Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility.

To better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterise transcription factors that are relevant for this process. Our method uses a linear mixed modelling approach to combine datasets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE dataset, we confirm already known and imply numerous novel transcription factors that play a role in the establishment or maintenance of open chromatin. In particular, our approach rediscovers many factors that have been annotated as pioneer factors

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries

Fossil biomass preserved as graphitic carbon in a late paleoproterozoic banded iron formation metamorphosed at more than 550°C

Metamorphism is thought to destroy microfossils, partly through devolatilization and graphitization of biogenic organic matter. However, the extent to which there is a loss of molecular, elemental and isotope signatures from biomass during high-temperature metamorphism is not clearly established. We report on graphitic structures inside and coating apatite grains from the c. 1850 Ma Michigamme silicate banded iron formation from Michigan, metamorphosed above 550°C. Traces of N, S, O, H, Ca and Fe are preserved in this graphitic carbon and X-ray spectra show traces of aliphatic groups. Graphitic carbon has an expanded lattice around 3.6 Å, forms microscopic concentrically-layered and radiating polygonal flakes and has homogeneous δ13C values around −22‰, identical to bulk analyses. Graphitic carbon inside apatite is associated with nanometre-size ammoniated phyllosilicate. Precursors of these metamorphic minerals and graphitic carbon originated from ferruginous clayrich sediments with biomass. We conclude that graphite coatings and inclusions in apatite grains indicate fluid remobilization during amphibolite-facies metamorphism of precursor biomass. This new evidence fills in observational gaps of metamorphosed biomass into graphite and supports the existence of biosignatures in the highly metamorphosed iron formation from the Eoarchean Akilia Association, which dates from the beginning of the sedimentary rock record

Auger de-excitation of metastable molecules at metallic surfaces

We study secondary electron emission from metallic surfaces due to Auger de-excitation of diatomic metastable molecules. Our approach is based on an effective model for the two active electrons involved in the process -- a molecular electron described by a linear combination of atomic orbitals when it is bound and a two-center Coulomb wave when it is not and a metal electron described by the eigenfunctions of a step potential -- and employs Keldysh Green's functions. Solving the Dyson equation for the retarded Green's function by exponential resummation we are able to treat time-nonlocal self-energies and to avoid the wide-band approximation.Results are presented for the de-excitation of \NitrogenDominantMetastableState\ on aluminum and tungsten and discussed in view of previous experimental and theoretical investigations. We find quantitative agreement with experimental data for tungsten indicating that the effective model captures the physics of the process quite well. For aluminum we predict secondary electron emission due to Auger de-excitation to be one to two orders of magnitude smaller than the one found for resonant charge-transfer and subsequent auto-detachment.Comment: 15 pages, 9 figures, revised version using an improved single-electron basi

Positively and negatively valenced customer engagement: the constructs and their organizational consequences

Until recently, the majority of academic research on customer engagement (CE) has focused on the concept’s positive valence that reflects consumers’ favorable brand-related cognitions, emotions, and behaviors, which typically contribute positively to brand performance. While the existence of negative CE manifestations has been recognized, little is known regarding their particular expressions, characteristics, and position in the broader nomological network, as explored in this chapter. While the antecedents and consequences of unidimensional and multidimensional negatively valenced CE (NVCE) have been explored in the literature, the consequences of multidimensional NVCE, particularly those at the organizational level, remain nebulous, as explored in this chapter. In addition, we examine organizational-level consequences of positively valenced CE (PVCE) that are contrasted to those of NVCE. To achieve these objectives, we first conceptualize positively and negatively valenced CE, followed by an exploration of their respective consequences. We conclude by offering specific managerial recommendations to increase positive CE whilst halting the concept’s negative expressions

Female Salamanders Experience Higher Parasitism Compared to Males: A Cost of Female Reproduction?

Males tend to experience higher rates of parasitism compared to females, a phenomenon associated with ecological factors, the fact that males engage in risky behaviors, and because testosterone is known to be immunosuppressive. However, females could experience higher rates of parasitism if energy is allocated from costly immune responses towards producing eggs. We used pooled data sets from laboratory experiments to investigate sex-specific differences in salamander (Plethodon cinereus) resistance to the emerging fungal pathogen Batrachochytrium dendrobatidis (‘‘Bd’’). Contrary to our predictions, we found that female salamanders had a higher prevalence of infection (~56%) and carried a higher Bd infection burden (455 zoospores equivalents per sample) compared to male salamanders (which had a Bd infection prevalence of ~24% and an average infection burden of 58 zoospore equivalents per sample). We also found that female reproductive investment (i.e., mass of eggs) positively correlated with Bd infection burden, suggesting that females who previously invested more into reproduction carried a higher Bd infection burden. Collectively, our findings might indicate that female salamanders experience a cost of reproduction in the form of decreased disease resistance

Ego-Splitting and the Transcendental Subject. Kant’s Original Insight and Husserl’s Reappraisal

In this paper, I contend that there are at least two essential traits that commonly define being an I: self-identity and self-consciousness. I argue that they bear quite an odd relation to each other in the sense that self-consciousness seems to jeopardize self-identity. My main concern is to elucidate this issue within the range of the transcendental philosophies of Immanuel Kant and Edmund Husserl. In the first section, I shall briefly consider Kant’s own rendition of the problem of the Egosplitting. My reading of the Kantian texts reveals that Kant himself was aware of this phenomenon but eventually deems it an unexplainable fact. The second part of the paper tackles the same problematic from the standpoint of Husserlian phenomenology. What Husserl’s extensive analyses on this topic bring to light is that the phenomenon of the Ego-splitting constitutes the bedrock not only of his thought but also of every philosophy that works within the framework of transcendental thinking

A machine learning pipeline for discriminant pathways identification

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a machine learning solution for molecular profiling with a recent network comparison method. The pipeline can identify changes occurring between specific sub-modules of networks built in a case-control biomarker study, discriminating key groups of genes whose interactions are modified by an underlying condition. The proposal is independent from the classification algorithm used. Three applications on genomewide data are presented regarding children susceptibility to air pollution and two neurodegenerative diseases: Parkinson's and Alzheimer's. Availability: Details about the software used for the experiments discussed in this paper are provided in the Appendix