Physics-informed Neural Networks for Solving Inverse Problems of Nonlinear Biot's Equations: Batch Training

In biomedical engineering, earthquake prediction, and underground energy harvesting, it is crucial to indirectly estimate the physical properties of porous media since the direct measurement of those are usually impractical/prohibitive. Here we apply the physics-informed neural networks to solve the inverse problem with regard to the nonlinear Biot's equations. Specifically, we consider batch training and explore the effect of different batch sizes. The results show that training with small batch sizes, i.e., a few examples per batch, provides better approximations (lower percentage error) of the physical parameters than using large batches or the full batch. The increased accuracy of the physical parameters, comes at the cost of longer training time. Specifically, we find the size should not be too small since a very small batch size requires a very long training time without a corresponding improvement in estimation accuracy. We find that a batch size of 8 or 32 is a good compromise, which is also robust to additive noise in the data. The learning rate also plays an important role and should be used as a hyperparameter.Comment: arXiv admin note: text overlap with arXiv:2002.0823

Spatially resolved spectroscopy of Coma cluster early-type galaxies - II:the minor axis dataset

We present minor axis, off set major axis and one diagonal long slit spectra for 10 E and S0 galaxies of the Coma cluster drawn from a magnitude-limited sample studied before. We derive rotation curves, velocity dispersion profiles and the H-3 and H-4 coefficients of the Hermite decomposition of the line of sight velocity distribution. Moreover, we derive the line index profiles of Mg, Fe and Hbeta line indices and assess their errors. The data will be used to construct dynamical models of the galaxies and study their stellar populations

DHA Improves Cognition and Prevents Dysfunction of Entorhinal Cortex Neurons in 3xTg-AD Mice

Defects in neuronal activity of the entorhinal cortex (EC) are suspected to underlie the symptoms of Alzheimer's disease (AD). Whereas neuroprotective effects of docosahexaenoic acid (DHA) have been described, the effects of DHA on the physiology of EC neurons remain unexplored in animal models of AD. Here, we show that DHA consumption improved object recognition (↑12%), preventing deficits observed in old 3xTg-AD mice (↓12%). Moreover, 3xTg-AD mice displayed seizure-like akinetic episodes, not detected in NonTg littermates and partly prevented by DHA (↓50%). Patch-clamp recording revealed that 3xTg-AD EC neurons displayed (i) loss of cell capacitance (CC), suggesting reduced membrane surface area; (ii) increase of firing rate versus injected current (F-I) curve associated with modified action potentials, and (iii) overactivation of glutamatergic synapses, without changes in synaptophysin levels. DHA consumption increased CC (↑12%) and decreased F-I slopes (↓21%), thereby preventing the opposite alterations observed in 3xTg-AD mice. Our results indicate that cognitive performance and basic physiology of EC neurons depend on DHA intake in a mouse model of AD

Dissecting the Red Sequence--II. Star Formation Histories of Early-Type Galaxies Throughout the Fundamental Plane

This analysis uses spectra of ~16,000 nearby SDSS quiescent galaxies to track variations in galaxy star formation histories along and perpendicular to the Fundamental Plane (FP). We sort galaxies by their FP properties (sigma, R_e, and I_e) and construct high S/N mean galaxy spectra that span the breadth and thickness of the FP. From these spectra, we determine mean luminosity-weighted ages, [Fe/H], [Mg/H], and [Mg/Fe] based on single stellar population models using the method described in Graves & Schiavon (2008). In agreement with previous work, the star formation histories of early-type galaxies are found to form a two-parameter family. The major trend is that mean age, [Fe/H], [Mg/H], and [Mg/Fe] all increase with sigma. However, no stellar population property shows any dependence on R_e at fixed sigma, suggesting that sigma and not dynamical mass (M_dyn ~ sigma^2 R_e) is the better predictor of past star formation history. In addition to the main trend with sigma, galaxies also show a range of population properties at fixed sigma that are strongly correlated with surface brightness residuals from the FP, such that higher surface brightness galaxies have younger mean ages, higher [Fe/H], higher [Mg/H], and lower [Mg/Fe] than lower-surface brightness galaxies. These latter trends are a major new constraint on star-formation histories.Comment: 23 pages, 14 figures. Accepted to Ap

Inter-annual growth of Arctic charr (Salvelinus alpinus, L.) in relation to climate variation

BACKGROUND: Major changes in climate have been observed in the Arctic and climate models predict further amplification of the enhanced greenhouse effect at high-latitudes leading to increased warming. We propose that warming in the Arctic may affect the annual growth conditions of the cold adapted Arctic charr and that such effects can already be detected retrospectrally using otolith data. RESULTS: Inter-annual growth of the circumpolar Arctic charr (Salvelinus alpinus, L.) was analysed in relation to climatic changes observed in the Arctic during the last two decades. Arctic charr were sampled from six locations at Qeqertarsuaq in West Greenland, where climate data have been recorded since 1990. Two fish populations met the criteria of homogeny and, consequently, only these were used in further analyses. The results demonstrate a complex coupling between annual growth rates and fluctuations in annual mean temperatures and precipitation. Significant changes in temporal patterns of growth were observed between cohorts of 1990 and 2004. CONCLUSION: Differences in pattern of growth appear to be a consequence of climatic changes over the last two decades and we thereby conclude that climatic affects short term and inter-annual growth as well as influencing long term shifts in age-specific growth patterns in population of Arctic charr

Identification of potential autoantigens in anti-CCP-positive and anti-CCP-negative rheumatoid arthritis using citrulline-specific protein arrays

Abstract The presence or absence of autoantibodies against citrullinated proteins (ACPAs) distinguishes two main groups of rheumatoid arthritis (RA) patients with different etiologies, prognoses, disease severities, and, presumably, disease pathogenesis. The heterogeneous responses of RA patients to various biologics, even among ACPA-positive patients, emphasize the need for further stratification of the patients. We used high-density protein array technology for fingerprinting of ACPA reactivity. Identification of the proteome recognized by ACPAs may be a step to stratify RA patients according to immune reactivity. Pooled plasma samples from 10 anti-CCP-negative and 15 anti-CCP-positive RA patients were assessed for ACPA content using a modified protein microarray containing 1631 different natively folded proteins citrullinated in situ by protein arginine deiminases (PADs) 2 and PAD4. IgG antibodies from anti-CCP-positive RA plasma showed high-intensity binding to 87 proteins citrullinated by PAD2 and 99 proteins citrullinated by PAD4 without binding significantly to the corresponding native proteins. Curiously, the binding of IgG antibodies in anti-CCP-negative plasma was also enhanced by PAD2- and PAD4-mediated citrullination of 29 and 26 proteins, respectively. For only four proteins, significantly more ACPA binding occurred after citrullination with PAD2 compared to citrullination with PAD4, while the opposite was true for one protein. We demonstrate that PAD2 and PAD4 are equally efficient in generating citrullinated autoantigens recognized by ACPAs. Patterns of proteins recognized by ACPAs may serve as a future diagnostic tool for further subtyping of RA patients

Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?

The urokinase receptor (uPAR) is a founding member of a small protein family with multiple Ly6/uPAR (LU) domains. The motif defining these LU domains contains five plesiotypic disulfide bonds stabilizing its prototypical three-fingered fold having three protruding loops. Notwithstanding the detailed knowledge on structure-function relationships in uPAR, one puzzling enigma remains unexplored. Why does the first LU domain in uPAR (DI) lack one of its consensus disulfide bonds, when the absence of this particular disulfide bond impairs the correct folding of other single LU domain-containing proteins? Here, using a variety of contemporary biophysical methods, we found that reintroducing the two missing half-cystines in uPAR DI caused the spontaneous formation of the corresponding consensus 7–8 LU domain disulfide bond. Importantly, constraints due to this cross-link impaired (i) the binding of uPAR to its primary ligand urokinase and (ii) the flexible interdomain assembly of the three LU domains in uPAR. We conclude that the evolutionary deletion of this particular disulfide bond in uPAR DI may have enabled the assembly of a high-affinity urokinase-binding cavity involving all three LU domains in uPAR. Of note, an analogous neofunctionalization occurred in snake venom α-neurotoxins upon loss of another pair of the plesiotypic LU domain half-cystines. In summary, elimination of the 7–8 consensus disulfide bond in the first LU domain of uPAR did have significant functional and structural consequences

Life and death of the Bose polaron

Spectroscopic and interferometric measurements complement each other in extracting the fundamental properties of quantum many-body systems. While spectroscopy provides precise measurements of equilibrated energies, interferometry can elucidate the dynamical evolution of the system. For an impurity immersed in a bosonic medium, both are equally important for understanding the quasiparticle physics of the Bose polaron. Here, we compare the interferometric and spectroscopic timescales to the underlying dynamical regimes of the impurity dynamics and the polaron lifetime, highlighting the capability of the interferometric approach to clearly resolve polaron dynamics. In particular, interferometric measurements of the coherence amplitude at strong interactions reveal faster quantum dynamics at large repulsive interaction strengths than at unitarity. These observations are in excellent agreement with a short-time theoretical prediction including both the continuum and the attractive polaron branch. For longer times, qualitative agreement with a many-body theoretical prediction which includes both branches is obtained. Moreover, the polaron energy is extracted from interferometric measurements of the observed phase velocity in agreement with previous spectroscopic results from weak to strong attractive interactions. Finally, the phase evolution allows for the measurement of an energetic equilibration timescale, describing the initial approach of the phase velocity to the polaron energy. Theoretically, this is shown to lie within the regime of universal dynamics revealing a fast initial evolution towards the formation of polarons. Our results give a comprehensive picture of the many-body physics governing the Bose polaron and thus validates the quasiparticle framework for further studies.Comment: 9 pages, 6 figure