Bidirectional Optimality Theory allows us to see a wide range of problems which would previously have been considered unrelated from a new perspective, the perspective of asymmetric relationships between input and output. For interpretation, the input is a form and the output a meaning, and for production the input is a meaning and the output is a form. A mismatch is any case where there is no ...

In this paper, we consider several variants of the pattern matching with mismatches problem. In particular, given a text T = t1t2 · · · tn and a pattern P = p1p2 · · · pm, we investigate the following problems: (1) pattern matching with mismatches: for every i, 1 ≤ i ≤ n −m + 1 output, the distance between P and titi+1 · · · ti+m−1; and (2) pattern matching with k mismatches: output those posit...

The development of the semantic web ensures that the facilitation of agent communication is an issue of increasing importance. It is usually assumed that agents are using the same ontology and hence can understand one another, but the dynamic and distributed nature of the semantic web mean that this is not always a valid assumption. In this paper, we describe a system under construction that ca...

HLA matching provides numerous benefits in organ transplantation including better graft function, fewer rejection episodes, longer graft survival, and the possibility of reduced immunosuppression. Mismatches are attended by more frequent rejection episodes that require increased immunosuppression that, in turn, can increase the risk of infection and malignancy. HLA mismatches also incur the ris...

Mismatch repair (MMR) corrects replication errors such as mismatched bases and loops in DNA. The evolutionarily conserved dimeric MMR protein MutS recognizes mismatches by stacking a phenylalanine of one subunit against one base of the mismatched pair. In all crystal structures of G:T mismatch-bound MutS, phenylalanine is stacked against thymine. To explore whether these structures reflect dire...

Monitoring and adaptation of multilayer systems are challenging, because the mismatches and adaptations are interrelated across the layers. This interrelation introduces two important but difficult questions. 1) When a system change causes mismatches in one layer, how to identify all the cascaded mismatches on the other layers? 2) When an adaptation is performed at one layer, how to find out al...

HLA matching between the donor and recipient improves the success of unrelated hematopoietic cell transplantation (HCT). Matched donors are available for only a minority of patients. Further information is needed to evaluate the limits of HLA mismatching. We examined the association of mortality with HLA-A, -B, -C, -DRB1, and -DQB1 mismatching in 948 patients who received a T-replete unrelated ...

We consider the problem of pattern matching with k mismatches, where there can be don't care or wild card characters in the pattern. Specifically, given a pattern P of length m and a text T of length n, we want to find all occurrences of P in T that have no more than k mismatches. The pattern can have don't care characters, which match any character. Without don't cares, the best known algorith...

Despite the potential of domain ontologies to provide consensual representations of domain-relevant knowledge, the open, distributed and decentralized nature of the Semantic Web means that individuals will rarely, if ever, countenance a common set of terminological and representational commitments during the ontology design process. More often than not, differences between ontologies are likely...