Open access models of publications: a strategy for improving 3R information retrieval?

Accessing 3R information for fundamental research is difficult for many reasons: the titles, abstracts, and author keywords of scientific articles do not contain the terms 3R, Reduce, Refine, Replace, alternatives or replacement. Mesh terms in Pubmed or thesaurus terms in Embase are rare and are not systematically attributed to scientific articles using animal experimentation or substitution methods. Reporting of animal conditions, animal and cell strains used for fundamental research are often incomplete in the Material and Methods section because authors have omitted them, but certainly also because publishers demand concision. The Material and Methods section is not indexed by bibliographic databases now used in life sciences, Pubmed, Embase, Scopus, or WOS (Web of Science). If Google scholar indexes full texts including the Material and Methods section, access to articles depends on whether the journal has been licensed by the researcher’s institution. The Gold Open Access model for journals specialized in animal experimentation or substitution methods is rare. Moreover, Green Open Access to 3R information is poorly developed: websites of journals specialized in animal experimentation or substitution methods do not even specify embargo periods preventing free diffusion of articles, and if, they are not included in the Sherpa, a publisher copyright policies & self-archiving information database. The archiving of full-text articles using animal experimentation into institutional Open Archives is not systematic yet, even for one of the largest free-full text archive of biomedical literature at the US, PMC (Pubmed Central). LAMDHI (Link Animal Models to Human Disease) is a free Web-based tool developed for providing biomedical researchers with a resource to compare animal models and locate them for their research. But corresponding full-text access to articles on animal models still depends on institutional academic licenses. Over the last five years, SYRCLE (Systematic Review Centre for Laboratory animal Experimentation) has developed educational activities focused on training of Dutch researchers to carry out systematic 3R reviews. SYRCLE also developed special filters that can help systematically search of 3R information in Pubmed or Embase. In Switzerland, researchers were sensitized to adopt strategies for finding relevant 3R information in 2012 and 2013 at the request of RESAL (Réseau des animaleries lémaniques) and LTK (Institut für LabortTierKunde). The ECVAM (European Center for Validation of Alternatives Methods) edited a complete, user-friendly, and free access guide to help untrained database users find 3R information in 2011. The guidelines ARRIVE (Animal Research Reporting of In Vivo Experiments) and GSPC (Gold Standard Publication Checklist) for accurate reporting of animal experimentation are also now available for researchers. These examples of different initiatives for better finding and reporting of animal experimentation and substitution methods are a good start. But 3R information circuits should be changed to really enhance 3R accessibility in the near future. It could be a Swiss case study of the spreading (and controversial) movement of Open Access models to scientific information. The Consortium of Swiss Academic Libraries could start negotiating for national licenses to some or all journal titles specialized in animal experimentation or substitutions methods for the best price for Swiss universities. A shorter embargo diffusion time for 3R articles should be negotiated with publishers. The embargo diffusion could be systematically indicated on publisher journal websites and on the Sherpa database for the development of Green Open Access to 3R information. Universities could adopt the practice of archiving all 3R, animal experimentation, and substitution methods articles in their Open Archives bibliographic databases. The switch from a classical publication model to a Gold Open Access model could be discussed with journals focusing on animal experimentation and/or substitution methods. As a result, a new kind of financial resource for publication should be created with the help of universities, libraries and the SNF (Swiss National Foundation). The reporting of animal experimentation conditions according to the recommended standards ARRIVE or GSPC should be accessible freely on Open Access platforms, ie Frontiers, Open Archives such as Infoscience at Ecole Polytechnique de Lausanne, or publishers’ open-access websites, as it is the already the case for Plos journals. Finally, Swiss 3R institutions could think about the financing and/or participation to the ontology development of the new German semantic search engine Go3R. A multidisciplinary team including veterinary and life sciences researchers as well as librarians could be created to evaluate the feasibility of the above options. RESAL, LTK, FNS, SAMS (Swiss Academy Medical Science), SGV (Swiss Laboratory Animal Science Association), Commission des Bibliothèques médicales, 3R Foundation should work together to obtain common 3R resources and tools at the Swiss National level for universities and veterinary offices, and to adopt common 3R information practices for the improvement of 3R information accessibility, experimental results and life science reproducibility. [1

Numerical modeling of cohesive sediment transport and bed morphology in estuaries

Célestin Leupi

Two major lines of investigation have been pursued in this thesis: (1) More efficient, robust and realistic numerical techniques are designed for the simulation of complex turbulent fluid flows; (2) A new algorithm and its analysis is performed in the context of multiphasic fluid flow, for a cohesive fine-grained sediment (fluid mud) transport in estuaries. Estuaries exist between marine and freshwater system where waters of different physical, chemical and biological composition meet, combine and disperse primarily due to tidal influences. In the present thesis, the behavior of cohesive sediment in estuaries is reviewed based on the existing literature. Basic theories and recent developments are introduced to describe the formation of fluid mud from a very dilute suspension and its motion down a natural river bed with complex bathymetry. The present work contributes to the numerical simulation of complex turbulent multiphasic fluid flows encountered in estuarine channels, with the aim of the better understanding of the underlying physical processes as well as predicting realistically the cohesive sediment transport and bed morphology in such a zone. The model is based on the mass preserving method by using the so-called Raviart-Thomas finite element on the unstructured mesh in the horizontal plane. In the vertical, the computational domain is divided into number of layers at predefined heights and the method uses a conventional conforming P1 finite element scheme, with the advantage that the lowermost and uppermost layers variable height allow a faithful representation of the time-varying bed and free surface, respectively. Concerning the modeling of turbulence, the research effort focuses on the turbulence two-equation k - ε closure for the vertical parameterization of eddy viscosity. More precisely, a robust up-to-date algorithm is used for this issue. The new methodology is developed with the aim to account for more general relevant effects in the closure. The proposed model offers the capability to cope with the stiffness problem introduced by the large difference between the solid phase flow time scale and the hydrodynamic one, by using a sub-cycling strategy, whereas the splitting scheme is adopted with the aim of stability and the positivity of the relevant turbulent variables. The flexibility of the model and its performance are evaluated on several free-surface flow configurations with increasing complexity : homogeneous unsteady non-uniform flows in plane open channel flows, U-shaped (193°) curved open channel flow. Concerning the cohesive sediment transport, most of the existing models in the literature assume the analogous transport characteristics with that of the coarse sediment and adopt the relevant developed sediment transport for the latter to treat the former. Moreover, these existing models do not account for the consolidation of the mud-bed. The present research effort focused on a novel methodology based on the realistic empirical relationships, which accounts for the mutually exclusive processes for re-suspension and/or erosion and deposition of fine sediment, whereas only a limited range of bed shear stresses is allowed for simultaneous erosion and deposition to occur. Hence, on this basis, the new model investigated the bed morphology evolution by taking into account of the fluidization and/or consolidation of the fluid mud, which was handled by modeling the bed in three layers: (i) the mud-bed layer, (ii) the partially consolidated bed and (iii) the fully consolidated bed. The prediction of deposition/re-suspension using these two different methods lead to a non negligible difference in the results. Therefore, investigation of the true mechanism of erosion/deposition processes for cohesive sediments and their implementation in the numerical model is very important. This suggests that a realistic prediction must account for the fresh mud-bed re-suspension once deposited, as well as the consolidation and/or fluidization of the mud-bed deposits. Finally, the capability and improvements of the model are demonstrated, and its predicting performance is successfully evaluated by applying it to the simulation of the Po River Estuary (PRE) in Italy, which is the main source of river water discharge into the Northern Adriatic Sea. The analysis showed that the consolidation/fluidization process at the bed may have important influence on the prediction of bed morphology evolution. The three-layer approach used in this thesis is a first attempt to model these processes in detail within a numerical model.

EPFL2005

Three essays on access to knowledge

Patrick Gaulé

The first chapter of this thesis, coauthored with Annamaria Conti, seeks to add an economic contribution to the current debate on using university licensing contracts to improve access to medicines in developing countries. We build a simple model in which we have a university licensing out an academic invention to a profit-maximizing pharmaceutical company. We compare three different types of licensing contracts that the university might use to enhance access to pharmaceuticals in the South: (1) an exclusive license limited to the North; (2) an exclusive license worldwide with a price cap in the South; and (3) an exclusive license worldwide with a price cap in the South and a clause specifying that the licensee would lose its exclusivity in the South if it does not supply the Southern market. We show that in a simple model with asymmetric information on production costs the latter type of contract dominates the two others. In the second chapter, coauthored with Nicolas Maystre, we reexamine the widely held belief that free availability of scientific articles increases the number of citations they receive. Since open access is relatively more attractive to authors of higher quality papers, regressing citations on open access and other controls yields upward-biased estimates. Using an instrumental variable approach, we find no significant effect of open access. Instead, self-selection of higher quality articles into open access explains at least part of the observed open access citation advantage. The third chapter uses an evidence-based approach to assess the difficulties faced by developing country scientists in accessing the scientific literature. I compare backward citations patterns of Swiss and Indian scientists in a database of 43'150 scientific papers published by scientists from either country in 2007. Controlling for fields and quality with citing journal fixed effects, I find that Indian scientists (1) have shorter references lists (2) are more likely to cite articles from open access journals and (3) are less likely to cite articles from expensive journals. The magnitude of the effects is small which can be explained by informal file sharing practices among scientists.

EPFL2009

Three essays on access to knowledge

Patrick Gaulé

EPFL2009

Numerical modeling of cohesive sediment transport and bed morphology in estuaries

Célestin Leupi

EPFL2005