Search

Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of reversals are called symmetric reversals, which, unfortunately, were largely ignored until recently. In this paper, we investigate the problem of sorting by symmetric reversals, which requires a series of symmetric reversals to transform one chromosome $A$ into the another chromosome $B$. The decision problem of sorting by symmetric reversals is referred to as {\em SSR} (when the input chromosomes $A$ and $B$ are given, we use {\em SSR(A,B)}) and the corresponding optimization version (i.e., when the answer for {\em SSR(A,B)} is yes, using the minimum number of symmetric reversals to convert $A$ to $B$), is referred to as {\em SMSR(A,B)}. The main results of this paper are summarized as follows, where the input is a pair of chromosomes $A$ and $B$ with $n$ repeats. (1) We present an $O(n^2)$ time algorithm to solve the decision problem {\em SSR(A,B)}, i.e., determine whether a chromosome $A$ can be transformed into $B$ by a series of symmetric reversals. (2) We design an $O(n^2)$ time algorithm for a special 2-balanced case of {\em SMSR(A,B)}, where chromosomes $A$ and $B$ both have duplication number 2 and every repeat appears twice in different orientations in $A$ and $B$. (3) We show that SMSR is NP-hard even if the duplication number of the input chromosomes are at most 2, hence showing that the above positive optimization result is the best possible. As a by-product, we show that the \emph{minimum Steiner tree} problem on \emph{circle graphs} is NP-hard, settling the complexity status of a 38-year old open problem., Comment: 35 pages, 12 figures

Photographing images is used as a common detection tool during the process of bridge maintenance. The edges in an image can provide a lot of valuable information, but the detection and extraction of edge details are often affected by the image noise. This study proposes an algorithm for wavelet transform to denoise the image before edge detection, which can improve the signal-to-noise ratio of the image and retain as much edge information as possible. In this study, four wavelet functions and four decomposition levels are used to decompose the image, filter the coefficients and reconstruct the image. The PSNR and MSE of the denoised images were compared, and the results showed that the sym5 wavelet function with three-level decomposition has the best overall denoising performance, in which the PSNR and MSE of the denoised images were 23.48 dB and 299.49, respectively. In this study, the canny algorithm was used to detect the edges of the images, and the detection results visually demonstrate the difference between before and after denoising. In order to further evaluate the denoising performance, this study also performed edge detection on images processed by both wavelet transform and the current widely used Gaussian filter, and it calculated the Pratt quality factor of the edge detection results, which were 0.53 and 0.47, respectively. This indicates that the use of wavelet transform to remove noise is more beneficial to the improvement of the subsequent edge detection results.

Developing a precise and reproducible bandgap tuning method that enables tailored design of materials is of crucial importance for optoelectronic devices. Towards this end, we report a sphere diameter engineering (SDE) technique to manipulate the bandgap of two-dimensional (2D) materials. A one-to-one correspondence with an ideal linear working curve is established between the bandgap of MoS2 and the sphere diameter in a continuous range as large as 360 meV. Fully uniform bandgap tuning of all the as-grown MoS2 crystals is realized due to the isotropic characteristic of the sphere. More intriguingly, both a decrease and an increase of the bandgap can be achieved by constructing a positive or negative curvature. By fusing individual spheres in the melted state, post-synthesis bandgap adjustment of the supported 2D materials can be realized. This SDE technique, showing good precision, uniformity and reproducibility with high efficiency, may further accelerate the potential applications of 2D materials. The bandgap of 2D molybdenum disulfide can be tuned uniformly, reproducibly and precisely over a large range by using a glass sphere support and changing the diameter of the spheres.

Developing a precise and reproducible bandgap tuning method that enables tailored design of materials is of crucial importance for optoelectronic devices. Towards this end, we report a sphere diameter engineering (SDE) technique to manipulate the bandgap of two-dimensional (2D) materials. A one-to-one correspondence with an ideal linear working curve is established between the bandgap of MoS2 and the sphere diameter in a continuous range as large as 360 meV. Fully uniform bandgap tuning of all the as-grown MoS2 crystals is realized due to the isotropic characteristic of the sphere. More intriguingly, both a decrease and an increase of the bandgap can be achieved by constructing a positive or negative curvature. By fusing individual spheres in the melted state, post-synthesis bandgap adjustment of the supported 2D materials can be realized. This SDE technique, showing good precision, uniformity and reproducibility with high efficiency, may further accelerate the potential applications of 2D materials.

A facile method has been developed to prepare flexible and uniform porous carbon film/Ni (PCF/Ni) double-layer structure for simply and rapidly assembling flexible electrochemical capacitor (EC). The PCF/Ni is obtained by ambient pressure chemical vapor deposition and subsequent partial etching of Ni foil. The thickness of PCF can be controlled by etching time. The PCF has a porous structure and tightly interface with Ni, resulting in a good conductivity and large surface area. The ECs based on PCF/Ni exhibits good electrical properties. Area (volumetric) capacitance of PCF/Ni electrode with PCF thickness of 0.52 μm reaches 0.31 mF/cm2 (5.96 F/cm3) at scan rate of 50 mV/s. Maximum volumetric (gravimetric) power density reaches 2.72 W/cm3 (9.05 kW/kg). The performance can be further improved by increasing the PCF thickness. Furthermore, the EC based on PCF/Ni has a very short time constant (~ 170 μs) and allows for operations at high rate up to 500 V/s.

It is well known that any set of n intervals in (Formula Presented) admits a non-monochromatic coloring with two colors and a conflict-free coloring with three colors. We investigate generalizations of this result to colorings of objects in more complex 1-dimensional spaces, namely so-called tree spaces and planar network spaces.

A short swap switches two elements with at most one element caught between them. Sorting permutation by short swaps asks to find a shortest short swap sequence to transform a permutation into another. A short swap can eliminate at most three inversions. It is still open for whether a permutation can be sorted by short swaps each of which can eliminate three inversions. In this paper, we present a polynomial time algorithm to solve the problem, which can decide whether a permutation can be sorted by short swaps each of which can eliminate 3 inversions in O(n) time, and if so, sort the permutation by such short swaps in O(n^2) time, where n is the number of elements in the permutation. A short swap can cause the total length of two element vectors to decrease by at most 4. We further propose an algorithm to recognize a permutation which can be sorted by short swaps each of which can cause the element vector length sum to decrease by 4 in O(n) time, and if so, sort the permutation by such short swaps in O(n^2) time. This improves upon the O(n^2) algorithm proposed by Heath and Vergara to decide whether a permutation is so called lucky.

A new and simple approach is proposed for the first time to fabricate free-standing amorphous carbon films (FS-ACFs) with controllable thickness by ambient pressure chemical vapor deposition (APCVD). The approach uses methane as the carbon source and Ni foil as the catalytic substrate, in which a large number of carbon atoms are trapped by controlling the experimental conditions during the APCVD growth process, and FS-ACFs are obtained by a simple corrosion of the Ni foil after APCVD growth. FS-ACFs having a uniform and continuous morphology with variable sizes over one hundred square centimeters and a controllable thickness of tens to hundreds of nanometers are synthesized by controlling the experimental conditions. Microstructure observations show that FS-ACFs have porous and transparent characteristics, which can be transferred or bent on different substrates, thus allowing for a variety of potential applications in electrochemistry. As a proof of concept, an electrochemical supercapacitor device directly assembled by using the FS-ACF exhibits an ultrashort time constant of 46 μs, a wide frequency range (∼kHz) for capacitive feature, and a good capacitance performance with an area specific capacitance of 0.28 mF cm−2 at a scan rate of 50 mV s−1. Furthermore, the FS-ACF-based supercapacitor shows a high power density with a maximum volumetric power density of 17.76 W cm−3.

The development of effective vaccines against difficult disease targets will require the identification of new subunit vaccination strategies that can induce and maintain effective immune responses in humans. Here we report on a phase 1a clinical trial using the AMA1 antigen from the blood-stage Plasmodium falciparum malaria parasite delivered either as recombinant protein formulated with Alhydrogel adjuvant with and without CPG 7909, or using recombinant vectored vaccines--chimpanzee adenovirus ChAd63 and the orthopoxvirus MVA. A variety of promising "mixed-modality" regimens were tested. All volunteers were primed with ChAd63, and then subsequently boosted with MVA and/or protein-in-adjuvant using either an 8- or 16-week prime-boost interval. We report on the safety of these regimens, as well as the T cell, B cell, and serum antibody responses. Notably, IgG antibody responses primed by ChAd63 were comparably boosted by AMA1 protein vaccine, irrespective of whether CPG 7909 was included in the Alhydrogel adjuvant. The ability to improve the potency of a relatively weak aluminium-based adjuvant in humans, by previously priming with an adenoviral vaccine vector encoding the same antigen, thus offers a novel vaccination strategy for difficult or neglected disease targets when access to more potent adjuvants is not possible.

At present, several provinces' power supply companies have established harmonic monitoring platform in China, by real-time monitoring the voltage and current of power grid, then upload these data to the main station to analyze and settle. The platform can collect about 1 TB(1TB=1000GB) data every day[12], these data contain all the indexes of power quality, but we can only use this platform to do some basal data analysis work, but not processing analysis with multi-indexes, so that it does not show strong supporting effort to the power grid operation. With the development of energy internet and the third industry, more and more unstructured data are impacting the power grid operation, how to make better use of big data technology to deal with the data from monitoring platform has became the focus of the power grid company. In this paper, some introduces of contents and characteristics of harmonic real-time monitoring platform and big data technology has been made, by comparing the way of using and settling data of platform to the big data technology, meanwhile by combining with the characteristics of power quality data, we analyze the combination of the two prospects. At last, the development direction of the advanced application for the harmonic line monitoring system is discussed in this paper.

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) I into I', with respect to a complete reference genome G, such that the number of adjacencies between G and I' is maximized. The problem is NP-complete and APX-hard, and admits a 1.2-approximation. However, the sequence input I is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when, (1) a scaffold S is given, the missing genes X = c(G) - c(S) can only be inserted in between the contigs, and the objective is to maximize the number of adjacencies between G and the filled S' and (2) a scaffold S is given, a subset of the missing genes X' subset X = c(G) - c(S) can only be inserted in between the contigs, and the objective is still to maximize the number of adjacencies between G and the filled S''. For problem (1), we present a simple NP-completeness proof, we then present a factor-2 greedy approximation algorithm, and finally we show that the problem is FPT when each gene appears at most d times in G. For problem (2), we prove that the problem is W[1]-hard and then we present a factor-2 FPT-approximation for the case when each gene appears at most d times in G.

To improve fuel economy and reduce operating costs are one of the future developments of the air transport. From another part, it is continually called for higher speed to satisfy the global reach and make the world as a neighbor. An airworthiness problem of supersonic civil aircraft is the propulsion system noise. The ACE (adaptive cycle engine) noise is explored at the state of takeoff based on the description and analysis of aero engine noise and supersonic air transport. The conceptual scheme of ACE is shown and then the calculation method of each component is studied, including fan, combustor, turbine and nozzle. The total noise level (EPN dB) is calculated and the impact of components noise is analyzed. The research shows that the ACE noise is lower than the supersonic aircraft Concorde but higher than actual subsonic civil engine. The nozzle and fan should be paid an attention at the noise suppression and the airport location for supersonic aircraft could be a condition of market acceptation.

Based on m-stems and semi-extensible structure, a model is presented to represent RNA planar pseudoknots, and corresponding dynamic programming algorithm is designed and implemented to predict arbitrary planer pseudoknots and simple non-planar pseudoknots with O(n4) time and O(n3) space. The algorithm folds total 245 sequences in the Pseudobase database, and the test results indicate that the algorithm has good accuracy, sensitivity and specificity. *Supported by National Natural Science Foundation of China (Grant Nos. 60573024 and 60573181), the Research Project of Shandong Economic University (01610784), and NSF of Shandong Provice (2005BS01014)

Hybrid carbon films composed of graphene film and porous carbon film may give full play to the advantages of both carbon materials, and have great potential for application in energy storage and conversion devices. Unfortunately, there are very few reports on fabrication of hybrid carbon films. Here we demonstrate a simple approach to fabricate free-standing sandwich-structured hybrid carbon film composed of porous amorphous carbon film and multilayer graphene film by chemical vapor deposition in a controllable and scalable way. Hybrid carbon films reveal good electrical conductivity, excellent flexibility, and good compatibility with substrate. Supercapacitors assembled by hybrid carbon films exhibit ultrahigh rate capability, wide frequency range, good capacitance performance, and high-power density. Moreover, this approach may provide a general path for fabrication of hybrid carbon materials with different structures by using different metals with high carbon solubility, and greatly expands the application scope of carbon materials.

This paper focuses on finding a spanning tree of a graph to maximize the number of its internal vertices. We present an approximation algorithm for this problem which can achieve a performance ratio $\frac{4}{3}$ on undirected simple graphs. This improves upon the best known approximation algorithm with performance ratio $\frac{5}{3}$ before. Our algorithm benefits from a new observation for bounding the number of internal vertices of a spanning tree, which reveals that a spanning tree of an undirected simple graph has less internal vertices than the edges a maximum path-cycle cover of that graph has. We can also give an example to show that the performance ratio $\frac{4}{3}$ is actually tight for this algorithm. To decide how difficult it is for this problem to be approximated, we show that finding a spanning tree of an undirected simple graph to maximize its internal vertices is Max-SNP-Hard., 15 pages, 1 figure

A biclustering problem consists of objects and an attribute vector for each object. Biclustering aims at finding a bicluster—a subset of objects that exhibit similar behavior across a subset of attributes, or vice versa. Biclustering in matrices with binary entries (“0”/“1”) can be simplified into the problem of finding submatrices with entries of “1.” In this paper, we consider a variant of the biclustering problem: the k-submatrix partition of binary matrices problem. The input of the problem contains an n×m matrix with entries (“0”/“1”) and a constant positive integer k. The k-submatrix partition of binary matrices problem is to find exactly k submatrices with entries of “1” such that these k submatrices are pairwise row and column exclusive and each row (column) in the matrix occurs in exactly one of the k submatrices. We discuss the complexity of the k-submatrix partition of binary matrices problem and show that the problem is NP-hard for any k≥3 by reduction from a biclustering problem in bipartite graphs.

This paper briefly reviews NP-hard optimization problems and theirin approximability. The hardness of solving CLIQUE problem isspecifically discussed. A dynamic-programming algorithm and its improvedversion for CLIQUE are reviewed and some additional analysis ispresented. The analysis implies that the improved algorithm, HEWN(hierarchical edge-weighted network), only provides a heuristic oruseful method, but cannot be called a polynomial algorithm.

Computability logic (CoL) is a formal theory of interactive computation. It understands computational problems as games played by two players: a machine and its environment, uses logical formalism to describe valid principles of computability and formulas to represent computational problems. Logic CL1 is a deductive system for a fragment of CoL. The logical vocabulary contains all of the operators of classical logic and choice operators, the atoms represent elementary games i.e. predicates of classical logic. In this paper, we present a program that takes a CL1-proof of an arbitrary formula $F$, and extract a winning strategy for $F$ from that proof then play $F$ using that strategy. We hope this paper would provide a starting point for further work in program extraction of the CoL-based arithmetic and other CoL-based applied systems., 1 figure

A review is presented of studies of polymeric membranes by applying positron annihilation lifetime spectroscopy (PALS). PALS has been used to study subnanometer-sized holes, to determine their size distribution and free-volume fractions, and to probe molecular-sized vacancies in glassy polymers. At present, PALS is believed to be a highly effective physical method for the examination of polymeric membranes.

This paper improves Itai and Rodeh's algorithm for finding a shortest cycle in an undirected unweighted graph. Given an undirected unweighted graph G with n vertices,the algorithm can determine a cycle whose length is at most k+1 where k is the length of the shortest cycle in G. The results of the experiment show that the improved algorithm runs faster than the original one when the input graph meets some special features.

Given an undirected graph with vertex and edge weights and a subset of vertices called terminals, the bounded size graph clustering (BSGC) problem is to partition the vertices into clusters of size at most a given budget such that each cluster contains at most one terminal and the total size of the clusters is minimized, where the size of a cluster is defined as the total vertex weight in the subset plus the total edge weight at the boundary of the cluster. For BSGC on trees, we present a pseudo-polynomial time exact algorithm, which can be modified via rounding to yield a (1+\epsilon)-approximation in polynomial time violating the given budget by a 1+\epsilon factor.

Given a graph G=(V,E) with real positive edge weights, where each edge (u, v) is labeled either + or – depending on whether u and v have been deemed to be similar or dissimilar, the problem of correlation clustering with l clusters is to partition the vertices of G into at most l clusters to minimize the total weight of + edges between clusters and – edges within clusters. This problem for general graphs is APX-complete. A fixed-parameter tractable (FPT) algorithm is presented, where the parameter k is defined as the maximum, over all blocks B of the graph, of the number of vertices that must be removed from B to obtain a forest.

The k-means clustering is one of the most popular schemes for discovering clusters in data. Its aim is to minimize the mean squared distance from each data to its nearest center. A lot of variants of Lloyd's heuristic have been studied. Unfortunately, many research results haven't given any approximate ratio. In this paper, an algorithm is presented which can obtain the optimal clustering with the ration of at most 2. The main idea of this algorithm is that k points are selected by means of a very simple, randomized seeding technique and then the local search is implemented to improve the accuracy. Some examples are selected to verify our algorithm and got better results both the speed and accuracy than the former methods. The main algorithmic contribution is that the input points are used as the candidate sets to obtain the optimal clustering with a constant ratio by means of local search technique and one method of selecting initial points.

A new kind of neural networks on solving shortest paths problem is presented, and the stability of the neural networks is proved. For a directed or undirected graph, the proposed neural network is always convergent to its single equilibrium, so that the shortest paths between every pair of nodes of the oriented graph are produced. This paper makes a new study on solving the optimization but not NP-hard problems by neural networks.

This paper gives an improved sufficient condition of ensuring the stability of delayed cellular neural networks (DCNN) by means of the analysis of a correspondent Lyapunov function. This result improved the limit given by Civalleri and gives an optional upper limit of the stability of DCNN.

It is difficult to reduce an NMR image's ringing artifacts and obtain better images. This paper uses the method of dyadic wavelets and self-adaptive threshold to process the images that have the ringing artifacts. The test results prove that the method is effective and it can process the NMR image's ringing artifacts. Finally the paper discusses using the fuzzy method.

In this paper the character of the associative memory is discussed emphatically from the viewpoint of the storage capacity and the associative ability of the network. The associative memory function can all be realized by utilizing the feedback network on competition. The competing classifying (CC) algorithm is presented here. Compared with any other associative memories that already exist, the neural network determined by the algorithm has very good performances such as high error-correcting capability, large storage capacity, no "rejected-point" and no spurious attractive center. The obtained network exceeds the storage capacity of HAM and BP networks.

The character of the associative memory is discussed emphatically from the viewpoint of the storage capacity and the associative ability of the network. The associative memory function can all be realized by utilizing the feedback network or the forward-feed network. The new algorithm, based on adaptive competing-classifying (ACC) algorithm, is presented here. Compared with other associative memories, the neural network determined by the algorithm has high error-correcting capability, large storage capacity, no "rejected-point" and no spurious attractive center. ACC algorithm can decrease the competition-number more than CC algorithm. The obtained network has the very strong ability of correcting errors and exceeds the storage capacity of HAM and BP networks.

Major surface proteins of Anaplasma marginale are vaccine candidates. We recently demonstrated that immunization of calves with outer membranes of the Florida strain of A. marginale resulted in protective immunity that correlated with a memory CD4(+) T-lymphocyte response specific for major surface protein 1 (MSP-1), MSP-2, and MSP-3 (W. C. Brown, V. Shkap, D. Zhu, T. C. McGuire, W. Tuo, T. F. McElwain, and G. H. Palmer, Infect. Immun. 66:5406-5413, 1998). As immunogens, these proteins have been shown to induce complete or partial protection against homologous challenge. To further define the T helper (Th) cell response to these and other A. marginale antigens and to determine conservation of Th cell epitopes among genetically distinct A. marginale strains, Th cell clones obtained prior to challenge from three immunized calves were characterized for antigen-specific responses. Nine distinct antigenic profiles were defined by 11 Th cell clones derived by stimulation with the Florida strain. Several clones responded to MSP-2, MSP-3, or both. All of these MSP-2- or MSP-3-specific clones and the majority of other clones that did not respond to MSPs recognized all bovine blood-passaged strains of A. marginale. These results demonstrate conservation of certain Th cell epitopes between MSP-2 and MSP-3 and show that Th cell epitopes in MSP-2, MSP-3, and undefined antigens are conserved among strains of A. marginale. Of seven clones that responded to the blood-passaged Virginia strain, two did not recognize antigen prepared from this strain cultured in tick cells, suggesting differences in the antigenic composition between these stages. Analysis of the cytokines expressed by the Th cells revealed that all clones expressed gamma interferon and tumor necrosis factor alpha, and most coexpressed interleukin-4. Our results provide a rationale for identifying Th cell epitopes conserved among different strains of A. marginale for inclusion in a nucleic acid or recombinant protein vaccine.

Genome rearrangement is an important area in computational biology. There are three basic operations, reversal, translocation and transposition. Here we study the translocation operations. Multi-chromosomal genomes frequently evolve by translocation events that exchange genetic material between two chromosomes. We focus on the signed case, where the direction of each gene is known. The signed translocation problem asks to find the minimum number of translocation operations as well as the sequence of translocation operations to transform one genome into the other. A linear-time algorithm that computes the minimum number of translocation operations was given in a linear-time algorithm for computing translocation distance between signed genomes [16]. However, that algorithm cannot give the optimum sequence of translocation operations. The best known algorithm that can give the optimum sequence of translocation operations for signed translocation problem runs in O(n2logn) time. In this paper, we design an O(n2) algorithm.

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g. orthology, paralogy, xenology). They are satisfiable if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp. paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations.