@article{3395,
  abstract     = {Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data.},
  author       = {Palero, Ferran and Abello, Pere and Macpherson, Enrique and Beaumont, Mark and Pascual, Marta},
  journal      = {Biological Journal of the Linnean Society},
  number       = {2},
  pages        = {407 -- 418},
  publisher    = {Wiley-Blackwell},
  title        = {{Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas}},
  doi          = {10.1111/j.1095-8312.2011.01728.x},
  volume       = {104},
  year         = {2011},
}

@article{3396,
  abstract     = {Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain undergo a characteristic tangential migration from rhombomere (r) 4, where they are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium such that they move apically between NCs towards the midline of the neuroepithelium instead of tangentially along the basal side of the neuroepithelium towards r6/7. However, direct experimental evaluation of this hypothesis is still lacking. Here, we have used a combination of biophysical cell adhesion measurements and high-resolution time-lapse microscopy to determine the role of NC cohesion in FBMN migration. We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity results in FBMNs positioned at the basal side of the neuroepithelium moving apically towards the neural tube midline instead of tangentially towards r6/7. In embryos with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results in fusion of the bilateral FBMN clusters over the apical midline of the neural tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin 2 (Cntn2) expression in these cells has little effect on apical FBMN movement, but reduces the fusion of the bilateral FBMN clusters in embryos with strongly diminished NC cohesion. These data provide direct experimental evidence that NC cohesion functions in tangential FBMN migration by restricting their apical movement.},
  author       = {Stockinger, Petra and Heisenberg, Carl-Philipp J and Maître, Jean-Léon},
  journal      = {Development},
  number       = {21},
  pages        = {4673 -- 4683},
  publisher    = {Company of Biologists},
  title        = {{Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube}},
  doi          = {10.1242/dev.071233},
  volume       = {138},
  year         = {2011},
}

@article{3397,
  abstract     = {Recent advances in microscopy techniques and biophysical measurements have provided novel insight into the molecular, cellular and biophysical basis of cell adhesion. However, comparably little is known about a core element of cell–cell adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss approaches to understand the nature and regulation of adhesion energy, and propose strategies to determine adhesion energy between cells in vitro and in vivo.},
  author       = {Maître, Jean-Léon and Heisenberg, Carl-Philipp J},
  journal      = {Current Opinion in Cell Biology},
  number       = {5},
  pages        = {508 -- 514},
  publisher    = {Elsevier},
  title        = {{The role of adhesion energy in controlling cell-cell contacts}},
  doi          = {10.1016/j.ceb.2011.07.004},
  volume       = {23},
  year         = {2011},
}

@article{3399,
  abstract     = {Context-dependent adjustment of mating tactics can drastically increase the mating success of behaviourally flexible animals. We used the ant Cardiocondyla obscurior as a model system to study adaptive adjustment of male mating tactics. This species shows a male diphenism of wingless fighter males and peaceful winged males. Whereas the wingless males stay and exclusively mate in the maternal colony, the mating behaviour of winged males is plastic. They copulate with female sexuals in their natal nests early in life but later disperse in search for sexuals outside. In this study, we observed the nest-leaving behaviour of winged males under different conditions and found that they adaptively adjust the timing of their dispersal to the availability of mating partners, as well as the presence, and even the type of competitors in their natal nests. In colonies with virgin female queens winged males stayed longest when they were the only male in the nest. They left earlier when mating partners were not available or when other males were present. In the presence of wingless, locally mating fighter males, winged males dispersed earlier than in the presence of docile, winged competitors. This suggests that C. obscurior males are capable of estimating their local breeding chances and adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive way, thus showing hitherto unknown behavioural plasticity in social insect males.},
  author       = {Cremer, Sylvia and Schrempf, Alexandra and Heinze, Jürgen},
  journal      = {PLoS One},
  number       = {3},
  publisher    = {Public Library of Science},
  title        = {{Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior}},
  doi          = {10.1371/journal.pone.0017323},
  volume       = {6},
  year         = {2011},
}

@article{3405,
  abstract     = {Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K+ channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.},
  author       = {Janovjak, Harald L and Sandoz, Guillaume and Isacoff, Ehud},
  journal      = {Nature Communications},
  number       = {232},
  pages        = {1 -- 6},
  publisher    = {Nature Publishing Group},
  title        = {{Modern ionotropic glutamate receptor with a K+ selectivity signature sequence}},
  doi          = {10.1038/ncomms1231},
  volume       = {2},
  year         = {2011},
}

@article{3429,
  abstract     = {Transcription factors are central to sustaining pluripotency, yet little is known about transcription factor dynamics in defining pluripotency in the early mammalian embryo. Here, we establish a fluorescence decay after photoactivation (FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription factor controlling pre-implantation development in the mouse embryo. FDAP measurements reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics, before there are any morphologically distinguishable differences or outward signs of lineage patterning. The differences revealed by FDAP are due to differences in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage tracing of the cells in the two distinct sub-populations demonstrates that the Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics are more likely to give rise to the pluripotent cell lineage that contributes to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences in total transcription factor expression levels, as a predictive measure of developmental cell lineage patterning in the early mouse embryo.},
  author       = {Plachta, Nicolas and Bollenbach, Mark Tobias and Pease, Shirley and Fraser, Scott and Pantazis, Periklis},
  journal      = {Nature Cell Biology},
  number       = {2},
  pages        = {117 -- 123},
  publisher    = {Nature Publishing Group},
  title        = {{Oct4 kinetics predict cell lineage patterning in the early mammalian embryo}},
  doi          = {10.1038/ncb2154},
  volume       = {13},
  year         = {2011},
}

@article{3505,
  abstract     = {Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells.},
  author       = {Sixt, Michael K and Lämmermann, Tim},
  journal      = {Cell Migration},
  pages        = {149 -- 165},
  publisher    = {Springer},
  title        = {{In vitro analysis of chemotactic leukocyte migration in 3D environments}},
  doi          = {10.1007/978-1-61779-207-6_11},
  volume       = {769},
  year         = {2011},
}

@article{3771,
  abstract     = {The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.},
  author       = {Pavan, Ana and Martins, Felipe and Santos, Fabrício and Ditchfield, Albert and Fernandes Redondo, Rodrigo A},
  journal      = {Biological Journal of the Linnean Society},
  number       = {3},
  pages        = {527 -- 539},
  publisher    = {Wiley-Blackwell},
  title        = {{Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.}},
  doi          = {10.1111/j.1095-8312.2010.01601.x},
  volume       = {102},
  year         = {2011},
}

@article{3778,
  author       = {Barton, Nicholas H},
  journal      = {Heredity},
  number       = {2},
  pages        = {205 -- 206},
  publisher    = {Nature Publishing Group},
  title        = {{Estimating linkage disequilibria}},
  doi          = {10.1038/hdy.2010.67},
  volume       = {106},
  year         = {2011},
}

@article{3781,
  abstract     = {We bound the difference in length of two curves in terms of their total curvatures and the Fréchet distance. The bound is independent of the dimension of the ambient Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and it generalizes a result by Fáry and Chakerian.},
  author       = {Fasy, Brittany Terese},
  journal      = {Acta Sci. Math. (Szeged)},
  number       = {1-2},
  pages        = {359 -- 367},
  publisher    = {Szegedi Tudományegyetem},
  title        = {{The difference in length of curves in R^n}},
  volume       = {77},
  year         = {2011},
}

@article{3784,
  abstract     = {Advanced stages of Scyllarus phyllosoma larvae were collected by demersal trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005. Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology is described and illustrated. This constitutes the second complete description of a Scyllaridae phyllosoma with its specific identity being validated by molecular techniques (the first was S. pygmaeus). These results also solved a long lasting taxonomic anomaly of several species assigned to the ancient genus Phyllosoma Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of S. arctus shows closer affinities with the American scyllarid Scyllarus depressus or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its sympatric species S. pygmaeus.},
  author       = {Palero, Ferran and Guerao, Guillermo and Clark, Paul and Abello, Pere},
  journal      = {Journal of the Marine Biological Association of the United Kingdom},
  number       = {2},
  pages        = {485 -- 492},
  publisher    = {Cambridge University Press},
  title        = {{Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological description}},
  doi          = {10.1017/S0025315410000287},
  volume       = {91},
  year         = {2011},
}

@inbook{3791,
  abstract     = {During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes.},
  author       = {Krens, Gabriel and Heisenberg, Carl-Philipp J},
  booktitle    = {Forces and Tension in Development},
  editor       = {Labouesse, Michel},
  pages        = {189 -- 213},
  publisher    = {Elsevier},
  title        = {{Cell sorting in development}},
  doi          = {10.1016/B978-0-12-385065-2.00006-2},
  volume       = {95},
  year         = {2011},
}

@inbook{3796,
  abstract     = {We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3.},
  author       = {Edelsbrunner, Herbert and Kerber, Michael},
  booktitle    = {Rainbow of Computer Science},
  editor       = {Calude, Cristian and Rozenberg, Grzegorz and Salomaa, Arto},
  pages        = {20 -- 35},
  publisher    = {Springer},
  title        = {{Covering and packing with spheres by diagonal distortion in R^n}},
  doi          = {10.1007/978-3-642-19391-0_2},
  volume       = {6570},
  year         = {2011},
}

@article{3965,
  abstract     = {The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.},
  author       = {Wang, Bei and Edelsbrunner, Herbert and Morozov, Dmitriy},
  journal      = {Journal of Experimental Algorithmics},
  number       = {2.2},
  pages        = {1 -- 13},
  publisher    = {ACM},
  title        = {{Computing elevation maxima by searching the Gauss sphere}},
  doi          = {10.1145/1963190.1970375},
  volume       = {16},
  year         = {2011},
}

@article{3303,
  abstract     = {Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. },
  author       = {Weissman, Daniel and Feldman, Marcus and Fisher, Daniel},
  journal      = {Genetics},
  number       = {4},
  pages        = {1389 -- 1410},
  publisher    = {Genetics Society of America},
  title        = {{The rate of fitness-valley crossing in sexual populations}},
  doi          = {10.1534/genetics.110.123240},
  volume       = {186},
  year         = {2010},
}

@inproceedings{10908,
  abstract     = {We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts.},
  author       = {Blanc, Régis and Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura},
  booktitle    = {Logic for Programming, Artificial Intelligence, and Reasoning},
  editor       = {Clarke, Edmund M and Voronkov, Andrei},
  isbn         = {9783642175107},
  issn         = {1611-3349},
  location     = {Dakar, Senegal},
  pages        = {103--118},
  publisher    = {Springer Nature},
  title        = {{ABC: Algebraic Bound Computation for loops}},
  doi          = {10.1007/978-3-642-17511-4_7},
  volume       = {6355},
  year         = {2010},
}

@inproceedings{10909,
  abstract     = {We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.},
  author       = {Chen, Chao and Freedman, Daniel},
  booktitle    = {Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms},
  location     = {Austin, TX, United States},
  pages        = {1594--1604},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Hardness results for homology localization}},
  doi          = {10.1137/1.9781611973075.129},
  year         = {2010},
}

@article{2409,
  abstract     = {Background: The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.

Results: We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.

Conclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict.},
  author       = {Kupczok, Anne and Schmidt, Heiko and Von Haeseler, Arndt},
  journal      = {Algorithms for Molecular Biology},
  number       = {1},
  publisher    = {BioMed Central},
  title        = {{Accuracy of phylogeny reconstruction methods combining overlapping gene data sets }},
  doi          = {10.1186/1748-7188-5-37},
  volume       = {5},
  year         = {2010},
}

@article{474,
  abstract     = {Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.},
  author       = {Barton, Nicholas H and Kelleher, Jerome and Etheridge, Alison},
  journal      = {Evolution},
  number       = {9},
  pages        = {2701 -- 2715},
  publisher    = {Wiley-Blackwell},
  title        = {{A new model for extinction and recolonization in two dimensions: Quantifying phylogeography}},
  doi          = {10.1111/j.1558-5646.2010.01019.x},
  volume       = {64},
  year         = {2010},
}

@inproceedings{488,
  abstract     = {Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of "regular" transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. },
  author       = {Alur, Rajeev and Cerny, Pavol},
  location     = {Chennai, India},
  pages        = {1 -- 12},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Expressiveness of streaming string transducers}},
  doi          = {10.4230/LIPIcs.FSTTCS.2010.1},
  volume       = {8},
  year         = {2010},
}