Citation and peer review of data: moving towards formal data publication

This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax

Predictors of anxiety after stroke: a systematic review of observational studies

Background: Anxiety disorders or symptoms are relatively common following stroke. A better understanding of the predictors of anxiety in stroke patients may improve the management of these disorders. The current review was conducted to determine the predictors of anxiety following stroke. Methods: Relevant articles concerning population, hospital or rehabilitation-based studies were identified by searching 10 electronic databases up to May 2014. Methodological quality appraisal, including the validity of prognostic models and data extraction were conducted by three reviewers. Results: A total of 18 studies were identified. Data from three population-based studies including 8130 patients, 8 hospital-based studies including 1199 patients, and 7 rehabilitation-based studies including 1103 patients was evaluated. Pre-stroke depression, stroke severity, early anxiety and dementia or cognitive impairment following stroke were the main predictors of post stroke anxiety. Older age, physical disability or impairment, and use of antidepressant drugs were not associated with presence of anxiety. Limitations of studies included wide variation in screening tools and cut-off scores, variability in the time frame of screening for anxiety, use of extensive exclusion criteria and questionable statistical internal and external validity of the models. Conclusions: Lack of methodological and statistical rigour affects the validity of proposed models to predict anxiety after stroke. Future research should focus on testing proposed models on both internal and external samples to ultimately inform future clinical practice

The Role of Grain Boundaries under Long-Time Radiation

Materials containing a high proportion of grain boundaries offer significant potential for the development of radiation-resistent structural materials. However, a proper understanding of the connection between the radiation-induced microstructural behaviour of grain boundary and its impact at long natural time scales is still missing. In this letter, point defect absorption at interfaces is summarised by a jump Robin-type condition at a coarse-grained level, wherein the role of interface microstructure is effectively taken into account. Then a concise formula linking the sink strength of a polycrystalline aggregate with its grain size is introduced, and is well compared with experimental observation. Based on the derived model, a coarse-grained formulation incorporating the coupled evolution of grain boundaries and point defects is proposed, so as to underpin the study of long-time morphological evolution of grains induced by irradiation. Our simulation results suggest that the presence of point defect sources within a grain further accelerates its shrinking process, and radiation tends to trigger the extension of twin boundary sections

Validity of ICD-9 and ICD-10 codes used to identify acute liver injury: a study in three European data sources

This is the peer reviewed version of the following article: Forns, J. [et al.]. Validity of ICD-9 and ICD-10 codes used to identify acute liver injury: a study in three European data sources. "Pharmacoepidemiology and drug safety", 6 Juny 2019, vol. 28, núm. 7, p. 965-975, which has been published in final form at 10.1002/pds.4803. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."Purpose Validating cases of acute liver injury (ALI) in health care data sources is challenging. Previous validation studies reported low positive predictive values (PPVs). Methods Case validation was undertaken in a study conducted from 2009 to 2014 assessing the risk of ALI in antidepressants users in databases in Spain (EpiChron and SIDIAP) and the Danish National Health Registers. Three ALI definitions were evaluated: primary (specific hospital discharge codes), secondary (specific and nonspecific hospital discharge codes), and tertiary (specific and nonspecific hospital and outpatient codes). The validation included review of patient profiles (EpiChron and SIDIAP) and of clinical data from medical records (EpiChron and Denmark). ALI cases were confirmed when liver enzyme values met a definition by an international working group. Results Overall PPVs (95% CIs) for the study ALI definitions were, for the primary ALI definition, 84% (60%-97%) (EpiChron), 60% (26%-88%) (SIDIAP), and 74% (60%-85%) (Denmark); for the secondary ALI definition, 65% (45%-81%) (EpiChron), 40% (19%-64%) (SIDIAP), and 70% (64%-77%) (Denmark); and for the tertiary ALI definition, 25% (18%-34%) (EpiChron), 8% (7%-9%) (SIDIAP), and 47% (42%-52%) (Denmark). The overall PPVs were higher for specific than for nonspecific codes and for hospital discharge than for outpatient codes. The nonspecific code “unspecified jaundice” had high PPVs in Denmark. Conclusions PPVs obtained apply to patients using antidepressants without preexisting liver disease or ALI risk factors. To maximize validity, studies on ALI should prioritize hospital specific discharge codes and should include hospital codes for unspecified jaundice. Case validation is required when ALI outpatient cases are considered.Peer ReviewedPostprint (author's final draft

STANDPOINTS ABOUT THE MANAGEMENT OF PRODUCTS DESIGN

In this paper the engineering design process is defined and the Product Design Specification is detailed. Subjects covered include form design, design for manufacture and assembly, materials and process for powder products selection. In general the simplest solution is the best and all professional engineers seek elegant and simple solutions. Design is not solely the achieving of technical solutions but also creating useful products which satisfy and appeal to their users. So along with the engineering science knowledge used the importance of communication, teamwork an project management cannot be underestimated.products, form design, project management

Consequences to flood management of using different probability distributions to estimate extreme rainfall

The design of flood defences, such as pumping stations, takes into consideration the predicted return periods of extreme precipitation depths. Most commonly these are estimated by fitting the Generalised Extreme Value (GEV) or the Generalised Pareto (GP) probability distributions to the annual maxima series or to the partial duration series. In this paper, annual maxima series of precipitation depths obtained from daily rainfall data measured at three selected stations in southeast UK are analysed using a range of probability distributions. These analyses demonstrate that GEV or GP distributions do not always provide the best fit to the data, and that extreme rainfall estimates for long return periods (e.g. 1 in 100 years) can differ by more than 40% depending on the distribution model used. Since a large number of properties in the UK and elsewhere currently benefit from flood defences designed using the GEV or GP probability distributions, the results from this study question whether the level of protection they offer are appropriate in locations where data demonstrate clearly that alternative probability distributions may have a better fit to the local rainfall data. This work: (a) raises awareness of the limitations of common practices in extreme rainfall analysis; (b) suggests a simple way forward to incorporate uncertainties that is easily applicable to local rainfall data worldwide; and thus (c) contributes to improve flood risk management. © 2012 Elsevier Ltd

Self-synchronization Phenomena in the Lugiato-Lefever Equation

The damped driven nonlinear Schr\"odinger equation (NLSE) has been used to understand a range of physical phenomena in diverse systems. Studying this equation in the context of optical hyper-parametric oscillators in anomalous-dispersion dissipative cavities, where NLSE is usually referred to as the Lugiato-Lefever equation (LLE), we are led to a new, reduced nonlinear oscillator model which uncovers the essence of the spontaneous creation of sharply peaked pulses in optical resonators. We identify attracting solutions for this model which correspond to stable cavity solitons and Turing patterns, and study their degree of stability. The reduced model embodies the fundamental connection between mode synchronization and spatiotemporal pattern formation, and represents a novel class of self-synchronization processes in which coupling between nonlinear oscillators is governed by energy and momentum conservation.Comment: This manuscript is published in Physical Review A. Copyright 2017 by the American Physical Society. arXiv admin note: text overlap with arXiv:1602.0852

PhOBF1, a petunia ocs element binding factor, plays an important role in antiviral RNA silencing.

Virus-induced gene silencing (VIGS) is a common reverse genetics strategy for characterizing the function of genes in plants. The detailed mechanism governing RNA silencing efficiency triggered by viruses is largely unclear. Here, we reveal that a petunia (Petunia hybrida) ocs element binding factor, PhOBF1, one of the basic leucine zipper (bZIP) transcription factors, was up-regulated by Tobacco rattle virus (TRV) infection. Simultaneous silencing of PhOBF1 and a reporter gene, phytoene desaturase (PDS) or chalcone synthase (CHS), by TRV-based VIGS led to a failure of the development of leaf photobleaching or the white-corollas phenotype. PhOBF1 silencing caused down-regulation of RNA silencing-related genes, including RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonautes (AGOs). After inoculation with the TRV-PhPDS, PhOBF1-RNAi lines exhibited a substantially impaired PDS silencing efficiency, whereas overexpression of PhOBF1 resulted in a recovery of the silencing phenotype (photobleaching) in systemic leaves. A compromised resistance to TRV and Tobacco mosaic virus was found in PhOBF1-RNAi lines, while PhOBF1-overexpressing lines displayed an enhanced resistance to their infections. Compared with wild-type plants, PhOBF1-silenced plants accumulated lower levels of free salicylic acid (SA), salicylic acid glucoside, and phenylalanine, contrarily to higher levels of those in plants overexpressing PhOBF1. Furthermore, transcripts of a number of genes associated with the shikimate and phenylpropanoid pathways were decreased or increased in PhOBF1-RNAi or PhOBF1-overexpressing lines, respectively. Taken together, the data suggest that PhOBF1 regulates TRV-induced RNA silencing efficiency through modulation of RDRs, DCLs, and AGOs mediated by the SA biosynthesis pathway

Systematic review of transition models for young people with long-term conditions: A report for NHS Diabetes.

Aims For many young people with Type 1 diabetes, transition from paediatric to adult care can result in a marked deterioration in glycaemic control. A systematic review assessed the effectiveness of transition models, or components of models, for managing the transition process in young people with long-term conditions, including Type 1 diabetes. This involved identifying (i) the main barriers and facilitators in implementing a successful transition programme, and (ii) the key issues for young people with long-term conditions and professionals involved in the transition process. Methods The following databases were searched from inception to August 2012: MEDLINE, EMBASE, PsychINFO, CINAHL, ASSIA, Social Services Abstracts, Academic Search Complete, Social Science Citation Index, Cochrane and Campbell Libraries. Selected studies included young people aged 11 to 25 diagnosed with long-term conditions who were in transition from paediatric to adult secondary health care services. Results 16 systematic reviews and 13 primary studies were included from 9992 records retrieved. No single transition model was uniquely effective. The most successful transitions centred around: young person-focused; age and developmentally appropriate content and delivery; self-management education; family participation; paediatric and adult collaboration; designated transition clinics; transition co-ordinator; young person’s portfolio; specific professionals training; multidisciplinary approach; structured process embedded in service delivery. There were no distinctive characteristics of condition-specific Type 1 diabetes services. Conclusion This important and timely review summarises the key factors that need to be considered for the development of transition programmes for young people with long-term conditions, including those with Type 1 diabetes