Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Unplanned complex suicide by self-strangulation associated with multiple sharp force injuries: a case report.

In cases of ligature strangulation, the importance of distinguishing self-inflicted death from homicide is crucial. This entails objective scene investigation, autopsy and anamnesis in order to elucidate the manner of death correctly. The authors report a case of unplanned complex suicide by means of self-strangulation and multiple sharp force injury. The use of more than one suicide method, consecutively--termed unplanned complex suicide--gives this case particular significance. A brief discussion on this uncommon method of suicide is presented, particularly relevant to the attending forensic physician. In addition, a short overview of the entity of complex suicide is given.

Treatment of rats with a self-selected hyperlipidic diet, increases the lipid content of the main adipose tissue sites in a proportion similar to that of the lipids in the rest of organs and tissues

Adipose tissue (AT) is distributed as large differentiated masses, and smaller depots covering vessels, and organs, as well as interspersed within them. The differences between types and size of cells makes AT one of the most disperse and complex organs. Lipid storage is partly shared by other tissues such as muscle and liver. We intended to obtain an approximate estimation of the size of lipid reserves stored outside the main fat depots. Both male and female rats were made overweight by 4-weeks feeding of a cafeteria diet. Total lipid content was analyzed in brain, liver, gastrocnemius muscle, four white AT sites: subcutaneous, perigonadal, retroperitoneal and mesenteric, two brown AT sites (interscapular and perirenal) and in a pool of the rest of organs and tissues (after discarding gut contents). Organ lipid content was estimated and tabulated for each individual rat. Food intake was measured daily. There was a surprisingly high proportion of lipid not accounted for by the main macroscopic AT sites, even when brain, liver and BAT main sites were discounted. Muscle contained about 8% of body lipids, liver 1-1.4%, four white AT sites lipid 28-63% of body lipid, and the rest of the body (including muscle) 38-44%. There was a good correlation between AT lipid and body lipid, but lipid in"other organs" was highly correlated too with body lipid. Brain lipid was not. Irrespective of dietary intake, accumulation of body fat was uniform both for the main lipid storage and handling organs: large masses of AT (but also liver, muscle), as well as in the"rest" of tissues. These storage sites, in specialized (adipose) or not-specialized (liver, muscle) tissues reacted in parallel against a hyperlipidic diet challenge. We postulate that body lipid stores are handled and regulated coordinately, with a more centralized and overall mechanisms than usually assumed.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Self-accelerating dolomite-for-calcite replacement: Self-organized dynamics of burial dolomitization and associated mineralization

A new dynamic model of dolomitization predicts a multitude of textural, paragenetic, geochemical and other properties of burial dolomites. The model is based on two postulates, (1) that the dolomitizing brine is Mg-rich but under saturated with both calcite and dolomite, and (2) that the dolomite-for-calcite replacement happens not by dissolution-precipitation as usually assumed, but by dolomite-growth-driven pressure solution of the calcite host. Crucially, the dolomite-for-calcite replacement turns out to be self-accelerating via Ca2 : the Ca2 released by each replacement increment accelerates the rate of the next, and so on. As a result, both pore-fluid Ca2 and replacement rate grow exponentially.

A case of suicide by self-injection of adrenaline.

Adrenaline (epinephrine) auto-injectors provide life-saving pre-hospital treatment for individuals experiencing anaphylaxis in a community setting. Errors in handling adrenaline auto-injectors, particularly by children and healthcare professionals, have been reported. Reports of adrenaline overdoses are limited in the medical literature. In most of these cases, accidental adrenaline administration results from medical error. Exogenous administration of catecholamine is responsible for cardiovascular and metabolic responses, which may cause supraventricular tachycardia, ventricular dysrhythmias and myocardial ischemia. The authors present a unique autopsy case involving a 34 year-old woman who intentionally self-injected adrenaline using an adrenaline auto-injector as part of a suicide plan. Catecholamines and metanephrines were measured in peripheral and cardiac blood as well as urine and vitreous humor. Based on the results of all postmortem investigations, the cause of death was determined to be cardiac dysrhythmia and cardiac arrest following adrenaline self-injection.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Thinking Outside the Box: Enhancing Science Teaching by Combining (Instead of Contrasting) Laboratory and Simulation Activities

The focus of the present work was on 10- to 12-year-old elementary school students’ conceptual learning outcomes in science in two specific inquiry-learning environments, laboratory and simulation. The main aim was to examine if it would be more beneficial to combine than contrast simulation and laboratory activities in science teaching. It was argued that the status quo where laboratories and simulations are seen as alternative or competing methods in science teaching is hardly an optimal solution to promote students’ learning and understanding in various science domains. It was hypothesized that it would make more sense and be more productive to combine laboratories and simulations. Several explanations and examples were provided to back up the hypothesis. In order to test whether learning with the combination of laboratory and simulation activities can result in better conceptual understanding in science than learning with laboratory or simulation activities alone, two experiments were conducted in the domain of electricity. In these experiments students constructed and studied electrical circuits in three different learning environments: laboratory (real circuits), simulation (virtual circuits), and simulation-laboratory combination (real and virtual circuits were used simultaneously). In order to measure and compare how these environments affected students’ conceptual understanding of circuits, a subject knowledge assessment questionnaire was administered before and after the experimentation. The results of the experiments were presented in four empirical studies. Three of the studies focused on learning outcomes between the conditions and one on learning processes. Study I analyzed learning outcomes from experiment I. The aim of the study was to investigate if it would be more beneficial to combine simulation and laboratory activities than to use them separately in teaching the concepts of simple electricity. Matched-trios were created based on the pre-test results of 66 elementary school students and divided randomly into a laboratory (real circuits), simulation (virtual circuits) and simulation-laboratory combination (real and virtual circuits simultaneously) conditions. In each condition students had 90 minutes to construct and study various circuits. The results showed that studying electrical circuits in the simulation–laboratory combination environment improved students’ conceptual understanding more than studying circuits in simulation and laboratory environments alone. Although there were no statistical differences between simulation and laboratory environments, the learning effect was more pronounced in the simulation condition where the students made clear progress during the intervention, whereas in the laboratory condition students’ conceptual understanding remained at an elementary level after the intervention. Study II analyzed learning outcomes from experiment II. The aim of the study was to investigate if and how learning outcomes in simulation and simulation-laboratory combination environments are mediated by implicit (only procedural guidance) and explicit (more structure and guidance for the discovery process) instruction in the context of simple DC circuits. Matched-quartets were created based on the pre-test results of 50 elementary school students and divided randomly into a simulation implicit (SI), simulation explicit (SE), combination implicit (CI) and combination explicit (CE) conditions. The results showed that when the students were working with the simulation alone, they were able to gain significantly greater amount of subject knowledge when they received metacognitive support (explicit instruction; SE) for the discovery process than when they received only procedural guidance (implicit instruction: SI). However, this additional scaffolding was not enough to reach the level of the students in the combination environment (CI and CE). A surprising finding in Study II was that instructional support had a different effect in the combination environment than in the simulation environment. In the combination environment explicit instruction (CE) did not seem to elicit much additional gain for students’ understanding of electric circuits compared to implicit instruction (CI). Instead, explicit instruction slowed down the inquiry process substantially in the combination environment. Study III analyzed from video data learning processes of those 50 students that participated in experiment II (cf. Study II above). The focus was on three specific learning processes: cognitive conflicts, self-explanations, and analogical encodings. The aim of the study was to find out possible explanations for the success of the combination condition in Experiments I and II. The video data provided clear evidence about the benefits of studying with the real and virtual circuits simultaneously (the combination conditions). Mostly the representations complemented each other, that is, one representation helped students to interpret and understand the outcomes they received from the other representation. However, there were also instances in which analogical encoding took place, that is, situations in which the slightly discrepant results between the representations ‘forced’ students to focus on those features that could be generalised across the two representations. No statistical differences were found in the amount of experienced cognitive conflicts and self-explanations between simulation and combination conditions, though in self-explanations there was a nascent trend in favour of the combination. There was also a clear tendency suggesting that explicit guidance increased the amount of self-explanations. Overall, the amount of cognitive conflicts and self-explanations was very low. The aim of the Study IV was twofold: the main aim was to provide an aggregated overview of the learning outcomes of experiments I and II; the secondary aim was to explore the relationship between the learning environments and students’ prior domain knowledge (low and high) in the experiments. Aggregated results of experiments I & II showed that on average, 91% of the students in the combination environment scored above the average of the laboratory environment, and 76% of them scored also above the average of the simulation environment. Seventy percent of the students in the simulation environment scored above the average of the laboratory environment. The results further showed that overall students seemed to benefit from combining simulations and laboratories regardless of their level of prior knowledge, that is, students with either low or high prior knowledge who studied circuits in the combination environment outperformed their counterparts who studied in the laboratory or simulation environment alone. The effect seemed to be slightly bigger among the students with low prior knowledge. However, more detailed inspection of the results showed that there were considerable differences between the experiments regarding how students with low and high prior knowledge benefitted from the combination: in Experiment I, especially students with low prior knowledge benefitted from the combination as compared to those students that used only the simulation, whereas in Experiment II, only students with high prior knowledge seemed to benefit from the combination relative to the simulation group. Regarding the differences between simulation and laboratory groups, the benefits of using a simulation seemed to be slightly higher among students with high prior knowledge. The results of the four empirical studies support the hypothesis concerning the benefits of using simulation along with laboratory activities to promote students’ conceptual understanding of electricity. It can be concluded that when teaching students about electricity, the students can gain better understanding when they have an opportunity to use the simulation and the real circuits in parallel than if they have only the real circuits or only a computer simulation available, even when the use of the simulation is supported with the explicit instruction. The outcomes of the empirical studies can be considered as the first unambiguous evidence on the (additional) benefits of combining laboratory and simulation activities in science education as compared to learning with laboratories and simulations alone.

Digital Humanities For Everyone’s Benefit?: interplay in social media with the great audience, high-esteemed researcher and self-conscious library

The National Library of Finland realizes the Digitization Project of Kindred Languages in 2012–15. The project is financially supported by the Kone Foundation. During this project the National Library of Finland has digitized and made available approximately 1200 monograph and more than 100 newspaper titles in several Uralic languages. The materials are available to both researchers and citizens in the National Library’s Fenno-Ugrica collection. The project will produce digitized materials in the Uralic languages as well as their development tools to support linguistic research and citizen science. The resulting materials will constitute the largest resource for the Uralic languages in the world. Through this project, researchers will gain access to corpora which they have not been able to study before and to which all users will have open access regardless of their place of residence. In my presentation, I will discuss 1) how we utilized the social media (Facebook, Twitter, VKontakte etc) to gain audience for our collection and 2) how the needs of researchers and laymen were met in crowdsourcing.

The physiology of inscription : Foucault's genealogy as curative science

In ''Nietzsche, Genealogy, History," Foucault suggests that genealogy is a sort of "curative science." The genealogist must be a physiologist and a pathologist as well as an historian, for his task is to decipher the marks that power relations and historical events leave on the subjugated body; "he must be able to diagnose the illnesses of the body, its conditions of weakness and strength, its breakdowns and resistances, to be in a position to judge philosophical discourse." But this claim seems to be incongruent with another major task of genealogy. After all, genealogy is supposed to show us that the things we take to be absolute are in fact discontinuous and historically situated: "Nothing in man-not even his body-is sufficiently stable to serve as the basis for self-recognition or for understanding other men." If this is true, then the subjugated body can never be restored to a healthy state because it has no essential or original nature. There are no universal standards by which we can even distinguish between healthy and unhealthy bodies. So in what sense is genealogy to be a "curative science"? In my thesis, I try to elucidate the complex relationship between genealogy and the body. I argue that genealogy can be a curative science even while it "multiplies our body and sets it against itself." Ifwe place a special emphasis on the role that transgression plays in Foucault's genealogical works, then the healthy body is precisely the body that resists universal standards and classifications. If genealogy is to be a curative science, then it must restore to the subjugated body an "identity" that transgresses its own limits and that constitutes itself, paradoxically, in the very effacement of identity. In the first chapter of my thesis, I examine the body's role as "surface of the inscription of events." Power relations inscribe on and around the body an identity or subjectivity that appears to be unified and universal, but which is in fact disparate and historically situated. The "subjected" body is the sick and pathologically weak body. In Chapters 2 and 3, I describe how it is possible for the unhealthy body to become healthy by resisting the subjectivity that has been inscribed upon it. Chapter 4 explains how Foucault's later works fit into this characterization of genealogy

Writing and science connections : integrated instruction and assessment

Learning to write is a daunting task for many young children. The purpose of this study was to examine the impact of a combined approach to writing instruction and assessment on the writing performance of students in two grade 3 classes. Five forms and traits of writing were purposefully connected during writing lessons while exhibiting links to the four strands of the grade 3 Ontario science curriculum. Students then had opportunities to engage in the writing process and to self-assess their compositions using either student-developed (experimental group/teacher-researcher's class) or teachercreated (control group/teacher-participant's class) rubrics. Paired samples t-tests revealed that both the experimental and control groups exhibited statistically significant growth from pretest to posttest on all five integrated writing units. Independent samples t-tests showed that the experimental group outperformed the control group on the persuasive + sentence fluency and procedure + word choice writing tasks. Pearson product-moment correlation r tests revealed significant correlations between the experimental group and the teacher-researcher on the recount + ideas and report + organization tasks, while students in the control group showed significant correlations with the teacher-researcher on the narrative + voice and procedure + word choice tasks. Significant correlations between the control group and the teacher-participant were evident on the persuasive + sentence fluency and procedure + word choice tasks. Qualitative analyses revealed five themes that highlighted how students' self-assessments and reflections can be used to guide teachers in their instructional decision making. These findings suggest that educators should adopt an integrated writing program in their classrooms, while working with students to create and utilize purposeful writing assessment tools.

Generator Matrix Based Search for Extremal Self-Dual Binary Error-Correcting Codes

Self-dual doubly even linear binary error-correcting codes, often referred to as Type II codes, are codes closely related to many combinatorial structures such as 5-designs. Extremal codes are codes that have the largest possible minimum distance for a given length and dimension. The existence of an extremal (72,36,16) Type II code is still open. Previous results show that the automorphism group of a putative code C with the aforementioned properties has order 5 or dividing 24. In this work, we present a method and the results of an exhaustive search showing that such a code C cannot admit an automorphism group Z6. In addition, we present so far unpublished construction of the extended Golay code by P. Becker. We generalize the notion and provide example of another Type II code that can be obtained in this fashion. Consequently, we relate Becker's construction to the construction of binary Type II codes from codes over GF(2^r) via the Gray map.

Impact of a Youth Development Camp on Participants’ Skills, Attitudes, and Views Towards Science and Scientific Inquiry

This mixed-methods research study sought to determine the impact of an informal science camp—the Youth Science Inquiry Development Camp (YSIDC)—on participants’ science inquiry skills, through self-assessment, as well as their views and attitudes towards science and scientific inquiry. Pre and post data were collected using quantitative surveys (SPSI, CARS), a qualitative survey (VOSI-E), interviews, and researcher’s observations. Paired sample t-tests from the quantitative surveys revealed that the YSIDC positively impacted participants’ science inquiry skills and attitudes towards science. Interviews supported these findings and provided contextual reasons for these impacts. Implications from this research would suggest that informal and formal educational institutions can increase science inquiry skills and promote positive views and attitudes towards science and scientific inquiry by using non-competitive cooperative learning strategies with a mixture of guided and open inquiry. Suggested directions for further research include measuring science inquiry skills directly and conducting longitudinal studies to determine the lasting effects of informal and formal science programs.

Imagination et individuation dans la philosophie de Spinoza : La science intuitive comme imagination libérée

La philosophie de Spinoza cherche à concilier et réunir trois horizons philosophiques fondamentaux : l’émanation néo-platonicienne (l’expression), le mécanisme cartésien (cause efficiente), et les catégories aristotéliciennes (Substance, attribut, mode). Ce premier point est pris pour acquis. Nous expliquerons que cette tentative sera rendue possible grâce à la conception nouvelle, au 17e siècle, de l’actualité de l’infini. Nous examinerons ensuite les conséquences de cette nouvelle interprétation, qui permet de rendre l’individu transparent à lui-même sur un plan d’immanence, expressif par rapport à une éminence qui le diffuse, mais déterminé dans une substantialité fictive entre objets finis. En proposant le pouvoir de l’imagination et des prophètes comme point de départ et principe actif du conatus, nous montrerons que la distinction, chez Spinoza, demeure toujours une fiction. Pour conclure, nous serons en mesure de signaler en quoi le Zarathoustra de Nietzsche relève d’une volonté de poursuivre le travail entrepris par Spinoza.

La doctrine de la science de Fichte : idéalisme spéculatif et réalisme pratique

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal