A Biased Topic Modeling Approach for Case Control Study from Health Related Social Media Postings

abstract: Online social networks are the hubs of social activity in cyberspace, and using them to exchange knowledge, experiences, and opinions is common. In this work, an advanced topic modeling framework is designed to analyse complex longitudinal health information from social media with minimal human annotation, and Adverse Drug Events and Reaction (ADR) information is extracted and automatically processed by using a biased topic modeling method. This framework improves and extends existing topic modelling algorithms that incorporate background knowledge. Using this approach, background knowledge such as ADR terms and other biomedical knowledge can be incorporated during the text mining process, with scores which indicate the presence of ADR being generated. A case control study has been performed on a data set of twitter timelines of women that announced their pregnancy, the goals of the study is to compare the ADR risk of medication usage from each medication category during the pregnancy. In addition, to evaluate the prediction power of this approach, another important aspect of personalized medicine was addressed: the prediction of medication usage through the identification of risk groups. During the prediction process, the health information from Twitter timeline, such as diseases, symptoms, treatments, effects, and etc., is summarized by the topic modelling processes and the summarization results is used for prediction. Dimension reduction and topic similarity measurement are integrated into this framework for timeline classification and prediction. This work could be applied to provide guidelines for FDA drug risk categories. Currently, this process is done based on laboratory results and reported cases. Finally, a multi-dimensional text data warehouse (MTD) to manage the output from the topic modelling is proposed. Some attempts have been also made to incorporate topic structure (ontology) and the MTD hierarchy. Results demonstrate that proposed methods show promise and this system represents a low-cost approach for drug safety early warning.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Exposure Assessment of Listeria Monocytogenes in Vacuum Packed Cold-smoked Salmon in the Republic of Ireland

Contamination of cold-smoked salmon with Listeria monocytogenes, a bacterium causing listeriosis, presents a risk to consumer health. The overall aim of this thesis was to investigate the prevalence and source of L. monocytogenes in different stages of vacuum packed cold-smoked salmon production chain/retail market and to develop a risk assessment model to quantitatively assess the risk of human listeriosis upon consumption of vacuum packed cold-smoked salmon. The study necessitated the identification of novel isolation techniques for the isolation and quantification of L. monocytogenes in vacuum packed cold-smoked salmon. The techniques currently used in isolation of L. monocytogenes from ready-to-eat food (EN/ISO 11290-01 and -02) were evaluated and were found to be 64 % effective in isolating L. monocytogenes. Use of 16S rRNA gene sequence analysis and molecular fingerprinting method multi-locus variable number tandem repeat analysis (MLVA) in combination with EN/ISO 11290-01 and -02 was found to be more effective (98 %) in quantification of L. monocytogenes in vacuum packed cold-smoked salmon. The prevalence of L. monocytogenes in five brands of vacuum packed cold-smoked salmon (n = 120) marketed in different retail outlets in the Republic of Ireland was 21.60%.The prevalence of L. monocytogenes surveyed in a vacuum packed cold-smoked salmon factory (n = 444) was 24.54 %. The final product (vacuum packed cold-smoked salmon) was contaminated with three major types of L. monocytogenes; one type originating from the raw material and the others colonising the production line. To validate these routes of contamination, 60 raw salmon were tagged and sampled after each stage of processing, the results showed that the final product was contaminated with 3 strain types of L. monocytogenes isolated from raw, curing and filleting stages of cold-smoking respectively. The prevalence and tagging results indicate the current ubiquitous nature of L. monocytogenes in vacuum packed cold-smoked salmon A product specific model was developed and validated under dynamic temperature conditions to predict the growth of L. monocytogenes in cold-smoked salmon taking into account the retail and consumer phases of the food pathways. The values of bias factor and accuracy factorof the modelwere close to unity, indicating good agreement between observations and predictions of the model. Finally a quantitative Monte Carlo risk assessment model was developed to assess likely human exposure and the probability of human illness by L. monocytogenes on cold-smoked iii salmon in Ireland. A surveillance study conducted at the retail level served as the starting point for the model with a mean prevalence of L. monocytogenes in vacuum packed cold-smoked salmon of 21.60 % and a mean count on contaminated vacuum packed cold-smoked salmon of 2.60 log10 CFU/g (95 % confidence interval 0.00 – 4.53 log10 CFU/g). The model predicted the annual log probability of illness by consuming contaminated vacuum packed cold-smoked salmon in a low risk and high risk population, with mean values -5.76 and -1.63, respectively (assuming weekly consumption). The model sensitivity analysis highlights the importance of reducing the initial contamination levels of L. monocytogenes on raw fish and the maintenance of proper storage conditions. Various ‗what-if‘ scenarios were studied to assess the likely impact on the log probability of illness per serving. Careful control of consumer storage temperature and time were identified as the best strategies to decrease the probability of illness. In conclusion, the results from this study indicated that sub-typing of the different strains using MLVA implicated a possible carryover of L. monocytogenes from the raw fish and in-house strain to the final product. Therefore, suitable processing parameters and pre- processing handling practices should be treated as important control measures to minimise the exposure to this pathogen. The product specific dynamic model developed in this study provides the sea food industry with a useful tool for effective management and optimization of product safety and may contribute to more realistic estimations of safety risks related to vacuum packed cold-smoked salmon. The results from the quantitative risk assessment developed in this thesis may help risk managers to make informed decisions with regard to possible control measures for L. monocytogenes in cold smoked salmon and therefore improve food safety

The use of precision cut lung slices and co-culture modelling to investigate the effect of human rhinovirus on cough and airway inflammation

Human Rhinovirus (hRV) is a major cause of upper respiratory tract infections (URTIs) and is linked to lower respiratory tract infections (LRTIs) and airway diseases exacerbations. Cough, airway inflammation and hypersensation are common symptoms of hRV infections however, the mechanisms involved remain elusive. A promising hypothesis is neuromodulation, whereby stimulation of transient receptor potential channels (TRPV4) in airway epithelial cells release ATP, subsequently activating the purinoreceptor P2X3 on vagal afferent nerve fibres. Here it is hypothesised that hRV infection will alter expression of channels and receptors known to be involved in cough and airway inflammation, causing lung tissue to become hyperresponsive to cough and bronchoconstrictive agents.A co-culture model of human airways using a lung epithelial cell line (A549 or Beas-2b) and astrocytes (1321N1 transfected with P2X3) to mimic neurones showed that activation of TRPV4 on lung epithelial cells led to ATP release which could evoke a measurable calcium influx into astrocytes. Additionally, A549 and Beas-2b cells responded differently to RV16 infection, with A549 cells exhibiting a reduced cytotoxicity, increased viability and proliferation compared to Beas-2b cells. Furthermore, RV16 infected ex vivo tissue showed limited impact on viability and cytotoxicity, reduced TEER measurements, increased bronchoconstriction and upregulated ICAM-1 protein expression. Finally, comparison of microfluidic devices to standard culture conditions demonstrated A549 cells could be cultured for 72 hours with similar rates of cell proliferation and viability, whilst PCLS could be cultured for 6 days with minimal impact on tissue viability or morphology.Overall, findings suggest that the TRPV4–ATP–P2X3 neuromodulation theory may play a role in the mechanism of cough and supports observations indicating hRV causes URTIs more frequently than LRTIs. Furthermore, hRV infection of ex vivo tissue appears promising as a model that can replicate in vivo and in vitro observations. Whilst the microfluidic devices used to replicate elements of the aforementioned models provide a promising start to better recapitulating the in vivo environment

Proceedings of the Salford Postgraduate Annual Research Conference (SPARC) 2011

These proceedings bring together a selection of papers from the 2011 Salford Postgraduate Annual Research Conference(SPARC). It includes papers from PhD students in the arts and social sciences, business, computing, science and engineering, education, environment, built environment and health sciences. Contributions from Salford researchers are published here alongside papers from students at the Universities of Anglia Ruskin, Birmingham City, Chester,De Montfort, Exeter, Leeds, Liverpool, Liverpool John Moores and Manchester

Restructuring the spaces under elevated expressways: a case study of the spaces below the Interstate-10 overpass at Perkins Road in Baton Rouge, Louisiana

General information about the development the United States Interstate System, different theories of urban design, and samples of projects developed under elevated highways structures were used to illustrate the issues associated to the development of elevated highway within urban areas. After building the framework for the study of the spaces below elevated highways a comprehensive study of the contextual, spatial, and functional characteristics of the spaces below the Interstate-10 at Perkins Road was conducted over a period of 9 months. As a result of this study a master plan was developed to addresses the issues affecting the spaces below the Interstate-10 overpass at Perkins Road and surrounding communities. The areas surrounding the Interstate-10 overpass are part large area known by locals as the Perkins Road Historic Business District. This area of northern Perkins Road is an active commercial corridor surrounded by large subdivisions. During the development of the Interstate-10 overpass on the 1960’s this area suffered drastic changes causing the removal of businesses and relocation of entire families. Despite these adverse effects Perkins Road commercial corridor has maintained its unique character but the under develop state of the spaces below the Interstate-10 overpass have restricted further development of the area

Applications

Volume 3 describes how resource-aware machine learning methods and techniques are used to successfully solve real-world problems. The book provides numerous specific application examples: in health and medicine for risk modelling, diagnosis, and treatment selection for diseases in electronics, steel production and milling for quality control during manufacturing processes in traffic, logistics for smart cities and for mobile communications

Urinary levels of toxic metals and pregnancy and newborn outcomes: biomonitoring of the IoMum cohort

Introdução: As mulheres grávidas estão sujeitas à exposição a vários metais tóxicos, o que pode ter um impacto significativo tanto na saúde materna como fetal, particularmente a exposição que ocorre durante o primeiro trimestre de gravidez. Este período representa uma janela de tempo de vulnerabilidade única, na qual a exposição pode afetar dramaticamente a saúde da mãe e do recém-nascido, tanto a curto como a longo prazo.   Objetivos: Avaliar a associação entre o nível de exposição das mulheres grávidas na coorte IoMum a quatro metais tóxicos - bismuto (Bi), tálio (Tl), níquel (Ni), e antimónio (Sb) - com características sociodemográficas da amostra do estudo, resultados da gravidez, e parâmetros antropométricos do recém-nascido. Métodos:  Este foi um estudo prospectivo baseado na coorte IoMum (registo de ensaio #NCT04010708, aprovação ética #292/17). As mulheres grávidas convidadas a participar neste estudo foram as que foram submetidas a ecografias de rotina do primeiro trimestre de Abril de 2018 a Abril de 2019 no Centro Hospitalar São João. Todas as mulheres com idade gestacional entre 10 semanas e 13 semanas mais 6 dias, vitalidade fetal confirmada e que assinaram o consentimento informado foram incluídas no estudo. Amostras de urina de participantes elegíveis foram analisadas utilizando a técnica ICP-MS para quantificar as concentrações urinárias de metais. Depois, utilizando testes estatísticos não paramétricos, foi avaliada a possível associação entre a exposição ao Bi, Tl, Ni, Sb e variáveis sociodemográficas da mãe, resultados da gravidez, e parâmetros antropométricos do recém-nascido. Resultados: A amostra do estudo correspondeu ao número de urinas recolhidas (n=349). As concentrações de metais urinários dos metais estudados foram, em µg/L: Bi 0,02 , Tl 0,02, Ni 4,3 e Sb 0,04. As taxas de detecção de cada metal (definidas como a percentagem de amostras com uma concentração de metal urinário ≥LOD) foram: 10,9% para Bi, 47,6% para Tl, 98,3% para Ni e 16,1% para Sb. A excreção mediana de Tl e Bi urinário foi associada à área de residência, com valores mais elevados para mulheres grávidas residentes em Valongo, em comparação com outros municípios. O aumento da idade materna foi associado a excreções urinárias mais elevadas de Bi, Sb, e Tl. Em relação ao índice de massa corporal anterior à gravidez, a excreção urinária de Bi, Ni, e Sb diminuiu consistentemente do peso normal para as mulheres obesas. A ocupação como profissional de saúde foi associada a excreções urinárias mais elevadas de Bi e Ni. Ocupações categorizadas como "alta exposição" - que incluíam profissionais de saúde, esteticistas, cabeleireiros, operadores de armazém, trabalhadores da indústria, cozinheiros, e profissionais de limpeza doméstica - foram também associadas a excreções mais elevadas de todos os metais. Em relação à exposição alimentar, a excreção de Tl urinário aumentou consistentemente com a frequência do consumo de peixe. Além disso, a excreção de Tl urinário aumentou consistentemente com o aumento das categorias antropométricas de peso ao nascimento, circunferência da cabeça ao nascimento, e comprimento ao nascimento. Finalmente, a mediana da excreção urinária de Ni foi muito mais elevada em mulheres que tiveram complicações no parto e em mulheres que tiveram um bebé com malformações. Conclusão: O presente estudo mostrou que algumas profissões podem aumentar a exposição das mulheres grávidas aos metais tóxicos estudados. Apesar disso, os níveis de exposição não são preocupantes quanto ao possível impacto na saúde materna ou do recém-nascido.Introduction: Pregnant women are subject to exposure to various toxic metals, which can have a significant impact on both maternal and fetal health, particularly exposure occurring during the first trimester of pregnancy. This period represents a time window of unique vulnerability, in which exposure can dramatically affect the health of the mother and newborn both on the short and on the long-term.   Aims: To evaluate the association between the level of exposure of pregnant women in the IoMum cohort to four toxic metals - bismuth (Bi), thallium (Tl), nickel (Ni), and antimony (Sb) - with sociodemographic characteristics of the study sample, pregnancy outcomes, and anthropometric parameters of the newborn. Methods:  This was a prospective study based on the IoMum cohort (trial registration #NCT04010708, ethical approval #292/17). Pregnant women invited to participate in this study were those who underwent routine first-trimester ultrasounds from April 2018 to April 2019 at Centro Hospitalar São João. All women with gestational age between 10 weeks and 13 weeks plus 6 days, confirmed foetal vitality and who signed the informed consent were included in the study. Spot urine samples from eligible participants were analyzed using the ICP-MS technique to quantify urinary concentrations of metals. Then, using non-parametric statistical tests, the possible association between exposure to Bi, Tl, Ni and Sb, and sociodemographic variables of the mother, pregnancy outcomes, and anthropometric parameters of the newborn was evaluated. Results: The study sample corresponded to the number of collected urines (n=349). The urinary metal concentrations of the studied metals were, in µg/L: Bi 0.02 , Tl 0.02, Ni 4.3 and Sb 0.04. The detection rates of each metal (defined as the percentage of samples with an urinary metal concentration ≥LOD) were: 10.9% for Bi, 47.6% for Tl, 98.3% for Ni and 16.1% for Sb. Median urinary Tl and Bi excretion was associated with residence area, with higher values for pregnant women residing in Valongo, compared to other municipalities. Increasing maternal age was associated with higher urinary excretions of Bi, Sb, and Tl. Regarding pre-pregnancy body mass index, Bi, Ni, and Sb urinary excretion consistently decreased from normal weight to obese women. Occupation as a health professional was associated with higher urinary excretion of Bi and Ni. Occupations categorized as "high exposure" - which included health professionals, aestheticians, hairdressing professionals, warehouse operators, industry workers, cooks, and housekeeping professionals - were also associated with higher excretions of all the metals. In relation to dietary exposure, urinary Tl excretion increased consistently with the frequency of fish consumption. In addition, urinary Tl excretion consistently increased with increasing anthropometric categories of birth weight, birth head circumference, and birth length Also, urinary Ni tended to show higher levels of excretion for adequate categories of birth head circumference and birth length. Finally, the median for urinary Ni excretion was much higher in women who had delivery complications and in women who have had a baby with malformations. Conclusion: The present study showed that some professions may increase the exposure of pregnant women to the studied toxic metals. Despite this, the levels of exposure are not of concern regarding possible impact on maternal or newborn health

Development of a 3D bioprinting and standalone bioreactor unit for the production and maintenance of bioscaffolds in vitro

The most common method for in vitro cell culture currently is to grow a specific cell type in isolation, in monolayer format, adhered to a 2D culture surface. This brings about many limitations in comparison to in vivo models due to altered cell phenotypes, as caused by the culturing technique itself, and the lack of naturally occurring cell-to-cell interactions. Three dimensional mammalian cell culture technologies have the potential to overcome these limitations, and provide models more representative of natural systems. Unfortunately, the cost and difficulty associated with achieving sustainable and useful 3D mammalian cell culture is still very high, preventing its widespread adoption across scientific platforms. In this research, we investigate the feasibility of developing and producing a visible light-based 3D stereolithographic bioprinter to produce 3D scaffolds for cell culture. Furthermore, we investigate the possibility of developing and implementing a forced perfusion bioreactor system, which would support the produced scaffold and improve longer-term culture conditions. The developed 3D bioprinter, and bioreactor designs were developed and tested alongside Poly (ethylene glycol) diacrylate (PEGDA), a versatile synthetic scaffold material. PEGDA itself was also evaluated for its printability, robustness in culture conditions over time, and its ability to maintain 3D mammalian cell culture. This research showed that both the developed 3D bioprinter, and bioreactor unit were capable of producing and maintaining an easily modifiable PEGDA scaffold, in culture conditions. In addition, the PEGDA formulation developed was shown to allow for the effective and reproducible 3D cell culture conditions over the medium term, with automated media feeding. The research presented here aimed to illustrate a proof of concept that the low-cost development and production of 3D culture scaffold production and maintenance systems was feasible to the scientific research environment. This technology can then be built upon, into a system that would then allow for the broader adoption and investigation of 3D cell culture as a tool within the scientific community.Thesis (MSc) -- Faculty of Science, Biotechnology Innovation Centre, 202