cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Triplet Repeat Expansion Generated by DNA Slippage Is Suppressed by Human Flap Endonuclease 1
Creators: name: Topal, Michael D.
name: Ruggiero, Bethany L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Human flap endonuclease 1 (h-FEN1) mutations have dramatic effects on repeat instability. Current models for repeat expansion predict that h-FEN1 protein prevents mutations by removing 5'-flaps generated at ends of Okazaki fragments by strand displacement synthesis. The models propose that hairpin formations within flaps containing repeats enable them to escape h-FEN1 cleavage. Friedreich's ataxia is caused by expansion mutations in a d(GAA)n repeat tract. Single-stranded d(GAA)n repeat tracts, however, do not form stable hairpins until the repeat tracts are quite long. Therefore, to understand how d(GAA)n repeat expansions survive h-FEN1 activity, we determined the effects of h-FEN1 on d(GAA)n repeat expansion during replication of a d(TTC)n repeat template. Replication initiated within the repeat tract generated significant expansion that was suppressed by the addition of h-FEN1 at the start of replication. The ability of h-FEN1 to suppress expansion implies that DNA slippage generates a 5'-flap in the nascent strand independent of strand displacement synthesis by an upstream polymerase. Delaying the addition of h-FEN1 to the replication reaction abolished the ability of h-FEN1 ability to suppress d(GAA)n repeat expansion products of all sizes, including sizes unable to hairpin. Use of model substrates demonstrated that h-FEN1 cleaves d(GAA)n 5'-flaps joined to double-stranded nonrepeat sequences but not those joined to double-stranded repeat tracts. The results provide evidence that, given the opportunity, short d(GAA)n repeat expansion products rearrange from 5'-flaps to stable internal loops inside the repeat tract. Long expansion products are predicted to form hairpinned flaps and internal loops. Once formed, these DNA conformations resist h-FEN1. The biological implications of the results are discussed.
S2-S3 from Computational analysis of hygromorphic self-shaping wood gridshell structures
Creators: name: Grönquist, Philippe
name: Prijanthy Panchadcharam
name: Wood, Dylan
name: Menges, Achim
name: Rüggeberg, Markus
name: Wittel, Falk K.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Mechanics
subject: 90599 Civil Engineering not elsewhere classified
subject: FOS: Civil engineering
subject: 30399 Macromolecular and Materials Chemistry not elsewhere classified
subject: FOS: Chemical sciences

description: Document: Figures S2 and S3
Bound states, scattering states and resonant states in PT-symmetric open quantum systems
Creators: name: Garmon, Savannah
name: Gianfreda, Mariagiovanna
name: Hatano, Naomichi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study a simple open quantum system with a PT-symmetric defect potential as a prototype to illustrate general features of PT-symmetric open quantum systems; however, the potential could be mimicked by a number of recent PT experiments. One key feature is the resonance in continuum (RIC), which appears in both the discrete spectrum and scattering spectrum. The RIC forms a standing wave extending throughout the spatial extent of the system, representing a resonance between the open environment and the central PT-symmetric potential. We illustrate that as one deforms the system parameters, the RIC may exit the continuum by splitting into a bound state and a virtual bound state at the band edge, a process that should be experimentally observable. We also study the exceptional points (EPs) at which two eigenvalues coalesce; we categorize these as either EP2As, at which two real-valued solutions coalesce before becoming complex-valued, or EP2Bs, for which the two solutions are complex on either side of the EP. The EP2As are associated with PT-symmetry breaking; we argue that these are more stable against parameter perturbation than the EP2Bs. We also study complex-valued solutions of the discrete spectrum for which the wave function is nevertheless spatially localized, something not allowed in traditional open quantum systems; we illustrate that these may form quasi-bound states in continuum (QBICs) under some circumstances. We also study the scattering properties of the system, including states that support invisible propagation and some general features of perfect transmission states. We finally construct scattering states that satisfy PT-symmetric boundary conditions; while these states do not conserve the traditional probability current, we introduce the PT-current that is preserved. The perfect transmission states appear as a special case of the PT-symmetric scattering states.
S4 from Computational analysis of hygromorphic self-shaping wood gridshell structures
Creators: name: Grönquist, Philippe
name: Prijanthy Panchadcharam
name: Wood, Dylan
name: Menges, Achim
name: Rüggeberg, Markus
name: Wittel, Falk K.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Mechanics
subject: 90599 Civil Engineering not elsewhere classified
subject: FOS: Civil engineering
subject: 30399 Macromolecular and Materials Chemistry not elsewhere classified
subject: FOS: Chemical sciences

description: Document: Matlab and Python codes including raw data
Fractional charge and spin errors in self-consistent Green's function theory
Creators: name: Phillips, Jordan J.
name: Kananenka, Alexei A.
name: Zgid, Dominika
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We examine fractional charge and spin errors in self-consistent Green's function theory within a second-order approximation (GF2). For GF2 it is known that the summation of diagrams resulting from the self-consistent solution of the Dyson equation removes the divergences pathological to second-order Moller-Plesset theory (MP2) for strong correlations. In the language often used in density functional theory contexts, this means GF2 has a greatly reduced fractional spin error relative to MP2. The natural question then is what effect, if any, does the Dyson summation have on the fractional charge error in GF2? To this end we generalize our previous implementation of GF2 to open-shell systems and analyze its fractional spin and charge errors. We find that like MP2, GF2 possesses only a very small fractional charge error, and consequently little many electron self-interaction error. This shows that GF2 improves on the critical failings of MP2, but without altering the positive features that make it desirable. Furthermore, we find that GF2 has both less fractional charge and fractional spin errors than typical hybrid density functionals as well as random phase approximation with exchange.
(1679) Geo Wigg
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Ubiquitylation of Neuronal Nitric-oxide Synthase by CHIP, a Chaperone-dependent E3 Ligase
Creators: name: Lau, Miranda
name: Morishima, Yoshihiro
name: Jenkins, Gary J.
name: Osawa, Yoichi
name: Peng, Hwei Ming
name: Patterson, Cam
name: Dunbar, Anwar Y.
name: Pratt, William B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: It is established that neuronal nitric-oxide synthase (nNOS) is ubiquitylated and proteasomally degraded. The proteasomal degradation of nNOS is enhanced by suicide inactivation of nNOS or by the inhibition of hsp90, which is a chaperone found in a native complex with nNOS. In the current study, we have examined whether CHIP, a chaperone-dependent E3 ubiquitin-protein isopeptide ligase that is known to ubiquitylate other hsp90-chaperoned proteins, could act as an ubiquitin ligase for nNOS. We found with the use of HEK293T or COS-7 cells and transient transfection methods that CHIP overexpression causes a decrease in immunodetectable levels of nNOS. The extent of the loss of nNOS is dependent on the amount of CHIP cDNA used for transfection. Lactacystin (10 microM), a selective proteasome inhibitor, attenuates the loss of nNOS in part by causing the nNOS to be found in a detergent-insoluble form. Immunoprecipitation of the nNOS and subsequent Western blotting with an anti-ubiquitin IgG shows an increase in nNOS-ubiquitin conjugates because of CHIP. Moreover, incubation of nNOS with a purified system containing an E1 ubiquitin-activating enzyme, an E2 ubiquitin carrier protein conjugating enzyme (UbcH5a), CHIP, glutathione S-transferase-tagged ubiquitin, and an ATP-generating system leads to the ubiquitylation of nNOS. The addition of purified hsp70 and hsp40 to this in vitro system greatly enhances the amount of nNOS-ubiquitin conjugates, suggesting that CHIP is an E3 ligase for nNOS whose action is facilitated by (and possibly requires) its interaction with nNOS-bound hsp70.
Weak Base Permeability Characteristics Influence the Intracellular Sequestration Site in the Multidrug-resistant Human Leukemic Cell Line HL-60
Creators: name: Gong, Yuping
name: Chatterji, Dev
name: Duvvuri, Muralikrishna
name: Krise, Jeffrey P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: A number of organelles contained within mammalian cells have been implicated in the selective sequestration of chemical entities including drug molecules. Specifically, weakly basic molecules have been shown to selectively associate with either the mitochondrial compartment or lysosomes; however, the structural basis for this differentiation has not been understood. To investigate this, we have identified a series of seven weakly basic compounds, all with pK(a) near neutrality, which have different sequestration sites within the multidrug-resistant HL-60 human leukemic cell line. Three of the compounds were selectively sequestered into the mitochondria of the cells, whereas the remainder were predominantly localized within lysosomes. Using specific chemical inhibitors to disrupt either mitochondrial or lysosomal accumulation capacity, we demonstrated that accumulation of these compounds into respective organelles are not competitive processes. Comparison of the permeability characteristics of these compounds as a function of pH revealed striking differences that correlate with the intracellular sequestration site. Only those compounds with significantly reduced permeability in the ionized state relative to the un-ionized state had the capacity to accumulate within lysosomes. Alternatively, those compounds with relatively pH-insensitive permeability selectively accumulated into mitochondria. Using novel quantitative assays for assaying drug accumulation into subcellular organelles, we demonstrated a correlation between these permeability characteristics and the lysosomal versus mitochondrial accumulation capacity of these compounds. Together, these results suggest that the selective accumulations of weakly basic compounds in either lysosomes and mitochondria occur via exclusive pathways governed by a unique permeability parameter.
details of behaviour classification methods from Migrating ospreys use thermal uplift over the open sea
Creators: name: Duriez, Olivier
name: PERON, Guillaume
name: Gremillet, David
name: Sforzi, Andrea
name: Monti, Flavio
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred km of open water. We equipped five juvenile ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 time slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explaining the transoceanic cosmopolitan distribution of osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors.
Schwinger boson mean field perspective on emergent spins in diluted Heisenberg antiferromagnets
Creators: name: Ghosh, Shivam
name: Changlani, Hitesh J.
name: Henley, Christopher L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Using an adaptation of Schwinger boson mean field theory (SBMFT) for nonuniform systems, we study the nature of low-energy spin excitations on the square and Bethe lattice at their percolation threshold. The optimal SBMFT parameters are interpreted as on-site potentials and pairing amplitudes, which enables an explanation of why emergent local moments develop in this system on dilution [L. Wang and A. W. Sandvik, Phys. Rev. Lett. 97, 117204 (2006); H.J. Changlani et al., ibid 111, 157201 (2013)] and why the corresponding single particle frequencies are driven to anomalously low values. We discuss how our mean field calculations suggest the strong link between the presence of sublattice imbalance and long range antiferromagnetic order, and why linear spin wave theory is inadequate for capturing this relation. Within the SBMFT framework, we also extract an energy scale for the interaction between emergent moments, which show qualitative agreement with many-body calculations.
description: 8 pages, 6 figures. Typos corrected, more explanations added after referee comments. Version closely matches published one. Selected as PRB Editor's suggestion
Adhesion Stimulates Direct PAK1/ERK2 Association and Leads to ERK-dependent PAK1 Thr 212 Phosphorylation
Creators: name: Mack, Christopher P.
name: Taylor, Joan M.
name: Doherty, Jason T.
name: Sundberg-Smith, Liisa J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The Rac1/Cdc42 effector p21-activated kinase (PAK) is activated by various signaling cascades including receptor-tyrosine kinases and integrins and regulates a number of processes such as cell proliferation and motility. PAK activity has been shown to be required for maximal activation of the canonical Ras/Raf/MEK/ERK Map kinase signaling cascade, likely because of PAK co-activation of Raf and MEK. Herein, we found that adhesion signaling also stimulates an association between PAK1 and ERK1/2. PAK1 and ERK1/2 co-immunoprecipitated from rat aortic smooth muscle cells (SMC) plated on fibronectin, and the two proteins co-localized in membrane ruffles and adhesion complexes following PDGF-BB or sphingosine 1-phosphate treatment, respectively. Far Western analysis demonstrated a direct association between the two proteins, and peptide mapping identified an ERK2 binding site within the autoinhibitory domain of PAK1. Interestingly, deletion of a major ERK binding site in PAK attenuates activation of an ERK-dependent serum-responsive element (SRE)-luciferase reporter gene, indicating that association between PAK and ERK is required to facilitate ERK signaling. We also show that ERK2 phosphorylates PAK1 on Thr(212) in vitro and that Thr(212) is phosphorylated in smooth muscle cells following PDGF-BB treatment in an adhesion- and MEK/ERK-dependent fashion. Expression of a phosphomimic variant, PAK-T212E, does not alter ERK association, but markedly attenuates downstream ERK signaling. Taken together, these data suggest that PAK1 may facilitate ERK signaling by serving as a scaffold to recruit Raf, MEK, and ERK to adhesion complexes, and that subsequent growth factor-stimulated phosphorylation of PAK-Thr(212) by ERK may serve to provide a negative feedback signal to control coordinate activation of ERK by growth factor- and matrix-induced signals.
Ribeiro_Supplementary_Analysis_ESM.docx from Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes.
Creators: name: Emanuell Duarte-Ribeiro
name: Davis, Aaron
name: Rivero-Vega, Rafael A.
name: Ortí, Guillermo
name: Betancur-R, Ricardo
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60301 Animal Systematics and Taxonomy
subject: 60310 Plant Systematics and Taxonomy

description: Supplementary material from “Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes”. It includes information regarding fossil calibration and divergence time estimation, assessing the robustness of lineage diversification analyses based on multiple taxonomic sampling schemes and other alternative statistics, and further supplementary analysis.
Development and Application of a High Resolution Melt (HRM) based test for the Rapid Screening of Leishmania infantum Genotypes
Creators: name: Buffi Gloria
name: Diotallevi Aurora
name: Ceccarelli Marcello
name: Andreoni Francesca
name: Bencardino Daniela
name: Abruzzese Michelealberto
name: Castelli Germano
name: Federica, Bruno
name: Fabrizio, Vitale
name: Magnani Mauro
name: Galluzzi Luca
Publisher: name: INFN Open Access Repository
Year: 2019

description: INTRODUCTION
 Leishmaniasis includes anthropo zoonotic infectious diseases caused by a protozoan of the Leishmania genus, associated with different clinical manifestations, affecting both humans and other vertebrates, including dogs The Mediterranean basin, including Italy, is considered an endemic area for both visceral and cutaneous leishmaniasis caused by L infantum The multi locus enzyme electrophoresis ( based on the electrophoretic mobility of several enzymes from promastigotes cultures, is considered the reference method for parasite typing Through this method, about 45 L infantum zymodemes (also termed MON) have been identified in humans in the Mediterranean basin 1 Among these, L infantum MON 1 is the most widespread, representing about 70 of all identified strains In Italy, canine infections showed a high prevalence of MON 1 91 with the remaining composed almost exclusively of MON 72 2 Since MLEE technique is cumbersome, time consuming and requires parasites isolation, several biomolecular approaches have been developed In particular, we identified the SNP 390 T>G in malic enzyme ( gene as a potential marker to differentiate the most common L infantum genotype, i e 390 T (corresponding to zymodemes MON 1 72 201 from all others. AIMS
 This study aimed to develop a Rapid Genotype Screening ( assay for L infantum genetic characterization in clinical samples using high resolution melt ( analysis, exploiting the polymorphism 390 T>G in the ME gene.
Ribeiro_Supplementary_Analysis_ESM.docx from Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes
Creators: name: Emanuell Duarte-Ribeiro
name: Davis, Aaron
name: Rivero-Vega, Rafael A.
name: Ortí, Guillermo
name: Betancur-R, Ricardo
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60301 Animal Systematics and Taxonomy
subject: 60310 Plant Systematics and Taxonomy

description: Supplementary material from “Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes”. It includes information regarding fossil calibration and divergence time estimation, assessing the robustness of lineage diversification analyses based on multiple taxonomic sampling schemes and other alternative statistics, and further supplementary analysis.
(1680) Elizabeth [Wigg]
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
HAT-P-50b, HAT-P-51b, HAT-P-52b, and HAT-P-53b: Three Transiting Hot Jupiters and a Transiting Hot Saturn From the HATNet Survey
Creators: name: Hartman, Joel D.
name: Bhatti, Waqas
name: Bakos, Gáspár Á.
name: Bieryla, Allyson
name: Kovács, Géza
name: Latham, David W.
name: Csubry, Zoltan
name: de Val-Borro, Miguel
name: Penev, Kaloyan
name: Buchhave, Lars A.
name: Torres, Guillermo
name: Howard, Andrew W.
name: Marcy, Geoff W.
name: Johnson, John A.
name: Isaacson, Howard
name: Sato, Bun'ei
name: Boisse, Isabelle
name: Falco, Emilio
name: Everett, Mark E.
name: Szklenar, Tamas
name: Fulton, Benjamin J.
name: Shporer, Avi
name: Kovács, Tamas
name: Hansen, Terese
name: Béky, Bence
name: Noyes, Robert W.
name: Lázár, József
name: Papp, Istvan
name: Sári, Pál
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We report the discovery and characterization of four transiting exoplanets by the HATNet survey. The planet HAT-P-50b has a mass of 1.35 M_J and a radius of 1.29 R_J, and orbits a bright (V = 11.8 mag) M = 1.27 M_sun, R = 1.70 R_sun star every P = 3.1220 days. The planet HAT-P-51b has a mass of 0.31 M_J and a radius of 1.29 R_J, and orbits a V = 13.4 mag, M = 0.98 M_sun, R = 1.04 R_sun star with a period of P = 4.2180 days. The planet HAT-P-52b has a mass of 0.82 M_J and a radius of 1.01 R_J, and orbits a V = 14.1 mag, M = 0.89 M_sun, R = 0.89 R_sun star with a period of P = 2.7536 days. The planet HAT-P-53b has a mass of 1.48 M_J and a radius of 1.32 R_J, and orbits a V = 13.7 mag, M = 1.09 M_sun, R = 1.21 R_sun star with a period of P = 1.9616 days. All four planets are consistent with having circular orbits and have masses and radii measured to better than 10% precision. The low stellar jitter and favorable R_P/R_star ratio for HAT-P-51 make it a promising target for measuring the Rossiter-McLaughlin effect for a Saturn-mass planet.
description: Submitted to AJ. 20 pages, 9 figures, 5 tables. Data available at http://hatnet.org/
(1676) Octavia Lucy Newbould Chadwick
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Analytical two-loop soft mass terms of sfermions in Extended GMSB models
Creators: name: Jelinski, Tomasz
name: Gluza, Janusz
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Analytical two-loop contributions to soft masses of sfermions are derived in the Extended GMSB (EGMSB) model with one superpotential coupling between matter and messenger superfields. Analytical results allows to study in detail the whole range of the ratio $F/M^2$ of the spurion $F$-term, $F$, to the messenger scale $M$. It is shown that if $F/M^2$ is of the order of $1$, then one- and two-loop contributions to soft masses are of the same magnitude and their interplay leads to novel sfermion mass patterns.
description: 8 pages, 5 figures. v2: typos corrected, figures added, discussion in the Sec. 5 extended
Approximate coherent states for nonlinear systems
Creators: name: Román-Ancheyta, R.
name: Récamier, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: On the basis of the f-deformed oscillator formalism, we propose to construct nonlinear coherent states for Hamiltonian systems having linear and quadratic terms in the the number operator by means of the two following definitions: i) as deformed annihilation operator coherent states (AOCS) and ii) as deformed displacement operator coherent states (DOCS). For the particular cases of the Morse and Modified Pöschl-Teller potentials, modeled as f-deformed oscillators (both supporting a finite number of bound states), the properties of their corresponding nonlinear coherent states, viewed as DOCS, are analyzed in terms of their occupation number distribution, their evolution on phase space, and their uncertainty relations.
description: 22 pages, 7 figures
Amphiregulin Is a Novel Growth Factor Involved in Normal Bone Development and in the Cellular Response to Parathyroid Hormone Stimulation
Creators: name: Qin, Ling
name: Lee, David C.
name: Partridge, Nicola C.
name: Tamasi, Joseph
name: Raggatt, Liza
name: Feyen, Jean H.M.
name: Li, Xin
name: DiCicco-Bloom, Emanuel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Parathyroid hormone (PTH) is the major mediator of calcium homeostasis and bone remodeling and is now known to be an effective drug for osteoporosis treatment. Yet the mechanisms responsible for its functions in bone are largely unknown. Here we report that the expression of amphiregulin (AR), a member of the epidermal growth factor (EGF) family, is rapidly and highly up-regulated by PTH in several osteoblastic cell lines and bone tissues. Other osteotropic hormones (1alpha,25-dihydroxyvitamin D3 and prostaglandin E2) also strongly stimulate AR expression. We found all EGF-like ligands and their receptors are expressed in osteoblasts, but AR is the only member that is highly regulated by PTH. Functional studies demonstrated that although AR is a potent growth factor for preosteoblasts, it completely inhibits further differentiation. AR also strongly and quickly stimulated Akt and ERK phosphorylation and c-fos and c-jun expression in an EGF receptor-dependent manner. Moreover, AR null mice displayed significantly less tibial trabecular bone than wild-type mice. Taken together, we have identified a novel growth factor that is PTH-regulated and appears to have an important role in bone metabolism.
Supplementary materials - Gazzola et al - Testudo hermanni from Continuous and discrete quantity discrimination in tortoises.
Creators: name: Gazzola, Andrea
name: Vallortigara, Giorgio
name: Pellitteri-Rosa, Daniele
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences

description: The ability to estimate quantity, which is crucially important in several aspects of animal behaviour (e.g. foraging), has been extensively investigated in most taxa, with the exception of reptiles. The few studies available, in lizards, report lack of spontaneous discrimination of quantity, which may suggest that reptiles could represent an exception in numerical abilities among vertebrates. We investigated the spontaneous ability of Hermann's tortoises (Testudo hermanni) to select the larger quantity of food items. Tortoises were able to choose the larger food item when exposed to two options differing in size, but equal in numerousness (0.25, 0.50, 0.67 and 0.75 ratio) and when presented with two groups differing in numerousness, but equal in size (1 versus 4, 2 versus 4, 2 versus 3 and 3 versus 4 items). The tortoises succeeded in both size and numerousness discrimination, and their performance appeared to depend on the ratio of items to be discriminated (thus following Weber's Law). These findings in chelonians provide evidence of an ancient system for the extrapolation of numerical magnitudes from given sets of elements, shared among vertebrates.
IGSN IDs: Identifying, Linking, & Citing Samples
Creators: name: Edmunds, Rorie
Publisher: name: Zenodo
Year: 2023
Subjects: IGSN IDs
Sample discovery
Connection metadata
Citation metrics
DataCite
ESIP

description: Presentation given to the ESIP Physical Sample Curation Cluster on Tuesday, 22 August 2023.
Amplification of Telomeric Arrays via Rolling-circle Mechanism
Creators: name: Makhov, Alexander M.
name: Rycovska, Adriana
name: Tomaska, Lubomir
name: Nosek, Jozef
name: Griffith, Jack D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Alternative (telomerase-independent) lengthening of telomeres mediated through homologous recombination is often accompanied by a generation of extrachromosomal telomeric circles (t-circles), whose role in direct promotion of recombinational telomere elongation has been recently demonstrated. Here we present evidence that t-circles in a natural telomerase-deficient system of mitochondria of the yeast Candida parapsilosis replicate independently of the linear chromosome via a rolling-circle mechanism. This is supported by an observation of (i) single-stranded DNA consisting of concatameric arrays of telomeric sequence, (ii) lasso-shaped molecules representing rolling-circle intermediates, and (iii) preferential incorporation of deoxyribonucleotides into telomeric fragments and t-circles. Analysis of naturally occurring variant t-circles revealed conserved motifs with potential function in driving the rolling-circle replication. These data indicate that extrachromosomal t-circles observed in a wide variety of organisms, including yeasts, plants, Xenopus laevis, and certain human cell lines, may represent independent replicons generating telomeric sequences and, thus, actively participating in telomere dynamics. Moreover, because of the promiscuous occurrence of t-circles across phyla, the results from yeast mitochondria have implications related to the primordial system of telomere maintenance, providing a paradigm for evolution of telomeres in nuclei of early eukaryotes.
Architecture of the Human Ndc80-Hec1 Complex, a Critical Constituent of the Outer Kinetochore
Creators: name: Ciferri, Claudio
name: Ferrari, Karin J.
name: De Lucall, Jennifer
name: Salmon, Edward D.
name: Wyman, Claire
name: Stark, Holger
name: Musacchio, Andrea
name: Kilmartin, John
name: Ristic, Dejan
name: Monzani, Silvia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The Ndc80 complex is a constituent of the outer plate of the kinetochore and plays a critical role in establishing the stable kinetochore-microtubule interactions required for chromosome segregation in mitosis. The Ndc80 complex is evolutionarily conserved and contains the four subunits Spc24, Spc25, Nuf2, and Ndc80 (whose human homologue is called Hec1). All four subunits are predicted to contain globular domains and extensive coiled coil regions. To gain an insight into the organization of the human Ndc80 complex, we reconstituted it using recombinant methods. The hydrodynamic properties of the recombinant Ndc80 complex are identical to those of the endogenous HeLa cell complex and are consistent with a 1:1:1:1 stoichiometry of the four subunits and a very elongated shape. Two tight Hec1-Nuf2 and Spc24-Spc25 subcomplexes, each stabilized by a parallel heterodimeric coiled coil, maintain this organization. These subcomplexes tetramerize via an interaction of the C- and N-terminal portions of the Hec1-Nuf2 and Spc24-Spc25 coiled coils, respectively. The recombinant complex displays normal kinetochore localization upon injection in HeLa cells and is therefore a faithful copy of the endogenous Ndc80 complex.
Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function
Creators: name: Scherrer, Arne
name: Agostini, Federica
name: Sebastiani, Daniel
name: Gross, E. K. U.
name: Vuilleumier, Rodolphe
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similarly to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach.
description: 13 pages, 5 figures, 4 tables
Supplementary materials - Gazzola et al - Testudo hermanni from Continuous and discrete quantity discrimination in tortoises
Creators: name: Gazzola, Andrea
name: Vallortigara, Giorgio
name: Pellitteri-Rosa, Daniele
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences

description: The ability to estimate quantity, which is crucially important in several aspects of animal behaviour (e.g. foraging), has been extensively investigated in most taxa, with the exception of reptiles. The few studies available, in lizards, report lack of spontaneous discrimination of quantity, which may suggest that reptiles could represent an exception in numerical abilities among vertebrates. We investigated the spontaneous ability of Hermann's tortoises (Testudo hermanni) to select the larger quantity of food items. Tortoises were able to choose the larger food item when exposed to two options differing in size, but equal in numerousness (0.25, 0.50, 0.67 and 0.75 ratio) and when presented with two groups differing in numerousness, but equal in size (1 versus 4, 2 versus 4, 2 versus 3 and 3 versus 4 items). The tortoises succeeded in both size and numerousness discrimination, and their performance appeared to depend on the ratio of items to be discriminated (thus following Weber's Law). These findings in chelonians provide evidence of an ancient system for the extrapolation of numerical magnitudes from given sets of elements, shared among vertebrates.
Diphoton production at Tevatron and the LHC in the NLO* approximation of the Parton Reggeization Approach
Creators: name: Nefedov, Maxim
name: Saleev, Vladimir
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The hadroproduction of prompt isolated photon pairs at high energies is studied in the NLO* framework of the Parton Reggeization Approach. The real part of the NLO corrections is computed, and the procedure for the subtraction of double counting between real parton emissions in the hard-scattering matrix element and unintegrated PDF is constructed for the amplitudes with Reggeized quarks in the initial state. The matrix element of the important NNLO subprocess RR->2gamma with full dependence on the transverse momenta of the initial-state Reggeized gluons is obtained. We compare obtained numerical results with diphoton spectra measured at Tevatron and the LHC, and find a good agreement of our predictions with experimental data at the high values of diphoton transverse momentum, pT, and especially at the pT larger than the diphoton invariant mass, M. In this multi-Regge kinematics region, the NLO correction is strongly suppressed, demonstrating the self-consistency of the Parton Reggeization Approach.
description: 23 pages, 12 figures, 1 table
Figure S6n from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Figure S6m from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
NFFA-Europe Pilot - D16.2 - Report on the first data services
Creators: name: Franzon, Marco
name: Osmenaj, Elda
name: Panighel, Mirco
name: Rodani, Tommaso
name: Brandino, Giuseppe Piero
name: Aversa, Rossella
Publisher: name: Zenodo
Year: 2022

description: This document describes the initial set of data services available in NFFA Europe Pilot.
description: WP16 - Implementing FAIR data approach within NEP
Figure S6n from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
On the search for artificial Dyson-like structures around pulsars
Creators: name: Osmanov, Z.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Popular Physics (physics.pop-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Assuming the possibility of existence of a supercivilization we extend the idea of Freeman Dyson considering pulsars instead of stars. It is shown that instead of a spherical shell the supercivilization must use ring-like constructions. We have found that a size of the "ring" should be of the order of $(10^{-4}-10^{-1})$AU with temperature interval $(300-600)$K for relatively slowly rotating pulsars and $(10-350)$AU with temperature interval $(300-700)$K for rapidly spinning neutron stars, respectively. Although for the latter the Dyson construction is unrealistically massive and cannot be considered seriously. Analyzing the stresses in terms of the radiation and wind flows it has been argued that they cannot significantly affect the ring construction. On the other hand, the ring in-plane unstable equilibrium can be restored by the energy which is small compared to the energy extracted from the star. This indicates that the search for infrared ring-like sources close to slowly rotating pulsars seems to be quite promising.
description: 9 pages, 4 figures
Figure S6o from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.