Published Research Data Research Articles

ABS-SmartComAgri: An Agent-Based Simulator of Smart Communication Protocols in Wireless Sensor Networks for Debugging in Precision Agriculture.

Smart communication protocols are becoming a key mechanism for improving communication performance in networks such as wireless sensor networks. However, the literature lacks mechanisms for simulating smart communication protocols in precision agriculture for decreasing production costs. In this context, the current work presents an agent-based simulator of smart communication protocols for efficiently managing pesticides. The simulator considers the needs of electric power, crop health, percentage of alive bugs and pesticide consumption. The current approach is illustrated with three different communication protocols respectively called (a) broadcast, (b) neighbor and (c) low-cost neighbor. The low-cost neighbor protocol obtained a statistically-significant reduction in the need of electric power over the neighbor protocol, with a very large difference according to the common interpretations about the Cohen’s d effect size. The presented simulator is called ABS-SmartComAgri and is freely distributed as open-source from a public research data repository. It ensures the reproducibility of experiments and allows other researchers to extend the current approach.

CARDIOVASCULAR AND METABOLIC IMPAIRMENT IN PATIENTS WITH OBSTRUCTIVE SLEEP APNEA

Since the moment when the obstructive nature of sleep apnea was first revealed, many new in-formation on this disease have been obtained. Now obstructive sleep apnea (OSA) recognized as an independent predictor of the development of impaired glucose tolerance (insulin resistance, fasting hyperglycaemia), type 2 diabetes mellitus (DM2), resistant arterial hypertension, cardio- vascular death. The problem of identifying and treating patients with OSA is still actual. In real clinical practice, there is a need for an integrated approach to the diagnosis and therapy of comorbid OSA patients with metabolic impairment and cardiovascular diseases. The aim of this review is to assess the clinical and pathogenesis features of metabolic impaired, carbohydrate metabolism, basic metabolism, eating behavior, body weight fluctuations in patients with ob-structive sleep apnea syndrome. Methods. In our work, we used a retrospective analysis of pub-lished clinical research data of domestic and foreign authors over the past 20 years. The review included studies with adequate design from the standpoint of «good clinical practice» (GCP) and evidence-based medicine. The conclusion . According to modern interpretation, obstructive sleep apnea is considered as an independent disease that has its pathogenic mechanisms, clinical and functional manifestations. There are several main causes of the effect of OSA on the metabolic component and the work of the cardiovascular system. Among them, intermittent hypoxemia, endothelial dysfunction, fluctuations in intrathoracic pressure, increased activity of the sympathetic nervous system, disturbance of the structure of sleep are leading. OSA is considered as a disease capable of disabling patients of working age, dramatically changing the quality of life, leading to early mortality due to cardiovascular disasters. Timely detection of clinical symptoms of OSA and the strategy of early administration of CPAP therapy significantly improve the quality of treatment and prognosis of comorbid patients.

Connecting Data Publication to the Research Workflow: A Preliminary Analysis

The data curation community has long encouraged researchers to document collected research data during active stages of the research workflow, to provide robust metadata earlier, and support research data publication and preservation. Data documentation with robust metadata is one of a number of steps in effective data publication. Data publication is the process of making digital research objects ‘FAIR’, i.e. findable, accessible, interoperable, and reusable; attributes increasingly expected by research communities, funders and society. Research data publishing workflows are the means to that end. Currently, however, much published research data remains inconsistently and inadequately documented by researchers. Documentation of data closer in time to data collection would help mitigate the high cost that repositories associate with the ingest process. More effective data publication and sharing should in principle result from early interactions between researchers and their selected data repository. This paper describes a short study undertaken by members of the Research Data Alliance (RDA) and World Data System (WDS) working group on Publishing Data Workflows. We present a collection of recent examples of data publication workflows that connect data repositories and publishing platforms with research activity ‘upstream’ of the ingest process. We re-articulate previous recommendations of the working group, to account for the varied upstream service components and platforms that support the flow of contextual and provenance information downstream. These workflows should be open and loosely coupled to support interoperability, including with preservation and publication environments. Our recommendations aim to stimulate further work on researchers’ views of data publishing and the extent to which available services and infrastructure facilitate the publication of FAIR data. We also aim to stimulate further dialogue about, and definition of, the roles and responsibilities of research data services and platform providers for the ‘FAIRness’ of research data publication workflows themselves.

Primary Research Data and Scholarly Communication

Abstract One of the questions that scholarly publishers have faced as a result of the increasing interest in research data is the relationship of journal articles to the research data behind those articles. From the 1970s forward, journals in the physical sciences published research data in the form of supplemental materials. Due to economic considerations and the sheer volume of data, this supplemental material was generally distributed in microform. In the late 1990s, some publishers began experimenting with digital distribution of research data. By the early 2000s, the volume of research data being submitted was causing problems for editors and reviewers. This tension was captured well in an editorial by Emilie Marcus in Cell in 2009. [1]

「研究データ公開」における人材と体制の問題 : 研究図書館の可能性(学術情報)

「研究データ公開」における人材と体制の問題 : 研究図書館の可能性(学術情報)

Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.

It is important for public data repositories to promote the reuse of archived data. In the growing field of omics science, however, the increasing number of submissions of high-throughput sequencing (HTSeq) data to public repositories prevents users from choosing a suitable data set from among the large number of search results. Repository users need to be able to set a threshold to reduce the number of results to obtain a suitable subset of high-quality data for reanalysis. We calculated the quality of sequencing data archived in a public data repository, the Sequence Read Archive (SRA), by using the quality control software FastQC. We obtained quality values for 1 171 313 experiments, which can be used to evaluate the suitability of data for reuse. We also visualized the data distribution in SRA by integrating the quality information and metadata of experiments and samples. We provide quality information of all of the archived sequencing data, which enable users to obtain sufficient quality sequencing data for reanalyses. The calculated quality data are available to the public in various formats. Our data also provide an example of enhancing the reuse of public data by adding metadata to published research data by a third party.

Strengthening Institutional Data Management and Promoting Data Sharing in the Social and Economic Sciences

In the German social and economic sciences there is a growing awareness of flexible data distribution and research data reuse, especially as increasing numbers of research funders recommend publishing research data as the basis for scientific insight. However, a data-sharing mentality has not yet been established in Germany attributable to researchers’ strong reservations about publishing their data. This attitude is exacerbated by the fact that, at present, there is no trusted national data sharing repository that covers the particular requirements of institutions regarding research data. This article discusses how this objective can be achieved with the project initiative SowiDataNet. The development of a community-driven data repository is a logically consistent and important step towards an attitude shift concerning data sharing in the social and economic sciences.

Survey on the number of published research data supported by Grant-in-Aid for Scientic Research

Survey on the number of published research data supported by Grant-in-Aid for Scientic Research

Evaluation of transcutaneous bilirubinometry in term neonates at Lagos State University Teaching Hospital, Ikeja, Lagos

Background: Serum bilirubin can be estimated using a technique that is real-time, noninvasive, painless, fast, and relatively inexpensive technique which is transcutaneous bilirubinometry (TcB). There is a paucity of published research data in Nigeria on TcB, and the aim of this study was to determine the correlation of TcB with total serum bilirubin (TSB) and in a group of term Nigerian neonates at Lagos State University Teaching Hospital (LASUTH) using the Konica Minolta JM-103. Materials and Methods: One hundred and fifty neonates were consecutively recruited at LASUTH, and detailed sociodemographic and clinical information was recorded with an interviewer-administered questionnaire. TcB readings were taken on the forehead, sternum, and abdomen of the calm neonate in a supine position, and blood samples for TSB estimation were drawn from a peripheral vein within 10 min of TcB measurement. Results: Eighty-nine (59.3%) neonates were male; 129 (86%) neonates were of 37–39 weeks' gestational age while 56 (37.3%) presented in the clinic after 48 h of life. Over 83% of the neonates had TcB values that were higher than TSB values, and the percentage of neonates with TSB values > 12 mg/dl was 45.2% compared with 56.8% obtained by TcB. The correlation of TcB with TSB using the Pearson's correlation was positive (r = 0.924). The mean error of TcB compared with the TSB level was independent of gender, gestational age, age at presentation, or birth weight. The measured bias by the Bland and Altman method was 0.97 mg/dl (95% confidence interval: 0.74–1.21) while imprecision was ± 2.96 mg/dl. The best correlation at the forehead was r = 0.928. Conclusion: Excellent correlation of TcB with TSB was obtained from this study, and it is envisaged that further researches will be carried out in dark skinned neonates and that the use of the JM-103 will be widely adopted as a screening tool in Nigeria.

D46 - Selection with a molecUlar PanEl foR Panitumumab EfficAcy in K-ras and n-ras wild type metastatic colorectal cancer (SUPER- PEAK)

Background: Currently we are able to exclude from anti-epidermal growth factor receptor (EGFR) treatment patients with putative refractory colorectal tumours (i.e. those harboring a RAS mutant status). However on the other hand a nonnegligible proportion of patients don't fully benefit from the use of chemotherapy in combination with anti-EGFR treatment (cetuximab or panitumumab), although in the absence of a mutation of the RAS genes. Published research data suggested that EGFR gene copy number, PIK3CA mutations, PTEN mutations or copy number variations and BRAF mutations may all represent predictive determinants for anti-EGFR therapy. However these factors were not incorporated into clinical practice particularly because prospective validation is lacking. Trial Design: The SUPER-PEAK is an ongoing, multicentre, biologically enriched, double blinded, prospectively stratified observational study. Patients receiving oxaliplatin, 5-fluorouracil and leucovorin (FOLFOX) plus panitumumab as per indication, are divided into 2 prognostic groups on the basis of their molecular profile: favourable and unfavourable (respectively high and low probability for improved RR). According to PIK3CA mutational status, BRAF mutational status and EGFR gene copy number (GCN), patients are prospectively allocated to either the favourable group (PIK3CA and BRAF wild type and EGFR GCN = 2.6) or the unfavourable group (PIK3CA mutation or BRAF mutation or EGFR GCN < 2.6). The study objective is to define a molecular panel able to identify patients more likely to benefit from the use of first-line panitumumab in combination with FOLFOX in terms of response rate (RR) as primary endpoint. Secondary endpoints include early tumour shrinkage (ETS), depth of response (DoR), median progression free-survival (PFS) and median overall survival (OS). To detect a difference in terms of RR among patients with an unfavourable profile and patients with a favourable profile assuming a probability alpha of 0.05 and beta of 0.10, the required sample size is 90 patients. (EudraCTnumber: 2015-001408-72)

Cómo analizar el impacto de los datos de investigación con métricas: modelos y servicios

This article is a summary of the different pathways to publish research data, of metrics for evaluating publishing and reuse, and of the existing services for measuring the reuse of research data. It is not yet possible to accurately analyze the metrics for open research data and this is one of the reasons why, in general, researchers do not include them in the assessment of their work. In order to further the use of these tools, it is necessary to increase the number of studies about these evaluation metrics.

Cardiac Hypertrophy: An Introduction to Molecular and Cellular Basis.

Ventricular hypertrophy is an ominous escalation of hemodynamically stressful conditions such as hypertension and valve disease. The pathophysiology of hypertrophy is complex and multifactorial, as it touches on several cellular and molecular systems. Understanding the molecular background of cardiac hypertrophy is essential in order to protect the myocardium from pathological remodeling, or slow down the destined progression to heart failure. In this review we highlight the most important molecular aspects of cardiac hypertrophic growth in light of the currently available published research data.

Lifestyle Factors that can Induce an Independent and Persistent Low-Grade Systemic Inflammatory Response: A Wholistic Approach

Subclinical inflammation was first shown in numerous chronic medical illnesses and in the early 1900s, activation of immune-inflammatory pathways was initially observed in a lifestyle-related disorder such as depression. A chronic mild inflammatory state is also a key feature of obesity as well as insulin resistance and other metabolic diseases. This particular form of immune process has given rise to the concept of “metaflammation” (metabolically triggered inflammation) because it can target vital organs and tissues that are critical for the regulation of metabolism, and ultimately disrupt systemic homoeostasis with detrimental health effects. However, accumulating evidence demonstrates a link between metaflammation and a number of lifestyle factors. Lifestyle variables such as ultra-endurance exercise, physical inactivity, extremes of sleep duration, cigarette smoking, burnout, anxiety, and depression can activate multiple immune-inflammatory pathways. Therefore, this review of the literature that bears hallmarks of a systematic review investigates and presents published research data of these lifestyle factors that can induce an independent and persistent low-grade systemic inflammatory response, within the human body, evaluated through the measurement of various biomarkers.

Stepping up Open Science Training for European Research

Open science refers to all things open in research and scholarly communication: from publications and research data to code, models and methods as well as quality evaluation based on open peer review. However, getting started with implementing open science might not be as straightforward for all stakeholders. For example, what do research funders expect in terms of open access to publications and/or research data? Where and how to publish research data? How to ensure that research results are reproducible? These are all legitimate questions and, in particular, early career researchers may benefit from additional guidance and training. In this paper we review the activities of the European-funded FOSTER project which organized and supported a wide range of targeted trainings for open science, based on face-to-face events and on a growing suite of e-learning courses. This article reviews the approach and experiences gained from the first two years of the project.

A Friendly Relationship between Endophytic Fungi and Medicinal Plants: A Systematic Review.

Endophytic fungi or endophytes exist widely inside the healthy tissues of living plants, and are important components of plant micro-ecosystems. Over the long period of evolution, some co-existing endophytes and their host plants have established a special relationship with one and another, which can significantly influence the formation of metabolic products in plants, then affect quality and quantity of crude drugs derived from medicinal plants. This paper will focus on the increasing knowledge of relationships between endophytic fungi and medicinal plants through reviewing of published research data obtained from the last 30 years. The analytical results indicate that the distribution and population structure of endophytes can be considerably affected by factors, such as the genetic background, age, and environmental conditions of their hosts. On the other hand, the endophytic fungi can also confer profound impacts on their host plants by enhancing their growth, increasing their fitness, strengthening their tolerances to abiotic and biotic stresses, and promoting their accumulation of secondary metabolites. All the changes are very important for the production of bioactive components in their hosts. Hence, it is essential to understand such relationships between endophytic fungi and their host medicinal plants. Such knowledge can be well exploited and applied for the production of better and more drugs from medicinal plants.

Advancing research data publishing practices for the social sciences: from archive activity to empowering researchers

Sharing and publishing social science research data have a long history in the UK, through long-standing agreements with government agencies for sharing survey data and the data policy, infrastructure, and data services supported by the Economic and Social Research Council. The UK Data Service and its predecessors developed data management, documentation, and publishing procedures and protocols that stand today as robust templates for data publishing. As the ESRC research data policy requires grant holders to submit their research data to the UK Data Service after a grant ends, setting standards and promoting them has been essential in raising the quality of the resulting research data being published. In the past, received data were all processed, documented, and published for reuse in-house. Recent investments have focused on guiding and training researchers in good data management practices and skills for creating shareable data, as well as a self-publishing repository system, ReShare. ReShare also receives data sets described in published data papers and achieves scientific quality assurance through peer review of submitted data sets before publication. Social science data are reused for research, to inform policy, in teaching and for methods learning. Over a 10 years period, responsive developments in system workflows, access control options, persistent identifiers, templates, and checks, together with targeted guidance for researchers, have helped raise the standard of self-publishing social science data. Lessons learned and developments in shifting publishing social science data from an archivist responsibility to a researcher process are showcased, as inspiration for institutions setting up a data repository.

A numerical simulation method for the flow around floating bodies in regular waves using a three-dimensional rectilinear grid system

The motion of a floating body and the free surface flow are the most important design considerations for ships and offshore platforms. In the present research, a numerical method is developed to simulate the motion of a floating body and the free surface using a fixed rectilinear grid system. The governing equations are the continuity equation and Navier–Stokes equations. The boundary of a moving body is defined by the interaction points of the body surface and the centerline of a grid. To simulate the free surface the Modified Marker-Density method is implemented. Ships advancing in regular waves, the interaction of waves by a fixed circular cylinder array and the response amplitude operators of an offshore platform are simulated and the results are compared with published research data to check the applicability. The numerical method developed in this research gives results good enough for application to the initial design stage.

Are Scientific Data Repositories Coping with Research Data Publishing?

Research data publishing is intended as the release of research data to make it possible for practitioners to (re)use them according to “open science” dynamics. There are three main actors called to deal with research data publishing practices: researchers, publishers, and data repositories. This study analyses the solutions offered by generalist scientific data repositories, i.e., repositories supporting the deposition of any type of research data. These repositories cannot make any assumption on the application domain. They are actually called to face with the almost open ended typologies of data used in science. The current practices promoted by such repositories are analysed with respect to eight key aspects of data publishing, i.e., dataset formatting, documentation, licensing, publication costs, validation, availability, discovery and access, and citation. From this analysis it emerges that these repositories implement well consolidated practices and pragmatic solutions for literature repositories. These practices and solutions can not totally meet the needs of management and use of datasets resources, especially in a context where rapid technological changes continuously open new exploitation prospects.

Correlation between impact factor and public availability of published research data in Information Science and Library Science journals

Scientists continuously generate research data but only a few of them are published. If these data were accessible and reusable, researchers could examine them and generate new knowledge. Our purpose is to determine whether there is a relationship between the impact factor and the policies concerning open availability of raw research data in journals of Information Science and Library Science (ISLS) subject category from the Web of Science database. We reviewed the policies related to public availability of papers and data sharing in the 85 journals included in the ISLS category of the Journal Citation Reports in 2012. The relationship between public availability of published data and impact factor of journals is analysed through different statistical tests. The variable statement of complementary material was accepted in 50 % of the journals; 65 % of the journals support reuse; 67 % of the journals specified in thematic or institutional repositories; the of the manuscript in a website was accepted in 69 % of the journals. We have found a 50 % of journals that include the possibility to deposit data as supplementary material, and more than 60 % accept reuse, storage in repositories and publication in websites. There is a clear positive relationship between being a top journal in impact factor ranking of JCR and having an open policy.

Making sense of journal research data policies

This article gives an overview of the findings from the first phase of the Jisc Journal Research Data Policy Registry pilot (JRDPR), which is currently under way. The project continues from the initial study, ‘Journal of Research Data policy bank’ (JoRD), carried out by Nottingham University’s Centre for Research Communication from 2012 to 2014. The project undertook an analysis of 250 journal research data policies to assess the feasibility of developing a policy registry to assist researchers and support staff to comply with research data publication requirements. The evidence shows that the current research data policy ecosystem is in critical need of standardization and harmonization if such services are to be built and implemented. To this end, the article proposes the next steps for the project with the objective of ultimately moving towards a modern research infrastructure based on machine-readable policies that support a more open scholarly communications environment.