A New Method for Species Identification via Protein-Coding and Non-Coding DNA Barcodes by Combining Machine Learning with Bioinformatic Methods

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75–100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62–98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60–99.37%) for 1094 brown algae queries, both using ITS barcodes

MICROSTRUCTURAL AND TRANSPORT-PROPERTIES OF LASER-ABLATED LUBA2CU3O7-DELTA THIN-FILMS

High-quality LuBa2Cu3O7-delta (LBCO) thin films have been grown on [100] LaAlO3 by pulsed laser deposition. Microstructural studies have indicated a high degree of c-axis orientation and an in-plane alignment. Transport measurements carried out on 10 mum wide microbridges of LBCO films have shown high critical current densities in the range 2-5 X 10(6) A cm-2 at 77 K. Self-field induced flux creep caused by transport currents has also been studied. However, the thickness-dependent effective microwave surface resistance, R(eff), measured using a microstrip resonator technique at the X band has shown a minimum at 3000 angstrom indicating film degradation above 3000 angstrom

EFFECT OF OXYGEN STOICHIOMETRY VARIATION ON T(C) IN ND1.85CE0.15CUO4-DELTA

The oxygen vacancy parameter, delta, in electron-doped superconducting Nd1.85Ce0.15CuO4-delta, has been varied by changing the sample-processing conditions. A T(c)-onset value of 19 K was obtained by quenching alone. T(c) onset as high as 24 K, T(c)(R = 0) = 17 K and DELTAT(90%-10%) = 3 K have been achieved for delta = 0.05 in argon-annealed single-phase Nd1.85Ce0.15CuO4-delta samples

SUPERCONDUCTIVITY AND VALENCE STATES OF CE, PR AND TB IN BULK LU1-XMXBA2CU3O7-DELTA (M = CE, PR AND TB) SYSTEMS

Bulk samples of composition Lu1-xMBa2Cu3O7-delta (M=Ce, Pr and Th) are examined with respect to the formation of 1-2-3 phase and the superconducting properties. Samples with M=Pr and Tb form a superconducting 1-2-3 phase for values of x less-than-or-equal-to 0.6. We observe that in case of M=Tb, the zero-resistance transition temperature, T(c(0)), is 85-86 K and independent of x for 0.1 less-than-or-equal-to x less-than-or-equal-to 0.3. For M=Pr, a maximum T(c(0)) of 86 K is observed for x=0.1. T(c(0)) decreases with increasing x for x>0.1 and the sample with x=0.6 is observed to be semiconducting down to 12 K. With M=Ce, samples of the composition Lu1-x-yCexCaBa2Cu3O7-delta form the superconducting 1-2-3 phase for x, y=0.1 and 0.15. Samples of the compositions Lu1-x-yPrxCaBa2Cu3O7-delta with x=0.1, 0.2, 0.3 and y=0.1, have lower T(c(0))'s than samples of a corresponding Pr content without Ca. We infer from our studies that the Pr ions are in the 3+ valence state for 0.1 less-than-or-equal-to x less-than-or-equal-to 0.3, the Th ions are mainly in the 3+ valence state for 0.t less-than-or-equal-to x less-than-or-equal-to 0.3, and the Ce ions are in the 4 + state

POSSIBLE OVERDOPING IN TLSRLACUO5 AND SUPERCONDUCTIVITY IN TLBALACUO5 BY ISOVALENT-CATION SUBSTITUTION

It is known that superconductivity in TlSrLaCuO5 is due to the overlap of empty Tl 6s band with the antibonding Cu 3d(x2-y2) band at the Fermi level. This motivated us to investigate the effects of isovalent-cation substitution in superconducting TlSrLaCuO5 and semiconducting TlBaLaCuO5. We have succeeded in inducing superconductivity in TIBaLaCuO5 by introducing Ca2+ at the Ba sites

SUPERCONDUCTIVITY IN THIN-FILMS OF THE COMPOSITION M(0.5)CA(0.5)BA(2)CU(3)O(7-DELTA) (M=LU, TB, TH)

We have grown in situ by laser ablation thin films of the composition M(0.5)Ca(0.5)Ba(2)CU(3)O(7-delta) (M=LU, Tb, Th). The significance of these investigations is that the compositions MBa(2)Cu(3)O(7-delta) (M = Lu, Tb, Th) do not form in single phase in bulk form and, in the case of Tb and Th, not even in thin film form. With partial replacement of the M element by Ca, we are able to grow thin films that are highly crystalline and preferentially oriented. Superconducting transition temperature of the films varies from congruent to 12 K to g 45 K. To the best of our knowledge, these are the first results reporting superconductivity in a 5f-element-based copper oxide system (in this case, M=Th)

SUPERCONDUCTIVITY AND VALENCE STATE OF TB IN LU1-XTBXBA2CU3O7-DELTA (0-LESS-THAN-OR-EQUAL-TO-X-LESS-THAN-OR-EQUAL-TO-0.7)

Although both lutetium and terbium do not form superconducting REBa2Cu3O7-delta, we report here the formation of superconducting phase in thin films. Films are highly c-axis oriented with high current densities (3.0x10(6) A cm-2 at 77 K) observed in Lu0.5Tb0.5Ba2Cu3O7-delta. X-ray photoelectron spectroscopic analysis of Tb in the above film indicates that Tb is in a trivalent state. Further, as the redox potential of Tb (Tb4+ +e- --> Tb3+:E0 = 3.1 V) is close to that of Pr (Pr4+ +e- -->Pr3+:E0 = 3.2 V), we suggest that Pr also would be in a trivalent state and the mechanism by which the latter depresses T(c) must be of trivalent origin

Superconductivity at 86-k in luba2cu3o7-delta thin-films

Superconductivity has been observed in thin films of LuBa2Cu3O7-delta, which otherwise does not form the 1:2:3 superconducting phase in bulk, presumably due to the small ionic radius of Lu. From this work, it is clear that the substrate influences the nucleation of the 1:2:3 superconducting phase in thin films. Results indicate that LuBa2Cu3O7-delta thin films with as good a quality as that achievable with YBa2Cu3O7-delta thin films can be realized; zero resistance transition temperature (T(c)) of 86 K and critical-current density (J(c)) of 5 X 10(5) A cm-2 at 77 K have been obtained

STRUCTURAL STABILITY OF LUBA2CU3O7-DELTA AND SUPERCONDUCTIVITY IN THIN-FILMS OF LU(1-X)M(X)BA(2)CU(3)O(7-DELTA) (M=PR, TB, AND CE)

We present here the results of our investigations of the structural and superconducting properties of thin films of Lu(1-x)M(x)Ba(2)Cu(3)O(7-delta) (M=Ce, Pr, and Tb), the three ambivalent rare-earth ions. Our results show that Pr and Tb ions are in the trivalent state and Ce ions are tetravalent. Structural (in)stability of the parent material LuBa2Cu3O7-delta forms the basis of our arguments. We suggest a simple model to account for the influence of Pr ions on superconductivity in cuprates