A detailed inventory of DNA copy number alterations in four commonly used Hodgkin's lymphoma cell lines

Background and Objectives Classical Hodgkin's lymphoma (cHL) is a common malignant lymphoma characterized by the presence of large, usually multinucleated malignant Hodgkin and Reed Sternberg (HRS) cells which are thought to be derived from germinal center B-cells. In cHL, the HRS cells constitute less than 1% of the tumor volume; consequently the profile of genetic aberrations in cHL is still poorly understood. Design and Methods In this study, we subjected four commonly used cHL cell lines to array comparative genomic hybridization (aCGH) in order to delineate known chromosomal aberrations in more detail and to search for small hitherto undetected genomic imbalances. Results The aCGH profiles of the four cell lines tested confirmed the complex patterns of rearrangements previously demonstrated with multicolor fluorescence in situ hybridization and chromosomal CGH (cCGH). Importantly, aCGH allowed a much more accurate delineation of imbalances as compared to previous studies performed at a chromosomal level of resolution. Furthermore, we detected 35 hitherto undetected aberrations including a homozygous deletion of chromosomal region 15q26.2 in the cell line HDLM2 encompasing RGMA and CHD2 and an amplification of the STAT6 gene in cell line L1236 leading to STAT6 overexpression. Finally, in cell line KM-H2 we found a 2.35 Mb deletion at 16q12.1 putatively defining a small critical region for the recurrent 16q deletion in cHL. This region contains the CYLD gene, a known suppressor gene of the NF-kappa B pathway. Interpretation and Conclusions aCGH was performed on four cHL cell lines leading to the improved delineation of known chromosomal imbalances and the detection of 35 hitherto undetected aberrations. More specifically, our results highlight STAT6 as a potential transcriptional target and identified RGMA, CHD2 and CYLD as candidate tumor suppressors in cHL

On the Optimal Space Complexity of Consensus for Anonymous Processes

The optimal space complexity of consensus in shared memory is a decades-old open problem. For a system of $n$ processes, no algorithm is known that uses a sublinear number of registers. However, the best known lower bound due to Fich, Herlihy, and Shavit requires $\Omega(\sqrt{n})$ registers. The special symmetric case of the problem where processes are anonymous (run the same algorithm) has also attracted attention. Even in this case, the best lower and upper bounds are still $\Omega(\sqrt{n})$ and $O(n)$. Moreover, Fich, Herlihy, and Shavit first proved their lower bound for anonymous processes, and then extended it to the general case. As such, resolving the anonymous case might be a significant step towards understanding and solving the general problem. In this work, we show that in a system of anonymous processes, any consensus algorithm satisfying nondeterministic solo termination has to use $\Omega(n)$ read-write registers in some execution. This implies an $\Omega(n)$ lower bound on the space complexity of deterministic obstruction-free and randomized wait-free consensus, matching the upper bound and closing the symmetric case of the open problem

Dva-ločno-tranzitivni dvo-valentni digrafi določenih redov

The topic of this paper is digraphs of in-valence and out-valence 2 that admit a 2-arc-transitive group of automorphisms. We classify such digraphs that satisfy certain additional conditions on their order. In particular, a classification of those with order ▫$kp$▫ or ▫$kp^{2}$▫ where ▫$k leq 14$▫ and ▫$p$▫ is a prime can be deduced from the results of this paper.Tema tega članka so digrafi vhodne in izhodne valence 2, ki dopuščajo 2-ločno-tranzitivno grupo avtomorfizmov. Klasificiramo takšne digrafe, ki zadoščajo določenim dodatnim pogojem glede njihovega reda. Tako je npr. mogoče s pomočjo rezultatov tega članka klasificirati tiste, ki imajo red ▫$kp$▫ ali ▫$kp^{2}$▫, kjer je ▫$k leq 14$▫ in je ▫$p$▫ praštevilo

Integrating sequence with FPC fingerprint maps

Recent advances in both clone fingerprinting and draft sequencing technology have made it increasingly common for species to have a bacterial artificial clone (BAC) fingerprint map, BAC end sequences (BESs) and draft genomic sequence. The FPC (fingerprinted contigs) software package contains three modules that maximize the value of these resources. The BSS (blast some sequence) module provides a way to easily view the results of aligning draft sequence to the BESs, and integrates the results with the following two modules. The MTP (minimal tiling path) module uses sequence and fingerprints to determine a minimal tiling path of clones. The DSI (draft sequence integration) module aligns draft sequences to FPC contigs, displays them alongside the contigs and identifies potential discrepancies; the alignment can be based on either individual BES alignments to the draft, or on the locations of BESs that have been assembled into the draft. FPC also supports high-throughput fingerprint map generation as its time-intensive functions have been parallelized for Unix-based desktops or servers with multiple CPUs. Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available

Advances in Discrete Applied Mathematics and Graph Theory

The present reprint contains twelve papers published in the Special Issue “Advances in Discrete Applied Mathematics and Graph Theory, 2021” of the MDPI Mathematics journal, which cover a wide range of topics connected to the theory and applications of Graph Theory and Discrete Applied Mathematics. The focus of the majority of papers is on recent advances in graph theory and applications in chemical graph theory. In particular, the topics studied include bipartite and multipartite Ramsey numbers, graph coloring and chromatic numbers, several varieties of domination (Double Roman, Quasi-Total Roman, Total 3-Roman) and two graph indices of interest in chemical graph theory (Sombor index, generalized ABC index), as well as hyperspaces of graphs and local inclusive distance vertex irregular graphs