A tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship

There is no clear-cut boundary between Free and Open Source Software and Open Scholarship, and the histories, practices, and fundamental principles between the two remain complex. In this study, we critically appraise the intersections and differences between the two movements. Based on our thematic comparison here, we conclude several key things. First, there is substantial scope for new communities of practice to form within scholarly communities that place sharing and collaboration/open participation at their focus. Second, Both the principles and practices of FOSS can be more deeply ingrained within scholarship, asserting a balance between pragmatism and social ideology. Third, at the present, Open Scholarship risks being subverted and compromised by commercial players. Fourth, the shift and acceleration towards a system of Open Scholarship will be greatly enhanced by a concurrent shift in recognising a broader range of practices and outputs beyond traditional peer review and research articles. In order to achieve this, we propose the formulation of a new type of institutional mandate. We believe that there is substantial need for research funders to invest in sustainable open scholarly infrastructure, and the communities that support them, to avoid the capture and enclosure of key research services that would prevent optimal researcher behaviours. Such a shift could ultimately lead to a healthier scientific culture, and a system where competition is replaced by collaboration, resources (including time and people) are shared and acknowledged more efficiently, and the research becomes inherently more rigorous, verified, and reproducible

Independent and combined effects of improved water, sanitation, and hygiene, and improved complementary feeding, on child stunting and anaemia in rural Zimbabwe: a cluster-randomised trial.

BACKGROUND: Child stunting reduces survival and impairs neurodevelopment. We tested the independent and combined effects of improved water, sanitation, and hygiene (WASH), and improved infant and young child feeding (IYCF) on stunting and anaemia in in Zimbabwe. METHODS: We did a cluster-randomised, community-based, 2 × 2 factorial trial in two rural districts in Zimbabwe. Clusters were defined as the catchment area of between one and four village health workers employed by the Zimbabwe Ministry of Health and Child Care. Women were eligible for inclusion if they permanently lived in clusters and were confirmed pregnant. Clusters were randomly assigned (1:1:1:1) to standard of care (52 clusters), IYCF (20 g of a small-quantity lipid-based nutrient supplement per day from age 6 to 18 months plus complementary feeding counselling; 53 clusters), WASH (construction of a ventilated improved pit latrine, provision of two handwashing stations, liquid soap, chlorine, and play space plus hygiene counselling; 53 clusters), or IYCF plus WASH (53 clusters). A constrained randomisation technique was used to achieve balance across the groups for 14 variables related to geography, demography, water access, and community-level sanitation coverage. Masking of participants and fieldworkers was not possible. The primary outcomes were infant length-for-age Z score and haemoglobin concentrations at 18 months of age among children born to mothers who were HIV negative during pregnancy. These outcomes were analysed in the intention-to-treat population. We estimated the effects of the interventions by comparing the two IYCF groups with the two non-IYCF groups and the two WASH groups with the two non-WASH groups, except for outcomes that had an important statistical interaction between the interventions. This trial is registered with ClinicalTrials.gov, number NCT01824940. FINDINGS: Between Nov 22, 2012, and March 27, 2015, 5280 pregnant women were enrolled from 211 clusters. 3686 children born to HIV-negative mothers were assessed at age 18 months (884 in the standard of care group from 52 clusters, 893 in the IYCF group from 53 clusters, 918 in the WASH group from 53 clusters, and 991 in the IYCF plus WASH group from 51 clusters). In the IYCF intervention groups, the mean length-for-age Z score was 0·16 (95% CI 0·08-0·23) higher and the mean haemoglobin concentration was 2·03 g/L (1·28-2·79) higher than those in the non-IYCF intervention groups. The IYCF intervention reduced the number of stunted children from 620 (35%) of 1792 to 514 (27%) of 1879, and the number of children with anaemia from 245 (13·9%) of 1759 to 193 (10·5%) of 1845. The WASH intervention had no effect on either primary outcome. Neither intervention reduced the prevalence of diarrhoea at 12 or 18 months. No trial-related serious adverse events, and only three trial-related adverse events, were reported. INTERPRETATION: Household-level elementary WASH interventions implemented in rural areas in low-income countries are unlikely to reduce stunting or anaemia and might not reduce diarrhoea. Implementation of these WASH interventions in combination with IYCF interventions is unlikely to reduce stunting or anaemia more than implementation of IYCF alone. FUNDING: Bill & Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Development Cooperation, UNICEF, and US National Institutes of Health.The SHINE trial is funded by the Bill & Melinda Gates Foundation (OPP1021542 and OPP113707); UK Department for International Development; Wellcome Trust, UK (093768/Z/10/Z, 108065/Z/15/Z and 203905/Z/16/Z); Swiss Agency for Development and Cooperation; US National Institutes of Health (2R01HD060338-06); and UNICEF (PCA-2017-0002)

A New, Discontinuous 2 Phases of Aging Model: Lessons from Drosophila melanogaster

International audienc

A birth–death model of ageing: from individual-based dynamics to evolutive differential inclusions

International audienc

Mitochondrial electron transport chain dysfunction during development does not extend lifespan in Drosophila melanogaster

International audienc

Organ-specific mediation of lifespan extension: More than a gut feeling?

International audienc

The Smurf transition: new insights on ageing from end-of-life studies in animal models

International audiencePurpose of review: Over the past 5 years, many articles were published concerning the prediction of high risk of mortality in apparently healthy adults, echoing the first description in 2011 of the Smurf phenotype, a harbinger of natural death in drosophila.Recent findings: These recent findings suggest that the end-of-life is molecularly and physiologically highly stereotyped, evolutionarily conserved and predictable.Summary: Taken altogether, these results from independent teams using multiple organisms including humans draw the lines of future directions in ageing research. The ability to identify and study individuals about to die of natural causes with no apparent diseases is a game-changer in this field. In addition, the public health applications are potentially of tremendous impact in our ageing societies and raise important ethical questions

Effects of the different parameters of the model on lifespan.

<p><b>A, B.</b> As <b><i>a</i></b> increases, lifespan decreases and Smurf Increase Rate (SIR) increases. <b>C, D.</b> When <b><i>b</i></b> increases, lifespan increases without affecting the SIR but the first Smurfs appear later. <b>E, F.</b> An increase of <b><i>k</i></b> decreases both lifespan and the SIR. Thus, by measuring lifespan and SIR of flies in two distinct conditions indicates which parameter is affected by the treatment.</p

Aging is a 2-phases process.

<p><b>A.</b> Aging is characterized by two distinct and consecutive phases. <u>Phase 1</u> is characterized by a time-dependent increase in the probability of at least one organ–the intestine–to fail. <u>Phase 2</u> is the terminal phase of life during which a large number of so-called age-related phenotypes occur concomitantly. <b>B.</b> Each phase can be described by a distinct equation. Phase 1 is defined by a linear equation (<b><i>y =</i> a <i>t +</i> b</b>–left panel) describing the time-dependent increase of the probability for an individual to turn Smurf. Phase 2 is characterized by a 1-phase exponential decay equation (<b><i>y = e</i></b>^{<b><i>-kt</i></b>}<b><i>)</i></b>–right panel) describing the survival of an isolated Smurf subpopulation. <b>C.</b> The longevity curve of a homogenous population (green line) of flies is the sum of the number of non-Smurfs flies (blue line) and living Smurfs (red line). The mathematical equations that lead to the different curves are given in the right panel. The model uses 3 parameters; <b><i>a</i></b> is the rate of apparition of the Smurfs in the whole population, <b>t</b>_<b>0</b> = <b>-<i>b/a</i></b> is the age at which the Smurfs appear in the population and <b>k</b> is the rate constant defining the Smurf longevity.</p

Positive selection of senescence through increased evolvability: ageing is not a by-product of evolution

30 sept. 2022For the past century, scientists have debated whether or not ageing is directly selected by evolution. Because ageing occurs, by definition, late in life - that is, after the organism’s development is complete - many people believe that it cannot be actively selected for as a process. Furthermore, because it reduces an individual’s fitness, it is thought unlikely to be selected for. In agreement with this viewpoint, numerous theories have been proposed in the last 75 years to explain the observation of its widespread presence in the realm of life. The bd model of ageing is based on a simple life-history trait model that we recently introduced. Our model suggests that senescence can be positively selected through evolution due to the increased evolvability it confers on organisms, not through a specific mechanism but through a ‘function ageing’, limiting organismal maintenance and reproduction. It confirms the substrate for mutation accumulation and antagonistic pleiotropy theories while providing an elegant explanation for the apparent tradeoff between longevity and fertility that led to the disposable soma theory without requiring an energy tradeoff. Furthermore, it predicts that the Lansing effect will be present in organisms that exhibit rapid post-reproductive senescence. This formal and numerical modeling of the evolution of ageing also provides new hints for testing the validity of existing theories