Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis

Detecting factors associated with transmission is important to understand disease epidemics, and to design effective public health measures. Clustering and terminal branch lengths (TBL) analyses are commonly applied to genomic data sets of Mycobacterium tuberculosis (MTB) to identify sub-populations with increased transmission. Here, I used a simulation-based approach to investigate what epidemiological processes influence the results of clustering and TBL analyses, and whether differences in transmission can be detected with these methods. I simulated MTB epidemics with different dynamics (latency, infectious period, transmission rate, basic reproductive number R0, sampling proportion, sampling period, and molecular clock), and found that all considered factors, except for the length of the infectious period, affect the results of clustering and TBL distributions. I show that standard interpretations of this type of analyses ignore two main caveats: (1) clustering results and TBL depend on many factors that have nothing to do with transmission, (2) clustering results and TBL do not tell anything about whether the epidemic is stable, growing, or shrinking, unless all the additional parameters that influence these metrics are known, or assumed identical between sub-populations. An important consequence is that the optimal SNP threshold for clustering depends on the epidemiological conditions, and that sub-populations with different epidemiological characteristics should not be analyzed with the same threshold. Finally, these results suggest that different clustering rates and TBL distributions, that are found consistently between different MTB lineages, are probably due to intrinsic bacterial factors, and do not indicate necessarily differences in transmission or evolutionary success

Study of the performance of a racing motorcycle by the optimal maneuver method

Study of the performance of a racing motorcycle by the optimal maneuver method. In particular on the gearbox. Parametric analysis of aerodynamic drag, centre of mass position and sprocket-pignon ratioopenEmbargo per motivi di segretezza e/o di proprietà dei risultati e informazioni di enti esterni o aziende private che hanno partecipato alla realizzazione del lavoro di ricerca relativo alla tes

RESTORATIVENESS AND ECOLOGICAL BEHAVIOURS: From methodological issues in self-report instruments to investigation of pattern of association

According to some studies, the positive, rewarding and restorative experiences that people have in natural environments could be one of the motivations to preserve and protect nature (Byrka, Hartig, & Kaiser, 2010; Collado & Corraliza, 2015; Hartig, Kaiser, & Strumse, 2007; Nisbet & Zelenski, 2011). Exposure to natural environments (and the obtained benefits) could influence the probability of implementing Ecological Behaviours (EBs) (Coldwell & Evans, 2017), that is those behaviours aimed at the care and protection of the environment (Hartig, Kaiser, & Bowler, 2001; Steg & Vlek, 2009). The research in this field is quite recent, and many issues are still open. Among the other, the present dissertation tries to face three main issues: the assessment of ecological behaviours, some methodological concerns about restorative effect of natural environment, and the role of other related constructs. The lack of consistency of instruments for EBs assessment makes it difficult to compare the studies and reflects a lack of consensus regarding which behaviours should actually be measured. In particular, psychologists often assess ecological behaviours with measurement instruments whose influence on the ecological system is not considered. A huge amount of studies regarding restorative experience and restorative environments are based on the assumption that the natural environments are more restorative than the urban ones. However, studies addressing this issue use a variety of research methods (concerning for example research design, measurement instruments, participants, kind of exposure to the environments) making it difficult to compare the findings and to draw conclusions. Finally, empirical evidences suggest that the effect of restorativeness on EBs is not a direct effect but is mediated by environmental attitudes (Berto & Barbiero, 2017; Byrka et al., 2010; Hartig et al., 2007; Whitburn, Linklater, & Milfont, 2019). Moreover, some authors suggest that the ability to perceive nature as a restorative environment is influenced by Connection to nature (e.g., Berto & Barbiero, 2017; Whitburn et al., 2019) that, in turn, is a requirement for action to protect nature (e.g., Berto & Barbiero, 2017; Clayton, 2012; Mayer & Frantz, 2004). Finally, some studies suggested that EBs and their antecedents (e.g., Hartig et al., 2001; Milfont, 2009; Noppers, Keizer, Bolderdijk, & Steg, 2014) could be bias by social desirability (SD) (Paulhus, 1984). However, no study has investigated all these variables in a single model. The present research intents to contribute to the study of association between restorativeness and EBs overcoming the limitations described above. First, the Pro-Environmental Behaviours Scale (PEBS; Markle, 2013) is, to our knowledge, the only scale based on an impact-oriented approach and on empirical evidence recognized by the environmental scientific community (Brower & Leon, 1999) to cover the three categories of EBs proposed by literature (Stern, 2000). For this reason, in the first study of this project we adapted the original PEBS to the Italian context (qualitative phase) and we verified its psychometric properties (e.g., factor structure) (quantitative phase). The original scale was slightly modified following a suggestion obtained in a focus group (n =17) and in a pilot study (n =18). On a sample of 765 Italian adults (70% female, mean [SD] age = 41.7 [12.2], 2 missing) results revealed a 4-factor structure (conservation, environmental citizenship, food, and transportation) of the Italian PEBS, like the original version (Markle, 2013), maintaining 15 of the 19 original items (CFI = .973; RMSEA = .037: WRMR = 1.047; \u3c7(84)2 = 170.63, p < .001; explained variance = 42%). Other psychometrics properties were \u201cgood\u201d or better. Results suggest that the Italian PEBS is a valid and reliable tool for assessing the principal EBs proposed by the literature as having a great impact on the environment. The second study of this project uses a meta-analysis aimed at estimating how much natural environments are perceived as being more restorative than urban environments. We investigated the role of moderator variables such as research design, kind of natural environment, participants, measurement instruments used or the context in which data were collected. PsycINFO, PsycARTICLES, Scopus, SpringerLINK, Web Of Science online databases were used to identity all peer-review articles on restorativeness published to date (k = 167). Reference sections of obtained papers were examined for additional studies. Only 22 studies met inclusion criteria (direct exposure to environment, comparison between one outdoor environment with natural element and one without natural element, and restorativeness measured by self-report scale) and were included in meta-analysis. Results showed that natural environments are perceived to be more restorative than urban environments (Cohen\u2019s d [C.I.] = 1.99 [1.38 - 2.61]). Significant heterogeneity between studies was found (Q(19) = 503.16, p < .001) and variability within studies was very high (I2 = 97%). However, subsequent univariate moderator analyses were not significant. Other methodological differences (e.g., lighting conditions) could explain this variability. We concluded that the variability in studies is more likely to be due to individuals differences (e.g., age, connections to nature, and environmental attitude) than to methodological differences. Finally, in the third study we investigated relationship between the perceived restorativeness, the environmental attitudes, the connection to nature, and the social desirability. The first aim of this study is to cover this lack by proposing an integrated model of antecedents of EBs. The second aim is to verify if the proposed model is valid for all the different EBs\u2019 categories proposed by literature (Stern, 2000): Conservation, Transportation, Food, and Environmental Citizenship. The model showed an excellent fit (CFI = 1.000; RMSEA = .000 [CI = .000 - .116]; SRMR = 0.031; \u3c7(4)2 = 3.412, p = .491; explained variance = 26%) and almost all the hypotheses were confirmed: connection to nature and environmental attitudes are the only two constructs \u2013 among the ones used in the model \u2013 with a direct effect on EBs; connection to nature have also indirect effects, via perceived restorativeness and via environmental attitudes; environmental attitudes are influenced by perceived restorativeness but they do not significantly mediate the effect of restorativeness on EBs; social desirability has an indirect effect on EBs via connection to nature but it did not have a direct relationship with environmental attitude. All models with the different EBs categories as outcomes showed a good fit, however, while connection to nature is confirmed as a predictor of all the four categories of EBs, the environmental attitudes predicts only Environmental Citizenship. In sum, our model suggests that connection to nature, besides being the strongest direct predictor of EBs, it is also an important predictor of perceived restorativeness and environmental attitudes. So, studies that have investigated the indirect effect of perceived restorativeness on EBs via environmental attitudes (Byrka et al., 2011; Collado & Corraliza, 2015; Hartig et al., 2007) without considering the role of the connection to nature could have overestimated the indirect effect

Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis

The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared to the average ("super-spreaders"). Here we used an Approximate Bayesian Computation approach to test whether multiple merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered eleven publicly available whole genome sequence data sets sampled from local MTB populations and outbreaks, and found that MMC had a better fit compared to the Kingman coalescent for ten of the eleven data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed, and that past findings based on the Kingman coalescent need to be revisited

Adaptation of the personal social capital brief scale for the measurement of the offline and online social capital in Italy

Social Capital refers to the resources associated with durable and trustworthy social connections. Social Capital can be developed through offline and online relationships. It can be distinguished between cognitive Social Capital (perception of trustworthiness, reciprocity, and support) and structural Social Capital (density of social networks and membership, and participation in groups and associations). It can also be distinguished between bonding Social Capital (resources associated with informal networks; i.e., neighbors, friends, colleagues) and bridging Social Capital (resources associated with formal networks; i.e., community service, cultural, religious or political groups/associations). The different forms and dimensions of Social Capital may have distinct effects on health outcomes and self-rated health. Therefore, public health researchers need valid and reliable instruments to investigate Social Capital. However, valid instruments including the measurement of online Social Capital are not available. The Personal Social Capital Scale aims to assess bonding and bridging Social Capital by means of cognitive and structural items. In the present investigation, three studies were carried out (N = 1149) to adapt the Personal Social Capital Scale to develop the Personal On-Offline Social Capital Brief Scale, a brief scale for measuring online and offline bonding and bridging Social Capital in Italy. Factorial structure and convergent/divergent validity in relation to scales measuring constructs with different patterns of relationships with bonding and bridging Social Capital (i.e., social support and stress; sense of community and health) were also investigated. Overall, these studies provide evidence of reliability and validity related to the internal structure of the Personal On-Offline Social Capital Brief Scale in measuring online and offline bonding and bridging Social Capital and discriminating them from similar constructs. This scale is a useful instrument for planning public health interventions

Exploring Perceived and Objective Measures of the Neighborhood Environment and Associations with Physical Activity among Adults: A Review and a Meta-Analytic Structural Equation Model

There is an urgent need to understand factors that promote physical activities (PA) because it is one of the modifiable risk factors for global mortality. None of the previous reviews considered both perceived and objective characteristics of the same environment. The first aim was to review the literature on studies investigating the relationship between PA behavior of adults and perceived and objective physical environment measures. The second aim was to verify the potential mediational role of the perceived measure in the relationship between the objective measure of the environment and PA using meta-analytic SEM. Only 15 studies reported a relationship between PA and both environmental measures. One of the most studied characteristics of the physical environment is the accessibility to recreational/PA facilities. Both objective and subjective measures of accessibility to PA facilities are associated with PA. Meta-SEM results suggest a significant effect of the objective accessibility to facilities on PA behavior ( = 0.15) and on the perceived measure ( = 0.10), but the indirect effect was not significant. No significant effect was found for the perceived measure on PA, suggesting that individuals’ level of awareness about their environments may have played a role. This prompts a need to create awareness campaigns

Modello Big Five di personalita' in adolescenti: Effetti di indicatori diversi del Livello Socio-Culturale personale e familiare

Per contribuire allo studio dell'associazione tra Livello Socio-Culturale e personalità in tema di salute, si è voluto verificare se indicatori diversi di LSC personale e familiare hanno effetti distinti sui fattori di personalità Big Five di adolescenti maschi (n = 50) e femmine (n = 107). A tale scopo, sono stati somministrati il Big-Five Questionnaire 2 per la valutazione della personalità e due brevi questionari (Questionario sugli Interessi Culturali e Scala Capitale Sociale Personale) per indagare il LSC personale. Per l'indagine sul LSC familiare i genitori (124 madri e 108 padri) hanno compilato anche il Questionario sull'Attività lavorativa. Utilizzando test statistici non parametrici (Test di Kruskal-Wallis e Test di Mann-Whitney) è stato possibile rilevare che il LSC personale e familiare ha effetti diversi sulla personalità di adolescenti maschi e femmine. Inoltre, è emerso che padre e madre influenzano in modo diverso i figli a seconda del genere. Infine, si è notata un'influenza del LSC diversa sulla personalità degli adolescenti rispetto a quella riscontrata sulla personalità adulta (Jonassaint et al., 2011; Khodadady et al., 2011)