cssi/SciSciGPT-SciSciNet huggingface dataset:
An osmolality/salinity-responsive enhancer 1 (OSRE1) in intron 1 promotes salinity induction of tilapia glutamine synthetase.

Euryhaline tilapia (Oreochromis mossambicus) are fish that tolerate a wide salinity range from fresh water to > 3× seawater. Even though the physiological effector mechanisms of osmoregulation that maintain plasma homeostasis in fresh water and seawater fish are well known, the corresponding molecular mechanisms that control switching between hyper- (fresh water) and hypo-osmoregulation (seawater) remain mostly elusive. In this study we show that hyperosmotic induction of glutamine synthetase represents a prominent part of this switch. Proteomics analysis of the O. mossambicus OmB cell line revealed that glutamine synthetase is transcriptionally regulated by hyperosmolality. Therefore, the 5′ regulatory sequence of O. mossambicus glutamine synthetase was investigated. Using an enhancer trapping assay, we discovered a novel osmosensitive mechanism by which intron 1 positively mediates glutamine synthetase transcription. Intron 1 includes a single, functional copy of an osmoresponsive element, osmolality/salinity-responsive enhancer 1 (OSRE1). Unlike for conventional enhancers, the hyperosmotic induction of glutamine synthetase by intron 1 is position dependent. But irrespective of intron 1 position, OSRE1 deletion from intron 1 abolishes hyperosmotic enhancer activity. These findings indicate that proper intron 1 positioning and the presence of an OSRE1 in intron 1 are required for precise enhancement of hyperosmotic glutamine synthetase expression.
An agent-based model of the foraging ascomycete hypothesis

Abstract Most trees host hundreds of species of fungi asymptomatically in their internal tissues, known collectively as fungal endophytes. The Foraging Ascomycete (FA) hypothesis proposed that some fungal endophytes inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia during periods of environmental stress. This dispersal strategy has recently been termed viaphytism and is now thought to apply to fungal groups beyond ascomycetes. Viaphytism implies that many fungi may be in continuous and cyclical flux between life stages as endophytes in the forest canopy and as wood-decomposing fungi on the forest floor. This cycle may represent a very common and previously-ignored process in the ecology of forests, with implications for forest health. The ecological consequences of the viaphyte lifestyle are complex, so we constructed an agent-based model to explore it. Our model is intended to serve as both an explicit conceptual explanation of viaphytism, and as an exploration of the conditions in which a strategy of endophytism accompanied by leaf dispersal may be advantageous for fungi. In a scenario of a viaphytic fungal species on a model forest landscape, without fungal competitors, viaphytism is predicted to be a plausible alternative to dispersal to substrates by spores alone, allowing the fungus to persist reliably in the landscape. In a scenario that allows competition from aggressively dispersed non-viaphytic fungi, the model predicts some competitive benefits to fungal dispersal via leaves. However, these benefits are conditional, requiring sufficient retention through time of endophyte infections by host trees, and sufficient host trees in the landscape. In the model, loss of these fungal populations can result from increased local disturbances of forest canopy, and deforestation.
Large Deflections of Inextensible Cantilevers: Modeling, Theory, and Simulation

A recent large deflection cantilever model is considered. The principal nonlinear effects come through the beam’s inextensibility – local arc length preservation – rather than traditional extensible effects attributed to fully restricted boundary conditions. Enforcing inextensibility leads to: nonlinear stiffness terms, which appear as quasilinear and semilinear effects, as well as nonlinear inertia effects, appearing as nonlocal terms that make the beam implicit in the acceleration. In this paper we discuss the derivation of the equations of motion via Hamilton’s principle with a Lagrange multiplier to enforce the effective inextensibility constraint . We then provide the functional framework for weak and strong solutions before presenting novel results on the existence and uniqueness of strong solutions. A distinguishing feature is that the two types of nonlinear terms present independent challenges: the quasilinear nature of the stiffness forces higher topologies for solutions, while the nonlocal inertia requires the consideration of Kelvin-Voigt type damping to close estimates. Finally, a modal approach is used to produce mathematically-oriented numerical simulations that provide insight into the features and limitations of the inextensible model.
Faster imaging simulation through complex systems: a coronagraphic example

End-to-end simulation of the influence of the optical train on the observed scene is important across optics and is particularly important for predicting the science yield of astronomical telescopes. As a consequence of their goal of suppressing starlight, coronagraphic instruments for high-contrast imaging have particularly complex field-dependent point-spread-functions (PSFs). The Roman Coronagraph Instrument (CGI), Hybrid Lyot Coronagraph (HLC) is one example. The purpose of the HLC is to image exoplanets and exozodiacal dust in order to understand dynamics of solar systems. This paper details how images of exoplanets and exozodiacal dust are simulated using some of the most recent PSFs generated for the CGI HLC imaging mode. First, PSFs are generated using physical optics propagation techniques. Then, the angular offset of pixels in image scenes, such as exozodiacal dust models, are used to create a library of interpolated PSFs using interpolation and rotation techniques, such that the interpolated PSFs correspond to angular offsets of the pixels. This means interpolation needs only be done once and an image can then be simulated by multiplying the vector array of the model astrophysical scene by the matrix array of the interpolated PSF data. This substantially reduces the time required to generate image simulations by reducing the process to matrix multiplication, allowing for faster scene analysis. We will detail the steps required to generate coronagraphic scenes, quantify the speed-up of our matrix approach versus other implementations, and provide example code for users who wish to simulate their own scenes using publicly available HLC PSFs.
Long time behavior of dynamic solution to Peierls–Nabarro dislocation model

In this paper we study the relaxation process of Peierls-Nabarro dislocation model, which is a gradient flow with singular nonlocal energy and double well potential describing how the materials relax to its equilibrium with the presence of a dislocation. We prove the dynamic solution to Peierls-Nabarro model will converge exponentially to a shifted steady profile which is uniquely determined.
Cryo-electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae

The extreme halophile Halococcus morrhuae (ATCC® 17082) contains a 108-nucleotide insertion in its 5S rRNA. Large rRNA expansions in Archaea are rare. This one almost doubles the length of the 5S rRNA. In order to understand how such an insertion is accommodated in the ribosome, we obtained a cryo-electron microscopy reconstruction of the native large subunit at subnanometer resolution. The insertion site forms a four-way junction that fully preserves the canonical 5S rRNA structure. Moving away from the junction site, the inserted region is conformationally flexible and does not pack tightly against the large subunit. The high salt requirement of the H. morrhuae ribosomes for their stability conflicted with the low salt threshold for cryo-electron microscopy procedures. Despite this obstacle, this is the first cryo-electron microscopy map of Halococcus ribosomes.
Community monitoring and crime: Evidence from Chicago's Safe Passage Program

Abstract This paper investigates the effect of community-based monitoring on crime in the context of a school safety initiative that employed community members to monitor city blocks during students' travel to and from school. Although we find that total crime decreased by 17% relative to neighboring non-treated blocks, these main effects are not the complete story. We find evidence of treatment spillovers in blocks closest to treated areas, but we also uncover cross-crime substitution within treated blocks, intertemporal reallocation of crime to non-monitored periods, and spatial displacement of crime into areas farther away from treated blocks. Our estimates of the benefit-cost ratio associated with each additional civilian-year of community monitoring are much larger than traditional estimates of each additional police officer-year.
Chimera States and Seizures in a Mouse Neuronal Model

Chimera states — the coexistence of synchrony and asynchrony in a nonlocally-coupled network of identical oscillators — are often used as a model framework for epileptic seizures. Here, we explore ...
Efficient Scale-Permuted Backbone with Learned Resource Distribution

Recently, SpineNet has demonstrated promising results on object detection and image classification over ResNet model. However, it is unclear if the improvement adds up when combining scale-permuted backbone with advanced efficient operations and compound scaling. Furthermore, SpineNet is built with a uniform resource distribution over operations. While this strategy seems to be prevalent for scale-decreased models, it may not be an optimal design for scale-permuted models. In this work, we propose a simple technique to combine efficient operations and compound scaling with a previously learned scale-permuted architecture. We demonstrate the efficiency of scale-permuted model can be further improved by learning a resource distribution over the entire network. The resulting efficient scale-permuted models outperform state-of-the-art EfficientNet-based models on object detection and achieve competitive performance on image classification and semantic segmentation.
Nonlinear descent on moduli of local systems

We establish a structure theorem for the integral points on moduli of special linear rank two local systems over surfaces, using mapping class group descent and boundedness results for systoles of local systems.
Fast randomized matrix and tensor interpolative decomposition using CountSketch

We propose a new fast randomized algorithm for interpolative decomposition of matrices which utilizes CountSketch. We then extend this approach to the tensor interpolative decomposition problem introduced by Biagioni et al. (J. Comput. Phys. 281(C), 116–134 (2015)). Theoretical performance guarantees are provided for both the matrix and tensor settings. Numerical experiments on both synthetic and real data demonstrate that our algorithms maintain the accuracy of competing methods, while running in less time, achieving at least an order of magnitude speedup on large matrices and tensors.
The Sun's Photospheric Convection Spectrum

Spectra of the cellular photospheric flows are determined from full-disk Doppler velocity observations acquired by the Helioseismic and Magnetic Imager (HMI) instrument on the Solar Dynamics Observatory spacecraft. Three different analysis methods are used to separately determine spectral coefficients representing the poloidal flows, the toroidal flows, and the radial flows. The amplitudes of these spectral coefficients are constrained by simulated data analyzed with the same procedures as the HMI data. We find that the total velocity spectrum rises smoothly to a peak at a wavenumber of about 120 (wavelength of about 35 Mm), which is typical of supergranules. The spectrum levels off out to wavenumbers of about 400, and then rises again to a peak at a wavenumber of about 3500 (wavelength of about 1200 km), which is typical of granules. The velocity spectrum is dominated by the poloidal flow component (horizontal flows with divergence but no curl) at wavenumbers above 30. The toroidal flow component (horizontal flows with curl but no divergence) dominates at wavenumbers less than 30. The radial flow velocity is only about 3% of the total flow velocity at the lowest wavenumbers, but increases in strength to become about 50% at wavenumbers near 4000. The spectrummore » compares well with the spectrum of giant cell flows at the lowest wavenumbers and with the spectrum of granulation from a 3D radiative-hydrodynamic simulation at the highest wavenumbers.« less
Optimizing coating performance for diffusion under cyclic moisture exposure

Fickian diffusion is often used to model moisture transport through barrier coatings, where the goal is to protect an underlying substrate from the onset of corrosion caused by buildup of water or other aggressive species. Such coatings are often exposed to cyclic moisture, either in laboratory testing or in service due to natural environmental fluctuations. In this paper, we use lattice Boltzmann numerical techniques to investigate the effects of reservoir cycling on moisture propagation and concentration at the substrate where corrosion onset occurs. We examine both the simple case of constant diffusivity, representing idealized Fickian diffusion, and diffusivity that depends on concentration via either a step or linear function, representing polymer network swelling. The use of a coating subject to swelling is shown to lead to highly variable equilibrium behavior. We show that the nature of the functional diffusivity has large effects on water concentration at the substrate, and has implications for material design and analysis to avoid corrosion.
IDENTIFYING AND QUANTIFYING RECURRENT NOVAE MASQUERADING AS CLASSICAL NOVAE

Recurrent novae (RNe) are cataclysmic variables with two or more nova eruptions within a century. Classical novae (CNe) are similar systems with only one such eruption. Many of the so-called CNe are actually RNe for which only one eruption has been discovered. Since RNe are candidate Type Ia supernova progenitors, it is important to know whether there are enough in our Galaxy to provide the supernova rate, and therefore to know how many RNe are masquerading as CNe. To quantify this, we collected all available information on the light curves and spectra of a Galactic, time-limited sample of 237 CNe and the 10 known RNe, as well as exhaustive discovery efficiency records. We recognize RNe as having (1) outburst amplitude smaller than 14.5 – 4.5 × log (t 3), (2) orbital period >0.6 days, (3) infrared colors of J – H > 0.7 mag and H – K > 0.1 mag, (4) FWHM of Hα > 2000 km s–1, (5) high excitation lines, such as Fe X or He II near peak, (6) eruption light curves with a plateau, and (7) white dwarf mass greater than 1.2 M ☉. Using these criteria, we identify V1721 Aql, DE Cir, CP Cru, KT Eri, V838 Her, V2672 Oph, V4160 Sgr, V4643 Sgr, V4739 Sgr, and V477 Sct as strong RN candidates. We evaluate the RN fraction among the known CNe using three methods to get 24% ± 4%, 12% ± 3%, and 35% ± 3%. With roughly a quarter of the 394 known Galactic novae actually being RNe, there should be approximately a hundred such systems masquerading as CNe.
On strongly quasiconvex subgroups

We develop a theory of \emph{strongly quasiconvex subgroups} of an arbitrary finitely generated group. Strong quasiconvexity generalizes quasiconvexity in hyperbolic groups and is preserved under quasi-isometry. We show that strongly quasiconvex subgroups are also more reflexive of the ambient groups geometry than the stable subgroups defined by Durham-Taylor, while still having many analogous properties to those of quasiconvex subgroups of hyperbolic groups. We characterize strongly quasiconvex subgroups in terms of the lower relative divergence of ambient groups with respect to them. We also study strong quasiconvexity and stability in relatively hyperbolic groups, right-angled Coxeter groups, and right-angled Artin groups. We give complete descriptions of strong quasiconvexity and stability in relatively hyperbolic groups and we characterize strongly quasiconvex special subgroups and stable special subgroups of two dimensional right-angled Coxeter groups. In the case of right-angled Artin groups, we prove that two notions of strong quasiconvexity and stability are equivalent when the right-angled Artin group is one-ended and the subgroups have infinite index. We also characterize non-trivial strongly quasiconvex subgroups of infinite index (i.e. non-trivial stable subgroups) in right-angled Artin groups by quadratic lower relative divergence, expanding the work of Koberda-Mangahas-Taylor on characterizing purely loxodromic subgroups of right-angled Artin groups.
Sign-Problem-Free Quantum Monte Carlo Study on Thermodynamic Properties and Magnetic Phase Transitions in Orbital-Active Itinerant Ferromagnets

Ferromagnetism of delocalized fermions is a fundamental aspect of condensed-matter physics but is difficult to describe using typical perturbative methods. Using nonperturbative simulations, scientists accurately determine the ferromagnetic transition temperature and other thermodynamic properties of a ferromagnetic metal.
A NARROW SHORT-DURATION GRB JET FROM A WIDE CENTRAL ENGINE

We use two-dimensional relativistic hydrodynamic numerical calculations to show that highly collimated relativistic jets can be produced in neutron star merger models of short-duration gamma-ray bursts (GRBs) without the need for a highly directed engine or a large net magnetic flux. Even a hydrodynamic engine generating a very wide sustained outflow on small scales can, in principle, produce a highly collimated relativistic jet, facilitated by a dense surrounding medium that provides a cocoon surrounding the jet core. An oblate geometry to the surrounding gas significantly enhances the collimation process. Previous numerical simulations have shown that the merger of two neutron stars produces an oblate, expanding cloud of dynamical ejecta. We show that this gas can efficiently collimate the central engine power much like the surrounding star does in long-duration GRB models. For typical short-duration GRB central engine parameters, we find jets with opening angles of an order of 10° in which a large fraction of the total outflow power of the central engine resides in highly relativistic material. These results predict large differences in the opening angles of outflows from binary neutron star mergers versus neutron star–black hole mergers.
Slow normal modes of proteins are accurately reproduced across different platforms.

The Protein data bank (PDB) (Berman et al 2000 Nucl. Acids Res. 28 235-42) contains the atomic structures of over 105 biomolecules with better than 2.8 A resolution. The listing of the identities and coordinates of the atoms comprising each macromolecule permits an analysis of the slow-time vibrational response of these large systems to minor perturbations. 3D video animations of individual modes of oscillation demonstrate how regions interdigitate to create cohesive collective motions, providing a comprehensive framework for and familiarity with the overall 3D architecture. Furthermore, the isolation and representation of the softest, slowest deformation coordinates provide opportunities for the development of mechanical models of enzyme function. The eigenvector decomposition, therefore, must be accurate, reliable as well as rapid to be generally reported upon. We obtain the eigenmodes of a 1.2 A 34 kDa PDB entry using either exclusively heavy atoms or partly or fully reduced atomic sets; Cartesian or internal coordinates; interatomic force fields derived either from a full Cartesian potential, a reduced atomic potential or a Gaussian distance-dependent potential; and independently developed software. These varied technologies are similar in that each maintains proper stereochemistry either by use of dihedral degrees of freedom which freezes bond lengths and bond angles, or by use of a full atomic potential that includes realistic bond length and angle restraints. We find that the shapes of the slowest eigenvectors are nearly identical, not merely similar.
Detectability of Local Group Dwarf Galaxy Analogues at High Redshifts

The dwarf galaxies of the Local Group are believed to be similar to the most abundant galaxies during the epoch of reionization (z 6). As a result of their proximity, there is a wealth of information that can be obtained about these galaxies; however, due to their low surface brightnesses, detecting their progenitors at high redshifts is challenging. We compare the physical properties of these dwarf galaxies to those of galaxies detected at high redshifts using Hubble Space Telescope and Spitzer observations and consider the promise of the upcoming James Webb Space Telescope on the prospects for detecting high-redshift analogues of these galaxies.
Moduli of products of stable varieties

We study the moduli space of a product of stable varieties over the field of complex numbers, as defined via the minimal model program. Our main results are: (a) taking products gives a well-defined morphism from the product of moduli spaces of stable varieties to the moduli space of a product of stable varieties; (b) this map is always finite etale; and (c) this map very often is an isomorphism. Our results generalize and complete the work of Van Opstall in dimension . The local results rely on a study of the cotangent complex using some derived algebro-geometric methods, while the global ones use some differential-geometric input.
IS THE ULTRA-HIGH ENERGY COSMIC-RAY EXCESS OBSERVED BY THE TELESCOPE ARRAY CORRELATED WITH ICECUBE NEUTRINOS?

The Telescope Array (TA) has observed a statistically signicant excess in cosmic-rays with energies above 57 EeV in a region of approximately 1150 square degrees centered on coordinates (R.A. = 146.7, Dec. = 43.2). We note that the location of this excess correlates with two of the 28 extraterrestrial neutrinos recently observed by IceCube. The overlap between the two IceCube neutrinos and the TA excess is statistically signicant at the 2 level. Furthermore, the spectrum and intensity of the IceCube neutrinos is consistent with a single source which would also produce the TA excess. Finally, we discuss possible source classes with the correct characteristics to explain the cosmic-ray and neutrino uxes with a single source. Subject headings: (ISM:) cosmic rays | gamma rays: theory | gamma rays: observations
Energy dynamics and current sheet structure in fluid and kinetic simulations of decaying magnetohydrodynamic turbulence

Simulations of decaying magnetohydrodynamic (MHD) turbulence are performed with a fluid and a kinetic code. The initial condition is an ensemble of long-wavelength, counter-propagating, shear-Alfven waves, which interact and rapidly generate strong MHD turbulence. The total energy is conserved and the rate of turbulent energy decay is very similar in both codes, although the fluid code has numerical dissipation, whereas the kinetic code has kinetic dissipation. The inertial range power spectrum index is similar in both the codes. The fluid code shows a perpendicular wavenumber spectral slope of k⊥−1.3. The kinetic code shows a spectral slope of k⊥−1.5 for smaller simulation domain, and k⊥−1.3 for larger domain. We estimate that collisionless damping mechanisms in the kinetic code can account for the dissipation of the observed nonlinear energy cascade. Current sheets are geometrically characterized. Their lengths and widths are in good agreement between the two codes. The length scales linearly with the d...
First-principles study of crystal and electronic structure of rare-earth cobaltites

Using density functional theory plus self-consistent Hubbard U (DFT + Usc) calculations, we have investigated the structural and electronic properties of the rare-earth cobaltites RCoO3 (R = Pr – Lu). Our calculations show the evolution of crystal and electronic structure of the insulating low-spin RCoO3 with increasing rare-earth atomic number (decreasing ionic radius), including the invariance of the Co-O bond distance (dCo–O), the decrease of the Co-O-Co bond angle (Θ), and the increase of the crystal field splitting (ΔCF) and band gap energy (Eg). Agreement with experiment for the latter improves considerably with the use of DFT + Usc and all trends are in good agreement with the experimental data. These trends enable a direct test of prior rationalizations of the trend in spin-gap associated with the spin crossover in this series, which is found to expose significant issues with simple band based arguments. We also examine the effect of placing the rare-earth f-electrons in the core region of the pse...
Developing Diagnostic Tools for Low-Burnup Reactor Samples

Determining the environment that a nuclear reactor's spent fuel has experienced is a challenging, critical task for reactor monitoring---to verify nonproliferation, for example. Certain isotopic ratios are reliable diagnostics for the total neutron exposure and cooling time of a sample, but many fail for very low burnup and very long cooling times. The authors derive new diagnostic tools for these scenarios and test them on archived samples by radiochemical analysis. The results show that multiple diagnostics can be used to identify self-consistency and systematic errors, such as fractionation, to guide future efforts in reactor forensics.
High-Dimensional Similarity Search with Quantum-Assisted Variational Autoencoder

Recent progress in quantum algorithms and hardware indicates the potential importance of quantum computing in the near future. However, finding suitable application areas remains an active area of research. Quantum machine learning is touted as a potential approach to demonstrate quantum advantage within both the gate-model and the adiabatic schemes. For instance, the Quantum-assisted Variational Autoencoder (QVAE) has been proposed as a quantum enhancement to the discrete VAE. We extend on previous work and study the real-world applicability of a QVAE by presenting a proof-of-concept for similarity search in large-scale high-dimensional datasets. While exact and fast similarity search algorithms are available for low dimensional datasets, scaling to high-dimensional data is non-trivial. We show how to construct a space-efficient search index based on the latent space representation of a QVAE. Our experiments show a correlation between the Hamming distance in the embedded space and the Euclidean distance in the original space on the Moderate Resolution Imaging Spectroradiometer (MODIS) dataset.Further, we find real-world speedups compared to linear search and demonstrate memory-efficient scaling to half a billion data points.
The Hamiltonian dynamics of magnetic confinement in toroidal domains

We consider a class of magnetic fields defined over the interior of a manifold $M$ which go to infinity at its boundary and whose direction near the boundary of $M$ is controlled by a closed 1-form $\sigma_\infty \in \Gamma(T^*\partial M)$. We are able to show that charged particles in the interior of $M$ under the influence of such fields can only escape the manifold through the zero locus of $\sigma_\infty$. In particular in the case where the 1-form is nowhere vanishing we conclude that the particles become confined to its interior for all time.
Eigenfunctions, transfer matrices, and absolutely continuous spectrum of one-dimensional Schrödinger operators

on L(R ) (and its half-line problem, H+, on L2(0,∞) with u(0) = 0 boundary conditions). We will focus on a new approach to the absolutely continuous spectrum σac(h) and, more generally, Σac(h), the essential support of the a.c. part of the spectral measures. What is new in our approach is that it relies on estimates on the transfer matrix, that is, the 2× 2 matrix TE(n,m) which takes (u(m+1) u(m) ) to (u(n+1) u(n) ) for solutions u of hu = Eu (in the continuum case use ( u′(x) u(x) ) instead of ( u(x+1) u(x) ) ). We let TE(n) ≡ TE(n, 0). For example, we will prove the following:
Decaying hidden dark matter in warped compactification

The recent PAMELA and ATIC/Fermi/HESS experiments have observed an excess of electrons and positrons, but not anti-protons, in the high energy cosmic rays. To explain this result, we construct a decaying hidden dark matter model in string theory compactification that incorporates the following two ingredients, the hidden dark matter scenario in warped compactification and the phenomenological proposal of hidden light particles that decay to the Standard Model. In this model, on higher dimensional warped branes, various warped Kaluza-Klein particles and the zero-mode of gauge field play roles of the hidden dark matter or mediators to the Standard Model.
Deep Learning and its Application to LHC Physics

Machine learning has played an important role in the analysis of high-energy physics data for decades. The emergence of deep learning in 2012 allowed for machine learning tools which could adeptly handle higher-dimensional and more complex problems than previously feasible. This review is aimed at the reader who is familiar with high-energy physics but not machine learning. The connections between machine learning and high-energy physics data analysis are explored, followed by an introduction to the core concepts of neural networks, examples of the key results demonstrating the power of deep learning for analysis of LHC data, and discussion of future prospects and concerns.
The algorithmic origins of life.

Although it has been notoriously difficult to pin down precisely what is it that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and, in particular, that top-down (or downward) causation—where higher levels influence and constrain the dynamics of lower levels in organizational hierarchies—may be a major contributor to the hierarchal structure of living systems. Here, we propose that the emergence of life may correspond to a physical transition associated with a shift in the causal structure, where information gains direct and context-dependent causal efficacy over the matter in which it is instantiated. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.
Notes on non-critical superstrings in various dimensions

We study non-critical superstrings propagating in d ? 6 dimensional Minkowski space or equivalently, superstrings propagating on the two-dimensional euclidean black hole tensored with d-dimensional Minkowski space. We point out a subtlety in the construction of supersymmetric theories in these backgrounds, and explain how this does not allow a consistent geometric interpretation in terms of fields propagating on a cigar-like spacetime. We explain the global symmetries of the various theories by using their description as the near horizon geometry of wrapped NS5-brane configurations. In the six-dimensional theory, we present a CFT description of the four dimensional moduli space and the global O(3) symmetry. The worldsheet action invariant under this symmetry contains both the = 2 sine-Liouville interaction and the cigar metric, thereby providing an example where the two interactions are naturally present in the same worldsheet lagrangian already at the non-dynamical level.
Surface Layer Accretion in Transitional and Conventional Disks: From Polycyclic Aromatic Hydrocarbons to Planets

'Transitional' T Tauri disks have optically thin holes with radii {approx}>10 AU, yet accrete up to the median T Tauri rate. Multiple planets inside the hole can torque the gas to high radial speeds over large distances, reducing the local surface density while maintaining accretion. Thus multi-planet systems, together with reductions in disk opacity due to grain growth, can explain how holes can be simultaneously transparent and accreting. There remains the problem of how outer disk gas diffuses into the hole. Here it has been proposed that the magnetorotational instability (MRI) erodes disk surface layers ionized by stellar X-rays. In contrast to previous work, we find that the extent to which surface layers are MRI-active is limited not by ohmic dissipation but by ambipolar diffusion, the latter measured by Am: the number of times a neutral hydrogen molecule collides with ions in a dynamical time. Simulations by Hawley and Stone showed that Am {approx} 100 is necessary for ions to drive MRI turbulence in neutral gas. We calculate that in X-ray-irradiated surface layers, Am typically varies from {approx}10{sup -3} to 1, depending on the abundance of charge-adsorbing polycyclic aromatic hydrocarbons, whose properties we infer from Spitzer observations. We conclude thatmore » ionization of H{sub 2} by X-rays and cosmic rays can sustain, at most, only weak MRI turbulence in surface layers 1-10 g cm{sup -2} thick, and that accretion rates in such layers are too small compared to observed accretion rates for the majority of disks.« less
Moduli spaces for D-branes at the tip of a cone

For physicists: We show that the quiver gauge theory derived from a Calabi-Yau cone via an exceptional collection of line bundles on the base has the original cone as a component of its classical moduli space. For mathematicians: We use data from the derived category of sheaves on a Fano surface to construct a quiver, and show that its moduli space of representations has a component which is isomorphic to the anticanonical cone over the surface.
Conservation of supergravity currents from Matrix theory

Abstract In recent work by Kabat and Taylor, certain Matrix theory quantities have been identified with the spatial moments of the supergravity stress-energy tensor, membrane current, and fivebrane current. In this paper we determine the relations between these moments required by current conservation, and prove that these relations hold as exact Matrix theory identities at finite N. This establishes conservation of the effective supergravity currents (averaged over the compact circle). In addition, the constraints of current conservation allow us to deduce Matrix theory quantities corresponding to moments of the spatial current of the longitudinal fivebrane charge, not previously identified.
Examining Collusion and Voting Biases Between Countries During the Eurovision Song Contest Since 1957

The Eurovision Song Contest (ESC) is an annual event which attracts millions of viewers. It is an interesting activity to examine since the participants of the competition represent a particular country's musical performance that will be awarded a set of scores from other participating countries based upon a quality assessment of a performance. There is a question of whether the countries will vote exclusively according to the artistic merit of the song, or if the vote will be a public signal of national support for another country. Since the competition aims to bring people together, any consistent biases in the awarding of scores would defeat the purpose of the celebration of expression and this has attracted researchers to investigate the supporting evidence for biases. This paper builds upon an approach which produces a set of random samples from an unbiased distribution of score allocation, and extends the methodology to use the full set of years of the competition's life span which has seen fundamental changes to the voting schemes adopted. By building up networks from statistically significant edge sets of vote allocations during a set of years, the results display a plausible network for the origins of the culture anchors for the preferences of the awarded votes. With 60 years of data, the results support the hypothesis of regional collusion and biases arising from proximity, culture and other irrelevant factors in regards to the music which that alone is intended to affect the judgment of the contest.
Formation and Reconnection of Three-Dimensional Current Sheets With a Guide Field in the Solar Corona

We analyze a series of three-dimensional magnetohydrodynamic numerical simulations of magnetic reconnection in a model solar corona to study the effect of the guide field component on quasi-steady state interchange reconnection in a pseudostreamer arcade configuration. This work extends the analysis of \citet{Edmondson2010b} by quantifying the mass density enhancement coherency scale in the current sheet associated with magnetic island formation during the nonlinear phase of plasmoid-unstable reconnection. We compare the results of four simulations of a zero, weak, moderate, and a strong guide field, $B_{GF}/B_0 = \lbrace 0.0 , 0.1 , 0.5 , 1.0 \rbrace$, to quantify the plasmoid density enhancement's longitudinal and transverse coherency scales as a function of the guide field strength. We derive these coherency scales from autocorrelation and wavelet analyses, and demonstrate how these scales may be used to interpret the density enhancement fluctuation's Fourier power spectra in terms of a structure formation range, an energy continuation range, and an inertial range---each population with a distinct spectral slope. We discuss the simulation results in the context of solar and heliospheric observations of pseudostreamer solar wind outflow and possible signatures of reconnection-generated structure.
Slim Fractals: The Geometry of Doubly Transient Chaos

Fractal geometry is inherent to chaotic systems, but this is not well understood in undriven dissipative processes, in which chaos necessarily vanishes over time. A new analysis leads to a novel framework for studying these systems and shows, for the first time, that they too can generically exhibit fractal behavior.
Substructural Observed Communication Semantics

Session-types specify communication protocols for communicating processes, and session-typed languages are often specified using substructural operational semantics given by multiset rewriting systems. We give an observed communication semantics for a session-typed language with recursion, where a process's observation is given by its external communications. To do so, we introduce fair executions for multiset rewriting systems, and extract observed communications from fair process executions. This semantics induces an intuitively reasonable notion of observational equivalence that we conjecture coincides with semantic equivalences induced by denotational semantics, bisimulations, and barbed congruences for these languages.
Synthesis, characterization, and finite size effects on electrical transport of nanoribbons of the charge density wave conductor NbSe3.

NbSe3 exhibits remarkable anisotropy in most of its physical properties and has been a model system for studies of quasi-one-dimensional charge density wave (CDW) phenomena. Herein, we report the synthesis, characterization, and electrical transport of single-crystalline NbSe3 nanoribbons by a facile one-step vapour transport process involving the transport of selenium powder onto a niobium foil substrate. Our investigations aid the understanding of the CDW nature of NbSe3 and the growth process of the material. They also indicate that NbSe3 nanoribbons have enhanced CDW properties compared to those of the bulk phase due to size confinement effects, thus expanding the search for new mesoscopic phenomena at the nanoscale level. Single nanoribbon measurements of the electrical resistance as a function of temperature show charge density wave transitions at 59 and 141 K. We also demonstrate significant enhancement in the depinning effect and sliding regimes mainly attributed to finite size effects. (Some figures may appear in colour only in the online journal)
Symmetries Near the Horizon

We consider a nearly-AdS2 gravity theory on the two-sided wormhole geometry. We construct three gauge-invariant operators in NAdS2 which move bulk matter relative to the dynamical boundaries. In a two-sided system, these operators satisfy an SL(2) algebra (up to non perturbative corrections). In a semiclassical limit, these generators act like SL(2) transformations of the boundary time, or conformal symmetries of the two sided boundary theory. These can be used to define an operator-state mapping. A particular large N and low temperature limit of the SYK model has precisely the same structure, and this construction of the exact generators also applies. We also discuss approximate, but simpler, constructions of the generators in the SYK model. These are closely related to the “size” operator and are connected to the maximal chaos behavior captured by out of time order correlators.
A Review of Pentaquark Calculations on the Lattice

We review lattice calculations of pentaquarks and discuss issues pertaining to interpolation fields, distinguishing the signal of pentaquarks from those of the KN scattering states, chiral symmetry, and ghost state contaminations.
MODEL STRUCTURAL INFERENCE USING LOCAL DYNAMIC OPERATORS

This paper focuses on the problem of quantifying the effects of model-structure uncertainty in the context of time-evolving dynamical systems. This is motivated by multi-model uncertainty in computer physics simulations: developers often make different modeling choices in numerical approximations and process simplifications, leading to different numerical codes that ostensibly represent the same underlying dynamics. We consider model-structure inference as a two-step methodology: the first step is to perform system identification on numerical codes for which it is possible to observe the full state; the second step is structural uncertainty quantification (UQ), in which the goal is to search candidate models "close" to the numerical code surrogates for those that best match a quantity-of-interest (QOI) from some empirical dataset. Specifically, we: (1) define a discrete, local representation of the structure of a partial differential equation, which we refer to as the "local dynamical operator" (LDO); (2) identify model structure non-intrusively from numerical code output; (3) non-intrusively construct a reduced order model (ROM) of the numerical model through POD-DEIM-Galerkin projection; (4) perturb the ROM dynamics to approximate the behavior of alternate model structures; and (5) apply Bayesian inference and energy conservation laws to calibrate a LDO to a given QOI. We demonstrate these techniques using the two-dimensional rotating shallow water (RSW) equations as an example system.
Maximum Principles for Boundary-Degenerate Second Order Linear Elliptic Differential Operators

We prove weak and strong maximum principles, including a Hopf lemma, for C 2 subsolutions to equations defined by linear, second-order, linear, elliptic partial differential operators whose principal symbols vanish along a portion of the domain boundary. The boundary regularity property of the C 2 subsolutions along this boundary vanishing locus ensures that these maximum principles hold irrespective of the sign of the Fichera function. Boundary conditions need only be prescribed on the complement in the domain boundary of the principal symbol's vanishing locus. We obtain uniqueness and a priori maximum principle estimates for C 2 solutions to boundary value and obstacle problems defined by these boundary-degenerate elliptic operators with partial Dirichlet or Neumann boundary conditions. We also prove weak maximum principles and uniqueness for W 1, 2 solutions to the corresponding variational equations and inequalities defined with the aide of weighted Sobolev spaces. The domain is allowed to be unbounde...
Sketch-Driven Regular Expression Generation from Natural Language and Examples

Recent systems for converting natural language descriptions into regular expressions (regexes) have achieved some success, but typically deal with short, formulaic text and can only produce simple ...
Are extreme dissipation events predictable in turbulent fluid flows

A method that combines dynamics and statistics for the underlying attractor allows for the extraction of characteristic states that precede laminarization events which subsequently lead to extreme dissipation episodes.
Controllability of spacecraft using only magnetic torques

Spacecraft attitude control using only magnetic torques is a time-varying system. Many designs have been proposed using linear quadratic regulator (LQR) and H∞ formulations. The existence of the solutions depends on the controllability of the linear time-varying systems, which has not been established. In this paper, the conditions of controllability for this linear time-varying system is derived.
Cyclic pursuit on compact manifolds

We study a form of cyclic pursuit on Riemannian manifolds with positive injectivity radius. We conjecture that on a compact manifold, the piecewise geodesic loop formed by connecting consecutive pursuit agents either collapses to a point in finite time or converges to a closed geodesic. The main result is that this conjecture is valid for nonpositively curved compact manifolds.
Xenon Bubble Chambers for Direct Dark Matter Detection

The search for dark matter is one of today's most exciting fields. As bigger detectors are being built to increase their sensitivity, background reduction is an ever more challenging issue. To this end, a new type of dark matter detector is proposed, a xenon bubble chamber, which would combine the strengths of liquid xenon TPCs, namely event by event energy resolution, with those of a bubble chamber, namely insensitivity to electronic recoils. In addition, it would be the first time ever that a dark matter detector is active on all three detection channels, ionization and scintillation characteristic of xenon detectors, and heat through bubble formation in superheated fluids. Preliminary simulations show that, depending on threshold, a discrimination of 99.99% to 99.9999+% can be achieved, which is on par or better than many current experiments. A prototype is being built at the University at Albany, SUNY. The prototype is currently undergoing seals, thermal, and compression testing.
Statistical models for the number of successful cyber intrusions

We propose several generalized linear models (GLMs) to predict the number of successful cyber intrusions (or “intrusions”) into an organization’s computer network, where the rate at which intrusion...
Rigidity for convex-cocompact actions on rank-one symmetric spaces

When a discrete group admits a convex-cocompact action on a non-compact rank-one symmetric space, there is a natural lower bound for the Hausdorff dimension of the limit set, given by the Ahlfors regular conformal dimension of the boundary of the group. We show that equality is achieved precisely when the group stabilizes an isometric copy of some non-compact rank-one symmetric space on which it acts with compact quotient. This generalizes a theorem of Bonk-Kleiner, who proved it in the case of real hyperbolic space. To prove our main theorem, we study tangents of Lipschitz differentiability spaces that are embedded in a Carnot group. We show that almost all tangents are isometric to Carnot subgroups, at least when they are rectifiably connected. This extends a theorem of Cheeger, who proved it for PI spaces that are embedded in Euclidean space.