Data Set for the Reporting of Malignant Odontogenic Tumors Explanations and Recommendations of the Guidelines From the International Collaboration on Cancer Reporting

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Point-contact Andreev reflection spectroscopy of heavy-fermion-metal/superconductor junctions

Our previous point-contact Andreev reflection studies of the heavy-fermion superconductor CeCoIn$_5$ using Au tips have shown two clear features: reduced Andreev signal and asymmetric background conductance [1]. To explore their physical origins, we have extended our measurements to point-contact junctions between single crystalline heavy-fermion metals and superconducting Nb tips. Differential conductance spectra are taken on junctions with three heavy-fermion metals, CeCoIn$_5$, CeRhIn$_5$, and YbAl$_3$, each with different electron mass. In contrast with Au/CeCoIn$_5$ junctions, Andreev signal is not reduced and no dependence on effective mass is observed. A possible explanation based on a two-fluid picture for heavy fermions is proposed. [1] W. K. Park et al., Phys. Rev. B 72 052509 (2005); W. K. Park et al., Proc. SPIE-Int. Soc. Opt. Eng. 5932 59321Q (2005); W. K. Park et al., Physica C (in press) (cond-mat/0606535).Comment: 2 pages, 2 figures, submitted to the SCES conference, Houston, Texas, USA, May 13-18, 200

Regional Conformational Flexibility Couples Substrate Specificity and Scissile Phosphate Diester Selectivity in Human Flap Endonuclease 1

Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5′-terminus/flap through the arch and recognition of a single nucleotide 3′-flap by the α2–α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2–α3 loop are disordered without substrate. Disorder within the arch explains how 5′-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1–DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1–DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble

The Basics of Water Waves Theory for Analogue Gravity

This chapter gives an introduction to the connection between the physics of water waves and analogue gravity. Only a basic knowledge of fluid mechanics is assumed as a prerequisite.Comment: 36 pages. Lecture Notes for the IX SIGRAV School on "Analogue Gravity", Como (Italy), May 201

Phosphate steering by Flap Endonuclease 1 promotes 5´-flap specificity and incision to prevent genome instability

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability

Phosphate steering by Flap Endonuclease 1 promotes 5´-flap specificity and incision to prevent genome instability

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability

Magnetism in Dense Quark Matter

We review the mechanisms via which an external magnetic field can affect the ground state of cold and dense quark matter. In the absence of a magnetic field, at asymptotically high densities, cold quark matter is in the Color-Flavor-Locked (CFL) phase of color superconductivity characterized by three scales: the superconducting gap, the gluon Meissner mass, and the baryonic chemical potential. When an applied magnetic field becomes comparable with each of these scales, new phases and/or condensates may emerge. They include the magnetic CFL (MCFL) phase that becomes relevant for fields of the order of the gap scale; the paramagnetic CFL, important when the field is of the order of the Meissner mass, and a spin-one condensate associated to the magnetic moment of the Cooper pairs, significant at fields of the order of the chemical potential. We discuss the equation of state (EoS) of MCFL matter for a large range of field values and consider possible applications of the magnetic effects on dense quark matter to the astrophysics of compact stars.Comment: To appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Ye

Coronal Shock Waves, EUV waves, and Their Relation to CMEs. I. Reconciliation of "EIT waves", Type II Radio Bursts, and Leading Edges of CMEs

We show examples of excitation of coronal waves by flare-related abrupt eruptions of magnetic rope structures. The waves presumably rapidly steepened into shocks and freely propagated afterwards like decelerating blast waves that showed up as Moreton waves and EUV waves. We propose a simple quantitative description for such shock waves to reconcile their observed propagation with drift rates of metric type II bursts and kinematics of leading edges of coronal mass ejections (CMEs). Taking account of different plasma density falloffs for propagation of a wave up and along the solar surface, we demonstrate a close correspondence between drift rates of type II bursts and speeds of EUV waves, Moreton waves, and CMEs observed in a few known events.Comment: 30 pages, 15 figures. Solar Physics, published online. The final publication is available at http://www.springerlink.co

TeV-scale bileptons, see-saw type II and lepton flavor violation in core-collapse supernova

Electrons and electron neutrinos in the inner core of the core-collapse supernova are highly degenerate and therefore numerous during a few seconds of explosion. In contrast, leptons of other flavors are non-degenerate and therefore relatively scarce. This is due to lepton flavor conservation. If this conservation law is broken by some non-standard interactions, electron neutrinos are converted to muon and tau-neutrinos, and electrons - to muons. This affects the supernova dynamics and the supernova neutrino signal. We consider lepton flavor violating interactions mediated by scalar bileptons, i.e. heavy scalars with lepton number 2. It is shown that in case of TeV-mass bileptons the electron fermi gas is equilibrated with non-electron species inside the inner supernova core at a time-scale of order of (1-100) ms. In particular, a scalar triplet which generates neutrino masses through the see-saw type II mechanism is considered. It is found that supernova core is sensitive to yet unprobed values of masses and couplings of the triplet.Comment: accepted to Eur.Phys.J.