Miracle-dz/UniFAR-FTUs huggingface dataset:
Making meaningful estimates of nest survival with model-based methods

Model-based methods for analyzing nest survival can be used to investigate effects of continuous and categorical covariates and to produce less biased and more precise estimates of nest survival than design-based methods. Herein, we modeled avian nest survival using the logistic-exposure method, demonstrated how to make meaningful model-based estimates of nest survival, and provided examples using SAS. To produce estimates of nest survival with model-based methods, one first fits a model to the data and then uses that model to produce estimates for specific values of covariates in the model. Covariate values can be based on the sample (e.g., means for continuous covariates and proportions for categorical covariates), however, the sample of nests (and nest-days) is usually non-random and therefore may not be representative of the population of interest. Alternatively, nest-survival estimates can be based on covariate values that the investigator believes are more representative of the population to try and reduce bias resulting from non-random sampling. We discuss a general method that can be used to reduce bias by adjusting estimates for nests that were never observed. We illustrate the method with an example that involves estimating period survival when daily survival varies by date. When the survival model includes interactions among covariates, main effects can be misleading; it is therefore important to present survival estimates as functions of the interacting covariates. When support exists for multiple models, predictions should be generated from each model and then averaged to produce survival and precision estimates that account for model selection uncertainty. We offer some suggestions for presenting model-based results from studies of avian nest survival.
Repeated Caffeine Intake Suppresses Cerebral Grey Matter Responses to Chronic Sleep Restriction in an A1 Adenosine Receptor-Dependent Manner

Evidence has shown that both sleep loss and daily caffeine intake can induce changes in grey matter (GM). Caffeine is frequently used to combat sleepiness and impaired performance caused by insufficient sleep. It is unclear 1) whether daily use of caffeine could prevent or exacerbate the GM alterations induced by chronic sleep restriction, and 2) whether the potential impact on GM plasticity depends on individual differences in the availability of adenosine receptors, which are involved in mediating effects of caffeine on sleep and waking function. In this double-blind, randomized, controlled study, 36 healthy adults (aged 28.9 ± 5.2 y/o; 15 females; habitual daily caffeine intake < 450 mg; 29 homozygous C/C allele carriers of the A2A adenosine receptor (A2AR) gene variant rs5751876 of ADORA2A) underwent a 9-day laboratory visit consisting of one adaption day, 2 baseline days (BL), 5-day sleep restriction (CSR, 5 h time-in-bed), and a recovery day (REC) after an 8-h sleep opportunity. Nineteen participants received 300 mg caffeine in coffee through the 5 days of CSR (CAFF group), while 17 matched participants received decaffeinated coffee (DECAF group). We measured the GM morphology on the 2nd BL Day, 5th CSR Day, and REC Day. Moreover, we used [18F]-CPFPX PET to quantify the baseline availability of A1 adenosine receptors (A1R) and their relation to GM plasticity. The voxel-wise multimodal whole-brain analysis on T1-weighted images controlled for variances of cerebral blood flow indicated a significant interaction between caffeine and CSR in four brain regions: 1) right temporal-occipital region, 2) right thalamus, 3) left dorsolateral, and 4) dorsomedial prefrontal region. The post-hoc analyses indicated increased GM intensity in the DECAF group in all four regions but decreased GM in the thalamus as well as dorsolateral and dorsomedial prefrontal regions in the CAFF group after sleep restriction. Furthermore, lower baseline subcortical A1R availability predicted larger reduction in the CAFF group after CSR of all brain regions except for the caffeine-associated thalamic reduction. In conclusion, our data suggest an adaptive upregulation in GM after 5-day CSR, while concomitant use of caffeine instead leads to a GM reduction. The lack of consistent association with individual A1R availability may suggest that CSR and caffeine affect GM plasticity predominantly by a different mechanism. Future studies on the role of adenosine A2A receptors (ADORA2A) in CSR-induced GM plasticity are warranted.
Essays in Macroeconometrics

This dissertation consists of three independent chapters on econometric methods for macroeconomic analysis. In the first chapter, I propose to estimate structural impulse response functions from macroeconomic time series by doing Bayesian inference on the Structural Vector Moving Average representation of the data. This approach has two advantages over Structural Vector Autoregression analysis: It imposes prior information directly on the impulse responses in a flexible and transparent manner, and it can handle noninvertible impulse response functions. The second chapter, which is coauthored with B. J. Bates, J. H. Stock, and M. W. Watson, considers the estimation of dynamic factor models when there is temporal instability in the factor loadings. We show that the principal components estimator is robust to empirically large amounts of instability. The robustness carries over to regressions based on estimated factors, but not to estimation of the number of factors. In the third chapter, I develop shrinkage methods for smoothing an estimated impulse response function. I propose a data-dependent criterion for selecting the degree of smoothing to optimally trade off bias and variance, and I devise novel shrinkage confidence sets with valid frequentist coverage.
Charm beyond the Standard Model: Probing possible manifestations of new dynamics in charm transitions

CP violation has been observed in the K and B meson systems and can possibly be accommodated within the KM ansatz in the Standard Model. However, it has been argued for long that to generate the observed matter-antimatter asymmetry, CP violation in excess of what can be accommodated within the SM is necessary. With current results from CDF and LHCb on the asymmetry in D → ππ and D → KK the ambiguity on whether D physics can or is showing hints of new dynamics has been given a new life. While there are reasonable arguments that the role of new dynamics in these asymmetries is apparent, it can also be well argued that what we see can possibly be accommodated within the SM. As this is one of the very few tangible signals of possible new dynamics, it has become increasing important that charm comes under rigorous experimental scrutiny once again. SM contribution to rare charm decays are tiny and hence they stand ripe for the intervention of new dynamics. These modes are dominated by long distance contributions and for new dynamics to produce any enhancements to the decay rates, the short distance contribution to these modes have to be enhanced by orders of magnitude, a task which is difficult in most new dynamics scenarios. Of course, there is a way out. Asymmetries are insensitive to long distance contributions and are usually driven by short distance physics. There are certain scenarios of new dynamics in which asymmetries like the forward-backward asymmetry (AcFB) and the CP asymmetry in the forward-backward asymmetry (A FB) can be enhanced by orders of magnitude above SM expectations in the inclusive decay modes D → X u ll. Although AcFB remains around a modest value of 1% in these scenarios, A FB can be as large as O(10 ). Three body final states are also important modes that can show hints of new dynamics and are richer in experimental observables than two body modes where only the decay rates and the difference in those of conjugate states can be probed. Some three body decay modes of both the charged and the neutral D meson system can show CP violation and a detailed 2D Dalitz plot analysis needs to be done. Although, this comes at a premium of statistics, a lot more can be learnt about the nature of new dynamics from this kind of an analysis. Also, CP asymmetries thus measured do not depend on the relative production of conjugate states, a case which is important in an environment where there are inherent production asymmetries. For four body decay modes, one can look into T-odd correlations. This can be done with a pair of pseudoscalars and a pair of leptons in the final state or with a hadronic final state
Hydrodynamic analysis of a mechanical pectoral fin in viscous flows

A two-DoF (degree of freedom) motion model was established for a mechanical pectoral fin. The secondary development of FLUENT (CFD code) software, which is based on the Reynolds-Averaged Navier-Stokes equations (RANS) was adopted. The methods of dynamic mesh and post-processing system of FLUNET were also fully used. The hydrodynamic performances of mechanical pectoral fin in viscous flows were calculated and the calculating results were compared with the latest experimental results. The influences of kinetic parameters on the pectoral fin hydrodynamics were analyzed, which was a basis for the later physical experiments.
Adiabatic theory : stability of systems with increasing gaps

Nous demontrons deux resultats concernant les hamiltoniens de la forme : H(t) = H 0 + V(t), ou H 0 a des lacunes spectrales croissantes et V(t) est un operateur regulier et borne. Tout d'abord, si H 0 possede un spectre discret et si V(t) est periodique en temps, nous etendons a l'operateur de Floquet correspondant certains criteres d'absence de spectre absolument continu. Le cas du rotateur pulse en dimension N est couvert par ce resultat. Ensuite, nous donnons une borne sur la croissance temporelle de l'energie moyenne. Dans le cas particulier d'un rotateur pulse de dimension N et d'un potentiel V(t) n-fois differentiable en temps, nous obtenons, pour (n ≥ 2): (Ψ 1 , H(t)ψ t ) ≤ const.t 2/n .
Parallel second order finite volume scheme for Maxwell’s equations with discontinuous dielectric permittivity on structured meshes

A second order finite volume scheme on structured meshes is presented for numerical solution of time dependent Maxwell’s equations with discontinuous dielectric permittivity. The scheme is based on approaches of Godunov, Van Leer and Lax Wendroff and employs a special technique for gradient calculation near dielectric permittivity discontinuities. The scheme was tested for problems with linear and curvilinear discontinuities. Test results demonstrate second order of convergence and support second order of approximation in space and time. A parallel implementation of the scheme based on geometric decomposition was developed. Computational region was partitioned into subregions. Computations in each subregion were carried out independently using halo cells. Test results indicate linear scalability. Parallel implementation was applied to modelling photonic crystal devices. Computational results for photonic crystal waveguide with a bend correctly confirm bend configurations and frequencies with zero reflection.
Beam-Based Measurements of Long Range Transverse Wakefields in CLIC Main Linac Accelerating Structure

The baseline design of CLIC (Compact Linear Collider) uses X-band accelerating structures in the main linacs. Every accelerating structure cell has four waveguides, terminated with individual RF loads, to damp the unwanted long-range transverse wakefields in order to maintain beam stability in multi-bunch operation. In order to experimentally verify the calculated suppression of wakefields, a prototype structure has been built and installed in FACET test facility at SLAC. The results of the measurements of the wakefields in the prototype structure, by means of positron and electron bunches, are presented.
Gemini/GRACES Spectroscopy of Stars in Triangulum II

The chemical abundance ratios and radial velocities for two stars in the recently discovered Triangulum II faint dwarf galaxy have been determined from high resolution, medium signal-to-noise ratio spectra from the Gemini-GRACES facility. These stars have stellar parameters and metallicities similar to those derived from their photometry and medium-resolution Ca II triplet spectra, and supports that Triangulum II has a metallicity spread consistent with chemical evolution in a dwarf galaxy. The elemental abundances show that both stars have typical calcium abundances and barium upper limits for their metallicities, but low magnesium and sodium. This chemical composition resembles some stars in dwarf galaxies, attributed to inhomogeneous mixing in a low star formation environment, and/or yields from only a few supernova events. One of our targets (Star40) has an enhancement in potassium, and resembles some stars in the unusual outer halo star cluster, NGC 2419. Our other target (Star46) appears to be a binary based on a change in its radial velocity (Delta v(rad) = 24.5 +/- 2.1 km/s). This is consistent with variations found in binary stars in other dwarf galaxies. While this serves as a reminder of the high binary fraction in these ultra faint dwarf galaxies, this particular object has had little impact on the previous determination of the velocity dispersion in Triangulum II.
Distinguishing the Confounding Factors: Policy Evaluation, High-Dimension and Variable Selection

Variable selection is an important question for policy evaluation when identification of the treatment effect relies on a conditional-on-observables strategy. Recent advances in variable selection methods, such as the Lasso, have been deemed useful for the econometrics of policy evaluation. The Lasso approach focuses on the computational feasibility of exhaustive model selection borrowing from procedures developed in a high-dimensional context. However, it has been seldom applied in policy evaluation works because it raises other di culties such as the choice of a parameter that sets the trade-o between t and sparsity. Two Lasso-based treatment e ect estimators are reviewed and compared on an empirical application, on which they perform well. This paper also illustrates the pitfalls of variable selection in a policy evaluation context.
A shorter proof of the distance energy of complete multipartite graphs

Abstract Caporossi, Chasser and Furtula in [Les Cahiers du GERAD (2009) G-2009-64] conjectured that the distance energy of a complete multipartite graph of order n with r ≥ 2 parts, each of size at least 2, is equal to 4(n − r). Stevanovic, Milosevic, Hic and Pokorny in [MATCH Commun. Math. Comput. Chem. 70 (2013), no. 1, 157-162. ] proved the conjecture, and then Zhang in [Linear Algebra Appl. 450 (2014), 108-120. ] gave another proof. We give a shorter proof of this conjecture using the interlacing inequalities of a positve semi-definite rank-1 perturbation to a real symmetric matrix.
Kaon Photoproduction: From an Experimental Point of View

Today, laboratory experiments conducted worldwide continue to search for undiscovered excited states of the nucleon. The database has been continually updated over the past years to allow for nearly model-independent partial wave analyses (PWA) to be carried out in the search for such undiscovered states. The photoproduction of mesons, such as kaons, has been studied extensively in the past. However, there is still much information that can be gathered and learned from the photoproduction of the kaon. Recent coupled-channel analyses have found strong sensitivity of the K + L channel to several higher mass nucleon resonances. Various experiments have provided new and interesting results that are discussed in this short review.
Assessment of land ownership fragmentation by multiple criteria

In this contribution, a simple way of assessing land ownership fragmentation by evaluating land consolidation projects on the basis of multiple criteria is proposed. Obviously, for the criteria that describe fragmentation directly (number of plots, co-owners per plot and plots per owner), minimum values are regarded as favourable. Average size of the plot in a low-fragmentation situation is, of course, higher and is an expected benefit. Distances in spider/radar plots (star coordinates) or the Euclidean distance from an ‘ideal point’ are used as well to measure the (de)fragmentation. Post- and pre-consolidation ratios reflect the changes. Rankings based on the calculated values help to identify problematic cases. Thus proposed system takes into account not only the ownership fragmentation, number and size of plots, but also the co-ownership shares. Its application is demonstrated using the data on 50 finished projects of land consolidation in Slovakia.
Securing software systems via fuzz testing and verification

Software security has been growing in importance due to the increasing reliance on various systems such as computers, smartphones, and Internet-of-Things devices. Security weaknesseses, or vulnerabilities, range in various aspects, from the systematic levels such as designing defects, to implementation errors such as language-specific program crashes. The multifaceted nature of vulnerabilities poses significant challenges to secure different systems. In fact, multilevel approaches have to be applied to reveal vulnerabilities or solidify the systems. Generally, there are two categories of approaches to securing a system, namely testing and verification. The former tries to generate test cases to trigger erroneous behaviors in the underlying programs. The latter models the system in an abstracted description to prove the absence of certain security defects. In this thesis, we will describe our efforts in greybox fuzz testing and type checking based verification in securing different levels of software systems. Firstly, we apply greybox fuzz testing (or fuzzing) to detect implementation vulnerabilities. These vulnerabilities are usually subtle that it is rather complicated to formally verify the absence of the corresponding defects. We target on two levels of vulnerabilities. One is to improve the fuzzing directedness of executing towards specific target program locations to reveal crash induced vulnerabilities such as buffer-overflow, use-after-free, etc. To emphasize existing challenges in directed fuzzing, we propose HAWKEYE to feature four desired properties for directedness. With the statically analyzed results on the target program and its target locations, HAWKEYE applies multiple dynamic strategies for seed prioritization, power scheduling and mutation. The experimental results on various real-world programs showed that HAWKEYE significantly outperforms the state-of-the-art greybox fuzzers AFL and AFLGo in reaching i
Multilevel adaptive radial basis function approximation using error indicators

Multilevel Adaptive Radial Basis Function Approximation using Error Indicators Qi Zhang In some approximation problems, sampling from the target function can be both expensive and time-consuming. It would be convenient to have a method for indicating where the approximation quality is poor, so that generation of new data provides the user with greater accuracy where needed. In this thesis, the author describes a new adaptive algorithm for Radial Basis Function (RBF) interpolation which aims to assess the local approximation quality and adds or removes points as required to improve the error in the specified region. For a multiquadric and Gaussian approximation, one has the flexibility of a shape parameter which one can use to keep the condition number of the interpolation matrix to a moderate size. In this adaptive error indicator (AEI) method, an adaptive shape parameter is applied. Numerical results for test functions which appear in the literature are given for one, two, and three dimensions, to show that this method performs well. A turbine blade design problem form GE Power (Rugby, UK) is considered and the AEI method is applied to this problem. Moreover, a new multilevel approximation scheme is introduced in this thesis by coupling it with the adaptive error indicator. Preliminary numerical results from this Multilevel Adaptive Error Indicator (MAEI) approximation method are shown. These indicate that the MAEI is able to express the target function well. Moreover, it provides a highly efficient sampling.
Tagging molecular clouds in turbulent air

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Solutions of L\'evy-driven SDEs with unbounded coefficients as Feller processes

Let $(L_t)_{t \geq 0}$ be a $k$-dimensional L\'evy process and $\sigma: \mathbb{R}^d \to \mathbb{R}^{d \times k}$ a continuous function such that the L\'evy-driven stochastic differential equation (SDE) $$dX_t = \sigma(X_{t-}) \, dL_t, \qquad X_0 \sim \mu$$ has a unique weak solution. We show that the solution is a Feller process whose domain of the generator contains the smooth functions with compact support if, and only if, the L\'evy measure $\nu$ of the driving L\'evy process $(L_t)_{t \geq 0}$ satisfies $$\nu(\{y \in \mathbb{R}^k; |\sigma(x)y+x|
Non-rotating and slowly rotating white dwarfs in classical physics

The equilibrium configurations of uniformly rotating white dwarfs are calculated in the framework of classical physics. The Chandrasekhar and the Salpeter equations of state are used to describe the white dwarf matter. The Hartle formalism is applied to the integration of the equations of hydrostatic equilibrium and field equations. The equations of structure have been expanded in powers of the angular velocity Ω of the white dwarf, and terms of higher order than Ω� have been neglected.All parameters of rotating white dwarfs such as the total mass, polar and equatorial radii, eccentricity, moment of inertia, angular velocity, angular momentum, gravitational potential and quadrupole moment have been calculated numerically within this approximation.
Image similarity/distance measures: what is really behind MSE and SSIM?

ABSTRACT Similarity/distance measures play an important role in various signal/image processing applications such as classification, clustering, change detection and matching. In most cases, maybe excluding visual perception, the distance measure should be amplitude/intensity translation invariant what means that it depends only on the relative difference of compared variables/parameters, but not on their absolute values. The two most popular measures: mean squared error (MSE) and structural similarity (SSIM) index used in image processing have been analysed theoretically and experimentally by showing their origin, similarities/differences and main properties. Both measures depend on the same parameters: sample means, standard deviations and correlation coefficient. It has been shown that SSIM originates from the two generalised Dice measures and thus inherit their main property scale invariance. Consequently, this property leads to the dependence of the measure on absolute mean and standard deviation values. Similarly, MSE depends on the absolute standard deviation values. A new composite similarity/distance measure based on means, standard deviations and correlation coefficient (CMSC) which has been proposed recently exhibits translation invariance property with respect to means and standard deviations. Experiments on simulated and real data corrupted with various types of distortions: mean shift, contrast stretching, noise (additive/multiplicative, impulsive) and blurring, supported theoretical results.