Partial Ovoids and Partial Spreads of Classical Finite Polar Spaces

2000 Mathematics Subject Classification: 05B25, 51E20.We survey the main results on ovoids and spreads, large maximal partial ovoids and large maximal partial spreads, and on small maximal partial ovoids and small maximal partial spreads in classical finite polar spaces. We also discuss the main results on the spectrum problem on maximal partial ovoids and maximal partial spreads in classical finite polar spaces.The research of the fourth author was also supported by the Project Combined algorithmic and the oretical study of combinatorial structur es between the Fund for Scientific Research Flanders-Belgium (FWO-Flanders) and the Bulgarian Academy of Science

SigsPack, a package for cancer mutational signatures

BACKGROUND: Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studies, and some of them have been linked to known oncogenic processes. Identification of the processes contributing to mutations observed in a sample is potentially informative to understand the cancer etiology. RESULTS: We present here SigsPack, a Bioconductor package to estimate a sample's exposure to mutational processes described by a set of mutational signatures. The package also provides functions to estimate stability of these exposures, using bootstrapping. The performance of exposure and exposure stability estimations have been validated using synthetic and real data. Finally, the package provides tools to normalize the mutation frequencies with respect to the tri-nucleotide contents of the regions probed in the experiment. The importance of this effect is illustrated in an example. CONCLUSION: SigsPack provides a complete set of tools for individual sample exposure estimation, and for mutation catalogue & mutational signatures normalization

New particle-hole symmetries and the extended interacting boson model

We describe shape coexistence and intruder many-particle-hole (mp-nh)excitations in the extended interacting boson model EIBM and EIBM-2,combining both the particle-hole and the charge degree of freedom.Besides the concept of I-spin multiplets and subsequently $SU(4)$ multiplets, we touch upon the existence of particle-hole mixed symmetry states. We furthermore describe regular and intrudermany-particle-hole excitations in one nucleus on an equal footing, creating (annihilating) particle-hole pairs using the K-spin operatorand studying possible mixing between these states. As a limiting case,we treat the coupling of two IBM-1 Hamiltonians, each decribing the regular and intruder excitations respectively, in particular lookingat the $U(5)$-$SU(3)$ dynamical symmetry coupling. We apply such coupling scheme to the Po isotopes

Shape coexistence in atomic nuclei and its spectroscopic fingerprints

In the present discussion we concentrate on shape coexistence asobtained within a deformed single-particle field as well as startingfrom the spherical shell-model, incorporating deformationeffects via the residual proton-neutron quadrupole interaction. Wediscuss in particular the appearance of shape coexisting phenomena inthe Pb region. In a second part then, we present a number ofexperimental fingerprints that allow to recognize the appearance ofshape coexisting phenomena or of shape mixing through the use ofselective experiments (e.g. band structure, spectroscopic factors,static moments, E0 properties and alpha-decay)

Identification and ranking of recurrent neo-epitopes in cancer

BACKGROUND: Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognition process lies antigen presentation from somatic mutations. These neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. METHOS: We carefully screen TCGA data sets for recurrent somatic amino acid exchanges and apply MHC class I binding predictions. RESULTS: We propose a method for in silico selection and prioritization of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. While the percentage of patients carrying a specific neo-epitope and HLA-type combination is relatively small, the sheer number of new patients leads to surprisingly high reoccurence numbers. We identify 769 epitopes which are expected to occur in 77629 patients per year. CONCLUSION: While our candidate list will definitely contain false positives, the results provide an objective order for wet-lab testing of reusable neo-epitopes. Thus recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options

Identification and ranking of recurrent neo-epitopes in cancer

Neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. We propose a method for in silico selection of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. This is achieved by carefully screening 33 TCGA data sets for recurrent somatic amino acid exchanges and, for the 1,055 resulting recurrent variants, applying MHC class I binding prediction algorithms. A preliminary confirmation of epitope binding and recognition by CD8 T cells has been carried out for a couple of candidates in humanized mice. Recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options