Detection of Histidine Kinase Activities of Bacteriophytochromes with Phos-tag™ Acrylamide Gel Electrophoresis

Phosphorylation is a key regulatory mechanism of cellular functions, and a majority of known bacteriophytochromes (BphPs) act as histidine kinases (HKs) in two-component signaling. These red/far-red light-sensing HKs play a role in diverse light responses in bacteria. In this chapter, we introduce protocols to easily track the net kinase and phosphatase activities of BphP HKs. The protocols provided here apply Phos-tag™ acrylamide gel electrophoresis for protein samples under controlled illumination conditions. They can be applied to BphP HKs and with a few modifications to photoreceptor HKs in general.peerReviewe

Rural Leisure Time in the Making : Self-Created Youth Activities and Leisure Time in Sparsely Populated Rural Finland

This chapter discusses leisure activities as individually and socially constructed everyday life spaces for rural youth in Finland. The chapter portrays local ‘do-it-yourself’ (DIY) or ‘do-it-together’ (DIT) youth cultures in the sparsely populated Finnish countryside. Discussion about free time activities in the countryside often focuses on the lack of arranged, adult-led activities and long distances that prevent participation in hobbies. This may overlook the meaning-making of young people themselves, who may be—or may have to be—very innovative in arranging activities on their own. The chapter shows that in sparsely populated regions, characterised by long distances and a small number of peers, self-created youth spaces become significant rationalities of leisure. Young people turned, for example, public or semi-public village spaces into their own, youth culturally important spaces where they could get together. In addition, homes, nature and online communities offered spaces for self-created activities. However, some of these spaces could also become stigmatised and subject to moral conflicts in the communities. Even in small communities, these spaces are rarely open for all young people: local youth cultures often involve non-articulated practices of inclusion and exclusion. The focus of this chapter is on the most sparsely populated areas of Finland. The chapter is based on qualitative longitudinal data from three different regions: from a withering industrial region in eastern Finland, a region characterised by agriculture and forestry in central Finland, and the northernmost Sámi homeland.peerReviewe

Capturing the Breadth and Dynamics of the Temporal Processes with Frequency Transition Network Analysis : A Primer and Tutorial

This chapter presents Frequency-Based Transition Network Analysis (FTNA), a novel method to model the relational dynamics and the transitions between states or events based on the frequency of occurrence of transitions. Compared to TNA based on Markov models, FTNA is well-suited when the research focus is on describing, summarizing, or visually analyzing the observed data without the probabilistic assumptions and constraints. Compared to process mining, FTNA leverages statistical techniques such as pruning, bootstrapping and permutation to validate and compare models. Moreover, FTNA employs networks as a lens to represent and analyze transitions, which provides a rich family of metrics and analyses such as centrality measures, communities and patterns. In this chapter, we offer an introduction to the method and its main features, along with a step-by-step tutorial in R using a case study in group collaboration.peerReviewe

Minimizing extractivism through 3D printing with law and policy support

The concept of ‘extractivism’ refers to the mindset and processes that facilitate for-profit large-scale exploitation of natural resources. Extractivism has a strong connection with how the markets work in this era of factory mass-production. This article seeks to understand if and how 3D printing (3DP), guided by effective legislation and policy, could help reduce overproduction practices and minimize resource extraction, thereby limiting the consumeristic attitude on which the concept of extractivism is based. The research utilized scenario building, following a multiphased-qualitative approach involving literature review, an expert workshop, and two focus group interviews. The primary outcome includes four scenarios for the year 2032, which are from most-likely, normative, optimistic, and pessimistic perspectives. Since the normative scenario calls for action to reach a preferable future, further analysis involved mapping out the strategies for utilizing 3DP to reduce extractivism. The findings support positioning 3DP as a low-volume production tool for prolonging product lifecycle and material value, highlighting the strategic areas of ‘material circulation’ and ‘product upgrade and repair-reuse systems’. Key legal and policy actions that could support these approaches are also identified, which primarily pertain to the fields of IPR and environmental legislation.peerReviewe

Identifying key components for multiobjective forest management decisions: A case study of state-owned Finnish forests

Finland’s state-owned forests provide multiple public values, including timber production, biodiversity conservation, and recreational use, often leading to trade-offs between conflicting objectives. The use of multiobjective optimization (MOO) helps navigate these trade-offs, but its effectiveness depends on how well the problem is formulated. While MOO studies in forest management typically focus on solving optimization models, they often overlook the crucial problem structuring phase. This study addresses that gap by identifying the key components required to formulate an MOO problem, based on perspectives from stakeholders and decision makers involved in Finnish state-owned forest management. Using semi-structured interviews with 20 participants, we identified six essential themes for MOO formulation: objective functions, decision options, constraints, available data, evaluation of objective functions, as well as uncertainty and risks. These themes reflect both commonly modeled components, such as timber production and economic returns, and less frequently integrated considerations, including biodiversity, recreational values, and risks associated with climate change and forest disturbances. Our findings contribute a replicable participatory approach for eliciting MOO components through the engagement of stakeholders and decision makers. By highlighting the importance of problem structuring, the study supports the development of more transparent, context-sensitive, and acceptable MOO models. Engaging participants in this early phase reveals a broader range of forest management priorities than typically represented in conventional MOO models, offering opportunities for improved decision support in public forest governance.peerReviewe

Associations between cumulative family environmental stress exposures and hair cortisol concentrations among 2.5- and 5-year-olds with different social competences

There is a vast amount of research indicating the associations between prenatal and postnatal environmental stress exposures and the human hypothalamic-pituitary-adrenal (HPA) axis functioning in early childhood. However, less is known about the protective factors among these associations. This study aimed to examine the associations between cumulative family environmental stress (CFES) exposure and a child's hair cortisol concentration (HCC) at the ages of 2.5 (n = 213) and 5 (n = 372) years. We further analyzed whether toddlers' social competence (by The Brief Infant-Toddler Social and Emotional Assessment) and preschoolers' pro- or antisocial behavior (by The Multisource Assessment of Children's Social Competence) would moderate the associations between CFES and HCC. Results showed that neither pre- nor postnatal CFES exposure was associated with child's HCC. However, children with higher social competence had lower HCC at the age of 2.5 independent of the environmental stress. Moreover, at the age of 5 years, in males with lower antisocial behavior, the HCC levels decreased along with the increased prenatal CFES exposure. The effect sizes were small, and the results should be considered with caution. The study provides some indications that a child's social and emotional abilities contribute to HPA axis functioning and could protect a child from family environmental related stress exposure during early childhood. Moreover, there may be sex differences in these associations. Further research is needed to examine whether a child's socioemotional competence could protect against stress arising from the early rearing environment as well as its contributions to the maturation of a child’ stress regulation.peerReviewe

Rural Nordic Youth’s Transition to Upper Secondary School : Challenges and Dilemmas

Starting from the Nordic policy idea of equal educational opportunities for all children and youth, this chapter examines the challenges and dilemmas that some young people from rural regions in Finland, Norway, Denmark, and Sweden faced when they transitioned from lower to upper secondary school. The chapter highlights how the structural conditions of living in a rural area often, but not always, complicated the young people’s transition, forcing them to set priorities and opt out of certain interests and educational ‘options’, thus enacting their agency in relation to restricted options. It further highlights the challenges of enacting agency in relation to societal ideas of what represents a ‘successful’ transition, balancing ‘not wasting time’ with ‘buying oneself time’ and ‘keeping doors open’. Overall, and thanks to longitudinal interview data, the chapter demonstrates how the challenges and dilemmas accompanying the transition to upper secondary school played out over time and how the structural, symbolic, and affective dimensions of enacting transitions were present in different ways in different times.peerReviewe

Invariant Coordinate Selection and Fisher discriminant subspace beyond the case of two groups

Invariant Coordinate Selection (ICS) is a multivariate technique that relies on the simultaneous diagonalization of two scatter matrices. It serves various purposes, including its use as a dimension reduction tool prior to clustering or outlier detection. ICS’s theoretical foundation establishes why and when the identified subspace should contain relevant information by demonstrating its connection with the Fisher discriminant subspace (FDS). These general results have been examined in detail primarily for specific scatter combinations within a two-cluster framework. In this study, we expand these investigations to include more clusters and scatter combinations. Our analysis reveals the importance of distinguishing whether the group centers matrix has full rank. In the full-rank case, we establish deeper connections between ICS and FDS. We provide a detailed study of these relationships for three clusters when the group centers matrix has full rank and when it does not. Based on these expanded theoretical insights and supported by numerical studies, we conclude that ICS is indeed suitable for recovering the FDS under very general settings and cases of failure seem rare.peerReviewe

Towards Understanding the Developer Experience in Quantum Software Development

In this thematic analysis, we study how quantum software development challenges can be framed in terms of general developer experience and how these connections can enhance our understanding of quantum developer experience. As a result, general developer experience categories, quantum software development challenges, and the connections and parallels between the two are identified. These novel results help to understand quantum developer experience better than before, thus offering guidance to future research and practical implementations.peerReviewe

Rigidity and regularity for almost homogeneous spaces with Ricci curvature bounds

We say that a metric space X is (ϵ, G)-homogeneous if G ≤Iso(X) is a discrete group of isometries with diam(X/G) ≤ ϵ. A sequence of (ϵi, Gi)-homogeneous spaces Xi with ϵi → 0 is called a sequence of almost homogeneous spaces. In this paper we show that the Gromov-Hausdorff limit of a sequence of almost homogeneous RCD(K, N) spaces must be a nilpotent Lie group with Ric ≥ K. We also obtain a topological rigidity theorem for (ϵ, G)-homogeneous RCD(K, N) spaces, which generalizes a recent result by Wang. Indeed, if X is an (ϵ, G)-homogeneous RCD(K, N) space and G is an almost-crystallographic group, then X/G is bi-Hölder to an infranil orbifold. Moreover, we study (ϵ, G)homogeneous spaces in the smooth setting and prove rigidity and ϵ-regularity theorems for Riemannian orbifolds with Einstein metrics and bounded Ricci curvatures respectively.peerReviewe