Discriminating antigen and non-antigen using proteome dissimilarity:bacterial antigens

It has been postulated that immunogenicity results from the overall dissimilarity of pathogenic proteins versus the host proteome. We have sought to use this concept to discriminate between antigens and non-antigens of bacterial origin. Sets of 100 known antigenic and nonantigenic peptide sequences from bacteria were compared to human and mouse proteomes. Both antigenic and non-antigenic sequences lacked human or mouse homologues. Observed distributions were compared using the non-parametric Mann-Whitney test. The statistical null hypothesis was accepted, indicating that antigen and non-antigens did not differ significantly. Likewise, we were unable to determine a threshold able to separate meaningfully antigen from non-antigen. Thus, antigens cannot be predicted from pathogen genomes based solely on their dissimilarity to the human genome.

Discriminating antigen and non-antigen using proteome dissimilarity II:viral and fungal antigens

Immunogenicity arises via many synergistic mechanisms, yet the overall dissimilarity of pathogenic proteins versus the host proteome has been proposed as a key arbiter. We have previously explored this concept in relation to Bacterial antigens; here we extend our analysis to antigens of viral and fungal origin. Sets of known viral and fungal antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. Both antigenic and non-antigenic sequences lacked human or mouse homologues. Observed distributions were compared using the non-parametric Mann-Whitney test. The statistical null hypothesis was accepted, indicating that antigen and non-antigens did not differ significantly. Likewise, we could not determine a threshold able meaningfully to separate non-antigen from antigen. We conclude that viral and fungal antigens cannot be predicted from pathogen genomes based solely on their dissimilarity to mammalian genomes.

Gaussian process quantile regression using expectation propagation

Direct quantile regression involves estimating a given quantile of a response variable as a function of input variables. We present a new framework for direct quantile regression where a Gaussian process model is learned, minimising the expected tilted loss function. The integration required in learning is not analytically tractable so to speed up the learning we employ the Expectation Propagation algorithm. We describe how this work relates to other quantile regression methods and apply the method on both synthetic and real data sets. The method is shown to be competitive with state of the art methods whilst allowing for the leverage of the full Gaussian process probabilistic framework.

Application of MARS for the Construction of Nonparametric Models

2000 Mathematics Subject Classification: 62G08, 62P30.

Applications of data envelopment analysis in education

Non-parametric methods for efficiency evaluation were designed to analyse industries comprising multi-input multi-output producers and lacking data on market prices. Education is a typical example. In this chapter, we review applications of DEA in secondary and tertiary education, focusing on the opportunities that this offers for benchmarking at institutional level. At secondary level, we investigate also the disaggregation of efficiency measures into pupil-level and school-level effects. For higher education, while many analyses concern overall institutional efficiency, we examine also studies that take a more disaggregated approach, centred either around the performance of specific functional areas or that of individual employees.

Without women: Masculinities, gay male sexual culture and sexual behaviors in Miami, Florida

Recent studies have reported alarmingly high rates of HIV infection and risky sexual behaviors among gay men in Miami, Florida. Previous research has suggested that the risky sexual behaviors of many gay men reflect the pursuit of intimacy and love, and that barriers to intimate relationships among gay men may stem from traditional masculinity norms. This dissertation examines the meanings which gay men ascribe to their sexual behaviors, as well as the intersections of those meanings with both traditional masculinity constructions and Miami's gay male sexual culture. ^ The study is based upon participant observation, print media content analysis, surveys and ethnographic interviews of a purposive snowball sample of 30 Cuban American, Puerto Rican, African American and Anglo gay men who reside in Miami-Dade County, Florida. Analysis of research questions was accomplished through grounded theory methods and descriptive and non-parametric statistics, including Pearson chi-square, Fisher's Exact and Mann-Whitney U tests. ^ The study shows that culturally-specified masculinity norms vary in the relative importance ascribed to heterosexual prowess, economic providership and competitiveness. These cultural differences appear important not only to the timing of sexual awareness and to the strength of homosexual stereotyping as effeminacy, but also to men's strategies in coming out as gay. The meanings men attributed to their sexual behaviors were, however, constructed in response to both inherited masculinity norms and the hypermasculine structure of Miami's gay male sexual culture. In addition to providing an ethnographic account of this subculture, the study elaborates men's issues relative to casual sex and committed relationships. Unprotected anal intercourse with casual partners during the previous twelve months was associated with growing up without one's father in the home, having been teased for effeminacy during childhood, being defensive about one's masculinity, not trusting men, having been cheated on by boyfriends, and believing that long-term gay male relationships are problematic. ^ It is concluded that the continuing epidemic of HIV infections among local gay men, as well as the hypermasculine form of the gay sexual subculture itself, are nihilistic symptoms embedded in the masculinist gender structure of the larger society. ^

How do partnerships lead to a competitive advantage? Applying the resource based view to nascent social ventures

This dissertation is one of the earliest to systematically apply and empirically test the resource-based view (RBV) in the context of nascent social ventures in a large scale study. Social ventures are entrepreneurial ventures organized as nonprofit, for-profit, or hybrid organizations whose primary purpose is to address unmet social needs and create social value. Nascent social ventures face resource gaps and engage in partnerships or alliances as one means to access external resources. These partnerships with different sectors facilitate social venture innovative and earned income strategies, and assist in the development of adequate heterogeneous resource conditions that impact competitive advantage. Competitive advantage in the context of nascent social ventures is achieved through the creation of value and the achievement of venture development activities and launching. The relationships between partnerships, heterogeneous resource conditions, strategies, and competitive advantage are analyzed in the context of nascent social ventures that participated in business plan competitions. A content analysis of 179 social venture business plans and an exploratory follow-up survey of 72 of these ventures are used to analyze these relationships using regression, ANOVA, correlations, t-tests, and non-parametric statistics. The findings suggest a significant positive relationship between competitive advantage and partnership diversity, heterogeneous resource conditions, social innovation, and earned income. Social capital is the type of resource most significantly related to competitive advantage. Founder previous start-up experience, client location, and business plan completeness are also found to be significant in the relationship between partnership diversity and competitive advantage. Finally the findings suggest that hybrid social ventures create a greater competitive advantage than nonprofit or for-profit social ventures. Consequently, this dissertation not only provides academics further insight into the factors that impact nascent social value creation, venture development, and ability to launch, but also offers practitioners guidance on how best to organize certain processes to create a competitive advantage. As a result more insight is gained into the nascent social venture creation process and how these ventures can have a greater impact on society.

Monitoring the Accuracy of Multiple Occupancy Forecasts

Corporate executives closely monitor the accuracy of their hotels' occupancy fore- casts since important decisions are based upon these predictions. This study lists the criteria for selecting an appropriate error measure. It discusses several evaluation methods focusing on statistical significance tests and demonstrates the use of two adequate evaluation methods: Mincer- Zamowitz's efficiency test and Wilcoxon's Non-Parametric Matched-Pairs Signed- Ranks test.

O estrategista em perspectiva: um estudo sobre o processo de formação de estratégias no ramo varejista de construção civil de Natal e região metropolitana

The strategy research have been widespread for many years and, more recently, the process of formation of the strategies in the individual perspective has also gained attention in academia. Confirming this trend, the goal of this study is to discuss the process of formation of the strategies from an individual perspective based on the three dimensions of the strategic process (change, thinking and formation) proposed by De Wit and Meyer (2004). To this end, this exploratory-descriptive study used the factor analysis techniques, non-parametric correlation and linear regression to analyze data collected from the decision makers of the 93 retail in the industry of construction supplies in the Natal and metropolitan area. As a result, we have that the formation factors of the dimensions investigated were identified in the majority, thus confirming the existence of paradoxes in the strategic process, and that there is a relationship between logical thinking and deliberate formation with the hierarchical level of decision makers.

Distribuição de derivados de petróleo por redes de polidutos: uma abordagem através de algoritmos evolucionários híbridos para um problema triobjetivo

An important problem faced by the oil industry is to distribute multiple oil products through pipelines. Distribution is done in a network composed of refineries (source nodes), storage parks (intermediate nodes), and terminals (demand nodes) interconnected by a set of pipelines transporting oil and derivatives between adjacent areas. Constraints related to storage limits, delivery time, sources availability, sending and receiving limits, among others, must be satisfied. Some researchers deal with this problem under a discrete viewpoint in which the flow in the network is seen as batches sending. Usually, there is no separation device between batches of different products and the losses due to interfaces may be significant. Minimizing delivery time is a typical objective adopted by engineers when scheduling products sending in pipeline networks. However, costs incurred due to losses in interfaces cannot be disregarded. The cost also depends on pumping expenses, which are mostly due to the electricity cost. Since industrial electricity tariff varies over the day, pumping at different time periods have different cost. This work presents an experimental investigation of computational methods designed to deal with the problem of distributing oil derivatives in networks considering three minimization objectives simultaneously: delivery time, losses due to interfaces and electricity cost. The problem is NP-hard and is addressed with hybrid evolutionary algorithms. Hybridizations are mainly focused on Transgenetic Algorithms and classical multi-objective evolutionary algorithm architectures such as MOEA/D, NSGA2 and SPEA2. Three architectures named MOTA/D, NSTA and SPETA are applied to the problem. An experimental study compares the algorithms on thirty test cases. To analyse the results obtained with the algorithms Pareto-compliant quality indicators are used and the significance of the results evaluated with non-parametric statistical tests.

Estimativas, variabilidade e análise de tendência da evapotranspiração de referência em perímetros irrigados, no semiárido do nordeste brasileiro

The variability / climate change has generated great concern worldwide, is one of the major issues as global warming, which can is affecting the availability of water resources in irrigated perimeters. In the semiarid region of Northeastern Brazil it is known that there is a predominance of drought, but it is not enough known about trends in climate series of joint water loss by evaporation and transpiration (evapotranspiration). Therefore, this study aimed to analyze whether there is increase and / or decrease evidence in the regime of reference evapotranspiration (ETo), for the monthly, annual and interdecadal scales in irrigated polo towns of Juazeiro, BA (9 ° 24'S, 40 ° 26'W and 375,5m) and Petrolina, PE (09 ° 09'S, 40 ° 22'W and 376m), which is the main analysis objective. The daily meteorological data were provided by EMBRAPA Semiárido for the period from 01.01.1976 to 31.12.2014, estimated the daily ETo using the standard method of Penman-Monteith (EToPM) parameterized by Smith (1991). Other methods of more simplified estimatives were calculated and compared to EToPM, as the ones following: Solar Radiation (EToRS), Linacre (EToL), Hargreaves and Samani (EToHS) and the method of Class A pan (EToTCA). The main statistical analysis were non-parametric tests of homogeneity (Run), trend (Mann-kendall), magnitude of the trend (Sen) and early trend detection (Mann-Whitney). The statistical significance adopted was 5 and / or 1%. The Analysis of Variance - ANOVA was used to detect if there is a significant difference in mean interdecadal mean. For comparison between the methods of ETo, it were used the correlation test (r), the Student t test and Tukey levels of 5% significance. Finally, statistics Willmott et al. (1985) statistics was used to evaluate the concordance index and performance of simplified methods compared to the standard method. It obtained as main results that there was a decrease in the time series of EToPM in irrigated areas of Juazeiro, BA and Petrolina, PE, significant respectively at 1 and 5%, with an annual magnitude of -14.5 mm (Juazeiro) and -7.7 mm (Petrolina) and early trend in 1996. The methods which had better for better agreement with EToPM were EToRS with very good performance, in both locations, followed by the method of EToL with good performance (Juazeiro) and median (Petrolina). EToHS had the worst performance (bad) for both locations. It is suggested that this decrease of EToPM can be associated with the increase in irrigated agricultural areas and the construction of Sobradinho lake upstream of the perimeters.

Anomaly detection from time-changing environmental sensor data streams

This thesis stems from the project with real-time environmental monitoring company EMSAT Corporation. They were looking for methods to automatically ag spikes and other anomalies in their environmental sensor data streams. The problem presents several challenges: near real-time anomaly detection, absence of labeled data and time-changing data streams. Here, we address this problem using both a statistical parametric approach as well as a non-parametric approach like Kernel Density Estimation (KDE). The main contribution of this thesis is extending the KDE to work more effectively for evolving data streams, particularly in presence of concept drift. To address that, we have developed a framework for integrating Adaptive Windowing (ADWIN) change detection algorithm with KDE. We have tested this approach on several real world data sets and received positive feedback from our industry collaborator. Some results appearing in this thesis have been presented at ECML PKDD 2015 Doctoral Consortium.

Text-messaging as a Tool for Medication Adherence and Behavior Change in Disease Management among Patients with Coronary Heart Disease

Background: Evidence-based medication and lifestyle modification are important for secondary prevention of cardiovascular disease but are underutilized. Mobile health strategies could address this gap but existing evidence is mixed. Therefore, we piloted a pre-post study to assess the impact of patient-directed text messages as a means of improving medication adherence and modifying major health risk behaviors among coronary heart disease (CHD) patients in Hainan, China.

Methods: 92 CVD patients were surveyed between June and August 2015 (before the intervention) and then between October and December 2015 (after 12 week intervention) about (a) medication use (b) smoking status,(c) fruit and vegetable consumption, and (d) physical activity uptake. Acceptability of text-messaging intervention was assessed at follow-up. Descriptive statistics, along with paired comparisons between the pre and post outcomes were conducted using both parametric (t-test) and non-parametric (Wilcoxon signed rank test) methods.

Results: The number of respondents at follow-up was 82 (89% retention rate). Significant improvements were observed for medication adherence (P<0.001) and for the number of cigarettes smoked per day (P=.022). However there was no change in the number of smokers who quitted smoking at follow-up. There were insignificant changes for physical activity (P=0.91) and fruit and vegetable consumption.

Flexible strategies for association analysis with genomic phenotypes

Thesis (Ph.D.)--University of Washington, 2016-08

Estimation du paramètre d'une copule archimedienne en présence de censure dépendante

Les méthodes classiques d’analyse de survie notamment la méthode non paramétrique de Kaplan et Meier (1958) supposent l’indépendance entre les variables d’intérêt et de censure. Mais, cette hypothèse d’indépendance n’étant pas toujours soutenable, plusieurs auteurs ont élaboré des méthodes pour prendre en compte la dépendance. La plupart de ces méthodes émettent des hypothèses sur cette dépendance. Dans ce mémoire, nous avons proposé une méthode d’estimation de la dépendance en présence de censure dépendante qui utilise le copula-graphic estimator pour les copules archimédiennes (Rivest etWells, 2001) et suppose la connaissance de la distribution de la variable de censure. Nous avons ensuite étudié la consistance de cet estimateur à travers des simulations avant de l’appliquer sur un jeu de données réelles.