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

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

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

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

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

Men's and women's experiences of violence and traumatic events in rural Cote d'Ivoire before, during and after a period of armed conflict.

OBJECTIVE: We assessed men's and women's experiences of gender based violence and other traumatic events in Côte d'Ivoire, a West African conflict-affected setting, before, during and after a period of active armed conflict (2000-2007). DESIGN: Cross-sectional, household survey. SETTING: 12 rural communities directly impacted by the Crisis in Côte d'Ivoire, spanning regions controlled by government forces, rebels and UN peacekeepers in 2008. PARTICIPANTS: 2678 men and women aged 15-49 years. PRIMARY OUTCOME MEASURES: Violence exposures measured since age 15. Questions included intimate partner physical and sexual violence; physical and sexual violence by others (including combatants) and exposure to traumatic events before, during and after the Crisis period (2000-2007). RESULTS: Physical and/or sexual violence since age 15 was reported by 57.1% women and 40.2% men (p=0.01); 29.9% women and 12.3% men reported exposure to any violence in the past year. Nearly 1 in 10 women (9.9%) and 5.9% men (p=0.03) were forced to have sex by a non-partner since age 15, and 14.8% women and 3.3% men (p=0.00) reported their first sexual experience was forced. Combatants were rarely reported as sexual violence perpetrators (0.3% women). After the Crisis, intimate partner physical violence was the most frequently reported form of violence and highest among women (20.9% women, 9.9% men, p=0.00). Fearing for their life was reported by men and women before, during and after the Crisis. CONCLUSIONS: Sexual violence in conflict remains a critical international policy concern. However, men and women experience different types of violence before, during and after conflict. In many conflict settings, other forms of violence, including intimate partner violence, may be more widespread than conflict-related sexual violence. Alongside service provision for rape survivors, our findings underscore the need for postconflict reconstruction efforts to invest in programmes to prevent and respond to intimate partner violence and trauma

Magnetic resonance angiography signal intensity as a marker of hemodynamic impairment in intracranial arterial stenosis.

BackgroundIntracranial arterial stenosis (ICAS) is the predominant cause of ischemic stroke and transient ischemic attack in Asia. Change of signal intensities (SI) across an ICAS on magnetic resonance angiography (MRA) may reflect its hemodynamic severity.MethodsIn-patients with a symptomatic single ICAS detected on 3D time-of-flight MRA were recruited from 2 hospitals. Baseline and 1-year follow-up data were collected. Signal intensity ratio (SIR) [ =  (mean post-stenotic SI -mean background SI)/(mean pre-stenotic SI - mean background SI)] was evaluated on baseline MRA to represent change of SIs across an ICAS. Acute infarct volume was measured on baseline diffusion-weighted images (DWI). Relationships between SIR and baseline characteristics as well as 1y outcomes were evaluated.ResultsThirty-six subjects (86.1% males, mean age 55.0) were recruited. Overall, mean SIR was 0.84±0.23. Mean SIRs were not significantly different between the 23 (63.9%) anatomically severe stenoses and the 13 (36.1%) anatomically moderate stenoses (0.80±0.23 versus 0.92±0.21, p = 0.126). SIR was significantly, linearly and negatively correlated to acute infarct volume on DWI (Spearman correlation coefficient -0.471, p = 0.011). Two patients (5.6%) had recurrent ischemic strokes at 1y, not related to SIR values.ConclusionsChange of signal intensities across an ICAS on MRA may reflect its hemodynamic and functional severity. Future studies are warranted to further verify the relationships between this index and prognosis of patients with symptomatic ICAS