Dissection of molecular and histological subtypes of papillary thyroid cancer using alternative splicing profiles

Despite growing evidence of the relevance of alternative splicing (AS) to cancer development and progression, the biological implications of AS for tumor behaviors, including papillary thyroid cancer (PTC), remain elusive. With the aim of further understanding the molecular and histological subtypes of PTC, we in this study explored whether AS events might act as new molecular determinants. For this purpose, AS profiles were analyzed in RNA-sequencing data from The Cancer Genome Atlas (TCGA) and from a Korean patient dataset. A total of 23 distinct exon-skipping (ES) events that correlated significantly with PTC oncogenic activity and differentiation scores were identified. The two top-ranked ES events, NUMA1_17515 in exon 18 of NUMA1 and TUBB3_38175 in exon 6 of TUBB3, showed high correlations with oncogenic activities and discriminated histological and molecular subtypes of PTC. Furthermore, two novel intron-retention (IR) events for TUBB3 were uncovered. All ES and IR events for the TUBB3 gene were predicted to induce nonsense-mediated mRNA decay. The relative abundances of intron reads in the PTC dataset from TCGA showed IR levels to differ significantly among PTC subtypes, possibly reflecting their different tumor behaviors. This study provides a landscape of AS changes among PTC subtypes and identified two significant AS events, NUMA1_17515 and TUBB3_38175, as potential AS biomarkers for PTC subclassification and characterization. The AS events identified in this study may be involved in the development of phenotypic differences underlying the functional characteristics and histological differentiation of PTCs.Subject terms: Cancer genomics, RNA splicing     

Variable range hopping conduction in semiconductor nanocrystal solids

The temperature and electrical field dependent conductivity of n-type CdSe nanocrystal thin films is investigated. In the low electrical field regime, the conductivity follows sigma approximately exp([-(T(*)/T)(1/2)] in the temperature range 10相似文献   

Scale dependence of branching in arterial and bronchial trees

Although models of branching in arterial and bronchial trees often predict a dependence of bifurcation parameters on the scale of the bifurcating vessels, direct verification of this dependence by comparison with data is uncommon. We compare measurements of bifurcation parameters of airways and arterial trees of different mammals as a function of scale to general features predicted by theoretical models based on minimization of pumping power and network volume. We find that the size dependence is more complex than existing theories based solely on energy and volume minimization explain, and suggest additional factors that may govern the branching at different scales.     

0-pi transitions in Josephson junctions with antiferromagnetic interlayers

We show that the dc Josephson current through superconductor-antiferromagnet-superconductor (S-AF-S) junctions manifests a remarkable atomic-scale dependence on the interlayer thickness. At low temperatures the junction is either a 0 or pi junction depending on whether the AF interlayer consists of an even or odd number of atomic layers. This is associated with different symmetries of the AF interlayers in the two cases. In the junction with odd AF interlayers an additional pi- 0 transition can take place as a function of temperature. This originates from the interplay of spin-split Andreev bound states. Experimental implications of these theoretical findings are discussed.     

Glass transition of miscible binary polymer-polymer thin films

The average glass transition temperatures, Tg, of thin homopolymer films exhibit a thickness dependence, Tg(h), associated with a confinement effect and with polymer-segment-interface interactions. The Tg's of completely miscible thin film blends of tetramethyl bisphenol-A polycarbonate (TMPC) and deuterated polystyrene (dPS), supported by SiO(x)/Si, decrease with decreasing h for PS weight fractions phi >0.1. This dependence is similar to that of PS and opposite to that of TMPC thin films. Based on an assessment of Tg(h, phi), we suggest that the Tg(h, phi) of miscible blends should be rationalized, additionally, in terms of the notion of a self-concentration and associated heterogeneous component dynamics.     

Photobleaching on Photonic Crystal Enhanced Fluorescence Surfaces

The effect of resonant fluorescent enhancement from a photonic crystal surface upon the fluorescent photobleaching rate of Cyanine-5 labeled protein has been investigated. We show that the enhanced excitation mechanism for photonic crystal enhanced fluorescence, in which the device surface resonantly couples light from an excitation laser, accelerates photobleaching in proportion to the coupling efficiency of the laser to the photonic crystal. We also show that the enhanced extraction mechanism, in which the photonic crystal directs emitted photons approximately normal to the surface, does not play a role in the rate of photobleaching. We show that the photobleaching rate of dye molecules on the photonic crystal surface is accelerated by 30x compared to an ordinary glass surface, but substantial signal gain is still evident, even after extended periods of continuous illumination at the resonant condition.     

Base‐dependent selectivity of an SNAr reaction

A detailed kinetic analysis and computational study of an S_NAr reaction between 2,5,6‐trifluoronicotinonitrile, 2 , and the ambident 3‐isopropoxy‐1H‐pyrazol‐5‐amine, 3 , is presented. The selectivity with respect to the reaction at the primary amino group of 2 , to give the desired product, 2,5‐difluoro‐6‐[(3‐isopropoxy‐1H‐pyrazol‐5‐yl)amino]nicotinonitrile, 1 , is strongly dependent upon reaction conditions. Reaction is found to proceed via both uncatalysed and base catalysed routes, and selectivity towards 1 is strongly enhanced in the presence of the base diazabicyclo[2,2,2]octane (DABCO). Computational studies in tetrahydrofuran solution at the B3LYP/6‐31G* level of theory have provided valuable insight into alternative kinetically indistinguishable reaction pathways. The results suggest that for reaction at the primary amino group, proton removal by DABCO accompanying amine addition allows avoidance of a high‐energy, zwitterionic Meisenheimer intermediate. Reactions at the alternative pyrazole nitrogen atoms are less sensitive to the presence of base because of stabilisation of the Meisenheimer zwitterions by intramolecular hydrogen bonding. Copyright © 2010 John Wiley & Sons, Ltd.     

Closed Unstretchable Knotless Ribbons and the Wunderlich Functional

In 1962, Wunderlich published the article “On a developable Möbius band,” in which he attempted to determine the equilibrium shape of a free standing Möbius band. In line with Sadowsky’s pioneering works on Möbius bands of infinitesimal width, Wunderlich used an energy minimization principle, which asserts that the equilibrium shape of the Möbius band has the lowest bending energy among all possible shapes of the band. By using the developability of the band, Wunderlich reduced the bending energy from a surface integral to a line integral without assuming that the width of the band is small. Although Wunderlich did not completely succeed in determining the equilibrium shape of the Möbius band, his dimensionally reduced energy integral is arguably one of the most important developments in the field. In this work, we provide a rigorous justification of the validity of the Wunderlich integral and fully formulate the energy minimization problem associated with finding the equilibrium shapes of closed bands, including both orientable and nonorientable bands with arbitrary number of twists. This includes characterizing the function space of the energy functional, dealing with the isometry and local injectivity constraints, and deriving the Euler–Lagrange equations. Special attention is given to connecting edge conditions, regularity properties of the deformed bands, determination of the parameter space needed to ensure that the deformation is surjective, reduction in isometry constraints, and deriving matching conditions and jump conditions associated with the Euler–Lagrange equations.

     

Dopant-modulated pair interaction in cuprate superconductors

A comparison of recent experimental STM data with single-impurity and many-impurity Bogoliubov-de Gennes calculations strongly suggests that random out-of-plane dopant atoms in cuprates modulate the pair interaction locally. This type of disorder is crucial to understanding the nanoscale electronic inhomogeneity observed in BSCCO-2212, and can reproduce observed correlations between the positions of impurity atoms and various aspects of the local density of states such as the gap magnitude and the height of the coherence peaks. Our results imply that each dopant atom modulates the pair interaction on a length scale of order one lattice constant.     

Equivalent Theories and Changing Hamiltonian Observables in General Relativity

Change and local spatial variation are missing in Hamiltonian general relativity according to the most common definition of observables as having 0 Poisson bracket with all first-class constraints. But other definitions of observables have been proposed. In pursuit of Hamiltonian–Lagrangian equivalence, Pons, Salisbury and Sundermeyer use the Anderson–Bergmann–Castellani gauge generator G, a tuned sum of first-class constraints. Kucha? waived the 0 Poisson bracket condition for the Hamiltonian constraint to achieve changing observables. A systematic combination of the two reforms might use the gauge generator but permit non-zero Lie derivative Poisson brackets for the external gauge symmetry of General Relativity. Fortunately one can test definitions of observables by calculation using two formulations of a theory, one without gauge freedom and one with gauge freedom. The formulations, being empirically equivalent, must have equivalent observables. For de Broglie-Proca non-gauge massive electromagnetism, all constraints are second-class, so everything is observable. Demanding equivalent observables from gauge Stueckelberg–Utiyama electromagnetism, one finds that the usual definition fails while the Pons–Salisbury–Sundermeyer definition with G succeeds. This definition does not readily yield change in GR, however. Should GR’s external gauge freedom of general relativity share with internal gauge symmetries the 0 Poisson bracket (invariance), or is covariance (a transformation rule) sufficient? A graviton mass breaks the gauge symmetry (general covariance), but it can be restored by parametrization with clock fields. By requiring equivalent observables, one can test whether observables should have 0 or the Lie derivative as the Poisson bracket with the gauge generator G. The latter definition is vindicated by calculation. While this conclusion has been reported previously, here the calculation is given in some detail.