Meshfree finite differences for vector Poisson and pressure Poisson equations with electric boundary conditions

We demonstrate how meshfree finite difference methods can be applied to solve vector Poisson problems with electric boundary conditions. In these, the tangential velocity and the incompressibility of the vector field are prescribed at the boundary. Even on irregular domains with only convex corners, canonical nodal-based finite elements may converge to the wrong solution due to a version of the Babuska paradox. In turn, straightforward meshfree finite differences converge to the true solution, and even high-order accuracy can be achieved in a simple fashion. The methodology is then extended to a specific pressure Poisson equation reformulation of the Navier-Stokes equations that possesses the same type of boundary conditions. The resulting numerical approach is second order accurate and allows for a simple switching between an explicit and implicit treatment of the viscosity terms.Comment: 19 pages, 7 figure

Complexity of biogeographic pattern in the endangered crayfish Austropotamobius italicus in northern Italy: molecular insights of conservation concern.

The protection of freshwater biodiversity has become a priority task for conservation practices, as freshwater ecosystems host high levels of cryptic diversity, while also record similarly high rates of extinction. The Italian white-clawed crayfish Austropotamobius italicus is an endemic freshwater crustacean, threatened by several anthropogenic impacts such as habitat fragmentation, pol- lution, invasion of exotics, and climate change. Previous phylogenetic studies conducted in Italy pointed out a complex phylogeographic framework for the species, with four different subspecies currently recognized. Conserva- tion efforts, particularly when involving restocking and reintroduction, require a detailed knowledge of their pop- ulation genetics. In this study we describe the genetic structure of A. italicus populations in northern Italy (Lombardy Alpine foothills and northern Apennines) by using the informative mitochondrial marker cytochrome c oxidase subunit I, in order to assess their current evolu- tionary diversity and past phylogeographic history from a conservation perspective. Our results contribute to the mapping of the contact area among A. i. carsicus and A. i. carinthiacus in the Orobie Larian Prealps. Moreinterestingly, we highlight the existence of two deeply differentiated evolutionary lineages within A. i. carsicus, showing alternative phylogeographic patterns and past demographic trends. We propose to consider these two clades as distinct molecular operational taxonomic units for the conservation of this endangered crayfish

Strong and auxiliary forms of the semi-Lagrangian method for incompressible flows

We present a review of the semi-Lagrangian method for advection-diusion and incompressible Navier-Stokes equations discretized with high-order methods. In particular, we compare the strong form where the departure points are computed directly via backwards integration with the auxiliary form where an auxiliary advection equation is solved instead; the latter is also referred to as Operator Integration Factor Splitting (OIFS) scheme. For intermediate size of time steps the auxiliary form is preferrable but for large time steps only the strong form is stable

An efficient method for the incompressible Navier-Stokes equations on irregular domains with no-slip boundary conditions, high order up to the boundary

Common efficient schemes for the incompressible Navier-Stokes equations, such as projection or fractional step methods, have limited temporal accuracy as a result of matrix splitting errors, or introduce errors near the domain boundaries (which destroy uniform convergence to the solution). In this paper we recast the incompressible (constant density) Navier-Stokes equations (with the velocity prescribed at the boundary) as an equivalent system, for the primary variables velocity and pressure. We do this in the usual way away from the boundaries, by replacing the incompressibility condition on the velocity by a Poisson equation for the pressure. The key difference from the usual approaches occurs at the boundaries, where we use boundary conditions that unequivocally allow the pressure to be recovered from knowledge of the velocity at any fixed time. This avoids the common difficulty of an, apparently, over-determined Poisson problem. Since in this alternative formulation the pressure can be accurately and efficiently recovered from the velocity, the recast equations are ideal for numerical marching methods. The new system can be discretized using a variety of methods, in principle to any desired order of accuracy. In this work we illustrate the approach with a 2-D second order finite difference scheme on a Cartesian grid, and devise an algorithm to solve the equations on domains with curved (non-conforming) boundaries, including a case with a non-trivial topology (a circular obstruction inside the domain). This algorithm achieves second order accuracy (in L-infinity), for both the velocity and the pressure. The scheme has a natural extension to 3-D.Comment: 50 pages, 14 figure

Excessive antigen reactivity may underlie the clinical aggressiveness of chronic lymphocytic leukemia stereotyped subset #8

Subset #8 is a distinctive subset of patients with chronic lymphocytic leukemia (CLL) defined by the expression of stereotyped IGHV4-39/IGKV1(D)-39 B-cell receptors. Subset #8 patients experience aggressive disease and exhibit the highest risk for Richter transformation among all CLL. In order to obtain biological insight into this behavior, we profiled the antigen reactivity and signaling capacity of subset #8 vs other clinically aggressive stereotyped subsets, namely subsets #1 and #2. Twenty-seven monoclonal antibodies (mAbs) from subsets #1, #2, and #8 CLL clones were prepared as recombinant human immunoglobulin G1 and used as primary antibodies in enzyme-linked immuno-sorbent assays against representatives of the major classes of established antigenic targets for CLL. Subset #8 CLL mAbs exhibited broad polyreactivity as they bound to all antigens tested, in clear contrast with the mAbs from the other subsets. Antigen challenge of primary CLL cells indicated that the promiscuous antigen-binding activity of subset #8 mAbs could lead to significant cell activation, again in contrast to the less responsive CLL cells from subsets #1 and #2. These features constitute a distinctive profile for CLL subset #8, supporting the existence of distinct mechanisms of aggressiveness in different immunogenetic subsets of CLL

Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments

Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution

Search for gamma ray bursts at Chacaltaya

A search for gamma-ray bursts in the GeV–TeV energy range has been performed by INCA, an air shower array working at 5200 m of altitude at the Chacaltaya Laboratory (Bolivia). The altitude of the detector and the use of the “single-particle technique” allows to lower the energy threshold up to few GeVs. No significant signals are observed during the occurrences of 125 GRBs detected by BATSE, and the obtained upper limits on the energy fluence in the interval 1–103 (1–102) GeV, range from 3.2 (8.6) ×10 −5 to 2.6 (7.0) ×10−2 erg cm −2 depending on the zenith angle of the events. These limits, thanks to the extreme altitude of INCA, are the lowest ever obtained in the sub-TeV energy region by a ground-based experiment