The tumour suppressor p53 protein plays a central role in the DNA damage response/checkpoint pathways leading to DNA repair, cell cycle arrest, apoptosis and senescence. The activation of p53-mediated pathways is primarily facilitated by the binding of tetrameric p53 to two 'half-sites', each consisting of a decameric p53 response element (RE). Functional REs are directly adjacent or separated by a small number of 1-13 'spacer' base pairs (bp). The p53 RE is detected by exact or inexact matches to the palindromic sequence represented by the regular expression [AG][AG][AG]C[AT][TA]G[TC][TC][TC] or a position weight matrix (PWM). The use of matrix-based and regular expression pattern-matching techniques, however, leads to an overwhelming number of false positives. A more specific model, which combines multiple factors known to influence p53-dependent transcription, is required for accurate detection of the binding sites. In this thesis, we present a logistic regression based model which integrates sequence information and epigenetic information to predict human p53 binding sites. Sequence information includes the PWM score and the spacer length between the two half-sites of the observed binding site. To integrate epigenetic information, we analyzed the surrounding region of the binding site for the presence of mono- and trimethylation patterns of histone H3 lysine 4 (H3K4). Our model showed a high level of performance on both a high-resolution data set of functional p53 binding sites from the experimental literature (ChIP data) and the whole human genome. Comparing our model with a simpler sequence-only model, we demonstrated that the prediction accuracy of the sequence-only model could be improved by incorporating epigenetic information, such as the two histone modification marks H3K4me1 and H3K4me3.

This thesis examines how regional-level factors combined with firm-level factors influence innovation in an emerging economy – India. Past literature has shown that differences in both country contexts and firm-level factors influence innovation. The bulk of this literature tended to focus on developed economies. The handful of studies that have considered contextual differences have studied these at the country-level or within regional blocks such as regions of Europe or Africa. There is a paucity of research, which investigates how differences in state-level factors within a single country combined with firm-level factors influence innovation within firms. Therefore, it is an open question whether the findings derived from developed economies and country-level studies apply equally to emerging economies, particularly at the state level within a single country. Thus, there is a gap in the literature regarding our understanding of the impact of combined state- and firm-level factors on innovation within a single country. This thesis aims to contribute to a better understanding of how state and firm-level factors drive innovation in India, an emerging economy. India is selected because it is a fast-growing emerging economy that is increasingly being integrated into the globalized world economy and thus understanding how these factors influence innovation in an emerging economy would complement the literature that focuses on developed countries. Moreover, India is a huge country with substantial varieties in resources, capabilities, institutions (both formal and informal institutions) as well as ethnic, religious, and cultural varieties. Contextually, these state-level differences are quite different from regions in the developed world where institutional differences tend to be relatively consistent (less varieties). Thus, the insights generated from this study of the Indian context complement prior research by identifying the state and firm factors that combine to drive firm-level innovation. This study also extends the innovation literature by focussing on state-level differences within a single emerging economy, for which there is limited research. The findings could also have practical managerial and policy implications. From a policy perspective, policymakers in India can get a deeper understanding of the relevant factors that influence firm-level innovation so that they can direct policy and resources to promote innovation in their respective states. From a managerial perspective, managers can also get a better understanding of strategies and investments they should take to enhance innovation within their firms. This study is based on data gathered from various sources including the World Bank Enterprise Survey and several sources from within India (Indiastat.com, NCAER State Investment Potential Index, India Innovation Index). The World Bank Enterprise Survey provides firm-level data while state-level data were obtained from the other reputable sources in India. The data were analyzed using logistic regression and multi-level modeling, given that firms are nested within states, thus, we can simultaneously model the micro and macro levels to assess the relevance of the regional context. The results of this study show that regional factors such as regulatory quality, corruption, and rule of law barriers negatively influence innovation in firms that invest in internal R&D to promote innovation. The results also show that regions that devote a higher proportion of their gross domestic product to innovation achieve higher levels of innovation. Further, regions that have higher levels of human capital stock (more skilled workers) and export technology tend to be more innovative. At the firm level, investments in both internal and external R&D and those that have highly experienced managers are more innovative than their peers. These results suggest that governments and policymakers can increase innovative activities of firms by providing a highly skilled labor force, invest heavily in R&D, reduce corruption, regulatory quality, and the rule of law barriers. For firm-level managers, this study indicates that higher levels of managerial capability and greater investments in both internal and external R&D can enhance the technical and innovative capabilities (absorptive capacity) of their firms. This may result in a competitive advantage through increased innovation.

This project is dedicated to the problem of vehicle classification using inductive loop sensors. We created the dataset that contains more than 11000 labeled inductive loop signatures collected at different times and from different parts of the world. Multiple classification methods and their optimizations were employed to the vehicle classification. Final model that combines K-nearest neighbors and logistic regression achieves 94\% accuracy on classification scheme with 9 classes. The vehicle classifier was implemented in C++.

No description available.

The purpose of this thesis was to use a quantitative method to expand on previous research in the field of start-up success prediction. This was accomplished by including more criteria in the study, which was made possible by the Crunchbase database, which is the largest available information source for start-ups. Furthermore, the data used in this thesis was limited to Western European start-ups only in order to study the effects of limiting the data to a certain geographical region on the prediction models, which to our knowledge has not been done before in this type of research. The quantitative method used was machine learning and specifically the three machine learning predictors used in this thesis were Logistic Regression, Random Forest and K-nearest Neighbor (KNN). All three models proposed and evaluated have a better prediction accuracy than guessing the outcome at random. When tested on data previously unknown to the model, Random Forest produced the greatest results, predicting a successful company as a success and a failed company as a failure with 79 percent accuracy. With accuracies of 65 percent and 59 percent, respectively, both logistic regression and K-Nearest Neighbor (KNN) were close behind. / Syftet med denna avhandling var att använda en kvantitativ metod för att utöka tidigare forskning inom modellering av framgångsfaktorer för start-ups genom maskininlärning. Detta kunde åstadkommas genom att inkludera fler kriterier i studien än vad som har gjorts tidigare, vilket möjliggjordes av Crunchbase-databasen, som är den största tillgängliga informationskällan för nystartade företag. Dessutom är den data som användes i denna avhandling begränsad till endast västeuropeiska start-ups för att studera effekterna av att begränsa data till ett visst geografiskt område i prediktionsmodellerna, vilket inte har gjorts tidigare i denna typ av forskning. Den kvantitativa metoden som användes var maskininlärning och specifikt var de tre maskininlärningsmodellerna som användes i denna avhandling Logistic Regression, Random Forest och K-Nearest Neighbor (KNN). Alla tre modeller som inkluderats och utvärderats har en bättre förutsägelsesnoggrannhet än att gissa resultatet slumpmässigt. När modellerna testades med data som tidigare varit okänd för modellerna, gav Random Forest det bästa resultatet och predikterade ett framgångsrikt företag korrekt och ett misslyckat företag korrekt med 79 procents noggrannhet. Nära efter kom både K-Nearest Neighbor (KNN) och Logistic Regression med respektive noggrannheter på 65 och 59 procent.

No description available.

This research addresses the novel application of design of experiment, artificial neural net-works and logistic regression to study the effect of demographic characteristics on the risk of acquiring HIV infection among the antenatal clinic attendees in South Africa. The annual antenatal HIV survey is the only major national indicator for HIV prevalence in South Africa. This is a vital technique to understand the changes in the HIV epidemic over time. The annual antenatal clinic data contains the following demographic characteristics for each pregnant woman; age (herein called mother's age), partner's age (herein father's age), population group (race), level of education, gravidity (number of pregnancies), parity (number of children born), HIV and syphilis status. This project applied a screening design of experiment technique to rank the effects of individual demographic characteristics on the risk of acquiring an HIV infection. There are a various screening design techniques such as fractional or full factorial and Plackett-Burman designs. In this work, a two-level fractional factorial design was selected for the purposes of screening. In addition to screening designs, this project employed response surface methodologies (RSM) to estimate interaction and quadratic effects of demographic characteristics using a central composite face-centered and a Box-Behnken design. Furthermore, this research presents the novel application of multi-layer perceptron’s (MLP) neural networks to model the demographic characteristics of antenatal clinic attendees. A review report was produced to study the application of neural networks to modelling HIV/AIDS around the world. The latter report is important to enhance our understanding of the extent to which neural networks have been applied to study the HIV/AIDS pandemic. Finally, a binary logistic regression technique was employed to benchmark the results obtained by the design of experiments and neural networks methodologies. The two-level fractional factorial design demonstrated that HIV prevalence was highly sensitive to changes in the mother's age (15-55 years) and level of her education (Grades 0-13). The central composite face centered and Box-Behnken designs employed to study the individual and interaction effects of demographic characteristics on the spread of HIV in South Africa, demonstrated that HIV status of an antenatal clinic attendee was highly sensitive to changes in pregnant mother's age and her educational level. In addition, the interaction of the mother's age with other demographic characteristics was also found to be an important determinant of the risk of acquiring an HIV infection. Furthermore, the central composite face centered and Box-Behnken designs illustrated that, individual-ally the pregnant mother's parity and her partner's age had no marked effect on her HIV status. However, the pregnant woman’s parity and her male partner’s age did show marked effects on her HIV status in “two way interactions with other demographic characteristics”. The multilayer perceptron (MLP) sensitivity test also showed that the age of the pregnant woman had the greatest effect on the risk of acquiring an HIV infection, while her gravidity and syphilis status had the lowest effects. The outcome of the MLP modelling produced the same results obtained by the screening and response surface methodologies. The binary logistic regression technique was compared with a Box-Behnken design to further elucidate the differential effects of demographic characteristics on the risk of acquiring HIV amongst pregnant women. The two methodologies indicated that the age of the pregnant woman and her level of education had the most profound effects on her risk of acquiring an HIV infection. To facilitate the comparison of the performance of the classifiers used in this study, a receiver operating characteristics (ROC) curve was applied. Theoretically, an ROC analysis provides tools to select optimal models and to discard suboptimal ones independent from the cost context or the classification distribution. SAS Enterprise MinerTM was employed to develop the required receiver-of-characteristics (ROC) curves. To validate the results obtained by the above classification methodologies, a credit scoring add-on in SAS Enterprise MinerTM was used to build binary target scorecards comprised of HIV positive and negative datasets for probability determination. The process involved grouping variables using weights-of-evidence (WOE), prior to performing a logistic regression to produce predicted probabilities. The process of creating bins for the scorecard enables the study of the inherent relationship between demographic characteristics and an in-dividual’s HIV status. This technique increases the understanding of the risk ranking ability of the scorecard method, while offering an added advantage of being predictive.

This research addresses the novel application of design of experiment, artificial neural net-works and logistic regression to study the effect of demographic characteristics on the risk of acquiring HIV infection among the antenatal clinic attendees in South Africa. The annual antenatal HIV survey is the only major national indicator for HIV prevalence in South Africa. This is a vital technique to understand the changes in the HIV epidemic over time. The annual antenatal clinic data contains the following demographic characteristics for each pregnant woman; age (herein called mother's age), partner's age (herein father's age), population group (race), level of education, gravidity (number of pregnancies), parity (number of children born), HIV and syphilis status. This project applied a screening design of experiment technique to rank the effects of individual demographic characteristics on the risk of acquiring an HIV infection. There are a various screening design techniques such as fractional or full factorial and Plackett-Burman designs. In this work, a two-level fractional factorial design was selected for the purposes of screening. In addition to screening designs, this project employed response surface methodologies (RSM) to estimate interaction and quadratic effects of demographic characteristics using a central composite face-centered and a Box-Behnken design. Furthermore, this research presents the novel application of multi-layer perceptron’s (MLP) neural networks to model the demographic characteristics of antenatal clinic attendees. A review report was produced to study the application of neural networks to modelling HIV/AIDS around the world. The latter report is important to enhance our understanding of the extent to which neural networks have been applied to study the HIV/AIDS pandemic. Finally, a binary logistic regression technique was employed to benchmark the results obtained by the design of experiments and neural networks methodologies. The two-level fractional factorial design demonstrated that HIV prevalence was highly sensitive to changes in the mother's age (15-55 years) and level of her education (Grades 0-13). The central composite face centered and Box-Behnken designs employed to study the individual and interaction effects of demographic characteristics on the spread of HIV in South Africa, demonstrated that HIV status of an antenatal clinic attendee was highly sensitive to changes in pregnant mother's age and her educational level. In addition, the interaction of the mother's age with other demographic characteristics was also found to be an important determinant of the risk of acquiring an HIV infection. Furthermore, the central composite face centered and Box-Behnken designs illustrated that, individual-ally the pregnant mother's parity and her partner's age had no marked effect on her HIV status. However, the pregnant woman’s parity and her male partner’s age did show marked effects on her HIV status in “two way interactions with other demographic characteristics”. The multilayer perceptron (MLP) sensitivity test also showed that the age of the pregnant woman had the greatest effect on the risk of acquiring an HIV infection, while her gravidity and syphilis status had the lowest effects. The outcome of the MLP modelling produced the same results obtained by the screening and response surface methodologies. The binary logistic regression technique was compared with a Box-Behnken design to further elucidate the differential effects of demographic characteristics on the risk of acquiring HIV amongst pregnant women. The two methodologies indicated that the age of the pregnant woman and her level of education had the most profound effects on her risk of acquiring an HIV infection. To facilitate the comparison of the performance of the classifiers used in this study, a receiver operating characteristics (ROC) curve was applied. Theoretically, an ROC analysis provides tools to select optimal models and to discard suboptimal ones independent from the cost context or the classification distribution. SAS Enterprise MinerTM was employed to develop the required receiver-of-characteristics (ROC) curves. To validate the results obtained by the above classification methodologies, a credit scoring add-on in SAS Enterprise MinerTM was used to build binary target scorecards comprised of HIV positive and negative datasets for probability determination. The process involved grouping variables using weights-of-evidence (WOE), prior to performing a logistic regression to produce predicted probabilities. The process of creating bins for the scorecard enables the study of the inherent relationship between demographic characteristics and an in-dividual’s HIV status. This technique increases the understanding of the risk ranking ability of the scorecard method, while offering an added advantage of being predictive.

BACKGROUND:Interruption of vector-borne transmission of Trypanosoma cruzi remains an unrealized objective in many Latin American countries. The task of vector control is complicated by the emergence of vector insects in urban areas.METHODS:Utilizing data from a large-scale vector control program in Arequipa, Peru, we explored the spatial patterns of infestation by Triatoma infestans in an urban and peri-urban landscape. Multilevel logistic regression was utilized to assess the associations between household infestation and household- and locality-level socio-environmental measures.RESULTS:Of 37,229 households inspected for infestation, 6,982 (18.8% / 95% CI: 18.4 - 19.2%) were infested by T. infestans. Eighty clusters of infestation were identified, ranging in area from 0.1 to 68.7 hectares and containing as few as one and as many as 1,139 infested households. Spatial dependence between infested households was significant at distances up to 2,000 meters. Household T. infestans infestation was associated with household- and locality-level factors, including housing density, elevation, land surface temperature, and locality type.CONCLUSIONS:High levels of T. infestans infestation, characterized by spatial heterogeneity, were found across extensive urban and peri-urban areas prior to vector control. Several environmental and social factors, which may directly or indirectly influence the biology and behavior of T. infestans, were associated with infestation. Spatial clustering of infestation in the urban context may both challenge and inform surveillance and control of vector reemergence after insecticide intervention.

Das Verkehrsmittelwahlverhalten von Menschen ist komplex. So spielen soziodemografische, sozioökonomische sowie raum- und siedlungsstrukturelle Merkmale eine Rolle. In dieser Arbeit wird dieses Verhalten untersucht. Dabei wird eine homogene Grundgesamtheit geschaffen, welche alle Personen beinhaltet, die sowohl über eine Dauerkarte des öffentlichen Personenverkehrs als auch einen Personenkraftwagen verfügen. Anhand derer soll eine deskriptive Analyse und eine multinomiale logistische Regression Aufschluss geben, ob es Unterschiede zwischen den jeweiligen Nutzergruppen gibt. So lässt sich die Gruppe der ÖV-Nutzer durch folgende Charakteristiken beschreiben: der Großteil sind Frauen, sowie Personen, die eine hohe schulische und berufliche Bildung besitzen. Des Weiteren werden eher weniger Wege mit dem ÖV als mit dem PKW zurückgelegt. Erwerbstätige hingegen entscheiden sich eher für den PKW. / Human behavior towards the choice of transportation varies in very complex ways such as sociodemographics, socioeconomics as well as settlement structures. For this paper a homogenous population is created from season ticket holders for public transportation and car owners. Based on this population a descriptive analysis followed by a multinomial logistic regression is supposed to generate the differences between the user groups. The group of users of the public transportation system can be characterized as followed: the majority of users are women as well as highly educated people. Within this specific group distances are more likely to be covered by public transportation rather than by car. However the working population prefers to go by passenger car.