Symmetric Submodular Function Minimization Under Hereditary Family Constraints

We present an efficient algorithm to find non-empty minimizers of a symmetric submodular function over any family of sets closed under inclusion. This for example includes families defined by a cardinality constraint, a knapsack constraint, a matroid independence constraint, or any combination of such constraints. Our algorithm make $O(n^3)$ oracle calls to the submodular function where $n$ is the cardinality of the ground set. In contrast, the problem of minimizing a general submodular function under a cardinality constraint is known to be inapproximable within $o(\sqrt{n/\log n})$ (Svitkina and Fleischer [2008]). The algorithm is similar to an algorithm of Nagamochi and Ibaraki [1998] to find all nontrivial inclusionwise minimal minimizers of a symmetric submodular function over a set of cardinality $n$ using $O(n^3)$ oracle calls. Their procedure in turn is based on Queyranne's algorithm [1998] to minimize a symmetric submodularComment: 13 pages, Submitted to SODA 201

The gaseous extent of galaxies and the origin of Lyman alpha absorption systems. IV: Lyman alpha absorbers arising in a galaxy group

We present new GHRS observations of Lyman alpha absorption lines associated with a group of galaxies towards the QSO 1545+2101. We have identified eight distinct Lyman alpha absorption features in the spectrum of QSO 1545+2101 at a mean redshift of z=0.2648 with a velocity dispersion of 163 km/s. A group of galaxies is detected in the vicinity of this QSO at a mean redshift of z=0.2645 and velocity dispersion 239 km/s. The identification of discrete absorption systems indicates that they arise in clouds of neutral hydrogen rather than in a diffuse intragroup medium. Our analysis suggests that the Lyman alpha absorption lines are associated with individual galaxies in the group, although a one-to-one relationship between absorbers and galaxies is difficult to establish in such a dense environment.Comment: 16 pages, 3 figures. Accepted for publication in Ap

Long-distance autumn migration across the Sahara by painted lady butterflies: exploiting resource pulses in the tropical savannah

The painted lady, Vanessa cardui, is a migratory butterfly that performs an annual multi-generational migration between Europe and North Africa. Its seasonal appearance south of the Sahara in autumn is well known and has led to the suggestion that it results from extremely long migratory flights by European butterflies to seasonally exploit the Sahel and the tropical savannah. However, this possibility has remained unproven. Here, we analyse the isotopic composition of butterflies from seven European and seven African countries to provide new support for this hypothesis. Each individual was assigned a geographical natal origin, based on its wing stable hydrogen isotope (¿2Hw) value and a predicted ¿2Hw basemap for Europe and northern Africa. Natal assignments of autumn migrants collected south of the Sahara confirmed long-distance movements (of 4000 km or more) starting in Europe. Samples from Maghreb revealed a mixed origin of migrants, with most individuals with a European origin, but others having originated in the Sahel. Therefore, autumn movements are not only directed to northwestern Africa, but also include southward and northward flights across the Sahara. Through this remarkable behaviour, the productive but highly seasonal region south of the Sahara is incorporated into the migratory circuit of V. cardui.K.A.H. was funded by an operating grant and D.X.S. by an NSERC visiting fellowship from Environment Canada. Funding to R.V. and G.T. was provided by the Committee for Research and Exploration of National Geographic (grant no. 9528-14) and by the Spanish Ministerio de Economía y Competitividad (CGL2013-48277-P). G.T. is supported by the Marie Curie Actions FP7-PEOPLE-2013-IOF (project 622716) and the grant BP-A00275 (AGAUR-Generalitat de Catalunya). Expeditions in Morocco were funded by Antoni Jonch Cooperació.Peer Reviewe

Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences

Background: Lineage specific differentiation of human embryonic stem cells (hESCs) is largely mediated by specific growth factors and extracellular matrix molecules. Growth factors initiate a cascade of signals which control gene transcription and cell fate specification. There is a lot of interest in inducing hESCs to an endoderm fate which serves as a pathway towards more functional cell types like the pancreatic cells. Research over the past decade has established several robust pathways for deriving endoderm from hESCs, with the capability of further maturation. However, in our experience, the functional maturity of these endoderm derivatives, specifically to pancreatic lineage, largely depends on specific pathway of endoderm induction. Hence it will be of interest to understand the underlying mechanism mediating such induction and how it is translated to further maturation. In this work we analyze the regulatory interactions mediating different pathways of endoderm induction by identifying co-regulated transcription factors.Results: hESCs were induced towards endoderm using activin A and 4 different growth factors (FGF2 (F), BMP4 (B), PI3KI (P), and WNT3A (W)) and their combinations thereof, resulting in 15 total experimental conditions. At the end of differentiation each condition was analyzed by qRT-PCR for 12 relevant endoderm related transcription factors (TFs). As a first approach, we used hierarchical clustering to identify which growth factor combinations favor up-regulation of different genes. In the next step we identified sets of co-regulated transcription factors using a biclustering algorithm. The high variability of experimental data was addressed by integrating the biclustering formulation with bootstrap re-sampling to identify robust networks of co-regulated transcription factors. Our results show that the transition from early to late endoderm is favored by FGF2 as well as WNT3A treatments under high activin. However, induction of late endoderm markers is relatively favored by WNT3A under high activin.Conclusions: Use of FGF2, WNT3A or PI3K inhibition with high activin A may serve well in definitive endoderm induction followed by WNT3A specific signaling to direct the definitive endoderm into late endodermal lineages. Other combinations, though still feasible for endoderm induction, appear less promising for pancreatic endoderm specification in our experiments. © 2012 Mathew et al.; licensee BioMed Central Ltd

Large eddy simulation of partial cavitation around a 2D plane-convex hydrofoil

Investigations of attached partial cavitation are important because to prevent damages in hydrulic machinery and to reduce the costs. As expected computational fluid dynamics (CFD) methods have been developed for more than 40 years to understand this phenomenon and to improve the machinery designs, as pumps and hydraulic turbines. However, cavitation appears at high Reynolds numbers, so that, the traditional turbulence models Reynolds-averaged Navier-Stokes (RANS)Postprint (published version

Small tails tell tall tales - intra-individual variation in the stable isotope values of fish fin

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