Acting, predicting and intervening in a socio-hydrological world

This paper asks a simple question: if humans and their actions co-evolve with hydrological systems (Sivapalan et al., 2012), what is the role of hydrological scientists, who are also humans, within this system? To put it more directly, as traditionally there is a supposed separation of scientists and society, can we maintain this separation as socio-hydrologists studying a socio-hydrological world? This paper argues that we cannot, using four linked sections. The first section draws directly upon the concern of science-technology studies to make a case to the (socio-hydrological) community that we need to be sensitive to constructivist accounts of science in general and socio-hydrology in particular. I review three positions taken by such accounts and apply them to hydrological science, supported with specific examples: (a) the ways in which scientific activities frame socio-hydrological research, such that at least some of the knowledge that we obtain is constructed by precisely what we do; (b) the need to attend to how socio-hydrological knowledge is used in decision-making, as evidence suggests that hydrological knowledge does not flow simply from science into policy; and (c) the observation that those who do not normally label themselves as socio-hydrologists may actually have a profound knowledge of socio-hydrology. The second section provides an empirical basis for considering these three issues by detailing the history of the practice of roughness parameterisation, using parameters like Manning's n, in hydrological and hydraulic models for flood inundation mapping. This history sustains the third section that is a more general consideration of one type of socio-hydrological practice: predictive modelling. I show that as part of a socio-hydrological analysis, hydrological prediction needs to be thought through much more carefully: not only because hydrological prediction exists to help inform decisions that are made about water management; but also because those predictions contain assumptions, the predictions are only correct in so far as those assumptions hold, and for those assumptions to hold, the socio-hydrological system (i.e. the world) has to be shaped so as to include them. Here, I add to the ``normal'' view that ideally our models should represent the world around us, to argue that for our models (and hence our predictions) to be valid, we have to make the world look like our models. Decisions over how the world is modelled may transform the world as much as they represent the world. Thus, socio-hydrological modelling has to become a socially accountable process such that the world is transformed, through the implications of modelling, in a fair and just manner. This leads into the final section of the paper where I consider how socio-hydrological research may be made more socially accountable, in a way that is both sensitive to the constructivist critique (Sect. 1), but which retains the contribution that hydrologists might make to socio-hydrological studies. This includes (1) working with conflict and controversy in hydrological science, rather than trying to eliminate them; (2) using hydrological events to avoid becoming locked into our own frames of explanation and prediction; (3) being empirical and experimental but in a socio-hydrological sense; and (4) co-producing socio-hydrological predictions. I will show how this might be done through a project that specifically developed predictive models for making interventions in river catchments to increase high river flow attenuation. Therein, I found myself becoming detached from my normal disciplinary networks and attached to the co-production of a predictive hydrological model with communities normally excluded from the practice of hydrological science.

The striatal long noncoding RNA Abhd11os is neuroprotective against an N-terminal fragment of mutant huntingtin in vivo.

A large number of gene products that are enriched in the striatum have ill-defined functions, although they may have key roles in age-dependent neurodegenerative diseases affecting the striatum, especially Huntington disease (HD). In the present study, we focused on Abhd11os, (called ABHD11-AS1 in human) which is a putative long noncoding RNA (lncRNA) whose expression is enriched in the mouse striatum. We confirm that despite the presence of 2 small open reading frames (ORFs) in its sequence, Abhd11os is not translated into a detectable peptide in living cells. We demonstrate that Abhd11os levels are markedly reduced in different mouse models of HD. We performed in vivo experiments in mice using lentiviral vectors encoding either Abhd11os or a small hairpin RNA targeting Abhd11os. Results show that Abhd11os overexpression produces neuroprotection against an N-terminal fragment of mutant huntingtin, whereas Abhd11os knockdown is protoxic. These novel results indicate that the loss lncRNA Abhd11os likely contribute to striatal vulnerability in HD. Our study emphasizes that lncRNA may play crucial roles in neurodegenerative diseases.

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

Assessment of the levels of degradation in fat co- and by-products for feed uses and their relationships with some lipid composition parameters

This paper discusses the levels of degradation of some co- and byproducts of the food chain intended for feed uses. As the first part of a research project, 'Feeding Fats Safety', financed by the sixth Framework Programme-EC, a total of 123 samples were collected from 10 European countries, corresponding to fat co- and byproducts such as animal fats, fish oils, acid oils from refining, recycled cooking oils, and other. Several composition and degradation parameters (moisture, acid value, diacylglycerols and monoacylglycerols, peroxides, secondary oxidation products, polymers of triacylglycerols, fatty acid composition, tocopherols, and tocotrienols) were evaluated. These findings led to the conclusion that some fat by- and coproducts, such as fish oils, lecithins, and acid oils, show poor, nonstandardized quality and that production processes need to be greatly improved. Conclusions are also put forward about the applicability and utility of each analytical parameter for characterization and quality control.

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.

Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.

Timing of visual stimuli in V1 and V5/MT: fMRI and TMS

Time perception is used in our day-to-day activities. While we understand quite well how our brain processes vision, touch or taste, brain mechanisms subserving time perception remain largely understudied. In this study, we extended an experiment of previous master thesis run by Tatiana Kenel-Pierre. We focused on time perception in the range of milliseconds. Previous studies have demonstrated the involvement of visual areas V1 and V5/MT in the encoding of temporal information of visual stimuli. Based on these previous findings the aim of the present study was to understand if temporal information was encoded in V1 and extrastriate area V5/MT in different spatial frames i.e., head- centered versus eye-centered. To this purpose we asked eleven healthy volunteers to perform a temporal discrimination task of visual stimuli. Stimuli were presented at 4 different spatial positions (i.e., different combinations of retinotopic and spatiotopic position). While participants were engaged in this task we interfered with the activity of the right dorsal V1 and the right V5/MT with transcranial magnetic stimulation (TMS). Our preliminary results showed that TMS over both V1 and V5/MT impaired temporal discrimination of visual stimuli presented at specific spatial coordinates. But whereas TMS over V1 impaired temporal discrimination of stimuli presented in the lower left quadrant, TMS over V5/MT affected temporal discrimination of stimuli presented at the top left quadrant. Although it is always difficult to draw conclusions from preliminary results, we could tentatively say that our data seem to suggest that both V1 and V5/MT encode visual temporal information in specific spatial frames.

Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Fourier-based registration for robust forward-looking sonar mosaicing in low-visibility underwater environments

Vehicle operations in underwater environments are often compromised by poor visibility conditions. For instance, the perception range of optical devices is heavily constrained in turbid waters, thus complicating navigation and mapping tasks in environments such as harbors, bays, or rivers. A new generation of high-definition forward-looking sonars providing acoustic imagery at high frame rates has recently emerged as a promising alternative for working under these challenging conditions. However, the characteristics of the sonar data introduce difficulties in image registration, a key step in mosaicing and motion estimation applications. In this work, we propose the use of a Fourier-based registration technique capable of handling the low resolution, noise, and artifacts associated with sonar image formation. When compared to a state-of-the art region-based technique, our approach shows superior performance in the alignment of both consecutive and nonconsecutive views as well as higher robustness in featureless environments. The method is used to compute pose constraints between sonar frames that, integrated inside a global alignment framework, enable the rendering of consistent acoustic mosaics with high detail and increased resolution. An extensive experimental section is reported showing results in relevant field applications, such as ship hull inspection and harbor mapping

Beyond the obvious : three acts in educational drama

Researching research is not a common theme in educational drama. Nor is the educational drama process from a participant perspective a typical focus of research, at least not if the participants are disabled. Yet this is the theme of this thesis, a drama in three acts. The aim of this thesis is to describe, analyse, and discuss both the ways in which research within educational drama can be carried out and represented, and the experiences of the participants of the educational drama process. The theoretical framework that steers the research process is built up of two pairs of frames, each of them, like Russian nesting dolls, containing further frames. The first frame, relating to the outcomes of conducting research in educational drama, comprises philosophical, representational, and personal theories. As the second question asks what educational drama is, the subject related frame is built up of pedagogical, drama educational, and aesthetic theories. The study in its entirety follows the structure of the researcher’s hermeneutical learning process and takes the form of a journey starting from what is familiar, stretching towards what is new and different, and finally returning back to the beginning with a new view on what was there at the start. The thesis consists of two separate but related studies. The first, a familiar study conducted earlier, Alpha in Act I, was carried out among upper secondary school pupils. In the second, the new and therefore unfamiliar study, Omega in Act III, the participants are adult individuals who are physically and communicatively disabled. In between these two Acts an element of “Verfremdung” where the Alpha study is systematically scrutinized as the purpose is to teach and to manage the reader to think. Meta-discussions on the philosophical issues of the study are conducted throughout the text, parallel to the empirical parts. The outcomes of the first research question show that philosophical, methodical, and representational consistency is crucial for research. While this may sound like stating the obvious, this has nevertheless not always been considered fact, especially not within qualitative research. The outcomes further stress that representational issues are also to be recognized when presenting non-rational aspects of educational drama. By wording the world, through the use of visualising language, the surplus of meanings of educational drama can be, as they are within this study, made visible, sensible, and almost tangible, not only cognitively understandable. The outcomes of the second question point to the different foci of the studies, with Alpha focusing on the rationally retold experiences and Omega focusing on nonrational experiences. The outcomes expose educational drama as a learning process comprising doing, reflecting, and being. The doing aspect communicates the concrete efforts in creating a piece of theatre, while the being aspect relates experiences of being as situated, embodied and sensuous, reciprocal, empowering, aesthetic and artistic, and existential. Reflection is the twine that runs throughout the process and connects both doing and being. In summary, the outcomes could be formulated as “learning from learning how to make theatre”.

Delay reduction in courts of justice – possibilities and challenges of process improvement in professional public organizations

Delays in the justice system have been undermining the functioning and performance of the court system all over the world for decades. Despite the widespread concern about delays, the solutions have not kept up with the growth of the problem. The delay problem existing in the justice courts processes is a good example of the growing need and pressure in professional public organizations to start improving their business process performance.This study analyses the possibilities and challenges of process improvement in professional public organizations. The study is based on experiences gained in two longitudinal action research improvement projects conducted in two separate Finnish law instances; in the Helsinki Court of Appeal and in the Insurance Court. The thesis has two objectives. First objective is to study what kinds of factors in court system operations cause delays and unmanageable backlogs and how to reduce and prevent delays. Based on the lessons learned from the case projects the objective is to give new insights on the critical factors of process improvement conducted in professional public organizations. Four main areas and factors behind the delay problem is identified: 1) goal setting and performance measurement practices, 2) the process control system, 3) production and capacity planning procedures, and 4) process roles and responsibilities. The appropriate improvement solutions include tools to enhance project planning and scheduling and monitoring the agreed time-frames for different phases of the handling process and pending inventory. The study introduces the identified critical factors in different phases of process improvement work carried out in professional public organizations, the ways the critical factors can be incorporated to the different stages of the projects, and discusses the role of external facilitator in assisting process improvement work and in enhancing ownership towards the solutions and improvement. The study highlights the need to concentrate on the critical factors aiming to get the employees to challenge their existing ways of conducting work, analyze their own processes, and create procedures for diffusing the process improvement culture instead of merely concentrating of finding tools, techniques, and solutions appropriate for applications from the manufacturing sector

Influence of the sample area in the variability of losses in the mechanical harvesting of soybeans

The mechanical harvesting is an important stage in the production process of soybeans and, in this process; the loss of a significant number of grains is common. Despite the existence of mechanisms to monitor these losses, it is still essential to use sampling methods to quantify them. Assuming that the size of the sample area affects the reliability and variability between samples in quantifying losses, this paper aimed to analyze the variability and feasibility of using different sizes of sample area (1, 2 and 3 m²) in quantifying losses in the mechanical harvesting of soybeans. Were sampled 36 sites and the cutting losses, losses by other mechanisms of the combine and total losses were evaluated, as well as the water content in seeds, straw distribution and crop productivity. Data were subjected to statistical analysis (descriptive statistics and analysis of variance) and Statistical Control Process (SCP). The coefficients of variation were similar for the three frames available. Combine losses showed stable behavior, whereas cutting losses and total losses showed unstable behavior. The frame size did not affect the quantification and variability of losses in the mechanical harvesting of soybeans, thus a frame of 1 m² can be used for determining losses.

Innovation management of biorefineries in Finnish forest sector

The aim of this report is to give a comprehensive overview of the opportunities integrated biorefining can offer to Finnish forest industry companies and to assess what changes it would require from these companies to implement biorefining into their business. Also the strengths and weaknesses of the Finnish forest industry companies connected to biorefining are examined through innovation management theory frames, industry comparisons, company examples and couple of case-examples. The conclusions of the report include the statement that the Finnish forest industry has a good starting point for biorefinering and many advantages compared to other countries and industries. Unfortunately the history of the industry is holding it back and the thinking patterns would have to be altered to a more innovative and co-operational direction.

Experiences among primary school teachers in Tanzania

The overall aim of the study was to explore primary school teachers’ experiences of constraints to their work, and actions taken for improvement after undergoing in-service courses in the Education Quality Improvement through Pedagogy program. The research interest was thus to deepen the understanding of teachers’ experiences of constraints to their work and experiences of actions taken to improve classroom actions. In order to achieve this ambition, the study was conducted with primary school teachers in Shinyanga district-Tanzania. Two research questions guided the study: What do teachers experience as constraints to their work? The second: How have teachers improved their classroom actions after undergoing professional development courses? The theoretical framework of the study is centred on limiting and enabling frames on teachers’ work and professional development. In order to understand the classroom situations, qualitative research was designed applying a phenomenological approach with semi-structured interview, observation and videotaping to collect data. Forty experienced primary school teachers from ten primary schools participated in the study. The results of the first research question indicate that teachers face many constraints in their work. Three categories identified as interactional, environmental and professional role constraints. The most critical experienced by all teachers is teaching in large classes and inadequate teaching and learning materials. The results of the second research question show that teachers’ actions taken for improving their work were influenced by professional development activities. Three main categories including expanded interaction, expanded use of environment and expanded professional roles were identified. Generally, the knowledge generated is relevant for viewing teachers’ experiences of the challenges they encounter in teaching and the importance of professional development beyond the sampled respondents. The results suggest that constant provision of teachers’ professional development could improve teaching performance.

Pursuit of change versus organizational inertia: a study on strategic renewal in the Finnish broadcasting company

This doctoral dissertation explores the intra-organizational dynamics of a strategic renewal process. The main research question is how the pursuit of change and organizational inertia co-exist, intertwine, and collide in organizational cognition and capabilities during the strategic renewal. It is a comprehensive study on how organizational capabilities, organizational cognition, and structure enhance and inhibit change. Theoretically, the study is positioned in the modern tradition of strategy research, using the dynamic capability view and the organizational and managerial cognition research tradition as the main theoretical frames. Empirically, the study is a longitudinal case study of the Finnish Broadcasting Company (Yle), following the organizational changes during the years of 2011-1014. The analysis is based on both quantitative and qualitative data, which was collected during the research process using surveys, interviews, and archives. The main theoretical contribution is the application of the two theoretical approaches in one study. Empirically, the study contributes to operationalization of the concepts related to the dynamic capability view and organizational cognition, in a media context that is going through drastic changes due to digitalization. Furthermore, the case of a public broadcasting company extends the application of the theoretical concepts to the context of public management. The results suggest that renewal is a complex process, in which an organization’s perceptions intertwine with the strategic actions and decision-making. The change evolves pathdependently: the past experiences, routines, and organizational structures tend to dictate the future visions, desires, and actions. The study also reveals how the public nature of an organization adds to the tensions between change and organizational inertia, and hampers the decision-making. The doctoral dissertation consists of six research papers, each of which explores the phenomenon under study from a different perspective.

The 42-kDa coat protein of Andean potato mottle virus acts as a transcriptional activator in yeast

Interactions of viral proteins play an important role in the virus life cycle, especially in capsid assembly. Andean potato mottle comovirus (APMoV) is a plant RNA virus with a virion formed by two coat proteins (CP42 and CP22). Both APMoV coat protein open reading frames were cloned into pGBT9 and pGAD10, two-hybrid system vectors. HF7c yeast cells transformed with the p9CP42 construct grew on yeast dropout selection media lacking tryptophan and histidine. Clones also exhibited ß-galactosidase activity in both qualitative and quantitative assays. These results suggest that CP42 protein contains an amino acid motif able to activate transcription of His3 and lacZ reporter genes in Saccharomyces cerevisiae. Several deletions of the CP42 gene were cloned into the pGBT9 vector to locate the region involved in this activation. CP42 constructions lacking 12 residues from the C-terminal region and another one with 267 residues deleted from the N-terminus are still able to activate transcription of reporter genes. However, transcription activation was not observed with construction p9CP42deltaC57, which does not contain the last 57 amino acid residues. These results demonstrate that a transcription activation domain is present at the C-terminus of CP42 between residues 267 and 374.