Using customised image processing for noise reduction to extract data from early 20th century African newspapers

A research report submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Science in Engineering, 2017The images from the African articles dataset presented challenges to the Optical Character Recognition (OCR) tool. Despite successful binerisation in the Image Processing step of the pipeline, noise remained in the foreground of the images. This noise caused the OCR tool to misinterpret the text from the images and thus needed removal from the foreground. The technique involved the application of the Maximally Stable Extremal Region (MSER) algorithm, borrowed from Scene-Text Detection, and supervised machine learning classifiers. The algorithm creates regions from the foreground elements. Regions are classifiable into noise and characters based on the characteristics of their shapes. Classifiers were trained to recognise noise and characters. The technique is useful for a researcher wanting to process and analyse the large dataset. They could semi-automate the foreground noise-removal process using this technique. This would allow for better quality OCR output, for use in the Text Analysis step of the pipeline. Better OCR quality means less compromises would be required at the Text Analysis step. These concessions can lead to false results when searching noisy text. Fewer compromises means simpler, less error-prone analysis and more trustworthy results. The technique was tested against specifically selected images from the dataset which exhibited noise. It involved a number of steps. Training regions were selected and manually classified. After training and running many classifiers, the highest performing classifier was selected. The classifier categorised regions from all images. New images were created by removing noise regions from the original images. To discover whether an improvement in the OCR output was achieved, a text comparison was conducted. OCR text was generated from both the original and processed images. The two outputs of each image were compared for similarity against the test text. The test text was a manually created version of the expected OCR output per image. The similarity test for both original and processed images produced a score. A change in the similarity score indicated whether the technique had successfully removed noise or not. The test results showed that blotches in the foreground could be removed, and OCR output improved. Bleed-through and page fold noise was not removable. For images affected by noise blotches, this technique can be applied and hence less concessions will be needed when processing the text generated from those images.CK201

Nucleosome positioning in Arabidopsis

The aim of this project was to test hypotheses relating to nucleosome positioning in Arabidopsis to provide a basis for better understanding of epigenetic transcriptional regulation in plants. Prior to this study, virtually no information existed regarding nucleosome positioning in plants. Eukaryote chromosomes consist of chromatin, composed of nucleosomes separated by linker DNA of variable lengths. Nucleosomes consist of 147 bp of DNA wrapped 1.7 times around a histone octamer. Whilst no consensus nucleosome positioning DNA sequence exists, sequence preferences influence positioning, and contribute to the complex epigenetic processes which act to control transcriptional activity. These details of the underlying mechanisms are known to differ between the plant and animal kingdoms. High-throughput sequencing technologies were utilised to generate large datasets of mono- and di-nucleosome sequences from wild-type Arabidopsis. These enabled genome-wide analysis and inference of plant-specific patterns of nucleosome positioning and sequence properties. Further data were generated from a methyltransferase antisense (MET1) which is depleted in methylated CG epigenetic marks. The internal distributions of dinucleotides within Arabidopsis nucleosomes were similar to those observed in non-plant eukaryotes. A unique periodicity in the distribution of linker lengths was detected in Arabidopsis wild type chromatin. In contrast, the MET1 antisense line displayed the expected periodicity, indicating systematic differences in chromatin organisation. There was a significant increase in nucleosome occupancy within exons compared with introns. However, this difference was less marked in the MET1 antisense. Specific patterns of nucleosome phasing were observed around transcription start sites. Linker lengths within rRNA gene clusters associated with nucleolar organiser regions (NORs) differed depending on chromosome of origin, suggesting differences in higher order chromatin structure between the NORs. Comparison of the nucleosome position and DNA methylation within the rRNA gene cluster revealed interesting differences between the two regions, which may reflect interactions affecting chromatin structure and transcriptional regulation

Incoherent light in tapered graded-index fibre: a study of transmission and modal noise

© 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license, http://creativecommons.org/licenses/by/4.0/We investigated the impact of taper length on light transmission through tapered graded-index fibres. We tested commercial fibres from Thorlabs and a custom graded-index fibre using both coherent and incoherent light sources. Our experimental results show optimum performance for taper transition lengths of 25 mm, although our simulations suggest further improvement may be possible for even shorter transition lengths. We also measured the modal noise power fluctuations caused by bending the fibre. Here, we observe that the custom fibre tapers have the highest transmission but suffer from the most modal noise. Accordingly, we find that the commercial graded-index fibre tapers promise practical usage as a beam mode-field converter, as they have lower power fluctuations but retain relatively high transmission if compared to commercial small core step-index fibre.Peer reviewe

Modifying the lipid content and composition of plant seeds: engineering the production of LC-PUFA

Omega-3 fatty acids are characterized by a double bond at the third carbon atom from the end of the carbon chain. Latterly, long chain polyunsaturated omega-3 fatty acids such as eicosapentaenoic acid (EPA; 20:5Δ5,8,11,14,17) and docosahexanoic acid (DHA; 22:6 Δ4,7,10,13,16,19), which typically only enter the human diet via the consumption of oily fish, have attracted much attention. The health benefits of the omega-3 LC-PUFAs EPA and DHA are now well established. Given the desire for a sustainable supply of omega-LC-PUFA, efforts have focused on enhancing the composition of vegetable oils to include these important fatty acids. Specifically, EPA and DHA have been the focus of much study, with the ultimate goal of producing a terrestrial plant-based source of these so-called fish oils. Over the last decade, many genes encoding the primary LC-PUFA biosynthetic activities have been identified and characterized. This has allowed the reconstitution of the LC-PUFA biosynthetic pathway in oilseed crops, producing transgenic plants engineered to accumulate omega-3 LC-PUFA to levels similar to that found in fish oil. In this review, we will describe the most recent developments in this field and the challenges of overwriting endogenous seed lipid metabolism to maximize the accumulation of these important fatty acids

The supply of fish oil to aquaculture: a role for transgenic oilseed crops?

The importance of an alternative and sustainable supply of omega-3 long chain polyunsaturated fatty acids (LC omega-3) has long been established. As these biologically active fatty acids have a role in nutrition and health, there is an ever increasing demand for oils containing LC omega-3 e.g. eicosapentaenoic (EPA) and docosahexaenoic acid (DHA). These fatty acids are produced by micoroganisms and enter our diet through the consumption of fish. However, in order that the nutritional requirements of fish in aquaculture are met and sufficient levels are deposited to meet the requirements of human consumers, EPA and DHA must be supplied in excess. Given the importance of the aquaculture industry in delivering healthy foodstuff, the question of how to resource the supply of LC omega-3 then arises; traditional sources of EPA and DHA (fish oil) are challenged, whilst vegetable oils do not contain EPA or DHA. Therefore research efforts have focused on the successful reconstitution of LC omega-3 biosynthesis in oilseed crops. The production of EPA and DHA in the seed oil of agricultural crops has the capacity to deliver large volumes of these fatty acids. The expression of optimised combinations of the genes required to produce these fatty acids in the seed of the crop Camelina sativa has been achieved and the utility of this approach demonstrated. This represents a significant breakthrough – the provision of an effective alternative to the use of omega-3 fish oil by the global aquaculture industry

A transgenic Camelina sativa seed oil effectively replaces fish oil as a dietary source of eicosapentaenoic acid in mice

Background: Fish currently supplies only 40% of the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) required to allow all individuals globally to meet the minimum intake recommendation of 500 mg/d. Therefore, alternative sustainable sources are needed. Objective: The main objective was to investigate the ability of genetically engineered Camelina sativa (20% EPA) oil (CO) to enrich tissue EPA and DHA relative to an EPA-rich fish oil (FO) in mammals. Methods: Six-week-old male C57BL/6J mice were fed for 10 wk either a palm oil–containing control (C) diet or diets supplemented with EPA-CO or FO, with the C, low-EPA CO (COL), high-EPA CO (COH), low-EPA FO (FOL), and high-EPA FO (FOH) diets providing 0, 0.4, 3.4, 0.3, and 2.9 g EPA/kg diet, respectively. Liver, muscle, and brain were collected for fatty acid analysis, and blood glucose and serum lipids were quantified. The expression of selected hepatic genes involved in EPA and DHA biosynthesis and in modulating their cellular impact was determined. Results: The oils were well tolerated, with significantly greater weight gain in the COH and FOH groups relative to the C group (P < 0.001). Significantly lower (36–38%) blood glucose concentrations were evident in the FOH and COH mice relative to C mice (P < 0.01). Hepatic EPA concentrations were higher in all EPA groups relative to the C group (P < 0.001), with concentrations of 0.0, 0.4, 2.9, 0.2, and 3.6 g/100 g liver total lipids in the C, COL, COH, FOL, and FOH groups, respectively. Comparable dose-independent enrichments of liver DHA were observed in mice fed CO and FO diets (P < 0.001). Relative to the C group, lower fatty acid desaturase 1 (Fads1) expression (P < 0.005) was observed in the COH and FOH groups. Higher fatty acid desaturase 2 (Fads2), peroxisome proliferator–activated receptor α (Ppara), and peroxisome proliferator–activated receptor γ (Pparg) (P < 0.005) expressions were induced by CO. No impact of treatment on liver X receptor α (Lxra) or sterol regulatory element-binding protein 1c (Srebp1c) was evident. Conclusions: Oil from transgenic Camelina is a bioavailable source of EPA in mice. These data provide support for the future assessment of this oil in a human feeding trial

A nutritionally-enhanced oil from transgenic Camelina sativa effectively replaces fish oil as a source of eicosapentaenoic acid for fish

For humans a daily intake of up to 500mg omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA) is recommended, amounting to an annual requirement of 1.25 million metric tonnes (mt) for a population of 7 billion people. The annual global supply of n-3 LC-PUFA cannot meet this level of requirement and so there is a large gap between supply and demand. The dietary source of n-3 LC-PUFA, fish and seafood, is increasingly provided by aquaculture but using fish oil in feeds to supply n-3 LC-PUFA is unsustainable. Therefore, new sources of n-3 LC-PUFA are required to supply the demand from aquaculture and direct human consumption. One approach is metabolically engineering oilseed crops to synthesize n-3 LC-PUFA in seeds. Transgenic Camelina sativa expressing algal genes was used to produce an oil containing n-3 LC-PUFA to replace fish oil in salmon feeds. The oil had no detrimental effects on fish performance, metabolic responses or the nutritional quality of the fillets of the farmed fish

Nutritional evaluation of an EPA-DHA oil from transgenic Camelina sativa in feeds for post-smolt Atlantic salmon (Salmo salar L.)

Vegetable oils (VO) are possible substitutes for fish oil in aquafeeds but their use is limited by their lack of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA). However, oilseed crops can be modified to produce n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, representing a potential option to fill the gap between supply and demand of these important nutrients. Camelina sativa was metabolically engineered to produce a seed oil with around 15 % total n-3 LC-PUFA to potentially substitute for fish oil in salmon feeds. Post-smolt Atlantic salmon (Salmo salar) were fed for 11-weeks with one of three experimental diets containing either fish oil (FO), wild-type Camelina oil (WCO) or transgenic Camelina oil (DCO) as added lipid source to evaluate fish performance, nutrient digestibility, tissue n-3 LC-PUFA, and metabolic impact determined by liver transcriptome analysis. The DCO diet did not affect any of the performance or health parameters studied and enhanced apparent digestibility of EPA and DHA compared to the WCO diet. The level of total n-3 LC-PUFA was higher in all the tissues of DCO-fed fish than in WCO-fed fish with levels in liver similar to those in fish fed FO. Endogenous LC-PUFA biosynthetic activity was observed in fish fed both the Camelina oil diets as indicated by the liver transcriptome and levels of intermediate metabolites such as docosapentaenoic acid, with data suggesting that the dietary combination of EPA and DHA inhibited desaturation and elongation activities. Expression of genes involved in phospholipid and triacylglycerol metabolism followed a similar pattern in fish fed DCO and WCO despite the difference in n-3 LC-PUFA contents

Evaluation of a high-EPA oil from transgenic Camelina sativa in feeds for Atlantic salmon (Salmo salar L.): Effects on tissue fatty acid composition, histology and gene expression

Currently, one alternative for dietary fish oil (FO) in aquafeeds is vegetable oils (VO) that are devoid of omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFAs). Entirely new sources of n-3 LC-PUFA such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids through de novo production are a potential solution to fill the gap between supply and demand of these important nutrients. Camelina sativa was metabolically engineered to produce a seed oil (ECO) with N20% EPA and its potential to substitute for FO in Atlantic salmon feeds was tested. Fish were fed with one of the three experimental diets containing FO, wild-type camelina oil (WCO) or ECO as the sole lipid sources for 7 weeks. Inclusion of ECO did not affect any of the performance parameters studied and enhanced apparent digestibility of individual n-6 and n-3 PUFA compared to dietaryWCO. High levels of EPA were maintained in brain, liver and intestine (pyloric caeca), and levels of DPA and DHA were increased in liver and intestine of fish fed ECO compared to fish fed WCO likely due to increased LC-PUFA biosynthesis based on up-regulation of the genes. Fish fed ECO showed slight lipid accumulation within hepatocytes similar to that with WCO, although not significantly different to fish fed FO. The regulation of a small number of genes could be attributed to the specific effect of ECO (311 features) with metabolismbeing the most affected category. The EPA oil from transgenic Camelina (ECO) could be used as a substitute for FO, however it is a hybrid oil containing both FO (EPA) and VO (18:2n-6) fatty acid signatures that resulted in similarly mixed metabolic and physiological responses

Mitigating Modal Noise in Multimode Circular Fibres by Optical Agitation using a Galvanometer

© 2024 The Author(s). Published by Oxford University Press on behalf of Royal Astronomical Society. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Modal noise appears due to the non-uniform and unstable distribution of light intensity among the finite number of modes in multimode fibres. It is an important limiting factor in measuring radial velocity precisely by fibre-fed high-resolution spectrographs. The problem can become particularly severe as the fibre's core become smaller and the number of modes that can propagate reduces. Thus, mitigating modal noise in relatively small core fibres still remains a challenge. We present here a novel technique to suppress modal noise. Two movable mirrors in the form of a galvanometer reimage the mode-pattern of an input fibre to an output fibre. The mixing of modes coupled to the output fibre can be controlled by the movement of mirrors applying two sinusoidal signals through a voltage generator. We test the technique for four multimode circular fibres: 10 and 50 micron step-index, 50 micron graded-index, and a combination of 50 micron graded-index and 5:1 tapered fibres (GI50t). We present the results of mode suppression both in terms of the direct image of the output fibre and spectrum of white light obtained with the high-resolution spectrograph. We found that the galvanometer mitigated modal noise in all the tested fibres, but was most useful for smaller core fibres. However, there is a trade-off between the modal noise reduction and light-loss. The GI50t provides the best result with about 60% mitigation of modal noise at a cost of about 5% output light-loss. Our solution is easy to use and can be implemented in fibre-fed spectrographs.Peer reviewe