Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Quantum Gravity as a Dissipative Deterministic System

It is argued that the so-called holographic principle will obstruct attempts to produce physically realistic models for the unification of general relativity with quantum mechanics, unless determinism in the latter is restored. The notion of time in GR is so different from the usual one in elementary particle physics that we believe that certain versions of hidden variable theories can -- and must -- be revived. A completely natural procedure is proposed, in which the dissipation of information plays an essential role. Unlike earlier attempts, it allows us to use strictly continuous and differentiable classical field theories as a starting point (although discrete variables, leading to fermionic degrees of freedom, are also welcome), and we show how an effective Hilbert space of quantum states naturally emerges when one attempts to describe the solutions statistically. Our theory removes some of the mysteries of the holographic principle; apparently non-local features are to be expected when the quantum degrees of freedom of the world are projected onto a lower-dimensional black hole horizon. Various examples and models illustrate the points we wish to make, notably a model showing that massless, non interacting neutrinos are deterministic.Comment: 20 pages plain TeX, 2 figures PostScript. Added some further explanations, and the definitions of `beable' and `changeable'. A minor error correcte

Monopole Condensation and Color Confinement

New evidence is discussed of monopole condensation in the vacuum of SU(2) and SU(3) gauge theories. Monopoles defined by different abelian projections do condense in the transition to the confined phase and show the same behavior. For SU(2) critical indices are determined by finite size scaling analysis and the results agree with the 3d Ising Model, as expected.Comment: LATTICE98(confinement),3 pages,4 figure

A Mean Field Approximation to the Worldsheet Model of Planar phi^3 Field Theory

We develop an approximation scheme for our worldsheet model of the sum of planar diagrams based on mean field theory. At finite coupling the mean field equations show a weak coupling solution that resembles the perturbative diagrams and a strong coupling solution that seems to represent a tensionless soup of field quanta. With a certain amount of fine-tuning, we find a solution of the mean field equations that seems to support string formation.Comment: 27 pages, 10 figures, typos corrected, appendix on slowly varying mean fields adde

Vortices versus monopoles in color confinement

We construct the creation operator of a vortex for SU(2) pure gauge theory using the methods developed for monopoles. We interpret its vacuum expectation value as a disorder parameter for the deconfinement phase transition and find that it behaves in the vacuum in a similar way to monopoles. Results are extrapolated to the thermodynamical limit using finite-size scaling.Comment: Talk presented at Lattice2000 (Topology and Vacuum), 4 page

Black Hole Evaporation without Information Loss

An approach to black hole quantization is proposed wherein it is assumed that quantum coherence is preserved. A consequence of this is that the Penrose diagram describing gravitational collapse will show the same topological structure as flat Minkowski space. After giving our motivations for such a quantization procedure we formulate the background field approximation, in which particles are divided into "hard" particles and "soft" particles. The background space-time metric depends both on the in-states and on the out-states. We present some model calculations and extensive discussions. In particular, we show, in the context of a toy model, that the $S$-matrix describing soft particles in the hard particle background of a collapsing star is unitary, nevertheless, the spectrum of particles is shown to be approximately thermal. We also conclude that there is an important topological constraint on functional integrals.Comment: 35 pages (including Figures); TEX, 3 figures in postscrip

Subcritical String and Large N QCD

We pursue the possibility of using subcritical string theory in 4 space-time dimensions to establish a string dual for large N QCD. In particular we study the even G-parity sector of the 4 dimensional Neveu-Schwarz dual resonance model as the natural candidate for this string theory. Our point of view is that the open string dynamics given by this model will {\it determine} the appropriate subcritical closed string theory, a tree level background of which should describe the sum of planar multi-loop open string diagrams. We examine the one loop open string diagram, which contains information about the closed string spectrum at weak coupling. Higher loop open string diagrams will be needed to determine closed string interactions. We also analyze the field theory limit of the one loop open string diagram and recover the correct running coupling behavior of the limiting gauge theory.Comment: 18 pages, 2 figures, error in eqs 46 and 47 correcte

Chern-Simons term in the 4-dimensional SU(2) Higgs Model

Using Seiberg's definition for the geometric charge in SU(2) lattice gauge theory, we have managed to apply it also to the Chern-Simons term. We checked the periodic structure and determined the Chern-Simons density on small lattices $L^4$ and $L^3 \times 2,\, 4$ with L=4,\, 6,\mbox{ and }8 near the critical region in the SU(2) Higgs model. The data indicate that tunneling is increased at high temperature.Comment: 7 pages plus 4 PS figure

Symmetry breaking via fermion 4-point functions

We construct the effective action and gap equations for nonperturbative fermion 4-point functions. Our results apply to situations in which fermion masses can be ignored, which is the case for theories of strong flavor interactions involving standard quarks and leptons above the electroweak scale. The structure of the gap equations is different from what a naive generalization of the 2-point case would suggest, and we find for example that gauge exchanges are insufficient to generate nonperturbative 4-point functions when the number of colors is large.Comment: 36 pages, uses Revtex and eps files for figure