ANALYSIS OF POPULUS TREMULOIDES CLONAL VARIATION AND DELINEATION IN THE OTTAWA NATIONAL FOREST

The technique of delineating Populus tremuloides (Michx.) clonal colonies based on morphology and phenology has been utilized in many studies and forestry applications since the 1950s. Recently, the availability and robustness of molecular markers has challenged the validity of such approaches for accurate clonal identification. However, genetically sampling an entire stand is largely impractical or impossible. For that reason, it is often necessary to delineate putative genet boundaries for a more selective approach when genetically analyzing a clonal population. Here I re-evaluated the usefulness of phenotypic delineation by: (1) genetically identifying clonal colonies using nuclear microsatellite markers, (2) assessing phenotypic inter- and intraclonal agreement, and (3) determining the accuracy of visible characters to correctly assign ramets to their respective genets. The long-term soil productivity study plot 28 was chosen for analysis and is located in the Ottawa National Forest, MI (46° 37'60.0" N, 89° 12'42.7" W). In total, 32 genets were identified from 181 stems using seven microsatellite markers. The average genet size was 5.5 ramets and six of the largest were selected for phenotypic analyses. Phenotypic analyses included budbreak timing, DBH, bark thickness, bark color or brightness, leaf senescence, leaf serrations, and leaf length ratio. All phenotypic characters, except for DBH, were useful for the analysis of inter- and intraclonal variation and phenotypic delineation. Generally, phenotypic expression was related to genotype with multiple response permutation procedure (MRPP) intraclonal distance values ranging from 0.148 and 0.427 and an observed MRPP delta value=0.221 when the expected delta=0.5. The phenotypic traits, though, overlapped significantly among some clones. When stems were assigned into phenotypic groups, six phenotypic groups were identified with each group containing a dominant genotype or clonal colony. All phenotypic groups contained stems from at least two clonal colonies and no clonal colony was entirely contained within one phenotypic group. These results demonstrate that phenotype varies with genotype and stand clonality can be determined using phenotypic characters, but phenotypic delineation is less precise. I therefore recommend that some genetic identification follow any phenotypic delineation. The amount of genetic identification required for clonal confirmation is likely to vary based on stand and environmental conditions. Further analysis, however, is needed to test these findings in other forest stands and populations.

High-performance liquid chromatography (HPLC) and high-performance liquid chromatography mass spectrometry (HPLC/MS) for the analysis of date rape drugs

The drugs studied in this work have been reportedly used to commit drug-facilitated sexual assault (DFSA), commonly known as "date rape". Detection of the drugs was performed using high-performance liquid chromatography with ultraviolet detection (HPLC/UV) and identified with high performance-liquid chromatography mass spectrometry (HPLC/MS) using selected ion monitoring (SIM). The objective of this study was to develop a single HPLC method for the simultaneous detection, identification and quantitation of these drugs. The following drugs were simultaneously analyzed: Gamma-hydroxybutyrate (GHB), scopolamine, lysergic acid diethylamide, ketamine, flunitrazepam, and diphenhydramine. The results showed increased sensitivity with electrospray (ES) ionization versus atmospheric pressure chemical ionization (APCI) using HPLC/MS. HPLC/ES/MS was approximately six times more sensitive than HPLC/APCI/MS and about fifty times more sensitive than HPLC/UV. A limit of detection (LOD) of 100 ppb was achieved for drug analysis using this method. The average linear regression coefficient of correlation squared (r2) was 0.933 for HPLC/UV and 0.998 for HPLC/ES/MS. The detection limits achieved by this method allowed for the detection of drug dosages used in beverage tampering. This method can be used to screen beverages suspected of drug tampering. The results of this study demonstrated that solid phase microextraction (SPME) did not improve sensitivity as an extraction technique when compared to direct injections of the drug standards.

Hilbert Space Valued Signal Plus Noise Models: Analysis of Structural Breaks under High Dimensionality and Temporal Dependence

This thesis is concerned with change point analysis for time series, i.e. with detection of structural breaks in time-ordered, random data. This long-standing research field regained popularity over the last few years and is still undergoing, as statistical analysis in general, a transformation to high-dimensional problems. We focus on the fundamental »change in the mean« problem and provide extensions of the classical non-parametric Darling-Erdős-type cumulative sum (CUSUM) testing and estimation theory within highdimensional Hilbert space settings. In the first part we contribute to (long run) principal component based testing methods for Hilbert space valued time series under a rather broad (abrupt, epidemic, gradual, multiple) change setting and under dependence. For the dependence structure we consider either traditional m-dependence assumptions or more recently developed m-approximability conditions which cover, e.g., MA, AR and ARCH models. We derive Gumbel and Brownian bridge type approximations of the distribution of the test statistic under the null hypothesis of no change and consistency conditions under the alternative. A new formulation of the test statistic using projections on subspaces allows us to simplify the standard proof techniques and to weaken common assumptions on the covariance structure. Furthermore, we propose to adjust the principal components by an implicit estimation of a (possible) change direction. This approach adds flexibility to projection based methods, weakens typical technical conditions and provides better consistency properties under the alternative. In the second part we contribute to estimation methods for common changes in the means of panels of Hilbert space valued time series. We analyze weighted CUSUM estimates within a recently proposed »high-dimensional low sample size (HDLSS)« framework, where the sample size is fixed but the number of panels increases. We derive sharp conditions on »pointwise asymptotic accuracy« or »uniform asymptotic accuracy« of those estimates in terms of the weighting function. Particularly, we prove that a covariance-based correction of Darling-Erdős-type CUSUM estimates is required to guarantee uniform asymptotic accuracy under moderate dependence conditions within panels and that these conditions are fulfilled, e.g., by any MA(1) time series. As a counterexample we show that for AR(1) time series, close to the non-stationary case, the dependence is too strong and uniform asymptotic accuracy cannot be ensured. Finally, we conduct simulations to demonstrate that our results are practically applicable and that our methodological suggestions are advantageous.

“A long-term mortality analysis of subsidized firms in rural areas: an empirical study in the Portuguese Alentejo region”

Studies have demonstrated that public policies to support private firms’ investment have the ability to promote entrepreneurship, but the sustainability of subsidized firms has not often been analysed. This paper aims to examine this dimension specifically through evaluating the mortality of subsidized firms in the long-term. The analysis focuses on a case study of the LEADER+ Programme in the Alentejo region of Portugal. With this purpose, the paper examines the activity status (active or not active) of 154 private, rural, for-profit firms in Alentejo that had received a subsidy to support investment between 2002 and 2008 under the LEADER+ Programme. The methodology is based on binary choice models in order to study the probability of these firms still being active. The explanatory variables used are the following: (1) the characteristics of entrepreneurs and managers’ strategic decisions, (2) firm profile and characteristics, (3) regional economic environment. Data assessment showed that the cumulative mortality rate of firms on 31st December 2013 is over 20 %. Interpretation of the regression model revealed that he probability of firms’ survival increases with higher investment, firm age and regional business concentration, whereas the number of applications made by firms has a negative impact on their survival. So it seems that for subsidized firms the amount of investment is as important as its frequency.

Integrated molecular analysis of endometrial carcinoma: translation of biomarker profiles into the clinical practice

The Cancer Genome Atlas (TCGA) collaborative project identified four distinct prognostic groups of endometrial carcinoma (EC) based on molecular alterations: (i) the ultramutated subtype that encompassed POLE mutated (POLE) cases; (ii) the hypermutated subtype, characterized by MisMatch Repair deficiency (MMRd); (iii) the copy-number high subtype, with p53 abnormal/mutated features (p53abn); (iv) the copy-number low subtype, known as No Specific Molecular Profile (NSMP). Although the prognostic value of TCGA molecular classification, NSMP tumors present a wide variability in molecular alterations and biological aggressiveness. This study aims to investigate the impact of ARID1A and CTNNB1/β-catenin alterations by targeted Next-generation sequencing (NGS) and immunohistochemistry (IHC) in a consecutive series of 125 molecularly classified ECs. NGS and IHC were used to assign surrogate TCGA groups and to identify molecular alterations of multiple target genes including POLE, PTEN, ARID1A, CTNNB1, TP53. Associations with clinicopathologic parameters, molecular subtypes, and outcomes identified NSMP category as the most heterogeneous group in terms of clinicopathologic features and outcome. Integration of surrogate TCGA molecular classification with ARID1A and β-catenin analysis showed NSMP cases with ARID1A mutation characterized by the worst outcome with early recurrence, while NSMP tumors with ARID1A wild-type and β-catenin alteration had indolent clinicopathologic features and no recurrence. This study indicates how the identification of ARID1A and β-catenin alterations in EC represents a simple and effective way to characterize NSMP tumor aggressiveness and metastatic potential.

Analysis of COVID-related symptoms from a database of Italian tweets

Twitter is a highly popular social media which on one hand allows information transmission in real time and on the other hand represents a source of open access homogeneous text data. We propose an analysis of the most common self-reported COVID symptoms from a dataset of Italian tweets to investigate the evolution of the pandemic in Italy from the end of September 2020 to the end of January 2021. After manually filtering tweets actually describing COVID symptoms from the database - which contains words related to fever, cough and sore throat - we discuss usefulness of such filtering. We then compare our time series with the daily data of new hospitalisations in Italy, with the aim of building a simple linear regression model that accounts for the delay which is observed from the tweets mentioning individual symptoms to new hospitalisations. We discuss both the results and limitations of linear regression given that our data suggests that the relationship between time series of symptoms tweets and of new hospitalisations changes towards the end of the acquisition.

Biomimetic surfaces for greener coastal infrastructures: an analysis of factors that contribute to make artificial structures more “natural”

The growing ecological awareness of Ocean Sprawl impacts is promoting the adoption of eco-engineering strategies to enhance the ecological performance of coastal infrastructures. Biomimicry, as an eco-engineering tool, aims to design infrastructure more suitable for wildlife by manipulating structural factors to mimic natural habitats. However, little is known about the extent to which natural and artificial substrates differ in their structure and to what extent such differences affect the biota. To fill these knowledge gaps and consequently design biomimetic surfaces, I initially explored how much physical structure diverges between various types of natural and artificial substrates and tested to what extent differences in physical structure and material composition affect the epibenthic communities. By mean of an in-field mensurative experiment and a systematic review coupled with a meta-analysis, I found that, although communities tended to differ between natural and artificial coastal habitats, both physical structure and material composition reported an overall mild effect on epibenthic communities. However, an informed choice of building material and an appropriate combination of multiple structural manipulations can promote ecological benefits at multiple levels, from increasing the ecological performance in situ to reducing the impacts during the production process. Thus, I combined my findings in a final experiment, still in progress, where I am testing the combined role of shape, brightness and inclination of biomimetic surfaces I have designed in producing benefits at multiple levels. Overall, I suggest that biomimicry has the potential to increase the ecological value of artificial habitats especially when a wide range of aspects is simultaneously considered. Indeed, none of the structural factors, individually, can fully mimic the “natural conditions” to effectively improve the ecological performance of the artificial substrates. This emphasizes the need to include in future works a multi-level perspective to fully achieve the great potential of biomimicry.

Analysis of technological accidents triggered by natural events (Natech) in the perspective of climate change

The severe accidents deriving from the impact of natural events on industrial installations have become a matter of growing concern in the last decades. In the literature, these events are typically referred to as Natech accidents. Several peculiarities distinguish them from conventional industrial accidents caused by internal factors, such as the possible occurrence of multiple simultaneous failures, and the enhanced probability of cascading events. The research project provides a comprehensive overview of Natech accidents that occurred in the Chemical and Process Industry, allowing for the identification of relevant aspects of Natech events. Quantified event trees and probability of ignition are derived from the collected dataset, providing a step forward in the quantitative risk assessment of Natech accidents. The investigation of past Natech accidents also demonstrated that wildfires may cause technological accidents. Climate change and global warming are promoting the conditions for wildfire development and rapid spread. Hence, ensuring the safety of industrial facilities exposed to wildfires is paramount. This was achieved defining safety distances between wildland vegetation and industrial equipment items. In addition, an innovative methodology for the vulnerability assessment of Natech and Domino scenarios triggered by wildfires was developed. The approach accounted for the dynamic behaviour of wildfire events and related technological scenarios. Besides, the performance of the emergency response and the related intervention time in the case of cascading events caused by natural events were evaluated. Overall, the tools presented in this thesis represent a step forward in the Quantitative Risk Assessment of Natech accidents. The methodologies developed also provide a solid basis for the definition of effective strategies for risk mitigation and reduction. These aspects are crucial to improve the resilience of industrial plants to natural hazards, especially considering the effects that climate change may have on the severity of such events.

Multi-scale analysis of active landslides using two-pass differential interferometry

Landslides are common features of the landscape of the north-central Apennine mountain range and cause frequent damage to human facilities and infrastructure. Most of these landslides move periodically with moderate velocities and, only after particular rainfall events, some accelerate abruptly. Synthetic aperture radar interferometry (InSAR) provides a particularly convenient method for studying deforming slopes. We use standard two-pass interferometry, taking advantage of the short revisit time of the Sentinel-1 satellites. In this paper we present the results of the InSAR analysis developed on several study areas in central and Northern Italian Apennines. The aims of the work described within the articles contained in this paper, concern: i) the potential of the standard two-pass interferometric technique for the recognition of active landslides; ii) the exploration of the potential related to the displacement time series resulting from a two-pass multiple time-scale InSAR analysis; iii) the evaluation of the possibility of making comparisons with climate forcing for cognitive and risk assessment purposes. Our analysis successfully identified more than 400 InSAR deformation signals (IDS) in the different study areas corresponding to active slope movements. The comparison between IDSs and thematic maps allowed us to identify the main characteristics of the slopes most prone to landslides. The analysis of displacement time series derived from monthly interferometric stacks or single 6-day interferograms allowed the establishment of landslide activity thresholds. This information, combined with the displacement time series, allowed the relationship between ground deformation and climate forcing to be successfully investigated. The InSAR data also gave access to the possibility of validating geographical warning systems and comparing the activity state of landslides with triggering probability thresholds.

Analysis of urban infrastructure for sustainable mobility through instrumented bicycles for students

In Europe almost 80% of the continent's population lives in cities. It is estimated that by 2030 most regions in Europe which contain major cities will have even more inhabitants on 35–60% more than now. This process generates a consequent elevate human pressure on the natural environment, especially around large urban agglomerations. Cities could be seen as an ecosystem, represented by the dominance of humans that re-distribute organisms and fluxes and represent the result of co-evolving human and natural systems, emerging from the interactions between humans, natural and infrastructures. Roads have a relevant role in building links between urban components, creating the basis on which it is founded the urban ecosystem itself. This thesis is focused on the research for a comprehensive model, framed in European urban health & wellbeing programme, aimed to evaluate the determinants of health in urban populations. Through bicycles, GPS and sensor kits, specially developed and produced by University of Bologna for this purpose, it has been possible to conduct on Bologna different direct observations that oriented the novelty of the research: the categorization of university students cyclists, connection among environmental data awareness and level of cycling, and an early identification of urban attributes able to impact on road air quality and level of cycling. The categorization of university students’ cyclist has been defined through GPS analysis and focused survey, that both permit to identify behavioural and technical variables and attitudes towards urban cycling. The statistic relationship between level of cycling, seen as number of bicycles passages per lane and pollutants level, has been investigated through an inverse regression model, defined and tested through SPSS software on the basis of the data harvest. The research project that represents a sort of dynamic mobility laboratory on two wheels, that permits to harvest and study detected parameters.

Contributions to the performance analysis of continuum parallel robots

Continuum parallel robots (CPRs) are manipulators employing multiple flexible beams arranged in parallel and connected to a rigid end-effector. CPRs promise higher payload and accuracy than serial CRs while keeping great flexibility. As the risk of injury during accidental contacts between a human and a CPR should be reduced, CPRs may be used in large-scale collaborative tasks or assisted robotic surgery. There exist various CPR designs, but the prototype conception is rarely based on performance considerations, and the CPRs realization in mainly based on intuitions or rigid-link parallel manipulators architectures. This thesis focuses on the performance analysis of CPRs, and the tools needed for such evaluation, such as workspace computation algorithms. In particular, workspace computation strategies for CPRs are essential for the performance assessment, since the CPRs workspace may be used as a performance index or it can serve for optimal-design tools. Two new workspace computation algorithms are proposed in this manuscript, the former focusing on the workspace volume computation and the certification of its numerical results, while the latter aims at computing the workspace boundary only. Due to the elastic nature of CPRs, a key performance indicator for these robots is the stability of their equilibrium configurations. This thesis proposes the experimental validation of the equilibrium stability assessment on a real prototype, demonstrating limitations of some commonly used assumptions. Additionally, a performance index measuring the distance to instability is originally proposed in this manuscript. Differently from the majority of the existing approaches, the clear advantage of the proposed index is a sound physical meaning; accordingly, the index can be used for a more straightforward performance quantification, and to derive robot specifications.

Analysis Of The Dna Fourier Transform-infrared Microspectroscopic Signature Using An All-reflecting Objective.

The Fourier transform-infrared (FT-IR) signature of dry samples of DNA and DNA-polypeptide complexes, as studied by IR microspectroscopy using a diamond attenuated total reflection (ATR) objective, has revealed important discriminatory characteristics relative to the PO2(-) vibrational stretchings. However, DNA IR marks that provide information on the sample's richness in hydrogen bonds have not been resolved in the spectral profiles obtained with this objective. Here we investigated the performance of an all reflecting objective (ARO) for analysis of the FT-IR signal of hydrogen bonds in DNA samples differing in base richness types (salmon testis vs calf thymus). The results obtained using the ARO indicate prominent band peaks at the spectral region representative of the vibration of nitrogenous base hydrogen bonds and of NH and NH2 groups. The band areas at this spectral region differ in agreement with the DNA base richness type when using the ARO. A peak assigned to adenine was more evident in the AT-rich salmon DNA using either the ARO or the ATR objective. It is concluded that, for the discrimination of DNA IR hydrogen bond vibrations associated with varying base type proportions, the use of an ARO is recommended.

Is Thyroid Stunning Clinically Relevant? A Retrospective Analysis Of 208 Patients.

Current guidelines have advised against the performance of (131)I-iodide diagnostic whole body scintigraphy (dxWBS) to minimize the occurrence of stunning, and to guarantee the efficiency of radioiodine therapy (RIT). The aim of the study was to evaluate the impact of stunning on the efficacy of RIT and disease outcome. This retrospective analysis included 208 patients with differentiated thyroid cancer managed according to a same protocol and followed up for 12-159 months (mean 30 ± 69 months). Patients received RIT in doses ranging from 3,700 to 11,100 MBq (100 mCi to 300 mCi). Post-RIT-whole body scintigraphy images were performed 10 days after RIT in all patients. In addition, images were also performed 24-48 hours after therapy in 22 patients. Outcome was classified as no evidence of disease (NED), stable disease (SD) and progressive disease (PD). Thyroid stunning occurred in 40 patients (19.2%), including 26 patients with NED and 14 patients with SD. A multivariate analysis showed no association between disease outcome and the occurrence of stunning (p = 0.3476). The efficacy of RIT and disease outcome do not seem to be related to thyroid stunning.

Combined Analysis Of νμ Disappearance And νμ→νe Appearance In Minos Using Accelerator And Atmospheric Neutrinos.

We report on a new analysis of neutrino oscillations in MINOS using the complete set of accelerator and atmospheric data. The analysis combines the ν(μ) disappearance and ν(e) appearance data using the three-flavor formalism. We measure |Δm(32)(2)| = [2.28-2.46] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.35-0.65 (90% C.L.) in the normal hierarchy, and |Δm(32)(2)| = [2.32-2.53] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.34-0.67 (90% C.L.) in the inverted hierarchy. The data also constrain δ(CP), the θ(23} octant degeneracy and the mass hierarchy; we disfavor 36% (11%) of this three-parameter space at 68% (90%) C.L.

Phylogenetic Analysis Of The Microbial Community In Hypersaline Petroleum Produced Water From The Campos Basin.

In this work the archaea and eubacteria community of a hypersaline produced water from the Campos Basin that had been transported and discharged to an onshore storage facility was evaluated by 16S recombinant RNA (rRNA) gene sequence analysis. The produced water had a hypersaline salt content of 10 (w/v), had a carbon oxygen demand (COD) of 4,300 mg/l and contains phenol and other aromatic compounds. The high salt and COD content and the presence of toxic phenolic compounds present a problem for conventional discharge to open seawater. In previous studies, we demonstrated that the COD and phenolic content could be largely removed under aerobic conditions, without dilution, by either addition of phenol degrading Haloarchaea or the addition of nutrients alone. In this study our goal was to characterize the microbial community to gain further insight into the persistence of reservoir community members in the produced water and the potential for bioremediation of COD and toxic contaminants. Members of the archaea community were consistent with previously identified communities from mesothermic reservoirs. All identified archaea were located within the phylum Euryarchaeota, with 98 % being identified as methanogens while 2 % could not be affiliated with any known genus. Of the identified archaea, 37 % were identified as members of the strictly carbon-dioxide-reducing genus Methanoplanus and 59 % as members of the acetoclastic genus Methanosaeta. No Haloarchaea were detected, consistent with the need to add these organisms for COD and aromatic removal. Marinobacter and Halomonas dominated the eubacterial community. The presence of these genera is consistent with the ability to stimulate COD and aromatic removal with nutrient addition. In addition, anaerobic members of the phyla Thermotogae, Firmicutes, and unclassified eubacteria were identified and may represent reservoir organisms associated with the conversion hydrocarbons to methane.