Bound and unbound substructures in Galaxy-scale Dark Matter haloes

We analyse the coarse-grained phase-space structure of the six Galaxy-scale dark matter haloes of the Aquarius Project using a state-of-the-art 6D substructure finder. Within r_50, we find that about 35% of the mass is in identifiable substructures, predominantly tidal streams, but including about 14% in self-bound subhaloes. The slope of the differential substructure mass function is close to -2, which should be compared to around -1.9 for the population of self-bound subhaloes. Near r_50 about 60% of the mass is in substructures, with about 30% in self-bound subhaloes. The inner 35 kpc of the highest resolution simulation has only 0.5% of its mass in self-bound subhaloes, but 3.3% in detected substructure, again primarily tidal streams. The densest tidal streams near the solar position have a 3-D mass density about 1% of the local mean, and populate the high velocity tail of the velocity distribution.Comment: Submitted to MNRAS on 12/10/2010, 11 pages, 10 figure

Solution Structure of the Tctex1 Dimer Reveals a Mechanism for Dynein-Cargo Interactions

SummaryTctex1 is a light chain found in both cytoplasmic and flagellar dyneins and is involved in many fundamental cellular activities, including rhodopsin transport within photoreceptors, and may function in the non-Mendelian transmission of t haplotypes in mice. Here, we present the NMR solution structure for the Tctex1 dimer from Chlamydomonas axonemal inner dynein arm I1. Structural comparisons reveal a strong similarity with the LC8 dynein light chain dimer, including formation of a strand-switched β sheet interface. Analysis of the Tctex1 structure enables the dynein intermediate chain binding site to be identified and suggests a mechanism by which cargo proteins might be attached to this microtubule motor complex. Comparison with the alternate dynein light chain rp3 reveals how the specificity of dynein-cargo interactions mediated by these dynein components is achieved. In addition, this structure provides insight into the consequences of the mutations found in the t haplotype forms of this protein

Application of random coherence order selection in gradient-enhanced multidimensional NMR

Development of multidimensional NMR is essential to many applications, for example in high resolution structural studies of biomolecules. Multidimensional techniques enable separation of NMR signals over several dimensions, improving signal resolution, whilst also allowing identification of new connectivities. However, these advantages come at a significant cost. The Fourier transform theorem requires acquisition of a grid of regularly spaced points to satisfy the Nyquist criterion, while frequency discrimination and acquisition of a pure phase spectrum require acquisition of both quadrature components for each time point in every indirect (non-acquisition) dimension, adding a factor of 2$^{N−1}$ to the number of free-induction decays which must be acquired, where $N$ is the number of dimensions. Compressed sensing (CS) ℓ$_{1}$-norm minimisation in combination with non-uniform sampling (NUS) has been shown to be extremely successful in overcoming the Nyquist criterion. Previously, maximum entropy reconstruction has also been used to overcome the limitation of frequency discrimination, processing data acquired with only one quadrature component at a given time interval, known as random phase detection (RPD), allowing a factor of two reduction in the number of points for each indirect dimension (Maciejewski et al. 2011 $\small \textit{PNAS}$ 108 16640). However, whilst this approach can be easily applied in situations where the quadrature components are acquired as amplitude modulated data, the same principle is not easily extended to phase modulated (P-/N-type) experiments where data is acquired in the form exp ($\textit{iωt}$) or exp (−$\textit{iωt}$), and which make up many of the multidimensional experiments used in modern NMR. Here we demonstrate a modification of the CS ℓ$_1$-norm approach to allow random coherence order selection (RCS) for phase modulated experiments; we generalise the nomenclature for RCS and RPD as random quadrature detection (RQD). With this method, the power of RQD can be extended to the full suite of experiments available to modern NMR spectroscopy, allowing resolution enhancements for all indirect dimensions; alone or in combination with NUS, RQD can be used to improve experimental resolution, or shorten experiment times, of considerable benefit to the challenging applications undertaken by modern NMR.This is the final version of the article. It first appeared from IOP Publishing via http://dx.doi.org/10.1088/1742-6596/699/1/01200

A proposed syntax for Minimotif Semantics, version 1

<p>Abstract</p> <p>Background</p> <p>One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.</p> <p>Results</p> <p>Herein, we present a structured syntax of minimotifs and their functional annotation. A syntax-based model of minimotif function with established minimotif sequence definitions was implemented using a relational database management system (RDBMS). To assess the usefulness of our standardized semantics, a series of database queries and stored procedures were used to classify SH3 domain binding minimotifs into 10 groups spanning 700 unique binding sequences.</p> <p>Conclusion</p> <p>Our derived minimotif syntax is currently being used to normalize minimotif covalent chemistry and functional definitions within the MnM database. Analysis of SH3 binding minimotif data spanning many different studies within our database reveals unique attributes and frequencies which can be used to classify different types of binding minimotifs. Implementation of the syntax in the relational database enables the application of many different analysis protocols of minimotif data and is an important tool that will help to better understand specificity of minimotif-driven molecular interactions with proteins.</p

SubHaloes going Notts: The SubHalo-Finder Comparison Project

We present a detailed comparison of the substructure properties of a single Milky Way sized dark matter halo from the Aquarius suite at five different resolutions, as identified by a variety of different (sub-)halo finders for simulations of cosmic structure formation. These finders span a wide range of techniques and methodologies to extract and quantify substructures within a larger non-homogeneous background density (e.g. a host halo). This includes real-space, phase-space, velocity-space and time- space based finders, as well as finders employing a Voronoi tessellation, friends-of-friends techniques, or refined meshes as the starting point for locating substructure.A common post-processing pipeline was used to uniformly analyse the particle lists provided by each finder. We extract quantitative and comparable measures for the subhaloes, primarily focusing on mass and the peak of the rotation curve for this particular study. We find that all of the finders agree extremely well on the presence and location of substructure and even for properties relating to the inner part part of the subhalo (e.g. the maximum value of the rotation curve). For properties that rely on particles near the outer edge of the subhalo the agreement is at around the 20 per cent level. We find that basic properties (mass, maximum circular velocity) of a subhalo can be reliably recovered if the subhalo contains more than 100 particles although its presence can be reliably inferred for a lower particle number limit of 20. We finally note that the logarithmic slope of the subhalo cumulative number count is remarkably consistent and <1 for all the finders that reached high resolution. If correct, this would indicate that the larger and more massive, respectively, substructures are the most dynamically interesting and that higher levels of the (sub-)subhalo hierarchy become progressively less important.Comment: 16 pages, 7 figures, 2 tables, Accepted for MNRA

The Evaluation of Optic Nerves Using 7 Tesla 'Silent' Zero Echo Time Imaging in Patients with Leber's Hereditary Optic Neuropathy with or without Idebenone Treatment

Magnetic Resonance Imaging (MRI) of the Optic Nerve is difficult due to the fine extended nature of the structure, strong local magnetic field distortions induced by anatomy, and large motion artefacts associated with eye movement. To address these problems we used a Zero Echo Time (ZTE) MRI sequence with an Adiabatic SPectral Inversion Recovery (ASPIR) fat suppression pulse which also imbues the images with Magnetisation Transfer contrast. We investigated an application of the sequence for imaging the optic nerve in subjects with Leber's hereditary optic neuropathy (LHON). Of particular note is the sequence's near-silent operation, which can enhance image quality of the optic nerve by reducing the occurrence of involuntary saccades induced during Magnetic Resonance (MR) scanning

Haloes gone MAD: The Halo-Finder Comparison Project

[abridged] We present a detailed comparison of fundamental dark matter halo properties retrieved by a substantial number of different halo finders. These codes span a wide range of techniques including friends-of-friends (FOF), spherical-overdensity (SO) and phase-space based algorithms. We further introduce a robust (and publicly available) suite of test scenarios that allows halo finder developers to compare the performance of their codes against those presented here. This set includes mock haloes containing various levels and distributions of substructure at a range of resolutions as well as a cosmological simulation of the large-scale structure of the universe. All the halo finding codes tested could successfully recover the spatial location of our mock haloes. They further returned lists of particles (potentially) belonging to the object that led to coinciding values for the maximum of the circular velocity profile and the radius where it is reached. All the finders based in configuration space struggled to recover substructure that was located close to the centre of the host halo and the radial dependence of the mass recovered varies from finder to finder. Those finders based in phase space could resolve central substructure although they found difficulties in accurately recovering its properties. Via a resolution study we found that most of the finders could not reliably recover substructure containing fewer than 30-40 particles. However, also here the phase space finders excelled by resolving substructure down to 10-20 particles. By comparing the halo finders using a high resolution cosmological volume we found that they agree remarkably well on fundamental properties of astrophysical significance (e.g. mass, position, velocity, and peak of the rotation curve).Comment: 27 interesting pages, 20 beautiful figures, and 4 informative tables accepted for publication in MNRAS. The high-resolution version of the paper as well as all the test cases and analysis can be found at the web site http://popia.ft.uam.es/HaloesGoingMA

NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR

Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform