Bidirectional Mendelian Randomization and Multiphenotype GWAS Show Causality and Shared Pathophysiology Between Depression and Type 2 Diabetes

OBJECTIVE

Depression is a common comorbidity of type 2 diabetes. We assessed the causal relationships and shared genetics between them.

RESEARCH DESIGN AND METHODS

We applied two-sample, bidirectional Mendelian randomization (MR) to assess causality between type 2 diabetes and depression. We investigated potential mediation using two-step MR. To identify shared genetics, we performed 1) genome-wide association studies (GWAS) separately and 2) multiphenotype GWAS (MP-GWAS) of type 2 diabetes (19,344 case subjects, 463,641 control subjects) and depression using major depressive disorder (MDD) (5,262 case subjects, 86,275 control subjects) and self-reported depressive symptoms (n = 153,079) in the UK Biobank. We analyzed expression quantitative trait locus (eQTL) data from public databases to identify target genes in relevant tissues.

RESULTS

MR demonstrated a significant causal effect of depression on type 2 diabetes (odds ratio 1.26 [95% CI 1.11-1.44], P = 5.46 × 10-4) but not in the reverse direction. Mediation analysis indicated that 36.5% (12.4-57.6%, P = 0.0499) of the effect from depression on type 2 diabetes was mediated by BMI. GWAS of type 2 diabetes and depressive symptoms did not identify shared loci. MP-GWAS identified seven shared loci mapped to TCF7L2, CDKAL1, IGF2BP2, SPRY2, CCND2-AS1, IRS1, CDKN2B-AS1. MDD has not brought any significant association in either GWAS or MP-GWAS. Most MP-GWAS loci had an eQTL, including single nucleotide polymorphisms implicating the cell cycle gene CCND2 in pancreatic islets and brain and the insulin signaling gene IRS1 in adipose tissue, suggesting a multitissue and pleiotropic underlying mechanism.

CONCLUSIONS

Our results highlight the importance to prevent type 2 diabetes at the onset of depressive symptoms and the need to maintain a healthy weight in the context of its effect on depression and type 2 diabetes comorbidity.

Sympathetic nervous activation, mitochondrial dysfunction and outcome in acutely decompensated cirrhosis: the metabolomic prognostic models (CLIF-C MET)

BACKGROUND AND AIMS

Current prognostic scores of patients with acutely decompensated cirrhosis (AD), particularly those with acute-on-chronic liver failure (ACLF), underestimate the risk of mortality. This is probably because systemic inflammation (SI), the major driver of AD/ACLF, is not reflected in the scores. SI induces metabolic changes, which impair delivery of the necessary energy for the immune reaction. This investigation aimed to identify metabolites associated with short-term (28-day) death and to design metabolomic prognostic models.

METHODS

Two prospective multicentre large cohorts from Europe for investigating ACLF and development of ACLF, CANONIC (discovery, n=831) and PREDICT (validation, n=851), were explored by untargeted serum metabolomics to identify and validate metabolites which could allow improved prognostic modelling.

RESULTS

Three prognostic metabolites strongly associated with death were selected to build the models. 4-Hydroxy-3-methoxyphenylglycol sulfate is a norepinephrine derivative, which may be derived from the brainstem response to SI. Additionally, galacturonic acid and hexanoylcarnitine are associated with mitochondrial dysfunction. Model 1 included only these three prognostic metabolites and age. Model 2 was built around 4-hydroxy-3-methoxyphenylglycol sulfate, hexanoylcarnitine, bilirubin, international normalised ratio (INR) and age. In the discovery cohort, both models were more accurate in predicting death within 7, 14 and 28 days after admission compared with MELDNa score (C-index: 0.9267, 0.9002 and 0.8424, and 0.9369, 0.9206 and 0.8529, with model 1 and model 2, respectively). Similar results were found in the validation cohort (C-index: 0.940, 0.834 and 0.791, and 0.947, 0.857 and 0.810, with model 1 and model 2, respectively). Also, in ACLF, model 1 and model 2 outperformed MELDNa 7, 14 and 28 days after admission for prediction of mortality.

CONCLUSIONS

Models including metabolites (CLIF-C MET) reflecting SI, mitochondrial dysfunction and sympathetic system activation are better predictors of short-term mortality than scores based only on organ dysfunction (eg, MELDNa), especially in patients with ACLF.

A systematic review of artificial intelligence impact assessments

Artificial intelligence (AI) is producing highly beneficial impacts in many domains, from transport to healthcare, from energy distribution to marketing, but it also raises concerns about undesirable ethical and social consequences. AI impact assessments (AI-IAs) are a way of identifying positive and negative impacts early on to safeguard AI's benefits and avoid its downsides. This article describes the first systematic review of these AI-IAs. Working with a population of 181 documents, the authors identified 38 actual AI-IAs and subjected them to a rigorous qualitative analysis with regard to their purpose, scope, organisational context, expected issues, timeframe, process and methods, transparency and challenges. The review demonstrates some convergence between AI-IAs. It also shows that the field is not yet at the point of full agreement on content, structure and implementation. The article suggests that AI-IAs are best understood as means to stimulate reflection and discussion concerning the social and ethical consequences of AI ecosystems. Based on the analysis of existing AI-IAs, the authors describe a baseline process of implementing AI-IAs that can be implemented by AI developers and vendors and that can be used as a critical yardstick by regulators and external observers to evaluate organisations' approaches to AI.

Toward equitable open research: stakeholder co-created recommendations for research institutions, funders and researchers

Open Research aims to make research more accessible, transparent, reproducible, shared and collaborative. Doing so is meant to democratize and diversify access to knowledge and knowledge production, and ensure that research is useful outside of academic contexts. Increasing equity is therefore a key aim of the Open Research movement, yet mounting evidence demonstrates that the practices of Open Research are implemented in ways that undermine this. In response, we convened a diverse community of researchers, research managers and funders to co-create actionable recommendations for supporting the equitable implementation of Open Research. Using a co-creative modified Delphi method, we generated consensus-driven recommendations that address three key problem areas: the resource-intensive nature of Open Research, the high cost of article processing charges, and obstructive reward and recognition practices at funders and research institutions that undermine the implementation of Open Research. In this paper, we provide an overview of these issues, a detailed description of the co-creative process, and present the recommendations and the debates that surrounded them. We discuss these recommendations in relation to other recently published ones and conclude that implementing ours requires 'global thinking' to ensure that a systemic and inclusive approach to change is taken.

Responsible Innovation and De Jure Standardisation: An In-Depth Exploration of Moral Motives, Barriers, and Facilitators

Standardisation is increasingly seen as a means to insert ethics in innovation processes. We examine the institutionalisation of responsible innovation in de jure standardisation as this is an important but unexplored research area. In de jure standardisation, stakeholders collaborate in committees to develop standards. We adopt the anticipation, inclusion, reflexivity, and responsiveness responsible innovation framework as our theoretical lens. Our study suggests that responsible standardisation processes should embody forms of these four dimensions. We investigate the institutionalisation of these dimensions and identify 96 factors that can motivate, hinder, or facilitate responsible standardisation. Factors were found through in-depth interviews with managers of a standard developing organisation. These are subsequently validated/rejected using surveys completed by committee representatives. The results suggest that the social desirability of standards is not self-evident. This study could pave the way for future research on responsible standardisation processes, complementing research on legitimacy, responsible innovation, and standardisation.

The politics of scaling

A fixation on 'scaling up' has captured current innovation discourses and, with it, political and economic life at large. Perhaps most visible in the rise of platform technologies, big data and concerns about a new era of monopolies, scalability thinking has also permeated public policy in the search for solutions to 'grand societal challenges', 'mission-oriented innovation' or transformations through experimental 'living labs'. In this paper, we explore this scalability zeitgeist as a key ordering logic of current initiatives in innovation and public policy. We are interested in how the explicit preoccupation with scalability reconfigures political and economic power by invading problem diagnoses and normative understandings of how society and social change function. The paper explores three empirical sites - platform technologies, living labs and experimental development economics - to analyze how scalability thinking is rationalized and operationalized. We suggest that social analysis of science and technology needs to come to terms with the 'politics of scaling' as a powerful corollary of the 'politics of technology', lest we accept the permanent absence from key sites where decisions about the future are made. We focus in on three constitutive elements of the politics of scaling: solutionism, experimentalism and future-oriented valuation. Our analysis seeks to expand our vocabulary for understanding and questioning current modes of innovation that increasingly value scaling as an end in itself, and to open up new spaces for alternative trajectories of social transformation.

The Societal Readiness Thinking Tool: A Practical Resource for Maturing the Societal Readiness of Research Projects

In this paper, we introduce the Societal Readiness (SR) Thinking Tool to aid researchers and innovators in developing research projects with greater responsiveness to societal values, needs, and expectations. The need for societally-focused approaches to research and innovation-complementary to Technology Readiness (TR) frameworks-is presented. Insights from responsible research and innovation (RRI) concepts and practice, organized across critical stages of project-life cycles are discussed with reference to the development of the SR Thinking Tool. The tool is designed to complement not only shortfalls in TR approaches, but also improve upon other efforts to integrate RRI, sustainability, and design thinking in research and innovation cycles. Operationalization and early-stage user tests of the Tool are reported, along with discussion of potential future iterations and applications.

A high-resolution temporal and geospatial content analysis of Twitter posts related to the COVID-19 pandemic

The COVID-19 pandemic has deeply impacted all aspects of social, professional, and financial life, with concerns and responses being readily published in online social media worldwide. This study employs probabilistic text mining techniques for a large-scale, high-resolution, temporal, and geospatial content analysis of Twitter related discussions. Analysis considered 20,230,833 English language original COVID-19-related tweets with global origin retrieved between January 25, 2020 and April 30, 2020. Fine grain topic analysis identified 91 meaningful topics. Most of the topics showed a temporal evolution with local maxima, underlining the short-lived character of discussions in Twitter. When compared to real-world events, temporal popularity curves showed a good correlation with and quick response to real-world triggers. Geospatial analysis of topics showed that approximately 30% of original English language tweets were contributed by USA-based users, while overall more than 60% of the English language tweets were contributed by users from countries with an official language other than English. High-resolution temporal and geospatial analysis of Twitter content shows potential for political, economic, and social monitoring on a global and national level.

What goes on in digital behaviour change interventions for weight loss maintenance targeting physical activity: A scoping review

OBJECTIVE

To identify the core components of digital behaviour change interventions for weight loss maintenance targeting physical activity, in terms of: (i) behaviour change techniques, (ii) mechanisms of action, (iii) modes of delivery, (iv) dose and (v) tailoring/personalization. In addition, the links between these components were investigated.

METHODS

A literature search was performed in five electronic databases: PubMed, Embase, CINHAL, PsycINFO and Web of Science. Two reviewers independently screened the identified articles and extracted data related with the study characteristics and behaviour change techniques, mechanism of action, mode of delivery, dose, and tailoring, using standardized classifications whenever available (e.g. behaviour change techniques taxonomy).

RESULTS

Seventeen articles reporting 11 original studies were selected. Two studies were protocols, 9 studies presented results for weight change and all but one showed no significant differences between the intervention and control groups. Eight studies (73%) provided adequate information on behaviour change techniques. Five studies (45%) provided partial information about how the behaviour change techniques were linked to mechanisms of action, and only one study (0.9%) described these links for all the techniques. Around half of the studies reported the modes through which behaviour change techniques were delivered. Descriptions of dose were present in most studies, but with minimal information. The use of tailoring or personalization approaches was mentioned in eight studies (73%), but descriptions of what was tailored and how were minimal.

CONCLUSIONS

The compilation of information regarding intervention components was difficult due to the lack of information and systematization in reporting across papers. This is particularly true for the reporting of the links between behaviour change techniques and the other core intervention components. This information is crucial to help us understand in the context of behaviour change interventions what works or does not work, how it works and why.

Premature consent and patient duties

This paper addresses the problem of 'premature consent'. The term 'premature consent' (introduced in a 2018 paper by J.K. Davis) denotes patient decisions that are: (i) formulated prior to discussion with the appropriate healthcare professional (HCP); (ii) based on information from unreliable sources (e.g. parts of the internet); and (iii) resolutely maintained despite the HCP having provided alternative reliable information. HCPs are not obliged to respect premature consent patients' demands for unindicated treatments. But why? What is it that premature consent patients do or get wrong? Davis has argued that premature consent patients are incompetent and misinformed. We argue that this view is not sustainable. A more plausible position asserts that premature consent threatens the integrity of the medical profession. We argue that this gives rise to a negative patient duty (to not obstruct HCPs in upholding the integrity of the medical profession) which premature consent patients fail to honour. We argue for a further positive duty of good faith engagement in shared decision-making. This implies willingness to potentially revise or justify one's evaluative bases (core assumptions, beliefs, values, etc.). Fundamentally, the problem with premature consent patients is that certain of their evaluative bases are not open to revision. They therefore fail in their duty to participate faithfully in the shared decision-making process.

Effect of Trehalose and Sucrose in Post-thaw Quality of Crassostrea angulata Sperm

Sperm cryopreservation can be a helpful tool in reproductive management and preservation of biodiversity. However, the freezing methodologies lead to some damage in structure and function of cells that may compromise post-thaw sperm activity. Cryoprotectant supplementation with sugars proved to be a successful strategy to reduce cryodamage in sperm of several species, once allowing to stabilize the plasma membrane constituents. Therefore, this study intends to understand the effects of sugars in the plasma membrane, DNA integrity, and oxidative response during Portuguese oyster sperm cryopreservation. Three cryoprotectants solutions with an initial concentration of 20% dimethyl sulfoxide (DMSO) and 20% DMSO complemented with 0.9 M trehalose or sucrose in artificial seawater were employed. Sperm samples of mature males were individually collected and diluted 1:10 (v/v) in artificial seawater followed by addition of cryoprotectants [1:1 (v/v)]. Thereafter, sperm was loaded into 0.5 ml straws, maintained at 4°C for 10 min, frozen in a programmable biofreezer at -6°C/min from 0 to -70°C, and stored in liquid nitrogen. Samples were thawed in a 37°C bath for 10 s. Several techniques were performed to evaluate post-thaw quality. Sperm motility and DNA integrity were analyzed by using computer-assisted sperm analysis (CASA) software and comet assay. Flow cytometry was employed to determine membrane and acrosome integrity and to detect intracellular reactive oxygen species (ROS) and apoptosis activity. Lipid peroxidation was determined by malondialdehyde (MDA) detection by using spectrophotometry. Sperm antioxidant capacity was evaluated through glutathione peroxidase, glutathione reductase, and superoxide dismutase. Motility was not affected by the extenders containing sugars; these compounds did not reduce the DNA damage. However, both the trehalose and sucrose protected plasma membrane of cells by increasing cell viability and significantly reducing MDA content. The same finding was observed for the ROS, where live cells registered significantly lower levels of ROS in samples cryopreserved with sugars. The activity of antioxidant enzymes was higher in treatments supplemented with sugars, although not significant. In conclusion, the addition of sugars seems to play an important role in protecting the Crassostrea angulata sperm membrane during cryopreservation, showing potential to improve the post-thaw sperm quality and protect the cells from cryoinjuries.

Ethics appraisal procedure in 79,670 Marie Skłodowska-Curie proposals from the entire European HORIZON 2020 research and innovation program (2014-2020): A retrospective analysis

INTRODUCTION

Horizon 2020 was the most significant EU Research and Innovation programme ever implemented and included the Marie Skłodowska-Curie Actions (MSCA). Proposals submitted to the MSCA actions awere subject to the Ethics Appraisal Procedure. In this work we explored the ethics appraisal procedure in MSCA H2020.

METHODS

Using a retrospective analysis of pooled anonymized data, we explored the ethics appraisal procedure on proposals submitted to Marie Skłodowska-Curie Actions (MSCA) during the entire Horizon 2020 program period (N = 79,670).

RESULTS

Our results showed that one of the most frequently identified ethics categories was Data protection. We also detected slight differences between applicants' and the ethics reviewers' awareness of ethical issues. Trajectory analysis of all ethics screened proposals appearing on main lists showed that a minimal portion of all screened submissions required additional ethics checks in the project implementation phase.

CONCLUSION

Personal data protection is one of the most represented ethics categories indicated among MSCA actions which exhaust ethics assessment efforts and may lead to "overkills" in ethics requirements. Excluding the majority of personal data protection assessment from the ethics assessment, except for parts which are directly related to ethics like "Informed consent procedures", might be necessary in the future. A gap in understanding of ethics issues between applicants and reviewers' points to the necessity to further educate researchers on research ethics issues.

Nonverbal Auditory Cues Allow Relationship Quality to be Inferred During Conversations

The claim that nonverbal cues provide more information than the linguistic content of a conversational exchange (the Mehrabian Conjecture) has been widely cited and equally widely disputed, mainly on methodological grounds. Most studies that have tested the Conjecture have used individual words or short phrases spoken by actors imitating emotions. While cue recognition is certainly important, speech evolved to manage interactions and relationships rather than simple information exchange. In a cross-cultural design, we tested participants’ ability to identify the quality of the interaction (rapport) in naturalistic third party conversations in their own and a less familiar language, using full auditory content versus audio clips whose verbal content has been digitally altered to differing extents. We found that, using nonverbal content alone, people are 75–90% as accurate as they are with full audio cues in identifying positive vs negative relationships, and 45–53% as accurate in identifying eight different relationship types. The results broadly support Mehrabian’s claim that a significant amount of information about others’ social relationships is conveyed in the nonverbal component of speech.

Metformin Use and Cognitive Function in Older Adults With Type 2 Diabetes Following a Mediterranean Diet Intervention

Background and Purpose: Both adherence to the Mediterranean diet (MedDiet) and the use of metformin could benefit the cognitive performance of individuals with type 2 diabetes, but evidence is still controversial. We examined the association between metformin use and cognition in older adults with type 2 diabetes following a MedDiet intervention. Methods: Prospective cohort study framed in the PREDIMED-Plus-Cognition sub-study. The PREDIMED-Plus clinical trial aims to compare the cardiovascular effect of two MedDiet interventions, with and without energy restriction, in individuals with overweight/obesity and metabolic syndrome. The present sub-study included 487 cognitively normal subjects (50.5% women, mean ± SD age of 65.2 ± 4.7 years), 30.4% of them (N = 148) with type 2 diabetes. A comprehensive battery of neurocognitive tests was administered at baseline and after 1 and 3 years. Individuals with type 2 diabetes that exhibited a good glycemic control trajectory, either using or not using metformin, were compared to one another and to individuals without diabetes using mixed-effects models with inverse probability of treatment weights. Results: Most subjects with type 2 diabetes (83.1%) presented a good and stable glycemic control trajectory. Before engaging in the MedDiet intervention, subjects using metformin scored higher in executive functions (Cohen's d = 0.51), memory (Cohen's d = 0.38) and global cognition (Cohen's d = 0.48) than those not using metformin. However, these differences were not sustained during the 3 years of follow-up, as individuals not using metformin experienced greater improvements in memory (β = 0.38 vs. β = 0.10, P = 0.036), executive functions (β = 0.36 vs. β = 0.02, P = 0.005) and global cognition (β = 0.29 vs. β = -0.02, P = 0.001) that combined with a higher MedDiet adherence (12.6 vs. 11.5 points, P = 0.031). Finally, subjects without diabetes presented greater improvements in memory than subjects with diabetes irrespective of their exposure to metformin (β = 0.55 vs. β = 0.10, P < 0.001). However, subjects with diabetes not using metformin, compared to subjects without diabetes, presented greater improvements in executive functions (β = 0.33 vs. β = 0.08, P = 0.032) and displayed a higher MedDiet adherence (12.6 points vs. 11.6 points, P = 0.046). Conclusions: Although both metformin and MedDiet interventions are good candidates for future cognitive decline preventive studies, a higher adherence to the MedDiet could even outweigh the potential neuroprotective effects of metformin in subjects with diabetes.

Important Topics for Fostering Research Integrity by Research Performing and Research Funding Organizations: A Delphi Consensus Study

To foster research integrity (RI), it is necessary to address the institutional and system-of-science factors that influence researchers' behavior. Consequently, research performing and research funding organizations (RPOs and RFOs) could develop comprehensive RI policies outlining the concrete steps they will take to foster RI. So far, there is no consensus on which topics are important to address in RI policies. Therefore, we conducted a three round Delphi survey study to explore which RI topics to address in institutional RI policies by seeking consensus from research policy experts and institutional leaders. A total of 68 RPO and 52 RFO experts, representing different disciplines, countries and genders, completed one, two or all rounds of the study. There was consensus among the experts on the importance of 12 RI topics for RPOs and 11 for RFOs. The topics that ranked highest for RPOs concerned education and training, supervision and mentoring, dealing with RI breaches, and supporting a responsible research process (e.g. through quality assurance). The highest ranked RFO topics concerned dealing with breaches of RI, conflicts of interest, and setting expectations on RPOs (e.g. about educating researchers about RI). Together with the research policy experts and institutional leaders, we developed a comprehensive overview of topics important for inclusion in the RI policies of RPOs and RFOs. The topics reflect preference for a preventative approach to RI, coupled with procedures for dealing with RI breaches. RPOs and RFOs should address each of these topics in order to support researchers in conducting responsible research.

3D Modelling of Mass Transfer into Bio-Composite

A three-dimensional model structure that allows considering interphase layer around permeable inclusions is developed to predict water vapor permeability in composite materials made of a matrix Poly(3-HydroxyButyrate-co-3-HydroxyValerate) (PHBV) including Wheat Straw Fiber (WSF) particles. About 500 two-phase structures corresponding to composites of different particles volume fractions (5.14-11.4-19.52 % v/v) generated using experimental particles' size distribution have permitted to capture all the variability of the experimental material. These structures have served as a basis to create three-phase structures including interphase zone of altered polymer property surrounding each particle. Finite Element Method (FEM) applied on these structures has permitted to calculate the relative permeability (ratio between composite and neat matrix permeability P/Pm). The numerical results of the two-phase model are consistent with the experimental data for volume fraction lower than 11.4 %v/v but the large upturn of the experimental relative permeability for highest volume fraction is not well represented by the two-phase model. Among hypothesis made to explain model's deviation, the presence of an interphase with its own transfer properties is numerically tested: numerical exploration made with the three-phase model proves that an interphase of 5 µm thick, with diffusivity of Di≥1×10-10 m2·s-1, would explain the large upturn of permeability at high volume fraction.

A data-driven metapopulation model for the Belgian COVID-19 epidemic: assessing the impact of lockdown and exit strategies

BACKGROUND

In response to the ongoing COVID-19 pandemic, several countries adopted measures of social distancing to a different degree. For many countries, after successfully curbing the initial wave, lockdown measures were gradually lifted. In Belgium, such relief started on May 4th with phase 1, followed by several subsequent phases over the next few weeks.

METHODS

We analysed the expected impact of relaxing stringent lockdown measures taken according to the phased Belgian exit strategy. We developed a stochastic, data-informed, meta-population model that accounts for mixing and mobility of the age-structured population of Belgium. The model is calibrated to daily hospitalization data and is able to reproduce the outbreak at the national level. We consider different scenarios for relieving the lockdown, quantified in terms of relative reductions in pre-pandemic social mixing and mobility. We validate our assumptions by making comparisons with social contact data collected during and after the lockdown.

RESULTS

Our model is able to successfully describe the initial wave of COVID-19 in Belgium and identifies interactions during leisure/other activities as pivotal in the exit strategy. Indeed, we find a smaller impact of school re-openings as compared to restarting leisure activities and re-openings of work places. We also assess the impact of case isolation of new (suspected) infections, and find that it allows re-establishing relatively more social interactions while still ensuring epidemic control. Scenarios predicting a second wave of hospitalizations were not observed, suggesting that the per-contact probability of infection has changed with respect to the pre-lockdown period.

CONCLUSIONS

Contacts during leisure activities are found to be most influential, followed by professional contacts and school contacts, respectively, for an impending second wave of COVID-19. Regular re-assessment of social contacts in the population is therefore crucial to adjust to evolving behavioral changes that can affect epidemic diffusion.

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner

BACKGROUND

IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5' and/or 3' end, internal editings or untemplated 3' end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification and functional exploration of isomiR expression in small RNA-seq datasets, accessible to users with no computational skills.

METHODS

IsomiR Window enables the discovery of isomiRs and identification of all annotated non-coding RNAs in RNA-seq datasets from animals and plants. It comprises two main components: the IsomiR Window pipeline for data processing; and the IsomiR Window Browser interface. It integrates over ten third-party softwares for the analysis of small-RNA-seq data and holds a new algorithm that allows the detection of all possible types of isomiRs. These include 3' and 5'end isomiRs, 3' end tailings, isomiRs with single nucleotide polymorphisms (SNPs) or potential RNA editings, as well as all possible fuzzy combinations. IsomiR Window includes all required databases for analysis and annotation, and is freely distributed as a Linux virtual machine, including all required software.

RESULTS

IsomiR Window processes several datasets in an automated manner, without restrictions of input file size. It generates high quality interactive figures and tables which can be exported into different formats. The performance of isomiR detection and quantification was assessed using simulated small-RNA-seq data. For correctly mapped reads, it identified different types of isomiRs with high confidence and 100% accuracy. The analysis of a small RNA-seq data from Basal Cell Carcinomas (BCCs) using isomiR Window confirmed that miR-183-5p is up-regulated in Nodular BCCs, but revealed that this effect was predominantly due to a novel 5'end variant. This variant displays a different seed region motif and 1756 isoform-exclusive mRNA targets that are significantly associated with disease pathways, underscoring the biological relevance of isomiR-focused analysis. IsomiR Window is available at https://isomir.fc.ul.pt/ .

Practices for Research Integrity Promotion in Research Performing Organisations and Research Funding Organisations: A Scoping Review

Research integrity (RI) is a continuously developing concept, and increasing emphasis is put on creating RI promotion practices. This study aimed to map the existing RI guidance documents at research performing organisations (RPOs) and research funding organisations (RFOs). A search of bibliographic databases and grey literature sources was performed, and retrieved documents were screened for eligibility. The search of bibliographical databases and reference lists of selected articles identified a total of 92 documents while the search of grey literature sources identified 118 documents for analysis. The retrieved documents were analysed based on their geographical origin, research field and organisational origin (RPO or RFO) of RI practices, types of guidance presented in them, and target groups to which RI practices are directed. Most of the identified practices were developed for research in general, and are applicable to all research fields (n = 117) and medical sciences (n = 78). They were mostly written in the form of guidelines (n = 136) and targeted researchers (n = 167). A comprehensive search of the existing RI promotion practices showed that initiatives mostly come from RPOs while only a few RI practices originate from RFOs. This study showed that more RI guidance documents are needed for natural sciences, social sciences, and humanities since only a small number of documents was developed specifically for these research fields. The explored documents and the gaps in knowledge identified in this study can be used for further development of RI promotion practices in RPOs and RFOs.

The Present Shock and Time Re-appropriation in the Pandemic Era : Missed Opportunities for Science Education

The crisis due to the COVID-19 pandemic led most people all over the world to deal with a change in their perception and organization of time. This happened also, and mainly, within the educational institutions, where students and teachers had to rearrange their teaching/learning dynamics because of the forced education at a distance. In this paper, we present an exploratory qualitative study with secondary school students aimed to investigate how they were experiencing their learning during lockdown and how, in particular, learning of science contributed to rearranging their daily lifetime rituals. In order to design and carry out our investigation, we borrowed constructs coming from a research field rather unusual for science education: the field of sociology of time. The main result concerns the discovery of the potential of the dichotomy between alienation from time and time re-appropriation. The former is a construct elaborated by the sociologist Hartmut Rosa to describe the society of acceleration in the "era of future shock". The latter represents an elaboration of the construct of appropriation that the authors had operationally defined, starting from Bakhtin's original idea, to describe the nexus between physics learning and identity. Thanks to the elaboration of the notion of time re-appropriation as feature of the "era of present shock", the study unveils how school science, instead of preparing the young to navigate our fast-changing and complex society, tends to create "bubbles of rituals" that detach learning from societal concern.

Consolidating RRI and Open Science: understanding the potential for transformative change

In European research and innovation policy, Responsible Research and Innovation (RRI) and Open Science (OS) encompass two co-existing sets of ambitions concerning systemic change in the practice of research and innovation. This paper is an exploratory attempt to uncover synergies and differences between RRI and OS, by interrogating what motivates their respective transformative agendas. We offer two storylines that account for the specific contexts and dynamics from which RRI and OS have emerged, which in turn offer entrance points to further unpacking what 'opening up' to society means with respect to the transformative change agendas that are implicit in the two agendas. We compare differences regarding the 'how' of opening up in light of the 'why' to explore common areas of emphasis in both OS and RRI. We argue that while both agendas align with mission-oriented narratives around grand societal challenges, OS tends to emphasize efficiency and technical optimisation over RRI's emphasis on normative concerns and democracy deficits, and that the two agendas thus contrast in their relative legitimate emphasis on doable outcomes versus desirable outcomes. In our conclusion, we reflect on the future outlook for RRI and OS' co-existence and uptake, and on what their respective ambitions for transformation might mean for science-society scholars and scholarship.

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

The two As resistance arsRBC operons of Pseudomonas putida KT2440 are followed by a downstream gene called arsH that encodes an NADPH-dependent flavin mononucleotide reductase. In this work, we show that the arsH1 and (to a lesser extent) arsH2 genes of P. putida KT2440 strengthened its tolerance to both inorganic As(V) and As(III) and relieved the oxidative stress undergone by cells exposed to either oxyanion. Furthermore, overexpression of arsH1 and arsH2 endowed P. putida with a high tolerance to the oxidative stress caused by diamide (a drainer of metabolic NADPH) in the absence of any arsenic. To examine whether the activity of ArsH was linked to a direct action on the arsenic compounds tested, arsH1 and arsH2 genes were expressed in Escherichia coli, which has an endogenous arsRBC operon but lacks an arsH ortholog. The resulting clones both deployed a lower production of reactive oxygen species (ROS) when exposed to As salts and had a superior endurance to physiological redox insults. These results suggest that besides the claimed direct action on organoarsenicals, ArsH contributes to relieve toxicity of As species by mediating reduction of ROS produced in vivo upon exposure to the oxyanion, e.g. by generating FMNH2 to fuel ROS-quenching activities.

Addressing research integrity challenges: from penalising individual perpetrators to fostering research ecosystem quality care

Concern for and interest in research integrity has increased significantly during recent decades, both in academic and in policy discourse. Both in terms of diagnostics and in terms of therapy, the tendency in integrity discourse has been to focus on strategies of individualisation (detecting and punishing individual deviance). Other contributions to the integrity debate, however, focus more explicitly on environmental factors, e.g. on the quality and resilience of research ecosystems, on institutional rather than individual responsibilities, and on the quality of the research culture. One example of this is the Bonn PRINTEGER Statement. This editorial to the LSSP thematic series (article collection) entitled Addressing integrity challenges in research: the institutional dimension invites authors to contribute to the research integrity debate. Notably, we are interested in submissions addressing issues such as institutional responsibilities, changes in the research climate, duties of research managers and research performing or research funding organisations (RPOs and RFOs) as well as new approaches to integrity education.

Teaching Responsible Research and Innovation: A Phronetic Perspective

Across the European research area and beyond, efforts are being mobilized to align research and innovation processes and products with societal values and needs, and to create mechanisms for inclusive priority setting and knowledge production. A central concern is how to foster a culture of "Responsible Research and Innovation" (RRI) among scientists and engineers. This paper focuses on RRI teaching at higher education institutions. On the basis of interviews and reviews of academic and policy documents, it highlights the generic aspects of teaching aimed at invoking a sense of care and societal obligation, and provides a set of exemplary cases of RRI-related teaching. It argues that the Aristotelian concept of phronesis can capture core properties of the objectives of RRI-related teaching activities. Teaching should nurture the students' capacity in terms of practical wisdom, practical ethics, or administrative ability in order to enable them to act virtuously and responsibly in contexts which are often characterized by uncertainty, contention, and controversy.

Classification of red blood cell shapes in flow using outlier tolerant machine learning

The manual evaluation, classification and counting of biological objects demands for an enormous expenditure of time and subjective human input may be a source of error. Investigating the shape of red blood cells (RBCs) in microcapillary Poiseuille flow, we overcome this drawback by introducing a convolutional neural regression network for an automatic, outlier tolerant shape classification. From our experiments we expect two stable geometries: the so-called 'slipper' and 'croissant' shapes depending on the prevailing flow conditions and the cell-intrinsic parameters. Whereas croissants mostly occur at low shear rates, slippers evolve at higher flow velocities. With our method, we are able to find the transition point between both 'phases' of stable shapes which is of high interest to ensuing theoretical studies and numerical simulations. Using statistically based thresholds, from our data, we obtain so-called phase diagrams which are compared to manual evaluations. Prospectively, our concept allows us to perform objective analyses of measurements for a variety of flow conditions and to receive comparable results. Moreover, the proposed procedure enables unbiased studies on the influence of drugs on flow properties of single RBCs and the resulting macroscopic change of the flow behavior of whole blood.

Influence of the initial chemical conditions on the rational design of silica particles

The influence of the water content in the initial composition on the size of silica particles produced using the Stöber process is well known. We have shown that there are three morphological regimes defined by compositional boundaries. At low water levels (below stoichiometric ratio of water:tetraethoxysilane), very high surface area and aggregated structures are formed; at high water content (>40 wt%) similar structures are also seen. Between these two boundary conditions, discrete particles are formed whose size are dictated by the water content. Within the compositional regime that enables the classical Stöber silica, the structural evolution shows a more rapid attainment of final particle size than the rate of formation of silica supporting the monomer addition hypothesis. The clearer understanding of the role of the initial composition on the output of this synthesis method will be of considerable use for the establishment of reliable reproducible silica production for future industrial adoption.

Policy coherence to achieve the SDGs: using integrated simulation models to assess effective policies

Coherently addressing the 17 Sustainable Development Goals requires planning tools that guide policy makers. Given the integrative nature of the SDGs, we believe that integrative modelling techniques are especially useful for this purpose. In this paper, we present and demonstrate the use of the new System Dynamics based iSDG family of models. We use a national model for Tanzania to analyse impacts of substantial investments in photovoltaic capacity. Our focus is on the impacts on three SDGs: SDG 3 on healthy lives and well-being, SDG 4 on education, and SDG 7 on energy. In our simulations, the investments in photovoltaics positively affect life expectancy, years of schooling and access to electricity. More importantly, the progress on these dimensions synergizes and leads to broader system-wide impacts. While this one national example illustrates the anticipated impact of an intervention in one specific area on several SDGs, the iSDG model can be used to support similar analyses for policies related to all the 17 SDGs, both individually and concurrently. We believe that integrated models such as the iSDG model can bring interlinks to the forefront and facilitate a shift to a discussion on development grounded in systems thinking.