73 research outputs found
EBV in Hodgkin Lymphoma
Up to 40% of Hodgkin lymphoma (HL) cases are associated with the Epstein-Barr virus (EBV). Clonal viral genomes can be found in the HL tumor cells, the Hodgkin Reed-Sternberg cells (HRS). The latent infection results in expression of the viral oncogenes LMP1 and LMP2A which contribute to generate the particular phenotype of the HRS cells. EBV does not only undergo epigenetic changes of its genome during latency, but also induces epigenetic changes in the host genome. The presence of EBV may alter the composition and activity of the immune cells surrounding the HRS cells. EBV favours a Th1 reaction, but this attempt at a cell mediated immune response appears to be ineffective. The presence of EBV in HL is associated with several clinicopathological characteristics: It is more frequent in cases with mixed cellular histology, in males, in children and older adults, and in developing countries, while the young-adult onset HL of nodular sclerosis type in industrialized countries is typically EBV-negative. Countries in the Mediterranean area often show an intermediate epidemiological pattern. Recent studies suggest a genetic predisposition to develop EBV-associated HL. Circulating EBV-DNA may serve as a biomarker to monitor response to therapy, and eventually, EBV will become a target for therapeutic intervention also in HL
Matching Patterns with Variables Under Edit Distance
A pattern is a string of variables and terminal letters. We say that
matches a word , consisting only of terminal letters, if can be
obtained by replacing the variables of by terminal words. The matching
problem, i.e., deciding whether a given pattern matches a given word, was
heavily investigated: it is NP-complete in general, but can be solved
efficiently for classes of patterns with restricted structure. If we are
interested in what is the minimum Hamming distance between and any word
obtained by replacing the variables of by terminal words (so matching
under Hamming distance), one can devise efficient algorithms and matching
conditional lower bounds for the class of regular patterns (in which no
variable occurs twice), as well as for classes of patterns where we allow
unbounded repetitions of variables, but restrict the structure of the pattern,
i.e., the way the occurrences of different variables can be interleaved.
Moreover, under Hamming distance, if a variable occurs more than once and its
occurrences can be interleaved arbitrarily with those of other variables, even
if each of these occurs just once, the matching problem is intractable. In this
paper, we consider the problem of matching patterns with variables under edit
distance. We still obtain efficient algorithms and matching conditional lower
bounds for the class of regular patterns, but show that the problem becomes, in
this case, intractable already for unary patterns, consisting of repeated
occurrences of a single variable interleaved with terminals
Matching Patterns with Variables Under Hamming Distance
A pattern ? is a string of variables and terminal letters. We say that ? matches a word w, consisting only of terminal letters, if w can be obtained by replacing the variables of ? by terminal words. The matching problem, i.e., deciding whether a given pattern matches a given word, was heavily investigated: it is NP-complete in general, but can be solved efficiently for classes of patterns with restricted structure. In this paper, we approach this problem in a generalized setting, by considering approximate pattern matching under Hamming distance. More precisely, we are interested in what is the minimum Hamming distance between w and any word u obtained by replacing the variables of ? by terminal words. Firstly, we address the class of regular patterns (in which no variable occurs twice) and propose efficient algorithms for this problem, as well as matching conditional lower bounds. We show that the problem can still be solved efficiently if we allow repeated variables, but restrict the way the different variables can be interleaved according to a locality parameter. However, as soon as we allow a variable to occur more than once and its occurrences can be interleaved arbitrarily with those of other variables, even if none of them occurs more than once, the problem becomes intractable
Combinatorial Algorithms for Subsequence Matching: A Survey
In this paper we provide an overview of a series of recent results regarding
algorithms for searching for subsequences in words or for the analysis of the
sets of subsequences occurring in a word.Comment: This is a revised version of the paper with the same title which
appeared in the Proceedings of NCMA 2022, EPTCS 367, 2022, pp. 11-27 (DOI:
10.4204/EPTCS.367.2). The revision consists in citing a series of relevant
references which were not covered in the initial version, and commenting on
how they relate to the results we survey. arXiv admin note: text overlap with
arXiv:2206.1389
Longest Common Subsequence with Gap Constraints
We consider the longest common subsequence problem in the context of
subsequences with gap constraints. In particular, following Day et al. 2022, we
consider the setting when the distance (i. e., the gap) between two consecutive
symbols of the subsequence has to be between a lower and an upper bound (which
may depend on the position of those symbols in the subsequence or on the
symbols bordering the gap) as well as the case where the entire subsequence is
found in a bounded range (defined by a single upper bound), considered by
Kosche et al. 2022. In all these cases, we present effcient algorithms for
determining the length of the longest common constrained subsequence between
two given strings
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