The Swap Matching Problem Revisited

In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using the model, we devise two efficient algorithms to solve the swap matching problem. The resulting algorithms are adaptations of the classic shift-and algorithm. For patterns having length similar to the word-size of the target machine, both the algorithms run in linear time considering a fixed alphabet.Comment: 23 pages, 3 Figures and 17 Table

Covering Problems for Partial Words and for Indeterminate Strings

We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding position. We also consider covering partial words, which are a special case of indeterminate strings where each non-solid symbol is a don't care symbol. We prove that indeterminate string covering problem and partial word covering problem are NP-complete for binary alphabet and show that both problems are fixed-parameter tractable with respect to $k$, the number of non-solid symbols. For the indeterminate string covering problem we obtain a $2^{O(k \log k)} + n k^{O(1)}$-time algorithm. For the partial word covering problem we obtain a $2^{O(\sqrt{k}\log k)} + nk^{O(1)}$-time algorithm. We prove that, unless the Exponential Time Hypothesis is false, no $2^{o(\sqrt{k})} n^{O(1)}$-time solution exists for either problem, which shows that our algorithm for this case is close to optimal. We also present an algorithm for both problems which is feasible in practice.Comment: full version (simplified and corrected); preliminary version appeared at ISAAC 2014; 14 pages, 4 figure

An unclassified tibial plateau fracture: Reverse Schatzker type IV.

The most commonly accepted system of classification for tibia plateau fractures is that of Schatzker. Increasingly, both high energy injuries and atypical osteoporotic fragility failures have led to more complex, unusual and previously undescribed fracture patterns being recognized. We present a case of a patient with a previously unreported pattern of tibia plateau fracture and knee dislocation. We highlight the challenges confronted and present the management and the outcomes of his injury. A 28-year old male motorcyclist was involved in a head on collision with a truck and was transferred by helicopter to our level 1 major trauma centre emergency department. His injuries were a circumferential degloving injury to his left leg and a right lateral tibial plateau fracture/knee dislocation. The pattern of the lateral tibial plateau fracture was unique and did not fit any recognised classification system. The patient received a spanning external fixator initially and after latency of 12 days for soft tissue resuscitation he underwent definite fixation through an antero-lateral approach to the proximal tibia with two cannulated 6.5 mm partially threaded screws and an additional lateral proximal tibia plate in buttress mode. A hinged knee brace was applied with unrestricted range of motion post-operatively and free weight bearing were permitted post operatively. At the 6 months follow up, the patient walks without aids and with no limp. Examination revealed a stable joint and full range of motion. Plain radiographs revealed that the fracture healed with good alignment and the fixation remained stable. High energy injuries can lead to more complicated fracture patterns, which challenge the orthopaedic surgeons in their management. It is crucial to understand the individual fracture pattern and the possible challenges that may occur. This study reports a lateral tibia plateau fracture/dislocation which perhaps is best described as a reverse Schatzker IV type fracture

Functional microRNA high throughput screening reveals miR-9 as a central regulator of liver oncogenesis by affecting the PPARA-CDH1 pathway

Background: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths, reflecting the aggressiveness of this type of cancer and the absence of effective therapeutic regimens. MicroRNAs have been involved in the pathogenesis of different types of cancers, including liver cancer. Our aim was to identify microRNAs that have both functional and clinical relevance in HCC and examine their downstream signaling effectors. Methods: MicroRNA and gene expression levels were measured by quantitative real-time PCR in HCC tumors and controls. A TargetScan algorithm was used to identify miR-9 downstream direct targets. Results: A high-throughput screen of the human microRNAome revealed 28 microRNAs as regulators of liver cancer cell invasiveness. MiR-9, miR-21 and miR-224 were the top inducers of HCC invasiveness and also their expression was increased in HCC relative to control liver tissues. Integration of the microRNA screen and expression data revealed miR-9 as the top microRNA, having both functional and clinical significance. MiR-9 levels correlated with HCC tumor stage and miR-9 overexpression induced SNU-449 and HepG2 cell growth, invasiveness and their ability to form colonies in soft agar. Bioinformatics and 3’UTR luciferase analyses identified E-cadherin (CDH1) and peroxisome proliferator-activated receptor alpha (PPARA) as direct downstream effectors of miR-9 activity. Inhibition of PPARA suppressed CDH1 mRNA levels, suggesting that miR-9 regulates CDH1 expression directly through binding in its 3’UTR and indirectly through PPARA. On the other hand, miR-9 inhibition of overexpression suppressed HCC tumorigenicity and invasiveness. PPARA and CDH1 mRNA levels were decreased in HCC relative to controls and were inversely correlated with miR-9 levels. Conclusions: Taken together, this study revealed the involvement of the miR-9/PPARA/CDH1 signaling pathway in HCC oncogenesis

On Quasiperiodic Morphisms

Weakly and strongly quasiperiodic morphisms are tools introduced to study quasiperiodic words. Formally they map respectively at least one or any non-quasiperiodic word to a quasiperiodic word. Considering them both on finite and infinite words, we get four families of morphisms between which we study relations. We provide algorithms to decide whether a morphism is strongly quasiperiodic on finite words or on infinite words.Comment: 12 page

Surface electronic properties of undoped InAlN alloys

The variation in surface electronic properties of undoped c-plane InxAl1−xN alloys has been investigated across the composition range using a combination of high-resolution x-ray photoemission spectroscopy and single-field Hall effect measurements. For the In-rich alloys, electron accumulation layers, accompanied by a downward band bending, are present at the surface, with a decrease to approximately flatband conditions with increasing Al composition. However, for the Al-rich alloys, the undoped samples were found to be insulating with approximate midgap pinning of the surface Fermi level observed

Efficient Seeds Computation Revisited

The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a given string, and the shortest seed problem is of much higher algorithmic difficulty. The problem is not well understood, no linear time algorithm is known. In the paper we give linear time algorithms for some of its versions --- computing shortest left-seed array, longest left-seed array and checking for seeds of a given length. The algorithm for the last problem is used to compute the seed array of a string (i.e., the shortest seeds for all the prefixes of the string) in $O(n^2)$ time. We describe also a simpler alternative algorithm computing efficiently the shortest seeds. As a by-product we obtain an $O(n\log{(n/m)})$ time algorithm checking if the shortest seed has length at least $m$ and finding the corresponding seed. We also correct some important details missing in the previously known shortest-seed algorithm (Iliopoulos et al., 1996).Comment: 14 pages, accepted to CPM 201