<p> The Archean pyroclastic conglomerate studied has six clast types which can be condensed to four clast families based on lithology. The quartz clasts have an average strain of X:Y:Z=1.21:1:0.55 while the pumice clasts have an average strain of X:Y:Z=1.27:1:0.47. The difference is strain between these clast families can be attributed to their different viscosities. The quartz clasts have an assumed viscosity ratio between the clasts and the matrix of unity and are taken to represent the strain in the rock as a whole. The sulphide and black clasts have strain ratios much higher than the quartz because of recrystallization of the sulphide and cleavage formation effecting the black clasts.</p> <p> The sedimentary structure of the deposit and its position between mafic pillow basalts indicate that the deposit is a result of the deposition of a subaqueous pyroclastic debris flow in a proximal environment.</p> / Thesis / Bachelor of Science (BSc)

Multiple strain path changes during forming lead to complex geometrically necessary dislocation (GND) development in strain gradient fields, inducing internal stresses that contribute to the Bauschinger effect, residual stresses, and springback which alters the final geometrical shape of the part. In order to analyze and design improved processing routes, models must capture the evolution of these internal stresses. However, most models capture the effects of these stresses via phenomenological approaches that require calibration to each new material and strain path. The development of models that capture the underlying physics at the sub-grain level is underway but requires in-depth studies of dislocation behavior (at the relevant meso length scale) in order to guide and validate them. The novel experimental campaign central to this thesis aims to tackle this problem by capturing unprecedented data of dislocation activity for several sheet metals during multiple strain path deformation. The resultant insights provide a new window into multi-path forming of metals, while also aiding the development and validation of two crystal plasticity (CP) models by collaborators at the University of New Hampshire (UNH). The models incorporate internal stresses at the grain and sub-grain levels, respectively. The hardening response due to strain path change during forming of AA6016-T4 was studied at the macro- and micro-level via combined experiments and an elasto-plastic self-consistent (EPSC) model. The experiments demonstrated that possible recombination and/or redirection of dislocations onto different slip systems under strain path change allowed for a gradual elasto-plastic transition, in comparison to a much sharper response upon continued deformation under the same strain path due to buildup and immediate activation of backstresses. The phenomenological backstress law of the EPSC model underpredicted the yield stress response for the strain path change deformations, possibly due to missing sub-grain GND development and an accurate description of associated backstresses. A more detailed experimental study of multi-path deformation for the AA6016-T4 was required in order to guide development of a strain gradient elasto-visco plasticity self-consistent model (SG-EVPSC); the model includes sub-grain strain gradient fields, and related internal stress fields. Total dislocation and GND density were tracked at various points of the deformation, and a complete 3D statistical volume element was characterized, to enable accurate modeling of the microstructure. The tests revealed a relatively lower yield stress response following strain path change, presumably aided by lower latent hardening than self hardening; the tests then showed a rapid accumulation of dislocations on the newly activated slip systems resulting in much higher final dislocation density without affecting the ductility of the pre-strained material. Interestingly, GND development was dominated by the precipitates instead of grain boundaries. These observations are vital for an accurate forming prediction from CPFEA models. Finally, optimized forming conditions of continuous bending under tension produced a ratcheting strain path resulting in a gradual GND development and a more complete retained austenite transformation in quenched-&-partitioned- and TRIP-assisted bainitic ferritic-1180 steels increasing their ductility by at least 360%.

Cardiac magnetic resonance (CMR)-derived left ventricular (LV) global longitudinal strain (GLS) provides incremental prognostic information on various cardiovascular diseases but has not yet been investigated comprehensively in patients with Takotsubo syndrome (TS). This study evaluated the prognostic value of feature tracking (FT) GLS, tissue tracking (TT) GLS, and fast manual long axis strain (LAS) in 147 patients with TS, who underwent CMR at a median of 2 days after admission. Long-term mortality was assessed 3 years after the acute event. In contrast to LV ejection fraction and tissue characteristics, impaired FT-GLS, TT-GLS and fast manual LAS were associated with adverse outcome. The best cutoff points for the prediction of long-term mortality were similar with all three approaches: FT-GLS −11.28%, TT-GLS −11.45%, and fast manual LAS −10.86%. Long-term mortality rates were significantly higher in patients with FT-GLS > −11.28% (25.0% versus 9.8%; p = 0.029), TT-GLS > −11.45% (20.0% versus 5.4%; p = 0.016), and LAS > −10.86% (23.3% versus 6.6%; p = 0.014). However, in multivariable analysis, diabetes mellitus (p = 0.001), atrial fibrillation (p = 0.001), malignancy (p = 0.006), and physical triggers (p = 0.006) outperformed measures of myocardial strain and emerged as the strongest, independent predictors of long-term mortality in TS. In conclusion, CMR-based longitudinal strain provides valuable prognostic information in patients with TS, regardless of the utilized technique of assessment. Long-term mortality, however, is mainly determined by comorbidities.

Through the last decades several nonlocal models of linear elasticity have been introduced as enhancements of the Cauchy-elastic model, often with the purpose of providing an improved mechanical description of solids at the microscale level. Although many efforts have been devoted to the analytical formulation of these advanced constitutive models, a definitive interpretation of the relevant static quantities is still incomplete and Finite Element (FE) solvers are practically unavailable. In this thesis, after providing a mechanical interpretation to the static quantities involved in strain gradient (of Mindlin type) elastic materials, an overview on the possible quadrilateral Hermitian finite elements is given to treat quasi-static plane problems. Beside the classical finite elements inspired by those adopted for modeling Kirchhoff plates, an alternative quadrilateral self-constrained finite element formulated through Lagrange multipliers is also proposed. With reference to a hexagonal lattice structure, for which the equivalent constitutive tensors have been recently derived as closed-form expressions, the developed FE codes are exploited to assess the reliability of modelling lattices through higher-order constitutive equations. These analyses are developed for one-dimensional and two dimensional problems, where the former are considered for both homogeneous layers (with a finite size in one direction) and rod-type structures (with a finite uniform cross section along one direction). It is confirmed that higher-order modelling improves the mechanical description. In particular, the macroscale response is shown to be strongly affected by higher-order contributions in the presence of extreme elastic contrast between microstructural elements. Indeed, in this last case, only higher-order modeling captures a non-null residual stiffness, which vanishes in the framework of classical models. Therefore, higher-order modeling becomes important not only to describe the mechanical response at a microlevel, but also for macrolevel modelling, when extreme mechanical properties are addressed. The presented results pave the way to a refined modelling of architected materials leading to improved design of microstructures displaying innovative mechanical features.

The human gut microbiome is home to many hundreds of different microbes which play a crucial role in human physiology. For most of them, little is known about how their genetic diversity translates into functional traits and how they interact with their host, which is to some extent due to the lack of isolate genomes. Cultivation-free metagenomic approaches yield extensive amounts of bacterial genetic data, and recently developed algorithms allow strain-level resolution and reconstruction of bacterial genomes from metagenomes, yet bacterial within-species diversity and transmission dynamics after fecal microbiota transplantation remain largely unexplored over cohorts and using these technological advances. To investigate bacterial within-species diversity I first undertook large-scale exploratory studies to characterize the population-level genomic makeup of the two key human gut microbes Eubacterium rectale and Akkermansia muciniphila , leveraging many hundreds of bacterial draft genomes reconstructed from short-read shotgun metagenomics datasets from all around the planet. For E. rectale , I extended previous observations about clustering of subspecies with geography, which suggested isolation by distance and the putative ancestral loss of four distinct motility operons, rendering a subspecies specifically found in Europe immotile. For A. muciniphila, I found that there are several closely related but undescribed Akkermansia spp. in the human gut that are all likely human-specific but are differentially associated with host body mass index, showcasing metabolic differences and distinct co-abundance patterns with putative cognate phages . For both species, I discovered distinct subspecies-level genetic variation in structural polysaccharide synthesis operons. Next, utilizing a complementary strain-resolved approach to track strains between individuals, I undertook a fecal microbiota transplantation (FMT) meta-analysis integrating 24 distinct clinical metagenomic datasets. I found that patients with an infectious disease or those who underwent antibiotic treatment displayed increased donor strain uptake and that some bacterial clades engraft more consistently than others. Furthermore, I developed a machine-learning framework that allows optimizing microbial parameters - such as bacterial richness - in the recipient after FMT based on donor microbiome features, representing first steps towards making a rational donor choice. Taken together, in my work I extended the strain-level understanding of human gut commensals and showcased that genomes from metagenomes can be suitable to conduct large-scale bacterial population genetics studies on other understudied human gut commensals. I further confirmed that strain-resolved metagenomics allows tracking of strains and thus inference of strain engraftment characteristics in an FMT meta-analysis, revealing important differences in engraftment over cohorts and species and paving the way towards better designed FMTs. I believe that my work is an important contribution to the field of microbiome research, showcasing the power of shotgun metagenomics, modern algorithms and large-scale data analysis to reveal previously unattainable insights about the human gut microbiome.

The shear stress in an unsaturated soil increases rapidly with limited shear strain to a peak value and then drops gradually with a further increase in the shear strain until a residual value is reached. In other words, there is a significant strain-softening behavior under large shear deformation. A variety of geotechnical structures (e.g., slopes, foundations, retaining walls and piles) associated with unsaturated soils typically undergo a large progressive deformation prior to reaching failure conditions due to the influence of environmental factors (e.g., rainfall infiltration and wetting-drying cycles). As a result, the shear strength of soils in sliding zones typically reduces from a peak to a residual value with the progressive development of large shear deformation, while the shear strength of soils in other zones are still at the peak level. In other words, in many scenarios the strain-softening behavior of unsaturated soils can significantly influence the mechanical behavior of geo-structures. Therefore, a thorough understanding of the shear strength behavior of unsaturated soils during strain-softening is required to reliably interpret the mechanical behavior of geo-structures that undergo large shear deformation. Significant advances have been made during the last thirty years to understand and model the strain-softening behavior of unsaturated soils. Most of these studies however focus on the strain-softening behavior within a relatively small shear deformation due to the limitations of the experimental apparatuses. Only limited experimental studies under large shear deformation were reported based on the modified suction-controlled ring shear apparatus. Therefore, more investigations are still required to provide a comprehensive understanding of the shear strength behavior of unsaturated soils during strain-softening under large shear deformation. Studies presented in this thesis are directed towards investigating the shear strength behavior of unsaturated soils during strain-softening and its application in geotechnical engineering practice. The following studies have been conducted: (i) A state-of-the-art review of the strain-softening behavior of unsaturated soils published in the literature during the past three decades is summarized. The physical mechanisms and modelling methods of the strain-softening behavior and the peak, critical and residual shear strength of unsaturated soils are investigated. (ii) A disturbed state concept model is proposed to predict the variation of shear stress in unsaturated soils during strain-softening process under drained condition. Five sets of experimental data gathered from the literature on unsaturated soils varying from coarse- to fine-grained soils are used to verify the proposed model. The proposed model can provide reasonable predictions for the strain-softening stress-strain relationships of various types of unsaturated soils. The model is simple in concept and all the required parameters can be obtained from conventional saturated and unsaturated shearing tests and pressure plate tests. (iii) Two sets of suction-controlled multistage ring shear tests are conducted on unsaturated SP-SM soil and Indian Head till (IHT), respectively. The variation of the shear stress, void ratio, and water content of specimens during shearing (the shear displacement reaches 100 mm) under multi levels of net normal stress and matric suction are described and discussed. The influence of matric suction and net normal stress on the residual shear strength envelops of unsaturated soils are critically discussed. (iv) A model for predicting the residual shear strength for a wide range of unsaturated soils comprising coarse- to fine-grained soils is developed in terms of two stress state variables (i.e., the net normal stress and matric suction) by using the soil water characteristic curve as a tool. The model is formulated and validated based on experimental data in a series of suction-controlled ring shear tests using the axis-translation technique, including the two sets of tests (SP-SM and IHT) conducted in this research and another three sets of tests (SM, SC-SM and CH) gathered from the literature. The fitting parameters are related to the plasticity index (Iₚ); thus, only four basic parameters (i.e., cᵣ', φᵣ', Sᵣ and Iₚ) are included in this approach. (v) A series of slope stability analyses of a landslide in unsaturated condition are conducted using Geoslope software based on the peak and residual shear strength parameters. The analyses results highlight the role of residual shear strength in the slope stability of unsaturated soils. In summary, the mechanical behavior of unsaturated soils under large shear deformation is comprehensively investigated in this thesis. The experimental results of the suction-controlled ring shear tests reported in this research contribute towards understanding the fundamental shear strength behavior of unsaturated soils during strain-softening under large shear deformation. The models proposed in this research provide simple tools to predict the shear strength of unsaturated soils under different levels of shear deformation.

The genus Mycobacterium contains many pathogenic bacteria that are known to cause serious diseases in humans. One of the most well-known of these bacteria is Mycobacterium tuberculosis, or Mtb, which is the causative agent of tuberculosis. It infects nearly one-third of the world’s population and kills 1.4 million people annually. Another important mycobacterial pathogen is Mycobacterium abscessus, or Mabs, which causes respiratory infections in cystic fibrosis patients. One of the biggest difficulties in combating these pathogens is the lack of effective diagnostics, as current strategies hold many pitfalls and can be unreliable. One common method used is sputum smear microscopy which involves acid fast staining of the bacteria present in a patient’s sputum. This method of detection fails to detect more than 50% of infections and is unable to differentiate between species of mycobacterium. This project introduces a novel method of mycobacterial diagnostics using binary deoxyribozymes (DNAzymes). Binary DNAzymes recognize bacteria-specific nucleic acid sequences and bind to them, forming a catalytic core which cleaves a substrate molecule. This cleavage separates a quencher molecule from a fluorophore, which results in a fluorescent output. This flexible assay platform has great potential for the detection of Mtb or Mabs. Our data shows the specificity of the DNAzymes allowing for a differential diagnosis of various species of Mycobacteria. It also shows the limit of detection of this technology and its additional utility in molecular typing of Mtb clinical isolates as well as drug resistance characterization. This multipurpose tool can contribute to disease management in multiple ways.

There has been extensive research conducted on recidivism among serious juvenile offenders. This study examines juvenile recidivism through the lenses of General Strain Theory (GST). GST has been used in previous studies to explain recidivism, however, secure placement and its effect on juvenile mental health, has not been studied. The purpose of this study is to test for a relationship between emotional responses like anger and hostility and secure placement, utilizing the Pathways to Desistance data. I will also examine if anger and hostility act as a mediator between secure placement and recidivism. Pathways to Desistance was a prospective study of serious juvenile offenders in Phoenix, Arizona (N = 654) and Philadelphia, Pennsylvania (N = 700). Specifically, I examined if secure placement, as measured by length of time spent in a secure facility (i.e., detention center), affects self-reported offending and criminal history. Anger and hostility were measured using the Brief Symptom Inventory (BSI; Derogatis and Melisaratos, 1983). If results suggested that assigning juveniles to a secure placement does evoke negative emotional responses which in turn increase the likelihood of recidivism, policy reflecting a more constructive deterrent and rehabilitation for juveniles would need to be created.

Experiments were conducted on ASTM A572 50 and A992 steel over a range of intermediate strain rates in order to determine material strength properties of structural members subjected to dynamic loadings. The yield and ultimate tensile stress (UTS) of the steels were determined at increasing strain rates using a hydraulic apparatus and compared to static values obtained from ASTM E8 standardized tensile experiments. Results revealed that A572-50 steel exhibited an increase in yield stress of up to 35% and UTS of up to 20% as strain rate increased from 0.002 to 2.0 s-1. A992 steel demonstrated a similar increase in yield stress of up to 45% and UTS of up to 20%. Ratios of dynamic-to-static strengths were used to develop dynamic increase factor curves spanning the range of strain rates studied. These curves provide designers with material property values required for accurate and economical design of protective structures.

Laying hen welfare is gaining importance in the United States and several states have passed legislation for a welfareriendly housing environment, which has forced the egg industry to explore alternative housing environments. For this reason, our first objective was to determine the effect of housing environment and laying hen strain on production performance and egg quality. Results showed that production performance of the hens raised in the alternative housing system was similar to the conventional system. The second objective was to compare the eggshell and cloacal microbiology. Our results indicated that the microbial load observed was higher in the alternative system compared to the conventional system. The third objective was to determine the effects of housing environment and laying hen strain on tibia and femur bone properties. The results demonstrated that the alternative system provided better tibia and femur bone characteristics, but it varied among laying hen strains.