Miracle-dz/UniFAR-FTUs huggingface dataset:
Joint modeling of correlated binary outcomes: HIV-1 and HSV-2 co-infection

Herpes Simplex Virus Type 2 (HSV-2) facilitates the sexual acquisition and transmission of HIV-1 infection and is highly prevalent in most regions experiencing severe HIV epidemics. In sub-Saharan Africa, where HIV infection is a public health burden, the prevalence of HSV-2 is substantially high. The high prevalence of HSV-2 and the association between HSV-2 infection and HIV-1 acquisition could play a significant role in the spread of HIV-1 in the region. The objective of our study was to identify risk factors for HSV-2 and HIV-1 infections among men in sub-Saharan Africa. We used a joint response model that accommodates the interdependence between the two infections in assessing their risk factors. Simulation studies show superiority of the joint response model compared to the traditional models which ignore the dependence between the two infections. We found higher odds of having HSV-2/HIV-1 among older men, in men who had multiple sexual partners, abused alcohol, or reported symptoms of sexually transmitted infections. These findings suggest that interventions that identify and control the risk factors of the two infections should be part of HIV-1 prevention programs in sub-Saharan Africa where antiretroviral therapy is not readily available.
Development and Characterization of DNA Hybridization Reaction on PDMS Microchip

This report describes the fabrication of PDMS (polydemethylsiloxane)-glass microchip and the use of it to perform DNA hybridization reaction. The PDMS-glass microchip was fabricated using replica molding and photolithographic techniques. The whole microchip was 5cm3cm and the dimensions of the microfluidic channels were 50um wide and 40um deep. To investigate the hybridization reaction in the microchip, streptavidin was firstly immobilized on the microchip. After washing, biotin labeled DNA probe was introduced to the channel and captured by the immobilized streptavidin. Then the complementary DNA chain and the SYBR-GREEN-1 dye were introduced and the hybridization reaction was performed inside the channel. The results were examined by the fluorescent detecting system. With this experimental setup, the microchip was able to quantify the DNA with sensitivity down to 10ug/ml. This report also describes surface modification and blocking to reduce background and nonspecific adsorption.
A comparison of second order convection discretization schemes for incompressible fluid flow

The paper addresses the problem of convection discretization by extension and application of numerical schemes used in compressible flows: SONIC-A, SONIC-B, UNO2, MUSCL and MINMOD to predict steady incompressible recirculating convection dominated flows. A new scheme, SONIC-Q, is proposed together with a third-order non-oscillatory practice for pressure interpolation in non-staggered grids. Finite-volume calculations of the Navier-Stokes equations of a standard 2D driven square cavity standard test case and the laminar flow over a fence using primitive variables and non-staggered grid systems have shown that the schemes are alternatives to the conventional ones used in general algorithms for incompressible recirculating flows. In general these composite high-order schemes have proved to be good candidates to overcome the problems of false-diffusion and unboundedness encountered in non-composite high-order upwind schemes used in incompressible flows.
Compound fiber ring resonator: theory

A compound fiber ring resonator is made with a Fabry–Perot etalon built inside a fiber ring that is fed through a 2 × 2 directional single-mode fiber coupler. It is theoretically analyzed by an unfolded equivalent model and a transfer-matrix method. The output intensities are presented, and four cases are discussed. The results may be useful in applications such as fiber spectrum analyzers, sensors, and lasers.
Are upconverting Ln3+ based nanoparticles any good for deep tissue imaging with retention of optical sectioning?

An effective strategy is presented to make spherical Ln3+ doped NaYF4 nanoparticles that show upconversion, with the aim of deep-tissue optical imaging. Upconversion is the conversion of two or more low-energy photons into one of higher energy, e.g. 980 nm to 545 and 680 nm and 980 nm to 800 nm. In order to avoid the formation of nanoparticles with an aspect ratio, we developed a strategy in which subsequent shells were grown on spherical seed nanoparticles. The last shell is undoped in order to improve the optical properties. In addition, a simple intercalation strategy involving the oleate ligands on the surface has been developed to make the nanoparticles dispersible in aqueous solutions and physiological buffers. Two-photon upconversion laser scanning microscopy (TPULSM) and two-photon upconversion wide-field microscopy (TPUWFM) have been tested for their suitability in deep-tissue imaging with retention of lateral and depth resolution (also called optical sectioning). TPULSM can be used up to ~ 600 μm deep, but takes inordinately long times to acquire, which is due to the fact that the absorption cross section of Yb3+ is low, the quantum yield of the upconversion process are << 1%, and the Ln3+ excited states are up to several hundreds of μs. Hence UCNPs in general are not very bright (i.e. large emitted photon flux). The TPUWFM seems more promising because acquisition times are only several minutes, with depth profiling up to 400 μm. We show the first optical sectioning with this technique in the brain of a mouse, through a thin shaved skull.
Universal critical behavior in the ferromagnetic supercondutor

W. T. Jin,1,∗,† Zheng Zhou,2,∗ Wei Li,2,3,∗,‡ S. Nandi,4 B. Ouladdiaf,5 Zheng Yan,2,§ Xinyuan Wei,2 Xuguang Xu,6 W. H. Jiao,7 N. Qureshi,5 Y. Xiao,8 Y. Su,1 G. H. Cao,9 and Th. Brückel4,1 1Jülich Centre for Neutron Science JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstraße 1, D-85747 Garching, Germany 2State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China 3Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China 4Jülich Centre for Neutron Science JCNS and Peter Grünberg Institut PGI, JARA-FIT, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany 5Institut Laue Langevin, 71 rue des Martyrs, BP156, 38042 Grenoble Cedex 9, France 6School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China 7School of Science, Zhejiang University of Science and Technology, Hangzhou 310023, China 8School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China 9Department of Physics, Zhejiang University, Hangzhou 310027, China (Dated: April 18, 2019)
The Organization of Plant Turnaround Maintenance in Process-Based Industries: Analytical Framework and Generic Processes

Plant turnaround maintenance is a fundamental asset management in capital intensive process-based industries. The successful implementation of turnaround maintenance among others depends on the appropriate provision of institution and organization for the governance of the event. However, it is not uncommon for senior management of these companies to focus their attention on the engineering, business, and economic aspects of the event. This tendency has left several gaps in the knowledge and understanding of the organizational dimensions of this event. To a remarkable degree, it is rare to find literature on organizational characteristics of plant turnaround maintenance. This paper proposes an analytic framework for examining the organizational dimensions of the plant turnaround by describing six core generic processes through the general concepts of institution and organization namely rules, roles, and groups. The generic processes include formation of turnaround maintenance organization, resource mobilization and management, communication, conflict management, contracts management, and relationships with external organizations. The framework provides means for the understanding of turnaround maintenance organization from the social science standpoint that was scarcely addressed in the management circles.
Joint probabilistic data association for autonomous navigation

A new autonomous navigation scheme based on the joint probabilistic data association (JPDA) approach that processes landmark detections in the field of view (FOV) of an on-board sensor is developed. These detections-some true, some false-are associated to a set of stored landmarks and used to update the state of the vehicle. The results obtained from Monte Carlo simulations prove the ability of this navigation filter to perform in very high false alarm environments. In the different environmental conditions tested in the simulations, the performance of the JPDA navigation filter (JPDANF) is very close to that of the filter based on perfect data association. The very efficient cluster decomposition algorithm presented for the purpose of the navigation problem can also be used in many multitarget tracking applications. >
Missing Values in Linear Regression: Imputations Using An Error-Contaminated Linear Predictor

The problem of missing values problem is common in all branches of statistics and especially in regression analysis. Here we consider estimation of the regression parameters in the presence of missingness in the response. The usual method is to replace the missing value by its predicted value based on the available observations without any correction for the disturbance term. Instead we suggest a method which corrects the usual predictor with a guess of the disturbance term based on the available residuals. Comparison between the two methods shows that the latter leads to better results.
Radio emission in a random magnetic field : radio haloes and the structure of the magnetic field in the Coma cluster

Μodels of cluster radio haloes have been constructed allowing for a random magnetic field. The resulting halo is far from smooth, both in intensity and polarization. The magnetic field must therefore be tangled on sufficiently small scales to reduce intensity fluctuations to observed levels. The smoothness of the inner regions of the radio halo in the Coma cluster, with fluctuations at about the 5 per cent level at 1-arcmin resolution, indicates that the outer scale of magnetic field fluctuations is less than 15 kpc
Causality in (2+1)-dimensional gravity

A method is presented to characterize fully the evolution of an arbitrary set of spinless particles in (unquantized) (2+1)-dimensional gravity theory. The method produces a complete series of time ordered Cauchy surfaces, which are being triangulated. By construction, closed timelike curves never arise, even if the initial conditions contain a Gott pair. In particular the author's construction shows that the configuration proposed by Carrol et al. (1992) in which a Gott pair is formed in a closed universe, nevertheless does not admit closed timelike curves; this universe has a finite lifetime, ending in a 'big crunch'.
M2599-SEARLE PRINT.indd

It has been claimed that trust has a number of signifi cant benefi ts for organizations and their employees. Studies indicate both direct and indirect benefi ts, such as improved performance, enhanced prosocial behaviours, reduced costs (see Searle et al., 2011a for review). A direct relationship has been identifi ed between trust and organizational eff ectiveness, effi ciency and performance (Whitney, 1994; Kramer and Tyler, 1996; Davis and Landa, 1999; Mayer and Davis, 1999; Dirks and Ferrin, 2002). Trust has been found to improve organizational performance indirectly by fostering desirable workrelated behaviours and creating a more conducive climate for cooperative organizational performance (Zand, 1972; Konovsky and Pugh, 1994; Kramer, 1999). In addition, trust has been linked to enhanced knowledge sharing and innovation, discretionary behaviours, higher motivation and positive attitudes (Searle et al., 2011a). Studies demonstrate that employees with high trust in their organizations put greater eff ort into their roles and work more cooperatively with others (Podsakoff et al., 1990; Konovsky and Pugh, 1994; Pillai et al., 1999). In contrast, those who do not trust their organizations work less eff ectively (Dirks and Ferrin, 2001), engage in counterproductive behaviours (Bies and Tripp, 1996), or leave (Robinson, 1996). Thus trust has been connected to positive human behaviours in the workplace that support the achievement of the organization’s goals. This clearly resonates with the central premise of human resource management (HRM), with its emphasis on the facilitation of behaviours which, from the organization’s perspective, are positive and desirable and that result in levels of employee commitment and performance that support the achievement of the corporate objectives. Torrington et al. (2005: 14) explicitly make this link when they observe that employees who do not trust their employer are instrumental in their orientation and ‘will make ineffectual the work of any HRM function’. Discussions of ‘high performance’ HRM implicitly and explicitly include trust as a factor, and Blunsdon and Reed (2003) demonstrated that trust levels are determined not only by individuals’ experiences and dispositions but also by features of the workplace itself and that interventions by management make a diff erence.
Laser-generated pair production and Hawking-Unruh radiation

Laser-produced electron-positron pair production has been under discussion in the literature since 1969. Large numbers of positrons have been generated by lasers for a few years in studies which are also related to the studies of the physics of the fast ignitor laser fusion concept. For electron-positron pair production in vacuum due to vacuum polarization as predicted by Heisenberg (1934) with electrostatic fields, high-frequency laser fields with intensities around 10 28 W/cm 2 are necessary and may be available within a number of years. A similar electron acceleration by gravitation near black holes denoted as Hawking-Unruh radiation was discussed in 1985 by McDonald. The conditions are considered in view of the earlier work on pair production, change of statistics for electrons in relativistic black body radiation, and an Einstein recoil mechanism with a consequence of a physical foundation of the fine structure constant.
Simulations of merging disk galaxies

The conditions under which identical disk-halo galaxies merge and the structure of the resulting merger remnants are studied with N-body simulations. The progenitor galaxies possess truncated exponential disks and ''live'' 1/r /sup 2/ halos; the intrinsic stability of these models is assessed. For both galaxy spins aligned with the orbital angular momentum, a large number of encounters are investigated on a variety of orbits to derive an accurate merging cross section. Merging occurs primarily from bound and marginally unbound orbits with a degree of overlap at pericenter. A fairly sharp distinction between ''prompt'' and ''slow'' merging may be established, based on the strength of orbital braking induced by the encounter. Impulse approximation predictions fail for resonant alignment of spin and orbital angular momenta. For a single interpenetrating parabolic encounter, a variety of relative disk orientations at pericenter are studied. The transfer of orbital to internal energy depends sensitively on both the degree of alignment of galaxy spins with the orbital angular momentum, and the extent of ''overlap'' or ''intersection'' of the disks at pericenter. A small fraction of escaping mass carries away a substantial fraction of the total angular momentum. Merger remnants are typically roughly oblate systems, although some mustmore » be classed as prolate or triaxial. Many properties of the remnants agree well with those observed for bright ellipticals: projected surface density profiles have the Hubble form, with core radii appreciably smaller than the progenitor peak rotation velocity; a radial separation of disk and halo populations (metallicity gradient) is preserved; rotation curves for the remnants exhibit peak velocities much lower than those of the progenitor; and the remnants have extended, diffuse envelopes. « less
The extended finite element method (XFEM) for solidification problems

An enriched finite element method for the multi‐dimensional Stefan problems is presented. In this method the standard finite element basis is enriched with a discontinuity in the derivative of the temperature normal to the interface. The approximation can then represent the phase interface and the associated discontinuity in the temperature gradient within an element. The phase interface can be evolved without re‐meshing or the use of artificial heat capacity techniques. The interface is described by a level set function that is updated by a stabilized finite element scheme. Several examples are solved by the proposed method to demonstrate the accuracy and robustness of the method. Copyright © 2001 John Wiley & Sons, Ltd.
Geodesic motion and confinement in van Stockum space–time

Geodesic motion of test particles in van Stockum space–time, which represents the internal gravitational field produced by a rigidly rotating dust cylinder, is studied. In particular, it is found that confinement occurs quite generally in the radial direction, while the motion in the axial direction is free. The possible relevance of the confinement to the extragalactic jet formation is pointed out.
Flush‐mounted probes in the divertor plates of Tokamak de Varennes

Arrays of 12 flush‐mounted Langmuir probes have been installed in both the upper and lower outboard divertor plates of TdeV (Tokamak de Varennes). Measurements of electron temperature and density are obtained using a novel method of analysis which assumes that charge collection is dominated by the finite size of the electrostatic sheath. The technique is validated by comparing measurements from a cylindrical and a flush probe which are operated simultaneously in the same plasma.
Multiple shape recognition using pairwise geometric histogram based algorithms

Pairwise geometric histogram (PGH) based algorithms have previously been shown to be a robust solution for the recognition of arbitrary 2D shapes in the presence of occlusion and scene clutter (Evans et al., 1993). The method is both statistically founded and complete in the sense that a shape may be reconstructed from its PGH representation (Riocreuz et al., 1994). The generality of this method has been further reinforced by an analysis of its scaleability which concludes that, if used appropriately, it is suitable for the recognition of very large numbers of objects (Ashbrook et al., 1995). The present authors demonstrate the application of PGHs to recognition tasks involving very large model training sets.
The Morphology of Several Tornadic Storms on 20 May 1977

Abstract Sixteen tornadic storms occurred in the afternoon and evening hours of 20 May 1977 and the early morning hours of 21 May 1977. Three storms, two of them tornadic, have been selected for detailed study. One of the tornadic storms was observed for 2 h during its growth stage prior to becoming tornadic. Radar displays indicated that it merged with a more mature but intensifying storm to its north. After this apparent merger, the storm to the north dissipated and the southern storm continued to become more vigorous and eventually produced a tornado. These storms displayed common structural similarities to another tornadic storm which was observed during its mature stage several hours earlier. Despite differences in the environments in which these storms grew, they share a characteristic structure and evolution as can be determined by this sample of their lifetimes.
THE STABILITY OF EVAPORATING THIN LIQUID FILMS IN THE PRESENCE OF SURFACTANT. I. LUBRICATION APPROXIMATION AND LINEAR ANALYSIS

The dynamics of an evaporating wetting liquid film in the presence of dissolved surfactant is investigated. The solid substrate is planar and is subjected to heating. The liquid–vapor interface is a two-dimensional continuum characterized by specific adsorption, interfacial viscosity, and surface tension, which depend on the surfactant subsurface concentration and temperature. In the case of small density, viscosity, and thermal conductivity of the vapor phase (compared to the respective values for the liquid phase), at small Reynolds and large Peclet numbers and for thin films, the lubrication approximation model can be applied. The effect of the van der Waals disjoining pressure is taken into account. The appearing dimensionless groups, defined in terms of the real physical parameters, can vary by several orders of magnitude depending on the film initial thickness, temperature difference, and type of surfactants. The developed linear theory describes the competition among the various instabilities. The .
Harmonic components of finite-amplitude sound in a focused Gaussian beam

The harmonic components of finite-amplitude focused sounds emitted from a Gaussian source is examined by theory and experiments. Assuming that the radial distributions of amplitude and phase for each harmonic component are independent of the excitation level, the simplified equations for Fourier coefficients to express the distorted sound are derived. The equations were numerically solved by finite difference method to get the amplitudes and phases of harmonic components. The waveform was observed at different positions in the focused Gaussian beam realized by a circular concave piezo electrictransducer with a back electrode fabricated in the shape of star. The experi mentalresults for the first four harmonic components agreed well with the computed results. The present computation is convenient for analyzing the finite-amplitude focused Gaussian beam.
Regularised estimation for ARMAX process with measurements subject to outliers

ARMAX models are widely used in control engineering for both system description and control design. They can accurately describe a large class of real processes with relatively low complexity, but do not take into account observation errors, which can be particularly important in applications like filtering and fault diagnosis. Due to the intrinsic dependence in ARMAX process output, a single outlier may contaminate multiple data entries and completely spoil the conventional least-squares estimate. In this study, the authors develop a novel Moving Horizon Estimator that is not only robust to outliers but also able to reveal outliers. By utilising the fact that outliers are extreme errors that occur infrequently, the estimation problem is formulated as a least-squares optimisation problem with outliers explicitly modelled and regularised with l 1 -norm to induce sparsity. A coordinate descent-based solver is developed to obtain iterative algorithms with guaranteed convergence and closed-form solution available to each coordinate sub-problem per iteration. Due to the explicit modelling of outlier vectors, the impact of an outlier on multiple time instants can be estimated and mitigated. Simulation tests demonstrate that the proposed algorithm can effectively cope with outliers, even for the case when the commonly used Huber's M-estimation approach breaks down.
A re-examination of the quantum theory of optical cavities with moving mirrors

The quantization of linearly polarized light in an ideal optical cavity with moving boundaries is re-examined. The mathematical results of the earlier study by Moore are obtained using more conventional techniques. In contrast to Moore, it is shown that the theory does possess a Hamiltonian and a Schrodinger picture when any suitable Lagrangian coordinate system is chosen. It is demonstrated that the quantum, as well as the classical, physics is independent of the choice of Lagrangian coordinate system.