Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Analysis of the influence of pre-loading in the rating life calculation of tapered roller bearings applied to lightweight front-axle differentials

For intricate automotive systems that enclose several components, such as gearboxes, an important aspect of the design is defining the correct assembly parameters. A proper assembly can ensure optimized operating conditions and therefore the components can achieve a longer life. In the case of the support bearings applied to front-axle lightweight differentials, the assembly preload is a major aspect for an adequate performance of the system. During the design phase it is imperative to define reference values to this preload, so the application would endure its requirements. However, with the assistance of computer simulations, it is possible to determine an optimum condition of operation, i.e. optimum pre-load, which would increase the system reliability. This paper presents a study on the influence of preload on the rating life of tapered roller bearings applied to light-weight front axle differentials, evaluating how preload affects several key parameters such as rating life and displacement of components, taking into account the flexibility of the surrounding differential housing. Copyright © 2012 SAE International.

Setting parameters in MRP for the effective management of bought-out inventory in a JIT assembly environment

In recent years, UK industry has seen an explosive growth in the number of `Computer Aided Production Management' (CAPM) system installations. Of the many CAPM systems, materials requirement planning/manufacturing resource planning (MRP/MRPII) is the most widely implemented. Despite the huge investments in MRP systems, over 80 percent are said to have failed within 3 to 5 years of installation. Many people now assume that Just-In-Time (JIT) is the best manufacturing technique. However, those who have implemented JIT have found that it also has many problems. The author argues that the success of a manufacturing company will not be due to a system which complies with a single technique; but due to the integration of many techniques and the ability to make them complement each other in a specific manufacturing environment. This dissertation examines the potential for integrating MRP with JIT and Two-Bin systems to reduce operational costs involved in managing bought-out inventory. Within this framework it shows that controlling MRP is essential to facilitate the integrating process. The behaviour of MRP systems is dependent on the complex interactions between the numerous control parameters used. Methodologies/models are developed to set these parameters. The models are based on the Pareto principle. The idea is to use business targets to set a coherent set of parameters, which not only enables those business targets to be realised, but also facilitates JIT implementation. It illustrates this approach in the context of an actual manufacturing plant - IBM Havant. (IBM Havant is a high volume electronics assembly plant with the majority of the materials bought-out). The parameter setting models are applicable to control bought-out items in a wide range of industries and are not dependent on specific MRP software. The models have produced successful results in several companies and are now being developed as commercial products.

Effect of weak dipolar interaction on the magnetic properties of Ni nanoparticles assembly analyzed with different protocols

The effect of weak dipolar interactions (DIs) between Ni nanoparticles (NPs) in samples with different Ni concentrations was investigated by performing a detailed characterization of their structural and magnetic properties. From the determination of several physical parameters of Ni NP assemblies, it was found that the ac and dc magnetic susceptibility measurements are valuable for identifying the DIs between NPs while hysteresis loops measurements showed to be very insensitive, provided that the strength of the DI field is much smaller than the maximum coercive field. Therefore, the sensitivity of the observed static and dynamical magnetic properties to the effect of weak DI depends on the measurement protocols used. (C) 2011 American Institute of Physics. [doi:10.1063/1.3556767]

Sensitivity to noise and ergodicity of an assembly line of cellular automata that classifies density

We investigate the sensitivity of the composite cellular automaton of H. Fuks [Phys. Rev. E 55, R2081 (1997)] to noise and assess the density classification performance of the resulting probabilistic cellular automaton (PCA) numerically. We conclude that the composite PCA performs the density classification task reliably only up to very small levels of noise. In particular, it cannot outperform the noisy Gacs-Kurdyumov-Levin automaton, an imperfect classifier, for any level of noise. While the original composite CA is nonergodic, analyses of relaxation times indicate that its noisy version is an ergodic automaton, with the relaxation times decaying algebraically over an extended range of parameters with an exponent very close (possibly equal) to the mean-field value.

Equilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation, and cluster distribution functions

We calculate the equilibrium thermodynamic properties, percolation threshold, and cluster distribution functions for a model of associating colloids, which consists of hard spherical particles having on their surfaces three short-ranged attractive sites (sticky spots) of two different types, A and B. The thermodynamic properties are calculated using Wertheim's perturbation theory of associating fluids. This also allows us to find the onset of self-assembly, which can be quantified by the maxima of the specific heat at constant volume. The percolation threshold is derived, under the no-loop assumption, for the correlated bond model: In all cases it is two percolated phases that become identical at a critical point, when one exists. Finally, the cluster size distributions are calculated by mapping the model onto an effective model, characterized by a-state-dependent-functionality (f) over bar and unique bonding probability (p) over bar. The mapping is based on the asymptotic limit of the cluster distributions functions of the generic model and the effective parameters are defined through the requirement that the equilibrium cluster distributions of the true and effective models have the same number-averaged and weight-averaged sizes at all densities and temperatures. We also study the model numerically in the case where BB interactions are missing. In this limit, AB bonds either provide branching between A-chains (Y-junctions) if epsilon(AB)/epsilon(AA) is small, or drive the formation of a hyperbranched polymer if epsilon(AB)/epsilon(AA) is large. We find that the theoretical predictions describe quite accurately the numerical data, especially in the region where Y-junctions are present. There is fairly good agreement between theoretical and numerical results both for the thermodynamic (number of bonds and phase coexistence) and the connectivity properties of the model (cluster size distributions and percolation locus).

Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal switching configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins

Viral self-assembly as a thermodynamic process

The protein shells, or capsids, of nearly all spherelike viruses adopt icosahedral symmetry. In the present Letter, we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral capsids constructed from structurally identical protein subunits and that this symmetry requires (at least) two internal switching configurations of the protein. Our results indicate that icosahedral symmetry is not a generic consequence of free energy minimization but requires optimization of internal structural parameters of the capsid proteins

A novel procedure for establishing clinching parameters for high strength steel sheet

The building industry has a particular interest in using clinching as a joining method for frame constructions of light-frame housing. Normally many clinch joints are required in joining of frames.In order to maximise the strength of the complete assembly, each clinch joint must be as sound as possible. Experimental testing is the main means of optimising a particular clinch joint. This includes shear strength testing and visual observation of joint cross-sections. The manufacturers of clinching equipment normally perform such experimental trials. Finite element analysis can also be used to optimise the tool geometry and the process parameter, X, which represents the thickness of the base of the joint. However, such procedures require dedicated software, a skilled operator, and test specimens in order to verify the finite element model. In addition, when using current technology several hours' computing time may be necessary. The objective of the study was to develop a simple calculation procedure for rapidly establishing an optimum value for the parameter X for a given tool combination. It should be possible to use the procedure on a daily basis, without stringent demands on the skill of the operator or the equipment. It is also desirable that the procedure would significantly decrease thenumber of shear strength tests required for verification. The experimental workinvolved tests in order to obtain an understanding of the behaviour of the sheets during clinching. The most notable observation concerned the stage of the process in which the upper sheet was initially bent, after which the deformation mechanism changed to shearing and elongation. The amount of deformation was measured relative to the original location of the upper sheet, and characterised as the C-measure. By understanding in detail the behaviour of the upper sheet, it waspossible to estimate a bending line function for the surface of the upper sheet. A procedure was developed, which makes it possible to estimate the process parameter X for each tool combination with a fixed die. The procedure is based on equating the volume of material on the punch side with the volume of the die. Detailed information concerning the behaviour of material on the punch side is required, assuming that the volume of die does not change during the process. The procedure was applied to shear strength testing of a sample material. The sample material was continuously hot-dip zinc-coated high-strength constructional steel,with a nominal thickness of 1.0 mm. The minimum Rp0.2 proof stress was 637 N/mm2. Such material has not yet been used extensively in light-frame housing, and little has been published on clinching of the material. The performance of the material is therefore of particular interest. Companies that use clinching on a daily basis stand to gain the greatest benefit from the procedure. By understanding the behaviour of sheets in different cases, it is possible to use data at an early stage for adjusting and optimising the process. In particular, the functionality of common tools can be increased since it is possible to characterise the complete range of existing tools. The study increases and broadens the amount ofbasic information concerning the clinching process. New approaches and points of view are presented and used for generating new knowledge.

Interplay between surface anisotropy and dipolar interactions in an assembly of nanomagnets

We study the interplay between the effects of surface anisotropy and dipolar interactions in monodisperse assemblies of nanomagnets with oriented anisotropy. We derive asymptotic formulas for the assembly magnetization, taking into account temperature, applied field, core and surface anisotropy, and dipolar interparticle interactions. We find that the interplay between surface anisotropy and dipolar interactions is well described by the analytical expression of the assembly magnetization derived here: the overall sign of the product of the two parameters governing the surface and the dipolar contributions determines whether intrinsic and collective terms compete or have synergistic effects on the magnetization. This is illustrated by the magnetization curves of γ-Fe2O3 nanoparticle assemblies in the low concentration limit.

Self-assembly of PS-PVP block copolymers and their complexes at the air/water interface

Une compréhension approfondie et un meilleur contrôle de l'auto-assemblage des copolymères diblocs (séquencés) et de leurs complexes à l'interface air/eau permettent la formation contrôlée de nanostructures dont les propriétés sont connues comme alternative à la nanolithographie. Dans cette thèse, des monocouches obtenues par les techniques de Langmuir et de Langmuir-Blodgett (LB) avec le copolymère dibloc polystyrène-poly(4-vinyl pyridine) (PS-PVP), seul ou complexé avec de petites molécules par liaison hydrogène [en particulier, le 3-n-pentadécylphénol (PDP)], ont été étudiées. Une partie importante de notre recherche a été consacrée à l'étude d'une monocouche assemblée atypique baptisée réseau de nanostries. Des monocouches LB composées de nanostries ont déjà été rapportées dans la littérature mais elles coexistent souvent avec d'autres morphologies, ce qui les rend inutilisables pour des applications potentielles. Nous avons déterminé les paramètres moléculaires et les conditions expérimentales qui contrôlent cette morphologie, la rendant très reproductible. Nous avons aussi proposé un mécanisme original pour la formation de cette morphologie. De plus, nous avons montré que l'utilisation de solvants à haut point d’ébullition, non couramment utilisés pour la préparation des films Langmuir, peut améliorer l'ordre des nanostries. En étudiant une large gamme de PS-PVP avec des rapports PS/PVP et des masses molaires différents, avec ou sans la présence de PDP, nous avons établi la dépendance des types principaux de morphologie (planaire, stries, nodules) en fonction de la composition et de la concentration des solutions. Ces observations ont mené à une discussion sur les mécanismes de formation des morphologies, incluant la cinétique, l’assemblage moléculaire et l’effet du démouillage. Nous avons aussi démontré pour la première fois que le plateau dans l'isotherme des PS-PVP/PDP avec morphologie de type nodules est relié à une transition ordre-ordre des nodules (héxagonal-tétragonal) qui se produit simultanément avec la réorientation du PDP, les deux aspects étant clairement observés par AFM. Ces études ouvrent aussi la voie à l'utilisation de films PS-PVP/PDP ultraminces comme masque. La capacité de produire des films nanostructurés bien contrôlés sur différents substrats a été démontrée et la stabilité des films a été vérifiée. Le retrait de la petite molécule des nanostructures a fait apparaître une structure interne à explorer lors d’études futures.

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc ¼ N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows b-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates b-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and smallangle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel b-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from diclofenac-meglumine supramolecular adducts

Meglumine is an aminocarbohydrate able to form supramolecular adducts with organic acids. The recognition is based on hydrogen bonds and the structures resulting from the complexation have high solubility in water. This property has been exploited by the pharmaceutical industry in the improvement of existing drugs, and the successful example of this approach involves the poorly soluble non-steroidal anti-inflammatory drugs (NSAIDs). Investigation of the thermal behavior of adduct obtained from meglumine and the NSAID diclofenac revealed that a polymer-like material is formed from the self-assembly of diclofenac-meglumine adducts in the melt. This polymer showed a high molecular weight around 2.0×105kDa. The kinetic parameters for the thermal decomposition step of the polymer were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15 and 20°Cmin-1, the Eα and Bα terms could be determined, and consequently the pre-exponential factor, Aα, as well as the kinetic model, g(α). © 2012 Elsevier B.V.

Coordinated dispersal and pre-isthmian assembly of the Central American ichthyofauna

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)