Van der Waals density functional: Self-consistent potential and the nature of the van der Waals bond

We derive the exchange-correlation potential corresponding to the nonlocal van der Waals density functional [M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004)]. We use this potential for a self-consistent calculation of the ground state properties of a number of van der Waals complexes as well as crystalline silicon. For the latter, where little or no van der Waals interaction is expected, we find that the results are mostly determined by semilocal exchange and correlation as in standard generalized gradient approximations (GGA), with the fully nonlocal term giving little effect. On the other hand, our results for the van der Waals complexes show that the self-consistency has little effect at equilibrium separations. This finding validates previous calculations with the same functional that treated the fully nonlocal term as a post GGA perturbation. A comparison of our results with wave-function calculations demonstrates the usefulness of our approach. The exchange-correlation potential also allows us to calculate Hellmann-Feynman forces, hence providing the means for efficient geometry relaxations as well as unleashing the potential use of other standard techniques that depend on the self-consistent charge distribution. The nature of the van der Waals bond is discussed in terms of the self-consistent bonding charge.Comment: submitted to Phys. Rev.

Bayesian correlated clustering to integrate multiple datasets

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct – but often complementary – information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured via parameters that describe the agreement among the datasets. Results: Using a set of 6 artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real S. cerevisiae datasets. In the 2-dataset case, we show that MDI’s performance is comparable to the present state of the art. We then move beyond the capabilities of current approaches and integrate gene expression, ChIP-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques – as well as to non-integrative approaches – demonstrate that MDI is very competitive, while also providing information that would be difficult or impossible to extract using other methods

The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola

Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in the common bean, Phaseolus vulgaris. P. syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene avrPphB (syn. hopAR1), which resides on PPHGI-1, a 106 kb genomic island. Loss of PPHGI-1 from P. syringae pv. phaseolicola 1302A following exposure to the hypersensitive resistance response (HR) leads to the evolution of strains with altered virulence. Here we have used fluorescent protein reporter systems to gain insight into the mobility of PPHGI-1. Confocal imaging of dual-labelled P. syringae pv. phaseolicola 1302A strain, F532 (dsRFP in chromosome and eGFP in PPHGI-1), revealed loss of PPHGI-1::eGFP encoded fluorescence during plant infection and when grown in vitro on extracted leaf apoplastic fluids. Fluorescence-activated cell sorting (FACS) of fluorescent and non-fluorescent PPHGI-1::eGFP F532 populations showed that cells lost fluorescence not only when the GI was deleted, but also when it had excised and was present as a circular episome. In addition to reduced expression of eGFP, quantitative PCR on sub-populations separated by FACS showed that transcription of other genes on PPHGI-1 (avrPphB and xerC) was also greatly reduced in F532 cells harbouring the excised PPHGI-1::eGFP episome. Our results show how virulence determinants located on mobile pathogenicity islands may be hidden from detection by host surveillance systems through the suppression of gene expression in the episomal state

A practical tool for managing change: cross-sectional psychometric assessment of the safe surgery organizational readiness tool

Background: Strengthening health systems through planned safety and quality improvement initiatives is an imperative to achieve more equitable, resilient, and effective care. And yet, years of organizational behavior research demonstrate that change initiatives often fall short because managers fail to account for organizational readiness for change. This finding remains true especially among surgical safety and quality improvement initiatives in low-income countries and middle-income countries. In this study, our aim was to psychometrically assess the construct validity and internal consistency of the Safe Surgery Organizational Readiness Tool (SSORT), a short survey tool designed to provide change leaders with insight into facility infrastructure that supports learning and readiness to undertake change. Materials and methods: To demonstrate generalizability and achieve a large sample size (n=1706) to conduct exploratory factor analysis (EFA) and confirmatory factor analysis (CFA), a collaboration between seven surgical and anesthesia safety and quality improvement initiatives was formed. Collected survey data from health care workers were divided into pilot, exploration, and confirmation samples. The pilot sample was used to assess feasibility. The exploration sample was used to conduct EFA, while the confirmation sample was used to conduct CFA. Factor internal consistency was assessed using Cronbach’s alpha coefficient. Results: Results of the EFA retained 9 of the 16 proposed factors associated with readiness to change. CFA results of the identified 9 factor model, measured by 28 survey items, demonstrated excellent fit to data. These factors (appropriateness, resistance to change, team efficacy, team learning orientation, team valence, communication about change, learning environment, vision for sustainability, and facility capacity) were also found to be internally consistent. Conclusion: Our findings suggest that communication, team learning, and supportive environment are components of change readiness that can be reliably measured prior to implementation of projects that promote surgical safety and quality improvement in low-income countries and middle-income countries. Future research can link performance on identified factors to outcomes that matter most to patients

Role of splice variants in the metastatic progression of prostate cancer

AS (alternative splicing) and its role in disease, especially cancer, has come to forefront in research over the last few years. Alterations in the ratio of splice variants have been widely observed in cancer. Splice variants of cancer-associated genes have functions that can alter cellular phenotype, ultimately altering metastatic potential. As metastases are the cause of approximately 90% of all human cancer deaths, it is crucial to understand how AS is dysregulated in metastatic disease. We highlight some recent studies into the relationship between altered AS of key genes and the initiation of prostate cancer metastasis. ©The Authors Journal compilation ©2012 Biochemical Society

From vigilance to violence : Tactics of mate retention in American undergraduates

Although the attraction and selection of mates are central to human reproduction, the retention of acquired mates is often necessary to actualize the promise of reproductive effort. Three empirical studies used act frequency methods to identify, assess the reported performance frequencies of, and evaluate the perceived effectiveness of 19 tactics and 104 acts of human mate guarding and retention. In Study 1 (N = 105), a hierarchical taxonomy of tactics was developed from a pool of nominated acts. We then assessed the reported performance frequencies of 19 retention tactics and 104 acts and tested three hypotheses derived from evolutionary models in an undergraduate sample (N = 102). Study 2 (N = 46) provided an independent test of these hypotheses by assessing the perceived effectiveness of each tactic. Discussion draws implications for sexual poaching, susceptibility to pair-bond defection, and the power of act frequency methods for preserving the proximate specificity and systemic complexity inherent in human mating processes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27156/1/0000151.pd

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

DNA sequence motifs and epigenetic modifications contribute to specific binding by a transcription factor, but the extent to which each feature determines occupancy in vivo is poorly understood. We addressed this question in erythroid cells by identifying DNA segments occupied by GATA1 and measuring the level of trimethylation of histone H3 lysine 27 (H3K27me3) and monomethylation of H3 lysine 4 (H3K4me1) along a 66 Mb region of mouse chromosome 7. While 91% of the GATA1-occupied segments contain the consensus binding-site motif WGATAR, only ∼0.7% of DNA segments with such a motif are occupied. Using a discriminative motif enumeration method, we identified additional motifs predictive of occupancy given the presence of WGATAR. The specific motif variant AGATAA and occurrence of multiple WGATAR motifs are both strong discriminators. Combining motifs to pair a WGATAR motif with a binding site motif for GATA1, EKLF or SP1 improves discriminative power. Epigenetic modifications are also strong determinants, with the factor-bound segments highly enriched for H3K4me1 and depleted of H3K27me3. Combining primary sequence and epigenetic determinants captures 52% of the GATA1-occupied DNA segments and substantially increases the specificity, to one out of seven segments with the required motif combination and epigenetic signals being bound

Sample-to-sample torque fluctuations in a system of coaxial randomly charged surfaces

Polarizable randomly charged dielectric objects have been recently shown to exhibit long-range lateral and normal interaction forces even when they are effectively net neutral. These forces stem from an interplay between the quenched statistics of random charges and the induced dielectric image charges. This type of interaction has recently been evoked to interpret measurements of Casimir forces in vacuo, where a precise analysis of such disorder-induced effects appears to be necessary. Here we consider the torque acting on a randomly charged dielectric surface (or a sphere) mounted on a central axle next to another randomly charged surface and show that although the resultant mean torque is zero, its sample-to-sample fluctuation exhibits a long-range behavior with the separation distance between the juxtaposed surfaces and that, in particular, its root-mean-square value scales with the total area of the surfaces. Therefore, the disorder-induced torque between two randomly charged surfaces is expected to be much more pronounced than the disorder-induced lateral force and may provide an effective way to determine possible disorder effects in experiments, in a manner that is independent of the usual normal force measurement.Comment: 7 pages, 3 fig