A novel end-to-end deep convolutional neural network based skin lesion classification framework

Background: Skin diseases are reported to contribute 1.79\% of the global burden of disease. The accurate diagnosis of specific skin diseases is known to be a challenging task due, in part, to variations in skin tone, texture, body hair, etc. Classification of skin lesions using machine learning is a demanding task, due to the varying shapes, sizes, colors, and vague boundaries of some lesions. The use of deep learning for the classification of skin lesion images has been shown to help diagnose the disease at its early stages. Recent studies have demonstrated that these models perform well in skin detection tasks, with high accuracy and efficiency. Objective: Our paper proposes an end-to-end framework for skin lesion classification, and our contributions are two-fold. Firstly, two fundamentally different algorithms are proposed for segmenting and extracting features from images during image preprocessing. Secondly, we present a deep convolutional neural network model, S-MobileNet that aims to classify 7 different types of skin lesions. Methods: We used the HAM10000 dataset, which consists of 10000 dermatoscopic images from different populations and is publicly available through the International Skin Imaging Collaboration (ISIC) Archive. The image data was preprocessed to make it suitable for modeling. Exploratory data analysis (EDA) was performed to understand various attributes and their relationships within the dataset. A modified version of a Gaussian filtering algorithm and SFTA was applied for image segmentation and feature extraction. The processed dataset was then fed into the S-MobileNet model. This model was designed to be lightweight and was analysed in three dimensions: using the Relu Activation function, the Mish activation function, and applying compression at intermediary layers. In addition, an alternative approach for compressing layers in the S-MobileNet architecture was applied to ensure a lightweight model that does not compromise on performance. Results: The model was trained using several experiments and assessed using various performance measures, including, loss, accuracy, precision, and the F1-score. Our results demonstrate an improvement in model performance when applying a preprocessing technique. The Mish activation function was shown to outperform Relu. Further, the classification accuracy of the compressed S-MobileNet was shown to outperform S-MobileNet. Conclusions: To conclude, our findings have shown that our proposed deep learning-based S-MobileNet model is the optimal approach for classifying skin lesion images in the HAM10000 dataset. In the future, our approach could be adapted and applied to other datasets, and validated to develop a skin lesion framework that can be utilised in real-time

Uphononongo lwamava omfundi, umzali kunye notitshala kwiziphazamisi ezingapheliyo zolusu nezifo zalo (chronic dermatological disorders) njengezithinteli ekufundeni

Abstract in English, Afrikaans and XhosaThe researcher observed that her son experienced his dermatological disorder as a barrier to learning. This personal experience made her wonder whether this might apply in the case of other learners too, and from this the aim of the research, namely to discover the extent to which dermatological disorders influence learning, was born. A qualitative case study involving interviews and questionnaires to explore the views of learners, parents, and teachers regarding chronic dermatological disorders was used. The findings indicated that while learning is indeed influenced by chronic dermatological disorders, parents and teachers are supportive of learners with these disorders. The following recommendations were made to overcome the learning barriers caused by chronic dermatological disorders: the forming of support groups, the use of social media and technology, inclusive education, the training of teachers in inclusive education, the implementation of educational policies relating to the health of learners, and collaboration between parents and teachers. Patience, endurance, consistent treatment, and understanding the problem are key survival techniques for learners with chronic dermatological disorders.Die navorser het waargeneem dat haar seun sy dermatologiese versteuring as ’n leerstruikelblok ervaar het. Hierdie persoonlike ervaring het haar laat wonder of dit ook op ander leerders van toepassing kon wees, en daaruit het die doel van die navorsing ontstaan, naamlik om die mate te bepaal waarin dermatologiese versteurings leer beïnvloed. ’n Kwalitatiewe gevallestudie, wat onderhoude en vraelyste behels het om die menings van leerders, ouers en onderwysers oor chroniese dermatologiese versteurings te verken, is gebruik. Die bevindings het daarop gedui dat, hoewel leer inderdaad deur chroniese dermatologiese versteurings beïnvloed word, ouers en onderwysers leerders met hierdie versteurings ondersteun. Die volgende aanbevelings is gemaak om die leerstruikelblokke wat deur chroniese dermatologiese versteurings veroorsaak word, te bowe te kom: die vestiging van steungroepe, die gebruik van sosiale media en tegnologie, inklusiewe onderwys, die opleiding van onderwys in inklusiewe onderwys, die inwerkingstelling van opvoedkundige beleide rakende die gesondheid van leerders, en samewerking tussen ouers en onderwysers. Geduld, volharding, konsekwente hantering, en begrip vir die probleem is belangrike oorlewingstegnieke vir leerders met chroniese dermatologiese versteurings.Umphandi ufumanise ukuba isithinteli esiphazamisa unyana wakhe solusu nezifo zalo sisithinteli ekufundeni kwakhe. La mava angawakhe amenze wazibuza ukuba ingaba oku kuyenzeka na nakwabanye abafundi, kwaze ukususela koku, injongo yophando ivele ekufumaniseni ubungakanani bempembelelo yezi ziphazamisi zolusu nezifo zalo ekufundeni. Kusetyenziswe ufundo-nzulu olwaziwa njenge-Qualitative case study oluquka udliwano-ndlebe kunye neencwadana zemibuzo ekuphononongeni iimbono zabafundi, abazali kunye nootitshala malunga neziphazamisi ezingapheliyo zolusu nezifo zalo. Okufunyenweyo kubonakalise ukuba nangona enyanisweni, ukufunda kunempembelelo kwiziphazamisi ezingapheliyo zolusu nezifo zalo, abazali nootitshala baya baxhasa abafundi abanazo ezi ziphazamisi. Ezi zindululo zilandelayo zenziwe ekoyiseni izithenteli zokufunda ezibangela iziphazamisi ezingapheliyo zolusu nezifo zalo: ukusekwa kwamaqela enkxaso, ukusetyenziswa kwamajelo oqhagamshelwano nge-intanethi nobuchwepheshe, imfundo equkwayo, ukuzalisekiswa kwemigaqo-nkqubo yemfundo enxulumene nempilo yabafundi kwakunye nentsebenziswano phakathi kwabazali nootitshala. Umonde, ukunyamezela, unyango olungaguqukiyo kunye nokuqonda ingxaki bobona buchule obuphambili empilweni yabafundi abaneziphazamisi ezingapheliyo zolusu nezifo zalo.Psychology of EducationM. Ed. (Psychology of Education

Tenascin-C: a marker and driver of inflammation

Tenascin-C, the founding member of the matricellular tenascin family, is a large multifunctional hexameric extracellular matrix (ECM) glycoprotein. It is abundantly expressed in the developing embryo but its expression becomes tightly regulated in the adult. However, during inflammatory responses tenascin-C becomes highly upregulated where it acts to create a local pro-inflammatory ‘niche’. In this proinflammatory role tenascin-C has been implicated in the pathogenesis of a variety of chronic inflammatory diseases including rheumatoid arthritis (RA) and inflammatory bowel disease (IBD), both of which are characterised by upregulated tenascin-C locally and systemically. The work of this thesis has looked to expand upon this earlier work, identifying tenascin-C as a key driver as well as marker of inflammation, and further probe its mechanistic role in the inflammatory response and utility as a biomarker of inflammatory disease. To answer the first question regarding tenascin-C’s role in pathological inflammation a murine Dextran Sulphate Sodium (DSS) model of chemically induced colitis was utilised. This thesis details the spatial and temporal expression of tenascin-C in the colon under basal conditions as well as the inflammatory state of the DSS model. Tenascin-C demonstrated a marked upregulation within the inflamed mucosa coinciding with the upregulation of other pro-inflammatory mediators and immune cell infiltration. Following this descriptive characterisation, subsequent studies probed the mechanistic relevance of this upregulation utilising the same model in combination with a tenascin-C knockout mouse. These studies showed a protective effect of tenascin-C’s genetic ablation on the severity of the colitis induced. This included reductions in gross pathology as well as histopathology including lower inflammation and tissue damage observed during the acute stage. Finally, with this mechanistic link clearly established between tenascin-C and the inflammatory diseased state this thesis aimed to explore tenascin-Cs utility as a disease marker, with a focus on RA. To this end, a number of novel immunoassays were established and validated for the measurement of tenascin-C and autoantibodies against in human serum samples. Screening of serum samples with these assays showed significantly higher levels of tenascin-C or autoantibodies against it in the serum of RA patients compared to healthy controls. These changes were not entirely RA specific however with a number of other inflammatory diseases tested also showing higher serum tenascin-C levels. The work described herein has utilised the DSS colitis model in combination with tenascin-C knockout mice to demonstrate the role of tenascin-C as a driver of inflammatory disease and has further shown translational relevance as a disease marker in human patients

Pain, sensation and biological responses following human skin puncture with microneedles

Future work should optimise the design of microneedle devices for clinical delivery of active molecules

Surgical site infection following major lower limb amputation : analysing the clinical effectiveness of antibiotic prophylaxis duration and skin preparation

Background: Major LLA remains a common operation in the United Kingdom with ⁓5000 procedures performed yearly. Amputations are described as ‘clean surgery’ and SSIs in this patient cohort have been previously under-reported. The true incidence lies between 13-35% and is associated with patient mortality, morbidity and implications on health economics. Previous work done in this thesis has demonstrated lack of consensus in clinical practice regarding perioperative antibiotic prophylaxis, and lack of high quality studies to formulate and sustain a common practice across the UK.Methods: A single centre RCT was designed to which a total of 161 patients were recruited and randomised to receive either a 5-day or a 24-hour prophylactic antibiotic course. Within the groups further allocation to skin preparation (alcoholic chlorhexidine Vs. alcoholic povidone iodine) was performed by stratification.Results: A total of 153 patients were included in the final analysis. Groups were well matched for comorbidities and demographics. The use of a 5-day course was associated with a statistically significant lower incidence of SSI(n=9, 11.5%) when compared to the 24-hour group (n=27, 36%) (P<0.001) and lower incidence of IWH(n=20, 25.6% Vs. n=40, 53.3% respectively) (P<0.001). History of diabetes, smoking, and transmetatarsal amputations performed, were statistically significant independent factors associated with an increase in SSI incidence (P=0.018, P=0.005, and P<0.001 respectively). Choice of skin preparation between alcoholic chlorhexidine and povidone iodine had no effect on the incidence of SSI / IWH (P=0.851 and P=0.326 respectively). The presence of SSI statistically significantly increased the post-operative length of hospital stay (from median 14 to 28 days, P=0.015)Conclusions: This is a Level 1 study which demonstrated that the use of a 5-day over a 24-hour antibiotic course can significantly reduce incidence and risk of SSI/IWH development. It has also highlighted 3 independent factors, 2 of which could be addressed during the preoperative optimisation stage to reduce the risk of developing an SSI post-operatively. The presence of SSI is associated with prolonged hospital stay, something which has significant implications on patient morbidity as well as incurring significant costs on healthcare resources.[Includes two articles published in Annals of vascular surgery (pages 254-267 of thesis, removed):https://doi.org/10.1016/j.avsg.2014.06.055 - A survey of perioperative management of major lower limb amputations : current UK practicehttps://doi.org/10.1016/j.avsg.2013.10.017 - The impact of previous surgery and revisions on outcome after major lower limb amputation

Evaluation of PD-L1 expression in various formalin-fixed paraffin embedded tumour tissue samples using SP263, SP142 and QR1 antibody clones

Background & objectives: Cancer cells can avoid immune destruction through the inhibitory ligand PD-L1. PD-1 is a surface cell receptor, part of the immunoglobulin family. Its ligand PD-L1 is expressed by tumour cells and stromal tumour infltrating lymphocytes (TIL). Methods: Forty-four cancer cases were included in this study (24 triple-negative breast cancers (TNBC), 10 non-small cell lung cancer (NSCLC) and 10 malignant melanoma cases). Three clones of monoclonal primary antibodies were compared: QR1 (Quartett), SP 142 and SP263 (Ventana). For visualization, ultraView Universal DAB Detection Kit from Ventana was used on an automated platform for immunohistochemical staining Ventana BenchMark GX. Results: Comparing the sensitivity of two different clones on same tissue samples from TNBC, we found that the QR1 clone gave higher percentage of positive cells than clone SP142, but there was no statistically significant difference. Comparing the sensitivity of two different clones on same tissue samples from malignant melanoma, the SP263 clone gave higher percentage of positive cells than the QR1 clone, but again the difference was not statistically significant. Comparing the sensitivity of two different clones on same tissue samples from NSCLC, we found higher percentage of positive cells using the QR1 clone in comparison with the SP142 clone, but once again, the difference was not statistically significant. Conclusion: The three different antibody clones from two manufacturers Ventana and Quartett, gave comparable results with no statistically significant difference in staining intensity/ percentage of positive tumour and/or immune cells. Therefore, different PD-L1 clones from different manufacturers can potentially be used to evaluate the PD- L1 status in different tumour tissues. Due to the serious implications of the PD-L1 analysis in further treatment decisions for cancer patients, every antibody clone, staining protocol and evaluation process should be carefully and meticulously validated