Registered reports: an early example and analysis

© 2019 Wiseman et al.The recent ‘replication crisis’ in psychology has focused attention on ways of increasing methodological rigor within the behavioral sciences. Part of this work has involved promoting ‘Registered Reports’, wherein journals peer review papers prior to data collection and publication. Although this approach is usually seen as a relatively recent development, we note that a prototype of this publishing model was initiated in the mid-1970s by parapsychologist Martin Johnson in the European Journal of Parapsychology (EJP). A retrospective and observational comparison of Registered and non-Registered Reports published in the EJP during a seventeen-year period provides circumstantial evidence to suggest that the approach helped to reduce questionable research practices. This paper aims both to bring Johnson’s pioneering work to a wider audience, and to investigate the positive role that Registered Reports may play in helping to promote higher methodological and statistical standards.Peer reviewe

Samples and data accessibility in research biobanks. An explorative survey

Biobanks, which contain human biological samples and/or data, provide a crucial contribution to the progress of biomedical research. However, the effective and efficient use of biobank resources depends on their accessibility. In fact, making bio-resources promptly accessible to everybody may increase the benefits for society. Furthermore, optimizing their use and ensuring their quality will promote scientific creativity and, in general, contribute to the progress of bio-medical research. Although this has become a rather common belief, several laboratories are still secretive and continue to withhold samples and data. In this study, we conducted a questionnairebased survey in order to investigate sample and data accessibility in research biobanks operating all over the world. The survey involved a total of 46 biobanks. Most of them gave permission to access their samples (95.7%) and data (85.4%), but free and unconditioned accessibility seemed not to be common practice. The analysis of the guidelines regarding the accessibility to resources of the biobanks that responded to the survey highlights three issues: (i) the request for applicants to explain what they would like to do with the resources requested; (ii) the role of funding, public or private, in the establishment of fruitful collaborations between biobanks and research labs; (iii) the request of co-authorship in order to give access to their data. These results suggest that economic and academic aspects are involved in determining the extent of sample and data sharing stored in biobanks. As a second step of this study, we investigated the reasons behind the high diversity of requirements to access biobank resources. The analysis of informative answers suggested that the different modalities of resource accessibility seem to be largely influenced by both social context and legislation of the countries where the biobanks operate

Investigating the potential impact of 1.5, 2 and 3 °C global warming levels on crop suitability and planting season over West Africa

West African rainfed agriculture is highly vulnerable to climate variability and change. Global warming is projected to result in higher regional warming and have a strong impact on agriculture. This study specifically examines the impact of global warming levels (GWLs) of 1.5°, 2° and 3 °C relative to 1971–2000 on crop suitability over West Africa. We used 10 Coupled Model Intercomparison Project Phase5 Global Climate Models (CMIP5 GCMs) downscaled by Coordinated Regional Downscaling Experiment (CORDEX) Rossby Centre’s regional Atmospheric model version 4, RCA4, to drive Ecocrop, a crop suitability model, for pearl millet, cassava, groundnut, cowpea, maize and plantain. The results show Ecocrop simulated crop suitability spatial representation with higher suitability, observed to the south of latitude 14°N and lower suitability to its north for 1971–2000 for all crops except for plantain (12°N). The model also simulates the best three planting months within the growing season from September-August over the past climate. Projected changes in crop suitability under the three GWLs 1.5–3.0 °C suggest a spatial suitability expansion for legume and cereal crops, notably in the central southern Sahel zone; root and tuber and plantain in the central Guinea-Savanna zone. In contrast, projected decreases in the crop suitability index value are predicted to the south of 14°N for cereals, root and tuber crops; nevertheless, the areas remain suitable for the crops. A delay of between 1-3 months is projected over the region during the planting month under the three GWLs for legumes, pearl millet and plantain. A two month delay in planting is projected in the south, notably over the Guinea and central Savanna zone with earlier planting of about three months in the Savanna-Sahel zones. The effect of GWL2.0 and GWL3.0 warming in comparison to GWL1.5 °C are more dramatic on cereals and root and tuber crops, especially cassava. All the projected changes in simulated crop suitability in response to climatic variables are statistically significant at 99% confidence level. There is also an increasing trend in the projected crop suitability change across the three warming except for cowpea. This study has implications for improving the resilience of crop production to climate changes, and more broadly, to food security in West Africa

Evidence in Practice – A Pilot Study Leveraging Companion Animal and Equine Health Data from Primary Care Veterinary Clinics in New Zealand

Veterinary practitioners have extensive knowledge of animal health from their day-to-day observations of clinical patients. There have been several recent initiatives to capture these data from electronic medical records for use in national surveillance systems and clinical research. In response, an approach to surveillance has been evolving that leverages existing computerized veterinary practice management systems to capture animal health data recorded by veterinarians. Work in the United Kingdom within the VetCompass program utilizes routinely recorded clinical data with the addition of further standardized fields. The current study describes a prototype system that was developed based on this approach. In a 4-week pilot study in New Zealand, clinical data on presentation reasons and diagnoses from a total of 344 patient consults were extracted from two veterinary clinics into a dedicated database and analyzed at the population level. New Zealand companion animal and equine veterinary practitioners were engaged to test the feasibility of this national practice-based health information and data system. Strategies to ensure continued engagement and submission of quality data by participating veterinarians were identified, as were important considerations for transitioning the pilot program to a sustainable large-scale and multi-species surveillance system that has the capacity to securely manage big data. The results further emphasized the need for a high degree of usability and smart interface design to make such a system work effectively in practice. The geospatial integration of data from multiple clinical practices into a common operating picture can be used to establish the baseline incidence of disease in New Zealand companion animal and equine populations, detect unusual trends that may indicate an emerging disease threat or welfare issue, improve the management of endemic and exotic infectious diseases, and support research activities. This pilot project is an important step toward developing a national surveillance system for companion animals and equines that moves beyond emerging infectious disease detection to provide important animal health information that can be used by a wide range of stakeholder groups, including participating veterinary practices

Controlled access under review : improving the governance of genomic data access

In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention

Forma mentis networks map how nursing and engineering students enhance their mindsets about innovation and health during professional growth

Reconstructing a "forma mentis", a mindset, and its changes, means capturing how individuals perceive topics, trends and experiences over time. To this aim we use forma mentis networks (FMNs), which enable direct, microscopic access to how individuals conceptually perceive knowledge and sentiment around a topic, providing richer contextual information than machine learning. FMNs build cognitive representations of stances through psycholinguistic tools like conceptual associations from semantic memory (free associations, i.e., one concept eliciting another) and affect norms (valence, i.e., how attractive a concept is). We test FMNs by investigating how Norwegian nursing and engineering students perceived innovation and health before and after a 2-month research project in e-health. We built and analysed FMNs by six individuals, based on 75 cues about innovation and health, and leading to 1,000 associations between 730 concepts. We repeated this procedure before and after the project. When investigating changes over time, individual FMNs highlighted drastic improvements in all students' stances towards "teamwork", "collaboration", "engineering" and "future", indicating the acquisition and strengthening of a positive belief about innovation. Nursing students improved their perception of "robots" and "technology" and related them to the future of nursing. A group-level analysis related these changes to the emergence, during the project, of conceptual associations about openness towards multidisciplinary collaboration, and a positive, leadershiporiented group dynamics. The whole group identified "mathematics" and "coding" as highly relevant concepts after the project. When investigating persistent associations, characterising the core of students' mindsets, network distance entropy and closeness identified as pivotal in the students' mindsets concepts related to "personal well-being", "professional growth" and "teamwork". This result aligns with and extends previous studies reporting the relevance of teamwork and personal well-being for Norwegian healthcare professionals, also within the novel e-health sector. Our analysis indicates that forma mentis networks are powerful proxies for detecting individual- and grouplevel mindset changes due to professional growth. FMNs open new scenarios for datainformed, multidisciplinary interventions aimed at professional training in innovation.publishedVersio

Lean requirements traceability automation enabled by model-driven engineering

Background: The benefits of requirements traceability, such as improvements in software product and process quality, early testing, and software maintenance, are widely described in the literature. Requirements traceability is a critical, widely accepted practice. However, very often it is not applied for fear of the additional costs associated with manual efforts or the use of additional tools. Methods: This article presents a “low-cost” mechanism for automating requirements traceability based on the model-driven paradigm and formalized by a metamodel for the creation and monitoring of traces and an integration process for traceability management. This approach can also be useful for information fusion in industry insofar that it facilitates data traceability. Results: This article extends an existing model-driven development methodology to incorporate traceability as part of its development tool. The tool has been used successfully by several companies in real software development projects, helping developers to manage ongoing changes in functional requirements. One of those projects is cited as an example in the paper. The authors’ current work leads them to conclude that a model-driven engineering approach, traditionally used only for the automatic generation of code in a software development process, can also be used to successfully automate and integrate traceability management without additional costs. The systematic evaluation of traceability management in industrial projects constitutes a promising area for future work.Junta de Andalucía AT17-5904-USEJunta de Andalucía US-1251532Ministerio de Ciencia, Innovación y Universidades PID2019-105455GB-C3

Enforcing public data archiving policies in academic publishing: A study of ecology journals

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.Comment: 35 pages, 1 figure, 1 tabl

Evidence based pathways to intervention for children with language disorders

Background: Paediatric SLT roles often involve planning individualised intervention for specific children (provided directly by SLTs or indirectly through non-SLTs), working collaboratively with families and education staff and providing advice and training. A tiered approach to service delivery is currently recommended, whereby services become increasingly specialised and individualised for children with greater needs.  Aims: To examine 1) evidence of intervention effectiveness for children with language disorders at different tiers and 2) evidence regarding SLT roles; and to propose an evidence-based model of SLT service delivery.  Methods: Controlled, peer-reviewed studies, meta-analyses and systematic reviews of interventions for children with language disorders are reviewed and their outcomes discussed, alongside the differing roles SLTs play in these interventions. We indicate where gaps in the evidence base exist and present a possible model of service delivery consistent with current evidence, and a flowchart to aid clinical decision making.  Main Contribution: The service delivery model presented resembles the tiered model commonly used in education services, but divides individualised (Tier 3) services into Tier3A: indirect intervention delivered by non-SLTs, and Tier 3B: direct intervention by an SLT. We report the evidence for intervention effectiveness and which children might best be served by each tier, the role SLTs could take within each, and the evidence of effectiveness of these roles. Regarding universal interventions provided to all children (Tier 1) and those targeted at children with language weaknesses (Tier 2), there is growing evidence that approaches led by education services can be effective when staff are highly trained and well-supported. There is currently limited evidence regarding additional benefit of SLT-specific roles at Tiers 1 and 2. With regard to individualised intervention (Tier 3): children with complex or pervasive language disorders progress significantly following direct individualised intervention (Tier 3B), whereas children with milder or less pervasive difficulties can make progress when intervention is managed by an SLT, but delivered indirectly by others (Tier 3A), provided they are well-trained, -supported and -monitored.  Conclusions: SLTs have a contribution to make at all tiers, but where prioritisation for clinical services is a necessity, we need to establish the benefits and cost-effectiveness of each contribution. Good evidence exists for SLTs delivering direct individualised intervention, and we should ensure that this is available to those children with pervasive and/or complex language impairments. In cases where service models are being provided which lack evidence, we strongly recommend that SLTs investigate the effectiveness of their approaches