Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining genotype groups and recursive partitioning: an application to human immunodeficiency virus type 1 genetics data

Summary. Understanding the relationship between human immunodeficiency virus type 1 genotypic markers of resistance and response to therapy presents an analytic challenge because of the high dimensionality of the viral genome and the complex interactions across sites on the genome. Recursive partitioning is a natural approach to classifying patients on the basis of covariates that capture information on the variability of a response variable and is therefore well suited to handling both of these features of the problem. In the human immunodeficiency virus genetics setting, we aim to classify patients on the basis of the genotypic characteristics of their infecting viral population so that the resulting groups explain the most variability in drug susceptibility phenotype. Recursive partitioning is also informative in identifying meaningful genotypic patterns that define the resulting classes. By combining dimension reduction techniques with recursive partitioning we can arrive at different classification schemes which are potentially more informative. Furthermore, the use of weighted distance metrics in the clustering algorithm allows us to update and potentially to improve on this classification scheme. An illustration of the relative benefits of the various approaches is provided by using 2559 protease sequences and the corresponding 50% inhibitory concentrations for Indinavir.
The dynamics of floating bodies in a regular wave environment

Theoretical and numerical investigations have been carried out on the use of the Integral Equation Method of solution for the Potential Theory problem of the interaction between a floating body and a train of regular waves in a two-dimensional domain. In particular, a numerical study has been carried out of the indirect method of solution of the integral equation resulting from a distribution of Green's Function sources over a boundary coincident with the immersed surface of the body. It is demonstrated that a significant increase in solution efficiency, with no loss of precision, can be effected by improvements in the general numerical techniques of solution together with the use of a polynomial type distribution of elements over the source boundary. It is also demonstrated that significant improvements in solution accuracy for rectangular aspects can be achieved by a slight 'rounding' of the submerged edges of the mathematical model. An experimental investigation of the interaction between a train of regular waves and a substantially rectangular floating body includes measurements of the reflection and transmission characteristics, for both the fixed and floating mode of the body, together with measurements of the body motions. The primary objective of the experimental study is the validation of theoretically predicted interaction parameters derived from the above methods. The experimental program was designed both to determine the extent of validity of Potential Theory within regimes where diffraction effects predominate, and also to determine the conditions under which the use of Potential Theory alone becomes invalid due to the significant presence of non-linear effects. As a consequence of the results of this investigation, recommendations are made both with regard to the possible achievement of further improvements in solution efficiency and, more importantly, with regard to a general improvement of solution accuracy by the inclusion of the above-mentioned non-linear effects in the theoretical formulations.
The impact of a slow interplanetary coronal mass ejection on Venus

We present Venus Express observations of the impact of a slow interplanetary coronal mass ejection (ICME), which struck Venus on 23 December 2006, creating unusual quasi steady state upstream conditions for the 2 h close to periapsis: an enhanced (∼ nT) interplanetary magnetic field (IMF), radially aligned with the Sun‐Venus line; and a dense (∼ cm−3) solar wind. Contrary to our current understanding and expectations, the ionosphere became partially demagnetized. We also find evidence for shocked sheathlike solar wind protons and electrons in the wake of Venus, and powerful (≈ nT2/Hz) foreshock whistler mode waves radiating from the bow shock at an unexpectedly low frequency (0.6 Hz). Given the abnormally high density of escaping heavy ions at the magnetopause boundary (295 cm−3, one of the highest of the whole mission) and the enhanced density of escaping heavy ions in the wake, we find that even weak ICMEs with no driving shocks can increase atmospheric loss rates at Venus and suggests that the Bx component of the IMF may be a factor in atmospheric escape rates.
Econometric Theory and Practice: Edgeworth Expansions for the Wald and GMM Statistics for Nonlinear Restrictions

An Edgeworth expansion is derived for the GMM distance statistic for a real-valued nonlinear restriction on a normal linear regression. The Edgeworth expansion takes the form F (x − n −1 α1x)+o(n −1 ), where F is the χ 2 distribution. We also provide a reÞnement of the Edgeworth expansion for the Wald statistic derived by Park and Phillips (1988), which takes the form F (x − n −1 (α1x + α2x 2 + α3x 3 )) +o(n −1 ). Our calculations show that the leading coefficient α1 is the same in these two expansions. This establishes that, to the order of approximation of the Edgeworth expansion, the GMM distance statistic has a superior approximation to the chi-square distribution than does the Wald statistic. We also update the Monte Carlo simulation of Gregory and Veall (1985) to include both heteroskedasticity-robust covariance matrix estimation and the GMM distance statistic. We Þnd that if the robust covariance matrix is calculated under the null, the GMM statistic has near perfect Þnite sample Type I error in our experiments, even in sample sizes as small as n =2 0.
Mesoscale convective systems during NAME

This work examines Mesoscale Convective Systems (MCS) observed during the North American Monsoon Experiment (NAME), using data of deployed instruments in Northwest Mexico like weather radar, atmospheric soundings and weather satellite. Satellite infrared images were used to define these meteorological phenomena during July-August 2004 period on the NAME core region. Eighty two MCS occurred during NAME in a summer season lightly more active than normal, due probably to a ridge position more to the south than normal. Southwesterly midlevel winds dominate in the region during inactive MCS formation periods, while easterly winds dominate during active periods. MCS initiation time was mostly between afternoon and evening, while their termination time was after midnight with an average MCS duration of 7.46 hours. Most of NAME MCS formed associated to synoptic ridges and inverted troughs. Few of them related to tropical cyclones. Most of the analyzed convective lines in this region were classifiable (70%), being most of them shear-parallel lines (69%). Not only the magnitude and direction of the midlevel and low-level wind shear vectors were important to MCS morphology, as is seen in weather radar images, but also the angle between these two wind shear vectors. Kinematic parameters were more important to MCS morphology than thermodynamic ones.
Designing of CK45 carbon steel and AISI 304 stainless steel dissimilar welds

Gas tungsten arc welding of CK45 and AISI304 stainless steel was performed through preparation of different types of samples using ER308L and ERNi-1 wires. Welded samples were studied by different techniques including optical metallography, scanning electron microscopy equipped with energy dispersive X-ray spectroscopy (SEM-EDS), X-ray diffraction, hardness measurements and impact test. It was observed that in the buttered specimen, the structure of the weld metal was completely austenitic while the microstructure of unbuttered sample was duplex ferritic-austenitic. M23C6-type carbides were observed within the weld metal of both as-weld specimen types. Effects of different post-weld heat treatments (PWHTs) were investigated. The experimented results concluded that simultaneous grain growth and carbides precipitation were competitive during PWHT. Also, there were not any indication related to sigma-phase in as-welded and PWHTed specimens due to their lower Cr/Ni ratios and insufficient preservation times.
Two‐stream approximations revisited: A new improvement and tests with GCM data

Two‐stream approximations (TSAs) are employed for multiple‐scattering calculations in most solar radiation schemes used in atmospheric general‐circulation models (GCMs). Two issues related to TSAs are addressed. First, a simple extension of the two‐stream formalism is presented that allows different parametrizations for different factors, such as water clouds, ice clouds and aerosols. A ‘tuned two‐stream approximation’ that uses this extension is then developed. Second, the accuracy of the tuned TSA and selected other TSAs is quantified using a global GCM‐generated dataset (nearly 25000 atmospheric columns with clouds, aerosols and absorbing gases).
Reflection and transmission of light in multilayers perturbed by picosecond strain pulse propagation

We derive analytical formulas for the modulation of the reflectance and transmittance of light normally incident on a multilayer thin-film structure whose refractive indices are perturbed by an ultrashort optical pulse. The formulas, expressed in compact form, should prove useful for analysis of a wide range of ultrashort time-scale experiments on multilayers as well as longer time-scale photoacoustic and photothermal experiments based on optical probing. We demonstrate our method by the analysis of the modulated reflectance variation of a SiO2/Cr structure in which picosecond acoustic pulses have been optically excited.
Transpiration-Cooled Hypersonic Flight Experiment: Setup, Flight Measurement, and Reconstruction

The present paper presents the in-flight measurement of the transpiration cooling experiment Aktive Kuhlung durch Transpiration im Versuch (often referred to as AKTiV) flown on the suborbital reentry configuration Sharp Edge Flight Experiment II (often referred to as SHEFEX II). Thermal response of the structure is measured just up- and downstream of a cooled sample with a noncooled reference setup on the opposite side of the vehicle. The measurement shows that the heat flux is reduced upon coolant exhaust. The maximum temperature reduction with 87 K is observed on the porous sample, while downstream the sample, the temperature is reduced by 75 K by film cooling. This corresponds to cooling efficiencies of 58 and 42% on the sample and downstream, respectively. The evaluation is supported by the semi-analytical tool HEATS, based on a transient heat balance at the surface. Comparison of the results with HEATS shows that the heat flux predicted with HEATS is in good concurrence with the measured temperatures.
A numerical study of a natural convection flow in a cavity

The solution to a benchmark problem of a differentially heated cavity flow with Ra=3.4×105 and Pr=0.71 was solicited for presentation at a special session entitled ‘Computational Predictability of Natural Convection Flows in Enclosures’ which was held at the First MIT Conference on Computational Fluid and Solid Mechanics. The objective of this paper is to present the results obtained using the ADINA System.
Impact of linear array geometry on direction-of-arrival estimation for a single source

The analysis is conducted using the Cramer-Rao lower bound simulations and performance modeling of maximum-likelihood estimation (MLE) while assuming a single source of illumination and additive white Gaussian noise. Particular attention is paid to the implementation of the MLE, the threshold signal-to-noise ratio (SNR), probability of outlier, and high SNR mean-squared-error (MSE) performance, which are evaluated and compared for uniform and nonuniform arrays. The conditions under which tradeoffs exist in choosing a particular geometry and their significance are determined. >
Iterative constrained least squares design of near perfect reconstruction pseudo QMF banks

This paper presents a simple and efficient method to design M-band near perfect reconstruction (NPR) pseudo quadrature mirror filter (QMF) banks. This method does not rely on a conventional computationally intensive nonlinear optimization method but rather on an iterative constrained least squares algorithm. The algorithm is rapidly converging, simple to implement and flexible. Its convergence does not depend on the starting point. Moreover an iteratively calculated weighting function can be used to shape the stopband of the prototype filter and perform the minimax or the gain constrained least squares approximation. Design examples and a MATLAB program implementing the proposed algorithm are included.
Random Point Attractors Versus Random Set Attractors

The notion of an attractor for a random dynamical system with respect to a general collection of deterministic sets is introduced. This comprises, in particular, global point attractors and global set attractors. After deriving a necessary and sufficient condition for existence of the corresponding attractors it is proved that a global set attractor always contains all unstable sets of all of its subsets. Then it is shown that in general random point attractors, in contrast to deterministic point attractors, do not support all invariant measures of the system. However, for white noise systems it holds that the minimal point attractor supports all invariant Markov measures of the system.
Dispersion Relations for Comb-Type Slow-Wave Structures

Asymptotically accurate dispersion relations for slow eigenwaves of a dense comb placed on the wall of a parallel-plate waveguide are given in closed form. The equations can be easily resolved numerically. An analysis of dispersion relations for combs, based on the above-mentioned equations, has advantages over commonly used methods because of the simplicity of the necessary calculations and clarity of results.
Multigene Genetic Programming Based Prediction of Concrete Fracture Parameters of Unnotched Specimens

This study explores the fracture energy of notched and unnotched concrete specimens subjected to the classical three-point bend test, instantiating a gradational step in the continued development of concrete fracture mechanics. An experimental campaign involving 18 notched test specimens and nine unnotched specimens of three different grades of concrete, an examination of the existing literature models for unnotched specimens, and a novel Multigene Genetic programming (MGGP) based concrete fracture energy model for unnotched specimens are integral to this study. As a salient result, the multiple approaches to quasi-brittle materials adopted in the study, highlighted the criticality of the determination of fracture energy, tensile strength and characteristic length for the crack width study. The failure modes of notched and unnotched specimens were found to be similar. The reported literature has mainly focused on a limited number of fracture energy influencing parameters. Therefore, six impact parameters have been chosen and incorporated into the present study to provide a more acceptable explanation of concrete fracture behaviour. A sensitivity analysis of the parameters and an error analysis of the model undertaken have established the accuracy and robustness of the developed MGGP model. Doi: 10.28991/CEJ-2023-09-02-011 Full Text: PDF
Interface estimates for the fully anisotropic Allen-Cahn equation and anisotropic mean curvature flow

In this paper, we prove that solutions of the anisotropic Allen-Cahn equation in double-obstacle form with kinetic term in {|φ|<1}, where A is a convex function, homogeneous of degree two, and β depends only on the direction of ∇φ, converge to an anisotropic mean-curvature flow Here VN and R denote respectively the normal velocity and the second fundamental form of the interface, and . We prove this in the case when the above flow admits a smooth solution, and we establish that the Hausdorff-distance between the zero-level set of φ and the interface of the flow is of order O(e2).
Parameter space map of an electron cyclotron resonance plasma in a compact chamber

Ion current density measurements were made in an electron cyclotron resonance (ECR) plasma reactor for both argon and oxygen discharges. Spatial changes in the ion current density were also recorded across the reactor diameter for changes in pressure and power. These measurements revealed a minimum in the ion current density on the reactor axis. This observation has been explained as a consequence of the shape of the ECR region, which, in turn, is dependent on the mode of coupling. Current density measurements were made as a function of reactor pressure and microwave power for two different axial locations in the system. A Langmuir probe was also used at these two locations to measure the electron temperature as a function of these process conditions. It was observed that the ion current density and/or plasma density measured downstream from the ECR zone, increased significantly in the low-pressure/high-microwave power region. Results from this region of the operating parameter space have not previously been reported. Further existing models do not predict this observed increase in plasma density or ion current density. It has been proposed that a rarefication of the gas in the ECR region, as a result of gas heating, has acted to increase the outward diffusion of electrons from the ECR zone and, thus, has increased the ambipolar diffusion of ions to the downstream location. This proposal has been partially validated by experimental results in which the ion energy was measured as a function of reactor pressure and gas flow rate. The shape of the oxygen parameter space map differs significantly from that for Ar. The principal reasons for these changes are a number of different inelastic electron scattering mechanisms which effect the transport electrons out of the ECR zone and through ambipolar diffusion also the transport of ions. The second factor is the production of negative ionic species which varies with reactor pressure and, thus, T/sub e/.
Improved stochastic physics schemes for global weather and climate models

The importance of probabilistic weather predictions and climate projections is growing. One of the key elements of the former is stochastic physics, schemes that perturb some uncertain processes in a general circulation model (GCM), such as physical parametrizations or diffusion. They help to increase the ensemble dispersion of ensemble prediction systems (EPS) and in some cases improve certain atmospheric processes by noise‐induced drifts. We have developed a new configuration of stochastic physics schemes for the Met Office Unified Model (MetUM). It consists of an improved Stochastic Kinetic Energy Backscatter v2 (SKEB2), plus the Stochastic Perturbation of Tendencies (SPT).
The puzzling behavior of HNCO isomers in molecular clouds

Context. Isocyanic acid (HNCO) has been observed in different physical environments in the interstellar medium (ISM) and in external galaxies. HNCO has several metastable isomers with a ground electronic singlet state: HOCN, HCNO, and HONC. The recent detection of fulminic acid (HCNO) in prestellar and protostellar cores and cyanic acid (HOCN) in warm molecular sources (e.g. hot cores) in the Galactic center proves that these species could also be common constituents of the ISM. Aims. To shed some light on the possible formation pathways of these species, we searched for HCNO in the sources where HOCN has been previously detected and vice versa. We have also included the low-mass protostar IRAS 16293-2422, where HNCO is found to be prominent. Methods. Using the new EMIR receivers at the IRAM 30-m telescope, we performed deep searches for three rotational transitions of HOCN and four of HCNO. Results. We report the detection of HOCN in four sources – three dense cores and the lukewarm corino L1527 – where HCNO has been previously observed. HOCN is tentatively detected toward the protostellar binary IRAS 16293-2422. However, HCNO has been detected neither in this source nor in the sources of the Galactic center where HOCN has been previously reported. The derived abundance ratios HCNO/HOCN are close to unity in quiescent clouds, while they are less than 0.01–0.1 in warm clouds. We attempt to explain these results by using both gas-phase and gas-grain chemical models.
Instability and chaotic behaviour in a free-surface flow

This paper describes some experimental observations of free-surface flows arising when fluid is poured over the end of a flat plate into a reservoir well below the plate. This class of flows was found to be highly unstable with over seven hundred qualitatively different flows being observed in the experiment. At very small values of the flux the liquid fell from the plate into the reservoir in the form of droplets which developed periodically at a number of sites on the underside of the plate. As the flux was increased these 'sites’ were able to sustain continuous, unbroken streams, and combinations of drip sites and continuous streams were possible. At still larger values of the flux there was a tendency for the liquid to fall in 'sheets’ and several combinations of’ sheet flows’ and continuous streams were observed, some of which flows exhibited a rather chaotic temporal behaviour. At even larger flux values the flow resembled that of the classic waterfall, but here there were also some unexpected instabilities where the attachment line of the free surface of the liquid with the plate developed corrugations.
Persistence in discrete Morse theory

The goal of this thesis is to bring together two different theories about critical points of a scalar function and their relation to topology: Discrete Morse theory and Persistent homology. While the goals and fundamental techniques are different, there are certain themes appearing in both theories that closely resemble each other. In certain cases, the two threads can be joined, leading to new insights beyond the classical realm of one particular theory.Discrete Morse theory provides combinatorial equivalents of several core concepts of classical Morse theory, such as discrete Morse functions, discrete gradient vector fields, critical points, and a cancelation theorem for the elimination of critical points of a vector field. Because of its simplicity, it not only maintains the intuition of the classical theory but allows to surpass it in a certain sense by providing explicit and canonical constructions that would become quite complicated in the smooth setting.Persistent homology quantifies topological features of a function. It defines the birth and death of homology classes at critical points, identifies pairs of these (persistence pairs), and provides a quantitative notion of their stability (persistence). Whereas (discrete) Morse theory makes statements about the homotopy type of the sublevel sets of a function, persistence is concerned with their homology. While homology is an invariant of homotopy equivalences, the converse is not true: not every map inducing an isomorphism in homology is a homotopy equivalence. In this thesis we establish a connection between both theories and use this combination to solve problems that are not easily accessibly by any single theory alone. In particular, we solve the problem of minimizing the number of critical points of a function on a surface within a certain tolerance from a given input function.