Miracle-dz/UniFAR-FTUs huggingface dataset:
Pairwise hybrid incompatibilities dominate allopatric speciation for a simple biophysical model of development

Understanding the origin of species is as Darwin called it “that mystery of mysteries”. Yet, how the processes of evolution give rise to non-interbreeding species is still not well understood. In an empirical search for a genetic basis, transcription factor DNA binding has been identiﬁed as an important factor in the development of reproductive isolation. Computational and theoretical models based on the biophysics of transcription factor DNA binding have provided a mechanistic basis of such incompatibilities between allopatrically evolving populations. However, gene transcription by such binding events occurs embedded within gene regulatory networks, so the importance of pair-wise interactions compared to higher-order interactions in speciation remains an open question. Theoretical arguments suggest that higher-order incompatibilities should arise more easily. Here, we show using simulations based on a simple biophysical genotype phenotype map of spatial patterning in development, that biophysics provides a stronger constraint, leading to pair-wise incompatibilities arising more quickly and being more numerous than higher-order incompatibilities. Further, we ﬁnd for small, drift dominated, populations that the growth of incompatibilities is largely determined by sequence entropy constraints alone; small populations give rise to incompatibilities more rapidly as the common ancestor is more likely to be slightly maladapted. This is also seen in models based solely on transcription factor DNA binding, showing that such simple models have considerable explanative power. We suggest the balance between sequence entropy and ﬁtness may play a universal role in the growth of incompatibilities in complex gene regulatory systems.
An automated segmentation method for three-dimensional carotid ultrasound images

We have developed an automated segmentation method for three-dimensional vascular ultrasound images. The method consists of two steps: an automated initial contour identification, followed by application of a geometrically deformable model (GDM). The formation of the initial contours requires the input of a single seed point by the user, and was shown to be insensitive to the placement of the seed within a structure. The GDM minimizes contour energy, providing a smoothed final result. It requires only three simple parameters, all with easily selectable values. The algorithm is fast, performing segmentation on a 336×352×200 volume in 25 s when running on a 100 MHz 9500 Power Macintosh prototype. The segmentation algorithm was tested on stenosed vessel phantoms with known geometry, and the segmentation of the cross-sectional areas was found to be within 3% of the true area. The algorithm was also applied to two sets of patient carotid images, one acquired with a mechanical scanner and the other with a freehand scanning system, with good results on both.
Non-Gaussian isocurvature perturbations in dark radiation

We study non-Gaussian properties of the isocurvature perturbations in the dark radiation, which consists of the active neutrinos and extra light species, if exist. We first derive expressions for the bispectra of primordial perturbations which are mixtures of curvature and dark radiation isocurvature perturbations. We also discuss CMB bispectra produced in our model and forecast CMB constraints on the non-linearity parameters based on the Fisher matrix analysis. Some concrete particle physics motivated models are presented in which large isocurvature perturbations in extra light species and/or the neutrino density isocurvature perturbations as well as their non-Gaussianities may be generated. Thus detections of non-Gaussianity in the dark radiation isocurvature perturbation will give us an opportunity to identify the origin of extra light species and lepton asymmetry.
Digital fundus imaging using a scanning laser ophthalmoscope

The authors describe the construction of a scanning laser ophthalmoscope interfaced to a computer, which has a number of significant advantages for digital retinal imaging. First, it has better uniformity of illumination than the fundus camera and operates at much lower light levels. Secondly, it permits imaging at various wavelengths with no consequent degradation in image quality; in particular, the value of imaging at infrared wavelengths to give greater tissue penetration is demonstrated. Finally, by introducing the capability for confocal imaging, tomographic images can be taken, improving the perceptibility of features situated deep in the retina. Typical images are shown to demonstrate the potential of this instrument.
R-matrix - Floquet theory of multiphoton processes: X. Theory of harmonic generation

The R-matrix - Floquet theory of multiphoton processes is extended to enable harmonic generation rates for a multi-electron atomic system interacting with a strong linearly polarized laser to be calculated. The matrix elements of the harmonic components are defined and several methods for their computation are described. In the two companion papers, applications of the theory to one-electron systems and to third-harmonic generation in magnesium are presented.
Development of cathode materials for the molten-carbonate fuel cell

The current emphasis of molten-carbonate fuel-cell research at Argonne National Laboratory is on developing cathode materials with better long-term stability than lithiated nickel oxide, which dissolves at the cathode and precipitates as nickel metal within the electrolyte tile. A methodology for evaluating candidate cathode materials has been adopted, and several materials have been prepared and tested for conductivity and short-term (<100 h) stability. The methodology and the preliminary results of materials testing are presented. Also, because the solubility of cathode materials in molten carbonates affects their long-term stability, techniques for determining solubility have been developed; the results of measurements on nickel oxide are presented.
Asymptotic analysis of an arbitrary anisotropic plate of variable thickness (sloping shell)

The leading terms of the asymptotics of the solution of the problem of elasticity theory for a thin plane with curved bases are constructed; in addition, the resulting problem (a two-dimensional model) is written out explicitly. Arbitrary anisotropy of elastic properties is allowed; moreover, these properties may depend on the “rapid” transversal and the “slow” longitudinal variables. The substantiation of these asymptotics is carried out on the basis of Korn's weighted inequality. The cases of laminated plates, sloping shells, and plates with sharp edges are discussed separately.
A Physics-Based, SPICE (Simulation Program with Integrated Circuit Emphasis)-Compatible Non-Quasi-Static MOS (Metal-Oxide-Semiconductor) Transient Model Based on the Collocation Method

The collocation method has been applied to derive a new SPICE (Simulation Program with Integrated Circuit Emphasis)-compatible non-quasi-static MOS (metal-oxide-semiconductor) transient model. Contrasting to the conventional approximation methods, the collocation method is simple for the model derivation and efficient in optimizing the variables of the continuity equation. The derived model is fully physics-based in that all the transient currents are directly expressed by only physically meaningful, optimized quantities. The model adequately predicts transient currents in the bias region such as the weak inversion region where conventional models show numerical difficulties.
The inverse problem of depth dose curve estimation

The inverse problem of the depth dose curve is formulated and a proposition for its solution is presented. The solution is based on the approximation of the observation equation with a numerical quadrature operator and the regularization of this inverse problem with a smoothness side constraint. The problem formulation is applicable for both the electron and the photon depth dose curve estimation. Moreover, the method is equivalent for, for example, all energies, field sizes and source-to-phantom distances. Simulations show that the estimation error is smaller with the proposed method than with direct linear interpolation. The main result of the paper, however, is the formulation of the problem that allows feasible extensions and modifications for different measurement situations.
Bridging scales from molecular simulations to classical thermodynamics: density functional theory of capillary condensation in nanopores

With the example of the capillary condensation of Lennard-Jones fluid in nanopores ranging from 1 to 10 nm, we show that the non-local density functional theory (NLDFT) with properly chosen parameters of intermolecular interactions bridges the scale gap from molecular simulations to macroscopic thermodynamics. On the one hand, NLDFT correctly approximates the results of Monte Carlo simulations (shift of vapour–liquid equilibrium, spinodals, density profiles, adsorption isotherms) for pores wider than about 2 nm. On the other hand, NLDFT smoothly merges (above 7–10 nm) with the Derjaguin–Broekhoff–de Boer equations which represent augmented Laplace–Kelvin equations of capillary condensation and desorption.
Cosmological evolution of a tachyon-quintom model of dark energy

In this work we study the cosmological evolution of a dark energy model with two scalar fields, i.e. the tachyon and the phantom tachyon. This model enables the equation of state w to change from w > −1 to w < −1 in the evolution of the universe. The phase-space analysis for such a system with inverse square potentials shows that there exists a unique stable critical point, which has power-law solution. In this paper, we also study another form of tachyon-quintom model with two fields, which involves the interactions between both fields.
A new equation of state for dark energy model

A new parameterization for the dark energy equation of state(EoS) is proposed and some of its cosmological consequences are also investigated. This new parameterization is the modification of Efstathiou' dark energy EoS parameterization. w(z) is a well behaved function for z >> 1 and has same behavior in z at low redshifts with Efstathiou' parameterization. In this parameterization there are two free parameter w0 and wa. We discuss the constraints on this model's parameters from current observational data. The best fit values of the cosmological parameters with 1σ confidence-level regions are: Ωm = 0.2735+0.0171−0.0163, w0 = −1.0537+0.1432−0.1511 and wa = 0.2738+0.8018−0.8288.
Super-acceleration from massless, minimally coupled ϕ4

We derive a simple form for the propagator of a massless, minimally coupled scalar in a locally de Sitter geometry of arbitrary spacetime dimension. We then employ it to compute the fully renormalized stress tensor at one- and two-loop orders for a massless, minimally coupled ϕ4 theory which is released in Bunch–Davies vacuum at t = 0 in co-moving coordinates. In this system, the uncertainty principle elevates the scalar above the minimum of its potential, resulting in a phase of super-acceleration. With the non-derivative self-interaction the scalar's breaking of de Sitter invariance becomes observable. It is also worth noting that the weak-energy condition is violated on cosmological scales. An interesting subsidiary result is that cancelling overlapping divergences in the stress tensor requires a conformal counterterm which has no effect on purely scalar diagrams.
An improved calculation of the non-Gaussian halo mass function

The abundance of collapsed objects in the universe, or halo mass function, is an important theoretical tool in studying the effects of primordially generated non-Gaussianities on the large scale structure. The non-Gaussian mass function has been calculated by several authors in different ways, typically by exploiting the smallness of certain parameters which naturally appear in the calculation, to set up a perturbative expansion. We improve upon the existing results for the mass function by combining path integral methods and saddle point techniques (which have been separately applied in previous approaches). Additionally, we carefully account for the various scale dependent combinations of small parameters which appear. Some of these combinations in fact become of order unity for large mass scales and at high redshifts, and must therefore be treated non-perturbatively. Our approach allows us to do this, and also to account for multi-scale density correlations which appear in the calculation. We thus derive an accurate expression for the mass function which is based on approximations that are valid over a larger range of mass scales and redshifts than those of other authors. By tracking the terms ignored in the analysis, we estimate theoretical errors for our result and also for the results of others. We also discuss the complications introduced by the choice of smoothing filter function, which we take to be a top-hat in real space, and which leads to the dominant errors in our expression. Finally, we present a detailed comparison between the various expressions for the mass functions, exploring the accuracy and range of validity of each.
PERICLES - PROMOTING AND ENHANCING REUSE OF INFORMATION THROUGHOUT THE CONTENT LIFECYCLE TAKING ACCOUNT OF EVOLVING SEMANTICS , APPLICATION TO EARTH AND SPACE SCIENCE DATA.

PERICLES (Promoting and Enhancing the Reuse of Information throughout the Content Lifecycle exploiting Evolving Semantics) is an FP7 project started on February 2013. It aims at preserving by design large and complex data sets. PERICLES is coordinated by King’s College London, UK and its partners are University of Borås (Sweden), CERTH-ITI (Greece), DotSoft (Greece), Georg-August-Universität Göttingen (Germany), University of Liverpool (UK), Space Application Services (Belgium), XEROX France and University of Edinburgh (UK). Two additional partners provide the two case studies: Tate Gallery (UK) brings the digital art and media case study and B.USOC (Belgian Users Support and Operations Centre) brings the space science case study. PERICLES addresses the life-cycle of large and complex data sets in order to cater for the evolution of context of data sets and user communities, including groups unanticipated when the data was created. Semantics of data sets are thus also expected to evolve and the project includes elements which could address the reuse of data sets at periods where the data providers and even their institutions are not available any more. B.USOC supports experiments on the International Space Station and is the curator of the collected data and operation history. The B.USOC operation team includes B.USOC and Space Applications Services personnel and is thus ideally configured to participate in this project. As a first test of the concept, B.USOC has chosen to analyse the SOLAR payload operating since 2008 on the ESA COLUMBUS module of the ISS. Observation data are prime candidates for long term data preservation as variabilities of the solar spectral irradiance have an influence on earth climate. The paradigm of these observations has already changed a lot in the last fifty years from a time where scientists were aiming at determining with high accuracy the “solar constant” which
Electron beam quality correction factors for plane-parallel ionization chambers: Monte Carlo calculations using the PENELOPE system

Simulations of three plane-parallel ionization chambers have been used to determine directly the chamber- and quality-dependent factors fc,Q, instead of the product (sw,air p)Q, and (or ) for a broad range of electron beam qualities (4–20 MeV) using divergent monoenergetic beams and phase-space data from two accelerators. An original calculation method has been used which circumvents the weakness of the so far assumed independence between stopping-power ratios and perturbation factors. Very detailed descriptions of the geometry and materials of the chambers have been obtained from the manufacturers, and prepared as input to the PENELOPE 2003 Monte Carlo system using a computer code that includes correlated sampling and particle splitting. Values of the beam quality factors have been determined for the case of an electron reference beam. The calculated values have been compared with those in the IAEA TRS-398 dosimetry protocol and the differences analysed. The results for a NACP-02 chamber show remarkably good agreement with TRS-398 at high electron beam qualities but differ slightly at low energies. Arguments to explain the differences include questioning the undemonstrated assumption that the NACP is a ‘perturbation-free’ chamber even at very low electron beam energies. Results for Wellhöfer PPC-40 and PPC-05 chambers cannot be compared with data from others for these chambers because no calculations or reliable experimental data exist. It has been found that the results for the PPC-40 are very close to those of a Roos chamber, but the values for the PPC-05 are considerably different from those of a Markus chamber, and rather approach those of a Roos chamber. Results for monoenergetic electrons and accelerator phase-space data have been compared to assess the need for detailed and costly simulations, finding very small differences. This questions the emphasis given in recent years to the use of ‘realistic’ source data for accurate electron beam dosimetry.
Can electroweak bubble walls run away?

In extensions of the Standard Model with SU(2) singlet scalar fields, there can be regions of parameter space for which the electroweak phase transition is first order already at the mean-field level of analysis. We show that in this case the phase interface (bubble wall) can become ultra-relativistic, with the relativistic gamma factor γ = (1−vwall2)−1/2 growing linearly with the wall's propagation distance. We provide a simple criterion for determining whether the bubble wall ``runs away'' in this way or if γ approaches a terminal value.
Constraining cosmic expansion and gravity with galaxy redshift surveys

We analyze the science reach of a next generation galaxy redshift survey such as BigBOSS to fit simultaneously for time varying dark energy equation of state and time- and scale-dependent gravity. The simultaneous fit avoids potential bias from assuming ΛCDM expansion or general relativity and leads to only modest degradation in constraints. Galaxy bias, fit freely in redshift bins, is self calibrated by spectroscopic measurements of redshift space distortions and causes little impact. The combination of galaxy redshift, cosmic microwave background, and supernova distance data can deliver 5-10% constraints on 6 model independent modified gravity quantities.
Thermal boundary resistance of mechanical contacts between solids at sub-ambient temperatures

The experimental values of the thermal boundary resistance occurring at interfaces between two solids at sub-ambient temperatures are reviewed. New data are presented in the temperature range from 4 K to 300 K for the thermal resistance between different metals (Cu, stainless steel), interlayered by various cryogenic bonding agents (Apiezon-N, Cryocon grease, In and InGa), or mechanically connected (dry) contacts. Depending on the contact materials, the thermal conductance varies between and at room temperature, and decreases approximately linearly by one order of magnitude between 200 K and 20 K. Our experimental data agree well with the data reported in the literature for the temperature range below 4 K and measurements near room temperature.
A direct probe of cosmological power spectra of the peculiar velocity field and the gravitational lensing magnification from photometric redshift surveys

The cosmological peculiar velocity field (deviations from the pure Hubble flow) of matter carries significant information on dark energy, dark matter and the underlying theory of gravity on large scales. Peculiar motions of galaxies introduce systematic deviations between the observed galaxy redshifts z and the corresponding cosmological redshifts zcos. A novel method for estimating the angular power spectrum of the peculiar velocity field based on observations of galaxy redshifts and apparent magnitudes m (or equivalently fluxes) is presented. This method exploits the fact that a mean relation between zcos and m of galaxies can be derived from all galaxies in a redshift-magnitude survey. Given a galaxy magnitude, it is shown that the zcos(m) relation yields its cosmological redshift with a 1σ error of σz ∼ 0.3 for a survey like Euclid ( ∼ 109 galaxies at z≲2), and can be used to constrain the angular power spectrum of z−zcos(m) with a high signal-to-noise ratio. At large angular separations corresponding to l≲15, we obtain significant constraints on the power spectrum of the peculiar velocity field. At 15≲l≲60, magnitude shifts in the zcos(m) relation caused by gravitational lensing magnification dominate, allowing us to probe the line-of-sight integral of the gravitational potential. Effects related to the environmental dependence in the luminosity function can easily be computed and their contamination removed from the estimated power spectra. The amplitude of the combined velocity and lensing power spectra at z ∼ 1 can be measured with ≲5% accuracy.
Dark matter assimilation into the baryon asymmetry

Pure singlets are typically disfavored as dark matter candidates, since they generically have a thermal relic abundance larger than the observed value. In this paper, we propose a new dark matter mechanism called “assimilation”, which takes advantage of the baryon asymmetry of the universe to generate the correct relic abundance of singlet dark matter. Through assimilation, dark matter itself is efficiently destroyed, but dark matter number is stored in new quasi-stable heavy states which carry the baryon asymmetry. The subsequent annihilation and late-time decay of these heavy states yields (symmetric) dark matter as well as (asymmetric) standard model baryons. We study in detail the case of pure bino dark matter by augmenting the minimal supersymmetric standard model with vector-like chiral multiplets. In the parameter range where this mechanism is effective, the LHC can discover long-lived charged particles which were responsible for assimilating dark matter.
Darstellung zeitabhängiger Veränderungen der Nasenschleimhaut unter Einsatz modernster Morphsoftware

Der Einblick in die Funktionsweise der Nase war bisher nur in Momentaufnahmen moglich. Endoskopische Photos ergaben Einzeldokumentationen der Funktionsweise der Nasenmuscheln. Die Darstellung der Muschelbewegung im Videofilm scheiterte bisher daran, uber einen langeren Zeitabschnitt Bilder von gleichem Ausschnitt und Blickwinkel zu erhalten. Dank des Einsatzes modernster S-VHS-Videotechnik, PC-Computertechnik (Targa+-Graphikkarte) und dem Softwareprogramm PC-Morph ist es uns gelungen, im Zeitraffer die Dynamik der unteren Muschel darzustellen. So konnten wir Ablauf und Zeitdauer des Abschwellvorganges nach Applikation von Nasentropfen und die Reboundphase visualisieren. Weiterhin war es moglich, die Wirksamkeit topisch applizierten Kortisons auf Nasenpolypen dynamisch zu dokumentieren.