scholarly journals FAIRifying Clinical Studies Metadata: A Registry for the Biomedical Research

2021 ◽  
Author(s):  
Vittorio Meloni ◽  
Alessandro Sulis ◽  
Cecilia Mascia ◽  
Francesca Frexia
Keyword(s):  
Clinical Trials ◽  
User Interface ◽  
Clinical Studies ◽  
Source Code ◽  
Use Case ◽  
Semantic Model ◽  
Current Implementation ◽  
Fair Principles ◽  
Rest Api ◽  
Clinical Domain

The data produced during a research project are too often collected for the sole purpose of the study, therefore hindering profitable reuse in similar contexts. The growing need to counteract this trend has recently led to the formalization of the FAIR principles that aim to make (meta)data Findable, Accessible, Interoperable and Reusable, for humans and machines. Since their introduction, efforts are ongoing to encourage FAIR principles adoption and to implement solutions based on them. This paper reports on the FAIR-compliant registry we developed to collect and serve metadata describing clinical trials. The design of the registry is based on the FAIR Data Point (FDP) specifications, the state-of-the-art reference for FAIRified metadata sharing. To map the metadata relevant to our use case, we have extended the DCAT-based semantic model of the FDP adopting well-established ontologies in the biomedical and clinical domain, like the Semanticscience Integrated Ontology (SIO). Current implementation is based on the Molgenis software and provides both a user interface and a REST API for metadata discovering. At present the registry is being loaded with the metadata of the 18 clinical studies included in the ‘I FAIR Program’, a project finalised to the dissemination of FAIR best practices among the clinical researchers in Sardinia (Italy). After a testing phase, the registry will be publicly available, while the new model and the source code will be released open source.

scholarly journals Towards FAIR protocols and workflows: the OpenPREDICT use case

2020 ◽  
Vol 6 ◽  
pp. e281
Author(s):  
Remzi Celebi ◽  
Joao Rebelo Moreira ◽  
Ahmed A. Hassan ◽  
Sandeep Ayyar ◽  
Lars Ridder ◽  
...  
Keyword(s):  
Drug Repurposing ◽  
Research Data ◽  
Use Case ◽  
Semantic Technologies ◽  
Semantic Model ◽  
Execution Traces ◽  
Fair Principles ◽  
Digital Objects ◽  
High Degree ◽  
Highly Cited

It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR principles to scientific workflows as well as the involved data. We apply and evaluate our approach on the case of the PREDICT workflow, a highly cited drug repurposing workflow. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. We propose a semantic model to address these specific requirements and was evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

scholarly journals Emerging Pharmacological Treatments for Cerebral Edema: Evidence from Clinical Studies

2020 ◽  
Vol 60 (1) ◽  
pp. 291-309 ◽  
Author(s):  
Jesse A. Stokum ◽  
Volodymyr Gerzanich ◽  
Kevin N. Sheth ◽  
W. Taylor Kimberly ◽  
J. Marc Simard
Keyword(s):  
Central Nervous System ◽  
Clinical Trials ◽  
Nervous System ◽  
Cerebral Edema ◽  
Clinical Studies ◽  
Central Nervous System Disease ◽  
Ancient Egypt ◽  
Nervous System Disease ◽  
Pharmacological Treatments ◽  
System Disease

Cerebral edema, a common and often fatal companion to most forms of acute central nervous system disease, has been recognized since the time of ancient Egypt. Unfortunately, our therapeutic armamentarium remains limited, in part due to historic limitations in our understanding of cerebral edema pathophysiology. Recent advancements have led to a number of clinical trials for novel therapeutics that could fundamentally alter the treatment of cerebral edema. In this review, we discuss these agents, their targets, and the data supporting their use, with a focus on agents that have progressed to clinical trials.

scholarly journals The case for introducing pre-registered confirmatory pharmacological pre-clinical studies

2018 ◽  
Vol 38 (5) ◽  
pp. 749-754 ◽  
Author(s):  
Olivia Kiwanuka ◽  
Bo-Michael Bellander ◽  
Anders Hånell
Keyword(s):  
Clinical Trial ◽  
Traumatic Brain Injury ◽  
Clinical Trials ◽  
Brain Injury ◽  
Network Analysis ◽  
Clinical Studies ◽  
Phase Iii ◽  
Phase Iii Clinical Trial ◽  
Phase Iii Clinical Trials ◽  
Experimental Drugs

When evaluating the design of pre-clinical studies in the field of traumatic brain injury, we found substantial differences compared to phase III clinical trials, which in part may explain the difficulties in translating promising experimental drugs into approved treatments. By using network analysis, we also found cases where a large proportion of the studies evaluating a pre-clinical treatment was performed by inter-related researchers, which is potentially problematic. Subjecting all pre-clinical trials to the rigor of a phase III clinical trial is, however, likely not practically achievable. Instead, we repeat the call for a distinction to be made between exploratory and confirmatory pre-clinical studies.

scholarly journals High-cited favorable studies for COVID-19 treatments ineffective in large trials

2022 ◽  
Author(s):  
John P.A. Ioannidis
Keyword(s):  
Clinical Trials ◽  
Randomized Controlled Trials ◽  
Clinical Studies ◽  
Observational Studies ◽  
Randomized Trials ◽  
Controlled Trials ◽  
Randomized Controlled ◽  
Wide Dissemination ◽  
Highly Cited Articles ◽  
Highly Cited

Importance. COVID-19 has resulted in massive production, publication and wide dissemination of clinical studies trying to identify effective treatments. However, several widely touted treatments failed to show effectiveness in large well-done randomized controlled trials (RCTs). Objective. To evaluate for COVID-19 treatments that showed no benefits in subsequent large RCTs how many of their most-cited clinical studies had declared favorable results for these interventions. Methods. Scopus (last update December 23, 2021) identified articles on lopinavir-ritonavir, hydroxycholoroquine/azithromycin, remdesivir, convalescent plasma, colchicine or interferon (index interventions) that represented clinical trials and that had received >150 citations. Their conclusions were assessed and correlated with study design features. The ten most recent citations for the most-cited article on each index intervention were examined on whether they were critical to the highly-cited study. Altmetric scores were also obtained. Findings. 40 articles of clinical studies on these index interventions had received >150 citations (7 exceeded 1,000 citations). 20/40 (50%) had favorable conclusions and 4 were equivocal. Highly-cited articles with favorable conclusions were rarely RCTs while those without favorable conclusions were mostly RCTs (3/20 vs 15/20, p=0.0003). Only 1 RCT with favorable conclusions had sample size >160. Citation counts correlated strongly with Altmetric scores, in particular news items. Only 9 (15%) of 60 recent citations to the most highly-cited studies with favorable or equivocal conclusions were critical to the highly-cited study. Conclusion. Many clinical studies with favorable conclusions for largely ineffective COVID-19 treatments are uncritically heavily cited and disseminated. Early observational studies and small randomized trials may cause spurious claims of effectiveness that get perpetuated.

scholarly journals Same but Different: Consistently Developing and Evolving Software Architecture Models and Their Implementation

2020 ◽  
pp. 87-112
Author(s):  
Marco Konersmann ◽  
Michael Goedicke
Keyword(s):  
Performance Evaluation ◽  
Software Architecture ◽  
Software Quality ◽  
Source Code ◽  
Use Case ◽  
Program Code ◽  
Separate Representation ◽  
Main Driver ◽  
Integrated Architecture ◽  
Architecture Specification

AbstractAs software architecture is a main driver for the software quality, source code is often accompanied by software architecture specifications. When the implementation is changed, the architecture specification is often not updated along with the code, which introduces inconsistencies between these artifacts. Such inconsistencies imply a risk of misunderstandings and errors during the development, maintenance, and evolution, causing serious degradation over the lifetime of the system. In this chapter we present the Explicitly Integrated Architecture approach and its tool Codeling, which remove the necessity for a separate representation of software architecture by integrating software architecture information with the program code. By using our approach, the specification can be extracted from the source code and changes in the specification can be propagated to the code. The integration of architecture information with the code leaves no room for inconsistencies between the artifacts and creates links between artifacts. We evaluate the approach and tool in a use case with real software in development and with a benchmark software, accompanied by a performance evaluation.

scholarly journals Comparative analysis of view technologies for the Spring application

2020 ◽  
Vol 14 ◽  
pp. 78-81
Author(s):  
Vadym Borys ◽  
Roman Slezenko ◽  
Beata Pańczyk
Keyword(s):  
Comparative Analysis ◽  
User Interface ◽  
Memory Performance ◽  
Performance Tests ◽  
Test Results ◽  
Rest Api

The goal of the article is to choose the most efficient user interface creation tools possible for Spring. The study compares 4 selected view technologies: JSP,  Thymeleaf, Wicket and Angular. Time and memory performance tests were carried out using Rest API in Spring. Test results allowed to identify the best solutions.

A comprehensive review of post-market clinical studies performed in adults with an Asian probiotic formulation

2010 ◽  
Vol 1 (1) ◽  
pp. 93-106 ◽  
Author(s):  
T. Tompkins ◽  
X. Xu ◽  
J. Ahmarani
Keyword(s):  
Clinical Trials ◽  
Clinical Studies ◽  
Clinical Findings ◽  
Chronic Diarrhoea ◽  
Helicobacter Pylori Eradication ◽  
Asian Populations ◽  
Post Market ◽  
Improve Compliance ◽  
Irritable Bowel ◽  
Study Designs

Probiotics as dietary supplements have been readily accepted by Asian populations. Use of certain probiotic preparations is widespread and the number of clinical trials undertaken with such products is unparalleled in western scientific literature. One such preparation, containing a combination of Enterococcus faecium R0026 and Bacillus subtilis R0179, has 23 publications on post-market clinical studies involving over 1,800 adults. The majority of these publications are printed in Chinese and Korean journals. This review examines the clinical findings with this probiotic combination. As mono-therapy, it has been used to overcome symptoms associated with chronic diarrhoea and irritable bowel syndrome. It has been used as co-adjuvant therapy with sulfasalazine and mesalazine to improve remission times in mild to moderate Ulcerative Colitis and to improve compliance with conventional triple therapy for Helicobacter pylori eradication. While the much of the data is preliminary and the study designs require refinement, the contribution of these trials should not be ignored. The information derived in this review will provide practitioners with practical information on appropriate applications for probiotic supplements, expected outcomes, dosing regimes, safety and reported adverse events. Furthermore, identification of problems in these trials should help researchers design better clinical trials when investigating probiotic products.

Lactulose in the Management of Constipation: A Current Review

1992 ◽  
Vol 26 (10) ◽  
pp. 1277-1282 ◽  
Author(s):  
Theresa V. Kot ◽  
Ngaire A. Pettit-Young
Keyword(s):  
Clinical Trials ◽  
Adverse Effects ◽  
Clinical Studies ◽  
Data Extraction ◽  
Point Of View ◽  
Data Synthesis ◽  
Study Selection ◽  
Beneficial Response ◽  
A Current

OBJECTIVE: To review the current published clinical studies evaluating the clinical efficacy and safety of lactulose compared with other laxatives or placebo. Adverse effects associated with lactulose are also reported. DATA SOURCES: Information was retrieved by searching the MEDLINE and EMBASE databases for clinical trials, abstracts, conference proceedings, and review articles dealing with lactulose. STUDY SELECTION: Emphasis was placed on clinical trials where lactulose was compared with other laxatives or placebo in patient populations where the diagnosis of constipation was reasonably established. DATA EXTRACTION: The methodology and results from clinical studies were evaluated. Assessment of the studies was made based on diagnosis of constipation, prior management of patients, follow-up of patients, dosage, and adverse effects. DATA SYNTHESIS: Clinical trials in geriatric patients, terminally ill patients, children, and normal and constipated subjects were reviewed. In most instances, lactulose was compared with a placebo, without incorporating the current education on dietary techniques for improving defecation. CONCLUSIONS: Generally, clinical trials have demonstrated a beneficial response compared with placebo, although sometimes that response has been only marginally better, from a clinical point of view.

Identification of Potential Reusable Subroutines in Recorded Automated Test Scripts

2018 ◽  
Vol 28 (01) ◽  
pp. 3-36
Author(s):  
Miroslav Bures ◽  
Martin Filipsky ◽  
Ivan Jelinek
Keyword(s):  
User Interface ◽  
Source Code ◽  
Automated Testing ◽  
Test Automation ◽  
Specific Test ◽  
Automated Test ◽  
Test Sets ◽  
Automated Process

In the automated testing based on actions in user interface of the tested application, one of the key challenges is maintenance of these tests. The maintenance overhead can be decreased by suitably structuring the test scripts, typically by employing reusable objects. To aid in the development, maintenance and refactoring of these test scripts, potentially reusable objects can be identified by a semi-automated process. In this paper, we propose a solution that identifies the potentially reusable objects in a set of automated test scripts and then provides developers with suggestions about these objects. During this process, we analyze the semantics of specific test steps using a system of abstract signatures. The solution can be used to identify the potentially reusable objects in both recorded automated test sets and tests programmed in an unstructured style. Moreover, compared to approaches that are based solely on searching for repetitive source code fragments, the proposed system identifies potentially reusable objects that are more relevant for test automation.

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