text:
- Methodology article
- Open Access
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
- Martin Bader1Email author,
- Mohamed I Abouelhoda2, 3 and
- Enno Ohlebusch1
© Bader et al; licensee BioMed Central Ltd. 2008
- Received: 14 March 2008
- Accepted: 04 December 2008
- Published: 04 December 2008
Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes.
In this paper, we present a new heuristic algorithm that directly constructs a phylogenetic tree w.r.t. the weighted reversal and transposition distance. Experimental results on previously published datasets show that constructing phylogenetic trees in this way results in better trees than constructing the trees w.r.t. the reversal distance, and recalculating the weight of the trees with the weighted reversal and transposition distance. An implementation of the algorithm can be obtained from the authors.
The possibility of creating phylogenetic trees directly w.r.t. the weighted reversal and transposition distance results in biologically more realistic scenarios. Our algorithm can solve today's most challenging biological datasets in a reasonable amount of time.
- Internal Node
- Steiner Tree
- Genome Rearrangement
- Median Solver
- Breakpoint Distance
During evolution both local and global mutations of DNA molecules occur. Local mutations (point mutations) consist of the substitution, insertion, or deletion of single nucleotides, while global mutations (genome rearrangements) change the DNA molecules on a large scale. In unichromosomal genomes, the most common rearrangements are inversions (also called reversals in bioinformatics), where a section of the genome is excised, reversed in orientation, and re-inserted. But also transpositions play a role. In a transposition, a section of the genome is excised and inserted at a new position in the genome; this may or may not also involve an inversion. Since genome rearrangements are rare compared to point mutations, they can give us valuable information about the evolutionary history of organisms. Moreover, because of the progress in large-scale sequencing in the last decade, hundreds of complete genomes are available to date. As a consequence, we are now able to tackle the problem of reconstructing the evolutionary history of genomes.
In the context of genome rearrangements, a unichromosomal genome is usually represented by an ordering of certain oriented markers (e.g., genes or synteny blocks [1]). Moreover, in the comparison of several genomes, it is typically assumed that the genomes have the same set {1,...,n} of markers. Thus, in the following a unichromosomal genome will be represented by a signed permutation of the sequence (1,...,n), where the sign indicates the corresponding orientation (strandedness) of the marker.
In the multiple genome rearrangement problem, one searches for a phylogenetic tree describing the most "plausible" rearrangement scenario for multiple genomes. Formally, given k genomes, find a tree T with the k genomes as leaf nodes and assign ancestral genomes to internal nodes of T such that the tree is optimal, i.e., the sum of rearrangement distances over all edges of the tree is minimal. The following rearrangement distances have been studied:
The breakpoint distance between two genomes is the smallest number of places where one genome must be broken so that the pieces can be rearranged to form the other genome. It can straightforwardly be computed in linear time.
The reversal distance between two genomes is the minimum number of reversals required to transform one genome into the other. It can also be computed in linear time [2, 3].
In the weighted reversal and transposition distance, the two types of operations are assigned (different) weights, and the rearrangement distance between two genomes is the minimum of the weights of all rearrangement sequences that transform one genome into the other (of course, the weight of a sequence is the sum of the weights of the operations in the sequence). The problem of computing the weighted reversal and transposition distance in polynomial time is yet unsolved, but we developed a 1.5 approximation algorithm that works well in practice [4, 5], extending the work of Hartman and Sharan for equally weighted reversals and transpositions [6].
Ordering of the mitochondrial genes in Drosophila melanogaster
Ordering of the mitochondrial genes in the two organisms.
D. melanogaster
L. forficatus
The multiple genome rearrangement problem was shown to be NP-hard for both the breakpoint and the reversal distance [7, 8]. This is true even if one considers only three genomes [7, 8]. To put it differently, the breakpoint and the reversal median problem are NP-hard. Recall that in the median problem, we are given a distance or dissimilarity measure d, three genomes g1, g2, and g3, and we want to find a genome M (a median) such that the sum is minimized.
Related work
Breakpoint distance
Sankoff and Blanchette [9] solved the multiple genome rearrangement problem for the breakpoint distance by solving the following problem for each tree topology: Given a tree topology T with the k genomes as leaf nodes, assign ancestral genomes to internal nodes of T such that the tree is optimal (among all trees with this topology). They proposed to use the breakpoint median problem in an iterative manner to refine rough initial guesses for internal nodes. The breakpoint median problem in turn can be reduced to the traveling salesman problem for which very good heuristics exist. The resulting software BPAnalysis, however, was rather slow. Moret et al. [10] provided a reimplementation of BPAnalysis called GRAPPA that resulted in a speedup by several orders of magnitude.
Reversal distance
Moret et al. [11] and Tang et al. [12] showed that using reversal medians instead of breakpoint medians in the method of Sankoff and Blanchette [9] yield better phylogenetic trees, and they further extended the GRAPPA software in this direction. Moreover, Bourque and Pevzner [13] pointed out that the use of the breakpoint distance for generating the tree is disadvantageous because it may result in a tree that is suboptimal under other rearrangement distances. Their own greedy method iteratively builds a phylogenetic tree, based on a heuristic for finding the reversal median (in case of multichromosomal genomes, translocations are taken into account as well). Their method is implemented in the software tool MGR. Wu and Gu devised algorithms that solve an equivalent Steiner tree problem. Besides a nearest path search algorithm on a simple grid [14] (simplifying the grid search algorithm of Sankoff et al. [15]), they also presented a neighbor perturbing algorithm that starts with a minimum spanning tree as a 2-approximation of the optimal Steiner tree and tries to iteratively improve the tree by searching for better Steiner nodes in the neighborhoods of the current nodes [16]. Recently, Bernt et al. [17] presented a software tool called amGRP which further significantly improves upon GRAPPA and MGR.
Weighted reversal and transposition distance
To the best of our knowledge, the approach of Cosner et al. [18] is the only one that (indirectly) takes weighted reversals and transpositions into account. In their method, they first use a heuristic to construct a phylogenetic tree according to the breakpoint distance as follows: Genomes are encoded as binary strings, a maximum parsimony technique for binary strings is employed, and then each internal node in the resulting phylogenetic tree is relabeled using BPAnalysis. Then, the weighted reversal and transposition distances on the edges of the tree are heuristically calculated with the software tool DERANGE II [19].
Our contribution
In this paper, we present a new heuristic algorithm for solving the multiple genome rearrangement problem. Our algorithm is the first one that tries to directly construct an optimal phylogenetic tree under the weighted reversal and transposition distance. We conducted experiments on previously published datasets, and the results are very promising. Because there is no other software tool that can deal with the weighted reversal and transposition distance, we conducted the same experiments with the reversal distance and compared our results with those delivered by other software tools. Although our program was not designed for the reversal distance, the results show that it can compete with state-of-the-art programs in this field.
In this paper, we consider genomes that consist of a single circular chromosome (like mitochondrial, chloroplast or bacterial genomes). Such genomes are modeled by signed circular permutations. A signed circular permutation π = (π1 ... π n ) is a permutation of (1...n), in which the indices are cyclic (i.e., n is followed by 1) and each element is labeled by plus or minus. We will use the term "permutation" as short hand for signed circular permutation. The reflection of a permutation π is the permutation (-π n ... π1). It is considered to be (biologically) equivalent to π. The permutation id = (+1 + 2...+n) is called the identity permutation. A segment π i ... π j (with j ≤ i) of a permutation π is a consecutive sequence of elements in π, with π i as first element and π j as last element. We consider three possible rearrangement operations on a permutation π. A transposition t(i, j, k) (with i <j and k <i or k > j) is an operation that cuts the segment π i ... πj-1out of π, and reinserts it before the element π k . A reversal r(i, j) (with i <j) is an operation that reverses the order of the elements of the segment π i ... πj-1. Additionally, the sign of every element in the segment is flipped. An inverted transposition tr(i, j, k) (with i <j and k <i or k > j) is the composition t(i, j, k) ◦ r(i, j) of a reversal and a transposition. In other words, the segment π i ... πj-1will be cut out of π, inverted, and reinserted before π k . A sequence of rearrangement operations op1, op2 ,..., op k applied to a permutation π yields the permutation = op k (opk-1(...(op1(π))...)). We also say that the sequence is a sorting sequence of p w.r.t. , as it sorts π into . A permutation lies on a sorting sequence op1, op2,...,op k of π if there is a j ≤ k such that op j (opj-1(...op1(π))...)) = . Each operation op is assigned a positive weight w(op). The weight of a sequence is the sum of the weights of its operations. An optimal sorting sequence between π and is a sequence of minimum weight transforming π into . The weighted genome rearrangement distance between π and (denoted by d(π, )) is the weight of an optimal sorting sequence between them. In this paper, we consider two different genome rearrangement distances, the reversal distance and the weighted reversal and transposition distance. For the reversal distance, we restrict the set of allowed operations to reversals. Each reversal has the weight 1, i.e. the reversal distance d r (π, ) is the minimum number of reversals required to transform π into . For the weighted reversal and transposition distance, the weight of an operation only depends on its type:w(op) = w r if op is a reversal, and w(op) = w t if op is a transposition or an inverted transposition. As reversals usually occur much more frequently than transpositions and inverted transpositions, we assume that w r ≤ w t . In fact, we assume that w r = 1 ≤ w t ≤ 2 because this results in a biologically meaningful balance between reversals and transpositions (see also in Section "Testing, Weight Ratios"). The weighted reversal and transposition distance between two permutations π and is denoted by d w (π, ), and a lower bound for this distance is d w (π, ) ≥ (w t /2)·(n - σ(π, )), where n is the size of the permutations and σ(π, ) is the score between the permutations π and (for details, see [4]). A median M(π1, π2, π3) of three permutations π1, π2, and π3 is the permutation that minimizes d(M, π1) + d(M, π2) + d(M,π3). Note that in general a median is not unique. An algorithm that solves the median problem (either exactly or heuristically) is called a median solver. A phylogenetic tree of a set of permutations (genomes) P = {π1,...,π n } is a tree T = (V, E), where V is the set of nodes and E is the set of edges of the tree. Each node is labeled by a permutation v i , and there is a bijection between the labels of the leaves and the permutations in P (i.e., any element of P is label of exactly one leaf). The weight of an edge (v i , v j ) is the distance d(v i , v j ). The weight of a tree w(T) is the sum of the weights of its edges. The phylogenetic reconstruction problem is to find a phylogenetic tree with minimum weight, given the set of permutations P.
The algorithm has two different phases. In the first phase, we use a fast heuristic that creates a tree. This heuristic does not rely on median solvers. In the second phase, this tree will be improved until it converges to a local optimum. We use two different improvement algorithms. One improves the tree topology, while the other improves the labeling of internal nodes by using a median solver. These two algorithms can be run alternatingly until the tree does not improve any further. In practice, the topology of the tree created in the first phase is already very good, so the algorithm for improving the topology has to be run only once. The whole algorithm was designed for the weighted reversal and transposition distance, however, it can also be used for other rearrangement distances as it only requires an algorithm that finds an optimal sorting sequence between two permutations, or at least a good approximation algorithm. Only the second improvement algorithm requires a median solver. We implemented the algorithm for the reversal distance and the weighted reversal and transposition distance. For the reversal distance, there is an efficient exact sorting algorithm [20, 21] and a branch-and-bound algorithm for the median that works well in practice [22]. For the weighted reversal and transposition distance, there is a 1.5-approximation for the sorting problem that works well in practice [4, 5]. As median solver, we extended Caprara's reversal median solver [22] such that it works on the lower bound for the weighted reversal and transposition distance instead of using the maximum cycle decomposition of the original algorithm. As the algorithm for the weighted reversal and transposition distance is often able to find exact solutions, especially for short distances, the median solver also finds an exact median w.r.t. the weighted reversal and transposition distance in many cases.
Creating the tree
We create the tree T iteratively, beginning with a tree whose set of nodes consists only of one arbitrary permutation of the set of input permutations P = {π1,...,π k }, i.e. T0 = (V0, E0) = ({π}, ∅) with π ∈ P.
In each step, we create the tree T i from the tree Ti-1by choosing a permutation π ∈ P\Vi-1that is not yet a node in the tree, and add this permutation as leaf node. This includes an update of the edge set, and can include the creation of a new internal node. The algorithm terminates when all input permutations are in the tree, i.e., T = T k . Choosing the next permutation π ∈ P to be added to the tree Ti-1, as well as determining its ancestor node, is done by a heuristic that minimizes the weight of the resulting tree T i . In contrast to previous algorithms, we do not use a median solver for this. Instead, we maintain for each edge (v, v') ∈ Ei-1a set of permutations, called the cloud of the edge. This cloud can be seen as sets of candidate nodes for internal nodes. For a formal definition of a cloud, we first must define the δ-vicinity of an edge.
Definition 1 Let (v, v') be an edge in a tree and let δ ∈ ℝ. The δ-vicinity of (v, v') is defined by Vic δ (v, v') = {s ∈ V | d(v, s) + d(s, v') ≤ d(v, v') + δ}
In the following, we often simply speak of the vicinity of an edge, assuming that δ is fixed.
Intuitively, this means that the d-vicinity of an edge (v, v') are all permutations w that lie "in between" v and v'. Splitting the edge into the two edges (v, w) and (w, v'), and adding the edge (w, π) will increase the weight of the tree by at most d(w, π) + δ. Thus, searching for new internal nodes in the vicinity of edges seems to be a good heuristic. However, even the 0-vicinity of an edge (v, v') can be of exponential size w.r.t. d(v, v'). Hence, it is not practicable to search the whole vicinities of the edges, and we have to restrict the search space somehow. In the following, we assume that d is a small, fixed number.
Definition 2 The cloud Cloud(v, v') of an edge (v, v') in a tree is a subset of Vic δ (v, v').
Of course, this definition is quite general and does not reflect how to generate "good" clouds. We will present a heuristic for generating clouds in the next section.
The resulting tree does not necessarily fulfill the definition of a phylogenetic tree, as a permutation π ∈ P may correspond to an internal node v instead of a leaf node. This can easily be fixed by creating an exact copy v' of v and adding the edge (v, v'), i.e. π corresponds now to the leaf v'.
Creating the clouds
The quality and size of the clouds are crucial for the quality of the resulting tree and the running time of the algorithm. Let us consider the two extremes. If the clouds are empty, the algorithm is reduced to Prim's algorithm that finds a minimum spanning tree of P. If the cloud of an edge (v, v') contains the whole vicinity of the edge, the algorithm will always find a best ancestral genome unless it is not in this vicinity. However, in this case the size of the cloud is exponential w.r.t. d(v, v'). Our goal is to find, for each edge (v, v'), a cloud of polynomial size w.r.t. d(v, v') that provides a good coverage of the vicinity of (v, v'). The main idea of our heuristic is to generate different optimal or near optimal sorting sequences between v and v' and to select a subset of the permutations that lie on these sorting sequences as the cloud of the edge. To avoid duplicates in the cloud, our algorithm proceeds as follows. First, we define the set C0 = {v}. Then, we iteratively generate the sets C i out of the sets Ci-1by applying to each permutation in Ci-1each operation that decreases the distance to v'. Then, we reduce the size of C i by selecting a fixed number of disjoint permutations from C i . As additional heuristic, we select the permutations from C i that minimize the distance to the closest permutation in the set of input permutations P that is not yet in the tree. These steps are repeated until we reach the permutation v', i.e. C m = {v'}. As cloud, we use the union of the sets C1 to Cm-1.
Note that the resulting cloud is a subset of Vic0(v, v'). However, this works only for the reversal distance, as we do not have an exact algorithm for the weighted reversal and transposition distance. In this case, we apply operations that decrease the lower bound instead of decreasing the real distance. Thus, the parameter δ depends on the approximation quality of the algorithm for generating the sorting sequence, and we cannot determine it exactly. However, the approximation quality of the algorithm is very good in practice [5], so we can assume that δ is small.
Improving the topology
Note that searching for the edge (w1, w2) is done by an exhaustive search for w1 in all nodes in V1 and all permutations in the clouds of all edges in E1, and similarly for w2. The improvement step is repeated until no further improvement is found.
Improving internal nodes
Due to the tree construction algorithm, usually some of the internal nodes are not the median of their neighboring nodes, although they are very close to the median in most cases. The second improvement algorithm further improves the tree by relabeling internal nodes until all internal nodes are the median of their neighbors. For this, we first must ensure that each internal node is of degree 3, since our median solver is designed to find the median of three nodes. Thus, for each internal node v with a degree of k > 3, we create a node v' which is an exact copy of v. We reconnect these two nodes such that v is connected to v' and two of its former neighbors, while v' is connected to v and all other neighbors of v. Thus v has now a degree of 3, and v' has a degree of k - 1. We repeat this until all internal nodes have a degree of 3.
Now, for each internal node v, we calculate the median M of its three neighboring nodes. If the sum of the distances of the neighbor nodes to M is less than the sum of the distances of the neighbor nodes to v, we replace v with M. For the reversal distance, we used the exact Caprara median solver, which maximizes the number of cycles in the multiple breakpoint graph and then checks the pairwise distances towards the calculated median (for details, see [22]). For the weighted reversal and transposition distance, we extended Caparara's median solver such that it minimizes the sum of the lower bounds between the calculated median and each of the three input permutations, and then checks the pairwise distances towards the calculated median. Note that there is no efficient exact median solver known for the weighted reversal and transposition distance. However, the median solver finds an exact median w.r.t. the lower bound for the weighted reversal and transposition distance. Thus, we only get inaccuracies by using the approximation algorithm for the weighted reversal and transposition distance, and therefore the approximation ratio of our median solver is as least as good as the approximation ratio of the pairwise distances, which is very good in practice.
The improvement of internal nodes is repeated until the tree does not improve any further, i.e. each node is the median of its neighboring nodes.
Data sets
We tested our algorithm on the following three biological datasets, which can be considered as benchmarks for phylogenetic reconstruction algorithms based on genome rearrangements.
This dataset contains 13 chloroplast DNAs of the flowering plant family Campanulaceae, where each genome contains 105 markers. It was created by Cosner et al. as test case for their new method MPBE [18], and at that time was ranked among the most challenging datasets for genome rearrangement algorithms.
This dataset contains 11 metazoan mitochondrial DNAs with 36 different markers. In the context of genome rearrangement algorithms, it was first used in [23]. In the year 2002, Bourque and Pevzner published a tree with 150 reversals, showing that MGR outperforms GRAPPA, as GRAPPA was only able to find a tree with 175 reversals in more than 48 hours [13]. However, GRAPPA has been improved ever since, and the current version is now able to find a tree with 159 reversals in 68 seconds (see Subsection "Experimental results").
This dataset contains 62 protostome mitochondrial DNAs with 36 different markers. It was first published in [24] and later adjusted in [17] to be used as test scenario for amGRP. The increased amount of data and the larger genome distances make this dataset much more complicated than the metazoan dataset.
Weight ratios
Two circular genomes (represented by n markers) are identical if the number of breakpoints between them is zero and the number of cycles in the breakpoint graph is n, respectively (for details, see [25]). Thus, a sequence of rearrangement operations that transforms one genome into the other must reduce the number of breakpoints to zero and increase the number of cycles to n, respectively. Because a reversal removes at most two breakpoints and generates at most one new cycle, while a transposition removes at most three breakpoints and generates at most two new cycles, transpositions are generally favored if the weight ratio is 1:1 (w r : w t ). On the other hand, if the weight ratio is 1:2 and one uses Eriksen's (1 + ϵ)-approximation algorithm [26], then an optimal sequence of rearrangements will consist almost solely of reversals. In our opinion, a realistic weight ratio for most biological datasets must be somewhere between these two extremes. Exemplarily, we are using the weight ratio 1:1.5.
We performed tests for the weighted reversal and transposition distance with the weight ratios 1:2, 1:1.5, and 1:1. The weight w r for reversals was fixed to 1, while the weight w t for transpositions was set to the corresponding values. We tested our program with different tree improvement strategies: No tree improvement (phylo-n), using only the tree perturbation to improve the topology (phylo-t), using only the median solver to improve the inner nodes (phylo-m), and the combination of both strategies (phylo-tm). Since the result of our algorithm depends on which permutation of the set P was chosen as first node, we performed one run for each permutation in P as start node.
Other tools using the reversal distance
As there is no other algorithm that can handle the weighted reversal and transposition distance, we also performed all tests mentioned above with the reversal distance, and compared our results with the results of the following programs.
We used the current version 2.0 [27], which contains some serious improvements above older versions, especially it includes a median solver. The best results were achieved with the parameters -t4 -T4 -n4 -e -m -a -C (for details see the GRAPPA manual). Using DCM-GRAPPA [28] only improved the running times, but usually resulted in worse trees.
We used the current version 2.01. The best results were achieved with the triplet resolution heuristic disabled. Note that the heuristics h3 and h5 are no longer available, thus we could not reproduce some of the results given in [13] and [17].
We used the version of April 2007. The best results were achieved with the "skewest" heuristic. As amGRP relies on randomness, we performed 50 runs for each data set. Note that this results in a similar number of runs and overall running time for amGRP and our program when using the reversal distance on the protostomes data set. In Subsection "Experimental results", we will only report the result of the best of these runs. For more information about the variance of the output of amGRP, the reader is referred to [17].
All tests were performed on a standard PC (Athlon 64 3200+ 2 GHz CPU, 512 kB L2 Cache, 4 GB RAM, 1000 MHz Bus Speed, Debian Kernel 2.6.22, GCC 4.1.2).
Comparing the results
While comparing the trees according to the reversal distance is straightforward, one might also be interested in comparing the trees according to the weighted reversal and transposition distance. The only other approach that tackles this task is the one of Cosner et al. [18], however in a very indirect way. First, a phylogenetic tree is generated according to the breakpoint distance, using a maximum parsimony technique for obtaining the tree topology and the software tool BPAnalysis for obtaining the labeling of internal nodes. Then, the weighted reversal and transposition distances of the edges of the tree are heuristically calculated with the software tool DERANGE II [19]. Since BPAnalysis is no longer state-of-the-art and software tools have improved ever since, we investigated whether it is worthwhile to create a tree according to the reversal distance, and then to recalculate the weights of the edges using the weighted reversal and transposition distance. The experiments showed that using DERANGE II or the algorithm devised in [4] led to very similar results, thus we only provide the results of the latter algorithm. To avoid misleading results by using an approximation algorithm, we also recalculated the weights of the edges using the lower bound for the weighted reversal and transposition distance, resulting in a lower bound for the tree weight for a given topology and labeling of internal nodes. To put it differently, recalculating the tree weight with an exact algorithm for the weighted reversal and transposition distance cannot give us a result that is lower than this value. This approach was only feasible for MGR and amGRP because GRAPPA does not report the permutations at internal nodes. One might also ask if using Eriksen's (1 + ϵ)-approximation algorithm [26] would lead to better results for the weight rato 1:2. However, comparing the calculated tree weights with the lower bounds showed that the approximation ratio of our algorithm is very good in practice, especially for this weight ratio, so we did not perform further tests with Eriksen's algorithm.
Experimental results
Weighted reversal and transposition distance
Results for the Campanulaceae dataset.
62 (62)
62 (62)
62 (62)
62 (62)
63 (63)
63 (63)
51.5 (51)
50 (49.5)
50 (49.5)
50 (49.5)
52.5 (52)
56 (55)
40 (39)
39 (38)
38 (37)
39 (38)
42 (41)
49 (47)
Results for the metazoan dataset.
153 (153)
151 (151)
146 (145)
146 (146)
142 (141)
151 (151)
125 (125)
123.5 (123.5)
119.5 (119.5)
120.5 (120.5)
125.5 (123.5)
134.5 (129)
87 (87)
87 (87)
85 (85)
85 (85)
110 (106)
116 (107)
Results for the protostomes dataset.
501 (497)
498 (494)
490 (487)
488 (485)
496 (490)
522 (520)
400.5 (399)
400 (398.5)
392.5 (392.5)
392 (392)
431.5 (418)
446.5 (441.5)
365 (347)
388 (363)
Reversal distance
Results for the reversal distance.
Our algorithm achieves two improvements over previous works on this topic. First, it does not rely on a specific genome rearrangement distance. It can be used for any genome rearrangement distance as long as there is at least a good approximation algorithm for generating a sorting sequence between two genomes. Second, it avoids median solvers as long as possible. The median problem is NP-hard for the breakpoint distance and the reversal distance, and most likely also for the other genome rearrangement distances. Although solving the median problem may be feasible for small problems, it is getting more and more complicated for larger genomes. Thus, in our opinion, median solvers should be avoided as long as possible. We have shown that our algorithm can compete with the currently best algorithms w.r.t. the reversal distance. To the best of our knowledge, our algorithm is currently the only one that directly tackles the phylogenetic reconstruction problem for the weighted reversal and transposition distance.
We implemented the algorithm in C++. The program is open source and can be obtained from the authors.
This work was supported by DFG-grant Oh 53/5-1. The authors wish to thank Jijun Tang for providing DCM-GRAPPA, Guillaume Bourque and Glenn Tesler for providing MGR, and Matthias Bernt for providing amGRP and his helpful comments on finding the best parameters for it.
Authors' Affiliations
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- Hannenhalli S, Pevzner P: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. Journal of the ACM 1999, 46: 1–27.View ArticleGoogle Scholar
- Tannier E, Bergeron A, Sagot MF: Advances on sorting by reversals. Discrete Applied Mathematics 2007, 155: 881–888.View ArticleGoogle Scholar
- Caprara A: The Reversal Median Problem. INFORMS Journal on Computing 2003, 15: 93–113.View ArticleGoogle Scholar
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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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GHOST IN THE SHELL 3.5 out of 10; Directed by Rupert Sanders; Written by Jamie Moss; Starring Scarlett Johansson, Takeshi Kitano, Pilou Asbaek and Michael Pitt; Rated PG-13 for intense sequences of sci-fi violence, suggestive content and some disturbing images; Running time 106 minutes; In wide release March 31, 2017.
The original Ghost in the Shell is a benchmark in Japanese animation. Taking its cues from Akira that came before, Ghost continued the trend of going to new levels of excellence in animation and into a world that no one could have imagined. It and its manga (essentially Japanese graphic novels) have influenced nearly every science fiction film of the last 30 years, so it was exciting to think what we would finally get to see on the big screen. The result, while beautifully shot and filmed, is but a pale imitation of what it should have been and is an intensely cold and shallow film.
Major (Scarlett Johansson) is a new breed of cyborg – an artificial body (shell) controlled by a living person's mind (ghost). Drafted into a risky experiment after a terrorist attack, Major awakens from death to find herself in a body she doesn't know and into a world she can't understand. A year later, she is now the perfect weapon and routinely and easily takes out thugs, terrorists and other threats to Tokyo. During the middle of an op, she discovers that a rogue known only as Kuze (Michael Pitt) is using cyborgs to hack into the minds of and kill the scientists of the Hanka Robotics corporation, the same one that brought her back to life. As she and her partner Batou (Pilou Asbaek) track him down, they are led deeper into a spiraling conspiracy that will have Major questioning reality and everything she has ever known.
Gorgeously shot, Ghost in the Shell manages to do the impossible and truly bring an anime to life. Scenes are crafted with the greatest care that gives the whole thing a gritty, dreamlike and nightmarish feeling that hits every high note from the source material. Iconic moments are perfectly recreated while the disturbing imagery will have people wincing. Despite being a PG-13 film, this pushes the boundaries of the rating and gets away with more than expected.
But much like a Fabergé egg, the glitter and shine is superficial and falls apart if the outside is cracked open.
Originally, Ghost in the Shell had layers that audiences could mine to find insights on humanity, religion and philosophy. This version is simply an excuse to have an extremely attractive woman whirl around in a skintight suit and shoot people in the face. There is no subtlety or intrigue, just excessive action superimposed on dry dialogue that is meant to sound smart but smacks of pop culture.
Not to mention how in love it is with its mythology. The middle is so long and drawn out that even fans will find themselves yawning and waiting for it to be over. For a film that runs barely over an hour and half, it felt like the epic it isn't.
And then there's the whitewashing issue. Already problematic for casting a Caucasian woman in the role of an Asian character, that isn't its biggest problem. The worst was that the one character who speaks Japanese, Major's boss, Aramaki (Takeshi Kitano), is constantly spoken down to by the white characters, and even Major who refuses to talk with him in his language. Throw in a sympathetic character speaking broken English just to make a scene more emotional as well as literally turning multiple Asian characters Caucasian, and it moves from annoying to disgusting.
So, while this easily could have been one of the most groundbreaking and riveting movies of the year, it is too beset by problems that would have kept a film with a lesser pedigree from ever being made. Yes, it's one of the best-looking things out there, and the filmmakers deserve a modicum of credit for attempting it, but that doesn't excuse its multitude of flaws. Rewatch the anime or go see Get Out, Logan, Power Rangers or any of the other great films out right now that are either masterpieces or just a lot of fun.
3.5 out of 10
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Tags: manga , Scarlett Johansson , anime , ghost in the shell


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Florida Panthers
Florida Panthers' Dan Ellis embraces the competition to be backup goalie
Backup goalie Dan Ellis' position with the Florida Panthers was compromised the day general manager Dale Tallon signed Al Montoya.
Ellis says he has no plans to go anywhere. Montoya doesn't, either.
With Roberto Luongo firmly entrenched as Florida's starting goalie, Ellis and Montoya are in camp vying to be the Panthers' backup, although Tallon made it clear on July 1 that Montoya was signed to do the job.
"It's not a concern of mine," Ellis said before starting Wednesday's preseason opener against Dallas at BB&T Center.
"It was a decision made by Dale and you have to respect that. But if I can lose my job in 20 days, I don't see why I can't win it back in 20 days. That's my focus and I don't worry about anything else."
With Montoya and Luongo taking the night off, Ellis played the first two periods of Florida's eventual 4-3 shootout loss.
Things didn't start well for Ellis against his former teammates — Ellis came to the Panthers from Dallas at the March trade deadline — as the Stars scored twice in the first period.
Ellis stopped all five shots faced in the second and left with the score tied at 2.
Ellis' play at the end of last season all but forced Tallon to go out and get another goalie off the free agency market. When he played in place of Luongo last spring, Ellis struggled to stop the puck.
Ellis ended the year going 0-5-1 with Florida, stopping just 84 percent of the shots he faced.
On Wednesday, Ellis said he wasn't surprised Florida went after Montoya — who had two pretty good years in Winnipeg — and suggested the competition is going to be good for him.
"Them signing Montoya has been the best thing for me," Ellis said. "I've really dove into myself, critiqued myself and things I need to improve on."
If all three of Florida's top goalies make it through training camp unscathed, Ellis is expected to be sent to Florida's AHL affiliate in San Antonio.
Coach Gerard Gallant said it's too early to begin speculating what the team will do in the coming weeks.
Both Montoya and Ellis would be paid their NHL salary if sent to the minors.
"This is what competition is all about," Gallant said. "We have three goaltenders with NHL experience and no one has said Montoya was brought in to backup anyone. It's about who wins the spot. You have to be fair to all your players."
Ellis said he has been through goalie battles in the past and he is ready for this one.
So, too, is Montoya.
Right now, he most definitely has the edge.
"Nothing has changed for me," Montoya said. "This is where I want to be, this is the team I want to play for. I take it as my job. I'm here to push [Luongo], here to push myself and here to help this team out."
Wednesday's game
▪ Dallas 4, Panthers 3 (SO): Ales Hemsky beat Michael Houser in the fourth round to lead the Stars to a shootout win.
Defenseman Shane O'Brien, in camp on a tryout, got the Panthers on the board in the second with a nice shot from the slot before center Dave Bolland made it 2-2 with 49.2 seconds left in the period.
The Panthers got a goal from Brandon Pirri early in the third before Alex Goligoski tied it off a pass from Tyler Seguin midway through the period.
coming UP
▪ Thursday: Off
▪ Friday: Practice at Coral Springs IceDen, 10 a.m.
▪ Saturday: Preseason doubleheader at Nashville, 4 and 8 p.m.


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I just realised when I went to post this today that I had completely forgotten to take a photo of my entry in Round 2 of this one - never mind
This time around the CJ is Frances (New2this) who is hosting the cj, she had a selection of sketches to choose from and I chose this one. I really liked the idea of the collage of photos but it was slightly tricky to scale down to the size of the cj. I do think though that I will try this sketch as a 12 x 12 layout
Here is the sketch
Here is my entry. I cut up bits from some of my many beachy type photos for the photo collage. I sprayed the background kraft card with some teal glimmer mist (my favourite product at the moment), I thought I would prick out and sew the wavy lines to represent the sea and my title round the edge of the photo collage reads I do like to be beside the seaside - which of course I do.
I just hope Frances likes it.
Please pardon the quality of the photos as I took them on my phone and I am not sure where the chequerboard effect sprung from!!


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Sunday, May 26, 2013
Season Review: You Can Ask For More.
4 comments:
Van Persie had one year left on his deal. We had to sell him. Unfortunately that is modern football - talent is concentrated where resources are greatest. Look at Dortmund. Lewandowski has a year left on his deal. Will they sell to Bayern for 25m or will they let him leave for free next year? I think the answer is obvious. As much as we like to think of ourselves as a big club, there are clubs bigger than us. Look around Europe. Atletico have lost Falcao and Aguero in consecutive years to oil funded rivals. Milan lost Zlatan and Thiago Silva. Portto lose players every year. Basically, only a handful of clubs can afford to keep their best players. I completely agree that performances in the domestic cups have been disgraceful but with regards to challenging for trophies that actually matter, i.e. the Champions League and the Premiership, the destinations of those can be pretty easy to narrow down. Is winning the FA Cup and finishing 4th really much better than just finishing 4th? Either way, we are a long way from the pinnacle of the sport. Whilst blame can be apportioned to the manager or the board, the fact is that there are much bigger clubs than us. This is the reality.
- 26 May 2013 at 18:57
Many of your o called " bigger clubs " are NOT bigger clubs they just have ownership with deeper pockets and a propensity to spend....3to 5 key signings and Arsene can crown his time with arsenal across the next 3to 5 years.
Now is the moment to seize the pinnacle... If w spend!
- 27 May 2013 at 04:11
- This comment has been removed by a blog administrator.
- 27 May 2013 at 12:28
Wenger has brought Arsenal to this level.He draws heighest salary without performance. Time to save Arsenal , time to say goodbye to the infamous pair of Wenger and Gazdi.
- 17 August 2013 at 14:51


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When it comes to taking pictures of animals, you are really going to want to get the best possible pictures you can get. This article will try and give you simple tips for taking great photos of animals.
There are two different types of animals you can photograph: your pets and the captive, and the wild animals.
According to Daniel mule, When taking photos of pets or animals in cages you really don't have as much to worry about except compositional techniques. The animals won't be moving like crazy and should be easier to handle. If its your own pet you could feed them some food and they'll stay still for sure. Daniel is arguably one of the foremost wildlife photographers. He is passionate about birds and is specializing in bird photography. In documenting birds through his photographs, he has developed a style of technical excellence combined with a captivating story. His journey included carrying his photography equipment and outdoor gear up high mountain peaks, across lakes and rivers, and over glaciers and lava fields.
Shooting wild creatures is somewhat trickier. These creatures are in the wild and keep running from individuals. You must sneak towards them and catch an injection of them brisk. In case you're capturing quick creatures like feathered creatures you must be additional fast as they could take off in seconds. Wildlife photography is not only a passion for Daniel, but a powerful medium to help conserve nature. He clicks his pictures with the motto "Every time he presses the button, he'll get one step closer to the Mother Nature".
At the point when taking creature shots you ought to attempt to keep the foundation basic. Attempt to maintain a strategic distance from excessively complex foundations that occupy the viewer.
To get great close up shots you should really think of getting a telephoto lens. There are some telephoto lenses built so you do not need a tripod. This is great as hauling a tripod around when taking shots of wild animals can be difficult, click here to read more.


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Hey guys,
After being on backorder for around 2 months, my SK450 + its Dead Cat conversion kit has finally arrived from HobbyKing.
Many thanks to Mr.Mohtashim for providing the frame!
Pictures of assembly and unpacking are attached below. I will keep the blog updated as the build progresses. Motors and ESCs are scheduled to arrive around 2nd-3rd March due to Chinese new year delays.


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The goal of achieving energy security provides a unique opportunity for cooperation between the United States, Canada, and Mexico. The United States and Canada have shaped their energy policies in response to the oil supply shocks of the 1970s and 1980s, while Mexico is currently experiencing a reduction in its own domestic oil supply. Energy security is often associated with energy independence and self-sufficiency for supply. This strategy remains impractical for the three North American countries because they are already interconnected in energy supply and demand. Due to the geographic distribution of raw fuels and need for exploration of unconventional resources, North American energy security will be better served by a policy of energy interdependence. The relationships forged through the North American Free Trade Agreement, the Security and Prosperity Partnership, and the North American Electrical Reliability Corporation have set a policy precedent for trilateral cooperation. Energy security is a crosscutting issue because it encompasses trade, labor flows, infrastructure, and defense. This study reviews the regulatory frameworks of the oil, natural gas, and electrical markets in the three North American countries to assess the energy security environment on the continent. It then proposes possible avenues for integrating the continental energy market, which could serve the greater purpose of increasing the sense of collective identity for North America.
About the author:
Alison Terry is a Master's candidate at the University of Denver's Josef Korbel School of International Studies. Her research interests include the geography of conflict and quantifying border permeability using GIS and remote sensing. She is a recipient of the US Geospatial Intelligence Foundation Graduate Scholarship for 2011-2012. Ms. Terry holds a Bachelor's Degree in Environmental Studies from Dartmouth College and has previously worked as a Biologist for the US Geological Survey.
Image courtesy of Christian Mehlführer.


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Firm leaders unveil new name, while reminding clients it's the same great service.
GREENVILLE, SC, October 20, 2017 – Leaders from Greene, Finney & Horton, LLP a boutique accounting and advisory firm, today announced the unveiling of the firm's new name. Rebranding efforts were initiated last month to represent the firm's current partners—while also preserving the firm's long-standing professional brand image.
"Effective and accurate branding and marketing are critical in today's competitive landscape. With a change in leadership, we wanted to ensure our brand was current. At the same time, we want to assure clients that despite the name change they will continue to receive the same excellence in our products and services they've come to expect and deserve," stated Larry Finney, Partner at Greene Finney.
Greene Finney provides the same level of sophisticated services as larger firms, but with a personal touch. Greene Finney provides audit and advisory services to local governments, nonprofits, and businesses. Additionally, Greene Finney offers outsourced accounting and advisory services supported by an advanced cloud-based platform. Our online system offers 24/7 convenience for clients and supports a collaborative working relationship with our professional team.
Partners Larry Finney, David Phillips, Ken Meadows, Denise Eidson, and Emily Sobczak will continue to lead the firm in providing quality services to our clients. Greene Finney, LLP officially announced its new name to clients earlier this month.
About Greene Finney, LLP
Greene Finney, LLP serves the audit, advisory, and accounting needs of businesses, governments, and nonprofits throughout the Carolinas. Their five offices are located in Greenville, SC; Spartanburg, SC; Mauldin, SC; Charleston, SC; and Asheville, NC. For more information, call (864) 232-5204 or visit our website at www.gfhllp.com.


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Preheat oven to 350ºF.
In the bowl, mix cream, butter and sugar together at least 3 minutes or until smooth.
Beat in vanilla and egg.
In a seperate bowl, combine baking powder with flour and add a litte at a time to wet the ingedients. The dough will be very stiff. If it becomes too stiff for your mixer turn out the dough onto a countertop surface. Wet your hands and finish off kneading the dough by hand.
Do not chill the dough. Divide into workable batches, roll out onto a floured surface and cut. You want these cookies to be on the thicker side.
Bake at 350 degrees for 6-8 minutes. Let cool on the cookie sheet until firm enough to transfer to a cooling rack.
Combine butter, powdered sugar and vanilla. Add milk slowly to reach desired consistency.
Color icing colors of choice for cookie shapes.
Place icing in assembled icing bags with Wilton® tip #2. Decorate each cookie shape.


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'Thor 2′ Posters: Heimdall Defends Asgard Against Malekith's Army
Apparently the best things come in pairs. The 'Thor 2' posters have been releasing in sets of two -- Loki and Odin, Jane and Sif, and now the Asgardian protector Heimdall and the Malekith-led army of Dark Elves get their share of the action.
It's funny to thing back on how great an uproar was had when Marvel first cast Idris Elba as the originally white character from the comics, and now it seems like 'Thor' wouldn't be the same without him. Marvel has even immortalized the character further by awarding him his own 'Thor 2' poster, displaying his towering stance as the guardian of the Bifrost. Simultaneously, EW debuted Malekith's (Christopher Eccleston) new sheet as he marches on his enemies with an army of Dark Elves backing him.
In 'Thor 2,' titled 'The Dark World,' Chris Hemsworth's Thor returns to the realm of Asgard to battle an ancient threat -- Malekith the Accursed and his army have returned to plunge the universe into darkness. The god of thunder and future king of Asgard must team up with the only person who can help defeat this villain, Tom Hiddleston's Loki, the bane of the Avengers' existence. Also starring are the returning Natalie Portman, Jaimie Alexander, Anthony Hopkins, Stellan Skarsgård and Kat Dennings, and newcomers like Adewale Akinnuoye-Agbaje.
'Thor 2' hits theaters November 8.


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Welcome to Build.Recycle.Net - Used Building Materials
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Vecoplan, LLC
VECOPLAN is the global leader in mechanical technologies for the processing of waste. We manufacture a complete line of Size Reduction Machinery including Shredders, Grinders & Chippers, as well as complete Size Reduction Systems used in Recycling.
We design, engineer, manufacture, install, and provide start-up training on, as well as ongoing parts and service for complete systems used to prepare and feed MSW or Biomass for use: as alternative fuel in the production of heat and power, as a feedstock for pelletizing, and as a feedstock for conversion to syngas, methanol, cellulosic ethanol, biodiesel, and other liquid biofuels. Vecoplan is also experienced with Tires, Wood, Carpet, and other industrial wastes.
Capabilities include unloading of raw feed-stocks, pre-shredding, ferrous separation, conveying, screening, air classification, optical sorting, re-shredding, non-ferrous separation, testing stations, storage, and metered feeding to the boiler, to the pelletizing machinery, to the liquid fuel conversion system, or to other waste conversion technologies.
Vecoplan, LLC
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Category crunch: UK pork sector in state of flux
By Katy Askew | 5 December 2012
Pork prices driven up by higher input costs
The UK pork sector hit the headlines when Dutch food group Vion announced plans to exit the market. The sudden withdrawal of a major player highlights the challenges pork processors are grappling with, including rising input costs and tough pricing negotiations. Nevertheless, as the sector embarks on a process of consolidation and capacity is taken out of the category, the balance of power could be shifting down the pork supply chain. In part one of our two-part category crunch, Katy Askew examines some of the issues facing the sector.
Dutch food group Vion's announcement that it plans to quit the UK has shone the spotlight on the country's pork sector.
The company ended months of speculation with the news it will sell its entire UK business, which employs 13,000 people across 38 manufacturing sites and generated revenue of EUR2.35bn (US$3.07bn) in fiscal 2011.
Vion appears to have made quick progress in finding a buyer for its pork processing business, which has estimated sales of EUR0.8bn and a workforce of around 5,000. Reports suggest the unit will fall into the hands of management in a private-equity backed buyout.
Vion's decision to exit the UK was not entirely unexpected, although the sudden and definitive nature of the move surprised many. Vion, which has been present in the UK since the late 1990s, has suffered a series of UK setbacks including, most recently, the controversial decision to close its loss making pork processing unit, Hall's of Broxburn.
As Vion outlined its decision to close Hall's, Peter Barr, chairman of the group's UK operations, blamed "significant over-capacity" in the pork industry. Excess supply is a problem for pork processors.
Sukhdev Joha, reader of management strategy at Royal Hollaway University of London and co-author of research report Bringing Home the Bacon, argues that, as capacity utilisation drops, profit margins follow.
"If you are operating at 80-90% capacity utilisation you make money, much below this and you are working to cover your costs... It is in the last 15-20% of production capacity that profits are made," Joha explains. "Over-capacity has far reaching consequences that impact the entire chain."
Joha argues the UK's supermarkets have a "trader mentality" toward their procurement of pork products, which they use as a loss-leader to drive footfall. According to Joha, this results in fluctuating demand, which in turn limits capacity utilisation in the sector.
However, Shore Capital analyst Clive Black insists that capacity has come out of the industry of late. "The UK pork industry is highly competitive, albeit the industry is benefiting from capacity reduction in recent years," he observes.
The sector is also benefiting from slow but steady revenue growth, which is being driven by higher prices. According to figures published by Kantar Worldpanel, fresh pork sales increased by 4.5% in the 52 weeks to 8 July, as price inflation of 5.9% offset a 2.3% drop in volumes. Sausage and ham prices offset a modest volume decline to boost total sales by 0.8% in the period. Only bacon saw volume in the 12 month period increase, as sales rose 0.7% on flat pricing.
While processors have been able to increase prices this does not, however, signal that they have it all their own way in negotiations with retailers. Around 70% of total pork sales are generated by the UK's top four multiples - Tesco, Asda, Sainsbury's and Morrisons. This sizeable share of the retail market means that, as in other supply chains, the supermarkets pack a considerable punch in pricing discussions.
Flemming Enevoldsen, chairman of processed meats at farmer-owned cooperative Danish Crown, tells just-food pricing negotiations with UK retailers are tough, especially given the current economic climate, which is marked by constrained consumer sentiment.
Enevoldsen, who is acting CEO of Danish Crown's UK arm Tulip, says: "Retailers are business people, they have to look after their business. It is never easy to increase prices with retailers, in particular in these years where you have a global, if not recession, at least period where the financial climate has cooled off."
Nevertheless, Enevoldsen says retailers are aware of the "broader picture" in the supply chain, with rising input costs putting processors and producers under pressure.
"Our customers - the retailers - are certainly bright enough to understand the broader picture. On thing is what informs their strategy moves, how they make their decisions, another is how they view the day-to-day business with their suppliers... I think it is fair to say that it is never easy to increase sales prices with retailers. But it is not because they don't understand the global supply chain."
Farm costs have risen steeply due to higher global feed prices. Drought in the US this year meant corn and soybean harvests have been significantly lower than previous years, while Russia cut its forecast wheat harvest in the summer due to poor weather conditions.
Another issue driving higher pig prices, Enevoldsen adds, is lower European pig meat production. "This is partly a reflection of the poor earnings being a pig farmer in the past years. It is also a reflection on many European countries having very slow and difficult procedures in place if you want to upgraded your production. And, of course, the most important factor is the financial crisis, which led to financing being more difficult to obtain amongst farmers."
European pig farmers have also had to overhaul their farming methods in order to prepare for the 2013 European welfare regulations that come into force in January.
These changes, which will ban the use of sow stalls, will not impact UK pig farmers who already adhere to higher standards of animal welfare. However, UK-reared pigs only account for about 50% of the nation's pork sales, a situation that has created a degree of uncertainty in the supply chain, with the possibility that imports from the EU could fall off.
According to Cranswick CEO Adam Couch, these factors meant the industry saw some spikes in pig meat prices in October and November and processors could be facing further volatile fluctuations in the coming months.
Couch concurs retailers are aware of the issues impacting the supply chain, although he too concedes these must also be balanced against the poor consumer sentiment that currently prevails in the market.
"Retailers are certainly aware of the difficult economic climate, obviously with their customers. But they are also attuned to the poor harvest that has created a lot of problems for pig producers the world over. We have had to respond in terms of the price we paid for pigs and the retailers, we are still in dialogue, but we are having very constructive conversations in order to keep these producers in business in the medium to long term," Couch tells just-food.
"If there isn't a whole chain responsibility taken on board then it leaves producers facing down the barrel of a gun. It resonates with both retailers and ourselves to get that price recovery through. There is a more responsible approach being taken in the wider context by both retailers and processors alike," Couch claims.
Panmure Gordon analyst Damien McNeela agrees an understanding of the troubles facing the supply chain has been a major factor prompting retailers to increase the price that they are willing to pay for pork products, particularly given the potential of further pork price rises following the introduction of the EU sow stall ban.
"Security of supply is the watchword amongst retailers and the uncertainty that the exit of Vion - one of the largest processors in the UK - creates amongst the retailers should be beneficial for other well invested, large scale meat players," he suggests.
Indeed, the UK's largest retailer Tesco recently unveiled plans to set up direct contracts with farmers. The company said that it will link the price that it pays pork producers to the cost of production. Moreover, Tesco said prices would be adjusted on a monthly basis to avoid a situation where farmers are locked into loss-making contracts if the cost of production swings significantly.
"Pig farmers will be consulted to determine a fair price for pork and this will be linked to the swings in feed price. The price of feed varies greatly: it can go up very quickly and it can go down very quickly. It will work both ways, but pig farmers will always get a fair price for their meat," a Tesco spokesperson explained.
The spokesman said the move was a "Tesco investment" and would not affect the price that consumers pay for pork. He also insisted that it would not "take processors out of the equation".
"The processors are still going to do the job they always did but Tesco will have the direct contract with the farmer."
The news has been roundly welcomed by the farming community. "British pig-keepers have been plagued by short-term supply chains and volatile costs, which have prevented them from investing in the future," National Pig Association general manager Dr Zoe Davies says. The Tesco contracts "could help transform British pig production", increasing transparency and promoting a more even sharing of risk and reward, Davies says.
Even as supply chain relationships adjust in response to a growing recognition of the need to promote stability, the nature of the UK pork sector remains highly competitive as pork processors compete for market share. Higher prices should be good news for the margins of pork producer. However, given the weak consumer sentiment currently prevailing in the UK, there is the possibility that higher prices could retard volume growth.
In part two of our Category Crunch, we will examine the divergent strategies employed by the country's pork majors as they look to grow sales in the face of weak consumer sentiment.
Sectors: Meat, poultry & eggs, Private label
Companies: Vion Food Group, Tesco, Danish Crown, Asda, Sainsbury's, Morrisons, Cranswick
Consuming issues: Wasting away
The problem of food waste is due to the low value people in the West put on cheap food. And cheap food is a product, in part, of the modern, industrial food system. However, amid some scepticism, the ...
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The company I work for is a sponsor for United Way. Last week we had our kick off to raise money for ALS. Yes, there were ice bucket challenges but in addition, we asked all the surrounding businesses in our area to donate something for our raffle. Not that I have my own business, but I was approached and asked to donate some type of paper crafts. So I have been busy packaging Halloween cards, Christmas cards, thank you cards and of course my waterfall folio mini albums!
Front cover
Inside photo mats and journaling tags
And of course a birthday themed album~
Here are a couple birthday cards I made as a request from a couple friends needing them. I've also been reorganizing and cleaning out all my space and cubby holes. I've come across papers I forgot I had so I started pulling them out to use them.
A friend of mine was in town for business but we were able to meet up for dinner before she had to fly back to California. Her birthday was in July so I made this mini album with her in mind. Other than the flowers and doily on the cover, all papers and embellishments are from Graphic 45 A Time To Celebrate.
Sorry for the poor photography.
That's all from me. Enjoy your day and happy Fall!


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JUST AFTER MIDNIGHT is here!
My newest novel was released by Lake Union (Amazon Publishing) on December 4th, 2018. It's called JUST AFTER MIDNIGHT, and it's currently available in Kindle, Paperback, Audiobook MP3 CD, and as an Audible Download. Feel free to get my email address from the "Contact Me" page and let me know what you think!
Now It's Easy to Keep Up with the News
Because you asked, I've created an easy way to subscribe to my blog so you never miss a deal alert, giveaway, or the latest publishing news. Just look at the bottom left of this or any of my pages. You'll see a space for your email address and a subscribe button. That's all there is to it!
A Scene Adaptation
I've released a specially made scene adaptation to introduce new readers to my novel DON'T LET ME GO. Think of it as a grand experiment in book trailers! Above are two little teaser videos. For the adapted scene itself, go to the Don't Let Me Go page or this special page devoted to the project.
A sneak peek at what's coming next
My next novel will be released by Lake Union (Amazon Publishing) on May 21st, 2019. It's called HAVE YOU SEEN LUIS VELEZ?, and it's especially close to my heart. It's available for preorder right now in Kindle, Paperback, and Audiobook MP3 CD. I can't wait to hear your thoughts on this one.


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Digital LCD Body Fat Analyzer Monitor Meter BMI Weight Loss Calculator
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Shows body fat by weight percentage and indication figure or body fat type
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Time function: 12 / 24 hour format selection
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Alarm clock function
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1 x CR2025 3V battery
1 x User manual
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Designed, engineered and hand crafted in Crewe, the Bentayga's styling is pure Bentley. Sculptural with an elegant, timeless execution, it perfectly balances athleticism with confidence. From the four round LED headlamps and large matrix grille, to the distinctive power line and muscular haunches, the Bentley DNA is apparent throughout. The Bentley Bentayga combines unparalleled luxury with effortless performance and everyday usability. With an all-new W12 powertrain, the Bentayga is the fastest, most powerful, most luxurious and most exclusive SUV in the world. It offers a true Bentley driving experience and showcases innovative technology features. The Bentley Bentayga boasts the world's finest automotive cabin, with unrivaled levels of precision. The detailing in metal, wood and leather, including meticulous tolerances between elements of trim – is the epitome of modern British luxury. This level of perfection is only achievable thanks to the exceptional craft and skill of Bentley's team in Crewe.
The Bentayga's wheel arches, fenders and bonnet deliver a balance between sportiness and SUV presence. The ultra-sharp Bentley power line and muscular rear haunch display a taut tension in side profile, as part of the largest single-piece aluminium pressing in the automotive world. Trademark Bentley features such as the large matrix grille and B-shaped wing vents afford the Bentayga a modern, dynamic elegance. The grille is flanked by four distinctive floating all-LED headlamps. The lights sit flush within the seamless super formed aluminium front fenders. Innovative design features, like the discreet headlamp washers contained within the outer lamp's body-colored centre, demonstrate remarkable attention to detail. To emphasize the go-anywhere nature of the Bentayga, the Bentley design team have integrated a stylish skid plate into the lower section of the front bumper, just below the floating wing motif. At the rear, within the segmented tail lights, a new 'B'-shaped illumination graphic is incorporated that affords the Bentayga an instantly recognizable and striking night-time signature.
An all-new twin-turbocharged 6.0-litre W12 engine is at the heart of the new Bentayga. The mighty 12-cylinder unit combines efficiency and refinement with ultra-luxurious levels of power and torque. With 600hp and 900 Nm delivering a 0-100Km time of 4.1 seconds and a top speed of 301km, making the Bentayga is the world's most powerful and fastest SUV. The new W12 uses both direct and indirect fuel injection. Switching seamlessly between the two technologies, the combination of these systems maximizes refinement, delivers low particulate emissions and maximizes power and torque delivery. The engine is mated to an eight-speed automatic gearbox. The transmission and four-wheel-drive system has been strengthened to handle the demands and high torque levels of off-road driving.
Inside the new Bentayga and you find the finest automotive interior in the world, with hand crafted wood and leather throughout, engineered with precision to deliver absolute perfection. The Bentayga's cockpit sets new standards for both luxury and precision, with meticulous tolerances between the exquisite veneered woods and metal elements. The dashboard takes the iconic Bentley 'wing' design as its inspiration, with the beautifully finished surfaces flowing gracefully from door to door over the top of the instrument binnacles, down under the centre console and back up around the passenger side fascia and foot well. Highly polished, hand crafted metal elements adorn the dashboard, centre console and doors. Trademark Bentley knurling on the drive mode selector, gear knob, iconic bulls-eye vents and organ pulls adds sophistication and tactile refinement. Sumptuous front seats individually hand crafted in Crewe and featuring 22-way adjustment including adjustable cushion and backrest bolsters, provide superb support and comfort for all conditions. This cosseted feeling is further enhanced with a six-program massage system, seat heating and ventilation. Activate the hands-free tailgate and not only is a large, practical storage space revealed, but also another of the Bentayga's unique features – the optional folding event seat. Ideal for those wishing to stop for a moment and enjoy a spectacular outdoor environment or pursuit, the innovative leather-trimmed folding seat matches exactly the style of the cabin seats and integrates seamlessly into the rear of the car with characteristic attention to detail.
Slated for sales sometime in 2016, this ultimate SUV is priced at $229,100 slightly ahead of the Mercedes-Benz G series.
The most expensive, powerful, luxurious and exclusive SUV in the world.
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Construction and regeneration company Morgan Sindall Group plc has announced its preliminary results today (18 February) for the year ended 31 December 2013.
Against a backdrop of continued challenging trading conditions, Morgan Sindall Group delivered strong operating cash flow with year end net cash of £70m (2012: £50m). Operating profit before amortisation and exceptional operating items was £33.6m (2012: £48.1m) on revenues of £2,095m (2012: £2,047m). Adjusted earnings per share were 60.9p (2012: 92.0p). The dividend for the year is 27.0p per share (2012: 27.0p). The Group's committed order book stands at £2.4bn (2012: £2.2bn) and the regeneration & development pipeline grew to £3.0bn (2012: £2.5bn).
Commenting on today's results, Chief Executive, John Morgan said:
"2013 has seen challenging conditions predominate across most of our markets, with competitive pressures impacting on margins and profitability. Notwithstanding this, the positive operating cash flow generated by the business has allowed us to make further investment in strategic assets, key skills and resources, which positions the Group well to benefit from future growth opportunities.
Looking ahead to 2014, although there are signs of improving conditions in some of our markets, it is anticipated that upward pressure on supply chain costs and skills availability will provide additional management challenges. Against this backdrop, we remain confident that our robust order book and on-going disciplined approach to contract selectivity will support the delivery of growth in this year and beyond."


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I really like Shishito Peppers. They are Japanese mild peppers that look like they would be spicy, but they are mild. Every once in a while you get one that is blazing hot, but you can't tell until you bite into it;o) You eat the skin and seeds, but not the stems. I love to have this at Izakaya (Japanese Style Pubs) or Yakitori/Robatayaki (Grilled Skewered Places) Restaurants. They usually grill them and they get nicely charred & blistered and have an essence of the charcoal. I figured out a super easy way to make these at home. They don't have the nice smokiness like the restaurant, but they turn out pretty tasty!
I make these in the Toaster Oven. These are coated in a little bit of Rice Bran Oil w/some salt sprinkled on top. I then put them in the toaster at 425 degrees for about 5 mins, turning them midway. I then put it on the toaster setting and bake them until they have a nice char to it, maybe another 5 mins or less. It depends on how much you want them cooked. I don't like them to have a raw crunch...
Shishito Peppers
I sprinkled some Katusobushi (Bonito Flakes), Soy Sauce & Ponzu on it. I served this with a Teriyaki Chicken Bowl that I made with leftover chicken from a previous night, salad with Japanese Onion Dressing (also made a previous night) & Kimchi. It was a very easy meal to make;o)


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The dance duo play a special gig in Dublin
Orbital have confirmed the venue for their show in IRELAND next month.
The duo will play at the Dublin Point on October 28. The show is in addition to already confirmed performances at the Electron Festival in Greece on September 8-9.
The band are also looking to add dates in South Africa (September 1-2), and Japan (November 24-26).
Orbital are currently working on their as-yet-untitled sixth studio album with Mickey Mann, who co-produced their second album and last year's 'The Middle Of Nowhere'. The album is not expected before the start of 2001.


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PTV DPS was founded in 1982 by Paul Palmer. Paul's extensive international experience at both an operational
and functional level within the FMCG transport sector allowed him to initially set up the business offering consultancy,
particularly at contracts logistic level.
Consultancy is still an important part of the business today, however as the business grew it highlighted the need for IT tools both for strategic and tactical purposes. At that time there were no suitable solutions available in the market, so DPS invested in the development of both route planning and scheduling systems. The software was then made available to the wider logistics market and branded as LogiX, now known as Route Optimiser.
In 1991 PTV DPS began expansion outside of the UK and now supplies its products and services throughout the world, with offices in
Europe and partners across the globe. DPS is proud of its Logistics heritage and is still a prominent supplier of choice within the sector,
remaining current and at the forefront of innovation as the sector evolves.
In 2007 DPS were the first worldwide to develop a browser-based Software as a Service (SaaS) vehicle routing and scheduling solution to appeal to a wider audience and the SME market.
The team is well established with several long serving members of staff from Logistics and IT backgrounds, many with hands on experience
of running complex transport operations who are highly qualified and committed to continuing professional development, with several members of
staff being members of Chartered Institute of Logistics & Transport and enthused with its founders entrepreneurial 'can do' attitude.
The core values of the business have always been of integrity and innovation. PTV DPS has an unrivalled commitment to quality and service. A collaborative and flexible approach has enabled DPS to respond to the precise needs of both new and long standing customers, providing the opportunity to develop versatility with additional functionality within the software. This has enabled PTV DPS to expand into different markets and enjoy a high level of repeat business, further building its reputation.
The multi-award winning Route Optimiser route planning and optimisation software is easy to use and friendly. The software helps its customers
to reduce transport costs through logistics planning and route optimization, whilst improving fleet utilization and driver productivity.
The software is now used not only within the transport and logistics sectors but also many vertical markets in collaboration with partners systems, and is available on all technology platforms.


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Flawless, radiant skin is the desire of every woman and shows off her health! The world today is contaminated with pollution and stress; top it up with a careless skin care regimen and you will see your once active skill turning dull and lifeless. Hence, skin rejuvenation is quintessential. A rejuvenated, revitalized skin gives you that extra dose of confidence, plus you will find yourself swarming with adorers. And, we bring to you some of the most amazing home remedies for skin rejuvenation that you can easily follow for a soft, clear and youthful skin!
Home Remedies for Skin Rejuvenation
1. Lemon Juice And Honey
Lemon juice helps rejuvenate skin by reducing age spots and other signs of aging. The vitamin C in lemon is a strong antioxidant that helps protect the skin from free radical damage. In addition, its bleaching properties help improve your overall skin complexion. Pour a few drops of honey on 1/2 of a lemon. Rub it gently on your face using upward strokes. Leave it on for 10 minutes and then rinse your face. Do this once or twice a week.
Alternatively, simply squeeze the juice from 1 lemon and apply it on the skin. Leave it on for about 15 minutes, then rinse it off with cool water. Use this remedy once daily. Another option is to mix together 1 teaspoon each of lemon juice and egg white, along with ½ teaspoon of milk cream. Apply this paste on your face. Wait 15 minutes, then rinse it off with cold water. Repeat once or twice a week.
2. Apricot
Apricots are rich in Vitamin A, C, and B as well as lycopene that make it an ideal skin rejuvenating agent. Soak 4 to 5 apricots in water and allow them to swell up. Make a pulp out of it and prepare a smooth mixture by blending the apricot pulp with 2 teaspoons of honey, 1/2 teaspoons of almond oil, and ½ teaspoons of lemon Juice. Apply in generous amounts on the face and allow to dry, say for about 20 minutes. Rinse off with cold water to reveal a shining skin.
3. Papaya, Honey And Lemon Juice
Papaya is rich in vitamins A, C and E, and has antioxidant properties that help in rejuvenating skin. It helps keep the skin soft, smooth and moisturized. In addition, the alpha hydroxy acids in papaya help exfoliate the skin. It also is beneficial in treating acne, blemishes, dark spots and other similar problems. Mix 2 tablespoons of mashed ripe papaya, 1 tablespoon of honey and ½ teaspoon of fresh lemon juice. Apply this on your face. After 15 minutes, wash it off with warm water. Finally, splash some cold water on your face. Use this face mask once a week to enjoy beautiful skin.
4. Banana, Milk Cream And Honey
Banana is excellent for rejuvenating your skin, especially dry skin, because of its moisturizing properties. It also helps fight wrinkles, fine lines and other signs of aging. Mash 1 small ripe banana. Add 2 tablespoons of milk cream, 1 tablespoon each of organic honey and oat flour, and a little water to make a paste. Apply this paste on your face, let it sit for 30 minutes, then rinse it off with lukewarm water.
Alternatively, mash a medium-size banana and mix it with 2 teaspoons of organic honey and a few drops of olive oil. Apply it on your face and rinse it off after 20 minutes.
Follow either of these remedies once or twice a week to enjoy radiant skin.
5. Cucumber And Yogurt
The high water content in cucumber is nourishing and hydrating for your skin. Its astringent and soothing properties benefit acne-prone and sunburned skin and help rejuvenate your skin. In addition, the antioxidant property in cucumber helps maintain clear, glowing and younger-looking skin. Mix together 2 teaspoons of grated cucumber and ½ cup of yogurt to make a face mask. Apply this on your face and neck. After 20 minutes, rinse it off with warm water. Use this face pack twice a week.
Alternatively, mix equal amounts of grated cucumber and watermelon pulp. Add a few drops of lemon juice to it, then apply it on your face. Allow it to dry, then wash it off with lukewarm water. Use this face pack a few times a week.
6. Yogurt, Turmeric Powder And Gram Flour
Yogurt is extremely beneficial for your skin. The lactic acid present in yogurt works like a natural cleanser, exfoliating agent and moisturizer. It can help replenish the lost glow and radiance of your skin. Prepare a mixture with 2 teaspoons of plain yogurt and ½ teaspoon each of turmeric powder and gram flour. Apply this paste on your face and neck. Allow it to dry, then rinse it off with cool water. Use this face pack once or twice a week.
Another option is to simply mix 2 teaspoons of organic honey in 2 tablespoons of plain yogurt. Apply it to your face, wait 15 minutes, then rinse it off with cool water. Use this remedy a few times a week.
7. Orange Peel And Gram Flour
Being rich in vitamin C, citric acid and other antioxidants, orange peels help reduce blemishes and maintain healthy and younger-looking skin. The peels help cleanse, exfoliate and tighten the skin. Dry the peels from a few oranges under the sun for a few days. Grind the peels into a fine powder. Mix 1 teaspoon of orange peel powder, 2 teaspoons of gram flour and enough water to make a paste. Apply the paste on your hands, neck and face. Wait 15 minutes, then rinse it off with warm water. Use this face mask once or twice a week.


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Can't remember seeing this posted before:
http://www.nba.com/warriors/interactive ... une07.html
Mildly interesting I'd say. I'm a little too much of a grumpy old fart for the playoff changes but I am all for more games against the closer teams to really build rivalries. Didn't it use to be 5 games against divisional teams before the last expansion or two?
Fitz blog
Discuss anything related to Golden State Warriors basketball here
Moderators: Mr. Crackerz, JREED, Guybrush, 32


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The National Flute Association has always functioned through inclusiveness and member participation. From the very beginning, NFA committees have played a critical role in guiding the organization's mission and policies. Over the years, members have founded a great depth and breadth of committees, following their own passions and seeking to move the NFA and greater flute community forward.
NFA committees perform many functions: highlight less prominent areas of flute musicianship, such as low and Baroque flutes, promote diversity and reach out to underserved communities, provide pedagogical guidance, and more. The hard work and dedication of these groups enabled the NFA to establish many core parts of its mission and traditions, from commissioning new music and creating scholarships and competitions to fostering the careers of young flutists.
In these pages, learn more about the work of NFA committees and browse the resources these groups have put together for the benefit of the flute community.
To learn more about a committee, or to explore how you might get involved, please contact the committee chair. Contact information can be found on the appointee roster.