Combining targeted panel-based resequencing and copy-number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

Inherited syndromic retinopathies are a highly heterogeneous group of diseases that involve retinal anomalies and systemic manifestations. They include retinal ciliopathies, other well-defined clinical syndromes presenting with retinal alterations and cases of non-specific multisystemic diseases. The heterogeneity of these conditions makes molecular and clinical characterization of patients challenging in daily clinical practice. We explored the capacity of targeted resequencing and copy-number variation analysis to improve diagnosis of a heterogeneous cohort of 47 patients mainly comprising atypical cases that did not clearly fit a specific clinical diagnosis. Thirty-three likely pathogenic variants were identified in 18 genes (ABCC6, ALMS1, BBS1, BBS2, BBS12, CEP41, CEP290, IFT172, IFT27, MKKS, MYO7A, OTX2, PDZD7, PEX1, RPGRIP1, USH2A, VPS13B, and WDPCP). Molecular findings and additional clinical reassessments made it possible to accurately characterize 14 probands (30% of the total). Notably, clinical refinement of complex phenotypes was achieved in 4 cases, including 2 de novo OTX2-related syndromes, a novel phenotypic association for the ciliary CEP41 gene, and the co-existence of biallelic USH2A variants and a Koolen-de-Vries syndrome–related 17q21.31 microdeletion. We demonstrate that combining next-generation sequencing and CNV analysis is a comprehensive and useful approach to unravel the extensive phenotypic and genotypic complexity of inherited syndromic retinopathiesFEDER (Fondo Europeo de Desarrollo Regional) | Ref. PI016/00425Instituto de Salud Carlos III | Ref. PT13/0010/001

Particle segregation associated with sub-sampling of feed at a typical UG2 concentrator

A dissertation submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in Metallurgical Engineering, Johannesburg, August 2017A particular Upper Group 2 (UG2) reef ore treating Concentrator Plant has been historically under-accounting in terms of 4T (Platinum, Palladium, Rhodium and Gold) content. It has been postulated that the main reason for the consistent under-accounting is due to the correct sub-sampling of finer particles and consequently under sub-sampling of the coarser particles present in the feed slurry streams into the plant. The test work presented involved a series of experimental studies designed to gain an understanding of the presence and extent of particle segregation in the intermediate hopper of a typical UG2 feed vezin sampling system. A total of three stages of test work were conducted, including vezin credibility and chronological sub-sample tests, tests on a re designed nozzle and mechanical hopper. The tests on sub-sampling of the feed material from the intermediate hopper performed on the current sampling arrangement (Stage 1, Test 1) demonstrated that segregation occurs in the intermediate hopper of the feed sampling system. A consistent bias was observed between the reject and official samples with the official samples having more fine particles and being higher in 4T grade than the reject samples. By means of a paired t-test, the calculated bias for % mass retained was deemed significant at the 95% confidence level. This outcome together with the size by assay analysis performed indicated that an under accounting scenario would result. Stage 2 test work involved the use of an alternative nozzle design at the outlet of the current intermediate hopper as a way of optimizing the current arrangement. The sub-sampling tests performed after this modification resulted in a more random distribution of fine and coarse particles in both the reject and official samples. The PSD’s for the reject and official samples were similar across all test runs however the 4T grade was not consistent. The calculated bias for % mass retained was not significant at the 95% confidence level. Stage 3 test work involved the application of a new hopper design which was equipped with an agitator in an attempt to reverse the segregation observed in the old hopper design. The ii new hopper also necessitated the introduction of an alternative sampling protocol where multiple primary increments were collected and the sub-sampling to produce an official and reject sample while agitation transpires created the platform for better suspension of all particles. The particle segregation in the intermediate hopper was reduced and the calculated bias for % mass retained was not significant at most measurements at the 90% and 95% confidence level. The change in nozzle and hopper design seemed to not have an impact on the overall 4T grade of the official sub-samples generated over the sampling campaign. There was a slight improvement in the % COV for the % +38μm from Stage 1 to Stage 2. With the inclusion of the new nozzle design to the mechanical hopper, the % COV for the % +75μm improved from 26.7% to 14.5%. In general, it is believed that the particle segregation which was so evident in the baseline test was significantly reduced with the incorporation of the alternative nozzle design and mechanical agitation. Compressed air agitation alone does not seem to keep all particles of varying size and density in suspension in the intermediate hopper. A future mechanical hopper prototype should be redesigned and fabricated from a cheaper yet robust material and should also be ergonomically improved. The incorporation of internal baffles inside the mechanical hopper should also be considered to reduce the impact of vortexing. An inspection port should also be integrated into the design to be able to view the agitator in operation and observe for vortexing of the slurry material or retention of residual solids in the hopper after sub-sampling takes place. Multiple air agitation points may also be considered in future designs of the mechanical hopper (for instance, an air agitation point above and below the pneumatic valve). It is recommended that any future investigation or test work around particle segregation in the intermediate hopper be conducted in a controlled testing environment. In this way, any random variation due to the process can be disregarded and the true bias (if any) can be determined and confirmed.XL201

Investigation of clusters and nano-particles in thermomechanically processed Ti-Mo steel

The study was focused on understanding the interphase precipitation and clustering phenomena in Ti-Mo alloyed HSLA steel. Combination of novel characterisation techniques enabled to characterise and classify precipitates, reveal conditions at the interfaces during formation of precipitates and study effect of deformation on the interphase precipitation

Petrography, chemical composition, and stratigraphic setting of the coals of North-Central Missouri

Under a grant from the National Air Pollution Control Administration, the Missouri Geological Survey undertook a core drilling program to learn more about the coals in north-central Missouri. The stratigraphic setting and chemical and petrographic characteristics of 43 complete samples of coal recovered from 13 diamond drill holes in the exploration program in north-central Missouri are major contributions of this study. These samples represent twelve different coal beds of the Atokan and Desmoinesian Series of the Pennsylvanian System of Missouri and range in thickness from 9.6 to 44.4 inches. They have an average thickness of 20.4 inches and a combined thickness of 71.8 feet. Detailec lithologic logs of the drill cores are an additional contribution of this investigation. In the seven county area of this report, there are an estimated 15.4 billion tons of coal resources. Of this total about 4.3 billion tons are classified as unmined coal reserves. Proximate and ultimate analyses, BTU and sulfur content including forms of sulfur are given for each of the coals sampled. The BTU content of the coals has an arithmetic mean of 10,447 as received. The arithmetic mean of the sulfur content of the coals is 4.69 percent as received of which 3.26 percent is pyritic, 1.39 percent is organic, and 0.04 percent is sulfate. The weighted average sulfur content based on thickness of the coal is 4.94 percent as received of which 3.37 percent is pyritic, 1.53 per cent is organic, and 0.04 percent is sulfate. The coals studied may be classified as high volatile bituminous. They have an arithmetic mean of 35.9 percent volatile matter and 13.8 percent moisture as received. The arithmetic mean of the fixed carbon content is 36.1 percent. Ash content is quite variable and ranges from 3.6 to 25.9 percent with an arithmetic mean of 11.9 percent. The maceral groups of vitrinite, inertinite, and exinite as well as mineral matter were identified and counted under reflected light from polished particulate sections of each of the 43 coal samples. This is the first time that such work has been done in Missouri. Vitrinite is the major maceral group present in the coals with an arithmetic mean of 80.1 percent. The vitrinite content of the coals increases irregularly towards the west in the study area. Inertinite has an arithmetic mean of 4.9 percent and exinite has an arithmetic mean of 2.5 per cent. Mineral matter is the second highest overall of the microscopic components studied, with an arithmetic mean of 12.5 percent. Practical uses of coal petrography in exploration and exploitation of coal mine lands are suggested. Other practical applications such as coal correlation, cost estimates in mining, and coal preparation are briefly described. A quantitative analysis was made of 74 elements with a mass spectrometer from seven selected coals. This was done by the U.S. Bureau of Mines at the request of the Missouri Geological Survey for this study. Most elements occur in the total coal sample in less concentration than the average amount of the same element found in crustal rocks of the earth. Sulfur, boron, silver, selenium, molybdenum, iodine, germanium, arsenic, and antimony are enriched in the total coal relative to the abundance of these nine elements in crustal rocks. The enrichment ratio ranges from 2 (antimony and arsenic) to 65 (sulfur) --Abstract, pages ii-iii

[Work in progress] Scalable, out-of-the box segmentation of individual particles from mineral samples acquired with micro CT

Minerals are indispensable for a functioning modern society. Yet, their supply is limited causing a need for optimizing their exploration and extraction both from ores and recyclable materials. Typically, these processes must be meticulously adapted to the precise properties of the processed particles, an extensive characterization of their shapes, appearances as well as the overall material composition. Current approaches perform this analysis based on bulk segmentation and characterization of particles imaged with a micro CT, and rely on rudimentary postprocessing techniques to separate touching particles. However, due to their inability to reliably perform this separation as well as the need to retrain or reconfigure methods for each new image, these approaches leave untapped potential to be leveraged. Here, we propose ParticleSeg3D, an instance segmentation method that is able to extract individual particles from large micro CT images taken from mineral samples embedded in an epoxy matrix. Our approach is based on the powerful nnU-Net framework, introduces a particle size normalization, makes use of a border-core representation to enable instance segmentation and is trained with a large dataset containing particles of numerous different materials and minerals. We demonstrate that ParticleSeg3D can be applied out-of-the box to a large variety of particle types, including materials and appearances that have not been part of the training set. Thus, no further manual annotations and retraining are required when applying the method to new mineral samples, enabling substantially higher scalability of experiments than existing methods. Our code and dataset are made publicly available

Characterization of dispersive and distributive mixing in a co-rotating twin-screw compounding extruder

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.A new design of closely intermeshing co-rotating twin-screw compounding extruder, developed at Brunel University, has been utilized in the development of quantitative techniques for characterization of dispersive and distributive mixing in thermoplastics materials prepared by extrusion compounding. Image analysis procedures were used to quantify mixing of polypropylene composites containing calcium carbonate filler using reflected light microscopy on polished surfaces, and transmitted light microscopy of microtomed pigmented sections. Stereological statistics have been applied to raw sample data; results are discussed in relation to mechanistic phenomena influencing particle agglomeration, dispersion and distribution of fillers in thermoplastics. Dispersive or intensive mixing determined from calcium carbonate filled polypropylene specimens showed that processing parameters had no significant influence except when filler was added midway along the machine although the melting zone was highlighted as having a marked effect on the rate of filler dispersion. Premixing of filler and polymer introduced additional agglomeration into the filler. A series of model experiments were undertaken to assess the influence of specific parameters. In this context moisture content emerged as having the single most important effect on filler compaction. Distributive or extensive mixing of carbon black pigmented specimens was very significantly affected by the presence of segmented disc elements at the end of the screws. These elements produced more than a six-fold increase in distributive mixing in the extrudate.Polymer Engineering Directorate of the Science and Engineering Research Council; Croxton and Garry Ltd

Reflection High-Energy Electron Diffraction Studies of Indium Phosphide (100) and Growth on Indium and Indium Nitride on Silicon (100)

Study of the effects of atomic hydrogen exposure on structure and morphology of semiconductor surfaces is important for fundamental properties and applications. In this dissertation, the electron yield of a hydrogen-cleaned indium phosphide (InP) surface was measured and correlated to the development of the surface morphology, which was monitored by in situ reflection high-energy electron diffraction (RHEED). Atomic hydrogen treatment produced a clean, well-ordered, and (2x4)-reconstructed InP(100) surface. The quantum efficiency, after activation to negative electron affinity, and the secondary electron emission were shown to increase with hydrogen cleaning time. RHEED patterns of low-index InP(100) surface were modified by the step structure and resulted in splitting of the specular beam at the out-of-phase diffraction condition. Quantitative RHEED showed reduction in the average terrace width and a decrease of the adatom-vacancy density with hydrogen exposure. This suggests that atomic hydrogen etching occurs preferentially at terrace edges, and thermal diffusion on the surface causes changes in the terrace edge morphology, which result in the observed decrease in the average terrace width. The results show that the decrease in the surface disorder, measured from the RHEED intensity-to-background ratio, correlated with the increased quantum efficiency. The growth of group-III metals on Si surfaces has become an attractive area of research because of its scientific importance and great potential in technological applications. In this work, the growth dynamics, structure, and morphology of indium (In) on a vicinal Si(100)-(2×1) surface by femtosecond pulsed laser deposition (fsPLD) were studied using in situ RHEED and ex situ atomic force microscopy. Indium was found to grow on Si(100) by the Stranski-Krastanove mode. At room temperature, the initial growth formed strained two-dimensional (2D) layers in the In(2×1) structure followed by growth of three-dimensional islands. During the 2D growth, the surface diffusion coefficient of deposited In on the In(2×1) layer was estimated to be in the order of 10−14 cm2/s, from recovery of the RHEED intensity. This was attributed to surface diffusion of In clusters by step flow mode. The results suggest that fsPLD of In removed the reconstruction of the Si(100)-(2×1) surface in the early growth and resulted in the initial In(2x1) structure. Next, growth of In on Si(100)-(2×1) was studied at temperature of 350–420°C and showed formation of In(4×3) structure. The growth stages, probed by RHEED intensity relaxation, proceed in a two-step process, formation of small In clusters and surface diffusion to the terrace step edges with activation energy of 1.4±0.2 eV and diffusion rate constant of 1.0±0.1x1011 s −1. The terrace width dynamics and the related surface processes were studied during growth of the In(4×3) phase with increase in film coverage. Finally, the fsPLD was used to grow nitride films of InN on Si(100) substrates. A buffer layer of In was grown on Si(100) by fsPLD prior to growth of InN and different nitridation procedures were used