Placing regenerators in optical networks to satisfy multiple sets of requests.

The placement of regenerators in optical networks has become an active area of research during the last years. Given a set of lightpaths in a network G and a positive integer d, regenerators must be placed in such a way that in any lightpath there are no more than d hops without meeting a regenerator. While most of the research has focused on heuristics and simulations, the first theoretical study of the problem has been recently provided in [10], where the considered cost function is the number of locations in the network hosting regenerators. Nevertheless, in many situations a more accurate estimation of the real cost of the network is given by the total number of regenerators placed at the nodes, and this is the cost function we consider. Furthermore, in our model we assume that we are given a finite set of p possible traffic patterns (each given by a set of lightpaths), and our objective is to place the minimum number of regenerators at the nodes so that each of the traffic patterns is satisfied. While this problem can be easily solved when d = 1 or p = 1, we prove that for any fixed d,p ≥ 2 it does not admit a PTASUnknown control sequence '\textsc', even if G has maximum degree at most 3 and the lightpaths have length O(d)(d). We complement this hardness result with a constant-factor approximation algorithm with ratio ln (d ·p). We then study the case where G is a path, proving that the problem is NP-hard for any d,p ≥ 2, even if there are two edges of the path such that any lightpath uses at least one of them. Interestingly, we show that the problem is polynomial-time solvable in paths when all the lightpaths share the first edge of the path, as well as when the number of lightpaths sharing an edge is bounded. Finally, we generalize our model in two natural directions, which allows us to capture the model of [10] as a particular case, and we settle some questions that were left open in [10]

Computational Prediction of MicroRNAs Encoded in Viral and Other Genomes

We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it seems that these small regulators have a more important role than has been previously thought. Most microRNAs have been detected by cloning and Northern blotting, but experimental methods are biased towards abundant microRNAs as well as being time-consuming. Computational detection methods must therefore be refined to serve as a faster, better, and more affordable method for microRNA detection. We also present data from a small study investigating the problems of computational miRNA prediction. Our findings suggest that the prediction of microRNA precursor candidates is fairly easy, while excluding false positives as well as exact prediction of the mature microRNA is hard. Finally, we discuss possible improvements to computational microRNA detection

Contemporary divergence in early life history in grayling (Thymallus thymallus)

<p>Abstract</p> <p>Background</p> <p>Following colonization of new habitats and subsequent selection, adaptation to environmental conditions might be expected to be rapid. In a mountain lake in Norway, Lesjaskogsvatnet, more than 20 distinct spawning demes of grayling have been established since the lake was colonized, some 20-25 generations ago. The demes spawn in tributaries consistently exhibiting either colder or warmer temperature conditions during spawning in spring and subsequent early development during early summer. In order to explore the degree of temperature-related divergence in early development, a multi-temperature common-garden experiment was performed on embryos from four different demes experiencing different spring temperatures.</p> <p>Results</p> <p>Early developmental characters were measured to test if individuals from the four demes respond differently to the treatment temperatures. There was clear evidence of among-deme differences (genotype - environment interactions) in larval growth and yolk-to-body-size conversion efficiency. Under the cold treatment regime, larval growth rates were highest for individuals belonging to cold streams. Individuals from warm streams had the highest yolk-consumption rate under cold conditions. As a consequence, yolk-to-body-mass conversion efficiency was highest for cold-deme individuals under cold conditions. As we observed response parallelism between individuals from demes belonging to similar thermal groups for these traits, some of the differentiation seems likely to result from local adaptation</p> <p>Conclusion</p> <p>The observed differences in length at age during early larval development most likely have a genetic component, even though both directional and random processes are likely to have influenced evolutionary change in the demes under study.</p

Supply Chain Control Principles in Local Food Production: A Norwegian Case Study

Based on an analysis of the supply chain of four producers of local specialty foods, we explore how planning and control principles can be applied to align supply chain capabilities and market requirements. It has been shown that local food struggles with market access, and that the supply chain is one of the obstacles preventing local food producers from gaining a solid market position. We identify a number of features of the local food chain, analyse the obstacles and develop generic designs and control principles for local food producers

Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays

Not until recently have custom made high-density oligonucleotide microarrays been available at an affordable price. The aim of this thesis was to design microarrays and analysis algorithms for DNA repair and DNA damage detection, and to apply the methods in real experiments. Thomassen et al. have used their custom designed whole genome-tiling microarrays for detection of transcriptional changes in Escherichia coli after exposure to DNA damageing reagents. The transcriptional changes in E. coli treated with UV light or the methylating reagent MNNG were shown to be larger and to include far more genes than previously reported. To optimize the data analysis for the custom made arrays, Thomassen and coworkers designed their own normalization and analysis algorithms, and showed these more suitable than established methods that are currently applied on custom tiling arrays. Among other findings several novel stress-induced transcripts were detected, of which one is predicted to be a UV-induced short transmembrane protein. Additionally, no upregulation of the previously described UV-inducible aidB is shown. In the MNNG study several genes are shown as downregulated in response to DNA damage although having upstream regulatory sequences similar to the established LexA box A and B. This indicates that the LexA regulon also might control gene repression and that the box A and B sequence can not alone answer for the LexA controlled gene regulation. Thomassen et al. have also custom designed a microarray for oncogenic fusion gene detection. Cancer specific fusion genes are often used to subgroup cancers and to define the optimal treatment, but currently the laboratory detection procedure is both laborious and tedious. In a blinded study on six cancer cell lines proof of principle was shown by detection of six out of six positive controls. The design and analysis methods for this microarray are now being refined to make a diagnostic fusion gene detection tool

Contact Representations of Graphs in 3D

We study contact representations of graphs in which vertices are represented by axis-aligned polyhedra in 3D and edges are realized by non-zero area common boundaries between corresponding polyhedra. We show that for every 3-connected planar graph, there exists a simultaneous representation of the graph and its dual with 3D boxes. We give a linear-time algorithm for constructing such a representation. This result extends the existing primal-dual contact representations of planar graphs in 2D using circles and triangles. While contact graphs in 2D directly correspond to planar graphs, we next study representations of non-planar graphs in 3D. In particular we consider representations of optimal 1-planar graphs. A graph is 1-planar if there exists a drawing in the plane where each edge is crossed at most once, and an optimal n-vertex 1-planar graph has the maximum (4n - 8) number of edges. We describe a linear-time algorithm for representing optimal 1-planar graphs without separating 4-cycles with 3D boxes. However, not every optimal 1-planar graph admits a representation with boxes. Hence, we consider contact representations with the next simplest axis-aligned 3D object, L-shaped polyhedra. We provide a quadratic-time algorithm for representing optimal 1-planar graph with L-shaped polyhedra

Low‐Temperature Heat Capacities and Thermodynamic Functions of Some Palladium and Platinum Group Chalcogenides. II. Dichalcogenides; PtS2, PtTe2, and PdTe2

Heat capacities of platinum disulfide, platinum ditelluride, and palladium ditelluride were measured in the range 5° to 350°K. They show the normal sigmoidal temperature dependence with no evidence of transitions or other anomalies. The derived heat capacity equations were integrated. Values of Cp, S°—S0°, H°—H0°, and —(F°—H0°)/T are tabulated for selected temperatures. At 298.15°K the entropies are 17.85 cal gfw—1 °K—1 for PtS2, 28.92 cal gfw—1 °K—1 for PtTe2 and 30.25 cal gfw—1 °K—1 for PdTe2. Thermodynamic values have been estimated for other dichalcogenides and related chalcogenides of the platinum group metals.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69847/2/JCPSA6-35-5-1670-1.pd

Size effect on magnetism of Fe thin films in Fe/Ir superlattices

In ferromagnetic thin films, the Curie temperature variation with the thickness is always considered as continuous when the thickness is varied from $n$ to $n+1$ atomic planes. We show that it is not the case for Fe in Fe/Ir superlattices. For an integer number of atomic planes, a unique magnetic transition is observed by susceptibility measurements, whereas two magnetic transitions are observed for fractional numbers of planes. This behavior is attributed to successive transitions of areas with $n$ and $n+1$ atomic planes, for which the $T_c$'s are not the same. Indeed, the magnetic correlation length is presumably shorter than the average size of the terraces. Monte carlo simulations are performed to support this explanation.Comment: LaTeX file with Revtex, 5 pages, 5 eps figures, to appear in Phys. Rev. Let

Recognizing and Drawing IC-planar Graphs

IC-planar graphs are those graphs that admit a drawing where no two crossed edges share an end-vertex and each edge is crossed at most once. They are a proper subfamily of the 1-planar graphs. Given an embedded IC-planar graph $G$ with $n$ vertices, we present an $O(n)$-time algorithm that computes a straight-line drawing of $G$ in quadratic area, and an $O(n^3)$-time algorithm that computes a straight-line drawing of $G$ with right-angle crossings in exponential area. Both these area requirements are worst-case optimal. We also show that it is NP-complete to test IC-planarity both in the general case and in the case in which a rotation system is fixed for the input graph. Furthermore, we describe a polynomial-time algorithm to test whether a set of matching edges can be added to a triangulated planar graph such that the resulting graph is IC-planar