Genetic analyses such as linkage and genome wide association studies (GWAS) have been extremely successful at identifying genomic regions that harbour genetic variants contributing to complex disorders. Over 90% of disease-associated variants from GWAS fall within non-coding regions (Maurano et al., 2012). However, pinpointing the causal variants has proven a major bottleneck to genetic research. To address this I have developed SuRFR, an R package for the ranked prioritisation of candidate causal variants by predicted function. SuRFR produces rank orderings of variants based upon functional genomic annotations, including DNase hypersensitivity signal, chromatin state, minor allele frequency, and conservation. The ranks for each annotation are combined into a final prioritisation rank using a weighting system that has been parametrised and tested through ten-fold cross-validation. SuRFR has been tested extensively upon a combination of synthetic and real datasets and has been shown to perform with high sensitivity and specificity. These analyses have provided insight into the extent to which different classes of functional annotation are most useful for the identification of known regulatory variants: the most important factor for identifying a true variant across all classes of regulatory variants is position relative to genes. I have also shown that SuRFR performs at least as well as its nearest competitors whilst benefiting from the advantages that come from being part of the R environment. I have applied SuRFR to several genomics projects, particularly the study of psychiatric illness, including genome sequencing of a large Scottish family with bipolar disorder. This has resulted in the prioritisation of such variants for future study.

Selecting the right project is critical for an organisation's success because resources are limited. From an economics perspective, the loss in opportunity for an organisation in doing the wrong project is expensive. This investment can be used for doing the right project for achieving competitive advantage and implementing business strategies. As a result, there are many frameworks with techniques and tools available in the literature for assisting organisations in project selection and prioritisation. All techniques or tools have their own advantages and disadvantages and these frameworks do not fit “one for all”. The framework can be business specific; therefore it is necessary to understand what the targeted industry considers as the “best practice”.

The landscape of security threats continues to evolve, with attacks becoming more serious and the number of vulnerabilities rising. To manage these threats, many security studies have been undertaken in recent years, mainly focusing on improving detection, prevention and response efficiency. Although there are security tools such as antivirus software and firewalls available to counter them, Intrusion Detection Systems and similar tools such as Intrusion Prevention Systems are still one of the most popular approaches. There are hundreds of published works related to intrusion detection that aim to increase the efficiency and reliability of detection, prevention and response systems. Whilst intrusion detection system technologies have advanced, there are still areas available to explore, particularly with respect to the process of selecting appropriate responses. Supporting a variety of response options, such as proactive, reactive and passive responses, enables security analysts to select the most appropriate response in different contexts. In view of that, a methodical approach that identifies important incidents as opposed to trivial ones is first needed. However, with thousands of incidents identified every day, relying upon manual processes to identify their importance and urgency is complicated, difficult, error-prone and time-consuming, and so prioritising them automatically would help security analysts to focus only on the most critical ones. The existing approaches to incident prioritisation provide various ways to prioritise incidents, but less attention has been given to adopting them into an automated response system. Although some studies have realised the advantages of prioritisation, they released no further studies showing they had continued to investigate the effectiveness of the process. This study concerns enhancing the incident prioritisation scheme to identify critical incidents based upon their criticality and urgency, in order to facilitate an autonomous mode for the response selection process in Intrusion Response Systems. To achieve this aim, this study proposed a novel framework which combines models and strategies identified from the comprehensive literature review. A model to estimate the level of risks of incidents is established, named the Risk Index Model (RIM). With different levels of risk, the Response Strategy Model (RSM) dynamically maps incidents into different types of response, with serious incidents being mapped to active responses in order to minimise their impact, while incidents with less impact have passive responses. The combination of these models provides a seamless way to map incidents automatically; however, it needs to be evaluated in terms of its effectiveness and performances. To demonstrate the results, an evaluation study with four stages was undertaken; these stages were a feasibility study of the RIM, comparison studies with industrial standards such as Common Vulnerabilities Scoring System (CVSS) and Snort, an examination of the effect of different strategies in the rating and ranking process, and a test of the effectiveness and performance of the Response Strategy Model (RSM). With promising results being gathered, a proof-of-concept study was conducted to demonstrate the framework using a live traffic network simulation with online assessment mode via the Security Incident Prioritisation Module (SIPM); this study was used to investigate its effectiveness and practicality. Through the results gathered, this study has demonstrated that the prioritisation process can feasibly be used to facilitate the response selection process in Intrusion Response Systems. The main contribution of this study is to have proposed, designed, evaluated and simulated a framework to support the incident prioritisation process for Intrusion Response Systems.

Purpose - The purpose of this master thesis is to investigate the possibilities to extend or change the base of IKEA’s SL classification and give recommendations concerning potential improvements.  Method - This thesis has an inductive research strategy since data has been collected to build theory rather than the other way around (Bryman and Bell, 2007). The data has been collected by qualitative research, mainly through interviews with employees at the different IKEA organisations. Empirics - The empirical data gathered describes the service level in practice at IKEA. In order to get an overview of the conflicting interests in the different functions, the chapter is divided into four themes; how IKEA works with SL, the purpose of SL, customer service and suggestion to the design of the SL classification. Theory - The theory has been based on our empirical findings in order to find the best solution for IKEA. The theory includes different classification models, the relationship between customer service and SL and is finished with a section on how to measure availability. Conclusions - The conclusion that could be drawn was that the purpose of the classification was not perceived in the same way within the company and that both internal and external information is needed. A new model is presented that takes into account the different products, buying situations, and customer reactions on OOS, which are important parameters for consumer perception of availability and customer service. By using this model IKEA will be able to fulfil the two, sometimes conflicting purposes; to secure the sales and increase customer satisfaction.

The New Zealand health system is two-tiered with elective treatments are performed by both publicly funded state hospitals and by private hospitals. Publicly funded operations are rationed using a prioritisation system which was introduced in 1998 to curtail expanding waiting lists for elective surgery. One of the aims of the new booking system was to generate national tools for prioritising patients in order to improve the equality of access to public elective surgery throughout New Zealand. However, priority scoring systems were not implemented in a consistent manner and access to elective surgery remains very unequal. Despite large media attention and a high public profile, waiting times have attracted little research in medical geography or within the wider social sciences community. The subject has been partly reserved for public health commentators within the medical field, who have found that variation in waiting times has much to do with the referral practices of physicians, the management of waiting lists by District Health Board (DHB) staff and the amount of private practice that occurs within each district. Most notably several studies have identified that in areas associated with high private admissions, patients tend to suffer higher waiting times for the same procedures in the public hospital system. This study examines the performance of the New Zealand Booking System (NZBS) during the years 2004 to 2007 to assess the equitable delivery of publicly funded elective surgery procedures. Waiting times (NBRS) and admissions (NMDS) datasets were sourced from the New Zealand Health and Information Service (NZHIS) of The Ministry of Health. Mean and Median waiting times were compared spatially between each of New Zealand’s 21 DHBs, compared with Australian waiting times and then broken down into five common medical specialties. Waiting times were then analysed by ethnicity, level of material deprivation and other individual factors using data from the 2006 New Zealand Census. Finally, rates of admissions were calculated for the public and private hospital sectors during the study period. These were used to correlate waiting times results with the amount of private practice in each DHB. ACC cases were extracted from the dataset to avoid bias in waiting times as much of this work is contracted out to the private sector and not subject to lengthy waiting times for treatment. A number of medical specialists and hospital administrators were interviewed to discuss results, explain prioritisation tools and management practices. Results showed large variations in the median waiting times of New Zealand DHBs. A north south gradient is observed in which southern DHBs suffer longer waits for care. Vastly better results were observed for Australian public hospitals than those seen in New Zealand. For waiting times as determined by individual factors, Maori and Pacific Island patients and those from lower socio-economic backgrounds suffered longer waiting times nationwide although, in certain DHBs inequalities for access to elective surgery were exacerbated. However, ethnic differences were more pronounced than socio-economic variations. Admissions results showed significant positive correlations between the amount of private practice and the waiting times experienced in each DHB which are supported by previous research. Feedback from interviews confirmed inconsistency in the use of scoring tools, manipulation occurring on behalf of the DHB management to achieve performance goals set by the Ministry of Health and provided some further explanation of the other quantitative results. Access to elective surgery is determined partly by location of residence, ethnicity, deprivation and where hospital resources are located but most importantly by the willingness to pay for treatment within the private hospital sector and the ability to manipulate the public prioritisation system.

This study concerns the decisions and expertise of speech and language therapists (sits) working with preschool children, in particular, the selection and prioritisation of newly referred youngsters for therapy. The literature review covers three aspects: the difficulties of identifying communication disorders in preschool children; the nature of speech & language therapy knowledge; the nature of the selection and prioritisation task. These three aspects provide the theoretical foundations of the study and gave rise to the selection of a multimethod and predominantly qualitative methodology. Using a series of knowledge elicitation tasks, the selection and prioritisation decision was explored. A small group of expert slts participated in semistructured interviews, case history analyses, focus group discussions and card sorting exercises. The results are summarised under three headings: the child, the process and the expertise. The study identifies areas considered significant in the discrimination of priority children. In particular, the co-consideration of the child's communication skills and the supporting communicative context emerged as the key categories. Features within these categories associated with priority and nonpriority children were identified. The process emerged as one whereby sits collected and evaluated baseline descriptions of the child and context. As these findings accumulated, they were judged as to their diagnostic and prognostic significance, as evidence of progress and as potential causes for sit concern. Substantial consensus was demonstrated between sits suggesting that the knowledge elicited emanated from a body of knowledge rather than being idiosyncratic. Even where variation occurred, patterns were evident, reflecting the possible existence of theories-of-action related to differing working contexts. The results are presented as theories-of-action which underpin slts decisions. As such they will be of support to junior sits in their understanding of the selection and prioritisation task and to more experienced slts in making their own decisions explicit.

Anthropogenic activities have drastically altered chemical exposure, with traces of synthetic chemicals detected ubiquitously in the environment. Many of these chemicals are thought to perturb endocrine function, leading to declines in reproductive health and fertility, and increases in the incidence of cancer, metabolic disorders and diabetes. There are over 90 million unique chemicals registered under the Chemical Abstracts Service (CAS), of which only 308,000 were subject to inventory and/or regulation, in September 2013. However, as a specific aim of the EU REACH regulations, the UK is obliged to reduce the chemical safety initiatives reliance on in vivo apical endpoints, promoting the development and validation of alternative mechanistic methods. The human health cost of endocrine disrupting chemical (EDC) exposure in the EU, has been estimated at €31 billion per annum. In light of the EU incentives, this study aims to evaluate current in silico and in vitro tools for EDC screening and hazard characterisation; testing the hypothesis that in silico virtual screening accurately predicts in vitro mechanistic assays. Nuclear receptor binding interactions are the current focus of in silico and in vitro tools to predict EDC mechanisms. To the author’s knowledge, no single study has quantitatively assessed the relationship between in silico nuclear receptor binding and in vitro mechanistic assays, in a comprehensive manner. Tripos ® SYBYL software was used to develop 3D-molecular models of nuclear receptor binding domains. The ligand binding pockets of estrogen (ERα and ERβ), androgen (AR), progesterone (PR) and peroxisome proliferator activated (PPARγ) receptors were successfully modelled from X-ray crystal structures. A database of putative-EDC ligands (n= 378), were computationally ‘docked’ to the pseudo-molecular targets, as a virtual screen for nuclear receptor activity. Relative to in vitro assays, the in silico screen demonstrated a sensitivity of 94.5%. The SYBYL Surflex-Dock method surpassed the OECD Toolbox ER-Profiler, DfW and binary classification models, in correctly identifying endocrine active substances (EAS). Aiming to evaluate the current in vitro tools for endocrine MoA, standardised ERα transactivation (HeLa9903), stably transfected AR transactivation (HeLa4-11) assays in addition to novel transiently transfected reporter gene assays, predicted the mechanism and potency of test substances prioritised from the in silico results (n = 10 potential-EDCs and 10 hormone controls). In conclusion, in silico SYBYL molecular modelling and Surflex-Dock virtual screening sensitively predicted the binding of ERα/β, AR, PR and PPARγ potential EDCs, and was identified as a potentially useful regulatory tool, to support EAS hazard identification.

No / Symptoms and signs (symptoms in brief) are the essential clinical manifestations for traditional Chinese medicine (TCM) diagnosis and treatments. To gain insights into the molecular mechanism of symptoms, this paper presents a network-based data mining method to integrate multiple phenotype-genotype data sources and predict the prioritizing gene rank list of symptoms. The result of this pilot study suggested some insights on the molecular mechanism of symptoms.

Yes / Smart city development is gaining considerable recognition in the systematic literature and international policies throughout the world. The study aims to identify the key barriers of smart cities from a review of existing literature and views of experts in this area. This work further makes an attempt on the prioritisation of barriers to recognise the most important barrier category and ranking of specific barriers within the categories to the development of smart cities in India. Through the existing literature, this work explored 31 barriers of smart cities development and divided them into six categories. This research work employed fuzzy Analytic Hierarchy Process (AHP) technique to prioritise the selected barriers. Findings reveal that ‘Governance’ is documented as the most significant category of barriers for smart city development followed by ‘Economic; ‘Technology’; ‘Social’; ‘Environmental’ and ‘Legal and Ethical’. In this work, authors also performed sensitivity analysis to validate the findings of study. This research is useful to the government and policymakers for eradicating the potential interferences in smart city development initiatives in developing countries like India.

Thesis (MEng)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Bridges are amongst the most important structures of any highway network. Once the bridge construction is complete and a bridge is put into service, it is subjected to deteriorations. An effective condition assessment, as a component of bridge management system, is therefore necessary to keep bridges in admissible conditions of safety and serviceability. In South Africa, some bridge authorities do not have sufficient funds to carry out bridge inspections at required intervals. In the case where bridge authorities have enough funds, a systematic inspection is performed, covering a number of bridges that are not in need of inspection. Inspection and maintenance for a limited number of bridges randomly chosen may result in an increase of the number of bridges in critical conditions. A bridge inspection prioritisation method that takes into account the need of inspection of bridges is therefore needed for South African highway bridges. This research provides a prioritisation method for concrete bridge inspections by integration of nonprofessional inspectors, imagery inspection and deterioration models. To achieve the research objectives of this study, a literature study has been carried out to understand bridge inspection practice in general and South African practice in particular. The literature helped also to identify previous works on bridge inspection prioritisation, the use of information from informal sources, imagery inspection and involvement of non-professionals in bridge inspection and use of deterioration models in bridge management. A survey has been conducted amongst South African bridge authorities in order to fill the literature gaps. Inventory and inspection data of bridges managed by South African National Roads Agency Limited (SANRAL) was used to develop a deterioration model by considering bridge characteristics such as bridge age, number of spans, and bridge type. Based on the literature review, results of surveys and estimated regression parameters, a bridge inspection prioritisation method has been developed. This method comprises three phases. The first phase is the initial screening that consists of an identification of bridges with critical defects that have not been repaired yet. These bridges, to which are added bridges that have not been inspected in the previous inspection, constitute the first inspection priority category. The second phase is an imagery screening which is an analysis of digital photographs for detection of defects that need urgent assessment by professional inspectors. The analysed photographs are taken by non-professional inspectors and uploaded to the Bridge Management System. The third phase is a grouping of bridges in inspection priority categories as a function of their physical characteristics and deteriorating factors using deterioration modelling. The method has been applied on SANRAL bridges using inspection ratings of 2011-2012. 422 SANRAL bridges have been categorised in the first inspection priority group by considering hydraulic related defects as critical. The third phase allowed to rank 522 possible combinations of bridges based on their characteristics. The developed method would help bridge authorities where inspection budget is limited, to prioritise bridge inspection as a function of needs of inspection. / AFRIKAANSE OPSOMMING: Brûe is ʼn belangrike deel van enige snelweg netwerk. Wanneer brugkonstruksie voltooi is en dit in diens gestel word, is die brug onderhewig aan skade en verval . 'n Doeltreffende toestandsassessering, as 'n komponent van ʼn brug bestuurstelsel, is dus nodig om brûe in ʼn toestand van veiligheid en diensbaarheid te hou. In Suid-Afrika het sommige brugowerhede nie genoeg fondse om bruginspeksies teen vereiste intervalle uit te voer nie. In die geval waar ʼn brugowerhede wel genoeg fondse het, word stelselmatige reekse inspeksies uitgevoer, waar brûe wat nie lukraaknoodwendig op daardie stadium inspeksie nodig het nie, ook soms ingesluit word. Inspeksie en onderhoud vir slegs 'n beperkte aantal brûe wat gekies word kan 'n toename veroorsaak in die aantal brûe wat in ʼn kritiese toestand is. 'n Bruginspeksie prioritiseringmetode wat brûe identifiseer vir inspeksie is dus nodig vir Suid-Afrikaanse brugowerhede. Hierdie navorsing stel 'n metode voor wat bruginspeksies prioritiseer deur gebruik te maak van nieprofessionele inspekteurs, inspeksie van foto’s en brugtoestandsvervalmodelle. Om die navorsings doelwitte van hierdie projek te bereik, is 'n literatuurstudie uitgevoer oor die praktyk van bruginspeksie in die algemeen, en meer spesifiek om die praktyk in Suid-Afrika te verstaan.. 'n Opname is voorts onder Suid-Afrikaanse brugowerhede uitgevoer om gapings in die literatuur aan te vul. Inventaris en inspeksie data van brûe wat bestuur word deur die Nasionale Padagentskap (SANRAL) is daarna gebruik om 'n toestand agteruitgangsmodel te ontwikkel deur die eienskappe soos brug ouderdom, aantal spanne en die tipe brug in ag te neem Gebaseer op die literatuur, resultate van opnames en beraamde regressie parameters is 'n brug inspeksie prioritiseringsmetode ontwikkel. Hierdie metode bestaan uit drie fases. Die eerste fase is die aanvanklike siftingsproses wat bestaan uit die identifisering van brûe met 'n kritiese defek wat nog nie herstel is sedert ʼn vorige inspeksie nie. Hierdie brûe, wat ingesluit word by ander brûe wat nie geïnspekteer was in die vorige inspeksie nie, is die eerste kategorie van inspeksie prioriteit. Die tweede fase is 'n ontleding van digitale foto's vir die opsporing van defekte wat dringende assessering deur professionele inspekteurs nodig het. Die foto's word geneem deur nie-professionele inspekteurs en dit word gelaai op die brug bestuurstelsel. Die derde fase is die groepering van brûe in inspeksie prioriteit kategorieë as 'n funksie van hul fisiese eienskappe en vervalfaktore met die hulp van agteruitgangsmodelle. Die metode is toegepas op die SANRAL brûe met die hulp van inspeksie graderings van 2011-2012. Deur die aanname van hidrouliese defekte as van kritiese belang, is 422 SANRAL brûe in die eerste inspeksie prioriteit gegroepeer. Die derde fase prioritiseer 522 moontlike kombinasies van brûe op grond van hul fisiese eienskappe. Die metode sal brugowerhede waar inspeksie begrotings beperk is, help om bruginspeksies te prioritiseer as 'n funksie van die noodsaaklikheid van inspeksie.