MassUntangler: a novel alignment tool for label-free liquid chromatography-mass spectrometry proteomic data

Liquid chromatography-mass spectrometry (LC-MS) has become an important analytical tool for quantitative proteomics and biomarker discovery. In the label-free differential LC-MS approach computational methods are required for an accurate alignment of peaks extrapolated from the experimental raw data accounting for retention time and m/z signals intensity, which are strongly affected by sample matrix and instrumental performance. A novel procedure "MassUntangler" for pairwise alignment has been developed, relying on a pattern-based matching algorithm integrated with filtering algorithms in a multi-step approach. The procedure has been optimized employing a two-step approach. Firstly, low-complexity LC-MS data derived from the enzymatic digestion of two standard proteins have been analyzed. Then, the algorithm's performance has been evaluated by comparing the results with other achieved using state-of-the-art alignment tools. In the second step, our algorithm has been used for the alignment of high-complexity LC-MS data consisting of peptides obtained by an Escherichia coli lysate available from a public repository previously used for the comparison of other alignment tools. MassUntangler gave excellent results in terms of precision scores (from 80% to 93%) and recall scores (from 68% to 89%), showing performances similar and even better than the previous developed tools. Considering the mass spectrometry sensitivity and accuracy, this approach allows the identification and quantification of peptides present in a biological sample at femtomole level with high confidence. The procedure's capability of aligning LC-MS data previously corrected for distortion in retention time has been studied through a hybrid approach, in which MassUntangler was interfaced with the OpenMS TOPP tool MapAligner. The hybrid aligner yielded better results, showing that an integration of different bioinformatic approaches for accurate label-free LC-MS data alignment should be used.     

Pointwise characterizations of Besov and Triebel–Lizorkin spaces and quasiconformal mappings

In this paper, the authors characterize, in terms of pointwise inequalities, the classical Besov spaces and Triebel–Lizorkin spaces for all s∈(0,1) and p,q∈(n/(n+s),∞], both in Rn and in the metric measure spaces enjoying the doubling and reverse doubling properties. Applying this characterization, the authors prove that quasiconformal mappings preserve on Rn for all s∈(0,1) and q∈(n/(n+s),∞]. A metric measure space version of the above morphism property is also established.     

Multiplication operators on the Bergman space via analytic continuation

In this paper, using the group-like property of local inverses of a finite Blaschke product ?, we will show that the largest C^?-algebra in the commutant of the multiplication operator M? by ? on the Bergman space is finite dimensional, and its dimension equals the number of connected components of the Riemann surface of ?−1°? over the unit disk. If the order of the Blaschke product ? is less than or equal to eight, then every C^?-algebra contained in the commutant of M? is abelian and hence the number of minimal reducing subspaces of M? equals the number of connected components of the Riemann surface of ?−1°? over the unit disk.     

A combinatorial formula for Macdonald polynomials

In this paper we use the combinatorics of alcove walks to give uniform combinatorial formulas for Macdonald polynomials for all Lie types. These formulas resemble the formulas of Haglund, Haiman and Loehr for Macdonald polynomials of type GLn. At q=0 these formulas specialize to the formula of Schwer for the Macdonald spherical function in terms of positively folded alcove walks and at q=t=0 these formulas specialize to the formula for the Weyl character in terms of the Littelmann path model (in the positively folded gallery form of Gaussent and Littelmann).     

Extended Deligne–Lusztig varieties for general and special linear groups

We give a generalisation of Deligne–Lusztig varieties for general and special linear groups over finite quotients of the ring of integers in a non-archimedean local field. Previously, a generalisation was given by Lusztig by attaching certain varieties to unramified maximal tori inside Borel subgroups. In this paper we associate a family of so-called extended Deligne–Lusztig varieties to all tamely ramified maximal tori of the group.Moreover, we analyse the structure of various generalised Deligne–Lusztig varieties, and show that the “unramified” varieties, including a certain natural generalisation, do not produce all the irreducible representations in general. On the other hand, we prove results which together with some computations of Lusztig show that for SL₂(Fq???/(?²)), with odd q, the extended Deligne–Lusztig varieties do indeed afford all the irreducible representations.     

Integral Menger curvature for surfaces

We develop the concept of integral Menger curvature for a large class of nonsmooth surfaces. We prove uniform Ahlfors regularity and a C1,λ-a priori bound for surfaces for which this functional is finite. In fact, it turns out that there is an explicit length scale R>0 which depends only on an upper bound E for the integral Menger curvature Mp(Σ) and the integrability exponent p, and not on the surface Σ itself; below that scale, each surface with energy smaller than E looks like a nearly flat disc with the amount of bending controlled by the (local) Mp-energy. Moreover, integral Menger curvature can be defined a priori for surfaces with self-intersections or branch points; we prove that a posteriori all such singularities are excluded for surfaces with finite integral Menger curvature. By means of slicing and iterative arguments we bootstrap the Hölder exponent λ up to the optimal one, λ=1−(8/p), thus establishing a new geometric ‘Morrey–Sobolev’ imbedding theorem.As two of the various possible variational applications we prove the existence of surfaces in given isotopy classes minimizing integral Menger curvature with a uniform bound on area, and of area minimizing surfaces subjected to a uniform bound on integral Menger curvature.     

Hochster's theta invariant and the Hodge–Riemann bilinear relations

Let R be an isolated hypersurface singularity, and let M and N be finitely generated R-modules. As R is a hypersurface, the torsion modules of M against N are eventually periodic of period two (i.e., for i?0). Since R has only an isolated singularity, these torsion modules are of finite length for i?0. The theta invariant of the pair (M,N) is defined by Hochster to be for i?0. H. Dao has conjectured that the theta invariant is zero for all pairs (M,N) when R has even dimension and contains a field. This paper proves this conjecture under the additional assumption that R is graded with its irrelevant maximal ideal giving the isolated singularity. We also give a careful analysis of the theta pairing when the dimension of R is odd, and relate it to a classical pairing on the smooth variety Proj(R).     

Fisher information and matrix-valued valuations

All continuous and affinely contravariant matrix-valued valuations on the Sobolev space W1,2(Rn) are completely classified. It is shown that there is a unique such valuation. This valuation turns out to be the Fisher information matrix.     

Smoothness of the moduli space of complexes of coherent sheaves on an abelian or a projective K3 surface

For an abelian or a projective K3 surface X over an algebraically closed field k, consider the moduli space of the objects E in Db(Coh(X)) satisfying and Hom(E,E)≅k. Then we can prove that is smooth and has a symplectic structure.