cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Where do I come from? Phylogenetic analysis of Bursatella leachii Blainville, 1817 (Mollusca: Gastropoda: Heterobranchia) from the Catalonian coast (NE Spain)
Creators: name: CÓRDOBA GONZÁLEZ, Darío
name: ENGUÍDANOS, Alba
name: VALDÉS, Ángel
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: Climate change and other human activities have contributed to the dispersal of species from tropical to temperate waters. This is the case of the sea hare Bursatella leachii, a species of unknown type locality, considered pantropical, which adapts very well to shallow bays and the less favorable conditions within ports and marinas. This species was first reported in the Mediterranean Sea in the 1940s, with increasing observation records ever since. The most accepted idea, based on molecular data, is that this species entered the Mediterranean through the Strait of Gibraltar and not through the Suez Canal (Lessepsian migration) as postulated in some previous works. To confirm these ideas, we collected B. leachii specimens from two locations (Delta del Ebro, Tarragona and Fòrum bathing area, Barcelona) on the coast of Catalonia, Spain (NW Mediterranean) and carried out both ML and Bayesian molecular analysis (MrBayes), in order to compare their sequences with specimens from the Atlantic (East and West), Indo-Pacific and other areas of the Mediterranean, obtained from GenBank; the morphology of different species of the genus was also compared. Our results show that specimens from Catalonia share haplotypes with specimens from both shores of the Atlantic (West and East) and from other locations in the Mediterranean Sea, but not with those from the Indo-Pacific even though all B. leachii from the different regions are morphologically the same. This confirms the hypothesis that B. leachii entered the Mediterranean Sea through the Strait of Gibraltar helped by favorable conditions such as warm currents, abundance of food and the adaptability of the larvae of the species, and not from the Red Sea by Lesepsian migration. It also indicates that the Atlantic Ocean is not a geographical barrier for the different species, because the larvae of B. leachii, being planktonic, can cross the Strait of Gibraltar and reach the Mediterranean Sea helped by warm currents such as the Algerian Current.
Additional file 1 of Translational development of ABCB5+ dermal mesenchymal stem cells for therapeutic induction of angiogenesis in non-healing diabetic foot ulcers
Creators: name: Kerstan, Andreas
name: Dieter, Kathrin
name: Niebergall-Roth, Elke
name: Klingele, Sabrina
name: Jünger, Michael
name: Hasslacher, Christoph
name: Daeschlein, Georg
name: Stemler, Lutz
name: Meyer-Pannwitt, Ulrich
name: Schubert, Kristin
name: Klausmann, Gerhard
name: Raab, Titus
name: Goebeler, Matthias
name: Kraft, Korinna
name: Esterlechner, Jasmina
name: Schröder, Hannes M.
name: Sadeghi, Samar
name: Ballikaya, Seda
name: Gasser, Martin
name: Waaga-Gasser, Ana M.
name: Murphy, George F.
name: Orgill, Dennis P.
name: Frank, Natasha Y.
name: Ganss, Christoph
name: Scharffetter-Kochanek, Karin
name: Frank, Markus H.
name: Kluth, Mark A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Table S1. Reported healing failure rates of diabetic foot ulcers. Table S2. Antibodies used for immunofluorescence evaluation. Table S3. Primers. Table S4. ABCB5+ MSC product release data. Table S5. LDPI measurements. Table S6. CD31 expression in the ischemic thigh muscle of OF1 mice with surgically induced hindlimb ischemia treated with vehicle or ABCB5+ MSCs. Table S7. Absolute wound surface area reduction from baseline by visit. Table S8. Patients with complete wound closure and with ≥30% wound surface area reduction by visit. Table S9. Wound exudation by visit. Table S10. Pain score by visit. Table S11. Quality of life scores by visit. Table S12. Serious treatment-emergent adverse events. Table S13. Vital signs. Table S14. Changes in physical examination findings from screening visit. Table S15. Controlled clinical trials evaluating the efficacy of cell-based adjunctive strategies to treat diabetic foot ulcers.
On a locally compact monoid of cofinite partial isometries of $\mathbb{N}$ with adjoined zero
Creators: name: Gutik, Oleg
name: Khylynskyi, Pavlo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Group Theory (math.GR)
subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 20M18, 20M20, 20M30, 22A15, 54A10, 54D45

description: Let $\mathscr{C}_\mathbb{N}$ be a monoid which is generated by the partial shift $α\colon n\mapsto n+1$ of the set of positive integers $\mathbb{N}$ and its inverse partial shift $β\colon n+1\mapsto n$. In this paper we prove that if $S$ is a submonoid of the monoid $\mathbf{I}\mathbb{N}_{\infty}$ of all partial cofinite isometries of positive integers which contains $\mathscr{C}_\mathbb{N}$ as a submonoid then every Hausdorff locally compact shift-continuous topology on $S$ with adjoined zero is either compact or discrete. Also we show that the similar statement holds for a locally compact semitopological semigroup $S$ with an adjoined compact ideal.
description: 15 pages. arXiv admin note: text overlap with arXiv:2104.14149, arXiv:2008.03159
Spin and lattice excitations of a BiFeO3 thin film and ceramics
Creators: name: Skiadopoulou, S.
name: Goian, V.
name: Kadlec, C.
name: Kadlec, F.
name: Bai, X. F.
name: Infante, I. C.
name: Dkhil, B.
name: Adamo, C.
name: Schlom, D. G.
name: Kamba, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present a comprehensive study of polar and magnetic excitations in BiFeO3 ceramics and a thin film epitaxially grown on an orthorhombic (110) TbScO3 substrate. Infrared reflectivity spectroscopy was performed at temperatures from 5 to 900 K for the ceramics and below room temperature for the thin film. All 13 polar phonons allowed by the factor-group analysis were observed in theceramic samples. The thin-film spectra revealed 12 phonon modes only and an additional weak excitation, probably of spin origin. On heating towards the ferroelectric phase transition near 1100 K, some phonons soften, leading to an increase in the static permittivity. In the ceramics, terahertz transmission spectra show five low-energy magnetic excitations including two which were not previously known to be infrared active; at 5 K, their frequencies are 53 and 56 cm-1. Heating induces softening of all magnetic modes. At a temperature of 5 K, applying an external magnetic field of up to 7 T irreversibly alters the intensities of some of these modes. The frequencies of the observed spin excitations provide support for the recently developed complex model of magnetic interactions in BiFeO3 (R.S. Fishman, Phys. Rev. B 87, 224419 (2013)). The simultaneous infrared and Raman activity of the spin excitations is consistent with their assignment to electromagnons.
The coupling of α 6 β 4 integrin to Ras-MAP kinase pathways mediated by Shc controls keratinocyte proliferation
Creators: name: Murgia, Chiara
name: Blumemberg, Miroslav
name: Der, Channing J.
name: Westwick, John K.
name: Giancotti, Filippo G.
name: Curatola, Anna Maria
name: Wary, Kishore K.
name: Pepe, Angela
name: Mainiero, Fabrizio
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1997

description: The signaling pathways linking integrins to nuclear events are incompletely understood. We have examined intracellular signaling by the alpha6beta4 integrin, a laminin receptor expressed in basal keratinocytes and other cells. Ligation of alpha6beta4 in primary human keratinocytes caused tyrosine phosphorylation of Shc, recruitment of Grb2, activation of Ras and stimulation of the MAP kinases Erk and Jnk. In contrast, ligation of the laminin- and collagen-binding integrins alpha3beta1 and alpha2beta1 did not cause these events. While the stimulation of Erk by alpha6beta4 was suppressed by dominant-negative Shc, Ras and RhoA, the activation of Jnk was inhibited by dominant-negative Ras and Rac1 and by the phosphoinositide 3-kinase inhibitor Wortmannin. Adhesion mediated by alpha6beta4 induced transcription from the Fos serum response element and promoted cell cycle progression in response to mitogens. In contrast, alpha3beta1- and alpha2beta1-dependent adhesion did not induce these events. These findings suggest that the coupling of alpha6beta4 integrin to the control of cell cycle progression mediated by Shc regulates the proliferation of basal keratinocytes and possibly other cells which are in contact with the basement membrane in vivo.
Controlled domain wall pinning in ferromagnetic nanowire by nanoparticles stray fields
Creators: name: Mironov, V. L.
name: Ermolaeva, O. L.
name: Skorohodov, E. V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We report the results of experimental investigations of controlled domain wall (DW) pinning in a ferromagnetic nanowire (NW) by stray fields of two uniformly magnetized bistable ferromagnetic nanoparticles (NPs) placed on either side of the NW and elongated parallel to the NW axis. We show by magnetic force microscopy measurements that DW pinning strength essentially depends on the orientation of the NP magnetic moments relative to the NW magnetization and can reach 20 mT. We also performed micromagnetic simulations confirming the influence of the magnetostatic interaction of the DW with the NP stray fields on the pinning strength. The possible realization of logic cell with switchable logic function is discussed.
Detecting Real-World Influence Through Twitter
Creators: name: Cossu, Jean-Val{è}re
name: Dugu{é}, Nicolas
name: Labatut, Vincent
Publisher: name: arXiv
Year: 2015
Subjects: subject: Social and Information Networks (cs.SI)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: In this paper, we investigate the issue of detecting the real-life influence of people based on their Twitter account. We propose an overview of common Twitter features used to characterize such accounts and their activity, and show that these are inefficient in this context. In particular, retweets and followers numbers, and Klout score are not relevant to our analysis. We thus propose several Machine Learning approaches based on Natural Language Processing and Social Network Analysis to label Twitter users as Influencers or not. We also rank them according to a predicted influence level. Our proposals are evaluated over the CLEF RepLab 2014 dataset, and outmatch state-of-the-art ranking methods.
Additional file 2 of Translational development of ABCB5+ dermal mesenchymal stem cells for therapeutic induction of angiogenesis in non-healing diabetic foot ulcers
Creators: name: Kerstan, Andreas
name: Dieter, Kathrin
name: Niebergall-Roth, Elke
name: Klingele, Sabrina
name: Jünger, Michael
name: Hasslacher, Christoph
name: Daeschlein, Georg
name: Stemler, Lutz
name: Meyer-Pannwitt, Ulrich
name: Schubert, Kristin
name: Klausmann, Gerhard
name: Raab, Titus
name: Goebeler, Matthias
name: Kraft, Korinna
name: Esterlechner, Jasmina
name: Schröder, Hannes M.
name: Sadeghi, Samar
name: Ballikaya, Seda
name: Gasser, Martin
name: Waaga-Gasser, Ana M.
name: Murphy, George F.
name: Orgill, Dennis P.
name: Frank, Natasha Y.
name: Ganss, Christoph
name: Scharffetter-Kochanek, Karin
name: Frank, Markus H.
name: Kluth, Mark A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Methods S1. Determination of the wound surface area.
3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae's Inner Colliding Winds
Creators: name: Madura, Thomas I.
name: Clementel, Nicola
name: Gull, Theodore R.
name: Kruip, Chael J. H.
name: Paardekooper, Jan-Pieter
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 M_Sun), highly eccentric (e ~ 0.9) binary star system Eta Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF journal publication and the benefits of using 3D visualization and 3D printing as tools to analyze data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics (SPH) simulations of Eta Carinae's inner (r ~ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (phi ~ 1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the fast (3000 km/s), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.
description: 15 pages, 14 figures, 12 interactive 3D figures, 1 embedded movie. Accepted for publication in MNRAS. To view 3D interactive figures and movie, use Adobe PDF viewer
String duality transformations in $f(R)$ gravity from Noether symmetry approach
Creators: name: Capozziello, Salvatore
name: Gionti, S. J. Gabriele
name: Vernieri, Daniele
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We select $f(R)$ gravity models that undergo scale factor duality transformations. As a starting point, we consider the tree-level effective gravitational action of bosonic String Theory coupled with the dilaton field. This theory inherits the Busher's duality of its parent String Theory. Using conformal transformations of the metric tensor, it is possible to map the tree-level dilaton-graviton string effective action into $f(R)$ gravity, relating the dilaton field to the Ricci scalar curvature. Furthermore, the duality can be framed under the standard of Noether symmetries and exact cosmological solutions are derived. Using suitable changes of variables, the string-based $f(R)$ Lagrangians are shown in cases where the duality transformation becomes a parity inversion.
description: v1: 13 pages; v2: minor rephrasings, published version
Neutral-current Hall effects in disordered graphene
Creators: name: Wang, Yilin
name: Cai, Xinghan
name: Reutt-Robey, Janice
name: Fuhrer, Michael S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A non-local Hall bar geometry is used to detect neutral-current Hall effects in graphene on silicon dioxide. Disorder is tuned by the addition of Au or Ir adatoms in ultra-high vacuum. A reproducible neutral-current Hall effect is found in both as-fabricated and adatom-decorated graphene. The Hall angle exhibits a complex but reproducible dependence on gate voltage and disorder, and notably breaks electron-hole symmetry. An exponential dependence on length between Hall and inverse-Hall probes indicates a neutral current relaxation length of approximately 300 nm. The short relaxation length and lack of precession in parallel magnetic field suggest that the neutral currents are valley currents. The near lack of temperature dependence from 7-300 K is unprecedented and promising for using controlled disorder for room temperature neutral-current electronics.
Angiotensin II stimulates ERK via two pathways in epithelial cells: protein kinase C suppresses a G-protein coupled receptor-EGF receptor transactivation pathway
Creators: name: Graves, Lee M.
name: Earp, H. Shelton
name: Li, Xiong
name: Lee, June Weon
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: In GN4 rat liver epithelial cells, angiotensin II (Ang II) produces intracellular calcium and protein kinase C (PKC) signals and stimulates ERK and JNK activity. JNK activation appears to be mediated by a calcium-dependent tyrosine kinase (CADTK). To define the ERK pathway, we established GN4 cells expressing an inhibitory Ras(N17). Induction of Ras(N17) blocked EGF- but not Ang II- or phorbol ester (TPA)-dependent ERK activation. In control cells, Ang II and TPA produced minimal increases in Ras-GTP level and Raf kinase activity. PKC depletion by chronic TPA exposure abolished TPA-dependent ERK activation but failed to diminish the effect of Ang II. In PKC-depleted cells, Ang II increased Ras-GTP level and activated Raf and ERK in a Ras-dependent manner. In PKC depleted cells, Ang II stimulated Shc and Cbl tyrosine phosphorylation, suggesting that without PKC, Ang II activates another tyrosine kinase. PKC-depletion did not alter Ang II-dependent tyrosine phosphorylation or activity of p125(FAK), CADTK, Fyn or Src, but PKC depletion or incubation with GF109203X resulted in Ang II-dependent EGF receptor tyrosine phosphorylation. In PKC-depleted cells, EGF receptor-specific tyrosine kinase inhibitors blocked Ang II-dependent EGF receptor and Cbl tyrosine phosphorylation, and ERK activation. In summary, Ang II can activate ERK via two pathways; the latent EGF receptor, Ras-dependent pathway is equipotent to the Ras-independent pathway, but is masked by PKC action. The prominence of this G-protein coupled receptor to EGF receptor pathway may vary between cell types depending upon modifiers such as PKC.
Supplemental Material from Fitness consequences of a non-recombining sex-ratio drive chromosome can explain its prevalence in the wild
Creators: name: Dyer, Kelly A.
name: Hall, David W.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: All ESM
Additional file 3 of Translational development of ABCB5+ dermal mesenchymal stem cells for therapeutic induction of angiogenesis in non-healing diabetic foot ulcers
Creators: name: Kerstan, Andreas
name: Dieter, Kathrin
name: Niebergall-Roth, Elke
name: Klingele, Sabrina
name: Jünger, Michael
name: Hasslacher, Christoph
name: Daeschlein, Georg
name: Stemler, Lutz
name: Meyer-Pannwitt, Ulrich
name: Schubert, Kristin
name: Klausmann, Gerhard
name: Raab, Titus
name: Goebeler, Matthias
name: Kraft, Korinna
name: Esterlechner, Jasmina
name: Schröder, Hannes M.
name: Sadeghi, Samar
name: Ballikaya, Seda
name: Gasser, Martin
name: Waaga-Gasser, Ana M.
name: Murphy, George F.
name: Orgill, Dennis P.
name: Frank, Natasha Y.
name: Ganss, Christoph
name: Scharffetter-Kochanek, Karin
name: Frank, Markus H.
name: Kluth, Mark A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3. Figure S1. Validation of the rabbit anti-human/mouse CD31 antibody. Figure S2. Blood flow recovery following surgically indcued hindlimb ischemia in OF1 mice.
Entanglement, noise, and the cumulant expansion
Creators: name: Drut, Joaquín E.
name: Porter, William J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Lattice (hep-lat)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We put forward a simpler and improved variation of a recently proposed method to overcome the signal-to-noise problem found in Monte Carlo calculations of the entanglement entropy of interacting fermions. The present method takes advantage of the approximate lognormal distributions that characterize the signal-to-noise properties of other approaches. In addition, we show that a simple rewriting of the formalism allows circumvention of the inversion of the restricted one-body density matrix in the calculation of the $n$-th Rényi entanglement entropy for $n>2$. We test our technique by implementing it in combination with the hybrid Monte Carlo algorithm and calculating the $n=2,3,4, \dots, 10$ Rényi entropies of the 1D attractive Hubbard model. We use that data to extrapolate to the von Neumann ($n=1$) and $n\to\infty$ cases.
description: Significantly expanded manuscript; improved presentation, new data and figures, new approach to the calculation of $n>2$ R\'enyi entropies. 8 pages, 8 figures
Evidence for a physical interaction between the Escherichia coli methyl-directed mismatch repair proteins MutL and UvrD
Creators: name: W.matson, Steven
name: Jordan, J. Ryan
name: Hall, Mark C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: UvrD (DNA helicase II) is an essential component of two major DNA repair pathways in Escherichia coli: methyl-directed mismatch repair and UvrABC-mediated nucleotide excision repair. In addition, it has an undefined role in the RecF recombination pathway and possibly in replication. In an effort to better understand the role of UvrD in these various aspects of DNA metabolism, a yeast two-hybrid screen was used to search for interacting protein partners. Screening of an E.coli genomic library revealed a potential interaction between UvrD and MutL, a component of the methyl-directed mismatch repair pathway. The interaction was confirmed by affinity chromatography using purified proteins. Deletion analysis demonstrated that the C-terminal 218 amino acids (residues 398-615) of MutL were sufficient to produce the two-hybrid interaction with UvrD. On the other hand, both the N- and C-termini of UvrD were required for interaction with MutL. The implications of this interaction for the mismatch repair mechanism are discussed.
First record of the zoanthid Savalia savaglia (Bertoloni, 1819) on the Atlantic French coast of the Bay of Biscay (north-east Atlantic)
Creators: name: CASAMAJOR, Marie-Noëlle De
name: SARTORETTO, Stéphane
name: ALTUNA, Alvaro
name: GOUILLIEUX, Benoît
name: RAVEL, Christophe
name: BUJAN, Stéphane
name: DEVAUX, Ludovic
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: This work aims to report the presence of Savalia savaglia in the Bay of Biscay on the French Basque coast. This is the most northerly observation reported on the north-east Atlantic area and the first for the French Atlantic coast. Colonies were observed on a remarkable circalittoral habitat with the engineer species Paramuricea cf. grayi (Johnson, 1861), at a depth of about 35 m, also previously unknown in this area. A description of the colonies is given as well as the environmental parameters that condition their development. This work details the distribution area of this species in the north-east Atlantic and contributes to the conservation issues of the marine protected area "Rocky Basque coast and offshore extension". Furthermore, it is suggested that S. savalia be included in the list of protected species of the Atlantic coast in the same way as in the Mediterranean Sea.
The Black Ring is Unstable
Creators: name: Santos, Jorge E.
name: Way, Benson
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study non-axisymmetric linearised gravitational perturbations of the Emparan-Reall black ring using numerical methods. We find an unstable mode whose onset lies within the "fat" branch of the black ring and continues into the "thin" branch. Together with previous results using Penrose inequalities that fat black rings are unstable, this provides numerical evidence that the entire black ring family is unstable.
description: 10 pages, 6 figures
Yeast PKA represses Msn2p/Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation
Creators: name: Ward, Mary P.
name: Smith, Angela
name: Garrett, Stephen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Yeast cAMP-dependent protein kinase (PKA) activity is essential for growth and antagonizes induction of the general stress response as well as accumulation of glycogen stores. Previous studies have suggested that the PKA effects on the two latter processes result in part from transcription repression. Here we show that transcription derepression that accompanies PKA depletion is dependent upon the presence of two redundant Zn2+-finger transcription factors, Msn2p and Msn4p. The Msn2p and Msn4p proteins were shown previously to act as positive transcriptional factors in the stress response pathway, and our results suggest that Msn2p and Msn4p also mediate PKA-dependent effects on stress response as well as glycogen accumulation genes. Interestingly, PKA activity is dispensable in a strain lacking Msn2p and Msn4p activity. Thus, Msn2p and Msn4p may antagonize PKAdependent growth by stimulating expression of genes that inhibit growth. In agreement with this model, Msn2p/Msn4p function is required for expression of a gene, YAK1, previously shown to antagonize PKA-dependent growth. These results suggest that Msn2p/Msn4p-dependent gene expression may account for all, or at least most, of the pleiotropic effects of yeast PKA, including growth regulation, response to stress and carbohydrate store accumulation.
Identification and count of immune cells of the marine gastropod Phorcus lineatus (Da Costa, 1778) from the El Jadida coastline (Atlantic coast, Morocco)
Creators: name: FAHMI, Fatiha
name: SIF, Jamila
name: ROUHI, Abdelali
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: The aim of the present work is the identification and counting of the different hemocytes composing the hemolymph of the marine gastropod Phorcus lineatus from the coast of El Jadida (Morocco). The originality of this work lies in the very little biological data on this species which is of great ecological importance and in the potential use of these results in future studies. For this purpose, two sampling sites with differing levels of pollution (Haouzia & Jorf-Lasfar) were selected. Microscopic observation of hemolymph smears allows the identification of three cell types: hyalinocytes, granulocytes and undifferentiated cells. Hyalinocytes have a cytoplasm without granules and represent about 80% of hemocytes. Granulocytes were less abundant (Haouzia: 12.96%; JorfLasfar: 14.52%) and contained numerous granules in the cytoplasm. Undifferentiated cells were distinguished by their small size and reduced cytoplasm, and represent less than 10% of the circulating hemocytes. In Haouzia, the total number of hemocytes (THN) in the hemolymph of Phorcus lineatus was 4.01 106 ± 2.49 105 cells.ml-1, whereas in Jorf-Lasfar, it was 4.27 106 ± 5.18 105 cells.ml-1. THN was not significantly different between both study sites.
Primordial Black Hole Dark Matter in the Context of Extra Dimensions
Creators: name: Friedlander, Avi
name: Mack, Katherine J.
name: Schon, Sarah
name: Song, Ningqiang
name: Vincent, Aaron C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Theories of large extra dimensions (LEDs) such as the Arkani-Hamed, Dimopoulos & Dvali scenario predict a "true" Planck scale $M_\star$ near the TeV scale, while the observed $M_{pl}$ is due to the geometric effect of compact extra dimensions. These theories allow for the creation of primordial black holes (PBHs) in the early Universe, from the collisional formation and subsequent accretion of black holes in the high-temperature plasma, leading to a novel cold dark matter (sub)component. Because of their existence in a higher-dimensional space, the usual relationship between mass, radius and temperature is modified, leading to distinct behaviour with respect to their 4-dimensional counterparts. Here, we derive the cosmological creation and evolution of such PBH candidates, including the greybody factors describing their evaporation, and obtain limits on LED PBHs from direct observation of evaporation products, effects on big bang nucleosynthesis, and the cosmic microwave background angular power spectrum. Our limits cover scenarios of 2 to 6 extra dimensions, and PBH masses ranging from 10 to $10^{21}$ g. We find that for two extra dimensions, LED PBHs represent a viable dark matter candidate with a range of possible black hole masses between $10^{17}$ and $10^{23}$ g depending on the Planck scale and reheating temperature. For $M_\star = 10$ TeV, this corresponds to PBH dark matter with a mass of $M \simeq 10^{21}$ g, unconstrained by current observations. We further refine and update constraints on "ordinary" four-dimension black holes.
description: 47 pages, 22 figures. Code available at https://github.com/songningqiang/CosmoLED. Corrected factor in Eq. 26, small changes to Fig. 4 and 5. Corrected values in Table II
Chaetonema cycloamphidum sp. nov. (Nematoda: Anoplostomatidae) from the Bohai Sea, China
Creators: name: GENG, Chunxiao
name: HUANG, Yong
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: A new species of free-living marine nematode belonging to genus Chaetonema is described from Tianjin coast along the Bohai Sea, China. Chaetonema cycloamphidum sp. nov. is characterized by its relatively smaller body size in the genus, narrow head with cephalic capsule, six outer labial setae unequal with four longer ones (3.8 head diameters) and two shorter ones (2 head diameters), amphidial fovea circular in males, buccal cavity cup-shaped without teeth, spicule arcuated with expanded proximal end and tapered distal end, gubernaculum plate-like with curved proximal end, a small ventral precloacal seta instead of precloacal supplement. The new species can easily be distinguished from its congeners by circular amphidial fovea, unequal outer labial setae and different shape of spicule and gubernaculum. Updated dichotomous key for the valid species of genus Chaetonema is given.
Supplementary Methods from Fungicide suppression of flight performance in the honeybee (Apis mellifera) and its amelioration by quercetin.
Creators: name: Ling-Hsiu Liao
name: Wen-Yen Wu
name: Dad, Azra
name: Berenbaum, May R.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: As a managed agricultural pollinator, the western honeybee Apis mellifera frequently encounters agrochemicals as contaminants of nectar and pollen. One such contaminant, the fungicide boscalid, is applied at bloom in orchards for fungal floral pathogen control. As an inhibitor of complex II in the mitochondrial electron transport chain of fungi, boscalid can potentially interfere with high energy-demanding activities of bees, including flight. We designed an indoor flight treadmill to evaluate impacts of ingesting boscalid and/or quercetin, a ubiquitous phytochemical in bee food that also affects mitochondrial respiration. Boscalid reduced the wingbeat frequencies of foragers during flight but did not alter the duration of flight. At the colony level, boscalid ingestion may thereby affect overall health by reducing forager efficiency. The consumption of quercetin, by contrast, led to higher adenosine triphosphate levels in flight muscles and a higher wingbeat frequency. Consuming the two compounds together increased wingbeat frequency, demonstrating a hitherto unrecognized mechanism by which dietary phytochemicals may act to ameliorate toxic effects of pesticides to promote honeybee health. In carrying out this work, we also introduce two methodological improvements for use in testing for pesticide effects on flight capacity—a ‘force-feeding’ to standardize flight fuel supply and a novel indoor flight treadmill.
Leptogenesis in Majoron Models without Domain Walls
Creators: name: Brune, Tim
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The emergence of domain walls is a well-known problem in Majoron models for neutrino mass generation. Here, we present extensions of the Majoron model by right-handed doublets and triplets that prevent domain walls from arising. These extensions are highly interesting in the context of Leptogenesis as they impact the conversion of a lepton asymmetry to a baryon asymmetry by Sphaleron processes.
description: replaced to match published version
Asymptotic behaviors of convolution powers of the Riemann zeta distribution
Creators: name: Aoyama, Takahiro
name: Namba, Ryuya
name: Ota, Koki
Publisher: name: arXiv
Year: 2022
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: Primary 60E, Secondary 11M

description: In probability theory, there exist discrete and continuous distributions. Generally speaking, we do not have sufficient kinds and properties of discrete ones compared to the continuous ones. In this paper, we treat the Riemann zeta distribution as a representative of few known discrete distributions with infinite supports. Some asymptotic behaviors of convolution powers of the Riemann zeta distribution are discussed.
description: 12 pages
Supplementary Methods from Fungicide suppression of flight performance in the honeybee (Apis mellifera) and its amelioration by quercetin
Creators: name: Ling-Hsiu Liao
name: Wen-Yen Wu
name: Dad, Azra
name: Berenbaum, May R.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Ecology
subject: 60801 Animal Behaviour

description: As a managed agricultural pollinator, the western honeybee Apis mellifera frequently encounters agrochemicals as contaminants of nectar and pollen. One such contaminant, the fungicide boscalid, is applied at bloom in orchards for fungal floral pathogen control. As an inhibitor of complex II in the mitochondrial electron transport chain of fungi, boscalid can potentially interfere with high energy-demanding activities of bees, including flight. We designed an indoor flight treadmill to evaluate impacts of ingesting boscalid and/or quercetin, a ubiquitous phytochemical in bee food that also affects mitochondrial respiration. Boscalid reduced the wingbeat frequencies of foragers during flight but did not alter the duration of flight. At the colony level, boscalid ingestion may thereby affect overall health by reducing forager efficiency. The consumption of quercetin, by contrast, led to higher adenosine triphosphate levels in flight muscles and a higher wingbeat frequency. Consuming the two compounds together increased wingbeat frequency, demonstrating a hitherto unrecognized mechanism by which dietary phytochemicals may act to ameliorate toxic effects of pesticides to promote honeybee health. In carrying out this work, we also introduce two methodological improvements for use in testing for pesticide effects on flight capacity—a ‘force-feeding’ to standardize flight fuel supply and a novel indoor flight treadmill.
Some histological data on the teeth organisation of Muraena helena Linnaeus, 1758 (Teleostei: Anguilliformes: Muraenidae)
Creators: name: SALLAMI, Balkis
name: MEUNIER, F.J.
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: The moray eel, Muraena helena, is a predatory fish that has lightly curved caniniform teeth. The teeth and the bony tissues of the jaws are studied through sections of undecalcified lower jaws. Teeth are constituted of a cone of orthodentine with a thin external layer of enameloid that is distinctly thicker at its apex. The dentinous walls of the pulp cavity are perfectly regular; they do not show folds in the pulp cavity, as opposed to some other predatory teleosts. The bony tissues show imbedded osteocytes characterized by typical multiramified osteocytic canalicles. We have also observed numerous specific tubules topped by an osteocyte, and crossing the primary bony layers orthogonally.
title: Prüfbericht G 2250 : Spritzeinrichtung mit unbemanntem Luftfahrzeug (UAV) Type Agrotop „iSDU“; Anerkannt als geeignet für das Spritzen/Sprühen im Weinbau (geprüft mit Multikopter EVO-X8)
Creators: name: JKI-Institut Für Anwendungstechnik Im Pflanzenschutz
Publisher: name: Bundesbehörden und Einrichtungen im Geschäftsbereich des Bundesministeriums für Ernährung und Landwirtschaft (BMEL)
Year: 2022
Subjects: subject: 630

description: Geräteprüfberichte des JKI
Supplementary Material from Machine-learned patterns suggest that diversification drives economic development.
Creators: name: Brummitt, Charles D.
name: Gómez-Liévano, Andrés
name: Hausmann, Ricardo
name: Bonds, Matthew H.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 60199 Biochemistry and Cell Biology not elsewhere classified
subject: 69999 Biological Sciences not elsewhere classified

description: Document with details on related literature, preprocessing the data, correlations among various indicators, and results of the model
On the double zeros of a partial theta function
Creators: name: Kostov, Vladimir Petrov
Publisher: name: arXiv
Year: 2015
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: The series $θ(q,x):=\sum _{j=0}^{\infty}q^{j(j+1)/2}x^j$ converges for $q\in [0,1)$, $x\in \mathbb{R}$, and defines a {\em partial theta function}. For any fixed $q\in (0,1)$ it has infinitely many negative zeros. For $q$ taking one of the {\em spectral} values $\tilde{q}_1$, $\tilde{q}_2$, $\ldots$ (where $0.3092493386\ldots =\tilde{q}_1
description: 1 figure
Tunable spin-polaron state in a singly clamped semiconducting carbon nanotube
Creators: name: Pistolesi, F.
name: Shekhter, R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We consider a semiconducting carbon nanotube (CNT) laying on a ferromagnetic insulating sub-strate with one end depassing the substrate and suspended over a metallic gate. We assume that the polarised substrate induces an exchange interaction acting as a local magnetic field for the electrons in the non-suspended CNT side. Generalizing the approach of I. Snyman and Yu.V. Nazarov [Phys. Rev. Lett. 108, 076805 (2012)] we show that one can generate electrostatically a tun-able spin-polarized polaronic state localized at the bending end of the CNT. We argue that at low temperatures manipulation and detection of the localised quantum spin state is possible.
TRF1 binds a bipartite telomeric site with extreme spatial flexibility
Creators: name: Rhodes, Daniela
name: Griffith, Jack D.
name: Fairall, Louise
name: Stansel, Rachel M.
name: Bianchi, Alessandro
name: De Lange, Titia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: TRF1 is a key player in telomere length regulation. Because length control was proposed to depend on the architecture of telomeres, we studied how TRF1 binds telomeric TTAGGG repeat DNA and alters its conformation. Although the single Myb-type helix-turn-helix motif of a TRF1 monomer can interact with telomeric DNA, TRF1 predominantly binds as a homodimer. Systematic Evolution of Ligands by Exponential enrichment (SELEX) with dimeric TRF1 revealed a bipartite telomeric recognition site with extreme spatial variability. Optimal sites have two copies of a 5'-YTAGGGTTR-3' half-site positioned without constraint on distance or orientation. Analysis of binding affinities and DNase I footprinting showed that both half-sites are simultaneously contacted by the TRF1 dimer, and electron microscopy revealed looping of the intervening DNA. We propose that a flexible segment in TRF1 allows the two Myb domains of the homodimer to interact independently with variably positioned half-sites. This unusual DNA binding mode is directly relevant to the proposed architectural role of TRF1.
Supplementary Material from Machine-learned patterns suggest that diversification drives economic development
Creators: name: Brummitt, Charles D.
name: Gómez-Liévano, Andrés
name: Hausmann, Ricardo
name: Bonds, Matthew H.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: 60114 Systems Biology
subject: FOS: Biological sciences
subject: 60199 Biochemistry and Cell Biology not elsewhere classified
subject: 69999 Biological Sciences not elsewhere classified

description: Document with details on related literature, preprocessing the data, correlations among various indicators, and results of the model
Supplementary document for An Investigation into the Structure of Crystalline Maltodextrin Particles by Second Harmonic Generation Microscopy - 6259283.pdf
Creators: name: Bennett, Elisha
name: Harvey, MacAulay
name: Cisek, Richard
name: Tokarz, Danielle
Publisher: name: Optica Publishing Group
Year: 2023
Subjects: Uncategorized

description: SHG intensity images of hydrated maize and B-type CMPs in a hydrogel
The relationships between fish length and otolith size and weight of the golden grey mullet Chelon auratus (Risso, 1810) (Mugiliformes, Mugilidae) collected from Köyceğiz Lagoon, Aegean Sea, Türkiye
Creators: name: REIS, İsmail
name: ATEŞ, Celal
name: JAWAD, Laith
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2023

description: Relationships between fish length and otolith length, width, and mass were examined in the golden grey mullet collected from Köyceğiz Lagoon, Aegean Sea, Türkiye. Chelon auratus is considered among the important commercial fishes in Turkey. Calculating the mathematical relationships between fish size and the otolith length, width, and weight will be significant in the future studies on the biology of this species, which include food and feeding and age and growth. The relationships otolith length-total fish length (TL), otolith weight- TL, and otolith width-TL were investigated using linear regression models for the relationships between otolith length-total fish length (TL) (TL = 3.96 x OL) and otolit width-TL (TL = 10.353 x OW ) and non-linear regression model for the relationship between otolith weight-TL (TL = 116.04 x OWe0.469 ). This study characterizes the first reference available on the relationship between fish size and otolith size and weight for Chelon auratus obtained from Köyceğiz Lagoon, Aegean Sea, Türkiye.
First record of the recently described Axinella venusta Idan, Shefer, Feldstein & Ilan, 2021 (Demospongiae: Axinellidae) in the western Mediterranean
Creators: name: DÍAZ, Julio A.
name: ORDINES, Francesc
name: MASSUTÍ, Enric
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2024

description: The sponge Axinella venusta Idan, Shefer, Feldstein & Ilan, 2021, recently described from the mesophotic zone off the coast of Israel (Levantine Sea), is recorded for second time from the western Mediterranean. Two specimens of A. venusta were collected at the summit of the Emile Baudot seamount, at the Mallorca channel (Balearic Islands). The specimens are described and the COI and 28S C1-C1 fragments sequenced. This record underlines the importance of seamounts as ecosystems of special interest for biodiversity research.
Wrapping of DNA around the E.coli RNA polymerase open promoter complex
Creators: name: Guthold, Martin
name: Bustamante, Carlos
name: Rivetti, Claudio
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: High-resolution atomic force microscopy (AFM) and biochemical methods were used to analyze the structure of Escherichia coli RNA polymerase.sigma(70) (RNAP) open promoter complex (RP(o)). A detailed analysis of a large number of molecules shows that the DNA contour length of RP(o) is reduced by approximately 30 nm (approximately 90 bp) relative to the free DNA. The DNA bend angle measured with different methods varied from 55 to 88 degrees. The contour length reduction and the DNA bend angle were much less in inactive RNAP-DNA complexes. These results, together with previously published observations, strongly support the notion that during transcription initiation, the promoter DNA wraps nearly 300 degrees around the polymerase. This amount of DNA bending requires an energy of 60 kJ/mol. The structural analysis of the open promoter complexes revealed that two-thirds of the DNA wrapped around the RNAP is part of a region upstream of the transcription start site, whereas the remaining one-third is part of the downstream region. Based on these data, a model of the sigma(70).RP(o) conformation is proposed.
Computation of local exchange coefficients in strongly interacting one-dimensional few-body systems: local density approximation and exact results
Creators: name: Marchukov, O. V.
name: Eriksen, E. H.
name: Midtgaard, J. M.
name: Kalaee, A. A. S.
name: Fedorov, D. V.
name: Jensen, A. S.
name: Zinner, N. T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: One-dimensional multi-component Fermi or Bose systems with strong zero-range interactions can be described in terms of local exchange coefficients and mapping the problem into a spin model is thus possible. For arbitrary external confining potentials the local exchanges are given by highly non-trivial geometric factors that depend solely on the geometry of the confinement through the single-particle eigenstates of the external potential. To obtain accurate effective Hamiltonians to describe such systems one needs to be able to compute these geometric factors with high precision which is difficult due to the computational complexity of the high-dimensional integrals involved. An approach using the local density approximation would therefore be a most welcome approximation due to its simplicity. Here we assess the accuracy of the local density approximation by going beyond the simple harmonic oscillator that has been the focus of previous studies and consider some double-wells of current experimental interest. We find that the local density approximation works quite well as long as the potentials resemble harmonic wells but break down for larger barriers. In order to explore the consequences of applying the local density approximation in a concrete setup we consider quantum state transfer in the effective spin models that one obtains. Here we find that even minute deviations in the local exchange coefficients between the exact and the local density approximation can induce large deviations in the fidelity of state transfer for four, five, and six particles.
description: 12 pages, 7 figures, 1 table, final version