Phenomenological power spectrum models for Hα\alpha emission line galaxies from the Nancy Grace Roman Space Telescope

The High Latitude Spectroscopic Survey (HLSS) is the reference baseline spectroscopic survey for NASA's Nancy Grace Roman space telescope, measuring redshifts of $\sim 10$M H$\alpha$ emission line galaxies over a $2000$ deg$^2$ footprint at $z=1-2$. In this work, we use a realistic Roman galaxy mock catalogue to explore optimal phenomenological modeling of the measured power spectrum. We consider two methods for modeling the redshift-space distortions (Kaiser squashing and another with a window function on $\beta$ that selects out the coherent radial infall pairwise velocities, $M_A$ and $M_B$, respectively), two models for the nonlinear impact of baryons that smears the BAO signal (a fixed ratio between the smearing scales in the perpendicular and parallel dimensions and another where these smearing scales are kept as a free parameters, P$_{dw}(k|k_*)$ and P$_{dw}(k|\Sigma_\perp,\Sigma_\parallel)$, respectively), and two analytical emulations of nonlinear growth (one employing the halo model and another formulated from simulated galaxy clustering of a semi-analytical model, $F_{HM}$ and $F_{SAM}$, respectively). We find that the best model combination employing $F_{HM}$ is $P_{dw}(k|k_*)*F_{HM}*M_B$, while the best combination employing $F_{SAM}$ is $P_{dw}(k|k_*)*F_{SAM}*M_B$, which leads to unbiased measurements of cosmological parameters. We compare these to the Effective Field Theory of Large-Scale Structure perturbation theory model $P_{EFT}(k|\Theta)$, and find that our simple phenomenological models are comparable across the entire redshift range for $k_{max}=0.25$ and $0.3$ $h$/Mpc. We expect the tools that we have developed to be useful in probing dark energy and testing gravity using Roman in an accurate and robust manner.Comment: 17 pages, 3 figures, 4 tables, Accepted to MNRAS 23 May 202

Sublattice symmetry breaking and Kondo-effect enhancement in strained graphene

Kondo physics in doped monolayer graphene is predicted to exhibit unusual features due to the linear vanishing of the pristine material's density of states at the Dirac point. Despite several attempts, conclusive experimental observation of the phenomenon remains elusive. One likely obstacle to identification is a very small Kondo temperature scale $T_K$ in situations where the chemical potential lies near the Dirac point. We propose tailored mechanical deformations of monolayer graphene as a means of revealing unique fingerprints of the Kondo effect. Inhomogeneous strains are known to produce specific alternating changes in the local density of states (LDOS) away from the Dirac point that signal sublattice symmetry breaking effects. Small LDOS changes can be amplified in an exponential increase or decrease of $T_K$ for magnetic impurities attached at different locations. We illustrate this behavior in two deformation geometries: a circular 'bubble' and a long fold, both described by Gaussian displacement profiles. We calculate the LDOS changes for modest strains and analyze the relevant Anderson impurity model describing a magnetic atom adsorbed in either a 'top-site' or a 'hollow-site' configuration. Numerical renormalization-group solutions of the impurity model suggest that higher expected $T_K$ values, combined with distinctive spatial patterns under variation of the point of graphene attachment, make the top-site configuration the more promising for experimental observation of signatures of the Kondo effect. The strong strain sensitivity of $T_K$ may lift top-site Kondo physics into the range experimentally accessible using local probes such as scanning tunneling microscopy.Comment: 19 pages, 7 figures (added Figs. 6 and 7 to version 1

The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction.

PINA is a novel ATPase and DNA helicase highly conserved in Archaea, the third domain of life. The PINA from Sulfolobus islandicus (SisPINA) forms a hexameric ring in crystal and solution. The protein is able to promote Holliday junction (HJ) migration and physically and functionally interacts with Hjc, the HJ specific endonuclease. Here, we show that SisPINA has direct physical interaction with Hjm (Hel308a), a helicase presumably targeting replication forks. In vitro biochemical analysis revealed that Hjm, Hjc, and SisPINA are able to coordinate HJ migration and cleavage in a concerted way. Deletion of the carboxyl 13 amino acid residues impaired the interaction between SisPINA and Hjm. Crystal structure analysis showed that the carboxyl 70 amino acid residues fold into a type II KH domain which, in other proteins, functions in binding RNA or ssDNA. The KH domain not only mediates the interactions of PINA with Hjm and Hjc but also regulates the hexameric assembly of PINA. Our results collectively suggest that SisPINA, Hjm and Hjc work together to function in replication fork regression, HJ formation and HJ cleavage

Interferon-gamma inducible protein 10 (IP10) induced cisplatin resistance of HCC after liver transplantation through ER stress signaling pathway.

Tumor recurrence remains an obstacle after liver surgery, especially in living donor liver transplantation (LDLT) for patients with hepatocellular carcinoma (HCC). The acute-phase liver graft injury might potentially induce poor response to chemotherapy in recurrent HCC after liver transplantation. We here intended to explore the mechanism and to identify a therapeutic target to overcome such chemoresistance. The associations among graft injury, overexpression of IP10 and multidrug resistant genes were investigated in a rat liver transplantation model, and further validated in clinical cohort. The role of IP10 on HCC cell proliferation and tumor growth under chemotherapy was studied both in vitro and in vivo. The underlying mechanism was revealed by detecting the activation of endoplasmic reticulum (ER) stress signaling pathways. Moreover, the effect of IP10 neutralizing antibody sensitizing cisplatin treatment was further explored. In rat liver transplantation model, significant up-regulation of IP10 associated with multidrug resistant genes was found in small-for-size liver graft. Clinically, high expression of circulating IP10 was significant correlated with tumor recurrence in HCC patients underwent LDLT. Overexpression of IP10 promoted HCC cell proliferation and tumor growth under cisplatin treatment by activation of ATF6/Grp78 signaling. IP10 neutralizing antibody sensitized cisplatin treatment in nude mice. The overexpression of IP10, which induced by liver graft injury, may lead to cisplatin resistance via ATF6/Grp78 ER stress signaling pathway. IP10 neutralizing antibody could be a potential adjuvant therapy to sensitize cisplatin treatment

Projected Multi-Agent Consensus Equilibrium (PMACE) for Distributed Reconstruction with Application to Ptychography

Multi-Agent Consensus Equilibrium (MACE) formulates an inverse imaging problem as a balance among multiple update agents such as data-fitting terms and denoisers. However, each such agent operates on a separate copy of the full image, leading to redundant memory use and slow convergence when each agent affects only a small subset of the full image. In this paper, we extend MACE to Projected Multi-Agent Consensus Equilibrium (PMACE), in which each agent updates only a projected component of the full image, thus greatly reducing memory use for some applications.We describe PMACE in terms of an equilibrium problem and an equivalent fixed point problem and show that in most cases the PMACE equilibrium is not the solution of an optimization problem. To demonstrate the value of PMACE, we apply it to the problem of ptychography, in which a sample is reconstructed from the diffraction patterns resulting from coherent X-ray illumination at multiple overlapping spots. In our PMACE formulation, each spot corresponds to a separate data-fitting agent, with the final solution found as an equilibrium among all the agents. Our results demonstrate that the PMACE reconstruction algorithm generates more accurate reconstructions at a lower computational cost than existing ptychography algorithms when the spots are sparsely sampled

Thioredoxin-1 maintains mechanistic target of rapamycin (mTOR) function during oxidative stress in cardiomyocytes

Thioredoxin 1 (Trx1) is a 12-kDa oxidoreductase that catalyzes thiol-disulfide exchange reactions to reduce proteins with disulfide bonds. As such, Trx1 helps protect the heart against stresses, such as ischemia and pressure overload. Mechanistic target of rapamycin (mTOR) is a serine/threonine kinase that regulates cell growth, metabolism, and survival. We have shown previously that mTOR activity is increased in response to myocardial ischemia-reperfusion injury. However, whether Trx1 interacts with mTOR to preserve heart function remains unknown. Using a substrate-trapping mutant of Trx1 (Trx1C35S), we show here that mTOR is a direct interacting partner of Trx1 in the heart. In response to H2O2 treatment in cardiomyocytes, mTOR exhibited a high molecular weight shift in non-reducing SDS-PAGE in a 2-mercaptoethanol-sensitive manner, suggesting that mTOR is oxidized and forms disulfide bonds with itself or other proteins. The mTOR oxidation was accompanied by reduced phosphorylation of endogenous substrates, such as S6 kinase (S6K) and 4E-binding protein 1 (4E-BP1) in cardiomyocytes. Immune complex kinase assays disclosed that H2O2 treatment diminished mTOR kinase activity, indicating that mTOR is inhibited by oxidation. Of note, Trx1 overexpression attenuated both H2O2-mediated mTOR oxidation and inhibition, whereas Trx1 knockdown increased mTOR oxidation and inhibition. Moreover, Trx1 normalized H2O2-induced down-regulation of metabolic genes and stimulation of cell death, and an mTOR inhibitor abolished Trx1-mediated rescue of gene expression. H2O2-induced oxidation and inhibition of mTOR were attenuated when Cys-1483 of mTOR was mutated to phenylalanine. These results suggest that Trx1 protects cardiomyocytes against stress by reducing mTOR at Cys-1483, thereby preserving the activity of mTOR and inhibiting cell death

Lineage tracing suggests that ovarian endosalpingiosis does not result from escape of oviductal epithelium

Most high‐grade serous carcinomas are thought to arise from Fallopian tube epithelium (FTE), but some likely arise outside of the tube, perhaps from ectopic tubal‐type epithelium known as endosalpingiosis. Importantly, the origin of endosalpingiosis is poorly understood. The proximity of the tubal fimbriae to the ovaries has led to the proposal that disruptions in the ovarian surface that occur during ovulation may allow detached FTE to implant in the ovary and form tubal‐type glands and cysts. An alternative model suggests that cells present in ectopic locations outside the Müllerian tract retain the capacity for multi‐lineage differentiation and can form glands with tubal‐type epithelium. We used double transgenic Ovgp1‐iCreERT2;R26RLSL‐eYFP mice, which express an eYFP reporter protein in OVGP1‐positive tissues following transient tamoxifen (TAM) treatment, to track the fate of oviductal epithelial cells. Cohorts of adult mice were given TAM to activate eYFP expression in oviductal epithelium, and ovaries were examined at time points ranging from 2 days to 12 months post‐TAM. To test whether superovulation might increase acquisition of endosalpingiosis, additional cohorts of TAM‐treated mice underwent up to five cycles of superovulation and ovaries were examined at 1, 6, and 12 months post‐TAM. Ovaries were sectioned in their entirety to identify endosalpingiosis. Immunohistochemical staining for PAX8, tubulin, OVGP1, and eYFP was employed to study endosalpingiosis lesions. Ovarian endosalpingiosis was identified in 14.2% of TAM‐treated adult mice. The endosalpingiotic inclusion glands and cysts were lined by secretory and ciliated cells and expressed PAX8, tubulin, OVGP1, and eYFP. Neither age nor superovulation was associated with a significant increase in endosalpingiosis. Endosalpingiosis was also occasionally present in the ovaries of pre‐pubertal mice. The findings imply that ovarian endosalpingiosis in the mouse does not likely arise as a consequence of detachment and implantation of tubal epithelium and other mechanisms may be relevant. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151844/1/path5308.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151844/2/path5308-sup-0001-FigS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151844/3/path5308_am.pd

Interacting models for twisted bilayer graphene: a quantum chemistry approach

The nature of correlated states in twisted bilayer graphene (TBG) at the magic angle has received intense attention in recent years. We present a numerical study of an interacting Bistritzer-MacDonald (IBM) model of TBG using a suite of methods in quantum chemistry, including Hartree-Fock, coupled cluster singles, doubles (CCSD), and perturbative triples (CCSD(T)), as well as a quantum chemistry formulation of the density matrix renormalization group method (DMRG). Our treatment of TBG is agnostic to gauge choices, and hence we present a new gauge-invariant formulation to detect the spontaneous symmetry breaking in interacting models. To benchmark our approach, we focus on a simplified spinless, valleyless IBM model. At integer filling ($\nu=0$), all numerical methods agree in terms of energy and $C_{2z} \mathcal{T}$ symmetry breaking. Additionally, as part of our benchmarking, we explore the impact of different schemes for removing ``double-counting'' in the IBM model. Our results at integer filling suggest that cross-validation of different IBM models may be needed for future studies of the TBG system. After benchmarking our approach at integer filling, we perform the first systematic study of the IBM model near integer filling (for $|\nu|< 0.2$). In this regime, we find that the ground state can be in a metallic and $C_{2z} \mathcal{T}$ symmetry breaking phase. The ground state appears to have low entropy, and therefore can be relatively well approximated by a single Slater determinant. Furthermore, we observe many low entropy states with energies very close to the ground state energy in the near integer filling regime

Controlling the Crucible : A Novel PvP Recommender Systems Framework for Destiny

Compared to conventional retail games, today's Massively Multiplayer Online Games (MMOGs) have become progressively more complex and volatile, living in a highly competitive market. Consumable resources in such games are nearly unlimited, making decisions to improve levels of engagement more challenging. Intelligent information filtering methods here can help players make smarter decisions, thereby improving performance, increasing level of engagement, and reducing the likelihood of early departure. In this paper, a novel approach towards building a hybrid multi-profile based recommender system for player-versus-player (PvP) content in the MMOG Destiny is presented. The framework groups the players based on three distinct traced behavioral aspects: base stats, cooldown stats, and weapon playstyle. Different combinations of these profiles are considered to make behavioral recommendations. An online evaluation was performed to investigate the usefulness of the proposed recommender framework to players of Destiny

OPENMENDEL: A Cooperative Programming Project for Statistical Genetics

Statistical methods for genomewide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software. In our view, a collaborative effort of statistical geneticists is required to develop open source software targeted to genetic epidemiology. Our attempt to meet this need is called the OPENMENDELproject (https://openmendel.github.io). It aims to (1) enable interactive and reproducible analyses with informative intermediate results, (2) scale to big data analytics, (3) embrace parallel and distributed computing, (4) adapt to rapid hardware evolution, (5) allow cloud computing, (6) allow integration of varied genetic data types, and (7) foster easy communication between clinicians, geneticists, statisticians, and computer scientists. This article reviews and makes recommendations to the genetic epidemiology community in the context of the OPENMENDEL project.Comment: 16 pages, 2 figures, 2 table