Near-optimal Assembly for Shotgun Sequencing with Noisy Reads

Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even when there is noise in the reads, one can successfully reconstruct with information requirements close to the noiseless fundamental limit. A new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. It is shown through analysis to perform well on the model, and through simulations to perform well on real genomes

An intercomparison of intraseasonal variability in general circulation models and observations

Low frequency oscillations appearing in three GCM seasonal cycle integrations are compared with the analyses of the European Center for Medium Range Weather Forecasting (ECMWF). All three models have the same resolution: 4 deg latitude by 5 deg longitude, with 9 levels. The dominant phase speeds and the differential vertical structure of the heating profiles in the GCMs are in general agreement with current theory involving the positive feedback between latent heating and moist static stability. All three GCMs fail to capture the detailed evolution in the different stages of the development and decay of the oscillation. The results suggest that an improvement in the boundary layer moisture processes may be crucial for a better simulation of the oscillation

K-Knuth Equivalence for Increasing Tableaux

A K-theoretic analogue of RSK insertion and Knuth equivalence relations was first introduced in 2006 by Buch, Kresch, Shimozono, Tamvakis, and Yong. The resulting K-Knuth equivalence relations on words and increasing tableaux on [n] has prompted investigation into the equivalence classes of tableaux arising from these relations. Of particular interest are the tableaux that are unique in their class, which we refer to as unique rectification targets (URTs). In this paper we give several new families of URTs and a bound on the length of intermediate words connecting two K-Knuth equivalent words. In addition, we describe an algorithm to determine if two words are K-Knuth equivalent and to compute all K-Knuth equivalence classes of tableaux on [n].Comment: 35 page

Functional renormalization group analysis of the half-filled one-dimensional extended Hubbard model

We study the phase diagram of the half-filled one-dimensional extended Hubbard model at weak coupling using a novel functional renormalization group (FRG) approach. The FRG method includes in a systematic manner the effects of the scattering processes involving electrons away from the Fermi points. Our results confirm the existence of a finite region of bond charge density wave, also known as a "bond order wave" near U=2V and clarify why earlier g-ology calculations have not found this phase. We argue that this is an example in which formally irrelevant corrections change the topology of the phase diagram. Whenever marginal terms lead to an accidental symmetry, this generalized FRG method may be crucial to characterize the phase diagram accurately.First author draf

Accurate molecular polarizabilities with coupled-cluster theory and machine learning

The molecular polarizability describes the tendency of a molecule to deform or polarize in response to an applied electric field. As such, this quantity governs key intra- and inter-molecular interactions such as induction and dispersion, plays a key role in determining the spectroscopic signatures of molecules, and is an essential ingredient in polarizable force fields and other empirical models for collective interactions. Compared to other ground-state properties, an accurate and reliable prediction of the molecular polarizability is considerably more difficult as this response quantity is quite sensitive to the description of the underlying molecular electronic structure. In this work, we present state-of-the-art quantum mechanical calculations of the static dipole polarizability tensors of 7,211 small organic molecules computed using linear-response coupled-cluster singles and doubles theory (LR-CCSD). Using a symmetry-adapted machine-learning based approach, we demonstrate that it is possible to predict the molecular polarizability with LR-CCSD accuracy at a negligible computational cost. The employed model is quite robust and transferable, yielding molecular polarizabilities for a diverse set of 52 larger molecules (which includes challenging conjugated systems, carbohydrates, small drugs, amino acids, nucleobases, and hydrocarbon isomers) at an accuracy that exceeds that of hybrid density functional theory (DFT). The atom-centered decomposition implicit in our machine-learning approach offers some insight into the shortcomings of DFT in the prediction of this fundamental quantity of interest

Does Osmotic Stress Affect Natural Product Expression in Fungi?

Acknowledgments: Russell Kerr acknowledges the assistance of Nadia Prigoda-Lee, Marius Grote, Kate McQuillan and Stephanie Duffy, and generous financial support from NSERC, the Canada Research Chair program, the Jeanne and Jean-Louis Lévesque Foundation and the Atlantic Canada Opportunities Agency. Ka-Lai Pang thanks the president of National Taiwan Ocean University, Ching-Fong Chang, for a special fund to attend the workshop held in Charlottetown, Canada in 2014 where this work was discussed. Rob Capon and Zhuo Shang acknowledge support from the University of Queensland, and the UQ Institute for Molecular Bioscience. Zhuo Shang acknowledges the provision of an International Postgraduate Research Scholarship (IPRS) and a Centennial Scholarship by the University of Queensland. Catherine Roullier acknowledges the assistance of Marie-Claude Boumard and Thibaut Robiou du Pont, and support from Region Pays de la Loire, FrancePeer reviewedPublisher PD

Phosphor- und Kalium-Bilanzen über 35 Jahre DOK-Versuch & geschätzte K-Nachlieferungsraten auf einem Lössboden

We calculated a phosphorus (P) and potassium (K) balance for the DOK-trial (Therwil, Switzerland) for a 35-years cropping period. In the DOK-trial, three cropping systems (D: biodynamic, O: bioorganic and K: conventional) are maintained on both a full (2) and a halved (1) fertilization level. Additionally, a treatment with no fertilization (N) and mineral fertilization (M; since 1985) are included. Balance inputs included fertilization, deposition, nutrients inputs by seeds, while in the outputs removal of nutrients by harvested plant material and leaching was considered. For P, the balance was positive for treatment M and treatment O2, but negative for the other treatments. The K-balance was positive only for treatment M, while treatments D2, O2 and K2 showed a slightly negative K-balance. In general, extensively maintained treatments on the halved fertilization level as well as treatment N show a negative P and K-Balance. Due to relatively constant K-concentrations and K-removal by crops in treatment N for the last 3 cropping periods (7 years each) we estimated a supply potential of K from loess soil of approximately 50 kg/ha * yr