Nilpotent Classical Mechanics

The formalism of nilpotent mechanics is introduced in the Lagrangian and Hamiltonian form. Systems are described using nilpotent, commuting coordinates $\eta$. Necessary geometrical notions and elements of generalized differential $\eta$-calculus are introduced. The so called $s-$geometry, in a special case when it is orthogonally related to a traceless symmetric form, shows some resemblances to the symplectic geometry. As an example of an $\eta$-system the nilpotent oscillator is introduced and its supersymmetrization considered. It is shown that the $R$-symmetry known for the Graded Superfield Oscillator (GSO) is present also here for the supersymmetric $\eta$-system. The generalized Poisson bracket for $(\eta,p)$-variables satisfies modified Leibniz rule and has nontrivial Jacobiator.Comment: 23 pages, no figures. Corrected version. 2 references adde

Contact complete integrability

Complete integrability in a symplectic setting means the existence of a Lagrangian foliation leaf-wise preserved by the dynamics. In the paper we describe complete integrability in a contact set-up as a more subtle structure: a flag of two foliations, Legendrian and co-Legendrian, and a holonomy-invariant transverse measure of the former in the latter. This turns out to be equivalent to the existence of a canonical $\R\ltimes \R^{n-1}$ structure on the leaves of the co-Legendrian foliation. Further, the above structure implies the existence of $n$ contact fields preserving a special contact 1-form, thus providing the geometric framework and establishing equivalence with previously known definitions of contact integrability. We also show that contact completely integrable systems are solvable in quadratures. We present an example of contact complete integrability: the billiard system inside an ellipsoid in pseudo-Euclidean space, restricted to the space of oriented null geodesics. We describe a surprising acceleration mechanism for closed light-like billiard trajectories

Invariants of pseudogroup actions: Homological methods and Finiteness theorem

We study the equivalence problem of submanifolds with respect to a transitive pseudogroup action. The corresponding differential invariants are determined via formal theory and lead to the notions of k-variants and k-covariants, even in the case of non-integrable pseudogroup. Their calculation is based on the cohomological machinery: We introduce a complex for covariants, define their cohomology and prove the finiteness theorem. This implies the well-known Lie-Tresse theorem about differential invariants. We also generalize this theorem to the case of pseudogroup action on differential equations.Comment: v2: some remarks and references addee

Special symplectic Lie groups and hypersymplectic Lie groups

A special symplectic Lie group is a triple $(G,\omega,\nabla)$ such that $G$ is a finite-dimensional real Lie group and $\omega$ is a left invariant symplectic form on $G$ which is parallel with respect to a left invariant affine structure $\nabla$. In this paper starting from a special symplectic Lie group we show how to ``deform" the standard Lie group structure on the (co)tangent bundle through the left invariant affine structure $\nabla$ such that the resulting Lie group admits families of left invariant hypersymplectic structures and thus becomes a hypersymplectic Lie group. We consider the affine cotangent extension problem and then introduce notions of post-affine structure and post-left-symmetric algebra which is the underlying algebraic structure of a special symplectic Lie algebra. Furthermore, we give a kind of double extensions of special symplectic Lie groups in terms of post-left-symmetric algebras.Comment: 32 page

Nambu-Poisson manifolds and associated n-ary Lie algebroids

We introduce an n-ary Lie algebroid canonically associated with a Nambu-Poisson manifold. We also prove that every Nambu-Poisson bracket defined on functions is induced by some differential operator on the exterior algebra, and characterize such operators. Some physical examples are presented

Poisson-Jacobi reduction of homogeneous tensors

The notion of homogeneous tensors is discussed. We show that there is a one-to-one correspondence between multivector fields on a manifold $M$, homogeneous with respect to a vector field $\Delta$ on $M$, and first-order polydifferential operators on a closed submanifold $N$ of codimension 1 such that $\Delta$ is transversal to $N$. This correspondence relates the Schouten-Nijenhuis bracket of multivector fields on $M$ to the Schouten-Jacobi bracket of first-order polydifferential operators on $N$ and generalizes the Poissonization of Jacobi manifolds. Actually, it can be viewed as a super-Poissonization. This procedure of passing from a homogeneous multivector field to a first-order polydifferential operator can be also understood as a sort of reduction; in the standard case -- a half of a Poisson reduction. A dual version of the above correspondence yields in particular the correspondence between $\Delta$-homogeneous symplectic structures on $M$ and contact structures on $N$.Comment: 19 pages, minor corrections, final version to appear in J. Phys. A: Math. Ge

Analysis of Multiple Sarcoma Expression Datasets: Implications for Classification, Oncogenic Pathway Activation and Chemotherapy Resistance

Background: Diagnosis of soft tissue sarcomas (STS) is challenging. Many remain unclassified (not-otherwise-specified, NOS) or grouped in controversial categories such as malignant fibrous histiocytoma (MFH), with unclear therapeutic value. We analyzed several independent microarray datasets, to identify a predictor, use it to classify unclassifiable sarcomas, and assess oncogenic pathway activation and chemotherapy response. Methodology/Principal Findings: We analyzed 5 independent datasets (325 tumor arrays). We developed and validated a predictor, which was used to reclassify MFH and NOS sarcomas. The molecular “match” between MFH and their predicted subtypes was assessed using genome-wide hierarchical clustering and Subclass-Mapping. Findings were validated in 15 paraffin samples profiled on the DASL platform. Bayesian models of oncogenic pathway activation and chemotherapy response were applied to individual STS samples. A 170-gene predictor was developed and independently validated (80-85% accuracy in all datasets). Most MFH and NOS tumors were reclassified as leiomyosarcomas, liposarcomas and fibrosarcomas. “Molecular match” between MFH and their predicted STS subtypes was confirmed both within and across datasets. This classification revealed previously unrecognized tissue differentiation lines (adipocyte, fibroblastic, smooth-muscle) and was reproduced in paraffin specimens. Different sarcoma subtypes demonstrated distinct oncogenic pathway activation patterns, and reclassified MFH tumors shared oncogenic pathway activation patterns with their predicted subtypes. These patterns were associated with predicted resistance to chemotherapeutic agents commonly used in sarcomas. Conclusions/Significance: STS profiling can aid in diagnosis through a predictor tracking distinct tissue differentiation in unclassified tumors, and in therapeutic management via oncogenic pathway activation and chemotherapy response assessment

Poisson structures for reduced non-holonomic systems

Borisov, Mamaev and Kilin have recently found certain Poisson structures with respect to which the reduced and rescaled systems of certain non-holonomic problems, involving rolling bodies without slipping, become Hamiltonian, the Hamiltonian function being the reduced energy. We study further the algebraic origin of these Poisson structures, showing that they are of rank two and therefore the mentioned rescaling is not necessary. We show that they are determined, up to a non-vanishing factor function, by the existence of a system of first-order differential equations providing two integrals of motion. We generalize the form of that Poisson structures and extend their domain of definition. We apply the theory to the rolling disk, the Routh's sphere, the ball rolling on a surface of revolution, and its special case of a ball rolling inside a cylinder.Comment: 22 page

Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes

Chromosome aberrations in two glioma cell lines were analyzed using biotinylated DNA library probes that specifically decorate chromosomes 1, 4, 7, 18 and 22 from pter to qter. Numerical changes, deletions and rearrangements of these chromosomes were radily visualized in metaphase spreads, as well as in early prophase and interphase nuclei. Complete chromosomes, deleted chromosomes and segments of translocated chromosomes were rapidly delineated in very complex karyotypes. Simultaneous hybridizations with additional subregional probes were used to further define aberrant chromosomes. Digital image analysis was used to quantitate the total complement of specific chromosomal DNAs in individual metaphase and interphase cells of each cell line. In spite of the fact that both glioma lines have been passaged in vitro for many years, an under-representation of chromosome 22 and an over-representation of chromosome 7 (specifically 7p) were observed. These observations agree with previous studies on gliomas. In addition, sequences of chromosome 4 were also found to be under-represented, especially in TC 593. These analyses indicate the power of these methods for pinpointing chromosome segments that are altered in specific types of tumors

Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1

Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i-->i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, alpha-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable alpha-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ~9 kcal/mol, but this was compensated by increased conformational entropy (TDS ≤ 7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by alpha-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases