No abstract

Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in single cells has been challenging, with copy-numberneutral and complex variants typically escaping detection. Here we describe single-cell tri-channel processing (scTRIP), a computational framework that integrates read depth, template strand and haplotype phase to comprehensively discover SVs in individual cells. We surveyed SV landscapes of 565 single cells, including transformed epithelial cells and patient-derived leukemic samples, to discover abundant SV classes, including inversions, translocations and complex DNA rearrangements. Analysis of the leukemic samples revealed four times more somatic SVs than cytogenetic karyotyping, submicroscopic copy-number alterations, oncogenic copy-neutral rearrangements and a subclonal chromothripsis event. Advancing current methods, single-cell tri-channel processing can directly measure SV mutational processes in individual cells, such as breakage-fusion-bridge cycles, facilitating studies of clonal evolution, genetic mosaicism and SV formation mechanisms, which could improve disease classification for precision medicine.

No abstract

The volume reflection phenomenon was detected while investigating 400 GeV proton interactions with bent silicon crystals in the external beam H8 of the CERN Super Proton Synchrotron. Such a process was observed for a wide interval of crystal orientations relative to the beam axis, and its efficiency exceeds 95%, thereby surpassing any previously observed value. These observations suggest new perspectives for the manipulation of high-energy beams, e.g., for collimation and extraction in new-generation hadron colliders, such as the CERN Large Hadron Collider.

The trend of volume reflection parameters (deflection angle and efficiency) in a bent (110) silicon crystal has been investigated as a function of the crystal curvature with 400 GeV/c protons on the H8 beam line at the CERN Super Proton Synchrotron. This Letter describes the analysis performed at six different curvatures showing that the optimal radius for volume reflection is approximately 10 times greater than the critical radius for channeling. A strong scattering of the beam by the planar potential is also observed for a bend radius close to the critical one.

Abstract. We classify the bipartite graphs G whose binomial edge ideal JG is Cohen-Macaulay. The connected components of such graphs can be obtained by gluing a finite number of basic blocks with two operations. In this context we prove the converse of a well-known result due to Hartshorne, showing that the Cohen-Macaulayness of these ideals is equivalent to the connectedness of their dual graphs. We study interesting properties also for non-bipartite graphs and in the unmixed case, constructing classes of bipartite graphs with JG unmixed and not Cohen-Macaulay.

Deflection due to planar channeling and volume reflection in short bent silicon crystals was observed for the first time for 150 GeV/c negative particles, pi(-) mesons, at one of the secondary beams of the CERN SPS. The deflection efficiency was about 30% for channeling and higher than 80% for volume reflection. Volume reflection occurs, in spite of the attractive character of the forces acting between the particles and the crystal planes, in a wide angular range of the crystal orientations determined by the crystal bend angle

Channeling in a short bent silicon crystal was investigated at the CERN SPS using 400-GeV/c protons with an angular spread much narrower than the critical channeling angle. Particle dechanneling due to multiple scattering on the atomic nuclei of the crystal was observed and its dechanneling length was measured to be about 1.5 mm. For a crystal with length comparable to such dechanneling length, an efficiency of 83.4% was recorded, which is close to the maximum value expected for a parallel beam and exceeds the previously known limitation of deflection efficiency for long crystal