Many empirical and theoretical studies show that workers obtain jobs through their social contacts. This paper attempts to investigate how the difference of individuals’ intrinsic abilities in obtaining their jobs affects the social network structure that emerges. When the probability of players who get job information by themselves is large enough, low-ability players will maintain more contacts than high-ability players do. We analyze the equilibrium network structures in homogeneous society and heterogeneous society respectively. For analyzing more complex cases that people are heterogeneous in their ability of obtaining jobs, we suggest a new equilibrium concept: Forward Induction Network Equilibrium (FINE), a refinement of pairwise stability equilibrium. According to FINE, the possible equilibrium network structures can be reduced drastically and the outcomes are either symmetric or close-to-symmetric equilibrium networks. We show that the difference of social contacts among overall individuals is no greater than one contact in the close-to-symmetric equilibrium networks.

In this thesis we describe subclasses of a class of graphs with three types of edges, called loopless mixed graphs (LMGs). The class of LMGs contains almost all known classes of graphs used in the literature of graphical Markov models. We focus in particular on the subclass of ribbonless graphs (RGs), which as special cases include undirected graphs, bidirected graphs, and directed acyclic graphs, as well as ancestral graphs and summary graphs. We define a unifying interpretation of independence structure for LMGs and pairwise and global Markov properties for RGs, discuss their maximality, and, in particular, prove the equivalence of pairwise and global Markov properties for graphoids defined over the nodes of RGs. Three subclasses of LMGs (MC, summary, and ancestral graphs) capture the modified independence model after marginalisation over unobserved variables and conditioning on selection variables of variables satisfying independence restrictions represented by a directed acyclic graph (DAG). We derive algorithms to generate these graphs from a given DAG or from a graph of a specific subclass, and we study the relationships between these classes of graphs. Finally, a manual and codes are provided that explain methods and functions in R for implementing and generating various graphs studied in this thesis.

The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles). To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit. I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers. In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.

The estimation of latent variable models with ordinal and continuous, or ranking variables is the research focus of this thesis. The existing estimation methods are discussed and a composite likelihood approach is developed. The main advantages of the new method are its low computational complexity which remains unchanged regardless of the model size, and that it yields an asymptotically unbiased, consistent, and normally distributed estimator. The thesis consists of four papers. The first one investigates the two main formulations of the unrestricted Thurstonian model for ranking data along with the corresponding identification constraints. It is found that the extra identifications constraints required in one of them lead to unreliable estimates unless the constraints coincide with the true values of the fixed parameters. In the second paper, a pairwise likelihood (PL) estimation is developed for factor analysis models with ordinal variables. The performance of PL is studied in terms of bias and mean squared error (MSE) and compared with that of the conventional estimation methods via a simulation study and through some real data examples. It is found that the PL estimates and standard errors have very small bias and MSE both decreasing with the sample size, and that the method is competitive to the conventional ones. The results of the first two papers lead to the next one where PL estimation is adjusted to the unrestricted Thurstonian ranking model. As before, the performance of the proposed approach is studied through a simulation study with respect to relative bias and relative MSE and in comparison with the conventional estimation methods. The conclusions are similar to those of the second paper. The last paper extends the PL estimation to the whole structural equation modeling framework where data may include both ordinal and continuous variables as well as covariates. The approach is demonstrated through an example run in R software. The code used has been incorporated in the R package lavaan (version 0.5-11).

Up to now, adolescent speakers have been the primary focus when researching contemporary variation in the language of Sweden’s urban areas. This study contributes to the growing body of research on the topic by examining and reporting on adult speakers of what is here referred to as förortssvenska (English: Suburban Swedish). This study focuses specifically on formal speech registers of eight young working-class men from Stockholm along with the perception and reception of their speech by two independent native-listener groups. The paper is the first to present quantifiable data on what has been previously referred to as a “staccato” rhythm in Suburban Swedish. Strong correlations are shown between prosodic rhythm as measured by the normalized pairwise variability index (nPVI) and speech speed to mean listener attitudes (R2=0.9). A strong correlation is also shown for nPVI’s influence on mean listener-projected ethnicity (R2=0.8). Alongside variation in rhythm, we also see phonemic variation that trends toward specific indexes of social identity as revealed by speaker interviews and native-listener assessments. Alongside linguistic variation among speakers, there is also significant variation within speaker peer groups. In addition to identifying specific linguistic features, the study examines social mechanisms revealed in interviews with and qualitative observations of speaker and listener participants. In exploratory fashion, ideas on variation, register ranges, meta-pragmatic stereotyping, and ethnic boundary-making are presented to make a case for treating contemporary urban variation in Swedish as a habitual semiotic extension of speaker identity. Indicators that contemporary urban variation in Swedish may be heading in the direction of sociolectal entrenchment are also discussed. / Hittills har unga talare varit det primära fokus för forskning av aktuell språklig variation i urbana Sverige. Denna studie bidrar till den växande mängden forskning i detta ämne genom att undersöka och rapportera om vuxna talare av det som här kallas för förortssvenska. Studien fokuserar specifikt på formella talregister bland åtta unga män från Stockholms arbetarklass, samt perception och mottagande av deras tal av två oberoende grupper av infödda lyssnare. Denna studie är den första som presenterar kvantifierbar data rörande den i tidigare forskning så kallade stackato-rytmen i förortssvenska. Starka korrelationer finns mellan, å ena sidan, prosodisk rytm mätt med the normalized pairwise variability index (nPVI) och talhastighet och, å den andra, de genomsnittliga lyssnarattityderna (R2=0,9). Det finns också en stark korrelation för nPVIs påverkan på genomsnittlig lyssnarprojicerad etnicitet (R2=0,8). Vid sidan av variation i rytm ser vi också fonemisk variation som trender mot specifika index för social identitet. Och vid sidan av variation i rytm bland talarna, finns också en stor variation inom kamratgrupperna. Förutom att den identifierar specifika lingvistiska drag, undersöker studien sociala mekanismer som framkommer i intervjuer med och kvalitativa observationer av talardeltagarna och lyssnardeltagarna. På ett explorativt sätt, lägger studien fram idéer om variation, registeromfång, meta-pragmatiska stereotyper och etniska gränsskapande för att framhäva argumentet för att behandla den aktuella förortsvariationen i svenska som en habituell avsiktlig utbyggnad av talarens identitet. Det diskuteras också indikatorer till att den aktuella urbana variationen i svenska kan vara på väg mot sociolektal stabilisering.

Meiosis is functionally conserved across eukaryotes, thus not expected to vary considerably among different species, and even less so among lineages within a species. However, recent studies showed that this is not necessarily the case in Arabidopsis arenosa. Genome scanning identified an excess differentiation in meiosis genes between A. arenosa diploids and tetraploids, interpreted as meiosis adaptation to the whole genome duplication in tetraploids and differentiation was also found between two diploid lineages. Thus, I present a population-based analysis of positive selection acting on meiosis proteins across multiple lineages of A. arenosa. I showed that meiosis proteins were under positive selection in all diploid lineages, mainly in the Pannonian and South-eastern Carpathian lineage. The evidence for positive selection in diploid lineages suggested differential pathways of meiosis adaptations in the species, probably reflecting the necessity to adapt to local environments, among all to temperature. The highest enrichment of amino acid substitutions (AASs) under positive selection was identified in tetraploids, in consistence with previous genome-scan results. As several interacting meiosis proteins were under positive selection in the same A. arenosa lineage, I hypothesize that the close...

Dans les essais randomisés conduits en oncologie médicale, l'effet des traitements est le plus souvent évalué sur plusieurs critères de jugement, dont un ou plusieurs critères de type temps jusqu'à événement. Une analyse globale de l'effet d'un traitement intègre les résultats observés sur l'ensemble des critères de jugement pertinent. Un des objectifs de notre travail était de réaliser une revue systématique de la littérature évaluant les méthodes de recueil, d'analyse et de rapport des événements indésirables et des critères de jugement rapportés par les patients dans les essais de phase III en oncologie médicale. Cette revue a mis en évidence une grande hétérogénéité des méthodes utilisées. De plus les rapports des essais omettaient souvent certaines informations indispensables pour évaluer la validité des résultats rapportés en toxicité ou sur les critères de jugement rapportés par les patients. Un autre objectif de cette thèse était de développer une extension de la méthode des comparaisons par paire généralisées permettant d'évaluer de façon non biaisée la propension au succès en présence de censure lorsqu'un des critères de jugement est de type temps jusqu'à événement. Cette thèse avait également pour objectif de montrer comment les comparaisons par paire pouvaient être utilisées afin d'évaluer la balance bénéfice-risque de traitements innovants dans les essais randomisés. De la même façon, la propension globale au succès permet d'évaluer le bénéfice thérapeutique global lorsqu'un effet positif est attendu sur plusieurs critères de jugement / In medical oncology randomized trials, treatment effect is usually assessed on several endpoints, including one or more time-to-event endpoints. An overall analysis of the treatment effect may include the outcomes observed on all the relevant endpoints. A systematic review of medical oncology phase III trials was conducted. We extracted the methods used to record, analyze and report adverse events and patient-reported outcomes. Our findings show that some methodological aspects of adverse events or patient-reported outcomes collection and analysis were poorly reported. Even when reported, the methods used were highly heterogeneous. Another objective was to develop an extension of the generalized pairwise comparison procedure for time-to-event variables. The extended procedure provides an unbiased estimation of the chance of a better outcome even in presence of highly censored observations. Then, we show how the chance of an overall better outcome can be used to assess the benefit-risk balance of treatment in randomized trials. When a benefit is expected on more than one endpoint, the chance of an overall better outcome assesses the overall therapeutic benefit. The test of the null hypothesis is more powerful than the test based on one single endpoint

Social media has become an important means of everyday communication. It is a mechanism for “sharing” and “resharing” of information. While social network platforms provide the means to users for resharing/reblogging (aka retweeting), it remains unclear what motivates users to share. Predicting the spread of content is quite important for several purposes such as viral marketing, popular news detection, personalized message recommendation and on-line advertisement. Social content systems store all the information produced in the interactions between users. However, to turn this data into information that allows us to extract patterns, it is important to consider the different phenomena involved in these interactions. In this work, two phenomena that influence the evolution of networks are studied for Twitter: diffusion of information and communication among users. Previous studies have shown that history of interaction among users and properties of the message are good attributes to understand the retweet behavior of users. Factors like content of message and time are less investigated. We propose a prediction model for retweet actions of users. It formulates a function which ranks the users according to how receptive they are to a particular message. The function generates a confidence score for the edges joining the initiator of the message and the followers. Two different pieces of information propagate through different users in the network. We divide the task of calculating confidence score into two parts. The first part is independent of the test tweet. It models transmission rate of the tie between the initiator and the follower. We call this as ‘Pairwise Influence Estimation’. The second part incorporates the tweet properties and user activeness as per time in the ranking function. The proposed model exploits all the dimensions of information dif-fusion process-influence, content and temporal properties. We have captured local aspects of diffusion. It has been observed that users do not read all the messages on their site. This results in shortcomings in the above models. Considering this, we first study the temporal behavior of users’ activities, which directly reflects their availability pertaining to the upcoming post. Also, as it is a continuous task of predicting retweet behavior, we design a user-centric, and temporally localized incremental classification model by considering the fact that users do not read all their tweets. We have tested the effectiveness of this model by using real data from Twitter. We demonstrate that the new proposed model is more accurate in describing the information propagation in microblog compared to the existing methods. Our model works well when we consider different classes of users depending on their activity patterns. In addition, we also investigate the parameters of the model for different classes of users. We report some interesting distinguishing patterns in retweeting behavior of users.

Ces travaux de thèse concernent la conception et l'étude d'algorithmes, d'une part pourprédire les quantités thermodynamiques et la structure secondaire des ARN, d'autre part pour l'alignement de séquences.Dans une première partie, nous appliquons un algorithme de Monte-Carlo pour approximer la densité d'états d'énergie des structures secondaires d'une séquence d'ARN, ou d'une hybridation de deux molécules d'ARN données. Nous montrons d'abord que la densité estimée par notre programme est aussi bonne que la densité exacte, et le temps d'exécution de notre programme est beaucoup plus rapide. Nous calculons ensuite la température de dénaturation d'une hybridation de deux molécules d'ARN. Nous montrons que nos températures de dénaturation sont plus proches des valeurs expérimentales que celles des deux autres programmes existants.Puis, dans une deuxième partie, nous implémentons un algorithme de programmation dynamique qui engendre des structures sous-optimales, dédié principalement à la prédiction des deux structures fonctionnelles des riboswitchs. Nous appliquons d'abord notre programme sur un riboswitch TPP dans lequel nous avons réussi à détecter les deux structures fonctionnelles. Nous montrons ensuite que les structures prédites par notre programme sont plus proches de la structure réelle par rapport aux cinq autres programmes existants, sur un échantillon de riboswitch purine.Enfin, dans une troisième partie, nous présentons un algorithme de recherche des alignements sous-optimaux de séquences pour améliorer la qualité d'alignement des séquences. Nous comparons d'abord nos alignement à ceux produits par l'algorithme de Needdleman-Wunsch. Nous prédissons plus d'alignements de référrence par rapport l'algorithme de Needdleman-Wunsch. Nous calculons ensuite les fréquences des paires de bases alignées et les entropies de position spécifique dans nos alignements sous-optimaux. Nous montrons que les entropies calculées à partir de notre programme sont plus corrélées que celles des autres programmes avec les positions des paires de résidus fiablement alignées selon BAliBASE. / This thesis concerns the design and study of algorithms, on the one hand to predict the thermodynamic quantities and the secondary structure of RNA, the other for sequence alignment.In the first part, we apply a Monte Carlo algorithm to approximate the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. We first show that the density estimated by our program is as good as the exact density, and the execution time of our program is much faster. We then calculate the melting temperature for a hybridization of two RNA sequences. We show that our melting temperatures are closer to experimental values than the other two programs.Then in the second part, we implement a dynamic programming algorithm that generates sub-optimal structures, mainly dedicated to the prediction of functional structures of riboswitchs. We first apply our program on a TPP riboswitch in which we were able to detect both functional structures. We then show that the structures predicted by our program are closer to the real structure compared to five other existing programs, on a sample of purine riboswitch.Finally, in the third part, we present a novel algorithm to produce sub-optimal pairwise alignments. We first compare our alignments to those produced by the algorithm of Needdleman-Wunsch. We predict more reference alignments than the algorithm of Needdleman-Wunsch. We then calculate the frequencies and position-specific entropies from our sub-optimal alignments. We show that entropies calculated from our program are more correlated than other programs with locations in the core block of BAliBASE reference alignments.

The formation and patterns of a monolayer are determined by the interplay of two fundamental interactions, adsorbate-substrate and intermolecular interactions. The binding strength between adsorbate and substrate affects the mobility of the adsorbate at the surface and the stability of the complex. The intermolecular interaction plays a significant role in the monolayer patterns on the epitaxial layer of the substrate. A monolayer can be formed either by a spontaneous self-assembly, or by fabrication via atomic-layer deposition (ALD). The physical and chemical properties of the resulting monolayer have a broad array of applications in fabricating functional materials for hydrophobic or hydrophilic surfaces, biological sensors, alternating the properties of the substrate, catalysis and forming ordered layered structures. In this dissertation, the investigation focuses primarily on the influence of the surface topology on the binding behaviour of adsorbate-surface complexes. The state of the art DFT-TS method is used to simulate the sulfur-containing amino acids at complex gold surfaces and examine the relationship between the binding strengths and the binding sites with various nearest neighbouring environments. The same method is also used to determine if a chemical reaction will take place for various catalytic silicon precursors at a silicon oxide surface. Simulating surface chemistry using the DFT-TS method requires intensive com- puting resources, including CPU use and computing time. Another focus of this dissertation is to increase the data generating speed by reducing the size of the sim- ulated systems without altering the outcome. A relatively small gold cluster is used to study the binding behaviours of small organic molecules on the cluster. The same strategy is also used to simulate the chemical reactions between various self-catalying silicon precursors and a water molecule. / Graduate / 2021-10-21