A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.Peer Reviewe

Housing prices and multiple employment nodes: is the relationship nonmonotonic?

Standard urban economic theory predicts that house prices will decline with distance from the central business district. Empirical results have been equivocal, however. Disjoints between theory and empirics may be due to a nonmonotonic relationship between house prices and access to employment arising from the negative externalities associated with proximity to multiple centres of employment. Based on data from Glasgow (Scotland), we use gravity-based measures of accessibility estimated using a flexible functional form that allows for nonmonotonicity. The results are thoroughly tested using recent advances in spatial econometrics. We find compelling evidence of a nonmonotonic effect in the accessibility measure and discuss the implications for planning and housing policy

Reflection of a Lieb-Liniger wave packet from the hard-wall potential

Nonequilibrium dynamics of a Lieb-Liniger system in the presence of the hard-wall potential is studied. We demonstrate that a time-dependent wave function, which describes quantum dynamics of a Lieb-Liniger wave packet comprised of N particles, can be found by solving an $N$-dimensional Fourier transform; this follows from the symmetry properties of the many-body eigenstates in the presence of the hard-wall potential. The presented formalism is employed to numerically calculate reflection of a few-body wave packet from the hard wall for various interaction strengths and incident momenta.Comment: revised version, improved notation, Fig. 5 adde

The Ethics of Corporate Governance

How should corporate directors determine what is the right decision? For at least the past 30 years the debate has raged as to whether shareholder value should take precedence over corporate social responsibility when crucial decisions arise. Directors face pressure, not least from ethical investors, to do the good thing when they seek to make the right choice. Corporate governance theory has tended to look to agency theory and the need of boards to curb excessive executive power to guide directors' decisions. While useful for those purposes, agency theory provides only limited guidance. Supplementing it with the alternatives - stakeholder theory and stewardship theory - tends to put directors in conflict with their legal obligations to work in the interests of shareholders. This paper seeks to reframe the discussion about corporate governance in terms of the ethical debate between consequential, teleological approaches to ethics and idealist, deontological ones, suggesting that directors are - for good reason - more inclined toward utilitarian judgments like those underpinning shareholder value. But the problems with shareholder value have become so great that a different framework is needed: strategic value, with an emphasis on long-term value creation judged from a decidedly utilitarian standpoint

Peptidylarginine Deiminase 3 (PAD3) Is Upregulated by Prolactin Stimulation of CID-9 Cells and Expressed in the Lactating Mouse Mammary Gland

Peptidylarginine deiminases (PADs) post-translationally convert arginine into neutral citrulline residues. Our past work shows that PADs are expressed in the canine and murine mammary glands; however, the mechanisms regulating PAD expression and the function of citrullination in the normal mammary gland are unclear. Therefore, the first objective herein was to investigate regulation of PAD expression in mammary epithelial cells. We first examined PAD levels in CID-9 cells, which were derived from the mammary gland of mid-pregnant mice. PAD3 expression is significantly higher than all other PAD isoforms and mediates protein citrullination in CID-9 cells. We next hypothesized that prolactin regulates PAD3 expression. To test this, CID-9 cells were stimulated with 5 mug/mL of prolactin for 48 hours which significantly increases PAD3 mRNA and protein expression. Use of a JAK2 inhibitor and a dominant negative (DN)-STAT5 adenovirus indicate that prolactin stimulation of PAD3 expression is mediated by the JAK2/STAT5 signaling pathway in CID-9 cells. In addition, the human PAD3 gene promoter is prolactin responsive in CID-9 cells. Our second objective was to investigate the expression and activity of PAD3 in the lactating mouse mammary gland. PAD3 expression in the mammary gland is highest on lactation day 9 and coincident with citrullinated proteins such as histones. Use of the PAD3 specific inhibitor, Cl4-amidine, indicates that PAD3, in part, can citrullinate proteins in L9 mammary glands. Collectively, our results show that upregulation of PAD3 is mediated by prolactin induction of the JAK2/STAT5 signaling pathway, and that PAD3 appears to citrullinate proteins during lactation

Integrability breakdown in longitudinaly trapped, one-dimensional bosonic gases

A system of identical bosons with short-range (contact) interactions is studied. Their motion is confined to one dimension by a tight lateral trapping potential and, additionally, subject to a weak harmonic confinement in the longitudinal direction. Finite delay time associated with penetration of quantum particles through each other in the course of a pairwise one-dimensional collision in the presence of the longitudinal potential makes the system non-integrable and, hence, provides a mechanism for relaxation to thermal equilibrium. To analyse this effect quantitatively in the limit of a non-degenerate gas, we develop a system of kinetic equations and solve it for small-amplitude monopole oscillations of the gas. The obtained damping rate is long enough to be neglected in a realistic cold-atom experiment, and therefore longitudinal trapping does not hinder integrable dynamics of atomic gases in the 1D regime

WARNING: Physics Envy May Be Hazardous To Your Wealth!

The quantitative aspirations of economists and financial analysts have for many years been based on the belief that it should be possible to build models of economic systems - and financial markets in particular - that are as predictive as those in physics. While this perspective has led to a number of important breakthroughs in economics, "physics envy" has also created a false sense of mathematical precision in some cases. We speculate on the origins of physics envy, and then describe an alternate perspective of economic behavior based on a new taxonomy of uncertainty. We illustrate the relevance of this taxonomy with two concrete examples: the classical harmonic oscillator with some new twists that make physics look more like economics, and a quantitative equity market-neutral strategy. We conclude by offering a new interpretation of tail events, proposing an "uncertainty checklist" with which our taxonomy can be implemented, and considering the role that quants played in the current financial crisis.Comment: v3 adds 2 reference

Understanding spatial and temporal processes of urban growth: cellular automata modelling

An understanding of the dynamic process of urban growth is a prerequisite to the prediction of land-cover change and the support of urban development planning and sustainable growth management. The spatial and temporal complexity inherent in urban growth requires the development of a new simulation approach, which should be process-oriented and have a strong interpretive element. In this paper the authors present an innovative methodology for understanding spatial processes and their temporal dynamics on two interrelated scales -- the municipality and project scale -- by means of a multistage framework and a dynamic weighting concept. The multistage framework is aimed at modelling local spatial processes and global temporal dynamics by the incorporation of explicit decisionmaking processes. It is divided into four stages: project planning, site selection, local growth, and temporal control. These four stages represent the interactions between top-down and bottom-up decisionmaking involved in land development in large-scale projects. Project-based cellular automata modelling is developed for interpreting the spatial and temporal logic between various projects that form the whole of urban growth. Use of dynamic weighting is an attempt to model local temporal dynamics at the project level as an extension of the local growth stage. As nonlinear function of temporal land development, dynamic weighting can link spatial processes and temporal patterns. The methodology is tested with reference to the urban growth of a fast growing city -- Wuhan, in the People's Republic of China -- from 1993 to 2000. The findings from this research suggest that this methodology can be used to interpret and visualise the dynamic process of urban growth temporally and transparently, globally and locally