Risk mapping for better governance in biobanking: the case of biobank.cy.

Introduction: Risk governance is central for the successful and ethical operation of biobanks and the continued social license for being custodians of samples and data. Risks in biobanking are often framed as risks for participants, whereas the biobank's risks are often considered as technical ones. Risk governance relies on identifying, assessing, mitigating and communicating all risks based on technical and standardized procedures. However, within such processes, biobank staff are often involved tangentially. In this study, the aim has been to conduct a risk mapping exercise bringing biobank staff as key actors into the process, making better sense of emerging structure of biobanks. Methods: Based on the qualitative research method of situational analysis as well as the card-based discussion and stakeholder engagement processes, risk mapping was conducted at the biobank setting as an interactive engagement exercise. The analyzed material comprises mainly of moderated group discussions. Results: The findings from the risk mapping activity are framed through an organismic metaphor: the biobank as a growing, living organism in a changing environment, where trust and sustainability are cross-cutting elements in making sense of the risks. Focusing on the situatedness of the dynamics within biobanking activity highlights the importance of prioritizing relations at the core of risk governance and promoting ethicality in the biobanking process by expanding the repertoire of considered risks. Conclusion: With the organismic metaphor, the research brings the diverse group of biobank staff to the central stage for risk governance, highlighting how accounting for such diversity and interdependencies at the biobank setting is a prerequisite for an adaptive risk governance.

Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation.

Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.

Dwarna: a blockchain solution for dynamic consent in biobanking.

Dynamic consent aims to empower research partners and facilitate active participation in the research process. Used within the context of biobanking, it gives individuals access to information and control to determine how and where their biospecimens and data should be used. We present Dwarna-a web portal for 'dynamic consent' that acts as a hub connecting the different stakeholders of the Malta Biobank: biobank managers, researchers, research partners, and the general public. The portal stores research partners' consent in a blockchain to create an immutable audit trail of research partners' consent changes. Dwarna's structure also presents a solution to the European Union's General Data Protection Regulation's right to erasure-a right that is seemingly incompatible with the blockchain model. Dwarna's transparent structure increases trustworthiness in the biobanking process by giving research partners more control over which research studies they participate in, by facilitating the withdrawal of consent and by making it possible to request that the biospecimen and associated data are destroyed.

Correction: Data in question: A survey of European biobank professionals on ethical, legal and societal challenges of biobank research.

[This corrects the article DOI: 10.1371/journal.pone.0221496.].

Data in question: A survey of European biobank professionals on ethical, legal and societal challenges of biobank research.

Biobanks have evolved, and their governance procedures have undergone important transformations. Our paper examines this issue by focusing on the perspective of the professionals working in management or scientific roles in research-based biobanks, who have an important impact on shaping these transformations. In particular, it highlights that recent advances in molecular medicine and genomic research have raised a range of ethical, legal and societal implications (ELSI) related to biobank-based research, impacting directly on regulations and local practices of informed consent (IC), private-public partnerships (PPPs), and engagement of participants. In our study, we investigate the ways that these concerns influence biobanking practices and assess the level of satisfaction of the cross-national biobanking research communities with the ELSI related procedures that are currently in place. We conducted an online survey among biobankers and researchers to investigate secondary use of data, informing and/or re-contacting participants, sharing of data with third parties from industry, participant engagement, and collaboration with industrial partners. Findings highlight the need for a more inclusive and transparent biobanking practice where biobanks are seen in a more active role in providing information and communicating with participants; the need to improve the current IC procedures and the role of biobanks in sharing of samples and data with industry partners and different countries, and the need for practical, tangible and hands-on ethical and legal guidance.

Conservation through the lens of (mal)adaptation: Concepts and meta-analysis.

Evolutionary approaches are gaining popularity in conservation science, with diverse strategies applied in efforts to support adaptive population outcomes. Yet conservation strategies differ in the type of adaptive outcomes they promote as conservation goals. For instance, strategies based on genetic or demographic rescue implicitly target adaptive population states whereas strategies utilizing transgenerational plasticity or evolutionary rescue implicitly target adaptive processes. These two goals are somewhat polar: adaptive state strategies optimize current population fitness, which should reduce phenotypic and/or genetic variance, reducing adaptability in changing or uncertain environments; adaptive process strategies increase genetic variance, causing maladaptation in the short term, but increase adaptability over the long term. Maladaptation refers to suboptimal population fitness, adaptation refers to optimal population fitness, and (mal)adaptation refers to the continuum of fitness variation from maladaptation to adaptation. Here, we present a conceptual classification for conservation that implicitly considers (mal)adaptation in the short-term and long-term outcomes of conservation strategies. We describe cases of how (mal)adaptation is implicated in traditional conservation strategies, as well as strategies that have potential as a conservation tool but are relatively underutilized. We use a meta-analysis of a small number of available studies to evaluate whether the different conservation strategies employed are better suited toward increasing population fitness across multiple generations. We found weakly increasing adaptation over time for transgenerational plasticity, genetic rescue, and evolutionary rescue. Demographic rescue was generally maladaptive, both immediately after conservation intervention and after several generations. Interspecific hybridization was adaptive only in the F1 generation, but then rapidly leads to maladaptation. Management decisions that are made to support the process of adaptation must adequately account for (mal)adaptation as a potential outcome and even as a tool to bolster adaptive capacity to changing conditions.

WASP (Write a Scientific Paper): Ethnography with children: Some considerations.

This paper introduces the key methodological challenges related to working with children within an ethnographic research design. After briefly identifying in-depth contextually rich data as the key aim of any ethnographic research, some of the particular challenges related to working with children are explored. These are described along two key axes: ethical issues related to power dynamics loaded in favour of the adult researcher, and practical, logistical barriers to generating data that are a true reflection of the young child's ideas and beliefs. 'Process assent' and 'ethical symmetry' are flagged as the key means of optimising ethicality, while the benefits of using the 'least adult role', and creative child centric activities are outlined as ways to generating and collecting trustworthy data.

Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health.

The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability-entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)-are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.

Humor as a Communication Strategy in Provider-Patient Communication in a Chronic Care Setting.

Humor is a potential communication strategy to accomplish various and potentially conflicting consultation goals. We investigated humor use and its reception in diabetes consultations by analyzing how and why humor emerges and its impact on the interaction. We did this by using an interactional sociolinguistics approach. We recorded 50 consultations in an Irish diabetes setting. Analysis of the humor events drew on framework analysis and on concepts from Conversation Analysis and pragmatics. The study also comprised interviews using tape-assisted recall. We identified 10 humor functions and two umbrella functions. A key finding is that most humor is relationship-protecting humor initiated by patients, that is, they voice serious messages and deal with emotional issues through humor. Our findings imply that patients' and providers' awareness of indirect communication strategies needs to be increased. We also recommend that researchers employ varied methods to adequately capture the interactive nature of humor.

Perceptions of Leadership: Comparing Canadian and Irish Physiotherapists' Views.

Purpose: To contribute to the growing body of research on leadership in physiotherapy by comparing leadership-related perceptions of physiotherapists in Ireland and in Canada. Methods: This article compares the results of a survey of Canadian physiotherapists with those of the same survey administered to Irish physiotherapists. The results of both studies have previously been reported and are used here to allow a cultural comparison of the perceptions of physiotherapists. The present study used two-portion Z-tests to compare the percentage of physiotherapists in Ireland who self-declared as a leader with the percentage of physiotherapists in Canada who did so. Results: Physiotherapists in both Ireland and Canada most often rated communication and professionalism as extremely important characteristics. Physiotherapists in Canada were more likely than those in Ireland to perceive themselves as leaders (Z=2.67, p < 0.05; 95% CI: 1.33, 9.87). Factors associated with self-declaration as a leader differed between the two countries. Conclusion: Physiotherapists in Canada and Ireland showed both similarities and differences in their perceptions of leadership characteristics. Results from this study may aid the development of future leadership training programmes specifically targeted at physiotherapists.

Objectif : Contribuer à la masse croissante de données de recherche sur le leadership en physiothérapie en comparant les perceptions liées au leadership chez les physiothérapeutes en Irlande et au Canada. Méthodes : Cet article compare les résultats d'un sondage des physiothérapeutes du Canada à ceux du même sondage administré à des physiothérapeutes en Irlande. Les résultats des deux études ont déjà fait l'objet de rapports et servent à établir une comparaison culturelle des perceptions relatives aux physiothérapeutes. Au cours de la présente étude, on a utilisé des tests-Z bilatéraux pour comparer le pourcentage des physiothérapeutes en Irlande qui se sont autodéclarés chefs de file à celui des physiothérapeute au Canada qui ont fait de même. Résultats : Les physiothérapeutes tant en Irlande qu'au Canada ont coté le plus souvent la communication et le professionnalisme comme caractéristiques « extrêmement importantes ¼. Les physiothérapeutes du Canada étaient plus susceptibles que ceux de l'Irlande de se percevoir comme des chefs de file (Z=2,67, p < 0.05; IC à 95%, 1,33 à 9,87). Les facteurs associés à l'autodéclaration comme chefs de file différaient entre les deux pays. Conclusion : Les physiothérapeutes au Canada et en Irlande ont montré à la fois des similitudes et des différences au niveau de leur perception des caractéristiques du leadership. Les résultats de cette étude peuvent aider à élaborer de futurs programmes de formation en leadership destinés spécialement aux physiothérapeutes.

The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding.

Additive diversity partitioning (α, ß, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (ß) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive ß) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

Obesity in question: understandings of body shape, self and normalcy among children in Malta.

Childhood obesity is a major public health concern in contemporary Malta. This article applies a critical realist approach to exploring body shape in young children, recognising fatness and obesity to be both a biologically and a socially constructed phenomenon. The agentic status of the child is central to the research design aimed at exploring understandings of body shape and how they impact on relational dynamics in the lived experiences of young children in Malta. Ethnographic methods were used in a school setting, working with children (n = 134) in two age groups: 5 and 10-year olds. The findings show a marked difference in the two groups. The obese 5-year-olds, buffered by robust protective strategies in their primary group, seem to be unaware of any difference in body shape. This situation changes in the older group where the fat body is stigmatised and obese children develop private coping strategies to deal with the physical disadvantages, taunting and exclusion by their peers. The data show that there is a culturally entrenched fluidity in the lay concept of obesity that impacts on the process of embodiment in young children and may have a lasting effect on body shape and weight.

Agonists of toll-like receptors 2 and 4 activate airway smooth muscle via mononuclear leukocytes.

RATIONALE: Toll-like receptors 2 and 4 (TLR2, TLR4) enable cellular responses to bacterial lipoproteins, LPS, and endogenous mediators of cell damage. They have an established role in the activation of leukocytes, endothelial cells, and some smooth muscle cell types, but their roles in airway smooth muscle are uncertain. OBJECTIVES: To determine the roles of TLRs in activation of airway smooth muscle. METHODS: Airway smooth muscle cells were cultured with TLR agonists, in the presence or absence of mononuclear leukocytes. MEASUREMENTS AND MAIN RESULTS: We observed expression of TLR2 and TLR4 mRNAs, which could be upregulated by treatment with proinflammatory cytokines in primary human airway smooth muscle, but no important functional responses to agonists of these TLRs were seen. Coincubation of airway smooth muscle with peripheral blood mononuclear cells, at concentrations as low as 250 mononuclear cells/ml, resulted in a marked cooperative response to TLR stimuli, and synergistic production of cytokines, including chemokines (interleukin [IL-]-8) and IL-6. This cooperative response was greater when monocytes were enriched and was transferable using supernatants from LPS-stimulated peripheral blood mononuclear cells. Activation of cocultures required IL-1 generation from mononuclear cells, and was blocked by IL-1 receptor antagonist, though IL-1 generation alone was not sufficient to account for the magnitude of mononuclear cell-dependent coculture activation. CONCLUSIONS: These data indicate that potent amplification of inflammation induced by TLR agonists, such as LPS, may be achieved by cooperativity between airway smooth muscle and leukocytes involved in immune surveillance or inflammation.

Heme oxygenase attenuates allergen-induced airway inflammation and hyperreactivity in guinea pigs.

Heme oxygenase (HO), the heme-degrading enzyme, has shown anti-inflammatory effects in several models of pulmonary diseases. HO is induced in airways during asthma; however, its functional role is unclear. Therefore, we evaluated the role of HO on airway inflammation [evaluated by bronchoalveolar lavage (BAL) cellularity and BAL levels of eotaxin, PGE(2), and proteins], mucus secretion (evaluated by analysis of MUC5AC gene expression and periodic acid-Schiff staining), oxidative stress (evaluated by quantification of 4-hydroxynonenal adducts and carbonylated protein levels in lung homogenates), and airway responsiveness to histamine in ovalbumin (OVA)-sensitized and multiple aerosol OVA or saline-challenged guinea pigs (6 challenges, once daily, OVA group and control group, respectively). Airway inflammation, mucus secretion, oxidative stress, and responsiveness were significantly increased in the OVA group compared with the control group. HO upregulation by repeated administrations of hemin (50 mg/kg i.p.) significantly decreased airway responsiveness in control animals and airway inflammation, mucus secretion, oxidative stress, and responsiveness in OVA animals. These effects were reversed by the concomitant administration of the HO inhibitor tin protoporphyrin-IX (50 micromol/kg i.p.). Repeated administrations of tin protoporphyrin-IX alone significantly increased airway responsiveness in control animals but did not modify airway inflammation, mucus secretion, oxidative stress, and responsiveness in OVA animals. These results suggest that upregulation of the HO pathway has a significant protective effect against airway inflammation, mucus hypersecretion, oxidative stress, and hyperresponsiveness in a model of allergic asthma in guinea pigs.

A new chromosomal locus associated with gut-modulated phenotypes in Salmonella enterica serotype typhimurium.

A cosmid DNA library had been constructed previously from 40-kb fragments of genomic DNA from a virulent invasive strain of Salmonella enterica serotype Typhimurium (TML) in an avirulent hypo-invasive Typhimurium strain (LT7). Selection of invasive clones from the library was attempted by iterative passage through a rabbit ileal organ culture. After the fourth passage, a clone, designated LT7(pHC20-2), was isolated. Exposure to both gut tissue and Caco-2 cells enhanced the growth, invasiveness for gut and Caco-2 cells, and flagellin expression of LT7(pHC20-2) although its invasiveness was less than that of strain TML. Expression of appendages (surface structures c. 60-70 nm diameter) was shown to play a role in but not to confer invasiveness, and was demonstrated in the absence of direct contact with eukaryotic cells. Exposure to gut tissue also affected the expression of several outer-membrane proteins (OMPs) in all four Salmonella strains--TML, LT7, LT7(pHC79), LT7(pHC20 2)--used in this work. As the genes involved in flagella, invasin and porin expression are distributed around the salmonella chromosome, it is possible that pHC20-2 encodes a pleiotropic regulator of genes involved in gastro-enteritic virulence and adaptation to the in-vivo gut environment. pHC20-2 mapped at c. centisome 25 on the salmonella chromosome close to, but distinct from, SPI-5.

Phthalate and alkyl phenol concentrations in soil following applications of inorganic fertiliser or sewage sludge to pasture and potential rates of ingestion by grazing ruminants.

Soil concentrations of dioctyl phthalate (DOP) and the alkyl phenols, octyl phenol (OP) and nonyl phenol (NP), after repeated surface applications of sewage sludge to pastures, were investigated. Liquid sludge was applied at a rate of 2.25 tonnes dry matter (DM) per hectare to each of three treated (T) plots on three occasions during the summer and two occasions in the early spring over a period of 2.5 years. Control (C) plots were treated with inorganic fertiliser containing amounts of nitrogen equivalent to those applied to the treated plots. At between 69 and 81 days after the application of sludge, 15 separate soil samples were collected from one half of each of the plots (Experiment 1). Concentrations (microg g(-1)) of DOP were higher (P < 0.001) than those of NP, while those of OP were generally below detectable levels. Mean soil concentrations of DOP were not significantly different in T and C plots [0.233 vs. 0.155 microg g(-1); standard error of the difference (SED) = 0.046; not significant (NS)], partly because there was already a relatively large amount of DOP present. NP concentrations were, however, significantly higher in T than in C plots (0.021 vs. 0.013 microg g(-1) SED = 0.002; P < 0.05). There was no consistent change over time in the mean soil concentrations of these compounds when sampled at intervals of 3-6 months. Concentrations in soil samples collected at monthly intervals following sludge application indicated that the variation in concentrations of these endocrine-disrupting compounds (EDC) was unrelated to time since sludge application. Rates of soil ingestion, expressed as the percentage of DM intake represented by soil, were higher during the winter than the summer (5.40 vs. 1.17; SED = 0.360; P < 0.001) and estimated daily intakes of DOP and NP were up to 150 microg and 8 microg, respectively. It is concluded that the application of sewage sludge to pasture does not increase soil concentrations of phthalate (as DOP) or alkyl phenols. Thus, the risk of increased exposure to these EDC as a result of sludge application is small. However, the small effect of sludge application on soil concentrations may be largely a reflection of the relatively high concentrations of DOP already present in the soil, which may be biologically significant.

Invasiveness of Salmonella serotypes Typhimurium and Enteritidis of human gastro-enteritic origin for rabbit ileum: role of LPS, plasmids and host factors.

An organ culture system involving explants of distal rabbit ileum was used to study the roles of lipopolysaccharide (LPS) and plasmids in primary invasiveness for enterocytes in situ of strains of Salmonella serotypes Typhimurium and Enteritidis. Long-chain LPS per se does not confer invasiveness on Typhimurium, as known avirulent, hypo-invasive strains express smooth LPS. However, the invasiveness of a naturally occurring rough isogenic derivative of Salmonella serotype Enteritidis PT 4 was about half that of its wild-type parent. Therefore, smooth LPS appears to play a secondary role in maximising invasiveness. No evidence was found to correlate primary invasiveness for gut of 18 strains of Typhimurium with plasmid profiles in general or with the 60-MDa serovar-specific virulence plasmid in particular. Evidence is presented that strongly suggests a seasonal variability in susceptibility of rabbit gut to invasion by Typhimurium. Although no explanation is given for this summer insusceptibility, the data indicate the importance of the physiological status of the host in relation to susceptibility to invasion by Salmonella.

Invasiveness of Salmonella serotypes Typhimurium, Choleraesuis and Dublin for rabbit terminal ileum in vitro.

Ten recent clinical isolates of Salmonella serotype Typhimurium from man that were tested for their invasiveness in rabbit ileal explants in vitro, were compared with Typhimurium strain TML, a well-characterised invasive strain isolated from a case of human gastro-enteritis. Nine of the 10 strains showed invasiveness that was comparable to that of strain TML. One isolate (GM3) was apparently substantially less invasive; electron microscopy showed this strain to be histotoxic - the probable reason for its reduced recovery from ileal mucosa and thus apparent 'low' invasiveness. Salmonella serotype Choleraesuis strain A50, isolated from a case of systemic salmonellosis in pigs, and serotype Dublin strain 3246, isolated from a case of systemic salmonellosis in calves, were also examined. Dublin strain 3246, when grown at 37 degrees C and used immediately in the invasion assay, damaged the mucosa in a manner similar to that of Typhimurium strain GM3, whereas Dublin strain 3246 grown at 37 degrees C and stored overnight at 4 degrees C did not. This was reflected in an apparently lower invasiveness of freshly grown organisms compared with that of organisms stored at 4 degrees C. In contrast, the histotoxicity of Typhimurium strain GM3 was not affected by storage at 4 degrees C. When stored at 4 degrees C, the levels of invasiveness of Choleraesuis strain A50 and Dublin strain 3246 were not significantly different from each other or from Typhimurium strain TML.