Outlier effects on robust joint modelling of longitudinal and survival data

Robust joint modelling is an emerging field of research. Through the advancements in electronic patient healthcare records, the popularly of joint modelling approaches has grown rapidly in recent years providing simultaneous analysis of longitudinal and survival data. This research advances previous work through the development of a novel robust joint modelling methodology for one of the most common types of standard joint models, that which links a linear mixed model with a Cox proportional hazards model. Through t-distributional assumptions, longitudinal outliers are accommodated with their detrimental impact being down weighed and thus providing more efficient and reliable estimates. The robust joint modelling technique and its major benefits are showcased through the analysis of Northern Irish end stage renal disease patients. With an ageing population and growing prevalence of chronic kidney disease within the United Kingdom, there is a pressing demand to investigate the detrimental relationship between the changing haemoglobin levels of haemodialysis patients and their survival. As outliers within the NI renal data were found to have significantly worse survival, identification of outlying individuals through robust joint modelling may aid nephrologists to improve patient's survival. A simulation study was also undertaken to explore the difference between robust and standard joint models in the presence of increasing proportions and extremity of longitudinal outliers. More efficient and reliable estimates were obtained by robust joint models with increasing contrast between the robust and standard joint models when a greater proportion of more extreme outliers are present. Through illustration of the gains in efficiency and reliability of parameters when outliers exist, the potential of robust joint modelling is evident. The research presented in this thesis highlights the benefits and stresses the need to utilise a more robust approach to joint modelling in the presence of longitudinal outliers.

Genomics and virulence factors of Fusobacterium necrophorum

Fusobacterium necrophorum, a Gram negative, anaerobic bacterium, is a common cause of acute pharyngitis and tonsillitis and a rare cause of more severe infections of the head and neck. At the beginning of the project, there was no available genome sequence for F. necrophorum. The aim of this project was to sequence the F. necrophorum genome and identify and study its putative virulence factors contained using in silico and in vitro analysis. Type strains JCM 3718 and JCM 3724,F. necrophorum subspecies necrophorum (Fnn) and funduliforme (Fnf), respectively, and strain ARU 01 (Fnf), isolated from a patient with LS, were commercially sequenced by Roche 454 GS-FLX+ next generation sequencing and assembled into contigs using Roche GS Assembler. Sequence data was annotated semi-automatically, using the xBASE pipeline, BLASTp and Pfam. The F. necrophorum genome was determined to be approximately 2.1 – 2.3 Mb in size, with an estimated 1,950 ORFs and includes genes for a leukotoxin, ecotin, haemolysin, haemagglutinin, haemin receptor, adhesin and type Vb and Vc secretion systems. The prevalence of the leukotoxin gene was investigated in strains JCM 3718, JCM 3724 and ARU 01, as well as a clinical collection of 25 Fnf strains, identified using biochemical and molecular tests. The leukotoxin operon was found to be universal within the strain collection by PCR. HL-60 cells subjected to aliquots of concentrated high molecular weight culture supernatant, predicted to contain the secreted leukotoxins of strains JCM 3718, JCM 3724 and ARU 01, were killed in a dose-dependent manner. The cytotoxic effect of the leukotoxin against human donor white blood cells was also tested to validate the HL-60 assay. The differences in the results between the two assays were not statistically significant. Ecotin, a serine protease inhibitor, was found to be present in 100 % of the strain collection and had a highly conserved sequence with primary and secondary binding sites exposed on opposing sides of the protein. During enzyme inhibition studies, a purified recombinant F. necrophorum ecotin protein inhibited human neutrophil elastase, a protease that degrades bacteria at inflammation sites, and human plasma kallikrein, a component of the host clotting cascade. The recombinant ecotin also prolonged human plasma clotting times by up to 7-fold for the extrinsic pathway, and up to 40-fold for the intrinsic pathway. The genome sequence data provides important information about F. necrophorum type strains and enables comparative study between strains and subspecies. Results from the leukotoxin and ecotin assays can be used to build up an understanding of how the organism behaves during infection.

Climate changes influence in occupational exposure to fungi and mycotoxins

Climate changes and their effects on fungal distribution and activity are aspects of concern regarding the human exposure to mycotoxins. An exhaustive search was made for papers available in scientific databases reposrting the influence that climate cchange has on fungi and mycotoxins. Also a review regarding fungal burden, collected between 2010 and 2015 in different settings, was done to support the discussion about future fungi and mycotoxins ocuupational exposure. A. flavus complex, E. graminerarum complex and F. verticilliodes were the most reported to be influenced by climate changes. We noted also that the analyzed Portuguese settings presented already an occupational problem due to their fungal burden. It will be important to know future climate changes to select what complexes/species and strains, and consequently the mycotoxins, we should consider as indicators of an occupational problem. In addition, epidemiologic studies are needed to increase knowledge about potential health effects related with the exposure to both risk factors.

Odour flux from litter of broiler chickens fed diets differing in protein levels and additives

The effect of dietary crude protein (CP) and additives on odour flux from broiler litter was investigated using 180 day-old Ross 308 male chicks randomly allocated to five dietary treatments with three replications of 12 birds each. A 5×3 factorial arrangement of treatments was employed. Factors were: diet (low CP, high CP, high CP+antibiotic, high CP+probiotic, high CP+saponin) and age (15, 29, 35 days). Low CP (LCP) and high CP (HCP) diets differed in CP levels by 4.5-5%. The low CP diets were supplemented with L-valine, L-isoleucine, L-arginine, L-lysine, D,L-methionine and L-threonine. The antibiotic used was Zn Bacitracin, the probiotic was a blend of three Bacillus subtilis strains and the saponin came from a blend of Yucca and Quillaja. Odorants were measured from litter headspace using a flux hood and selective ion flow tube mass spectrometry (SIFT-MS). Results were log tranformed and analysed by two-way ANOVA with repeated measures using JMP statistical software v.8, and means were separated by Tukey's HSD test at P<0.05.The results showed that LCP group produced lower flux of dimethyl amine, trimethyl amine, H2S, NH3 and phenol in litter compared to HCP group (P<0.05). Similarly, HCP+probiotic group produced lower flux of H2S (P<0.05) and HCP+saponin group produced lower flux of trimethylamine and phenol in litter compared to HCP group (P<0.05). The dietary treatments tended (P=0.065) to have higher flux of methanethiol in HCP group compared to others. There was a diet x age interaction for litter flux of diacetyl, acetoin, 3-methyl-1-butanol, 3-methylbutanal, ethanethiol, propionic acid and hexane (P<0.05). Concentrations of diacetyl, acetoin, propionic acid and hexane in litter were higher from LCP group compared to all other treatments on d 35 (P<0.05) but not on days 15 and 29. Thus, the low CP diet, Bacillus subtilis based probiotic and Yucca/Quillaja based saponin were effective in reducing the emissions of some key odorants from broiler litter.

Characterisation and quantification of changes in odorants from litter headspace of meat chickens fed diets varying in protein levels and additives

The effect of dietary crude protein (CP) and additives on odor flux from meat chicken litter was investigated using 180 day-old Ross 308 male chicks randomly allocated to five dietary treatments with three replicates of 12 birds each. A 5 × 3 factorial arrangement of treatments was employed. Factors were: diet (low CP, high CP, high CP+antibiotic, high CP+probiotic, high CP+saponin) and age (15, 29, 35 days). The antibiotic used was Zn bacitracin, the probiotic was a blend of three Bacillus subtilis strains and the saponin came from a blend of Yucca and Quillaja. Odorants were collected from litter headspace with a flux hood and measured using selective ion flow tube mass spectrometry (SIFT-MS). Litter moisture, water activity (Aw), and litter headspace odorant concentrations were correlated. The results showed that low CP group produced lower flux of dimethyl amine, trimethyl amine, H2S, NH3, and phenol in litter compared to high CP group (P < 0.05). Similarly, high CP+probiotic group produced lower flux of H2S (P < 0.05) and high CP+saponin group produced lower flux of trimethylamine and phenol in litter compared to high CP group (P < 0.05). The dietary treatments tended (P = 0.065) to have higher flux of methanethiol in high CP group compared to others. There was a diet × age interaction for litter flux of diacetyl, 3-hydroxy-2-butanone (acetoin), 3-methyl-1-butanol, 3-methylbutanal, ethanethiol, propionic acid, and hexane (P < 0.05). Concentrations of diacetyl, acetoin, propionic acid, and hexane in litter were higher from low CP group compared to all other treatments on d 35 (P < 0.05) but not on d 15 and 29. A high litter moisture increased water activity (P < 0.01) and favored the emissions of methyl mercaptan, hydrogen sulfide, dimethyl sulfide, ammonia, trimethyl amine, phenol, indole, and 3-methylindole over others. Thus, the low CP diet, Bacillus subtilis based probiotic and the blend of Yucca/Quillaja saponin were effective in reducing the emissions of some key odorants from meat chicken litter.

Characteristics and management of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemase in a tertiary hospital.

Background: The emergence of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemases is rare. We report an occurrence of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemases in a Chinese tertiary care hospital from November 2010 to December 2012. Methods: The clinical characteristics of 30 patients were described. The genetic relationship of isolates was determined by pulsed-field gel electrophoresis (PFGE). Carbapenemases were detected by modified Hodge test (MHT) and polymerase chain reactions (PCRs). Amplicons were sequenced and blasted to determine the genotype. Results: Most infected patients were from intensive care unit and had complex and serious underlying illnesses requiring mechanical ventilation. PFGE revealed that Klebsiella pneumoniae showed two major PFGE types. Two Klebsiella oxytoca had an indistinguishable PFGE pattern, while four Enterobacter cloacae were different strains. The sequencing studies showed Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemase in the 23 infected patients. The majority of patients had infections with the carbapenemase-producing Enterobacteriaceae (CPE) strain, most were successfully treated with a range of antibiotics and discharged. Conclusion: It is important to maintain a high index of suspicion to screen for carbapenemase-producing Enterobacteriaceae strains. Rapid identification of these strains and implementation of stringent procedures are the key to prevent major outbreaks in a hospital setting. Keywords:

Prevalence of colonizing bacteria and their association with primary bacteremias in hemodialysis of a university hospital

to be from 2.5 to 5.5 cases per 1,000 catheter-day. the clinical impact is relevant and increases the cost of the HD Unit. Methods: The present study is the irst of 2 phases. It was conducted from January to December of 2012, and included all patients and nurses who were in the HD Unit. The prevalence of Gramnegative bacilli (GNB) and methicillin-resistant Staphylococcus aureus (MrSA) colonizing the nasal passages and the skin is described. Also, phenotypic association was sought by genus, species and sensitivities between colonizing bacterial strains and blood cultures with GNB and MRSA. Results: the study included 70 patients and 10 nurses. the prevalence of nasal colonization in patients by GNB was 9% and 6% in the pericatheter, and no nursing GNB colonization was discovered. The prevalence of MRSA nasal colonization was 19% and 6% in the pericatheter for patients and in the nurses the nasal colonization was 50% and 10% in the hands. We identiied 29 cases of primary bacteremia. The primary bacteremia rate is 1.5 per 1,000 catheter-day or 0.4 episodes per patient per year. Conclusion: We demonstrated a high prevalence of MrSA colonization in patients and nurses in the HD Unit. No relationship was found between primary bacteremia by GNB and patients and nurses’ bacteria colonization by the phenotypic comparison.

Effect of nitrogen nutrition on yeast ecology and alcoholic fermentation

Mestrado Vinifera Euromaster - Instituto Superior de Agronomia - UL

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

From field to fermentation: characterisation and application of non-dairy cultures in dairy foods

This thesis investigates the phenotypic and genotypic diversity of non-dairy L. lactis strains and their application to dairy fermentations. A bank of non-dairy lactococci were isolated from grass, vegetables and the bovine rumen. Subsequent analysis of these L. lactis strains revealed seven strains to possess cremoris genotypes which did not correlate with their observed phenotypes. Multi-locus sequence typing (MLST) and average nucleotide identity (ANI) highlighted the genetic diversity of lactis and cremoris subspecies. The application of these non-dairy lactococci to cheese production was also assessed. In milk, non-dairy strains formed diverse volatile profiles and selected strains were used as adjuncts in a mini Gouda-type cheese system. Sensory analysis showed non-dairy strains to be strongly associated with the development of off-flavours and bitterness. However, microfluidisation appeared to reduce bitterness. A novel bacteriophage, ɸL47, was isolated using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. The phage, a member of the Siphoviridae, possessed a long tail fiber, previously unseen in dairy lactococcal phages. Genome sequencing revealed ɸL47 to be the largest sequenced lactococcal phage to date and owing to the high % similarity with ɸ949, a second member of the 949 group. Finally, to identify and characterise specific genes which may be important in niche adaptation and for applications to dairy fermentations, comparative genome sequence analysis was performed on L. lactis from corn (DPC6853), the bovine rumen (DPC6853) and grass (DPC6860). This study highlights the contribution of niche specialisation to the intra-species diversity of L. lactis and the adaptation of this organism to different environments. In summary this thesis describes the genetic diversity of L. lactis strains from outside the dairy environment and their potential application in dairy fermentations.

Combined Use of NMR, LC-ESIMS and Antifungal Tests for Rapid Detection of Bioactive Lipopeptides Produced by Bacillus

The science and technology interact with the art in several ways. Biotechnological coupled with analytical approaches can play an important role in protecting and preserving cultural heritage for future generations. Many microorganisms influenced by environmental conditions are the main responsible for biological contamination in built heritage. Biocides based on chemical compounds have been used to mitigate this problem. Thus, it is vitally important to develop proper remediation actions based on environmentally innocuous alternative. Bacillus specie is emerging as an optimistic alternative for built heritage treatment due to their capacity to produce secondary metabolites with antagonistic activities against many fungal pathogens. Therefore, the intent of this work was to access a rapid evaluation of antifungal potential of bioactive metabolites produced by Bacillus strains and simultaneously their characterization using spectroscopic (NMR) and chromatographic techniques (LCESI- MS). The high antifungal activity obtained for Bacillus sp. active compounds produced in this study confirms the great potential to suppress biodeteriogenic fungi growth on historical artworks. Additionally, the proposed methodology allowed to access bioactive metabolites produced without need of the laborious total previous isolation and could be used as a viable alternative to be employed for screening and production of new green biocides.

Mutation frequency of non-ESBL phenotype SENTRY (Asia-Pacific) isolates of Klebsiella pneumoniae conversion to an ESBL positive phenotype

Extended spectrum β-lactamases or ESBLs, which are derived from non-ESBL precursors by point mutation of β-lactamase genes (bla), are spreading rapidly all over the world and have caused considerable problems in the treatment of infections caused by bacteria which harbour them. The mechanism of this resistance is not fully understood and a better understanding of these mechanisms might significantly impact on choosing proper diagnostic and treatment strategies. Previous work on SHV β-lactamase gene, blaSHV, has shown that only Klebsiella pneumoniae strains which contain plasmid-borne blaSHV are able to mutate to phenotypically ESBL-positive strains and there was also evidence of an increase in blaSHV copy number. Therefore, it was hypothesised that although specific point mutation is essential for acquisition of ESBL activity, it is not yet enough, and blaSHV copy number amplification is also essential for an ESBL-positive phenotype, with homologous recombination being the likely mechanism of blaSHV copy number expansion. In this study, we investigated the mutation rate of non-ESBL expressing K. pneumoniae isolates to an ESBL-positive status by using the MSS-maximum likelihood method. Our data showed that blaSHV mutation rate of a non-ESBL expressing isolate is lower than the mutation rate of the other single base changes on the chromosome, even with a plasmid-borne blaSHV gene. On the other hand, mutation rate from a low MIC ESBL-positive (≤ 8 µg/mL for cefotaxime) to high MIC ESBL-positive (≥16 µg/mL for cefotaxime) is very high. This is because only gene copy number increase is needed which is probably mediated by homologous recombination that typically takes place at a much higher frequencies than point mutations. Using a subinhibitory concentration of novobiocin, as a homologous recombination inhibitor, revealed that this is the case.

Domestic violence in the urban fringe

Police call data for domestic violence incidents in the city of Brisbane were used to further explore the locational disadvantage thesis. it was hypothesised that the supposed additional burdens and stresses on disadvantaged families living in the outer suburbs may be reflected in significantly higher rates of reported domestic violence. Using an index of relative socioeconomic disadvantage and employing Analysis of variance (ANOVA) this research shows that significantly higher rates of reported domestic violence occur in the inner suburbs relative to the middle or outer suburbs of Brisbane. This finding adds further doubt to the magnitude of locational disadvantage impacts on outer suburban low income family households.

Phylogenetic analysis of polyomaviruses based on their complete genomes

Perez-Losada et al. [1] analyzed 72 complete genomes corresponding to nine mammalian (67 strains) and 2 avian (5 strains) polyomavirus species using maximum likelihood and Bayesian methods of phylogenetic inference. Because some data of 2 genomes in their work are now not available in GenBank, in this work, we analyze the phylogenetic relationship of the remaining 70 complete genomes corresponding to nine mammalian (65 strains) and two avian (5 strains) polyomavirus species using a dynamical language model approach developed by our group (Yu et al., [26]). This distance method does not require sequence alignment for deriving species phylogeny based on overall similarities of the complete genomes. Our best tree separates the bird polyomaviruses (avian polyomaviruses and goose hemorrhagic polymaviruses) from the mammalian polyomaviruses, which supports the idea of splitting the genus into two subgenera. Such a split is consistent with the different viral life strategies of each group. In the mammalian polyomavirus subgenera, mouse polyomaviruses (MPV), simian viruses 40 (SV40), BK viruses (BKV) and JC viruses (JCV) are grouped as different branches as expected. The topology of our best tree is quite similar to that of the tree constructed by Perez-Losada et al.

Modelling of inflatable rescue boats (IRBs) in surf conditions to reduce injuries

The Inflatable Rescue Boat (IRB) is arguably the most effective rescue tool used by the Australian surf lifesavers. The exceptional features of high mobility and rapid response have enabled it to become an icon on Australia's popular beaches. However, the IRB's extensive use within an environment that is as rugged as it is spectacular, has led it to become a danger to those who risk their lives to save others. Epidemiological research revealed lower limb injuries to be predominant, particularly the right leg. The common types of injuries were fractures and dislocations, as well as muscle or ligament strains and tears. The concern expressed by Surf Life Saving Queensland (SLSQ) and Surf Life Saving Australia (SLSA) led to a biomechanical investigation into this unique and relatively unresearched field. The aim of the research was to identify the causes of injury and propose processes that may reduce the instances and severity of injury to surf lifesavers during IRB operation. Following a review of related research, a design analysis of the craft was undertaken as an introduction to the craft, its design and uses. The mechanical characteristics of the vessel were then evaluated and the accelerations applied to the crew in the IRB were established through field tests. The data were then combined and modelled in the 3-D mathematical modelling and simulation package, MADYMO. A tool was created to compare various scenarios of boat design and methods of operation to determine possible mechanisms to reduce injuries. The results of this study showed that under simulated wave loading the boats flex around a pivot point determined by the position of the hinge in the floorboard. It was also found that the accelerations experienced by the crew exhibited similar characteristics to road vehicle accidents. Staged simulations indicated the attributes of an optimum foam in terms of thickness and density. Likewise, modelling of the boat and crew produced simulations that predicted realistic crew response to tested variables. Unfortunately, the observed lack of adherence to the SLSA footstrap Standard has impeded successful epidemiological and modelling outcomes. If uniformity of boat setup can be assured then epidemiological studies will be able to highlight the influence of implementing changes to the boat design. In conclusion, the research provided a tool to successfully link the epidemiology and injury diagnosis to the mechanical engineering design through the use of biomechanics. This was a novel application of the mathematical modelling software MADYMO. Other craft can also be investigated in this manner to provide solutions to the problem identified and therefore reduce risk of injury for the operators.