cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Strain-specific virulence phenotypes of Streptococcus pneumoniae assessed using the Chinchilla laniger model of otitis media.
Creators: name: Forbes, Michael L.
name: Horsey, Edward
name: Hiller, Natalia
name: Farrel J. Buchinsky
name: Hayes, Jay D.
name: Compliment, James M.
name: Hillman, Todd
name: Ezzo, Suzanne
name: Shen, Kai
name: Keefe, Randy
name: Barbadora, Karen
name: J. Christopher  Post
name: Hu, Fen Z.
name: Ehrlich, Garth D.
Publisher: name: Carnegie Mellon University
Year: 2008
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: BACKGROUND: Streptococcus pneumoniae [Sp] infection is associated with local and systemic disease. Our current understanding of the differential contributions of genetic strain variation, serotype, and host response to disease phenotype is incomplete. Using the chinchilla model of otitis media [OM] we investigated the disease phenotype generated by the laboratory strain TIGR4 and each of thirteen clinical strains (BS68-75, BS290, BS291, BS293, BS436 and BS437); eleven of the thirteen strains have been genomically sequenced. METHODOLOGY/PRINCIPAL FINDINGS: For each strain 100 colony forming units were injected bilaterally into the tympanic bullae of 6 young adult chinchillas under general anesthesia. All animals were examined daily for local and systemic disease by a blinded observer. Pneumatic otoscopy was used to evaluate local disease, and behavioral assessments served as the measure of systemic disease. Virulence scoring was performed using a 4-point scale to assess four clinical parameters [severity and rapidity of local disease onset; and severity and rapidity of systemic disease onset] during a 10-day evaluation period. Highly significant variation was observed among the strains in their ability to cause disease and moribundity. CONCLUSIONS/SIGNIFICANCE: As expected, there was a significant correlation between the rapidity of systemic disease onset and severity of systemic disease; however, there was little correlation between the severity of otoscopic changes and severity of systemic disease. Importantly, it was observed that different strains of the same serotype produced as broad an array of disease phenotypes as did strains of different serotypes. We attribute these phenotypic differences among the strains to the high degree of genomic plasticity that we have previously documented.
Mid-infrared Identification of 6 cm Radio Source Counterparts in the Extended Groth Strip
Creators: name: Willner, S. P.
name: Coil, A. L.
name: Goss, W. M.
name: Ashby, M. L. N.
name: Barmby, P.
name: Huang, J. -S.
name: Ivison, R.
name: Koo, D. C.
name: Egami, E.
name: Miyazaki, Satoshi
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A new 6-cm survey of almost 0.6 square degrees to a limit of 0.55-mJy/beam (10-sigma) finds 37 isolated radio sources and 7 radio source pairs (not necessarily physical companions). IRAC counterparts are identified for at least 92% of the radio sources within the area of deep IRAC coverage, which includes 31 isolated sources and 6 pairs. This contrasts with an identification rate of <74% to R<23.95 in visible light. Eight of the IRAC galaxies have power law spectral energy distributions, implying that the mid-infrared emission comes from a powerful AGN. The remaining 26 IRAC galaxies show stellar emission in the mid-infrared, probably in most of these galaxies because the stellar emission is bright enough to outshine an underlying AGN. The infrared colors suggest that the majority of these galaxies are bulge-dominated and have redshifts between approximately 0.5 and 1.0. Visible spectra from the DEEP2 redshift survey, available for 11 galaxies, are consistent with this suggestion. The IRAC galaxies fall into two distinct groups in a color-magnitude diagram, one group (the "stripe") includes all the AGN. The other group (the "blue clump") has blue 3.6 to 8 micron colors and a small range of 8 micron magnitudes. This separation should be useful in classifying galaxies found in other radio surveys.
description: Accepted by AJ
Physospermum cornubiense
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
Apiales
Apiaceae
Physospermum
Physospermum cornubiense

description: Ligusticum cornubiense Linnaeus, Centuria II Plantarum: 13. 1756.
"Habitat in Cornubia." RCN: 2013.
 Lectotype (Reduron in Jarvis & al. in Taxon 55: 213. 2006): [icon] " Smyrnium tenuifolium, nostras" in Ray, Syn. Meth. Stirp. Brit., ed. 3: 209, t. 8. 1724. - Epitype (Reduron in Jarvis & al. in Taxon 55: 213. 2006): " Tragoselinum maximum cornubiense umbella Candida N.11" in Herb. Buddle; Herb. Sloane 120: 37 (BM-SL).
 Current name: Physospermum cornubiense (L.) DC. (Apiaceae).
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 632, DOI: 10.5281/zenodo.291971
Additional file 1 of Sustained glymphatic transport and impaired drainage to the nasal cavity observed in multiciliated cell ciliopathies with hydrocephalus
Creators: name: Xue, Yuechuan
name: Gursky, Zachary
name: Monte, Brittany
name: Koundal, Sunil
name: Liu, Xiaodan
name: Lee, Hedok
name: Michurina, Tatyana V.
name: Mellanson, Kennelia A.
name: Zhao, Lucy
name: Nemajerova, Alice
name: Kahle, Kristopher T.
name: Takemaru, Ken-Ichi
name: Enikolopov, Grigori
name: Peunova, Natalia I.
name: Benveniste, Helene
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Hematology

description: Additional file 1: Figure S1. Automated quantification of AQP4 polarization index using CellProfiler.
Additional file 1 of Monocyte state 1 (MS1) cells in critically ill patients with sepsis or non-infectious conditions: association with disease course and host response
Creators: name: Leite, Giuseppe G. F.
name: de Brabander, Justin
name: Michels, Erik H. A.
name: Butler, Joe M.
name: Cremer, Olaf L.
name: Scicluna, Brendon P.
name: Sweeney, Timothy E.
name: Reyes, Miguel
name: Salomao, Reinaldo
name: Peters-Sengers, Hessel
name: van der Poll, Tom
Publisher: name: figshare
Year: 2024
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1. Supplementary materials, tables and figures.
A new method for real radiation at NNLO
Creators: name: Anastasiou, C.
name: Melnikov, Kirill
name: Petriello, Frank
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose a new method of computing real emission contributions to hard QCD processes. Our approach uses sector decomposition of the exclusive final-state phase space to enable extraction of all singularities of the real emission matrix elements before integration over any kinematic variable. The exact kinematics of the real emission process are preserved in all regions of phase space. Traditional approaches to extracting singularities from real emission matrix elements, such as phase space slicing and dipole subtraction, require both the determination of counterterms for double real emission amplitudes in singular kinematic limits and the integration of these contributions analytically to cancel the resulting singularities against virtual corrections. Our method addresses both of these issues. The implementation of constraints on the final-state phase space, including various jet algorithms, is simple using our approach. We illustrate our method using electron-positron --> jets at NNLO as an example.
description: 15 pages
Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics.
Creators: name: Byoungkoo  Lee
name: LeDuc, Philip
name: Schwartz, Russell
Publisher: name: Carnegie Mellon University
Year: 2008
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The environment inside a living cell is dramatically different from that found in in vitro models, presenting a problem for computational models of biochemistry that are only beginning to capture these differences. This deviation between idealized in vitro models and more realistic intracellular conditions is particularly problematic for models of molecular self-assembly, but also specifically hard to address because the large sizes and long assembly times of biological self-assembly systems force the use of highly simplified models. We have developed a prototype of a molecular self-assembly simulator based on the Green's function reaction dynamics (GFRD) model to achieve more realistic models of assembly in the crowded conditions of the cell without unduly sacrificing tractability. We tested the model on a simple representation of dimer assembly in a two-dimensional space. Our simulations verify that the model is computationally efficient, provides a realistic quantitative model of reaction kinetics in uncrowded conditions, and exhibits expected excluded volume effects under conditions of high crowding. This work confirms the effectiveness of the GFRD technique for more realistic coarse-grained modeling of self-assembly in crowded conditions and helps lay the groundwork for exploring the effects of in vivo crowding on more complex assembly systems.
VLA Radio Observations of the HST Frontier Fields Cluster Abell 2744: The Discovery of New Radio Relics
Creators: name: Pearce, C. J. J.
name: van Weeren, R. J.
name: Andrade-Santos, F.
name: Jones, C.
name: Forman, W. R.
name: Brüggen, M.
name: Bulbul, E.
name: Clarke, T. E.
name: Kraft, R. P.
name: Medezinski, E.
name: Mroczkowski, T.
name: Nonino, M.
name: Nulsen, P. E. J.
name: Randall, S. W.
name: Umetsu, K.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Cluster mergers leave distinct signatures in the ICM in the form of shocks and diffuse cluster radio sources that provide evidence for the acceleration of relativistic particles. However, the physics of particle acceleration in the ICM is still not fully understood. Here we present new 1-4 GHz Jansky Very Large Array (VLA) and archival Chandra observations of the HST Frontier Fields Cluster Abell 2744. In our new VLA images, we detect the previously known $\sim2.1$ Mpc radio halo and $\sim1.5$ Mpc radio relic. We carry out a radio spectral analysis from which we determine the relic's injection spectral index to be $α_{\rm{inj}} = -1.12 \pm 0.19$. This corresponds to a shock Mach number of $\mathcal{M}$ = 2.05$^{+0.31}_{-0.19}$ under the assumption of diffusive shock acceleration. We also find evidence for spectral steepening in the post-shock region. We do not find evidence for a significant correlation between the radio halo's spectral index and ICM temperature. In addition, we observe three new polarized diffuse sources and determine two of these to be newly discovered giant radio relics. These two relics are located in the southeastern and northwestern outskirts of the cluster. The corresponding integrated spectral indices measure $-1.81 \pm 0.26$ and $-0.63 \pm 0.21$ for the SE and NW relics, respectively. From an X-ray surface brightness profile we also detect a possible density jump of $R=1.39^{+0.34}_{-0.22}$ co-located with the newly discovered SE relic. This density jump would correspond to a shock front Mach number of $\mathcal{M}=1.26^{+0.25}_{-0.15}$.
description: accepted for publication in ApJ
Stochastic dynamics of uncoupled neural oscillators: Fokker-Planck studies with the finite element method.
Creators: name: Galán, Roberto F.
name: G Bard  Ermentrout
name: Urban, Nathan
Publisher: name: Carnegie Mellon University
Year: 2007
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: We have investigated the effect of the phase response curve on the dynamics of oscillators driven by noise in two limit cases that are especially relevant for neuroscience. Using the finite element method to solve the Fokker-Planck equation we have studied (i) the impact of noise on the regularity of the oscillations quantified as the coefficient of variation, (ii) stochastic synchronization of two uncoupled phase oscillators driven by correlated noise, and (iii) their cross-correlation function. We show that, in general, the limit of type II oscillators is more robust to noise and more efficient at synchronizing by correlated noise than type I.
Stem cells in the news: CNN and APC make headlines.
Creators: name: McCartney, Brooke M
name: Peifer, Mark
Publisher: name: Carnegie Mellon University
Year: 2003
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Stem cell self-renewal depends on their ability to divide asymmetrically, with one daughter retaining stem cell identity. This often involves precise orchestration of mitotic spindle orientation, but the machinery used to ensure this outcome is understood in only a handful of examples. In a recent issue of Science, Yamashita et al. provide new insights into the factors that control this process in the male germline of Drosophila, identifying roles for the centrosomal protein Centrosomin and tumor suppressor homologs of the APC family.
Early propagation of energetic particles across the mean field in turbulent plasmas
Creators: name: Laitinen, T.
name: Dalla, S.
name: Marriott, D.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Space Physics (physics.space-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Propagation of energetic particles across the mean field direction in turbulent magnetic fields is often described as spatial diffusion. Recently, it has been suggested that initially the particles propagate systematically along meandering field lines, and only later reach the time-asymptotic diffusive cross-field propagation. In this paper, we analyse cross-field propagation of 1--100 MeV protons in composite 2D-slab turbulence superposed on a constant background magnetic field, using full-orbit particle simulations, to study the non-diffusive phase of particle propagation with a wide range of turbulence parameters. We show that the early-time non-diffusive propagation of the particles is consistent with particle propagation along turbulently meandering field lines. This results in a wide cross-field extent of the particles already at the initial arrival of particles to a given distance along the mean field direction, unlike when using spatial diffusion particle transport models. The cross-field extent of the particle distribution remains constant for up to tens of hours in turbulence environment consistent with the inner heliosphere during solar energetic particle events. Subsequently, the particles escape from their initial meandering field lines, and the particle propagation across the mean field reaches time-asymptotic diffusion. Our analysis shows that in order to understand solar energetic particle event origins, particle transport modelling must include non-diffusive particle propagation along meandering field lines.
description: 11 pages, 9 figures; Accepted for publication in MNRAS
STED nanoscopy in living cells using Fluorogen Activating Proteins.
Creators: name: Fitzpatrick, James
name: Yan, Qi
name: Sieber, Jochen J.
name: Dyba, Marcus
name: Schwarz, Ulf
name: Szent-Gyorgyi, Christopher
name: Woolford, Carol
name: Berget, Peter B.
name: Waggoner, Alan
name: Bruchez, Marcel
Publisher: name: Carnegie Mellon University
Year: 2009
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: We demonstrate the effectiveness of a genetically encoded Malachite Green (MG) binding fluorogen activating protein (FAP) for live cell stimulated emission depletion nanoscopy (STED). Both extracellular and intracellular FAPs were tested in living cells using fluorogens with either membrane expressed FAP or as an intracellular FAP-actin fusion. Structures with FWHM of 110-122nm were observed. Depletion data however suggests a resolution of 70nm with the given instrument.
Stable triplet of uracil-uracil basepairs in a small antisense RNA.
Creators: name: Yiping  Zhan
name: Rule, Gordon
Publisher: name: Carnegie Mellon University
Year: 2005
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The interaction between ant (antirepressor) mRNA and its antisense RNA, sar (small antisense RNA), is important in regulation of the development of bacteriophage P22. Sar is 68-69 nucleotides in length and is believed to consist of two hairpin structures separated by a small inter-hairpin region, followed by a short 3' tail [Schaefer and McClure RNA 1997, 3, 141-156]. A novel feature of the proposed secondary structure of the first hairpin is a extremely rare triple U:U base stack. Heteronuclear NMR studies presented here show that the first hairpin does not possess a unique structure in the absence of the second hairpin. However, it acquires a well-defined structure within full length sar. Remarkably, the triple U:U stack appears to be a stable feature of the first hairpin, regardless of the presence or absence of the second hairpin.
Extracting Meaningful Keywords from Patent Claims Item
Creators: name: Rossi, J.
Publisher: name: University of Amsterdam / Amsterdam University of Applied Sciences
Year: 2024
Subjects: Information and Computing Sciences

description: The search for prior art is crucial in patent application processing, it consists in retrieving other documents relevant to the invention of the application. Most methods feed a search engine with keywords that are extracted by frequency-analysis methods. We suggest and demonstrate a new method that relies on the way information is provided in patent claims.
title: ADCO, Grènetier de Cîteaux : comptes (1497-1504) (11 H 1172), f. 00104
Creators: name: de la Côte-d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2019
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: comptes
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Grènetier de Cîteaux : comptes (1497-1504), Archives départementales de la Côte-d'Or, (11 H 1172). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Grènetier de Cîteaux : comptes (1497-1504), Archives départementales de la Côte-d'Or, (11 H 1172), f. 00104, in Projet CBMA - Corpus Burgundiae Medii Aevi \[Ressource en ligne\], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Cosmic Supernova Rates and the Hubble Sequence
Creators: name: Calura, F.
name: Matteucci, F.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We compute the type Ia, Ib/c and II supernova (SN) rates as functions of the cosmic time for galaxies of different morphological types. We use four different chemical evolution models, each one reproducing the features of a particular morphological type: E/S0, S0a/b, Sbc/d and Irr galaxies. We essentially describe the Hubble sequence by means of decreasing efficiency of star formation and increasing infall timescale. These models are used to study the evolution of the SN rates per unit luminosity and per unit mass as functions of cosmic time and as functions of the Hubble type. Our results indicate that: (i) the observed increase of the SN rate per unit luminosity and unit mass from early to late galaxy types is accounted for by our models. Our explanation of this effect is related to the fact that the latest Hubble types have the highest star formation rate per unit mass; (ii) By adopting a Scalo (1986) initial mass function in spiral disks, we find that massive single stars ending their lives as Wolf-Rayet objects are not sufficient to account for the observed type Ib/c SN rate per unit mass. Less massive stars in close binary systems can give instead a significant contribution to the local Ib/c SN rates. On the other hand, with the assumption of a Salpeter (1955) IMF for all galaxy types, single massive WR stars are sufficient to account for the observed type Ib/c SN rate. (iii) Our models allow us to reproduce the observed type Ia SN rate density up to redshift z~1. We predict an increasing type Ia SN rate density with redshift, reaching a peak at redshift z >= 3, because of the contribution of massive spheroids.
description: ApJ, accepted for publication. 17 pages, 11 figures
The phantom menaced: constraints on low-energy effective ghosts
Creators: name: Cline, James M.
name: Jeon, Sangyong
name: Moore, Guy D.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: It has been suggested that a scalar field with negative kinetic energy, or ``ghost,'' could be the source of the observed late-time cosmological acceleration. Naively, such theories should be ruled out by the catastrophic quantum instability of the vacuum. We derive phenomenological bounds on the Lorentz-violating ultraviolet cutoff Lambda which must apply to low-energy effective theories of ghosts, in order to keep the instability at unobservable levels. Assuming only that ghosts interact at least gravitationally, we show that Lambda < 3 MeV for consistency with the cosmic gamma ray background. We also show that theories of ghosts with a Lorentz-conserving cutoff are completely excluded.
description: 4 pages, 2 figures; fixed references. Version to appear in Phys.Rev.D
Scalar absorption by charged rotating black holes
Creators: name: Leite, Luiz C. S.
name: Benone, Carolina L.
name: Crispino, Luís C. B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We compute numerically the absorption cross section of planar massless scalar waves impinging upon a Kerr-Newman black hole with different incidence angles. We investigate the influence of the black hole electric charge and angular momentum in the absorption spectrum, comparing our numerical computations with analytical results for the limits of high and low frequency.
description: Accepted for publication in Physical Review D
A Central Limit Theorem for non-overlapping return times
Creators: name: Johnson, Oliver
Publisher: name: arXiv
Year: 2005
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 94A17; 60F05; 62H20

description: Define the non-overlapping return time of a random process to be the number of blocks that we wait before a particular block reappears. We prove a Central Limit Theorem based on these return times. This result has applications to entropy estimation, and to the problem of determining if digits have come from an independent equidistribted sequence. In the case of an equidistributed sequence, we use an argument based on negative association to prove convergence under weaker conditions.
Additional file 3 of Sustained glymphatic transport and impaired drainage to the nasal cavity observed in multiciliated cell ciliopathies with hydrocephalus
Creators: name: Xue, Yuechuan
name: Gursky, Zachary
name: Monte, Brittany
name: Koundal, Sunil
name: Liu, Xiaodan
name: Lee, Hedok
name: Michurina, Tatyana V.
name: Mellanson, Kennelia A.
name: Zhao, Lucy
name: Nemajerova, Alice
name: Kahle, Kristopher T.
name: Takemaru, Ken-Ichi
name: Enikolopov, Grigori
name: Peunova, Natalia I.
name: Benveniste, Helene
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Hematology

description: Additional file 3: Table S2. Physiological variables during MRI scanning.
Stabilization and analysis of intron lariats in vivo.
Creators: name: Conklin, Jamie
name: Goldman, Aaron
name: Antonio-Javier Lopez
Publisher: name: Carnegie Mellon University
Year: 2005
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The analysis of lariats produced in vivo during pre-mRNA splicing is a powerful tool for elucidation of regulatory mechanisms and identification of natural recursive splicing events. Nevertheless, this analysis is technically challenging because lariats normally have short half-lives. With appropriate controls, RT-PCR amplification and sequencing of the region spanning the 2'-5' phosophodiester bond at the branch junction can be a sensitive and versatile method for lariat analysis. This approach can be facilitated and enhanced by reducing the activity of debranching enzyme (DBR) in order to stabilize lariats. We have generated a set of plasmids for dsRNA-mediated knockdown of DBR under diverse conditions in transgenic Drosophila and in cultured cells. We describe the use of these plasmids and protocols for lariat analysis. We have generated transgenic Drosophila strains carrying a GAL4-regulated RNAi construct that allows selective knockdown of DBR in specific tissues or developmental stages, using the large collection of available GAL4 expression lines. These strains should prove useful for detailed developmental analyses of alternative and recursive splicing and for genetic analyses of splicing factors. Similar approaches should be readily adaptable to other organisms.
Planetary nebulae abundances and stellar evolution
Creators: name: Pottasch, S. R.
name: Bernard-Salas, J.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A summary is given of planetary nebulae abundances from ISO measurements. It is shown that these nebulae show abundance gradients (with galactocentric distance), which in the case of neon, argon, sulfur and oxygen (with four exceptions) are the same as HII regions and early type star abundance gradients. The abundance of these elements predicted from these gradients at the distance of the Sun from the center are exactly the solar abundance. Sulfur is the exception to this; the reason for this is discussed. The higher solar neon abundance is confirmed; this is discussed in terms of the results of helioseismology. Evidence is presented for oxygen destruction via ON cycling having occurred in the progenitors of four planetary nebulae with bilobal structure. These progenitor stars had a high mass, probably greater than 5 solar masses. This is deduced from the high values of He/H and N/H found in these nebulae. Formation of nitrogen, helium and carbon are discussed. The high mass progenitors which showed oxygen destruction are shown to have probably destroyed carbon as well. This is probably the result of hot bottom burning.
description: 9 pages, 2 Tables, 8 figures, A&A in press
Levisticum officinale W. D J. Koch
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
Apiales
Apiaceae
Levisticum
Levisticum officinale

description: Ligusticum levisticum Linnaeus, Species Plantarum 1: 250. 1753.
"Habitat in Apenninis Liguriae." RCN: 2009.
 Lectotype (Reduron in Jarvis & al. in Taxon 55: 213. 2006): Herb. Clifford: 97, Ligusticum 2 (BM-000558301).
 Current name: Levisticum officinale W.D J. Koch (Apiaceae).
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 632, DOI: 10.5281/zenodo.291971
Baryon production from cluster hadronization
Creators: name: Gieseke, Stefan
name: Kirchgaeßer, Patrick
name: Plätzer, Simon
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present an extension to the colour reconnection model in the Monte-Carlo event generator Herwig to account for the production of baryons and compare it to a series of observables for soft physics. The new model is able to improve the description of charged-particle mutliplicities and hadron flavour observables in pp collisions
description: 13 pages; v3: updated to match journal version
Direct Solution of Renormalization Group Equations of QCD in $x-$space: NLO Implementations at Leading Twist
Creators: name: Cafarella, Alessandro
name: Coriano', Claudio
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We illustrate the implementation of a method based on the use of recursion relations in (Bjorken) $x-$space for the solution of the evolution equations of QCD for all the leading twist distributions. The algorithm has the advantage of being very fast. The implementation that we release is written in C and is performed to next-to-leading order in $α_s$.
description: 31 pages, 15 figs, replaced with revised final version, to be published by Comp. Phys. Comm
title: ADCO, Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Cart. 32 (G 136), 745 folios, f. 1186
Creators: name: de la Côte d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Archives départementales de la Côte-d'Or, Cart. 32 (G 136), 745 folios, f. 1186, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Archives départementales de la Côte-d'Or, Cart. 32 (G 136), 745 folios, f. 1186, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Quantum field theory treatment of magnetic effects on a system of free electrons
Creators: name: Verzegnassi, C.
name: Germano, R.
name: Kurian, P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The effects of a magnetic field on the energy and on the spin of free electrons are computed in the framework of quantum field theory. In the case of a constant moderate field and with relatively slow electrons, the derived formulae are particularly simple. A comparison with the approaches of classical physics and of quantum mechanics shows essential differences and important analogies. The relevance to the magnetic effects of the initial polarization components of the electron states and the possible existence of special values of these quantities are discussed in the final conclusions, which might be useful to explain recent experiments on quasi-free electrons in chiral systems in biology.
Mirror symmetry for Del Pezzo surfaces: Vanishing cycles and coherent sheaves
Creators: name: Auroux, Denis
name: Katzarkov, Ludmil
name: Orlov, Dmitri
Publisher: name: arXiv
Year: 2005
Subjects: subject: Algebraic Geometry (math.AG)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics

description: We study homological mirror symmetry for Del Pezzo surfaces and their mirror Landau-Ginzburg models. In particular, we show that the derived category of coherent sheaves on a Del Pezzo surface X_k obtained by blowing up CP^2 at k points is equivalent to the derived category of vanishing cycles of a certain elliptic fibration W_k:M_k\to\C with k+3 singular fibers, equipped with a suitable symplectic form. Moreover, we also show that this mirror correspondence between derived categories can be extended to noncommutative deformations of X_k, and give an explicit correspondence between the deformation parameters for X_k and the cohomology class [B+iω]\in H^2(M_k,C).
description: 40 pages, 9 figures
Src Regulates Sequence-Dependent Beta-2 Adrenergic Receptor Recycling via Cortactin Phosphorylation.
Creators: name: Vistein, Rachel
name: Manojkumar Puthenveedu
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The recycling of internalized signaling receptors, which has direct functional consequences, is subject to multiple sequence and biochemical requirements. Why signaling receptors recycle via a specialized pathway, unlike many other proteins that recycle by bulk, is a fundamental unanswered question. Here, we show that these specialized pathways allow selective control of signaling receptor recycling by heterologous signaling. Using assays to visualize receptor recycling in living cells, we show that the recycling of the beta-2 adrenergic receptor (B2AR), a prototypic signaling receptor, is regulated by Src family kinases. The target of Src is cortactin, an essential factor for B2AR sorting into specialized recycling microdomains on the endosome. Phosphorylation of a single cortactin residue, Y466, regulates the rate of fission of B2AR recycling vesicles from these microdomains and, therefore, the rate of delivery of B2AR to the cell surface. Together, our results indicate that actin-stabilized microdomains that mediate signaling receptor recycling can serve as a functional point of convergence for crosstalk between signaling pathways.
Data: video-recall methods paper
Creators: name: Grimminger, Angela
name: Buschmeier, Hendrik
name: Lazarov, Stefan
Publisher: name: OSF
Year: 2025

description: These data sheets were used for the studies describing the video-recall method applied in project A02 "Monitoring the understanding of explanations". All variables in the statistical datasheets, as well as the data annotations are described in a text files located in the provided folders.
Petroselinum
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
Apiales
Apiaceae
Petroselinum

description: Ligusticum peregrinum Linnaeus, Species Plantarum, ed. 2, 1: 360. 1762.
"Habitat in Lusitania." RCN: 2014.
Type not designated.
Original material: Herb. Linn. No. 353.7 (LINN).
 Current name:  Petroselinum sp.  (Apiaceae).
 Note: It appears that this name probably threatens Petroselinum crispum (Mill.) Fuss and is therefore a candidate for rejection.
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 632, DOI: 10.5281/zenodo.291971
Specific labeling of threonine methyl groups for NMR studies of protein-nucleic acid complexes.
Creators: name: Kaustubh Sinha
name: Jen-Jacobson, Linda
name: Rule, Gordon
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Specific (13)C labeling of Thr methyl groups has been accomplished via the growth of a standard laboratory strain of Escherichia coli on [2-(13)C]glycerol in the presence of deuterated isoketovalerate, Ile, and Ala. Diversion of the label from the Thr biosynthetic pathway is suppressed by including Lys, Met, and Ile in the growth medium. This method complements the repertoire of methyl labeling schemes for NMR structural and dynamic studies of proteins and is particularly useful for the study of nucleic acid binding proteins because of the high propensity of Thr residues at protein-DNA and -RNA interfaces.
The galaxy-galaxy lensing contribution to the cosmic shear two point function
Creators: name: Bridle, Sarah
name: Abdalla, Filipe B.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We note that galaxy-galaxy lensing by non-spherical galaxy halos produces a net anti-correlation between the shear of background galaxies and the ellipticity of foreground galaxies. This anti-correlation would contaminate the tomographic cosmic shear two point function if the effect were not taken into account. We compare the size of the galaxy-galaxy lensing contribution to the change in the cosmic shear two-point correlation function due to a change in the dark energy equation of state w of 1%. We find them comparable on scales
description: 5 pages and 4 figures. Replaced to match journal version
Signal coupling to embedded pitch adapters in silicon sensors
Creators: name: Artuso, Marina
name: Betancourt, Christopher
name: Bezshyiko, Iaroslava
name: Blusk, Steven
name: Bruendler, Ruth
name: Bugiel, Szymon
name: Dasgupta, Roma
name: Dendek, Adam
name: Dey, Biplab
name: Ely, Scott
name: Lionetto, Federica
name: Petruzzo, Marco
name: Polyakov, Ivan
name: Rudolph, Matthew
name: Schindler, Heinrich
name: Steinkamp, Olaf
name: Stone, Sheldon
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: We have examined the effects of embedded pitch adapters on signal formation in n-substrate silicon microstrip sensors with data from beam tests and simulation. According to simulation, the presence of the pitch adapter metal layer changes the electric field inside the sensor, resulting in slowed signal formation on the nearby strips and a pick-up effect on the pitch adapter. This can result in an inefficiency to detect particles passing through the pitch adapter region. All these effects have been observed in the beam test data.
Spatially restricted G protein-coupled receptor activity via divergent endocytic compartments.
Creators: name: Jean-Alphonse, Frederic
name: Bowersox, Shanna
name: Chen, Stanford
name: Beard, Gemma
name: Manojkumar Puthenveedu
name: Hanyaloglu, Aylin C.
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Postendocytic sorting of G protein-coupled receptors (GPCRs) is driven by their interactions between highly diverse receptor sequence motifs with their interacting proteins, such as postsynaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1), zonula occludens-1 protein (zo-1) (PDZ) domain proteins. However, whether these diverse interactions provide an underlying functional specificity, in addition to driving sorting, is unknown. Here we identify GPCRs that recycle via distinct PDZ ligand/PDZ protein pairs that exploit their recycling machinery primarily for targeted endosomal localization and signaling specificity. The luteinizing hormone receptor (LHR) and β2-adrenergic receptor (B2AR), two GPCRs sorted to the regulated recycling pathway, underwent divergent trafficking to distinct endosomal compartments. Unlike B2AR, which traffics to early endosomes (EE), LHR internalizes to distinct pre-early endosomes (pre-EEs) for its recycling. Pre-EE localization required interactions of the LHR C-terminal tail with the PDZ protein GAIP-interacting protein C terminus, inhibiting its traffic to EEs. Rerouting the LHR to EEs, or EE-localized GPCRs to pre-EEs, spatially reprograms MAPK signaling. Furthermore, LHR-mediated activation of MAPK signaling requires internalization and is maintained upon loss of the EE compartment. We propose that combinatorial specificity between GPCR sorting sequences and interacting proteins dictates an unprecedented spatiotemporal control in GPCR signal activity.
Additional file 4 of Sustained glymphatic transport and impaired drainage to the nasal cavity observed in multiciliated cell ciliopathies with hydrocephalus
Creators: name: Xue, Yuechuan
name: Gursky, Zachary
name: Monte, Brittany
name: Koundal, Sunil
name: Liu, Xiaodan
name: Lee, Hedok
name: Michurina, Tatyana V.
name: Mellanson, Kennelia A.
name: Zhao, Lucy
name: Nemajerova, Alice
name: Kahle, Kristopher T.
name: Takemaru, Ken-Ichi
name: Enikolopov, Grigori
name: Peunova, Natalia I.
name: Benveniste, Helene
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Hematology

description: Additional file 4: Figure S2. Varying degree of hydrocephalus in FOXJ1-Cre;CEP164fl/fl mice.
Electric Dipole Moments in the MSSM at Large tan(beta)
Creators: name: Demir, Durmus
name: Lebedev, Oleg
name: Olive, Keith A.
name: Pospelov, Maxim
name: Ritz, Adam
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Within the minimal supersymmetric standard model (MSSM), the large tan(beta) regime can lead to important modifications in the pattern of CP-violating sources contributing to low energy electric dipole moments (EDMs). In particular, four-fermion CP-violating interactions induced by Higgs exchange should be accounted for alongside the constituent EDMs of quarks and electrons. To this end, we present a comprehensive analysis of three low energy EDM observables - namely the EDMs of thallium, mercury and the neutron - at large tan(beta), in terms of one- and two-loop contributions to the constituent EDMs and four-fermion interactions. We concentrate on the constrained MSSM as well as the MSSM with non-universal Higgs masses, and include the CP-violating phases of mu and A. Our results indicate that the atomic EDMs receive significant corrections from four-fermion operators, especially when Im(A) is the only CP-violating source, whereas the neutron EDM remains relatively insensitive to these effects. As a consequence, in a large portion of the parameter space, one cannot infer a separate bound on the electron EDM via the experimental constraint on the thallium EDM. Furthermore, we find that the electron EDM can be greatly reduced due to the destructive interference of one- and two-loop contributions with the latter being dominated by virtual staus.
description: 39 pages, 17 figures
Coupling Brain-Tumor Biophysical Models and Diffeomorphic Image Registration
Creators: name: Scheufele, Klaudius
name: Mang, Andreas
name: Gholami, Amir
name: Davatzikos, Christos
name: Biros, George
name: Mehl, Miriam
Publisher: name: arXiv
Year: 2017
Subjects: subject: Medical Physics (physics.med-ph)
subject: Image and Video Processing (eess.IV)
subject: Optimization and Control (math.OC)
subject: Tissues and Organs (q-bio.TO)
subject: FOS: Physical sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Mathematics
subject: FOS: Biological sciences
subject: 49K20, 49M15, 35K57, 65K10, 68W10

description: We present the SIBIA (Scalable Integrated Biophysics-based Image Analysis) framework for joint image registration and biophysical inversion and we apply it to analyse MR images of glioblastomas (primary brain tumors). In particular, we consider the following problem. Given the segmentation of a normal brain MRI and the segmentation of a cancer patient MRI, we wish to determine tumor growth parameters and a registration map so that if we "grow a tumor" (using our tumor model) in the normal segmented image and then register it to the patient segmented image, then the registration mismatch is as small as possible. We call this "the coupled problem" because it two-way couples the biophysical inversion and registration problems. In the image registration step we solve a large-deformation diffeomorphic registration problem parameterized by an Eulerian velocity field. In the biophysical inversion step we estimate parameters in a reaction-diffusion tumor growth model that is formulated as a partial differential equation. In this paper, our contributions are the introduction of a PDE-constrained optimization formulation of the coupled problem, the derivation of the optimality conditions, and the derivation of a Picard iterative scheme for the solution of the coupled problem. In addition, we perform several tests to experimentally assess the performance of our method on synthetic and clinical datasets. We demonstrate the convergence of the SIBIA optimization solver in different usage scenarios. We demonstrate that we can accurately solve the coupled problem in three dimensions ($256^3$ resolution) in a few minutes using 11 dual-x86 nodes. Also, we demonstrate that, with our coupled approach, we can successfully register normal MRI to tumor-bearing MRI while obtaining Dice coefficients that match those achieved when registering of normal-to-normal MRI.
description: 38 pages, 19 figures