Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Formulation and evaluation of poly (L-lactide-co-ε-caprolactone) loaded gliclazide biodegradable nanoparticles as a control release carrier

A biodegradable nanoparticle has been used frequently as drug delivery carrier due to its better encapsulation capacity, sustained/ control release property and less toxicity. Gliclazide (GLZ) is a second generation of hypoglycemic sulfonylurea and acts selectively on pancreatic ß cell to control diabetes mellitus. The objective of this study was to produce controlled release nanoparticles of Gliclazide using poly (L-lactide-co-ε-caprolactone) (PLCL). The method was optimized using design of experiments by employing a 3-factor, 3-level Design Expert (version 8.0.7.1) Statistical Design Software and was subjected to various characterization studies including Field Emission Scanning Electron Microscopy (FE-SEM), X-ray diffraction (XRD), Encapsulation efficiency (%EE), Particle Size Distribution (PSD), etc. Formulated nanoparticles were also subjected to Fourier Transform Infrared Spectroscopy (FT-IR), Differential Scanning Calorimetry (DSC) for studying interaction between drug and polymer and the effect of lyophilization (Freeze Drying) on developed nanoparticles.  The release profiles and encapsulation efficiencies are depended on the concentration of PLCL. These data demonstrated the efficacy of the biodegradable polymeric nanoparticles in controlling the gliclazide drug release profile as novel drug delivery system

Behavior of fresh and fouled railway ballast subjected to direct shear testing: Discrete element simulation

This paper presents the three-dimensional discrete element method (DEM) that was used to study the shear behavior of fresh and coal fouled ballast in direct shear testing. The volumetric changes and stress-strain behavior of fresh and fouled ballast were simulated and compared with the experimental results. Clump logic in particle flow code in three dimensions (PFC3D) incorporated in a subroutine was used to simulate irregular-shaped particles in which groups of 10-20 spherical balls were clumped together in appropriate sizes to simulate ballast particles. Fouled ballast with a various void contaminant index (VCI) ranging from 20 to 70% VCI was modeled by injecting a specified number of miniature spherical particles into the voids of fresh ballast. The DEM simulation captures the behavior of fresh and fouled ballast as observed in the laboratory, showing that the peak shear stress of the ballast assembly decreases and the dilation of fouled ballast increases with an increasing VCI. Furthermore, the DEM also provides insight to the distribution of contact force chains and particle displacement vectors, which cannot be determined experimentally. These micromechanical observations clearly justify the formation of a shear band and the evolution of volumetric changes during shearing. The reduced maximum contact force associated with increased particle contact area due to fouling explains the decreased breakage of fouled ballast. An acceptable agreement was found between the DEM model predictions and laboratory data. © 2014 American Society of Civil Engineers

The influence of rubber crumbs on the critical state behavior of waste mixtures

© The Authors, published by EDP Sciences. The practical application of waste materials such as steel furnace slag (SFS) and coal wash (CW) is becoming more prevalent in many geotechnical projects. It was found that the inclusion of rubber crumbs (RCs) from recycled tyres into mixtures of SFS and CW not only solves the problem of large stockpiles of waste tyres, it also can provide an energy-absorbing medium that will reduce track degradation. In order to investigate the influence of RC on the geotechnical properties of the granular waste matrix (SFS+CW+RC), a series of monotonic consolidated drained triaxial tests were conducted on waste mixtures. The test results reveal that the inclusion of RC significantly affects the geotechnical properties of the waste mixtures, especially their critical state behaviour. Specifically, the waste matrix can achieve a critical state with a low RC content (<20%), whereas those mixtures with higher RC contents (20-40%) cannot attain a critical state within the ultimate strain capacity that can be applied to specimens using the traditional triaxial equipment. Therefore, for the waste matrix with higher RC contents extrapolation of the measured volumetric strains had to be adopted to obtain the appropriate critical state parameters. Moreover, the influence of energy absorbing property by adding RC on the critical state behaviour has also been captured through an empirical equation

The Scottish Early Rheumatoid Arthritis (SERA) Study:an inception cohort and biobank

Background: The Scottish Early Rheumatoid Arthritis (SERA) study is an inception cohort of rheumatoid (RA) and undifferentiated arthritis (UA) patients that aims to provide a contemporary description of phenotype and outcome and facilitate discovery of phenotypic and prognostic biomarkers Methods: Demographic and clinical outcome data are collected from newly diagnosed RA/UA patients every 6 months from around Scotland. Health service utilization data is acquired from Information Services Division, NHS National Services Scotland. Plain radiographs of hands and feet are collected at baseline and 12 months. Additional samples of whole blood, plasma, serum and filtered urine are collected at baseline, 6 and 12 months Results: Results are available for 1073 patients; at baseline, 76 % were classified as RA and 24 % as UA. Median time from onset to first review was 163 days (IQR97-323). Methotrexate was first-line DMARD for 75 % patients. Disease activity, functional ability and health-related quality of life improved significantly between baseline and 24 months, however the proportion in any employment fell (51 to 38 %, p = 0.0005). 24 % patients reported symptoms of anxiety and/or depression at baseline. 35/391 (9 %) patients exhibited rapid radiographic progression after 12 months. The SERA Biobank has accrued 60,612 samples Conclusions: In routine care, newly diagnosed RA/UA patients experience significant improvements in disease activity, functional ability and health-related quality of life but have high rates of psychiatric symptoms and declining employment rates. The co-existence of a multi-domain description of phenotype and a comprehensive biobank will facilitate multi-platform translational research to identify predictive markers of phenotype and prognosis

Direct shear behavior of gravel-rubber mixtures: Discrete element modeling and microscopic investigations

In this paper, a newly developed 3-dimentional discrete element model (DEM) for gravel-rubber mixtures (GRMs), namely DEM4GRM, that is capable of accurately describing the macro-scale shear response (from small to large deformation) of GRMs in a direct shear box apparatus is presented. Rigid gravel grains are modelled as simple multi-shape clumps, while soft rubber particles are modeled by using deformable 35-ball body-centered-cubic clusters. Mixtures are prepared with different volumetric rubber content (VRC) at 0, 10, 25, 40 and 100%, statically compressed under 30, 60 and 100 kPa vertical stress and then sheared, by closely simulating a reference laboratory test procedure. The variation of micro-scale factors such as fabric, normal and tangential force anisotropy is carefully examined throughout the shearing process and described by means of novel micro-mechanical relationships valid for GRMs. Moreover, strong-force chains are scrutinized to identify the transition from rigid to soft granular skeleton and gain insights on the load transfer and deformation mechanisms of GRMs. It is shown that the development of the fabric and force anisotropy during shearing is closely related to the macro-scale shear strength of GRMs, and strongly depends on the VRC. Besides, strong-force chains appear to be primarily formed by gravel-gravel contacts (resulting in a rigid-like mechanical behavior) up to VRC = 30%, and by rubberrubber contacts (causing a soft-like mechanical response) beyond VRC = 60%. Alternatively, at 30% < VRC < 60%, gravel-rubber contacts are predominant in the strong-force network and an intermediate mechanical behavior is observed. This is consistent with the behavioral trends observed in the macro- and micro-mechanical responses

Dem Study on the Dynamic Performance of a Fouled Ballasted Track Under Repeated Traffic Loading

The fouling of ballast, resulting from upward intrusion of subgrade slurries, coal or other mineral ore dislodging from passing freight traffic, and the accumulation of debris among ballast grains, has been extensively reported as the primary cause for numerous disastrous railroad incidents. This paper presents a numerical study to examine the deformation and degradation responses of a coal-fouled ballasted track upon repeated traffic loading using the discrete element modeling (DEM). A particle degradation model considering Weibull statistics in tandem with a granular medium size effect is developed and employed to capture the continuous corner abrasion of angular ballast. The model had been calibrated by comparing the predicted shear stress–strain response with laboratory data obtained from large-scale direct shear testing. A series of cubical shear test simulations have been carried out to examine the dynamic performance of ballast assemblies with various coal fouling contents under cyclic loading. The results show that an increase in fouling content exacerbates the sleeper settlement, while decreasing the resilient modulus and the particle breakage in ballasted bed. Ballast beneath the sleeper experiences significant breakage compared to the crib ballast, and the extent of damage is mitigated with depth. Rigorous microscopic analysis is also presented in terms of interparticle contacts and contact network anisotropy of the ballast assembly. The micromechanical examinations show that the decrease in ballast breakage observed in fouled assemblies is predominantly attributed to the inevitable decrease in interparticle pressures as effected by the coating of ballast aggregates by the coal fines

Softrigid particle mixtures: direct shear behavior from macro to micro

This paper provides a summary of the main outcomes of a research activity aimed at facilitating the use of gravelrubber mixtures (GRMs) in geotechnical engineering applications. Specifically, the results of direct shear tests carried out on GRMs prepared at different volumetric rubber contents (VRC = 0, 10, 25, 40 and 100%) are reported and discussed. Moreover, an original 3D hybrid DEM numerical model for rigid-soft particle mixtures is presented, and its performance is assessed. Finally, using newly proposed constitutive equations, micro-scale factors such as fabric, force anisotropy and strong-force chains are systematically examined throughout the shearing process to gain insight on the micro-mechanical behavior of mixtures with varying VRC. RÉSUMÉ: Cet article résume les principaux résultats d'une activité de recherche visant à faciliter l'utilisation de mélanges graviercaoutchouc (GRM) dans les applications de génie géotechnique. Plus précisément, les résultats d'essais de cisaillement direct réalisés sur des GRM préparés à différentes teneurs volumétriques en caoutchouc (VRC = 0, 10, 25, 40 et 100%) sont rapportés et discutés. De plus, un modèle numérique DEM hybride 3D original pour les mélanges de particules rigides-molles est présenté et ses performances sont évaluées. Enfin, en utilisant les équations constitutives nouvellement proposées, des facteurs micro-échelles tels que le tissu, l'anisotropie de force et les chaînes de force forte sont systématiquement examinés tout au long du processus de cisaillement pour avoir un aperçu du comportement micro-mécanique des mélanges avec des VRC variables