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Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Efficient Optimization Algorithms for Nonlinear Data Analysis

Identification of low-dimensional structures and main sources of variation from multivariate data are fundamental tasks in data analysis. Many methods aimed at these tasks involve solution of an optimization problem. Thus, the objective of this thesis is to develop computationally efficient and theoretically justified methods for solving such problems. Most of the thesis is based on a statistical model, where ridges of the density estimated from the data are considered as relevant features. Finding ridges, that are generalized maxima, necessitates development of advanced optimization methods. An efficient and convergent trust region Newton method for projecting a point onto a ridge of the underlying density is developed for this purpose. The method is utilized in a differential equation-based approach for tracing ridges and computing projection coordinates along them. The density estimation is done nonparametrically by using Gaussian kernels. This allows application of ridge-based methods with only mild assumptions on the underlying structure of the data. The statistical model and the ridge finding methods are adapted to two different applications. The first one is extraction of curvilinear structures from noisy data mixed with background clutter. The second one is a novel nonlinear generalization of principal component analysis (PCA) and its extension to time series data. The methods have a wide range of potential applications, where most of the earlier approaches are inadequate. Examples include identification of faults from seismic data and identification of filaments from cosmological data. Applicability of the nonlinear PCA to climate analysis and reconstruction of periodic patterns from noisy time series data are also demonstrated. Other contributions of the thesis include development of an efficient semidefinite optimization method for embedding graphs into the Euclidean space. The method produces structure-preserving embeddings that maximize interpoint distances. It is primarily developed for dimensionality reduction, but has also potential applications in graph theory and various areas of physics, chemistry and engineering. Asymptotic behaviour of ridges and maxima of Gaussian kernel densities is also investigated when the kernel bandwidth approaches infinity. The results are applied to the nonlinear PCA and to finding significant maxima of such densities, which is a typical problem in visual object tracking.

Insights into the physiological function of cellular prion protein

Prions have been extensively studied since they represent a new class of infectious agents in which a protein, PrPsc (prion scrapie), appears to be the sole component of the infectious particle. They are responsible for transmissible spongiform encephalopathies, which affect both humans and animals. The mechanism of disease propagation is well understood and involves the interaction of PrPsc with its cellular isoform (PrPc) and subsequently abnormal structural conversion of the latter. PrPc is a glycoprotein anchored on the cell surface by a glycosylphosphatidylinositol moiety and expressed in most cell types but mainly in neurons. Prion diseases have been associated with the accumulation of the abnormally folded protein and its neurotoxic effects; however, it is not known if PrPc loss of function is an important component. New efforts are addressing this question and trying to characterize the physiological function of PrPc. At least four different mouse strains in which the PrP gene was ablated were generated and the results regarding their phenotype are controversial. Localization of PrPc on the cell membrane makes it a potential candidate for a ligand uptake, cell adhesion and recognition molecule or a membrane signaling molecule. Recent data have shown a potential role for PrPc in the metabolism of copper and moreover that this metal stimulates PrPc endocytosis. Our group has recently demonstrated that PrPc is a high affinity laminin ligand and that this interaction mediates neuronal cell adhesion and neurite extension and maintenance. Moreover, PrPc-caveolin-1 dependent coupling seems to trigger the tyrosine kinase Fyn activation. These data provide the first evidence for PrPc involvement in signal transduction.

Recent advances in angiotensin II signaling

Angiotensin II (Ang II)* is a multifunctional hormone that influences the function of cardiovascular cells through a complex series of intracellular signaling events initiated by the interaction of Ang II with AT1 and AT2 receptors. AT1 receptor activation leads to cell growth, vascular contraction, inflammatory responses and salt and water retention, whereas AT2 receptors induce apoptosis, vasodilation and natriuresis. These effects are mediated via complex, interacting signaling pathways involving stimulation of PLC and Ca2+ mobilization; activation of PLD, PLA2, PKC, MAP kinases and NAD(P)H oxidase, and stimulation of gene transcription. In addition, Ang II activates many intracellular tyrosine kinases that play a role in growth signaling and inflammation, such as Src, Pyk2, p130Cas, FAK and JAK/STAT. These events may be direct or indirect via transactivation of tyrosine kinase receptors, including PDGFR, EGFR and IGFR. Ang II induces a multitude of actions in various tissues, and the signaling events following occupancy and activation of Ang receptors are tightly controlled and extremely complex. Alterations of these highly regulated signaling pathways may be pivotal in structural and functional abnormalities that underlie pathological processes in cardiovascular diseases such as cardiac hypertrophy, hypertension and atherosclerosis.

NFAT transcription factors: from cell cycle to tumor development

The nuclear factor of activated T cells (NFAT) family of transcription factors has been primarily identified in immune cells; however, these proteins have been recently found to be functionally active in several other non-immune cell types. NFAT proteins are activated upon different stimuli that lead to increased intracellular calcium levels. Regardless of their widely known cytokine gene expression properties, NFATs have been shown to regulate other genes related to cell cycle progression, cell differentiation and apoptosis, revealing a broader role for these proteins in normal cell physiology. Several reports have addressed the participation of NFATs in many aspects of malignant cell transformation and tumorigenic processes. In this review, we will discuss the involvement of the different NFAT family members in the regulation of cell cycling, differentiation and tumor formation, and also its implications on oncogenesis. Better understanding the mechanisms by which NFATs regulate cell cycle and tumor-related events should be relevant for the development of rational anti-cancer therapies.

A mechanistic view of mitochondrial death decision pores

Mitochondria increase their outer and inner membrane permeability to solutes, protons and metabolites in response to a variety of extrinsic and intrinsic signaling events. The maintenance of cellular and intraorganelle ionic homeostasis, particularly for Ca2+, can determine cell survival or death. Mitochondrial death decision is centered on two processes: inner membrane permeabilization, such as that promoted by the mitochondrial permeability transition pore, formed across inner membranes when Ca2+ reaches a critical threshold, and mitochondrial outer membrane permeabilization, in which the pro-apoptotic proteins BID, BAX, and BAK play active roles. Membrane permeabilization leads to the release of apoptogenic proteins: cytochrome c, apoptosis-inducing factor, Smac/Diablo, HtrA2/Omi, and endonuclease G. Cytochrome c initiates the proteolytic activation of caspases, which in turn cleave hundreds of proteins to produce the morphological and biochemical changes of apoptosis. Voltage-dependent anion channel, cyclophilin D, adenine nucleotide translocase, and the pro-apoptotic proteins BID, BAX, and BAK may be part of the molecular composition of membrane pores leading to mitochondrial permeabilization, but this remains a central question to be resolved. Other transporting pores and channels, including the ceramide channel, the mitochondrial apoptosis-induced channel, as well as a non-specific outer membrane rupture may also be potential release pathways for these apoptogenic factors. In this review, we discuss the mechanistic models by which reactive oxygen species and caspases, via structural and conformational changes of membrane lipids and proteins, promote conditions for inner/outer membrane permeabilization, which may be followed by either opening of pores or a rupture of the outer mitochondrial membrane.

The modified 2VO ischemia protocol causes cognitive impairment similar to that induced by the standard method, but with a better survival rate

Permanent bilateral occlusion of the common carotid arteries (2VO) in the rat has been established as a valid experimental model to investigate the effects of chronic cerebral hypoperfusion on cognitive function and neurodegenerative processes. Our aim was to compare the cognitive and morphological outcomes following the standard 2VO procedure, in which there is concomitant artery ligation, with those of a modified protocol, with a 1-week interval between artery occlusions to avoid an abrupt reduction of cerebral blood flow, as assessed by animal performance in the water maze and damage extension to the hippocampus and striatum. Male Wistar rats (N = 47) aged 3 months were subjected to chronic hypoperfusion by permanent bilateral ligation of the common carotid arteries using either the standard or the modified protocol, with the right carotid being the first to be occluded. Three months after the surgical procedure, rat performance in the water maze was assessed to investigate long-term effects on spatial learning and memory and their brains were processed in order to estimate hippocampal volume and striatal area. Both groups of hypoperfused rats showed deficits in reference (F(8,172) = 7.0951, P < 0.00001) and working spatial memory [2nd (F(2,44) = 7.6884, P < 0.001), 3rd (F(2,44) = 21.481, P < 0.00001) and 4th trials (F(2,44) = 28.620, P < 0.0001)]; however, no evidence of tissue atrophy was found in the brain structures studied. Despite similar behavioral and morphological outcomes, the rats submitted to the modified protocol showed a significant increase in survival rate, during the 3 months of the experiment (P < 0.02).

Remodeling in the ischemic heart: the stepwise progression for heart

Abstract Coronary artery disease is the leading cause of death in the developed world and in developing countries. Acute mortality from acute myocardial infarction (MI) has decreased in the last decades. However, the incidence of heart failure (HF) in patients with healed infarcted areas is increasing. Therefore, HF prevention is a major challenge to the health system in order to reduce healthcare costs and to provide a better quality of life. Animal models of ischemia and infarction have been essential in providing precise information regarding cardiac remodeling. Several of these changes are maladaptive, and they progressively lead to ventricular dilatation and predispose to the development of arrhythmias, HF and death. These events depend on cell death due to necrosis and apoptosis and on activation of the inflammatory response soon after MI. Systemic and local neurohumoral activation has also been associated with maladaptive cardiac remodeling, predisposing to HF. In this review, we provide a timely description of the cardiovascular alterations that occur after MI at the cellular, neurohumoral and electrical level and discuss the repercussions of these alterations on electrical, mechanical and structural dysfunction of the heart. We also identify several areas where insufficient knowledge limits the adoption of better strategies to prevent HF development in chronically infarcted individuals.

Early neonatal echocardiographic findings in an experimental rabbit model of congenital diaphragmatic hernia

This study aimed to demonstrate that congenital diaphragmatic hernia (CDH) results in vascular abnormalities that are directly associated with the severity of pulmonary hypoplasia and hypertension. These events increase right ventricle (RV) afterload and may adversely affect disease management and patient survival. Our objective was to investigate cardiac function, specifically right ventricular changes, immediately after birth and relate them to myocardial histological findings in a CDH model. Pregnant New Zealand rabbits underwent the surgical procedure at 25 days of gestation (n=14). CDH was created in one fetus per horn (n=16), and the other fetuses were used as controls (n=20). At term (30 days), fetuses were removed, immediately dried and weighed before undergoing four-parameter echocardiography. The lungs and the heart were removed, weighed, and histologically analyzed. CDH animals had smaller total lung weight (P<0.005), left lung weight (P<0.005), and lung-to-body ratio (P<0.005). Echocardiography revealed a smaller left-to-right ventricle ratio (LV/RV, P<0.005) and larger diastolic right ventricle size (DRVS, P<0.007). Histologic analysis revealed a larger number of myocytes undergoing mitotic division (186 vs 132, P<0.05) in CDH hearts. Immediate RV dilation of CDH hearts is related to myocyte mitosis increase. This information may aid the design of future strategies to address pulmonary hypertension in CDH.

Man måste tänka själv : klasslärares uppfattningar av undervisning i de naturvetenskapliga läroämnena

A teacher´s perception of a school subject affects a teacher´s teaching and by extension pupils´ learning. The main purpose of this thesis is to describe the variation in the ways class-teachers perceive teaching within science subjects and to illustrate how these teachers choose to work and why they choose as they do. This purpose is operationalized into three central research questions concerning a teacher´s perception of teaching, teachers´ experiences of working methods in the subject and different aspects that are consciously present when the teacher makes his or her choice of working methods. These aspects are viewed from two different perspectives: a subject educational perspective and a teacher perspective. The theoretical background of the study is interdisciplinary. The thesis is a qualitative study where the research approach is phenomenographic. The empirical investigation was made as two separate studies: a semistructured interview study (N = 15) followed by a stimulated recall study (N = 3), a combined interview and video-observation. Results from the empirical investigation indicate that regarding aims for science education teachers wish to awaken or maintain the pupils´ interest in nature and science and that the pupils within the science subjects shall build a base for fundamental general knowledge. As motives for teaching the science subjects teachers view the subjects as a foundation for everyday life, planning and democracy but also for pupils´ further studies and a possible career in the field. The interdisciplinary key competences and the care for the pupils´ well being are aspects that are consciously present when teachers make their choice of working methods. A great variation can be found in the teachers´ perceptions of the science subjects as subjects and of the working methods within these subjects. Teachers describe lack of time on their own part as well as for the pupil´s learning. Results from the empirical investigation also indicate that teachers modestly focus on aims for the teaching and communication regarding these aims. There seems to be an existing need for increased and qualitatively improved inservice education within these subjects.

Marketing Brock University in the 1980's: assessing freshman student feedback in strategic planning approach

Universities have entered a period of rapid change and upheaval due to an external environment beyond their control which includes shifting demographic patterns, accelerating technology, funding shortages, and keener competition for students. Strategic planning, a comprehensive vision which challenges universities to take bold and creative measures to meet the threats and opportunities of the future, is an institutional imperative in the 1980's. This paper examines freshman student feedback in an effort to incorporate this important element into a strategic plan for Brock University, a small, predominantly liberal arts university in St. Catharines, Ontario. The study was designed to provide information on the characteristics of the 1985-86 pool of freshman registrants: their attitudes towards Brock's recruitment measures, their general university priorities, and their influences in regard to university selection (along with other demographical and attitudinal data). A survey involving fixed-alternative questions of a subjective and objective nature was administered in two large freshman classes at Brock in which a broad cross-section of academic programs was anticipated. Computer analysis of the data for the 357 respondents included total raw frequencies and rounded percentages, as well as subgroup cross-tabulation by geographic home area of respondent, academic major, and high school graduating average. The four directional hypotheses put forward were all substantiatied by the survey data, indicating that 1) the university's current recruitment program had been a positive influence during their university search 2) parents were the most influential group in the students' decisions related to university 3) respondents viewed institutional reputation as less of a priority than an enjoyable university lifestyle in a personal learning atmosphere 4) students had a decided preference for co-operative study and internship programs. Strategic planning recommendations included a reduction in the faculty/student ratio through faculty hirings to restore the close rapport between professors and students, increased recruitment presentations in Ontario high schools to enlarge the applicant pool, creation of an Office of Co-operative Study and Internship Programs, institutional emphasis on a "customer orientation", and an extension of research into student demographics and attitudinal data.

The influence of recreational ball hockey play on cardiovascular risk factors in sedentary males

Introduction: The prevalence of coronary artery disease (CAD) is ever increasing in western industrialized societies. An individuals overall risk for CAD may be quantified by integrating a number of factors including, but not limited to, cardiorespiratory fitness, body composition, blood lipid profile and blood pressure. It might be expected that interventions aimed at improving any or all of these independent factors might improve an individual 's overall risk. To this end, the influence of standard endurance type exercise on cardiorespiratory fitness, body composition, blood lipids and blood pressure, and by extension the reduction of coronary risk factors, is well documented. On the other hand, interval training (IT) has been shown to provide an extremely powerful stimulus for improving indices of cardiorespiratory function but the influence of this training type on coronary risk factors is unknown. Moreover, the vast majority of studies investigating the effects of IT on fitness have used laboratory type training protocols. As a result of this, the influence of participation in interval-type recreational sports on cardiorespiratory fitness and coronary risk factors is unknown. Aims: The aim of the present study was to evaluate the effectiveness of recreational ball hockey, a sport associated with interval-type activity patterns, on indices of aerobic function and coronary risk factors in sedentary men in the approximate age range of 30 - 60 years. Individual risk factors were compiled into an overall coronary risk factor score using the Framingham Point Scale (FPS). Methods: Twenty-four sedentary males (age range 30 - 60) participated in the study. Subject activity level was assessed apriori using questionnaire responses. All subjects (experimental and control) were assessed to have been inactive and sedentary prior to participation in the study. The experimental group (43 ± 3 years; 90 ± 3 kg) (n = 11) participated in one season of recreational ball hockey (our surrogate for IT). Member of this group played a total of 16 games during an 11 week span. During this time, the control group (43 ± 2 years; 89 ± 2 kg) (n = 11) performed no training and continued with their sedentary lifestyle. Prior to and following the ball hockey season, experimental and control subjects were tested for the following variables: 1) cardiorespiratory fitness (as V02 Max) 2) blood lipid profile 3) body composition 5) waist to hip ratio 6) blood glucose levels and 7) blood pressure. Subject V02 Max was assessed using the Rockport submaximal walking test on an indoor track. To assess body composition we determined body mass ratio (BMI), % body fat, % lean body mass and waist to hip ratio. The blood lipid profile included high density lipoprotein, low density lipoprotein and total cholesterol levels; in addition, the ratio of total cholesterol to high density was calculated. Blood triglycerides were also assessed. All data were analyzed using independent t - tests and all data are expressed as mean ± standard error. Statistical significance was accepted at p :S 0.05. Results: Pre-test values for all variables were similar between the experimental and control group. Moreover, although the intervention used in this study was associated with changes in some variables for subjects in the experimental group, subjects in the control group did not exhibit any changes over the same time period. BODY COMPOSITION: The % body fat of experimental subjects decreased by 4.6 ± 0.5%, from 28.1 ± 2.6 to 26.9 ± 2.5 % while that of the control group was unchanged at 22.7 ± 1.4 and 22.2 ± 1.3 %. However, lean body mass of experimental and control subjects did not change at 64.3 ± 1.3 versus 66.1 ± 1.3 kg and 65.5 ± 0.8 versus 64.7 ± 0.8 kg, respectively. In terms of body mass index and waist to hip ratio, neither the experimental nor the control group showed any significant change. Respective values for the waist to hip ratio and body mass index (pre and post) were as follows: 1 ± 0.1 vs 0.9 ± 0.1 (experimental) and 0.9 ± 0.1 versus 0.9 ± 0.1 (controls) while for BMI they were 29 ± 1.4 versus 29 ± 1.2 (experimental) and 26 ± 0.7 vs. 26 ± 0.7 (controls). CARDIORESPIRATORY FITNESS: In the experimental group, predicted values for absolute V02 Max increased by 10 ± 3% (i.e. 3.3 ± 0.1 to 3.6 ± 0.1 liters min -1 while that of control subjects did not change (3.4 ± 0.2 and 3.4 ± 0.2 liters min-I). In terms of relative values for V02 Max, the experimental group increased by 11 ± 2% (37 ± 1.4 to 41 ± 1.4 ml kg-l min-I) while that of control subjects did not change (41 ± 1.4 and 40 ± 1.4 ml kg-l min-I). BLOOD LIPIDS: Compared to pre-test values, post-test values for HDL were decreased by 14 ± 5 % in the experiment group (from 52.4 ± 4.4 to 45.2 ± 4.3 mg dl-l) while HDL data for the control group was unchanged (49.7 ± 3.6 and 48.3 ± 4.1 mg dl-l, respectively. On the other hand, LDL levels did not change for either the experimental or control group (110.2 ± 10.4 versus 112.3 ± 7.1 mg dl-1 and 106.1 ± 11.3 versus 127 ± 15.1 mg dl-1, respectively). Further, total cholesterol did not change in either the experimental or control group (181.3 ± 8.7 mg dl-1 versus 178.7± 4.9 mg dl-l) and 190.7 ± 12.2 versus 197.1 ± 16.1 mg dl-1, respectively). Similarly, the ratio of TC/HDL did not change for either the experimental or control group (3.8 ± 0.4 versus 4.5 ± 0.5 and 4 ± 0.4 versus 4.2 ± 0.4, respectively). Blood triglyceride levels were also not altered in either the experimental or control group (100.3 ± 19.6 versus 114.8 ± 15.3 mg dl-1 and 140 ± 23.5 versus 137.3 ± 17.9 mg dl-l, respectively). BLOOD GLUCOSE: Fasted blood glucose levels did not change in either the experimental or control group. Pre- and post-values for experimental and control groups were 92.5 ± 4.8 versus 93.3 ± 4.3 mg dl-l and 92.3 ± 11.3 versus 93.2 ± 2.6 mg dl-1 , respectively. BLOOD PRESSURE: No aspect of blood pressure was altered in either the experimental or control group. For example, pre- and post-test systolic blood pressures were 131 ± 2 versus 129 ± 2 mmHg (experimental) and 123 ± 2 and 125 ± 2 mmHg (controls), respectively. Pre- and post-test diastolic blood pressures were 84 ± 2 and 83 ± 2 mmHg (experimental) and 81 ± 1 versus 82 ± 1 mmHg, respectively. Similarly, calculated pulse pressure was not altered in the experimental or control as pre- and post-test values were 47 ± 1 versus 47 ± 2 mmlHg and 42 ± 2 versus 43 ± 2 mmHg, respectively. FRAMINGHAM POINT SCORE: The concerted changes reported above produced an increased risk in the Framingham Point Score for the subjects in the experimental group. For example, the pre- and post-test FPS increased from 1.4 ± 0.9 to 2.7 ± 0.7. On the other hand, pre- and post-test scores for the control group were 1.8 ± 1 versus 1.8 ± 0.9. Conclusions: Our data confirms previous studies showing that interval-type exercise is a useful intervention for increasing aerobic fitness. Moreover, the increase in V02 Max we found in response to limited participation in ball hockey (i.e. 16 games) suggests that recreational sport may help reduce this aspect of coronary risk in previously sedentary individual. On the other hand, our results showing little or no positive change in body composition, blood lipids or blood pressures suggest that one season of recreational sport in not in of itself a powerful enough stimulus to reduce the overall risk of coronary artery disease. In light of this, it is recommended that, in addition to participation in recreational sport, the performance of regular physical activity is used as an adjunct to provide a more powerful overall stimulus for decreasing coronary risk factors. LIMITATIONS: The increase in the FPS we found for the experimental group, indicative of an increased risk for coronary disease, was largely due to the large decrease in HDL we observed after compared to above one season of ball hockey. In light of the fact that cardiorespiratory fitness was increased and % body fat was decreased, as well as the fact that other parameters such as blood pressure showed positive (but non statistically significant) trends, the possibility that the decrease in HDL showed by our data was anomalous should be considered. FUTURE DIRECTIONS: The results of this study suggesting that recreational sport may be a potentially useful intervention in the reduction of CAD require to be corroborated by future studies specifically employing 1) more rigorous assessment of fitness and fitness change and 2) more prolonged or frequent participants.

Entering Youthwork Through Love's Many Pathways: A Poetic Rendition

Entering Youth work Through Love's Many Pathways is a text that wanders and digresses to places where, through poetic inquiry and a Spinozist and Sufi framework, the concepts of immanence, love and becoming can be explored. This thesis is framed as a walk through which the researcher / youth worker along with the reader, traverses through five pathways that she considers necessary in cultivating a meaningful relationship with the youth: opening, strength, listening, trust and unconditional compassion. By means of engaging the “self”, this thesis approaches youth work as a field that is relational and socially interconnected. In this sense, this poetic inquiry seeks to rupture predictable patterns of behaviour. One of the ways I do this is through found poetry. Through this specific form of poetic inquiry, I bring together various voices, an assemblage – Rumi, Rilke, Whitman, Lalla, Mirabai and Song of Songs – in order to find my voice and by extension, to help the youth find their voice through a human connection that goes beyond colour, race, gender etc. In other words, my aim is to actualize the experiences of becoming youth worker while being in a field of immanence where similarities are understood and differences respected. My hope is that this project may offer an example of understanding, celebration, and engagement of our mutual differences, while still being able to relate to one another through the many pathways of love.

Erie & Niagara Railway Collection, 1864-1884

William Alexander Thomson (1816-1878) was a promoter and developer of railway systems in western Ontario. He incorporated the Fort Erie Railroad Company in 1857, purchased the Erie and Ontario Railroad in 1863, and incorporated the Erie and Niagara Extension Railway Company in 1868 (later renamed the Canada Southern Railway). Thomson was also elected to the House of Commons for Welland in 1872, and re-elected in 1874. He was known for his support of public management of the currency and is seen as a pioneer advocate of government monetary policy. He was also an advocate of radical agrarian economic doctrine, believing that Canadian laws favoured mercantile interests over those of the producers of goods, and that this hindered national development.

Geology of Hebes Chasma, Valles Marineris, Mars

Hebes Chasma is an 8 km deep, 126 by 314 km, isolated basin that is partially filled with interior layered deposits (ILD), massive deposits of water altered strata. By analyzing the ILD’s structure, stratigraphy and mineralogy, as well as the perimeter faults exposed in the plateau adjacent to the chasma, the evolution and depositional history of Hebes Chasma is interpreted. Three distinct ILD units were found and are informally referred to as the Lower, Upper and Late ILDs. These units have differing layer thicknesses, layer attitudes, mineralogies and erosional landforms. Based on observations of the plateau, wall morphology and slump blocks within the chasma’s interior, chasma evolution appears to be controlled by cross-faults that progressively detached sections of the wall. A scenario involving the loss of subsurface volume and ash fall events is proposed as the dominant setting throughout Hebes’ geologic history.