Methods matter: computational modelling in public health policy and planning

This work is aimed at understanding and unifying information on epidemiological modelling methods and how those methods relate to public policy addressing human health, specifically in the context of infectious disease prevention, pandemic planning, and health behaviour change. This thesis employs multiple qualitative and quantitative methods, and presents as a manuscript of several individual, data-driven projects that are combined in a narrative arc. The first chapter introduces the scope and complexity of this interdisciplinary undertaking, describing several topical intersections of importance. The second chapter begins the presentation of original data, and describes in detail two exercises in computational epidemiological modelling pertinent to pandemic influenza planning and policy, and progresses in the next chapter to present additional original data on how the confidence of the public in modelling methodology may have an effect on their planned health behaviour change as recommended in public health policy. The thesis narrative continues in the final data-driven chapter to describe how health policymakers use modelling methods and scientific evidence to inform and construct health policies for the prevention of infectious diseases, and concludes with a narrative chapter that evaluates the breadth of this data and recommends strategies for the optimal use of modelling methodologies when informing public health policy in applied public health scenarios.

Synthesis and structural stability of metal-organic frameworks

Metal-organic frameworks (MOFs) have attracted significant attention during the past decade due to their high porosity, tunable structures, and controllable surface functionalities. Therefore many applications have been proposed for MOFs. All of them however are still in their infancy stage and have not yet been brought into the market place. In this thesis, the background of the MOF area is first briefly introduced. The main components and the motifs of designing MOFs are summarized, followed by their synthesis and postsynthetic modification methods. Several promising application areas of MOFs including gas storage and separation, catalysis and sensing are reviewed. The current status of commercialization of MOFs as new chemical products is also summarized. Examples of the design and synthesis of two new MOF structures Eu(4,4′,4′′,4′′′-(porphine-5,10,15,20-tetrayl)tetrakis(benzoic acid))·2H2O∙xDMF and Zn4O(azobenzene-4,4’-dicarboxylic acid)3∙xNMP are described. The first one contains free-base porphyrin centers and the second one has azobenzene components. Although the structures were synthesized as designed, unfortunately they did not possess the expected properties. The research idea to use MOFs as template materials to synthesize porous polymers is introduced. Several methods are discussed to grow PMMA into IRMOF-1 (Zn4O(benzene-1,4-dicarboxylate)3, IR stands for isoreticular) structure. High concentration of the monomers resulted in PMMA shell after MOF digestion while with low concentration of monomers no PMMA was left after digestion due to the small iii molecular weight. During the study of this chapter, Kitagawa and co-workers published several papers on the same topic, so this part of the research was terminated thereafter. Many MOFs are reported to be unstable in air due to the water molecules in air which greatly limited their applications. By incorporating a number of water repelling functional groups such as trifluoromethoxy group and methyl groups in the frameworks, the water stability of MOFs are shown to be significantly enhanced. Several MOFs inculding Banasorb-22 (Zn4O(2-trifluoromethoxybenzene-1,4-dicarboxylate)3), Banasorb-24 (Zn4O(2, 5-dimethylbenzene-1,4-dicarboxylate)3) and Banasorb-30 (Zn4O(2-methylbenzene-1,4-dicarboxylate)3) were synthesized and proved to have isostructures with IRMOF-1. Banasorb-22 was stable in boiling water steam for one week and Banasorb-30’s shelf life was over 10 months under ambient condition. For comparison, IRMOF-1’s structure collapses in air after a few hours to several days. Although MOF is a very popular research area nowadays, only a few studies have been reported on the mechanical properties of MOFs. Many of MOF’s applications involve high pressure conditions, so it is important to understand the behavior of MOFs under elivated pressures. The mechanical properties of IRMOF-1 and a new MOF structure Eu2(C12N2O4H6)3(DEF)0.87(H2O)2.13 were studied using diamond anvil cells at Advanced Photon Source. IRMOF-1 experienced an irriversible phase transtion to a nonporous phase followed by amorphization under high pressure. Eu2(C12N2O4H6)3(DEF)0.87(H2O)2.13 showed reversible compression under pressure up to 9.08GPa.

Improving drug discovery using hybrid softcomputing methods

Virtual screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface in order to find new hotspots, where ligands might potentially interact with, and which is implemented in last generation massively parallel GPU hardware, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods and concretely BINDSURF is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to improve accuracy of the scoring functions used in BINDSURF we propose a hybrid novel approach where neural networks (NNET) and support vector machines (SVM) methods are trained with databases of known active (drugs) and inactive compounds, being this information exploited afterwards to improve BINDSURF VS predictions.

Nutritional risk among surgery patients and associations with hospital stay and postoperative complications

Introduction and Objectives: Nutritional Risk Screening (NRS 2002) is employed to identify nutritional risk in the hospital setting and determine which patients would benefit from nutritional support. The aim of the present study was to identify nutritional risk in patients admitted to the surgery ward and determine possible associations with hospital stay and postoperative complications. Methods: Three hundred fifteen surgery patients were evaluated in the first 24 hours since admission. Evaluations involved the calculation of the body mass index, the determination of weight loss ≥ 5% in the previous six months and the assessment of nutritional risk using the NRS 2002. Hospital stay (in days) and postoperative complications were also recorded. Results: A total of 31.1% of the patients were classified as being "at risk", among whom 98.3% had food intake 50% lower than habitual intake, 65.9% had weight loss ≥ 5% in the previous six months, 64.7% had a diagnosis of neoplasm, 59.9% were aged ≥ 60 years and 59.9% were candidates for non-elective surgery. Postoperative complications were recorded in 4.4% of the overall sample and were more frequent in patients at nutritional risk (p < 0.000). Hospital stay was also longer among the patients at nutritional risk (p < 0.01). Conclusion: A high percentage of surgery patients were at nutritional risk in the present study and associations were found with age ≥ 60 years, a diagnosis of neoplasm, non-elective surgery of the gastrointestinal tract, a reduction in habitual food intake and weight loss. Patients at nutritional risk had a greater frequency of postoperative complications and a longer hospital stay.

A review of patients with advanced cervical cancer presenting to palliative care services at Queen Elizabeth Central Hospital in Blantyre, Malawi

Background Cervical cancer is the commonest cancer affecting women in Malawi, which has the highest rate of this disease in the world. Most cases are diagnosed at an advanced stage. Aim To describe the symptom burden, palliative care interventions, and outcomes of cervical cancer patients who entered care at Tiyanjane Clinic in Blantyre, Malawi, between January and December 2012. Methods We reviewed the case files of 72 patients presenting to our hospital-based palliative care service over one year. Results The mean age was 49.5 years. Twenty-six patients (36%) were HIVpositive and the majority of these (n = 22; 85%) were on antiretroviral medication at presentation to palliative care. Pain (n = 66; 92%), vaginal discharge (n = 44; 61%), and unpleasant odour (n = 37; 51%) were commonly reported. Over a third of patients (n = 26; 36%) reported pain in two or more sites. Fourteen patients (19%) reported vaginal bleeding. Spousal breakdown (through widowhood or divorce) was noted in over half (n = 41; 57%) of all cases. Pain relief was provided to 69 (96%) of the patients (morphine to 40 patients; 56%). Common interventions provided included metronidazole tablets (used vaginally), sanitary items, and counselling. At the end of the study period, 18 patients (25%) were still under the care of palliative services. Conclusions Access to medications such as morphine, metronidazole and tranexamic acid can improve quality of life, even when radiotherapy is limited. Health care teams require necessary skills and training, including how to perform a comprehensive assessment, with an emphasis on the provision of psychosexual counselling, to assist with the complexity of symptoms occurring in this vulnerable group.

Modelling and analysing cargo screening processes: a project outline

The efficiency of current cargo screening processes at sea and air ports is unknown as no benchmarks exists against which they could be measured. Some manufacturer benchmarks exist for individual sensors but we have not found any benchmarks that take a holistic view of the screening procedures assessing a combination of sensors and also taking operator variability into account. Just adding up resources and manpower used is not an effective way for assessing systems where human decision-making and operator compliance to rules play a vital role. For such systems more advanced assessment methods need to be used, taking into account that the cargo screening process is of a dynamic and stochastic nature. Our project aim is to develop a decision support tool (cargo-screening system simulator) that will map the right technology and manpower to the right commodity-threat combination in order to maximize detection rates. In this paper we present a project outline and highlight the research challenges we have identified so far. In addition we introduce our first case study, where we investigate the cargo screening process at the ferry port in Calais.

Análise de componentes arquitetônicos para potencialização da ventilação natural com ênfase em captadores de vento

The building envelope is the principal mean of interaction between indoors and environment, with direct influence on thermal and energy performance of the building. By intervening in the envelope, with the proposal of specific architectural elements, it is possible to promote the use of passive strategies of conditioning, such as natural ventilation. The cross ventilation is recommended by the NBR 15220-3 as the bioclimatic main strategy for the hot and humid climate of Natal/RN, offering among other benefits, the thermal comfort of occupants. The analysis tools of natural ventilation, on the other hand, cover a variety of techniques, from the simplified calculation methods to computer fluid dynamics, whose limitations are discussed in several papers, but without detailing the problems encountered. In this sense, the present study aims to evaluate the potential of wind catchers, envelope elements used to increase natural ventilation in the building, through CFD simplified simulation. Moreover, it seeks to quantify the limitations encountered during the analysis. For this, the procedure adopted to evaluate the elements implementation and efficiency was the CFD simulation, abbreviation for Computer Fluid Dynamics, with the software DesignBuilder CFD. It was defined a base case, where wind catchers were added with various settings, to compare them with each other and appreciate the differences in flows and air speeds encountered. Initially there has been done sensitivity tests for familiarization with the software and observe simulation patterns, mapping the settings used and simulation time for each case simulated. The results show the limitations encountered during the simulation process, as well as an overview of the efficiency and potential of wind catchers, with the increase of ventilation with the use of catchers, differences in air flow patterns and significant increase in air speeds indoors, besides changes found due to different element geometries. It is considered that the software used can help designers during preliminary analysis in the early stages of design

Use of BARD scoring system in non-alcoholic fatty liver disease patients and its correlation with ultrasonographic grading in Gizan, Saudi Arabia

Purpose: To assess the efficacy of the BARD scoring system in Saudi non‐alcoholic fatty liver disease (NAFLD) patients attending Gizan General Hospital and to identify the clinical variables associated with advanced fibrosis. . Methods: The cross-sectional study involved 120 patients aged ≥ 18 years who attended the Ultrasound Department of Gizan General Hospital, Gizan, Saudi Arabia, during January – June 2013. BARD scoring system comprised the following variables: body mass index (BMI) ≥ 28 = 1 point, aspartate aminotransferase/alanine aminotransferase (AST/ALT) ratio ≥ 0.8 = 2 points, and type 2 diabetes mellitus = 1 point. Results: Patients with advanced fibrosis were older (55.0 years) than patients with no/mild fibrosis (48.6 years), albeit not significantly so. A higher BMI was associated with advanced fibrosis in males, females and all study participants (p = 0.013, 0.016 and 0.001, respectively). Advanced fibrosis was more common in older patients with a higher weight to height ratio. Logistic regression suggested that age ≥ 50 years was associated with a 2.52-fold increase in the risk of advanced fibrosis, but this did not have a significant clinical impact (p = 0.087). BMI > 28 was associated with a 26.73-fold increased risk of advanced fibrosis, while AST/ALT ≥ 0.8 was associated with an 18.46-fold increased risk of advanced liver fibrosis (p = 0.002 and 0.006, respectively). Conclusion: The major risk factors for advanced fibrosis using BARD scoring system in patients with NAFLD were old age, BMI > 28, and AST/ALT ≥ 0.8. In addition, grade 3 ultrasonographic fatty liver significantly correlated with advanced fibrosis.

Estudo comparativo da utilização do nitrogênio como fluido alternativo após a injeção de vapor

Currently, due to part of world is focalized to petroleum, many researches with this theme have been advanced to make possible the production into reservoirs which were classified as unviable. Because of geological and operational challenges presented to oil recovery, more and more efficient methods which are economically successful have been searched. In this background, steam flood is in evidence mainly when it is combined with other procedures to purpose low costs and high recovery factors. This work utilized nitrogen as an alternative fluid after steam flood to adjust the best combination of alternation between these fluids in terms of time and rate injection. To describe the simplified economic profile, many analysis based on liquid cumulative production were performed. The completion interval and injection fluid rates were fixed and the oil viscosity was ranged at 300 cP, 1.000 cP and 3.000 cP. The results defined, for each viscosity, one specific model indicating the best period to stop the introduction of steam and insertion of nitrogen, when the first injected fluid reached its economic limit. Simulations in physics model defined from one-eighth nine-spot inverted were realized using the commercial simulator Steam, Thermal and Advanced Processes Reservoir Simulator STARS of Computer Modelling Group CMG

Subject response rates in case-control studies of cancer : time trends, study design determinants, and quality of reporting

Objectifs: Examiner les tendances temporelles, les déterminants en lien avec le design des études et la qualité des taux de réponse rapportés dans des études cas-témoins sur le cancer publiées lors des 30 dernières années. Méthodes: Une revue des études cas-témoins sur le cancer a été menée. Les critères d'inclusion étaient la publication (i) dans l’un de 15 grands périodiques ciblés et (ii) lors de quatre périodes de publication (1984-1986, 1995, 2005 et 2013) couvrant trois décennies. 370 études ont été sélectionnées et examinées. La méthodologie en lien avec le recrutement des sujets et la collecte de données, les caractéristiques de la population, les taux de participation et les raisons de la non-participation ont été extraites de ces études. Des statistiques descriptives ont été utilisées pour résumer la qualité des taux de réponse rapportés (en fonction de la quantité d’information disponible), les tendances temporelles et les déterminants des taux de réponse; des modèles de régression linéaire ont été utilisés pour analyser les tendances temporelles et les déterminants des taux de participation. Résultats: Dans l'ensemble, les qualités des taux de réponse rapportés et des raisons de non-participation étaient très faible, particulièrement chez les témoins. La participation a diminué au cours des 30 dernières années, et cette baisse est plus marquée dans les études menées après 2000. Lorsque l'on compare les taux de réponse dans les études récentes a ceux des études menées au cours de 1971 à 1980, il y a une plus grande baisse chez les témoins sélectionnés en population générale ( -17,04%, IC 95%: -23,17%, -10,91%) que chez les cas (-5,99%, IC 95%: -11,50%, -0,48%). Les déterminants statistiquement significatifs du taux de réponse chez les cas étaient: le type de cancer examiné, la localisation géographique de la population de l'étude, et le mode de collecte des données. Le seul déterminant statistiquement significatif du taux de réponse chez les témoins hospitaliers était leur localisation géographique. Le seul déterminant statistiquement significatif du taux de participation chez les témoins sélectionnés en population générale était le type de répondant (sujet uniquement ou accompagné d’une tierce personne). Conclusion: Le taux de participation dans les études cas-témoins sur le cancer semble avoir diminué au cours des 30 dernières années et cette baisse serait plus marquée dans les études récentes. Afin d'évaluer le niveau réel de non-participation et ses déterminants, ainsi que l'impact de la non-participation sur la validité des études, il est nécessaire que les études publiées utilisent une approche normalisée pour calculer leurs taux de participation et qu’elles rapportent ceux-ci de façon transparente.

Recent advances in explaining hedge fund returns:implicit factors and exposures

We survey articles covering how hedge fund returns are explained, using largely non-linear multifactor models that examine the non-linear pay-offs and exposures of hedge funds. We provide an integrated view of the implicit factor and statistical factor models that are largely able to explain the hedge fund return-generating process. We present their evolution through time by discussing pioneering studies that made a significant contribution to knowledge, and also recent innovative studies that examine hedge fund exposures using advanced econometric methods. This is the first review that analyzes very recent studies that explain a large part of hedge fund variation. We conclude by presenting some gaps for future research.

Subject response rates in case-control studies of cancer : time trends, study design determinants, and quality of reporting

Objectifs: Examiner les tendances temporelles, les déterminants en lien avec le design des études et la qualité des taux de réponse rapportés dans des études cas-témoins sur le cancer publiées lors des 30 dernières années. Méthodes: Une revue des études cas-témoins sur le cancer a été menée. Les critères d'inclusion étaient la publication (i) dans l’un de 15 grands périodiques ciblés et (ii) lors de quatre périodes de publication (1984-1986, 1995, 2005 et 2013) couvrant trois décennies. 370 études ont été sélectionnées et examinées. La méthodologie en lien avec le recrutement des sujets et la collecte de données, les caractéristiques de la population, les taux de participation et les raisons de la non-participation ont été extraites de ces études. Des statistiques descriptives ont été utilisées pour résumer la qualité des taux de réponse rapportés (en fonction de la quantité d’information disponible), les tendances temporelles et les déterminants des taux de réponse; des modèles de régression linéaire ont été utilisés pour analyser les tendances temporelles et les déterminants des taux de participation. Résultats: Dans l'ensemble, les qualités des taux de réponse rapportés et des raisons de non-participation étaient très faible, particulièrement chez les témoins. La participation a diminué au cours des 30 dernières années, et cette baisse est plus marquée dans les études menées après 2000. Lorsque l'on compare les taux de réponse dans les études récentes a ceux des études menées au cours de 1971 à 1980, il y a une plus grande baisse chez les témoins sélectionnés en population générale ( -17,04%, IC 95%: -23,17%, -10,91%) que chez les cas (-5,99%, IC 95%: -11,50%, -0,48%). Les déterminants statistiquement significatifs du taux de réponse chez les cas étaient: le type de cancer examiné, la localisation géographique de la population de l'étude, et le mode de collecte des données. Le seul déterminant statistiquement significatif du taux de réponse chez les témoins hospitaliers était leur localisation géographique. Le seul déterminant statistiquement significatif du taux de participation chez les témoins sélectionnés en population générale était le type de répondant (sujet uniquement ou accompagné d’une tierce personne). Conclusion: Le taux de participation dans les études cas-témoins sur le cancer semble avoir diminué au cours des 30 dernières années et cette baisse serait plus marquée dans les études récentes. Afin d'évaluer le niveau réel de non-participation et ses déterminants, ainsi que l'impact de la non-participation sur la validité des études, il est nécessaire que les études publiées utilisent une approche normalisée pour calculer leurs taux de participation et qu’elles rapportent ceux-ci de façon transparente.

A Diagnostic Calculator for Detecting Glaucoma on the Basis of Retinal Nerve Fiber Layer, Optic Disc, and Retinal Ganglion Cell Analysis by Optical Coherence Tomography

Purpose: The purpose of this study was to develop and validate a multivariate predictive model to detect glaucoma by using a combination of retinal nerve fiber layer (RNFL), retinal ganglion cell-inner plexiform (GCIPL), and optic disc parameters measured using spectral-domain optical coherence tomography (OCT). Methods: Five hundred eyes from 500 participants and 187 eyes of another 187 participants were included in the study and validation groups, respectively. Patients with glaucoma were classified in five groups based on visual field damage. Sensitivity and specificity of all glaucoma OCT parameters were analyzed. Receiver operating characteristic curves (ROC) and areas under the ROC (AUC) were compared. Three predictive multivariate models (quantitative, qualitative, and combined) that used a combination of the best OCT parameters were constructed. A diagnostic calculator was created using the combined multivariate model. Results: The best AUC parameters were: inferior RNFL, average RNFL, vertical cup/disc ratio, minimal GCIPL, and inferior-temporal GCIPL. Comparisons among the parameters did not show that the GCIPL parameters were better than those of the RNFL in early and advanced glaucoma. The highest AUC was in the combined predictive model (0.937; 95% confidence interval, 0.911–0.957) and was significantly (P = 0.0001) higher than the other isolated parameters considered in early and advanced glaucoma. The validation group displayed similar results to those of the study group. Conclusions: Best GCIPL, RNFL, and optic disc parameters showed a similar ability to detect glaucoma. The combined predictive formula improved the glaucoma detection compared to the best isolated parameters evaluated. The diagnostic calculator obtained good classification from participants in both the study and validation groups.

European Guidelines for soil and water bioengineering

Basic principles of soil and water bioengineering; Calculation of soil and water bioengineering stabilisation measures; Soils and water bioengineering methods; Maintenance of soil and water bioengineering structures; Eficience review of soil and water bioengineering methods