/n of that required by the conventional method; for the total number of additions, the latter is a bit more when N/spl les/8 and much fewer when N/spl ges/16 than the former. To validate the proposed algorithm, we take the case when n=3 as an example and apply it to motion-picture coding. The results show that our method is superior to MPEG-2 in speed and coding performance. The algorithm is clearly described and it is easy to make a computer program for implementation.
Azimuth‐dependent Es layer instability: A missing link found

[1] A number of features observed in association with nighttime midlatitude sporadic E (Es) have defied satisfactory explanation, until now. They include Es properties such as semitransparency, tilts, altitude modulation, plasma structure, and frontal structures with preferred alignment in azimuth. Other puzzling manifestations of Es include gigahertz scintillation and anomalously large electric fields (). All can now be interpreted self-consistently in terms of a recently discovered, azimuth-dependent Es layer instability [Cosgrove and Tsunoda, 2002b, 2003]. Zonal wind shear turns out to be responsible for both the initial formation of Es (wind shear theory) and its instability to vertical transport, the latter arising through an from Hall polarization. The meridional wind drives an important secondary polarization process that acts through conductivity perturbations to distort and produce a characteristic asymmetry in Es plasma structure, above and below the zonal wind shear node. Stability is restored through reduction in from the overlap of Es structures above and below the wind-shear node; overlap is produced by antiparallel horizontal transport. Temporal evolution therefore is a cyclical process of Es layer distortion and structure development, followed by horizontal overlap and vertical reconvergence. In this paper we elucidate the underlying physics and discuss how hitherto puzzling observations now provide supporting evidence for this instability. We further endorse the findings that Hall polarization and the Es layer instability must be playing major roles in the coupled electrodynamics and instability of the nighttime midlatitude ionosphere [Tsunoda and Cosgrove, 2001; Cosgrove and Tsunoda, 2004; Cosgrove et al., 2004].
Helminths associated with terrestrial slugs in Swedish agricultural fields

Abstract Slugs are important agricultural pests causing yearly yield losses. However, parasitizing helminths potentially could affect the size of the slug population. Here, a survey of terrestrial slug-parasitic helminths (nematodes and trematodes) was conducted for the first time in Sweden. In total, 268 terrestrial slugs were collected from 27 agricultural field edges in three seasons over 2020 and 2021 and dissected for presence of helminth parasites. Slugs belonging to the genus Arion were molecularly identified by mitochondrial DNA cytochrome c oxidase subunit I (COI) while parasites were identified using ribosomal RNA (18S). Overall, 13% of the collected slugs had helminth parasites and the likelihood of a slug being parasitized was highest in autumn. Slugs identified as Arion vulgaris were more likely to be parasitized than native slug species. The prevalence of nematodes and trematodes were similar; the dominant species found were Alloionema appendiculatum and Brachylaima thompsoni, respectively. This is the first record of the presence of these two species in Sweden.
Infographics in higher education: A scoping review

In education, infographics may be used to promote active learning and engage learners in the creation of more diverse learning artefacts. This study aims to analyze the application of infographics in higher education. The authors conducted a scoping review of the scientific articles to analyze the use of infographics across a variety of university subjects. The findings revealed that the most frequent educational practices were those that merged both ready-made infographics and students’ hands-on experience in creating their own infographics. Such learning activities facilitated the learning of the subject-related material and helped students to advance with the creation of this popular form of modern communication. The tasks including infographics also represented an enhanced mission of higher education as students were given opportunities to develop a number of personal and career readiness skills and capabilities simultaneously, such as digital, visual and information literacy, critical thinking, creativity, communication and collaboration skills. The educational recommendations and technological solutions proposed might diversify teaching and learning practices in higher education.
Genomic Characteristics and Molecular Epidemiology of Multidrug-Resistant Klebsiella pneumoniae Strains Carried by Wild Birds

Little is known about the pathogenic microorganisms carried by wild animals. This study found that the multidrug resistance phenotype of Klebsiella pneumoniae isolates carried by wild birds was mainly attributed to multidrug resistance plasmids, and these multidrug resistance plasmids from wild birds were closely related to human-infecting bacteria. ABSTRACT This study aimed to explore the relationship between wild birds and the transmission of multidrug-resistant strains. Klebsiella pneumoniae was isolated from fresh feces of captured wild birds and assessed by the broth microdilution method and comparative genomics. Four Klebsiella pneumoniae isolates showed different resistance phenotypes; S90-2 and S141 were both resistant to ampicillin, cefuroxime, and cefazolin, while M911-1 and S130-1 were sensitive to most of the 14 antibiotics tested. S90-2 belongs to sequence type 629 (ST629), and its genome includes 30 resistance genes, including blaCTX-M-14 and blaSHV-11, while its plasmid pS90-2.3 (IncR) carries qacEdelta1, sul1, and aph(3′)-Ib. S141 belongs to ST1662, and its genome includes a total of 27 resistance genes, including blaSHV-217. M911-1 is a new ST, carrying blaSHV-1 and fosA6, and its plasmid pM911-1.1 (novel) carries qnrS1, blaLAP-2, and tet(A). S130-1 belongs to ST3753, carrying blaSHV-11 and fosA6, and its plasmid pS130-1 [IncFIB(K)] carries only one resistance gene, tet(A). pM911-1.1 and pS90-2.3 do not have conjugative transfer ability, but their resistance gene fragments are derived from multiple homologous Enterobacteriaceae strain chromosomes or plasmids, and the formation of resistance gene fragments (multidrug resistance region) involves interactions between multiple mobile element genes, resulting in a complex and diverse resistance plasmid structure. The homologous plasmids related to pM911-1.1 and pS90-2.3 were mainly from isolated human-infecting bacteria in China, namely, K. pneumoniae and Escherichia coli. The multidrug-resistant K. pneumoniae isolates carried by wild birds in this study had drug resistance phenotypes conferred primarily by multidrug resistance plasmids that were closely related to human-infecting bacteria. IMPORTANCE Little is known about the pathogenic microorganisms carried by wild animals. This study found that the multidrug resistance phenotype of Klebsiella pneumoniae isolates carried by wild birds was mainly attributed to multidrug resistance plasmids, and these multidrug resistance plasmids from wild birds were closely related to human-infecting bacteria. Wild bird habitats overlap to a great extent with human and livestock habitats, which further increases the potential for horizontal transfer of multidrug-resistant bacteria among humans, animals, and the environment. Therefore, wild birds, as potential transmission hosts of multidrug-resistant bacteria, should be given attention and monitored.
An asymptotic theory for a class of initial-boundary value problems for weakly nonlinear wave equations with an application to a model of the galloping oscillations of overhead transmission

The aim of this paper is to contribute to the foundation of the asymptotic methods for initial-boundary value problems and initial value problems for weakly nonlinear hyperbolic partial differential equations of order two. In this paper an asymptotic theory for a class of initial-boundary value problems for weakly nonlinear wave equations is presented. The theory implies the well-posedness of the problem in the classical sense and the validity of formal approximations on long timescales.As an application of the theory, an initial-boundary value problem for a Rayleigh wave equation is studied in detail using a two-timescale perturbation method. From an aeroelastic analysis, it is shown that this initial-boundary value problem may be regarded as a model describing the growth of wind-induced oscillations of overhead transmission lines.
Retrieval validation during the European Aqua Thermodynamic Experiment

Atmospheric and surface thermodynamic parameters retrieved with advanced hyperspectral remote sensors aboard Earth observing satellites are critical to weather prediction and scientific research. The retrieval algorithms and retrieved parameters from satellite sounders must be validated to demonstrate the capability and accuracy of both observation and data processing systems. The European Aqua Thermodynamic Experiment (EAQUATE) was conducted not only for validation of the Atmospheric InfraRed Sounder on the Aqua satellite, but also for assessment of validation systems of both ground‐based and aircraft‐based instruments that will be used for other satellite systems, such as the Infrared Atmospheric Sounding Interferometer on the European MetOp satellite, the Cross‐track Infrared Sounder from the National Polar‐orbiting Operational Environmental Satellite System (NPOESS) Preparatory Project and the continuing series of NPOESS satellites. Detailed intercomparisons were conducted and presented using different retrieval methodologies: measurements from airborne ultraspectral Fourier transform spectrometers, aircraft in situ instruments, dedicated dropsondes and radiosondes, ground‐based Raman lidar, as well as the European Centre for Medium‐range Weather Forecasting modelled thermal structures. The results of this study not only illustrate the quality of the measurements and retrieval products, but also demonstrate the capability of the validation systems put in place to validate current and future hyperspectral sounding instruments and their scientific products. Copyright © 2007 Royal Meteorological Society
Modified nonequilibrium molecular dynamics for fluid flows with energy conservation

The nonequilibrium molecular dynamics generated by the SLLOD algorithm [so called due to its association with the DOLLS tensor algorithm (D. J. Evans and G. P. Morriss, Statistical Mechanics of Nonequilibrium Liquids (Academic, New York, 1990)] for fluid flow is considered. It is shown that, in the absence of time-dependent boundary conditions (e.g., shearing boundary conditions via explicit cell dynamics or Lees–Edwards boundary conditions), a conserved energy, H exists for the equations of motion. The phase space distribution generated by SLLOD dynamics can be explicitly derived from H. In the case of a fluid confined between two immobile boundaries undergoing planar Couette flow, the phase space distribution predicts a linear velocity profile, a fact which suggests the flow is field driven rather than boundary driven. For a general flow in the absence of time-dependent boundaries, it is shown that the SLLOD equations are no longer canonical in the laboratory momenta, and a modified form of the SLLOD dynamics is presented which is valid arbitrarily far from equilibrium for boundary conditions appropriate to the flow. From an analysis of the conserved energy for the new SLLOD equations in the absence of time-dependent boundary conditions, it is shown that the correct local thermodynamics is obtained. In addition, the idea of coupling each degree of freedom in the system to a Nose–Hoover chain thermostat is presented as a means of efficiently generating the phase space distribution.
Analysis method for motor characteristics with three-dimensional flux distribution

This paper investigates the static torque characteristics of a two-phase pancake-type DC brushless motor for DVD-ROM spindles or chip coolers to control their driving speed. The novel spindle motor is of the axial-winding and radial-air-gap type, which has inherent three-dimensional (3-D) flux distribution and therefore requires excessive computation time for computer-aided design and analysis. The paper describes an analytical method based on an equivalent magnetic circuit, where the permeance distribution per salient pole is calculated by the boundary-element method. The method is particularly suitable for solving partial differential equations, and since the basic voltage equation can be deduced, the detent torque can be calculated analytically by using the energy method. This approach is computationally efficient and useful in the optimal design of a motor whose flux distribution is inherently three-dimensional. The Maxwell 3D Field Simulator has verified the numerical results. Tests of a prototype of the newly designed two-phase spindle motor for CD/DVD-ROM drives have demonstrated the performance and illustrated potential applications.
Public expenditure in the UK: how measures matter

Summary. Studying spending over time requires reliable data. It is not clear that such data exist in the UK, however. The two published sources of functional spending numbers—the Office for National Statistics's ‘blue book’ and Her Majesty's Treasury's Public Expenditure Statistical Analyses (PESA)—rely on estimates of past spending, using a link year method, rather than recalculating actual spending figures when functional definitions change. We assess the various measures of spending in the UK. Specifically, we do two things. First, we present a new, third, set of spending numbers applying temporally consistent functional definitions to PESA microdata. Second, we compare the three measures. Our analyses indicate that the Office for National Statistics and PESA data differ quite markedly, especially for certain functions, i.e. in some cases the two measures imply completely different histories. The differences between the original PESA data and our new measures are less pronounced on average, though significant differences are evident, especially year by year.
Fitting power-law distributions to data with measurement errors

If X, which follows a power-law distribution, is observed subject to Gaussian measurement errore, then X + e is distributed as the convolution of the power-law and Gaussian distributions. Maximum-likelihood estimation of the parameters of the two distributions is considered. Large-sample formulae are given for the covariance matrix of the estimated parameters, and implementation of a small-sample method (the jackknife) is also described. Other topics dealt with are tests for goodness of fit of the posited distribution, and tests whether special cases (no measurement errors or an infinite upper limit to the power-law distribution) may be preferred. The application of the methodology is illustrated by fitting convolved distributions to masses of giant molecular clouds in M33 and the Large Magellanic Cloud (LMC), and to H I cloud masses in the LMC.
Spectrum estimation of nonuniformly sampled signals

Nonuniform sampling of signals, if properly used, may allow performing digital signal processing that does not suffer from the undesired effects of aliasing. This paper presents the results of research on estimating spectra of signals whose samples were taken at randomly distributed sampling instants. The paper determines the conditions under which a DFT-like spectrum estimator provides an unbiased approximation of the spectrum of the original continuous-time signal in an unlimited range of frequencies. It also provides analysis of the accuracy of such spectral estimation and identifies factors which decide the quality of the results. Not every random sampling scheme is suitable for performing alias free signal processing. The analysis presented here shows how to generate two suitable sampling schemes. Numerical examples illustrate the main thesis of the paper.
Statistics of coastal flood prevention

For the design of sea defences the main statistical issue is to estimate quantiles of the distribution of annual maximum sea levels for all coastal sites. Traditional procedures independently analyse data from each individual site; thus known spatial properties of the meteorological and astronomical tidal components of sea level are not exploited. By spatial modelling of the marginal behaviour and inter-site dependence of sea level annual maxima around the British coast we are able to examine risk assessment for coastlines and the issue of sensitivity to climatic change.
Stability of stagnation points in rotating flows

The Lifschitz and Hameiri theory for short-wave instabilities is used to show that any steady inviscid plane flow subjected (or not) to a Coriolis with perpendicular angular velocity vector is unstable to three-dimensional perturbations if Φ(x0)<0 on a stagnation point located at x0. Φ is the second invariant of the inertial tensor [Leblanc and Cambon, Phys. Fluids 9, 1307 (1997)]. The particular cases of zero absolute W(x0)+2Ω=0 and zero tilting W(x0)+4Ω=0 vorticities are also considered. The criterion is applied to Chaplygin’s non-symmetric dipolar vortex moving along a circular path, which is shown to be unstable.
Critical neutron scattering in CeSb

Diffuse critical neutron scattering above the antiferromagnetic first-order phase transition has been observed in the cerium monopnictide CeSb. Whereas the long-range ordering below TN=16.4K has type-A2/3 structure with superlattice peaks at q0=(2 pi / alpha ) (0,0,2/3) the fluctuations are of type-I antiferromagnetic (AF/I) structure and disappear when the long-range ordering occurs. This frustration indicates that the system is near a Lifshitz point. The longitudinal spin correlation is anisotropic and the transverse fluctuations are unobservably small. The authors analysed the critical behaviour by a mean-field treatment of a Hamiltonian that includes strong cubic anisotropy.