The ‘Cod-Multiple’: Modes of Existence of Fish, Science and People

Fish represent a politically regulated, scientifically researched, industrially processed, commercially marketed and socially contested living marine resource. Related to this, the incorporation of resource users and stakeholders into fisheries management is particularly important. Such involvement has recently improved in terms of frequency, but institutional frameworks often result in a lack of recognition and integration of the diverse ‘knowledges’ of stakeholders involved. Against this background, we aim to uncover the potentials of additional knowledge types for management purposes, paving the way toward a more collaborative management. We first conducted qualitative expert interviews with different stakeholder groups (e.g., commercial fisheries, eNGO and administration) to map various ‘knowledges’ about cod (Gadus morhua), a major resource species in the Western Baltic Sea to reveal the various experiences and epistemologies revolving around it. The second analytical step consisted of examining how these ‘knowledges’ structure, inform and often enter into conflict with perspectives on and assessments of fisheries management. Potentials were identified regarding enhanced stakeholder engagement in management processes that provide food for thought to seek change in sustainable management of fish stocks in the future. Our study is a pointer to the need to transform fisheries management in a more social and participatory way. We argue that sustainable natural resource management cannot be designed solely by integrating more ‘knowledges’ (knowledge sharing) but requires the creation of social contexts and institutions with stakeholder empowerment at the local level (power sharing) to sustainably manage natural resources such as commercially importance fish stocks.

Topology and Phase Transitions: A First Analytical Step towards the Definition of Sufficient Conditions

Different arguments led to supposing that the deep origin of phase transitions has to be identified with suitable topological changes of potential related submanifolds of configuration space of a physical system. An important step forward for this approach was achieved with two theorems stating that, for a wide class of physical systems, phase transitions should necessarily stem from topological changes of energy level submanifolds of the phase space. However, the sufficiency conditions are still a wide open question. In this study, a first important step forward was performed in this direction; in fact, a differential equation was worked out which describes how entropy varies as a function of total energy, and this variation is driven by the total energy dependence of a topology-related quantity of the relevant submanifolds of the phase space. Hence, general conditions can be in principle defined for topology-driven loss of differentiability of the entropy.

VOLTA: adVanced mOLecular neTwork Analysis

Motivation Network analysis is a powerful approach to investigate biological systems. It is often applied to study gene co-expression patterns derived from transcriptomics experiments. Even though co-expression analysis is widely used, there is still a lack of tools that are open and customizable on the basis of different network types and analysis scenarios (e.g. through function accessibility), but are also suitable for novice users by providing complete analysis pipelines. Results We developed VOLTA, a Python package suited for complex co-expression network analysis. VOLTA is designed to allow users direct access to the individual functions, while they are also provided with complete analysis pipelines. Moreover, VOLTA offers when possible multiple algorithms applicable to each analytical step (e.g. multiple community detection or clustering algorithms are provided), hence providing the user with the possibility to perform analysis tailored to their needs. This makes VOLTA highly suitable for experienced users who wish to build their own analysis pipelines for a wide range of networks as well as for novice users for which a ‘plug and play’ system is provided. Availability and implementation The package and used data are available at GitHub: https://github.com/fhaive/VOLTA and 10.5281/zenodo.5171719. Supplementary information Supplementary data are available at Bioinformatics online.

GIP: An open-source computational pipeline for mapping genomic instability from protists to cancer cells

One of the hallmarks of eukaryotic pathogens is the ability to genetically adapt to environmental change, causing for instance frequent drug resistance. Even though genome instability has been recognized as a key driver for microbial adaptation, most available computational tools focus just on one mutation type or analytical step. To overcome this limitation and better understand the role of genetic changes in enhancing microbial pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis across microbial populations. GIP allows batch processing of whole genome sequencing datasets, including read alignment, normalization, quantification of chromosomes, genes and genomic bins, and detection of single nucleotide and structural variants. GIP produces a comprehensive summary report providing sample statistics together with graphical representations of genomic features and tabulated results. GIP further includes a tool-suite that enables downstream custom comparisons of samples subsets. GIP is broadly applicable to different eukaryotic systems that exploit genome instability for adaptation, including Leishmania, Plasmodium, Candida, and cancer.

Value Chain as Tool of Strategic Management in Agro-Industrial Complex

Analyzing organization competitiveness by production costs is an important analytical step for units of agroindustrial complex (AIC). Such importance can be explained by specific features of markets, where AIC units operate: produce is uniform and standardized or poorly differentiated, price competition plays the essential role, therefore organizations with low costs are leaders on market. In this situation one of the most important parameters of strategic standing of the organization is its capability to compete by costs. Topicality of using the value chain is stipulated by importance of managing processes of raising competitiveness by costs and realizing strategy in general. The article studies practical and methodological issues of strategic analysis of production costs. It shows results of empirical research on managing processes of forming costs in AIC units and identifies key problems that can impact their successful development in the long run. Special attention was paid to changing approaches to managing processes of forming costs and potential profit, the shift of searching for opportunities of competitiveness by costs from internal environment to outer one. Recommendations on using value chains in AIC strategic management on state level were worked out. It was shown that effective cooperation of state and private AIC units could promote attainment of strategic goals of AIC development.

Gender and attitudes toward welfare state reform: Are women really social investment promoters?

This article contributes to the study of the demand side of welfare politics by investigating gender differences in social investment preferences systematically. Building on the different functions of social investment policies in creating, preserving, or mobilizing skills, we argue that women do not support social investment policies generally more strongly than men. Rather, women demand, in particular, policies to preserve their skills during career interruptions and help to mobilize their skills on the labour market. In a second analytical step, we examine women’s policy priorities if skill preservation and mobilization come at the expense of social compensation. We test our arguments for eight Western European countries with data from the INVEDUC survey. The confirmation of our arguments challenges a core assumption of the literatures on the social investment turn and women’s political realignment. We discuss the implication of our findings in the conclusion.

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in which longer contigs, ideally whole chromosomes/genomes, are formed from shorter NGS reads. However, the contigs generated from the de novo assembly are often very fragmented and rarely longer than a few kilo base pairs (kb). Therefore, a time-consuming extension process is routinely performed on the de novo assembled contigs. Results To facilitate this process, we propose a new tool for metagenome contig extension after de novo assembly. ContigExtender employs a novel recursive extending strategy that explores multiple extending paths to achieve highly accurate longer contigs. We demonstrate that ContigExtender outperforms existing tools in synthetic, animal, and human metagenomics datasets. Conclusions A novel software tool ContigExtender has been developed to assist and enhance the performance of metagenome de novo assembly. ContigExtender effectively extends contigs from a variety of sources and can be incorporated in most viral metagenomics analysis pipelines for a wide variety of applications, including pathogen detection and viral discovery.

EEG and fMRI Correlates of Insight: A Pilot Study

Insight is described as the sudden solution of a problem and is contrasted with an analytical, step-by-step approach. Traditionally, insight is thought to be associated with activity of the right hemisphere, whereas analytical solutions are thought to be associated with activity of the left hemisphere. However, empirical evidence as to the localization of insight-related brain activity is mixed and inconclusive. Some studies seem to confirm the traditional view, whereas others do not. Moreover, results of EEG and fMRI studies frequently contradict each other. In this study, EEG and fMRI data were recorded while subjects performed the remote association test and for each solved problem were asked to report whether the solution was reached analytically or insightfully. The data were analyzed in a 16-second fragment preceding the subject’s response. Source localization techniques were used in the analysis of EEG data. Based on EEG data, insightful as compared to analytical problem solving was accompanied by high-frequency synchronization in semantic cortical areas of the left hemisphere 10–12 s before the subject’s response. Based on fMRI data, however, insightful solutions were accompanied by increased activity in frontal and temporal regions of the right hemisphere. The results are interpreted in terms of different cognitive processes involved in insightful problem solving, which could be differently reflected in EEG and fMRI data.

Serum Myo-Inositol, Dimethyl Sulfone, and Valine in Combination with Creatinine Allow Accurate Assessment of Renal Insufficiency—A Proof of Concept

Evaluation of renal dysfunction includes estimation of glomerular filtration rate (eGFR) as the initial step and subsequent laboratory testing. We hypothesized that combined analysis of serum creatinine, myo-inositol, dimethyl sulfone, and valine would allow both assessment of renal dysfunction and precise GFR estimation. Bio-banked sera were analyzed using nuclear magnetic resonance spectroscopy (NMR). The metabolites were combined into a metabolite constellation (GFRNMR) using n = 95 training samples and tested in n = 189 independent samples. Tracer-measured GFR (mGFR) served as a reference. GFRNMR was compared to eGFR based on serum creatinine (eGFRCrea and eGFREKFC), cystatin C (eGFRCys-C), and their combination (eGFRCrea-Cys-C) when available. The renal biomarkers provided insights into individual renal and metabolic dysfunction profiles in selected mGFR-matched patients with otherwise homogenous clinical etiology. GFRNMR correlated better with mGFR (Pearson correlation coefficient r = 0.84 vs. 0.79 and 0.80). Overall percentages of eGFR values within 30% of mGFR for GFRNMR matched or exceeded those for eGFRCrea and eGFREKFC (81% vs. 64% and 74%), eGFRCys-C (81% vs. 72%), and eGFRCrea-Cys-C (81% vs. 81%). GFRNMR was independent of patients’ age and sex. The metabolite-based NMR approach combined metabolic characterization of renal dysfunction with precise GFR estimation in pediatric and adult patients in a single analytical step.

Decolonizing Refugee Studies, Standing up for Indigenous Justice: Challenges and Possibilities of a Politics of Place

This paper interrogates the challenges and potentials for solidarity between refugees and Indigenous peoples by bringing decolonial, anti-colonial and anti-imperialist critiques in different parts of the world, including in white settler colonies and in the Third World, into conversation with each other and with Refugee Studies. The first section of the paper offers two analytical steps towards decolonizing mainstream Refugee Studies. The first step involves identifying, analyzing and problematizing what we may call “an elephant in the room,” a parallax gap between Refugee Studies and studies of International Politics. The second analytical step is problematizing and challenging the popular discourses of charity and gratitude that dominate refugee discourses and narratives in the Global North. The second section of the paper engages in a more direct and detailed discussion about challenges to and possibilities for solidarity between refugees and Indigenous peoples. Articulating historical and contemporary parallels between refugee displacement from land and Indigenous dispossession of land, this section demonstrates that there are nevertheless no guarantees for political solidarity. It argues that potentials for solidarity are contingent on a politics of place, as articulated by Indigenous and non-Indigenous scholars; and also possibly on a reconceptualization and reorientation of refugee identity different from the ways it has been constituted in colonial discourses.