Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary trajectories, accessibility, and other metaphors: the case of C4 and CAM photosynthesis.

Are evolutionary outcomes predictable? Adaptations that show repeated evolutionary convergence across the Tree of Life provide a special opportunity to dissect the context surrounding their origins, and identify any commonalities that may predict why certain traits evolved many times in particular clades and yet never evolved in others. The remarkable convergence of C4 and Crassulacean Acid Metabolism (CAM) photosynthesis in vascular plants makes them exceptional model systems for understanding the repeated evolution of complex phenotypes. This review highlights what we have learned about the recurring assembly of C4 and CAM, focusing on the increasingly predictable stepwise evolutionary integration of anatomy and biochemistry. With the caveat that we currently understand C4 evolution better than we do CAM, I propose a general model that explains and unites C4 and CAM evolutionary trajectories. Available data suggest that anatomical modifications are the "rate-limiting step" in each trajectory, which in large part determines the evolutionary accessibility of both syndromes. The idea that organismal structure exerts a primary influence on innovation is discussed in the context of other systems. Whether the rate-limiting step occurs early or late in the evolutionary assembly of a new phenotype may have profound implications for its distribution across the Tree of Life. This article is protected by copyright. All rights reserved.
Diverse Temporal Properties of Gamma-Ray Burst Afterglows

The detection of delayed X-ray, optical, and radio emission, the "afterglow" associated with gamma-ray bursts (GRBs), is consistent with fireball models, in which the emission is produced by a relativistic expanding blast wave, driven by an expanding fireball at cosmological distances. The emission mechanisms of GRB afterglows have been discussed by many authors, and synchrotron radiation is believed to be the main mechanism. The observations show that the optical light curves of two observed gamma-ray bursts, GRB 970228 and GRB 970508, can be described by a simple power law, which seems to support the synchrotron radiation explanation. However, here we show that under some circumstances, inverse Compton scattering (ICS) may play an important role in the emission spectrum, and this may influence the temporal properties of GRB afterglows. We expect that the light curves of GRB afterglows may consist of multiple components, depending on the fireball parameters.
Residual defects following rapid thermal annealing of shallow boron and boron fluoride implants into preamorphized silicon

Shallow BF2 and B implants (42 keV, 2×1015 cm−2) were conducted at either liquid nitrogen or room temperature into deeply preamorphized (100) Si. Cross‐sectional transmission electron microscopy revealed that subsequent rapid thermal annealing (RTA) of the room‐temperature implanted BF2 sample in the temperature range 950–1150 °C for 10 s created three classes of secondary defects at three different depth levels. The depths corresponded closely to the projected range of the BF2 implant, the deep amorphous/crystalline interface, and the region immediately below the interface. In contrast, RTA of preamorphized Si with or without the shallow B implant both resulted in a high perfection surface region with secondary defects only in the region below the deep amorphous/crystalline interface. A phenomenological model for nucleation of the separate layers of defects is presented.
Recent Advances of Percolation Theory in Complex Networks

During the past two decades, percolation has long served as a basic paradigm for network resilience, community formation and so on in complex systems. While the percolation transition is known as one of the most robust continuous transitions, the percolation transitions occurring in complex systems are often of different types such as discontinuous, hybrid, and infinite-order phase transitions. Thus, percolation has received considerable attention in network science community. Here we present a very brief review of percolation theory recently developed, which includes those types of phase transitions, critical phenomena, and finite-size scaling theory. Moreover, we discuss potential applications of theoretical results and several open questions including universal behaviors.
$\Omega$ and $\phi$ in Au + Au ~collisions at \srt~= 200 and 11.5 GeV from a multiphase transport model

Within the framework of a multiphase transport model, we study the production and properties of $\Omega$ and $\phi$ in Au + Au collisions with a new set of parameters for $\sqrt{s_{NN}}$ = 200 GeV and with the original set of parameters for $\sqrt{s_{NN}}$ = 11.5 GeV, respectively. The AMPT model with the string melting version provides a reasonable description at $\sqrt{s_{NN}}$ = 200 GeV and while the AMPT model with default version describes the data well at $\sqrt{s_{NN}}$ = 11.5 GeV. It indicates that the system created at top RHIC energy is dominated by partonic interaction and while the hadronic interaction becomes important at lower beam energy, such as $\sqrt{s_{NN}}$ = 11.5 GeV. The comparison of $N(\Omega ^++\Omega^-)/[2N(\phi)]$ ratio between data and calculations further supports the argument. Our calculations can generally describe the data of nuclear modification factor as well as elliptic flow.
Variation of the fundamental constants over the cosmological time: veracity of Dirac’s intriguing hypothesis

We investigate how the universal constants, including the fine structure constant, have varied since the early universe close to the Planck energy scale (EP ∼ 1019 GeV) and, thus, how they have evolved over the cosmological time related to the temperature of the expanding universe. According to a previous paper (Nassif and Amaro de Faria, Jr. Phys. Rev. D, 86, 027703 (2012). doi:10.1103/PhysRevD.86. 027703), we have shown that the speed of light was much higher close to the Planck scale. In the present work, we will go further, first by showing that both the Planck constant and the electron charge were also too large in the early universe. However, we conclude that the fine structure constant (α ≅ 1/137) has remained invariant with the age and temperature of the universe, which is in agreement with laboratory tests and some observational data. Furthermore, we will obtain the divergence of the electron (or proton) mass and also the gravitational constant (G) at the Planck scale. Thus, we will be able to ver.
Spectral Properties of Analyzed and Forecast Global 500 mb fields

Abstract Global ECMWF data for winter and summer seasons are used to study the spectral structure of 500 mb analyzed height variance and forecast error variance, as well as the effect of spectral truncation in the height and temperature variance calculations. The high wavenumber region of the variance of the analyses is nearly homogeneous and isotropic and follows the −5 power law both in the zonal, two-dimensional and meridional wavenumber indexes. The high wavenumber region is dominated by transient waves. The low wavenumber region is dominated by the stationary part, being anisotropic and seasonally variable. The transition between the two regions is at wavenumbers 7–8. The temperature variance follows a −4 power law in the high wavenumber region. The ECMWF forecast error variance is dominated by the nonsystematic error, the maximum of which shifts from medium to long zonal waves during the forecast. The nonsystematic error variance spectrum is quite similar to the transient variance in the analyses.
Optimal Controller Parameter Design Using Simplex Optimization

This paper proposes a method of finding optimal controller parameters off line using Simplex parameter optimization. Given the system's specifications, one can use a scaler function or in other words, performance index function, in terms of controller parameters, to describe the performance of the system, such that when the function is minimized, the performance requirements are met. Minimization is initiated from a properly chosen point on the performance surface and a Simplex algorithm is used to search downhill on the performance surface.
A High-Resolution ROSAT X-Ray Study of Abell 4059

We present the analysis of ROSAT HRI and PSPC X-ray data on the compact cD type cluster Abell 4059. The central cD galaxy hosts the strong radio source PKS 2354-35. The central portion of the X-ray image shows two statistically significant X-ray emission minima and an orthogonal X-ray bar. As is the case in NGC 1275, the radio lobes in PKS 2354-35 lie perpendicularly to the X-ray bar and extend into the two X-ray minima. One suggestion is that the radio lobe plasma has displaced the X-ray plasma and created the X-ray holes. The radio plasma and the X-ray gas do have comparable pressures in the radio lobe area. However, the available radio images do not show radio emission that extends far enough to fill the two X-ray holes. An alternative scenario for the anticorrelated radio and X-ray structure is an rotating disk in the cooling flow region of Abell 4059. The ROSAT HRI surface brightness profile shows that there is a cooling flow around the central cD galaxy with a cooling rate of Ṁ=184+ 22−25 M☉ yr-1 within a radius of 156 kpc. However, the ROSAT PSPC spectrum of the central regions does not require a cooling flow and gives an upper limit to the cooling rate of Ṁ < 80 M☉ yr-1 (90% confidence level). The X-ray spectra of the central region indicate very little intrinsic absorption in the cluster, with an upper limit of ΔNH ≤ 4.0 × 1019 cm-2 for excess absorption in front of the cluster emission at the center of the cooling flow. On large scales, the cluster shows interesting spatial alignment between the major axes of the X-ray emission, cD galaxy, and the cluster potential. This is consistent with the anisotropic merger model for the formation of cD galaxies and the orientation of cD galaxy radio sources.
Bundle Geodesic Convolutional Neural Network for Multishell DWI Voxel Classiﬁcation

This work presents a Riemannian Deep Learning framework for extracting features with rotational invariance. Our main application is classiﬁcation of multishell Magnetic Resonance Diﬀusion Weighted Imaging (DWI) at single voxel level. To that extent, we extend a G-CNN learning architecture, ﬁrst in a generic way on a Riemannian manifold. It mainly consists of three layers: a lifting layer that locally represents and convolves data on tangent spaces to produce a family of functions deﬁned on the rotation groups of the tangent spaces, i.e., a section of a bundle of rotational functions on the manifold; a group convolution layer that convolves this section with rotation kernels to produce a new section; and a projection by maximisation to collapse this local data to form new manifold based functions. We propose an instantiation on the 2-dimensional sphere where the DWI orientation data is in general represented, and we use it for voxel classiﬁcation. We show that it provides a grey matter vs. non-grey matter classiﬁcation that is competitive with reported results in the literature.
Ellipsometric studies of electronic interband transitions in Cd x Hg 1-x Te

Ellipsometric measurements of the dielectric constant of ${\mathrm{Cd}}_{x}{\mathrm{Hg}}_{1\ensuremath{-}x}\mathrm{Te}$ alloys were performed at room temperature between 1.8 and 5.5 eV for samples covering the whole range of concentrations. The dependence of the ${E}_{1}$, ${E}_{1}+{\ensuremath{\Delta}}_{1}$, and ${E}_{2}$ threshold energies on $x$ was obtained: It is quadratic for ${E}_{1}$ and ${E}_{1}+{\ensuremath{\Delta}}_{1}$ and linear within experimental error for ${E}_{2}$. An upwards bowing is found for the spin-orbit splitting ${\ensuremath{\Delta}}_{1}$ as a function of $x$. The effect of alloying in broadening the observed structures is relatively small. However, a large decrease of excitonic effects in the ${E}_{1}$ and ${E}_{1}+{\ensuremath{\Delta}}_{1}$ gaps due to alloying has been observed. These results are discussed in the light of recent coherent-potential-approximation calculations.
A plane-wave pseudopotential study on III–V zinc-blende and wurtzite semiconductors under pressure

The results of a plane-wave pseudopotential study on the mechanical and electronic properties of twelve III-V zinc-blende (ZB) and wurtzite (WZ) semiconductors under pressure are presented. The lattice parameters, bulk moduli B-0, energy band types, band-gaps E-g(Gamma) at the Gamma point, and pressure dependences of E-g(Gamma) are investigated in detail. Our results show that the E-g(Gamma)-P relations can be classified into two distinct types for these ZB and WZ phases. A transformation from one type of E-g(Gamma)-P-relation to the other type is found to occur in some WZ phases. Linear relationships between the bulk moduli and the inverse of unit-cell volumes at P = 0 are also found for the ZB and WZ phases.
Density Matrix Approach to Local Hilbert Space Reduction

We present a density matrix approach for treating systems with a large or infinite number of degrees of freedom per site with exact diagonalization or the density matrix renormalization group. The method is demonstrated on the 1D Holstein model of electrons coupled to Einstein phonons. In this system, two or three optimized phonon modes per site give results as accurate as with 10-100 bare phonon levels per site.
Back to basics: The ‘met. enclosure’: Part 7 — Evaporation

The rate at which water evaporates from the ground and from vegetation is influenced by the relative humidity and temperature of the ah-, by the level of radiation, by wind speed and the amount of water available, by the nature of the surface (for example, its roughness) and the type of vegetation (for example, grassland, crops or forest). The state of the stomata of the plants is a further factor, since transpiration is lumped together under the general heading of evaporation. More precisely, the combined process should be termed evapotranspiration, but for brevity evaporation will be used here. Open water, snow and ice each present their own special conditions. As explained in an earlier article (Strangeways 1998), the net incoming energy at the ground’s surface is divided into three fluxes sensible heat, latent heat and soil heat fluxes according to the particular combination of circumstances, which vary with both time and place. Here we are concerned with the latent heat flux. Evaporation is expressed in the same units as precipitation the equivalent depth of liquid water, in millimetres, lost to the atmosphere as water vapour, over a period of time. By using the same units, water balances are easily calculated. To be clear exactly what type of evaporation is being discussed, several standard rates have been defined (Shuttleworth 1979). Penman (1948, 1956) developed the idea of potential evaporation the amount of water evaporated (per unit area, per unit time) from an extensive area of a free water surface. Although this method takes no account of the actual processes occurring within the water or in the air above, the concept bears some relation to reality. The idea of potential evapotranspiration the amount of water that can evaporate from a large area of vegetation when the soil is saturated (Gangopadhyaya et al. 1966) was a later development based on experimental evidence that, at the time, suggested that the type of vegetation had little effect on evaporation. However, it later became clear that the type of vegetation did have a significant effect (Tanner 1967), and the concept of reference crop evapotranspiration was introduced. In Penman’s original work, the evaporation was from grassland. There are now a number of variations on Penman’s original work, but Penman’s classical example is the one considered below. While it is difficult enough to measure the input of liquid and solid water as precipitation (Strangeways 1996a), it is considerably more difficult to measure the loss of water by evaporation.
Catalog of Galactic β Cephei Stars

We present an extensive and up-to-date catalog of Galactic β Cephei stars. This catalog is intended to give a comprehensive overview of observational characteristics of all known β Cephei stars, covering information until 2004 June. Ninety-three stars could be confirmed to be β Cephei stars. We use data from more than 250 papers published over the last nearly 100 years, and we provide over 45 notes on individual stars. For some stars we reanalyzed published data or conducted our own analyses. Sixty-one stars were rejected from the final β Cephei list, and 77 stars are suspected to be β Cephei stars. A list of critically selected pulsation frequencies for confirmed β Cephei stars is also presented. We analyze the β Cephei stars as a group, such as the distributions of their spectral types, projected rotational velocities, radial velocities, pulsation periods, and Galactic coordinates. We confirm that the majority of the β Cephei stars are multiperiodic pulsators. We show that, besides two exceptions, the β Cephei stars with high pulsation amplitudes are slow rotators. Those higher amplitude stars have angular rotational velocities in the same range as the high-amplitude δ Scuti stars (Prot ≳ 3 days). We construct a theoretical HR diagram that suggests that almost all 93 β Cephei stars are main-sequence objects. We discuss the observational boundaries of β Cephei pulsation and the physical parameters of the stars. We corroborate that the excited pulsation modes are near to the radial fundamental mode in frequency and we show that the mass distribution of the stars peaks at 12 M⊙. We point out that the theoretical instability strip of the β Cephei stars is filled neither at the cool nor at the hot end and attempt to explain this observation.
Bose-einstein condensation of trapped interacting spin-1 atoms

We investigate Bose-Einstein condensation of trapped spin-1 atoms with ferromagnetic or antiferromagnetic two-body contact interactions. We adopt the mean field theory and develop a Hartree-Fock-Popov type approximation in terms of a semiclassical two-fluid model. For antiferromagnetic interactions, our study reveals double condensations as atoms in the |m{sub F}=0> state never seem to condense under the constraints of both the conservation of total atom number N and magnetization M. For ferromagnetic interactions, however, triple condensations can occur. Our results can be conveniently understood in terms of the interplay of three factors: (anti)ferromagnetic atom-atom interactions, M conservation, and the miscibilities between and among different condensed components.
Anomalous self-diffusion in the ferromagnetic Ising chain with Kawasaki dynamics

We investigate the motion of a tagged spin in a ferromagnetic Ising chain evolving under Kawasaki dynamics. At equilibrium, the displacement is Gaussian, with a variance increasing as At1/2. The temperature dependence of the prefactor A is derived exactly. At low temperature, where the static correlation length ξ is large, the mean square displacement increases as (t/ξ2)2/3 in the coarsening regime, i.e., as a finite fraction of the mean square domain length. The case of totally asymmetric dynamics, where (+) (resp. (−)) spins move only to the right (resp. to the left), is also considered. In the steady state, the displacement variance increases as Bt2/3. The temperature dependence of the prefactor B is derived exactly, using the Kardar–Parisi–Zhang theory. At low temperature, the displacement variance increases as t/ξ2 in the coarsening regime, again proportionally to the mean square domain length.
The WARPS Survey. II. The log N-log S Relation and the X-Ray Evolution of Low-Luminosity Clusters of Galaxies

The strong negative evolution observed in previous X-ray-selected surveys of clusters of galaxies is evidence in favor of hierarchical models of the growth of structure in the universe. A large recent survey has, however, contradicted the low-redshift results, finding no evidence for evolution at z < 0.3. Here we present the first results from an X-ray-selected, flux- and surface brightness-limited deep survey for high-redshift clusters and groups of galaxies based on ROSAT PSPC pointed data. The log N-log S relation of all clusters in this survey is consistent with that of most previous surveys, but it occupies a flux range not previously covered (greater than 6 × 10-14 ergs cm-2 s-1 total flux in the 0.5-2 keV band). At high redshifts (z > 0.3) the cluster luminosities are in the range 4 × 1043-2 × 1044 h−250 ergs s-1, the luminosities of poor clusters. The number of high-redshift, low-luminosity clusters is consistent with no evolution of the X-ray luminosity function between redshifts of z ≈ 0.4 and z = 0, and it places a limit of a factor of less than 1.7 (at 90% confidence) on the amplitude of any pure negative density evolution of clusters of these luminosities, in contrast with the factor of ≈ 3 [corresponding to number density evolution ∝(1 + z)-2.5] found in the Einstein Extended Medium-Sensitivity Survey at similar redshifts but higher luminosities. Taken together, these results support hierarchical models in which there is mild negative evolution of the most luminous clusters at high redshift, but little or no evolution of the less luminous but more common optically poor clusters. Models involving preheating of the X-ray gas at an early epoch fit the observations, at least for Ω0 = 1.
Interface bonding of a ferromagnetic/semiconductor junction: A photoemission study of Fe/ZnSe(001)

We have probed the interface of a ferromagnetic/semiconductor (FM/SC) heterojunction by a combined high resolution photoemission spectroscopy and x-ray photoelectron diffraction study. Fe/ZnSe(001) is considered as an example of a very low reactivity interface system and it is expected to constitute large tunnel magnetoresistance devices. We focus on the interface atomic environment, on the microscopic processes of the interface formation and on the iron valence band. We show that the Fe contact with ZnSe induces a chemical conversion of the ZnSe outermost atomic layers. The main driving force that induces this rearrangement is the requirement for a stable Fe-Se bonding at the interface and a Se monolayer that floats at the Fe growth front. The released Zn atoms are incorporated in substitution in the Fe lattice position. This formation process is independent of the ZnSe surface termination (Zn or Se). The Fe valence-band evolution indicates that the d-states at the Fermi level show up even at submonolayer Fe coverage but that the Fe bulk character is only recovered above 10 monolayers. Indeed, the Fe Delta(1)-band states, theoretically predicted to dominate the tunneling conductance of Fe/ZnSe/Fe junctions, are strongly modified at the FM/SC interface.
Algebraic decomposition of the electromagnetic constitutive tensor. A step towards a pre‐metric based gravitation?

The aim of this paper is to provide an algebraic decomposition of the principal part of the electromagnetic constitutive tensor χμνρσ (a pre‐metric structure), in a sum of terms of the form \documentclass{article}\usepackage{amssymb}\pagestyle{empty}\begin{document}$$\[ \sum\limits_i Z_{(i)} ({g_{\mu \rho } }\limits_{(i)} {g_{\nu \sigma } }\limits_{(i)} - {g_{\mu \sigma } }\limits_{(i)} {g_{\nu \rho } }\limits_{(i)} ) \] $$\end{document} where the Z(i) are invariant scalars and gμν(i)unimodular conformal metrics. If the space‐time is also equipped with a volume measure, such a decomposition is equivalent to a similar decomposition of the associated area metric, where the gμν(i) are ordinary metrics. It has been recently argued [8] that, if such a particular decomposition should be available, it would then be possible to find a compatible connection and derived tensors.