5,855 research outputs found
A Visual Modeling Method for Spatiotemporal and Multidimensional Features in Epidemiological Analysis: Applied COVID-19 Aggregated Datasets
The visual modeling method enables flexible interactions with rich graphical
depictions of data and supports the exploration of the complexities of
epidemiological analysis. However, most epidemiology visualizations do not
support the combined analysis of objective factors that might influence the
transmission situation, resulting in a lack of quantitative and qualitative
evidence. To address this issue, we have developed a portrait-based visual
modeling method called +msRNAer. This method considers the spatiotemporal
features of virus transmission patterns and the multidimensional features of
objective risk factors in communities, enabling portrait-based exploration and
comparison in epidemiological analysis. We applied +msRNAer to aggregate
COVID-19-related datasets in New South Wales, Australia, which combined
COVID-19 case number trends, geo-information, intervention events, and
expert-supervised risk factors extracted from LGA-based censuses. We perfected
the +msRNAer workflow with collaborative views and evaluated its feasibility,
effectiveness, and usefulness through one user study and three subject-driven
case studies. Positive feedback from experts indicates that +msRNAer provides a
general understanding of analyzing comprehension that not only compares
relationships between cases in time-varying and risk factors through portraits
but also supports navigation in fundamental geographical, timeline, and other
factor comparisons. By adopting interactions, experts discovered functional and
practical implications for potential patterns of long-standing community
factors against the vulnerability faced by the pandemic. Experts confirmed that
+msRNAer is expected to deliver visual modeling benefits with spatiotemporal
and multidimensional features in other epidemiological analysis scenarios
Analysis of the current status of tuberculosis transmission in China based on a heterogeneity model
Tuberculosis (TB) is an infectious disease transmitted through the
respiratory system. China is one of the countries with a high burden of TB.
Since 2004, an average of more than 800,000 cases of active TB have been
reported each year in China. Analyzing the case data from 2004-2018, we find
significant differences in TB incidence by age group. Therefore, the effect of
age heterogeneous structure on TB transmission needs further study. We develop
a model of TB to explore the role of age heterogeneity as a factor in TB
transmission. The model is fitted numerically using the nonlinear least squares
method to obtain the key parameters in the model, and the basic reproduction
number Rv 0.8017 is calculated and the sensitivity anal-ysis of Rv to the
parameters is given. The simulation results show that reducing the number of
new infections in the elderly population and increasing the recovery rate of
elderly patients with the disease could significantly reduce the transmission
of tuberculosis. Furthermore the feasibility of achieving the goals of the WHO
End TB Strategy in China is assessed, and we obtain that with existing TB
control measures it will take another 30 years for China to reach the WHO goal
to reduce 90% of the number of new cases by year 2049. However, in theoretical
it is feasible to reach the WHO strategic goal of ending tuberculosis by 2035
if the group contact rate in the elderly population can be reduced though it is
difficulty to reduce the contact rate.Comment: We think this is a very interesting work that gives a good
understanding of the current TB transmission in China and assesses the
possibility of China achieving the 2035 TB control target and also explores
possible ways for how to prevent and control the TB in Chin
A Molecular Approach to the Diagnosis, Assessment, Monitoring and Treatment of Pulmonary Non-Tuberculous Mycobacterial Disease
Introduction: Non-Tuberculous Mycobacteria (NTM) can cause disease of the lungs and sinuses, lymph nodes, joints and central nervous system as well as disseminated infections in immunocompromised individuals. Efforts to tackle infections in NTM are hampered by a lack of reliable biomarkers for diagnosis, assessment of disease activity, and prognostication.
Aims: The broad aims of this thesis are:
1. to develop molecular assays capable of quantifying the 6 most common pathogenic mycobacteria (M. abscessus, M. avium, M. intracellulare, M. malmoense, M. kansasii, M. xenopi) and calculate comparative sensitivities and specificities for each assay.
2. to assess patients’ clinical course over 12 – 18 months by performing the developed molecular assays against DNA extracted from sputum from patients with NTM infection.
3. to assess dynamic bacterial changes of the lung microbiome in patients on treatment for NTM disease and those who are treatment na ve.
Methods: DNA was extracted from a total of 410 sputum samples obtained from 38 patients who were either:
• commencing treatment for either M. abscessus or Mycobacterium avium complex.
• considered colonised with M. abscessus or Mycobacterium avium complex (i.e. cultured NTM but were not deemed to have infection as they did not meet ATS or BTS criteria for disease).
• Diagnosed with cystic fibrosis (CF) or non-CF bronchiectasis but had never cultured NTM.
For the development of quantitative molecular assays, NTM hsp65 gene sequences were aligned and interrogated for areas of variability. These variable regions enabled the creation of species specific probes. In vitro sensitivity and specificity for each probe was determined by testing each probe against a panel of plasmids containing hsp65
gene inserts from different NTM species. Quantification accuracy was determined by using each assay against a mock community containing serial dilutions of target DNA.
Each sample was tested with the probes targeting: M. abscessus, M. avium and M. intracellulare producing a longitudinal assessment of NTM copy number during each patient’s clinical course.
In addition, a total of 64 samples from 16 patients underwent 16S rRNA gene sequencing to characterise longitudinal changes in the microbiome of both NTM disease and controls.
Results: In vitro sensitivity for the custom assays were 100% and specificity ranged from 91.6% to 100%. In terms of quantification accuracy, there was no significant difference between the measured results of each assay and the expected values when performed in singleplex. The assays were able to accurately determine NTM copy number to a theoretical limit of 10 copies/μl.
When used against samples derived from human sputum and using culture results as a gold standard, the sensitivity of the assay for M. abscessus was found to be 0.87 and 0.86 for MAC. The specificity of the assay for M. abscessus was 0.95 and 0.62 for MAC. The negative predictive value of the assay for M. abscessus was 0.98 and 0.95 for MAC. This resulted in an AUC of 0.92 for M. abscessus and 0.74 for MAC.
Longitudinal analysis of the lung microbiome using 16SrRNA gene sequencing showed that bacterial burden initially decreases after initiation of antibiotic therapy but begins to return to normal levels over several months of antibiotic therapy. This effect is mirrored by changes in alpha diversity. The decrease in bacterial burden and loss of alpha diversity was found to be secondary to significant changes in specific genera such as Veillonella and Streptococcus. The abundance of other Proteobacteria such as Pseudomonas remain relatively constant.
Conclusion: The molecular assay has shown high in vitro sensitivity and specificity for the detection and accurate quantification of the 6 most commonly pathogenic NTM species. The assays successfully identified NTM DNA from human sputum samples.
A notable association between NTM copy number and the cessation of one or more antibiotics existed (i.e. when one antibiotic was stopped because of patient intolerance, NTM copy number increased, often having been unrecordable prior to this). The qPCR assays developed in this thesis provide an affordable, real time and rapid measurement of NTM burden allowing clinicians to act on problematic results sooner than currently possible.
There was no significant difference between the microbiome in bronchiectasis and cystic fibrosis nor was there a significant difference between the microbiome in patients requiring treatment for NTM and those who did not. Patients receiving treatment experienced an initial decrease in bacterial burden over the first weeks of treatment followed by a gradual increase towards baseline over the next weeks to months. This change was mirrored in measures of alpha diversity. Changes in abundance and diversity were accounted for by decreases in specific bacteria whilst the abundance of other bacteria increased, occupying the microbial niche created. These bacteria (for example Pseudomonas spp) are often associated with morbidity.Open Acces
Assessing the water quality of selected public swimming pools within the Johannesburg area of the Gauteng province, South Africa
Abstract: A number of contaminants in public swimming pools have been recognised globally, all of which are detrimental to the quality of such amenities as well as to human health. Thus, swimming pool water may serve as a medium for the transmission of waterborne pathogens amongst swimmers unless appropriate preventive measures are properly implemented. Moreover, at certain times various researchers have linked the poor quality of swimming pool waters to pathogenic outbreaks. Despite such negative health impacts, studies focusing on the water quality of swimming pools are limited in South Africa. Even so, the quality of drinking water in most African countries is alarming, let alone the quality of public swimming pool water. As a result, the present study was carried out to assess the water quality of selected public swimming pools within the CoJ Metropolitan Municipality, in the Gauteng province in South Africa. The swimming pool water’s pH, electrical conductivity, temperature, free available chlorine, total chlorine, alkalinity, water hardness, and cyanuric acid were measured on site while the collected water samples were analysed at the laboratory for the presence microbiological agents (i.e. E. coli and total faecal coliforms). The results showed different degrees of unsatisfactory and non-compliance across all selected public swimming pools. The findings also indicated the presence of waterborne pathogens largely due to inadequate disinfection. It has also been established that the existing recirculation-filtration systems are not always working optimally (due to electrical load shedding) and water chemical imbalances, thus resulting in water quality non-compliance. Unfortunately, surrounding communities use such facilities for recreation and leisure time, despite their health and hazard potential. Based on the results of this study, it is recommended that the swimming pool waters must be effectively treated to inactivate and kill microbes, therefore providing chemically balanced water. Furthermore, water quality testing kits and water quality sensors can be used to measure multiple physical and chemical water quality parameters simultaneously and to provide instant results.M.Sc. (Environmental Management
Examining the Potential for Isotope Analyses of Carbon, Nitrogen, and Sulphur in Burned Bone from Experimental and Archaeological Contexts.
The aim of this project was to determine whether isotope analyses of carbon, nitrogen and sulphur can be conducted on collagen extracted from burned bone. This project was conducted in two phases: a controlled heating experiment and an archaeological application. The controlled heating experiment used cow (Bos taurus) bone to test the temperature thresholds for the conservation of δ13C, δ15N, and δ34S values. These samples were also used to test the efficacy of Fourier Transform Infrared spectroscopy (FTIR) and colour analysis, for determining the burning intensities experienced by bone burned in unknown conditions.
The experiment showed that δ13C values were relatively unchanged up to 400°C (<2‰ variation), while δ15N values were relatively stable up to 200°C (0.5‰ variation). Values of δ34S were also relatively stable up to 200°C (1.4‰ variation). Colour change and FTIR data were well correlated with the change in isotope ratios. Models estimating burning intensities were created from the FTIR data.
For the archaeological application, samples were selected from two early Anglo-Saxon cemetery sites: Elsham and Cleatham. Samples were selected from both inhumed and cremated individuals. Among the inhumed individuals δ13C values suggested a C3 terrestrial diet and δ15N values suggested protein derived largely from terrestrial herbivores, as expected for the early Anglo-Saxon period. However, δ34S values suggested the consumption of freshwater resources and that this consumption was related to both the age and sex of the individual.
The experimental data shows that there is potential for isotope analyses of cremated remains, as during the cremation process heat exposures are not uniform across the body. The samples selected for the archaeological application, however, were not successful. Bone samples heated in controlled conditions produced viable collagen for isotope analysis; however, there are several differences between experiments conducted in a muffle furnace and open-air pyre cremation that need to be investigated further. Additionally, the influence of taphonomy on collagen survival in burned bone needs to be quantified. Finally, methods of sample selection need to be improved to find bone samples from archaeologically cremated remains that are most likely to retain viable collagen. While there is significant research that must be conducted before this research can be widely applied there are a multitude of cultures that practised cremation throughout history and around the world that could be investigated through the analyses proposed in this project
Breaking Ub with Leishmania mexicana: a ubiquitin activating enzyme as a novel therapeutic target for leishmaniasis
Leishmaniasis is a neglected tropical disease, which inflicts a variety of gruesome pathologies on humans. The number of individuals afflicted with leishmaniasis is thought to vary between 0.7 and 1.2 million annually, of whom it is estimated that 20 to 40 thousand die. This problem is exemplary of inequality in healthcare – current leishmaniasis treatments are inadequate due to toxicity, cost, and ineffectiveness, so there is an urgent need for improved chemotherapies.
Ubiquitination is a biochemical pathway that has received attention in cancer research. It is the process of adding the ubiquitin protein as a post-translational modification to substrate proteins, using an enzymatic cascade comprised of enzymes termed E1s, E2s, and E3s. Ubiquitination can lead to degradation of substrate proteins, or otherwise modulate their function. As the name suggests, this modification can be found across eukaryotic cell biology. As such, interfering with ubiquitination may interfere with essential biological processes, which means ubiquitination may present a new therapeutic target for leishmaniasis.
Before ubiquitination inhibitors can be designed, components of the ubiquitination system must be identified. To this end, a bioinformatic screening campaign employed BLASTs and hidden Markov models, using characterised orthologs from model organisms as bait, to screen publicly-available Leishmania mexicana genome sequence databases, searching for genes encoding putative E1s, E2s, and E3s. To confirm some of these identifications on a protein level, activity-based probes, protein pulldowns, and mass spectrometry were used. Using an activity-based probe that emulates the structure of adenylated ubiquitin, E1s were identified, and their relative abundance quantified. A chemical crosslinker extended the reach of this probe, allowing the identification of an E2 (LmxM.33.0900). It is noted that L. mexicana has two E1s – unusual for a single celled organism. Of these E1s, LmxM.34.3060 was considerably more abundant than LmxM.23.0550 in both major life cycle stages of the in vitro Leishmania cultures.
It is important to describe the wider context of these enzymes – what is their interactome, what are their substrates? To study this, CRISPR was used to fuse a proximity-based labelling system, BioID, on genes of interest – LmxM.34.3060 and LmxM.33.0900. The E2 (LmxM.33.0900) was shown to interact with the E1 (LmxM.34.3060), validating the results from the activity-based probe and crosslinker experiments. Due to sequence homology with characterised orthologs, the E2 was hypothesised to function in the endoplasmic reticulum degradation pathway. Immunoprecipitations of a ubiquitin motif, diglycine, were conducted with a view to gathering information on the substrates of ubiquitin. Anti-diglycine peptides included some of those identified by BioID. Experiments examining ubiquitin’s role in the DNA damage response were also initiated, as were improvements to the proximity-based labelling system, however these were not followed to completion due to a lack of time and resources.
To examine the possibility of finding novel drug targets in the ubiquitination cascade, recombinant proteins were expressed. LmxM.34.3060 was expressed in a functional form, while a putative SUMO E2 (LmxM.02.0390) was functional after refolding. Expressed LmxM.33.0900 was not functional and could not be refolded into a functional form. Drug assays were conducted on LmxM.34.3060, which found an inhibitor of the human ortholog, TAK-243, to be 20-fold less effective against the Leishmania enzyme. Additional assays found an inhibitor that was 50-fold more effective at inhibiting the Leishmania enzyme as opposed to its human equivalent - 5'O-sulfamoyl adenosine. Furthermore, a new mechanism of action, inhibiting the E1, for was identified for drugs previously characterised to inhibit protein synthesis. LmxM.34.3060 underwent biophysical characterisation, with structural information obtained using SAXS and protein crystallography. A crystal structure was solved to 3.1 Å, with the in-solution SAXS structure complementary to this. TAK-243 was modelled into the LmxM.34.3060 structure and clashes were predicted, concurring with TAK-243’s reduced efficacy against the Leishmania enzyme in the drug assays.
This project aimed to characterise the potential of an understudied biochemical system to provide novel therapeutic targets for a neglected tropical pathogen. To achieve this aim it presents the identifications of two E1s, an interactome, a structure, and a potent, selective inhibitor of a Leishmania ubiquitin activating enzyme
Maternal immunometabolism adaptation in pregnancy
Pregnant women undergo a series of metabolic and immunologic changes to ensure provision of nutrients to, and prevent rejection of, the fetus. To ensure continuous supply of glucose to the fetus, the mother increases glucose production, glucose intolerance and insulin resistance. To meet her own energy demands, the mother transitions from lipid storage to lipolysis. To prevent rejection of the fetal semi-allograft, the mother’s immune system must be regulated, whilst maintaining protection against pathogens. Hypothesis: Well-recognised metabolic changes in pregnancy could impact maternal immune function. The aims of this project are to landscape the lipidomic profile using novel mass spectrometry techniques, and to determine whether monocytes undergo metabolic adaptation, if this occurs at 28 weeks of gestation, and if maternal obesity sabotages immunological adaptations. In addition, aims included investigation into the mechanisms which may protect the mother and fetus against SARS-CoV-2. Key findings unveiled significant phenotypic adaptations in the monocyte subsets during pregnancy, which are sabotaged by obesity. As the effect of maternal obesity is poorly understood, other immunological adaptations were investigated which revealed a shift to a Th1 and Th17 response which might contribute to the detrimental effects of obesity on pregnancy. At term, the monocytes illustrate a strong metabolic adaptation where their oxidative phosphorylation capabilities are reduced, confirmed by alterations in their mitochondria, with a downstream effect on their functionality with reduced production of lipid mediators and cytokines. While risk of infection with SARS-CoV-2 is low to pregnant women and the fetus, there is increased risk of preterm birth and admission into ICU. The fetus is relatively protected against infection, with cases of vertical transmission being rare. This thesis illustrates an elevated presence of soluble SARS-CoV-2 related molecules in breast milk and amniotic fluid which are postulated to act as decoy traps for the virus, which protects the neonate. In conclusion, this thesis has revealed novel findings into the immunometabolism adaptation to pregnancy
Rethinking established methodology in micromammal taphonomy: archaeological case studies from Orkney, UK (4th millennium BC – 15th century AD)
Micromammals (e.g. rodents, shrews), characterised by their small size, short lifespan and high reproduction rate, are known for rapid adaptability to changing conditions, inhabiting all environments besides the most frigid. They form a variety of relationships with other animals as well as humans, from being prey up to mutualism, commensalism and even taming and domestication. Changes occurring short or long-term within micromammal populations can be a useful proxy for natural as well as human-induced changes. However, their remains from archaeological contexts have seldom been investigated, with a scarcity of methodological studies and incomparability of published data often discouraging research.
Human impact on the environment is especially noticeable in the case of insular environments where humans are responsible for the majority of species introductions. This thesis examines a series of case studies from the Orkney islands off north-east Scotland to develop a micromammal zooarchaeological methodology and investigate the micromammal relationships with predators and human activity in this context. Specifically it has two main aims: 1) perform methodological research on obtained data to investigate established methods as well as to suggest new approaches to data analysis given what data are retrievable from studied assemblages; 2) apply the revised methodology to investigate a range of Orcadian sites, covering two main time periods of intensification of maritime contacts: Neolithic (4000 – 2000 BC) and Norse/mediaeval (600 – 1500 AD) ages. Analysis standardisation and reproducibility through coding in R is also introduced to deal with the large breath of obtained data.
The study provides conclusive results, broadening the understanding of micromammal taphonomy and a range of different assemblages and deposition patterns present within and around anthropic contexts. The breath of utilizable data retrievable from micromammal assemblages is comparable with typical zooarchaeological research on the remains of bigger species, for example including information on age of death or non-predatory taphonomic factors. Spatial and contextual data, particularly, proves to be crucial for understanding the impact of dispersal and burial processes on micromammal accumulations. Moreover, the necessity for consistent sieving is confirmed, lower effort sampling or sieving regimes failing to provide representative and comparable samples. The obtained data can be effectively analysed through statistical methods, including classifying algorithms, bypassing problems encountered in the case of multiple comparisons and deposition patterns. However, the results also show that actualistic research may not be directly comparable with archaeological material without considering non-predatory taphonomic factors and their impact on data representativeness.
Assemblages identified within the studied sites seem to be formed by a variety of factors. Identifiable predatory depositions could be attributed to both owls and diurnal raptors, taxa expected to be found considering modern Orkney fauna and dominant micromammal predators. Cases of non-predatory depositions included deaths of commensal species living and/or nesting within the anthropic environment, self-entrapment in anthropic features such as trenches or pits of single individuals and secondary accumulation in similar features due to dispersal. In general, each site shows multiple different patterns being present, with certain areas or context types (e.g. open/enclosed, natural/usage period/abandonment) exhibiting a predominance of a specific deposition. Intrusiveness is surprisingly rare and, where identified, is characterised by multiple intrusive species within the contexts, with singular species intrusiveness rarely being noted. Some evidence for human interaction with micromammals, direct or indirect, can be noted through additional taphonomic marks such as burning. However, a definitive interpretation of these marks, as of now, cannot be achieved
Metabolomics and biosensor approaches to the detection of fever associated diseases
Febrile illnesses are still a major cause of mortality and morbidity globally and the failure to detect and correctly diagnose a specific disease associated with fever is partly responsible for this. This thesis aimed to investigate a biosensor-based method for the detection of fever associated diseases and to further explore the molecular mechanisms and possible biomarkers of febrile illnesses by employing a metabolomics-based approach. The biosensor platform is based on a complementary metal oxide semiconductor technology, which has both technological and economic advantages. Due to the small size of the microchip, accurate signal processing becomes challenging and, thus, computational methods were developed and tested for the quantitative detection of antibodies in a solution tested on the biosensor platform. Three methods, one based on a deterministic approach and two others based on machine learning (ML) algorithms, were tested and compared for the detection of a reaction spot intensity using synthetically generated images. Next, in order to develop an immunoassay protocol for the detection of one specific fever associated infectious disease, human African trypanosomiasis (HAT), several steps were taken. First of all, a suitable and sensitive method of detection was selected, i.e. enzyme linked immunosorbent assay (ELISA). Next, four recombinant antigens currently used for the detection of HAT were selected based on previous evidence and developed using molecular cloning techniques in E.coli. These were tested on infected and control humans serum samples obtained from endemic regions of the Democratic Republic of Congo (DRC). Disposable poly-methyl methacrylate (PMMA) slides which were chemically functionalised were used on top of the chip as the immunoassay surface. Titrations for the selected antigens/antibody were tested using an indirect ELISA-like protocol and the best results after fitting a calibration curve were obtained for an antigen concentration of 2.5 µg/ml. The detection of the antibody to the trypanosome antigen invariant surface glycoprotein 65 (ISG65) proved to be successful and the protocol could be replicated for all the other antigens. However, technical challenges and the closure of the laboratory during the Covid-19 pandemic precluded my taking this part of the project to its conclusion. Following this, metabolomics datasets studying disparate febrile infectious illnesses obtained using liquid chromatography coupled to mass spectrometry (LC-MS) were used in order to investigate and detect possible metabolite-based biomarkers common to fever-associated diseases. A warping based method was developed in order to enable integration by alignment of disparate LC-MS metabolomics datasets. Integration was performed by correcting the RT drift between the datasets using fitted Gaussian Process regression models, a supervised ML method, which was followed by direct matching alignment using MZmine2. The correction was performed by using the standard reference mixture (SRM) information. Statistical analysis on the meta-dataset was performed using linear modelling implemented in the limma R-package. Comparison was made between infected and control samples and commonality was established using the fold change values obtained for the individual datasets. Annotation was carried out by matching the compounds against metabomlomics datasets and through mummichog software, which was also used for pathway analysis. The features obtained from this analysis which were putatively annotated were classified into categories (amino acids, sugars, lipids, nucleotides, etc.). Features in common to all datasets were used to make a connection to the previously established molecular basis of fever. Significant changes were identified to several metabolic pathways, with the most notable perturbations being within the kynurenine pathway, a branch of tryptophan metabolism. Also, features specific to each dataset were used to evaluate the accuracy of the fever biomarkers and investigate possible biomarkers for each different fever-associated disease
- …