cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Mutational analysis of essential septins reveals a role for septin-mediated signaling in filamentation.
Creators: name: Blankenship, Jill R.
name: Shaoji  Cheng
name: Woolford, Carol
name: Wenjie  Xu
name: Johnson, Tanner M.
name: P. David  Rogers
name: Saranna  Fanning
name: M. Hong  Nguyen
name: Clancy, Cornelius J.
name: Mitchell, Aaron
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Septin proteins are conserved structural proteins that often demarcate regions of cell division. The essential nature of the septin ring, composed of several septin proteins, complicates investigation of the functions of the ring, although careful analysis in the model yeast Saccharomyces cerevisiae has elucidated the role that septins play in the cell cycle. Mutation analysis of non-essential septins in the pathogenic fungus Candida albicans has shown that septins also have vital roles in CWR, hyphal formation, and pathogenesis. While mutations in non-essential septins have been useful in establishing phenotypes, the septin defect is so slight that identifying causative associations between septins and downstream effectors has been difficult. In this work, we describe Decreased Abundance by mRNA Perturbation (DAmP) alleles of essential septins, which display a more severe septin defect than the defect observed in deletions of non-essential septins. The septin-DAmP alleles have allowed us to genetically separate the role of septins in hyphal growth and CWR and to identify the cyclic AMP pathway as a pathway that likely acts in a parallel manner with septins in hyphal morphogenesis.
Photometric redshifts for the Kilo-Degree Survey. Machine-learning analysis with artificial neural networks
Creators: name: Bilicki, M.
name: Hoekstra, H.
name: Brown, M. J. I.
name: Amaro, V.
name: Blake, C.
name: Cavuoti, S.
name: de Jong, J. T. A.
name: Georgiou, C.
name: Hildebrandt, H.
name: Wolf, C.
name: Amon, A.
name: Brescia, M.
name: Brough, S.
name: Costa-Duarte, M. V.
name: Erben, T.
name: Glazebrook, K.
name: Grado, A.
name: Heymans, C.
name: Jarrett, T.
name: Joudaki, S.
name: Kuijken, K.
name: Longo, G.
name: Napolitano, N.
name: Parkinson, D.
name: Vellucci, C.
name: Kleijn, G. A. Verdoes
name: Wang, L.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present a machine-learning photometric redshift analysis of the Kilo-Degree Survey Data Release 3, using two neural-network based techniques: ANNz2 and MLPQNA. Despite limited coverage of spectroscopic training sets, these ML codes provide photo-zs of quality comparable to, if not better than, those from the BPZ code, at least up to zphot<0.9 and r<23.5. At the bright end of r<20, where very complete spectroscopic data overlapping with KiDS are available, the performance of the ML photo-zs clearly surpasses that of BPZ, currently the primary photo-z method for KiDS. Using the Galaxy And Mass Assembly (GAMA) spectroscopic survey as calibration, we furthermore study how photo-zs improve for bright sources when photometric parameters additional to magnitudes are included in the photo-z derivation, as well as when VIKING and WISE infrared bands are added. While the fiducial four-band ugri setup gives a photo-z bias $δz=-2e-4$ and scatter $σ_z<0.022$ at mean z = 0.23, combining magnitudes, colours, and galaxy sizes reduces the scatter by ~7% and the bias by an order of magnitude. Once the ugri and IR magnitudes are joined into 12-band photometry spanning up to 12 $μ$, the scatter decreases by more than 10% over the fiducial case. Finally, using the 12 bands together with optical colours and linear sizes gives $δz<4e-5$ and $σ_z<0.019$. This paper also serves as a reference for two public photo-z catalogues accompanying KiDS DR3, both obtained using the ANNz2 code. The first one, of general purpose, includes all the 39 million KiDS sources with four-band ugri measurements in DR3. The second dataset, optimized for low-redshift studies such as galaxy-galaxy lensing, is limited to r<20, and provides photo-zs of much better quality than in the full-depth case thanks to incorporating optical magnitudes, colours, and sizes in the GAMA-calibrated photo-z derivation.
description: A&A, in press. Data available from the KiDS website http://kids.strw.leidenuniv.nl/DR3/ml-photoz.php#annz2
Holographic model for the anomalous scalings of the cuprates
Creators: name: Blauvelt, Erin
name: Cremonini, Sera
name: Hoover, Anthony
name: Li, Li
name: Waskie, Steven
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We examine transport in a holographic model in which the dynamics of the charged degrees of freedom is described by the nonlinear Dirac-Born-Infeld (DBI) action. Axionic scalar fields are included to break translational invariance and generate momentum dissipation in the system. Scaling exponents are introduced by using geometries which are nonrelativistic and hyperscaling-violating in the infrared. In the probe DBI limit the theory reproduces the anomalous temperature dependence of the resistivity and Hall angle of the cuprate strange metals, $ρ\sim T$ and $\cotΘ_H \sim T^2$. These scaling laws would not be present without the nonlinear dynamics encoded by the DBI interactions. We further show that because of its richness the DBI theory supports a wide spectrum of temperature scalings. This model provides explicit examples in which transport is controlled by different relaxation times. On the other hand, when only one quantity sets the temperature scale of the system, the Hall angle and conductivity typically exhibit the same temperature behavior. We illustrate this point using new fully backreacted analytical dyonic black brane solutions.
description: v2: 6 pages+supplemental material, matches version published in PRD Rapid Communication
College Students and Eating Habits: A Study Using An Ecological Model for Healthy Behavior
Creators: name: Sogari, Giovanni
name: Velez-Argumedo, Catalina
name: Gómez, Miguel I.
name: Mora, Cristina
name: Sogari, Giovanni
name: Velez-Argumedo, Catalina
name: Gómez, Miguel I.
name: Mora, Cristina
Publisher: name: Unknown
Year: 2020
Subjects: Food Consumption/Nutrition/Food Safety

description: Gómez
Detection of possible glycine precursor molecule methylamine towards the hot molecular core G358.93$-$0.03 MM1
Creators: name: Manna, Arijit
name: Pal, Sabyasachi
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The search for the simplest amino acid, glycine (NH$_{2}$CH$_{2}$COOH), in the interstellar medium (ISM), has become a never-ending story for astrochemistry and astrophysics researchers because that molecule plays a possible connection between the Universe and the origin of life. In the last forty years, all searches for NH$_{2}$CH$_{2}$COOH in the ISM at millimeter and submillimeter wavelengths have failed. Since the detection of NH$_{2}$CH$_{2}$COOH in the ISM was extremely difficult, we aimed to search for the possible precursors of NH$_{2}$CH$_{2}$COOH. Earlier, many laboratory experiments have suggested that methylamine (CH$_{3}$NH$_{2}$) plays an important role in the ISM as a possible precursor of NH$_{2}$CH$_{2}$COOH. After spectral analysis using the local thermodynamic equilibrium (LTE) model, we identified the rotational emission lines of CH$_{3}$NH$_{2}$ towards the hot molecular core G358.93$-$0.03 MM1 using the Atacama Large Millimeter/Submillimeter Array (ALMA). The column density of CH$_{3}$NH$_{2}$ towards the G358.93$-$0.03 MM1 was estimated to be (1.10$\pm$0.31)$\times$10$^{17}$ cm$^{-2}$ with an excitation temperature of 180.8$\pm$25.5 K. The fractional abundance of CH$_{3}$NH$_{2}$ with respect to H$_{2}$ towards the G358.93$-$0.03 MM1 was (8.80$\pm$2.60)$\times$10$^{-8}$. The column density ratio of CH$_{3}$NH$_{2}$ and NH$_{2}$CN towards G358.93$-$0.03 MM1 was (1.86$\pm$0.95)$\times$10$^{2}$. The estimated fractional abundance of CH$_{3}$NH$_{2}$ towards the G358.93$-$0.03 MM1 agrees fairly well with the previous three-phase warm-up chemical modelling abundance of CH$_{3}$NH$_{2}$. We also discussed the possible formation mechanism of CH$_{3}$NH$_{2}$, and we find that CH$_{3}$NH$_{2}$ is most probably formed via the reactions of radical CH$_{3}$ and radical NH$_{2}$ on the grain surface of G358.93$-$0.03 MM1.
description: Published in New Astronomy
Relative merits of Phononics vs. Plasmonics: the energy balance approach
Creators: name: Khurgin, Jacob B
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The common feature of various plasmonic schemes is their ability to confine optical fields of surface plasmon polaritons (SPPs) into sub-wavelength volumes and thus achieve a large enhancement of linear and nonlinear optical properties. This ability, however, is severely limited by the large ohmic loss inherent to even the best of metals. However, in the mid and far infrared ranges of the spectrum there exists a viable alternative to metals, polar dielectrics and semiconductors in which dielectric permittivity (the real part) turns negative in the Reststrahlen region. This feature engenders the so-called surface phonon polaritons (SPhPs) capable of confining the field in a way akin to their plasmonic analogues, the SPPs. Since the damping rate of polar phonons is substantially less than that of free electrons, it is not unreasonable to expect that phononic devices may outperform their plasmonic counterparts. Yet a more rigorous analysis of the comparative merits of phononics and plasmonics reveals a more nuanced answer, namely that while phononic schemes do exhibit narrower resonances and can achieve a very high degree of energy concentration, most of the energy is contained in the form of lattice vibrations so that enhancement of the electric field, and hence the Purcell factor, is rather small compared to what can be achieved with metal nanoantennas. Still, the sheer narrowness of phononic resonances is expected to make phononics viable in applications where frequency selectivity is important.
Application of the Mixed Time-averaging Semiclassical Initial Value Representation method to Complex Molecular Spectra
Creators: name: Buchholz, Max
name: Grossmann, Frank
name: Ceotto, Michele
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The recently introduced mixed time-averaging semiclassical initial value representation molecular dynamics method for spectroscopic calculations [M. Buchholz, F. Grossmann, and M. Ceotto, J. Chem. Phys. 144, 094102 (2016)] is applied to systems with up to 61 dimensions, ruled by a condensed phase Caldeira-Leggett model potential. By calculating the ground state as well as the first few excited states of the system Morse oscillator, changes of both the harmonic frequency and the anharmonicity are determined. The method faithfully reproduces blueshift and redshift effects and the importance of the counter term, as previously suggested by other methods. Differently from previous methods, the present semiclassical method does not take advantage of the specific form of the potential and it can represent a practical tool that opens the route to direct ab initio semiclassical simulation of condensed phase systems.
description: 11 figures
On the Physics of Type I X-ray Bursts on Accreting Neutron Stars at High Accretion Rates
Creators: name: Cooper, Randall L.
name: Narayan, Ramesh
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We investigate the effect of the hot CNO cycle breakout reaction 15O(alpha,gamma)19Ne on the occurrence of type I X-ray bursts on accreting neutron stars. For f_rp
description: 4 pages, 1 figure, accepted by ApJL
Society-in-the-Loop: Programming the Algorithmic Social Contract
Creators: name: Rahwan, Iyad
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computers and Society (cs.CY)
subject: FOS: Computer and information sciences
subject: K.4.1, K.5.2

description: Recent rapid advances in Artificial Intelligence (AI) and Machine Learning have raised many questions about the regulatory and governance mechanisms for autonomous machines. Many commentators, scholars, and policy-makers now call for ensuring that algorithms governing our lives are transparent, fair, and accountable. Here, I propose a conceptual framework for the regulation of AI and algorithmic systems. I argue that we need tools to program, debug and maintain an algorithmic social contract, a pact between various human stakeholders, mediated by machines. To achieve this, we can adapt the concept of human-in-the-loop (HITL) from the fields of modeling and simulation, and interactive machine learning. In particular, I propose an agenda I call society-in-the-loop (SITL), which combines the HITL control paradigm with mechanisms for negotiating the values of various stakeholders affected by AI systems, and monitoring compliance with the agreement. In short, `SITL = HITL + Social Contract.'
description: (in press), Ethics of Information Technology, 2017
Ferromagnetism and Superconductivity in Quark Matter - Color magnetic superconductivity -
Creators: name: Tatsumi, Toshitaka
name: Maruyama, Tomoyuki
name: Nakano, Eiji
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A coexistent phase of spin polarization and color superconductivity in high-density QCD is studied at zero temperature. The axial-vector self-energy stemming from the Fock exchange term of the one-gluon-exchange interaction has a central role to cause spin polarization. As a significant feature, the Fermi surface is deformed by the axial-vector self-energy and then rotation symmetry is spontaneously broken down. The gap function results in being anisotropic in the momentum space in accordance with the deformation. It is found that spin polarization barely conflicts with color superconductivity, and almost coexists with it.
description: Proc. of Int. Workshop, "Finite Density QCD", 2003
Quantum Brownian motion under generalized position measurements: A converse Zeno scenario
Creators: name: Magazzù, L.
name: Talkner, P.
name: Hänggi, P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the quantum Brownian motion of a harmonic oscillator undergoing a sequence of generalized position measurements. Our exact analytical results capture the interplay of the measurement backaction and dissipation. Here we demonstrate that no freeze-in Zeno effect occurs upon increasing the monitoring frequency. A similar behavior is also found in the presence of generalized momentum measurements.
description: 22 pages, 5 figures
Murine orthostatic response during prolonged vertical studies: effect on cerebral blood flow measured by arterial spin-labeled MRI.
Creators: name: Foley, Lesley
name: T. Kevin  Hitchens
name: Kochanek, Patrick M.
name: Melick, John A.
name: Jackson, Edwin K.
name: Ho, Chien
Publisher: name: Carnegie Mellon University
Year: 2005
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: High-field MRI scanners are, in principle, well suited for mouse studies; however, many high-field magnets employ a vertical design that may influence the physiological state of the rodent. The purpose of this study was to investigate the orthostatic response of cerebral blood flow (CBF) in mice during a prolonged MR experiment in the vertical position. Arterial spin-labeled (ASL) MRI was performed at 4.7-Tesla with a 15-cm gradient insert that allowed horizontal and vertical CBF measurements to be obtained with the same scanner. For mice in the head-up (HU) vertical position, CBF decreased by approximately 40% compared to the horizontal position, although blood pressure did not differ. Furthermore, CBF values for vertically positioned mice treated with phenylephrine remained constant while blood pressure increased. These results support the conclusion that cerebral autoregulation was intact, albeit at a lower level. Since CBF recovers to near horizontal values by volume loading with saline, it appears that a decrease in central venous pressure (CVP) leading to an increase in sympathetic tone may be a contributing mechanism for lowered CBF. This suggests that using an HU vertical position for MRI in mice may have broader implications, especially for studies that rely on CBF (such as BOLD and fMRI).
Circulating trans fatty acids are associated with prostate cancer in Ghanaian and American men
Creators: name: Zewdu Minas, Tsion
name: Lord, Brittany D.
name: Zhang, Amy L.
name: Candia, Julián
name: Dorsey, Tiffany H.
name: S. Baker, Francine
name: Tang, Wei
name: Bailey‑Whyte, Maeve
name: J. Smith, Cheryl
name: M. Obadi, Obadi
name: Ajao, Anuoluwapo
name: Jordan, Symone V.
name: Tettey, Yao
name: Biritwum, Richard B.
name: A. Adjei, Andrew
name: Mensah, James E.
name: Hoover, Robert N.
name: Hsing, Ann W.
name: liu, Jia
name: Loffredo, Christopher A.
name: Yates, Clayton
name: Cook, Michael B.
name: Ambs, Stefan
Publisher: name: University of Limerick
Year: 2023
Subjects: classificationCode: 42
subject: Health sciences
subject: FOS: Health sciences

description: The association between fatty acids and prostate cancer remains poorly explored in African-descent populations. Here, we analyze 24 circulating fatty acids in 2934 men, including 1431 prostate cancer cases and 1503 population controls from Ghana and the United States, using CLIA-certified mass spectrometry-based assays. We investigate their associations with population groups (Ghanaian, African American, European American men), lifestyle fac?tors, the fatty acid desaturase (FADS) genetic locus, and prostate cancer. Blood levels of circulating fatty acids vary significantly between the three population groups, particularly trans, omega-3 and omega-6 fatty acids. FADS1/2 germline genetic variants and lifestyle factors explain some of the variation in fatty acid levels, with the FADS1/2 locus showing population-specific associations, suggesting differences in their control by germline genetic factors. All trans fatty acids, namely elaidic, palmitelaidic, and linoelaidic acids, associated with an increase in the odds of developing prostate cancer, independent of ancestry, geographic location, or potential confounders.
Calculating particle pair potentials from fluid-state pair correlations: Iterative Ornstein-Zernike Inversion
Creators: name: Heinen, Marco
Publisher: name: arXiv
Year: 2017
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: An iterative Monte Carlo inversion method for the calculation of particle pair potentials from given particle pair correlations is proposed in this paper. The new method, which is best referred to as Iterative Ornstein-Zernike Inversion, represents a generalization and an improvement of the established Iterative Boltzmann Inversion technique [Reith, Pütz \& Müller-Plathe, J. Comput. Chem. 24, 1624 (2003)]. Our modification of Iterative Boltzmann Inversion consists of replacing the potential of mean force as an approximant for the pair potential with another, generally more accurate approximant that is based on a trial bridge function in the Ornstein-Zernike integral equation formalism. As an input, the new method requires the particle pair correlations both in real space and in the Fourier conjugate wavenumber space. An accelerated iteration method is included in the discussion, by which the required number of iterations can be greatly reduced below that of the simple Picard iteration that underlies most common implementations of Iterative Boltzmann Inversion. Comprehensive tests with various pair potentials show that the new method generally surpasses the Iterative Boltzmann Inversion method in terms of reliability of the numerical solution for the particle pair potential.
description: Accepted for publication in J. Comput. Chem
Dynamical Evolution of Globular Clusters in Hierarchical Cosmology
Creators: name: Prieto, Jose L.
name: Gnedin, Oleg Y.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We test the hypothesis that metal-poor globular clusters form within disk galaxies at redshifts z>3. Numerical simulations demonstrate that giant gas clouds, which are cold and dense enough to produce massive star clusters, assemble naturally in hierarchical models of galaxy formation at high redshift. Do model clusters evolve into observed globular clusters or are they disrupted before present as a result of the dynamical evolution? To address this question, we calculate the orbits of model clusters in the time-variable gravitational potential of a Milky Way-sized galaxy, using the outputs of a cosmological N-body simulation. We find that at present the orbits are isotropic in the inner 50 kpc of the Galaxy and preferentially radial at larger distances. All clusters located outside 10 kpc from the center formed in satellite galaxies, some of which are now tidally disrupted and some of which survive as dwarf galaxies. The spatial distribution of model clusters is spheroidal and the fit to the density profile has a power-law slope of 2.7. The combination of two-body relaxation, tidal shocks, and stellar evolution drives the evolution of the cluster mass function from an initial power law to a peaked distribution, in agreement with observations. However, not all initial conditions and not all evolution scenarios are consistent with the observed mass function of the Galactic globular clusters. The successful models require the average cluster density to be constant initially for clusters of all mass and to remain constant with time. Synchronous formation of all clusters at a single epoch (z=4) and continuous formation over a span of 1.6 Gyr (between z=9 and z=3) are both consistent with the data. For both formation scenarios, we provide online catalogs of the main physical properties of model clusters.
description: 16 pages, submitted to ApJ, cluster catalogs are available online at http://www.astronomy.ohio-state.edu/~prieto/GC/
Priestleya tomentosa Druce
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fabales
Fabaceae
Priestleya
Priestleya tomentosa

description: Liparia villosa Linnaeus, Mantissa Plantarum Altera: 269. 1771, nom. illeg.
["Habitat in Aethiopia."] Sp. Pl. 2: 707 (1753). RCN: 5435.
 Replaced synonym: Borbonia tomentosa L. (1753).
 Lectotype (Schutte & Van Wyk in Taxon 42: 47. 1993): [icon] " Genista, Africana, tomentosa, folio cochleariformi, flore luteo" in Seba, Locupl. Rer. Nat. Thes. 1: 38, t. 24, f. 1. 1734.
 Current name: Priestleya tomentosa (L.) Druce (Fabaceae: Faboideae).
 Note: An illegitimate renaming of Borbonia tomentosa L. (1753) in Liparia, as noted by Schutte & Van Wyk.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
A new construction of universal spaces for asymptotic dimension
Creators: name: Bell, G. C.
name: Nagórko, A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: Primary 54F45, Secondary 54E15

description: For each $n$, we construct a separable metric space $\mathbb{U}_n$ that is universal in the coarse category of separable metric spaces with asymptotic dimension ($\mathop{asdim}$) at most $n$ and universal in the uniform category of separable metric spaces with uniform dimension ($\mathop{udim}$) at most $n$. Thus, $\mathbb{U}_n$ serves as a universal space for dimension $n$ in both the large-scale and infinitesimal topology. More precisely, we prove: \[ \mathop{asdim} \mathbb{U}_n = \mathop{udim} \mathbb{U}_n = n \] and such that for each separable metric space $X$, a) if $\mathop{asdim} X \leq n$, then $X$ is coarsely equivalent to a subset of $\mathbb{U}_n$; b) if $\mathop{udim} X \leq n$, then $X$ is uniformly homeomorphic to a subset of $\mathbb{U}_n$.
Multiple roles of a conserved GAF domain tyrosine residue in cyanobacterial and plant phytochromes.
Creators: name: Fischer, Amanda J.
name: Rockwell, Nathan C.
name: Jang, Abigail Y.
name: Ernst, Lauren A.
name: Waggoner, Alan
name: Duan, Yong
name: Hongxing  Lei
name: J. Clark  Lagarias
Publisher: name: Carnegie Mellon University
Year: 2005
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The phytochrome family of red/far-red photoreceptors has been optimized to support photochemical isomerization of a bound bilin chromophore, a process that triggers a conformational change and modulates biochemical output from the surrounding protein scaffold. Recent studies have established that the efficiency of this photochemical process is profoundly altered by mutation of a conserved tyrosine residue (Tyr176) within the bilin-binding GAF domain of the cyanobacterial phytochrome Cph1 [Fischer, A. J., and Lagarias, J. C. (2004) Harnessing phytochrome's glowing potential, Proc. Natl. Acad. Sci. U.S.A. 101, 17334-17339]. Here, we show that the equivalent mutation in plant phytochromes behaves similarly, indicating that the function of this tyrosine in the primary photochemical mechanism is conserved. Saturation mutagenesis of Tyr176 in Cph1 establishes that no other residue can support comparably efficient photoisomerization. The spectroscopic consequences of Tyr176 mutations also reveal that Tyr176 regulates the conversion of the porphyrin-like conformation of the bilin precursor to a more extended conformation. The porphyrin-binding ability of the Tyr176Arg mutant protein indicates that Tyr176 also regulates the ligand-binding specificity of apophytochrome. On the basis of the hydrogen-bonding ability of Tyr176 substitutions that support the nonphotochemical C15-Z,syn to C15-Z,anti interconversion, we propose that Tyr176 orients the carboxyl side chain of a conserved acidic residue to stabilize protonation of the bilin chromophore. A homology model of the GAF domain of Cph1 predicts a C5-Z,syn, C10-Z,syn, C15-Z,anti configuration for the chromophore and implicates Glu189 as the proposed acidic residue stabilizing the extended conformation, an interpretation consistent with site-directed mutagenesis of this conserved acidic residue.
Excited states using semistochastic heat-bath configuration interaction
Creators: name: Holmes, Adam A.
name: Umrigar, C. J.
name: Sharma, Sandeep
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We extend our recently-developed heat-bath configuration interaction (HCI) algorithm, and our semistochastic algorithm for performing multireference perturbation theory, to the calculation of excited-state wavefunctions and energies. We employ time-reversal symmetry, which reduces the memory requirements by more than a factor of two. An extrapolation technique is introduced to reliably extrapolate HCI energies to the Full CI limit. The resulting algorithm is used to compute the twelve lowest-lying potential energy surfaces of the carbon dimer using the cc-pV5Z basis set, with an estimated error in energy of 30-50 μHa compared to Full CI. The excitation energies obtained using our algorithm have a mean absolute deviation of 0.02 eV compared to experimental values. We also calculate the complete active-space (CAS) energies of the S0, S1, and T0 states of tetracene, which are of relevance to singlet fission, by fully correlating active spaces as large as 18 electrons in 36 orbitals.
Multiple motifs regulate apical sorting of p75 via a mechanism that involves dimerization and higher-order oligomerization.
Creators: name: Youker, Robert T.
name: Bruns, Jennifer R.
name: Costa, Simone A.
name: Rbaibi, Youssef
name: Lanni, Frederick
name: Kashlan, Ossama B.
name: Haibing Teng
name: Weisz, Ora A.
Publisher: name: Carnegie Mellon University
Year: 2013
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The sorting signals that direct proteins to the apical surface of polarized epithelial cells are complex and can include posttranslational modifications, such as N- and O-linked glycosylation. Efficient apical sorting of the neurotrophin receptor p75 is dependent on its O-glycosylated membrane proximal stalk, but how this domain mediates targeting is unknown. Protein oligomerization or clustering has been suggested as a common step in the segregation of all apical proteins. Like many apical proteins, p75 forms dimers, and we hypothesized that formation of higher-order clusters mediated by p75 dimerization and interactions of the stalk facilitate its apical sorting. Using fluorescence fluctuation techniques (photon-counting histogram and number and brightness analyses) to study p75 oligomerization status in vivo, we found that wild-type p75-green fluorescent protein forms clusters in the trans-Golgi network (TGN) but not at the plasma membrane. Disruption of either the dimerization motif or the stalk domain impaired both clustering and polarized delivery. Manipulation of O-glycan processing or depletion of multiple galectins expressed in Madin-Darby canine kidney cells had no effect on p75 sorting, suggesting that the stalk domain functions as a structural prop to position other determinants in the lumenal domain of p75 for oligomerization. Additionally, a p75 mutant with intact dimerization and stalk motifs but with a dominant basolateral sorting determinant (Δ250 mutant) did not form oligomers, consistent with a requirement for clustering in apical sorting. Artificially enhancing dimerization restored clustering to the Δ250 mutant but was insufficient to reroute this mutant to the apical surface. Together these studies demonstrate that clustering in the TGN is required for normal biosynthetic apical sorting of p75 but is not by itself sufficient to reroute a protein to the apical surface in the presence of a strong basolateral sorting determinant. Our studies shed new light on the hierarchy of polarized sorting signals and on the mechanisms by which newly synthesized proteins are segregated in the TGN for eventual apical delivery.
Double polarization asymmetry as a possible filter for $Θ^+$'s parity
Creators: name: Zhao, Q.
name: Al-Khalili, J. S.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We present an analysis of the Beam-Target double polarization asymmetry for the photoproduction of $Θ^+$ in $γn\to Θ^+ K^-$. We show that this quantity can serve as a filter for the determination of the $Θ^+$'s spin-parity assignment near threshold. It is highly selective between $1/2^+$ and $1/2^-$ configurations due to dynamical reasons.
description: Proofread version
Lippia americana Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Lamiales
Verbenaceae
Lippia
Lippia americana

description: Lippia americana Linnaeus, Species Plantarum 2: 633. 1753.
"Habitat in Vera Cruce." RCN: 4599.
 Lectotype (Moldenke in Phytologia 12: 76. 1965): Herb. Linn. No. 801.1 (LINN).
 Generitype of Lippia Linnaeus.
 Current name: Lippia americana L. (Verbenaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Stellar Encounters with Massive Star-Disk Systems
Creators: name: Moeckel, Nickolas
name: Bally, John
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The dense, clustered environment in which massive stars form can lead to interactions with neighboring stars. It has been hypothesized that collisions and mergers may contribute to the growth of the most massive stars. In this paper we extend the study of star-disk interactions to explore encounters between a massive protostar and a less massive cluster sibling using the publicly available SPH code GADGET-2. Collisions do not occur in the parameter space studied, but the end state of many encounters is an eccentric binary with a semi-major axis ~ 100 AU. Disk material is sometimes captured by the impactor. Most encounters result in disruption and destruction of the initial disk, and periodic torquing of the remnant disk. We consider the effect of the changing orientation of the disk on an accretion driven jet, and the evolution of the systems in the presence of on-going accretion from the parent core.
description: 11 pages, 10 figures, accepted to ApJ
Microdon capitatus Levyns
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Lamiales
Scrophulariaceae
Microdon
Microdon capitatus

description: Lippia ovata Linnaeus, Systema Naturae, ed. 12, 2: 423; Mantissa Plantarum: 89. 1767.
"Habitat ad Cap. b. spei." RCN: 4601.
Type not designated.
Original material: Herb. Linn. No. 801.2 (LINN).
 Current name: Microdon capitatus (P.J. Bergius) Levyns (Globulariaceae).
 Note: Although Rolfe (in J. Linn. Soc., Bot. 20: 347. 1884) noted the existence of 801.2 (LINN), he did not indicate it as type, and Hilliard (Tribe Selagineae: 12. 1999) did so, but with doubt ("Type: sheet no. 801.2 herb. LINN?").
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Comptonia peregrina J. M. Coult.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fagales
Myricaceae
Comptonia
Comptonia peregrina

description: Liquidambar aspleniifolia (Linnaeus) Linnaeus, Species Plantarum, ed. 2, 2: 1418. 1763.
"Habitat in America septentrionali." RCN: 7238.
 Basionym: Myrica aspleniifolia L. (1753).
Type not designated.
Original material: as basionym.
 Current name: Comptonia peregrina (L.) J.M. Coult. (Myricaceae).
 Note: Specific epithet spelled “asplenifolium” in the protologue.
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Comptonia peregrina J. M. Coult.
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Fagales
Myricaceae
Comptonia
Comptonia peregrina

description: Liquidambar peregrina Linnaeus, Species Plantarum 2: 999. 1753.
"Habitat in Canada." RCN: 7238.
 Lectotype (Reveal & al. in Huntia 7: 223. 1987): Kalm, Herb. Linn. No. 1134.3 (LINN).
 Current name: Comptonia peregrina (L.) J.M. Coult. (Myricaceae).
 Note: See discussion by Fernald (in Rhodora 40: 411. 1938).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Prospects for the Characterization and Confirmation of Transiting Exoplanets via the Rossiter-McLaughlin Effect
Creators: name: Gaudi, B. Scott
name: Winn, Joshua N.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The Rossiter-McLaughlin (RM) effect is the distortion of stellar spectral lines that occurs during eclipses or transits, due to stellar rotation. We assess the future prospects for using the RM effect to measure the alignment of planetary orbits with the spin axes of their parent stars, and to confirm exoplanetary transits. We compute the achievable accuracy for the parameters of interest, in general and for the 5 known cases of transiting exoplanets with bright host stars. We determine the requirements for detecting the effects of differential rotation. For transiting planets with small masses or long periods (as will be detected by forthcoming satellite missions), the velocity anomaly produced by the RM effect can be much larger than the orbital velocity of the star. For a terrestrial planet in the habitable zone of a Sun-like star found by the Kepler mission, it will be difficult to use the RM effect to confirm transits with current instruments, but it still may be easier than measuring the spectroscopic orbit.
description: 18 pages, 8 figures, one table. Minor changes. Accepted to ApJ, to appear in the Jan 20, 2007 issue (v655)
Liquidambar styraciflua Linnaeus 1753
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Saxifragales
Altingiaceae
Liquidambar
Liquidambar styraciflua

description: Liquidambar styraciflua Linnaeus, Species Plantarum 2: 999. 1753.
"Habitat in Virginia, Mexico." RCN: 7237.
 Lectotype (Wijnands, Bot. Commelins: 109. 1983): Kalm, Herb. Linn. No. 1134.1 (LINN).
 Generitype of Liquidambar Linnaeus (vide Green, Prop. Brit. Bot.: 189. 1929).
 Current name: Liquidambar styraciflua L. (Hamamelidaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Multifunctional RNA Processing Protein SRm160 Induces Apoptosis and Regulates Eye and Genital Development in Drosophila.
Creators: name: Fan, Yu-Jie
name: Aryn Gittis
name: Juge, François
name: Qiu, Chen
name: Xu, Yong-Zhen
name: Rabinow, Leonard
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: SRm160 is an SR-like protein implicated in multiple steps of RNA processing and nucleocytoplasmic export. Although its biochemical functions have been extensively described, its genetic interactions and potential participation in signaling pathways remain largely unknown, despite the fact that it is highly phosphorylated in both mammalian cells and Drosophila. To begin elucidating the functions of the protein in signaling and its potential role in developmental processes, we characterized mutant and overexpression SRm160 phenotypes in Drosophila and their interactions with the locus encoding the LAMMER protein kinase, Doa. SRm160 mutations are recessive lethal, while its overexpression generates phenotypes including roughened eyes and highly disorganized internal eye structure, which are due at least in part to aberrantly high levels of apoptosis. SRm160 is required for normal somatic sex determination, since its alleles strongly enhance a subtle sex transformation phenotype induced by Doa kinase alleles. Moreover, modification of SRm160 by DOA kinase appears to be necessary for its activity, since Doa alleles suppress phenotypes induced by SRm160 overexpression in the eye and enhance those in genital discs. Modification of SRm160 may occur through direct interaction because DOA kinase phosphorylates it in vitro. Remarkably, SRm160 protein was concentrated in the nuclei of precellular embryos but was very rapidly excluded from nuclei or degraded coincident with cellularization. Also of interest, transcripts are restricted almost exclusively to the developing nervous system in mature embryos.
Talauma rumphii Blume 1825
Creators: name: Jarvis, Charlie
Publisher: name: Linnaean Society of London in association with the Natural History Museum
Year: 2007
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Magnoliales
Magnoliaceae
Talauma
Talauma rumphii

description: Liriodendron liliifera Linnaeus, Species Plantarum, ed. 2, 1: 755. 1762.
"Habitat in Amboina." RCN: 3979.
 Lectotype (Merrill, Interpret. Rumph. Herb. Amb.: 224. 1917): [icon] "Sampacca montana" in Rumphius, Herb. Amboin. 2: 204, t. 69. 1741.
 Current name: Talauma rumphii Blume (Magnoliaceae).
description: Published as part of Jarvis, Charlie, 2007, Chapter 7: Linnaean Plant Names and their Types (part L), pp. 610-650 in Order out of Chaos. Linnaean Plant Types and their Types, London :Linnaean Society of London in association with the Natural History Museum on page 636, DOI: 10.5281/zenodo.291971
Search for Oxygen Emission from Warm-Hot Intergalactic Medium around A2218 with Suzaku
Creators: name: Takei, Yoh
name: Ohashi, Takaya
name: Henry, J. Patrick
name: Mitsuda, Kazuhisa
name: Fujimoto, Ryuichi
name: Tamura, Takayuki
name: Yamasaki, Noriko Y.
name: Hayashida, Kiyoshi
name: Tawa, Noriaki
name: Matsushita, Kyoko
name: Bautz, Mark W.
name: Hughes, John P.
name: Madejski, Grzegorz M.
name: Kelley, Richard L.
name: Arnaud, Keith A.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We searched for redshifted O emission lines from the possible warm-hot intergalactic medium (WHIM) surrounding the cluster of galaxies A2218 at z=0.1756 using the XIS instrument on Suzaku. This cluster is thought to have an elongated structure along the line of sight based on previous studies. We studied systematic uncertainties in the spectrum of the Galactic emission and in the soft X-ray response of the detectors due to the contamination building up on the XIS filters. We detected no significant redshifted O lines, and set a tight constraint on the intensity with upper limits for the surface brightness of OVII and OVIII lines of 1.1 x 10^-7 and 3.0 x 10^-7 photons cm^-2 s^-1 arcmin^-2, respectively. These upper limits are significantly lower than the previously reported fluxes from the WHIM around other clusters of galaxies. We also discuss the prospect for the detection of the WHIM lines with Suzaku XIS in the future.
description: 12 pages, 13 figures. Accepted for publication in PASJ Suzaku special issue (Vol.59, No.SP1)
Probing Neutralino Resonance Annihilation via Indirect Detection of Dark Matter
Creators: name: Baer, Howard
name: Farrill, Jorge O'
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The lightest neutralino of R-parity conserving supersymmetric models serves as a compelling candidate to account for the presence of cold dark matter in the universe. In the minimal supergravity (mSUGRA) model, a relic density can be found in accord with recent WMAP data for large values of the parameter $\tanβ$, where neutralino annihilation in the early universe occurs via the broad s-channel resonance of the pseudoscalar Higgs boson $A$. We map out rates for indirect detection of neutralinos via 1. detection of neutrinos arising from neutralino annihilation in the core of the earth or sun and 2. detection of gamma rays, antiprotons and positrons arising from neutralino annihilation in the galactic halo. If indeed $A$-resonance annihilation is the main sink for neutralinos in the early universe, then signals may occur in the gamma ray, antiproton and positron channels, while a signal in the neutrino channel would likely be absent. This is in contrast to the hyperbolic branch/focus point (HB/FP) region where {\it all} indirect detection signals are likely to occur, and also in contrast to the stau co-annihilation region, where {\it none} of the indirect signals are likely to occur.
description: 12 pages including 4 eps figures
A deep mosaic of [O III] 5007 A CCD images of the environment of the LBV star P Cygni
Creators: name: Boumis, P.
name: Meaburn, J.
name: Redman, M. P.
name: Mavromatakis, F.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A mosaic of six, deep, CCD images in the light of the [O III] 5007 A nebular emission line has been obtained with the 1.3-m Skinakas (Crete) telescope of the filamentary nebulosity surrounding P Cygni. The [O III] 5007 A line discriminates against confusing galactic H II regions along the same sight-lines and the new mosaic did not include the 4.8 mag. central star; a source of artifacts in the previous lower angular resolution observations. New giant `lobes' and `shells' are found to be clustered around P Cygni which must be the relics of historic eruptions between 2400 and up to ~10^5 yr ago.
description: 4 pages, 2 figures. Accepted for pubication by A&A Letters
The use of ocean colour, multispectral and hyperspectral measurements to study phytoplankton in Lake Trasimeno
Creators: name: Bresciani, Mariano
name: Giardino, Claudia
name: Cazzaniga Ilaria
name: Hommersom, A.
name: Luciani, G.
name: Della Bella, V.
name: Cingolani, A.
name: Charavgis, F.
Publisher: name: Zenodo
Year: 2019

description: Poster at LPS 2019, Milan Aims
 This study presents the application of integration of satellite remote sensing and in situ monitoring from optical sensors for assessing phytoplankton dynamics in Lake Trasimeno (Italy). The products are exploited to provide spatial and temporal information of chlorophyll-a concentrations (Chl-a) for both supporting the Water Framework Directive (EC/2000/60), and for evaluating seasonal trends and their possible relations with climate change.
Parametric Resonance in Quantum Electrodynamics Vacuum Birefringence
Creators: name: Arza, Ariel
name: Elias, Ricardo Gabriel
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Vacuum magnetic birefringence is one of the most interesting non-linear phenomena in quantum electrodynamics because it is a pure photon-photon result of the theory and it directly signalizes the violation of the classical superposition principle of electromagnetic fields in the full quantum theory. We perform analytical and numerical calculations when an electromagnetic wave interacts with an oscillating external magnetic field. We find that in an ideal cavity, when the external field frequency is around the electromagnetic wave frequency, the normal and parallel components of the wave suffer parametric resonance at different rates, producing a vacuum birefringence effect growing in time. We also study the case where there is no cavity and the oscillating magnetic field is spatially localized in a region of length $L$. In both cases we find also a rotation of the elliptical axis.