FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

Quantum Criticality in doped CePd_1-xRh_x Ferromagnet

CePd_1-xRh_x alloys exhibit a continuous evolution from ferromagnetism (T_C= 6.5 K) at x = 0 to a mixed valence (MV) state at x = 1. We have performed a detailed investigation on the suppression of the ferromagnetic (F) phase in this alloy using dc-(\chi_dc) and ac-susceptibility (\chi_ac), specific heat (C_m), resistivity (\rho) and thermal expansion (\beta) techniques. Our results show a continuous decrease of T_C (x) with negative curvature down to T_C = 3K at x*= 0.65, where a positive curvature takes over. Beyond x*, a cusp in cac is traced down to T_C* = 25 mK at x = 0.87, locating the critical concentration between x = 0.87 and 0.90. The quantum criticality of this region is recognized by the -log(T/T_0) dependence of C_m/T, which transforms into a T^-q (~0.5) one at x = 0.87. At high temperature, this system shows the onset of valence instability revealed by a deviation from Vegard's law (at x_V~0.75) and increasing hybridization effects on high temperature \chi_dc and \rho. Coincidentally, a Fermi liquid contribution to the specific heat arises from the MV component, which becomes dominant at the CeRh limit. In contrast to antiferromagnetic systems, no C_m/T flattening is observed for x > x_cr rather the mentioned power law divergence, which coincides with a change of sign of \beta. The coexistence of F and MV components and the sudden changes in the T dependencies are discussed in the context of randomly distributed magnetic and Kondo couplings.Comment: 11 pages, 11 figure

Interplay between superconductivity and magnetism in K-doped EuFe2As2

Superconductivity is found in 50% K-doped EuFe2As2 sample below 33 K. Our results of electrical resistivity, magnetic susceptibility and 57Fe and 151Eu Mossbauer spectroscopy provide clear evidence that the ordering of the Fe moments observed at 190 K in undoped EuFe2As2 is completely suppressed in our 50% K doped sample, thus there is no coexistence between the Fe magnetic order and the superconducting state. However, short range ordering of the Eu moments is coexisting with the superconducting state below 15 K. A bump in the susceptibility well below Tc as well as a slight broadening of the Fe Mossbauer line below 15 K evidence an interplay between the Eu magnetism and the superconducting state.Comment: 7 pages, 6 figure

Density fluctuations and single-particle dynamics in liquid lithium

The single-particle and collective dynamical properties of liquid lithium have been evaluated at several thermodynamic states near the triple point. This is performed within the framework of mode-coupling theory, using a self-consistent scheme which, starting from the known static structure of the liquid, allows the theoretical calculation of several dynamical properties. Special attention is devoted to several aspects of the single-particle dynamics, which are discussed as a function of the thermodynamic state. The results are compared with those of Molecular Dynamics simulations and other theoretical approaches.Comment: 31 pages (in preprint format), 14 figures. Submitted to Phys. Rev.

Superconductive "sodalite"-like clathrate calcium hydride at high pressures

Hydrogen-rich compounds hold promise as high-temperature superconductors under high pressures. Recent theoretical hydride structures on achieving high-pressure superconductivity are composed mainly of H2 fragments. Through a systematic investigation of Ca hydrides with different hydrogen contents using particle-swam optimization structural search, we show that in the stoichiometry CaH6 a body-centred cubic structure with hydrogen that forms unusual "sodalite" cages containing enclathrated Ca stabilizes above pressure 150 GPa. The stability of this structure is derived from the acceptance by two H2 of electrons donated by Ca forming a "H4" unit as the building block in the construction of the 3-dimensional sodalite cage. This unique structure has a partial occupation of the degenerated orbitals at the zone centre. The resultant dynamic Jahn-Teller effect helps to enhance electron-phonon coupling and leads to superconductivity of CaH6. A superconducting critical temperature (Tc) of 220-235 K at 150 GPa obtained from the solution of the Eliashberg equations is the highest among all hydrides studied thus far.Comment: 19 pages, 4 figure

Pressure effects on the electron-doped high Tc superconductor BaFe(2-x)Co(x)As(2)

Application of pressures or electron-doping through Co substitution into Fe sites transforms the itinerant antiferromagnet BaFe(2)As(2) into a superconductor with the Tc exceeding 20K. We carried out systematic transport measurements of BaFe(2-x)Co(x)As(2) superconductors in pressures up to 2.5GPa, and elucidate the interplay between the effects of electron-doping and pressures. For the underdoped sample with nominal composition x = 0.08, application of pressure strongly suppresses a magnetic instability while enhancing Tc by nearly a factor of two from 11K to 21K. In contrast, the optimally doped x=0.20 sample shows very little enhancement of Tc=22K under applied pressure. Our results strongly suggest that the proximity to a magnetic instability is the key to the mechanism of superconductivity in iron-pnictides.Comment: 5 figure

Evidence of two viscous relaxation processes in the collective dynamics of liquid lithium

New inelastic X-ray scattering experiments have been performed on liquid lithium in a wide wavevector range. With respect to the previous measurements, the instrumental resolution, improved up to 1.5 meV, allows to accurately investigate the dynamical processes determining the observed shape of the the dynamic structure factor, $S(Q,\omega)$. A detailed analysis of the lineshapes shows the co-existence of relaxation processes with both a slow and a fast characteristic timescales, and therefore that pictures of the relaxation mechanisms based on a simple viscoelastic model must be abandoned.Comment: 5 pages, 4 .PS figure

Sensory Measurements: Coordination and Standardization

Do sensory measurements deserve the label of “measurement”? We argue that they do. They fit with an epistemological view of measurement held in current philosophy of science, and they face the same kinds of epistemological challenges as physical measurements do: the problem of coordination and the problem of standardization. These problems are addressed through the process of “epistemic iteration,” for all measurements. We also argue for distinguishing the problem of standardization from the problem of coordination. To exemplify our claims, we draw on olfactory performance tests, especially studies linking olfactory decline to neurodegenerative disorders

Evidence of short time dynamical correlations in simple liquids

We report a molecular dynamics (MD) study of the collective dynamics of a simple monatomic liquid -interacting through a two body potential that mimics that of lithium- across the liquid-glass transition. In the glassy phase we find evidences of a fast relaxation process similar to that recently found in Lennard-Jones glasses. The origin of this process is ascribed to the topological disorder, i.e. to the dephasing of the different momentum $Q$ Fourier components of the actual normal modes of vibration of the disordered structure. More important, we find that the fast relaxation persists in the liquid phase with almost no temperature dependence of its characteristic parameters (strength and relaxation time). We conclude, therefore, that in the liquid phase well above the melting point, at variance with the usual assumption of {\it un-correlated} binary collisions, the short time particles motion is strongly {\it correlated} and can be described via a normal mode expansion of the atomic dynamics.Comment: 7 pages, 7 .eps figs. To appear in Phys. Rev.

Proceedings of the 2nd Workshop on Flavor Symmetries and Consequences in Accelerators and Cosmology (FLASY12)

These are the proceedings of the 2nd Workshop on Flavor Symmetries and Consequences in Accelerators and Cosmology, held 30 June 2012 - 4 July 2012, Dortmund, Germany.Comment: Order 400 pages, several figures including the group picture v2: corrected author list and contributio