The rate of convergence of some asymptotically chi-square distributed statistics by Stein's method

We build on recent works on Stein's method for functions of multivariate normal random variables to derive bounds for the rate of convergence of some asymptotically chi-square distributed statistics. We obtain some general bounds and establish some simple sufficient conditions for convergence rates of order $n^{-1}$ for smooth test functions. These general bounds are applied to Friedman's statistic for comparing $r$ treatments across $n$ trials and the family of power divergence statistics for goodness-of-fit across $n$ trials and $r$ classifications, with index parameter $\lambda\in\mathbb{R}$ (Pearson's statistic corresponds to $\lambda=1$). We obtain a $O(n^{-1})$ bound for the rate of convergence of Friedman's statistic for any number of treatments $r\geq2$. We also obtain a $O(n^{-1})$ bound on the rate of convergence of the power divergence statistics for any $r\geq2$ when $\lambda$ is a positive integer or any real number greater than 5. We conjecture that the $O(n^{-1})$ rate holds for any $\lambda\in\mathbb{R}$.Comment: 32 page

Semilocal momentum-space regularized chiral two-nucleon potentials up to fifth order

We introduce new semilocal two-nucleon potentials up to fifth order in the chiral expansion. We employ a simple regularization approach for the pion-exchange contributions which (i) maintains the long-range part of the interaction, (ii) is implemented in momentum space and (iii) can be straightforwardly applied to regularize many-body forces and current operators. We discuss in detail the two-nucleon contact interactions at fourth order and demonstrate that three terms out of fifteen used in previous calculations can be eliminated via suitably chosen unitary transformations. The removal of the redundant contact terms results in a drastic simplification of the fits to scattering data and leads to interactions which are much softer (i.e. more perturbative) than our recent semilocal coordinate-space regularized potentials. Using the pion-nucleon low-energy constants from matching pion-nucleon Roy-Steiner equations to chiral perturbation theory, we perform a comprehensive analysis of nucleon-nucleon scattering and the deuteron properties up to fifth chiral order and study the impact of the leading F-wave two-nucleon contact interactions which appear at sixth order. The resulting chiral potentials lead to an outstanding description of the proton-proton and neutron-proton scattering data from the self-consistent Granada-2013 database below the pion production threshold, which is significantly better than for any other chiral potential. For the first time, the chiral potentials match in precision and even outperform the available high-precision phenomenological potentials, while the number of adjustable parameters is, at the same time, reduced by about ~40%. Last but not least, we perform a detailed error analysis and, in particular, quantify for the first time the statistical uncertainties of the fourth- and the considered sixth-order contact interactions.Comment: 57 pages, 17 figures, 19 table

Low-Energy Scale Excitations in the Spectral Function of Organic Monolayer Systems

Using high-resolution photoemission spectroscopy we demonstrate that the electronic structure of several organic monolayer systems, in particular 1,4,5,8-naphthalene tetracarboxylic dianhydride and Copper-phtalocyanine on Ag(111), is characterized by a peculiar excitation feature right at the Fermi level. This feature displays a strong temperature dependence and is immediatly connected to the binding energy of the molecular states, determined by the coupling between the molecule and the substrate. At low temperatures, the line-width of this feature, appearing on top of the partly occupied lowest unoccupied molecular orbital of the free molecule, amounts to only $\approx 25$ meV, representing an unusually small energy scale for electronic excitations in these systems. We discuss possible origins, related e.g. to many-body excitations in the organic-metal adsorbate system, in particular a generalized Kondo scenario based on the single impurity Anderson model.Comment: 6 pages, 3 figures, accepted as PRB Rapid Communication

R-Parity Violation at the LHC

We investigate the phenomenology of the MSSM extended by a single R-parity violating coupling at the unification scale. For all R-parity violating couplings, we discuss the evolution of the particle spectra through the renormalization group equations and the nature of the lightest supersymmetric particle (LSP) within the CMSSM, as an example of a specific complete supersymmetric model. We use the nature of the LSP to classify the possible signatures. For each possible scenario we present in detail the current LHC bounds on the supersymmetric particle masses, typically obtained using simplified models. From this we determine the present coverage of R-parity violating models at the LHC. We find several gaps, in particular for a stau-LSP, which is easily obtained in R-parity violating models. Using the program CheckMATE we recast existing LHC searches to set limits on the parameters of all R-parity violating CMSSMs. We find that virtually all of them are either more strongly constrained or similarly constrained in comparison to the R-parity conserving CMSSM, including the $\bar U\bar D\bar D$ models. For each R-parity violating CMSSM we then give the explicit lower mass bounds on all relevant supersymmetric particles.Comment: 43 pages, 13 tables, 17 figures; updated Figs. 11-17 and Tab. 12 including NLO corrections; version accepted for publication in EPJ

Identifying networks with common organizational principles

Many complex systems can be represented as networks, and the problem of network comparison is becoming increasingly relevant. There are many techniques for network comparison, from simply comparing network summary statistics to sophisticated but computationally costly alignment-based approaches. Yet it remains challenging to accurately cluster networks that are of a different size and density, but hypothesized to be structurally similar. In this paper, we address this problem by introducing a new network comparison methodology that is aimed at identifying common organizational principles in networks. The methodology is simple, intuitive and applicable in a wide variety of settings ranging from the functional classification of proteins to tracking the evolution of a world trade network.Comment: 26 pages, 7 figure

Efficient method for estimating the number of communities in a network

While there exist a wide range of effective methods for community detection in networks, most of them require one to know in advance how many communities one is looking for. Here we present a method for estimating the number of communities in a network using a combination of Bayesian inference with a novel prior and an efficient Monte Carlo sampling scheme. We test the method extensively on both real and computer-generated networks, showing that it performs accurately and consistently, even in cases where groups are widely varying in size or structure.Comment: 13 pages, 4 figure

Fast and accurate read mapping with approximate seeds and multiple backtracking

We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai

Development of General Guidelines for the Planning of Stormwater Management Facilities: Application to Urban Watersheds in Kentucky

This report provides a planning methodology and a design tool to help determine the appropriate location and volume of detention basins required to control critical storm events. The technique involves using watershed characteristics including the SCS curve number, time of concentration, peak outflow rate, watershed area and the storage recurrence interval to help predict these detention volumes. Historical rainfall records are used in a revised continuous simulation program (SYNOP, Hydroscience, Inc,) to determine the rainfall excess from which runoff hydrographs are produced. Various combinations of the watershed characteristics were input and computer analyses done to obtain the required data base. A statistical analysis is performed in each computer analysis to obtain the statistics on the required volume. Graphs were drawn from these statistical results as functions of the watershed characteristics and the release rate. Entering the graphs with the governing watershed characteristics, the designer can obtain.a good estimate of the detention basin volume required

Going Rogue: The Supreme Court\u27s Newfound Hostility to Policy-Based Bivens Claims

In Ziglar v. Abbasi, 137 S. Ct. 1843 (2017), the Supreme Court held that a proposed Bivens remedy was subject to an exacting special factors analysis when the claim arises in a “new context.” In Ziglar itself, the Court found the context of the plaintiffs’ claims to be “new” because, in the Court’s view, they challenged “large-scale policy decisions concerning the conditions of confinement imposed on hundreds of prisoners.” Bivens claims for damages caused by unconstitutional policies, the Court suggested, were inappropriate. This Essay critically examines the Ziglar Court’s newfound hostility to policy-based Bivens claims. We show that an exemption for policy challenges can claim no support in the Court’s own development of the Bivens doctrine, or in the principles that animate the Court’s broader approach to government accountability law. Equally troubling, the policy exemption has already caused substantial confusion among lower courts. Judging that it lacks a legitimate predicate and defies coherent application, we conclude that the Court should pursue no further its hostility to policy-based Bivens claims

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants

BACKGROUND: Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra. The PMF process requires calibration, usually performed with external or internal calibrants of known molecular masses. RESULTS: We have introduced two novel MS calibration methods. The first method utilises the local similarity of peptide maps generated after separation of complex protein samples by two-dimensional gel electrophoresis. It computes a multiple peak-list alignment of the data set using a modified Minimum Spanning Tree (MST) algorithm. The second method exploits the idea that hundreds of MS samples are measured in parallel on one sample support. It improves the calibration coefficients by applying a two-dimensional Thin Plate Splines (TPS) smoothing algorithm. We studied the novel calibration methods utilising data generated by three different MALDI-TOF-MS instruments. We demonstrate that a PMF data set can be calibrated without resorting to external or relying on widely occurring internal calibrants. The methods developed here were implemented in R and are part of the BioConductor package mscalib available from . CONCLUSION: The MST calibration algorithm is well suited to calibrate MS spectra of protein samples resulting from two-dimensional gel electrophoretic separation. The TPS based calibration algorithm might be used to correct systematic mass measurement errors observed for large MS sample supports. As compared to other methods, our combined MS spectra calibration strategy increases the peptide/protein identification rate by an additional 5 – 15%