A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

LitDB - Keeping Track of Research Papers From Your Institute Made Simple

Background

In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities.

Results

We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a “crowd-sourcing” effort.

Conclusions

Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

     

Citrate usage in the leading causes of blindness: new possibilities for the old metabolite

Introduction

Citrate is an old metabolite which is best known for the role in the Krebs cycle. Citrate is widely used in many branches of medicine. In ophthalmology citrate is considered as a therapeutic agent and an useful diagnostic tool—biomarker.

Objectives

To summarize the published literature on citrate usage in the leading causes of blindness and highlight the new possibilities for this old metabolite.

Methods

We conducted a systematic search of the scientific literature about citrate usage in ophthalmology up to January 2018. The reference lists of identified articles were searched for providing in-depth information.

Results

This systematic review included 30 articles. The role of citrate in the leading causes of blindness is presented.

Conclusions

Citrate might help inhibit cataract progression, in case of questions confirm glaucoma diagnosis or improve cornea repair treatment as adjuvant agent (therapy of ulcerating cornea after alkali injury, crosslinking procedure). However, the knowledge about possible citrate usage in ophthalmology is not widely known. Promoting recent scientific knowledge about citrate usage in ophthalmology may not only benefit of medical improvement but may also limit economic costs caused by leading causes of blindness. Further studies on citrate usage in ophthalmology should continuously be the field of scientific interest.

     

Interactive processing and visualization of image data for biomedical and life science applications

Background

Applications in biomedical science and life science produce large data sets using increasingly powerful imaging devices and computer simulations. It is becoming increasingly difficult for scientists to explore and analyze these data using traditional tools. Interactive data processing and visualization tools can support scientists to overcome these limitations.

Results

We show that new data processing tools and visualization systems can be used successfully in biomedical and life science applications. We present an adaptive high-resolution display system suitable for biomedical image data, algorithms for analyzing and visualization protein surfaces and retinal optical coherence tomography data, and visualization tools for 3D gene expression data.

Conclusion

We demonstrated that interactive processing and visualization methods and systems can support scientists in a variety of biomedical and life science application areas concerned with massive data analysis.

     

The role of interdisciplinary research team in the impact of health apps in health and computer science publications: a systematic review

Background

Several studies have estimated the potential economic and social impact of the mHealth development. Considering the latest study by Institute for Healthcare Informatics, more than 165.000 apps of health and medicine are offered including all the stores from different platforms. Thus, the global mHealth market was an estimated $10.5 billion in 2014 and is expected to grow 33.5 percent annually between 2015 and 2020s. In fact, apps of Health have become the third-fastest growing category, only after games and utilities.

Methods

This study aims to identify, study and evaluate the role of interdisciplinary research teams in the development of articles and applications in the field of mHealth. It also aims to evaluate the impact that the development of mHealth has had on the health and computer science field, through the study of publications in specific databases for each area which have been published until nowadays.

Results

Interdisciplinary nature is strongly connected to the scientific quality of the journal in which the work is published. This way, there are significant differences in those works that are made up by an interdisciplinary research team because of they achieve to publish in journals with higher quartiles. There are already studies that warn of methodological deficits in some studies in mHealth, low accuracy and no reproducibility. Studies of low precision and poor reproducibility, coupled with the low evidence, provide low degrees of recommendation of the interventions targeted and therefore low applicability.

Conclusions

From the evidence of this study, working in interdisciplinary groups from different areas greatly enhances the quality of research work as well as the quality of the publications derived from its results.

     

From behind the curtain: talking about values in LCA

Purpose

Practitioners of life cycle assessment (LCA) acknowledge that more input from social scientists can help advance the cause of life cycle management (LCM). This commentary offers a social science perspective on a long-running question within LCA, namely, how the field should manage not only stakeholders’ values but also those of practitioners themselves.

Methods

More than 60 interviews were conducted with LCA practitioners and their industry clients. Qualitative data were also collected through participant observation at several LCA and LCM conferences, a study of the field’s history, and extensive content and discourse analysis of LCA publications and online forums.

Results and discussion

Results show that LCA practitioners’ values are informed partly by the knowledge acquired through their LCA work. At the same time, LCA standards and professional norms implicitly advise practitioners to keep those values out of their work as much as possible, so as not to compromise its apparent objectivity. By contrast, many social scientists contend openly that value-based judgments, based on “situated knowledge,” can actually enhance the rigor, accountability, and credibility of scientific assessments.

Conclusions

LCA practitioners’ own situated knowledge justifies not only the value choices required by LCA but also their evaluative judgments of contemporary life cycle-based sustainability initiatives. This more critical voice could advance the goals of LCM while also boosting the credibility of LCA more generally.

     

Bridge processes: a solution for LCI datasets independent of background databases

Introduction

New platforms are emerging that enable more data providers to publish life cycle inventory data.

Background

Providing datasets that are not complete LCA models results in fragments that are difficult for practitioners to integrate and use for LCA modeling. Additionally, when proxies are used to provide a technosphere input to a process that was not originally intended by the process authors, in most LCA software, this requires modifying the original process.

Results

The use of a bridge process, which is a process created to link two existing processes, is proposed as a solution.

Discussion

Benefits to bridge processes include increasing model transparency, facilitating dataset sharing and integration without compromising original dataset integrity and independence, providing a structure with which to make the data quality associated with process linkages explicit, and increasing model flexibility in the case that multiple bridges are provided. A drawback is that they add additional processes to existing LCA models which will increase their size.

Conclusions

Bridge processes can be an enabler in allowing users to integrate new datasets without modifying them to link to background databases or other processes they have available. They may not be the ideal long-term solution but provide a solution that works within the existing LCA data model.

     

What causes more LCA research—subjective values,objective problems,or scientific traditions?

Purpose

This paper aims to verify whether life cycle assessment (LCA) research can be mainly treated as a kind of pro-environmental behavior due to public environment concerns, or academic and research activities based on scientific traditions.

Methods

This paper uses the international comparisons method for modeling and SPSS 16.0 for data processing. The data in this study were obtained from the Human Development Report by the United Nations Development Programme and the Web of Science by the Institute for Scientific Information.

Results and discussion

Our empirical study shows that the two main factors influencing the outputs per capita of the research articles in LCA in a particular country are the value of Environmental Performance Index, which represents the overall environmental quality, as well as the outputs per capita of the research articles in environmental science and technology. The results of statistical analysis show two J-type curves: with the change of the independent variables, the dependent variable changes in the same direction, but at a rate that is first slow, then fast.

Conclusions

LCA research results from scientific traditions and can only develop based on fundamental research in environmental science and technology. Further, LCA research is a pro-environmental behavior due to actual and objective effects rather than subjective motives as more research on LCA can accompany, even in some degree may lead to better overall environmental qualities. However, although environmental concerns are likely to affect the number of LCA studies as an implicit variable, this has not been empirically confirmed in our optimization model.

     

The metabolome 18 years on: a concept comes of age

Background

The term ‘metabolome’ was introduced to the scientific literature in September 1998.

Aim and key scientific concepts of the review

To mark its 18-year-old ‘coming of age’, two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.

     

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository

Introduction

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific ‘mwTab’ flat file format.

Objectives

In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in ‘mwTab’ formatted files, we implemented a Python library and package. This Python package, named ‘mwtab’, is a parser for the domain-specific ‘mwTab’ flat file format, which provides facilities for reading, accessing, and writing ‘mwTab’ formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given ‘mwTab’ formatted file.

Methods

In order to develop the ‘mwtab’ package we used the official ‘mwTab’ format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator.

Results

The ‘mwtab’ package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating ‘mwTab’ formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, ‘pythonic’ access and manipulation of data and metadata. Also, the package provides facilities to convert ‘mwTab’ files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The ‘mwtab’ package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between ‘mwTab’ and JSONized formats in raw text and a variety of compressed binary file formats.

Conclusions

The ‘mwtab’ package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a ‘User Guide’, ‘Tutorial’, and ‘API Reference’. The GitHub repository also provides ‘mwtab’ package unit-tests via a continuous integration service.

     

Usage of cell nomenclature in biomedical literature

Background

Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial for science reproducibility and knowledge integration. There are efforts for standardisation of the cell nomenclature based on ontology development to support FAIR principles of the cell knowledge. However, it is important to analyse the usage of cell nomenclature in publications at a large scale for understanding the level of uptake of cell nomenclature in literature by scientists. In this study, we analyse the usage of cell nomenclature, both in Vivo, and in Vitro in biomedical literature by using text mining methods and present our results.

Results

We identified 59% of the cell type classes in the Cell Ontology and 13% of the cell line classes in the Cell Line Ontology in the literature. Our analysis showed that cell line nomenclature is much more ambiguous compared to the cell type nomenclature. However, trends indicate that standardised nomenclature for cell lines and cell types are being increasingly used in publications by the scientists.

Conclusions

Our findings provide an insight to understand how experimental cells are described in publications and may allow for an improved standardisation of cell type and cell line nomenclature as well as can be utilised to develop efficient text mining applications on cell types and cell lines. All data generated in this study is available at https://github.com/shenay/CellNomenclatureStudy.

     

Effectiveness of online learning on health researcher capacity to appropriately integrate sex,gender, or both in grant proposals

Background

To describe the effectiveness of online learning to augment academic capacity to consider sex and gender in the conduct of basic science, clinical research, and population health studies.

Method

The analysis compares pre- and post-test scores from 1441 individuals who completed the Canadian Institutes of Health Research Institute of Gender and Health’s interactive e-learning modules between February 2016 and May 2017. The tests measured knowledge, self-efficacy, and self-reported intent to change behavior for three competencies: (1) the ability to appropriately define and distinguish between sex-related versus gender-related variables, (2) the application of methods for integrating sex and gender, and (3) the critical appraisal of sex and gender integration in the design, methods, and analysis plan of research proposals and publications.

Results

Of the 543 individuals who completed the basic science module, 62% demonstrated improved knowledge, and 86% increased self-efficacy across all competencies. Gains in knowledge and self-efficacy also occurred among 84% and 77% of completers of the human data collection module (n?=?463) and among 73% and 82% of those who completed the secondary data analysis module (n?=?435). In aggregate, 95% of participants reported an intent to change their behavior with respect to sex and gender in health research.

Conclusions

Interactive online learning combined with feedback and self-assessment results in improved knowledge and self-efficacy for integrating sex and gender in health research.

     

Escher-FBA: a web application for interactive flux balance analysis

Background

Flux balance analysis (FBA) is a widely-used method for analyzing metabolic networks. However, most existing tools that implement FBA require downloading software and writing code. Furthermore, FBA generates predictions for metabolic networks with thousands of components, so meaningful changes in FBA solutions can be difficult to identify. These challenges make it difficult for beginners to learn how FBA works.

Results

To meet this need, we present Escher-FBA, a web application for interactive FBA simulations within a pathway visualization. Escher-FBA allows users to set flux bounds, knock out reactions, change objective functions, upload metabolic models, and generate high-quality figures without downloading software or writing code. We provide detailed instructions on how to use Escher-FBA to replicate several FBA simulations that generate real scientific hypotheses.

Conclusions

We designed Escher-FBA to be as intuitive as possible so that users can quickly and easily understand the core concepts of FBA. The web application can be accessed at https://sbrg.github.io/escher-fba.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Design and integration of a problem-based biofabrication course into an undergraduate biomedical engineering curriculum

Background

The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method.

Results

Students were assessed on a range of metrics designed to evaluate the format of the course, the efficacy of the format for teaching new topics and concepts, and the depth of the contribution this course made to students training for biological engineering careers. The evaluation showed that the problem-based format of the course was well suited to teaching students how to use the scientific method to investigate and uncover the fundamental biological design rules that govern the field of biofabrication.

Conclusions

We show that this approach is an efficient and effective method of translating emergent scientific principles from the lab bench to the classroom and training the next generation of biological and biomedical engineers for careers as researchers and industry practicians.

     

Pityriasis Versicolor: Treatment Update

Purpose of Review

To address the latest treatments used for pityriasis versicolor and identify those that have proven to be effective in recent publications.

Recent Findings

Even though Malassezia spp. have shown resistance to antifungals, classical treatments continue to be effective, and other novelty therapies including light therapies have shown promising results in the treatment of this condition.

Summary

Pityriasis versicolor is a common superficial fungal infection of the skin. There are numerous and diverse topical and systemic therapeutic options that are successful for the treatment and prophylaxis of this mycosis. New substances that act against the fungus through other mechanisms of action different from those used until now are expected in the near future.

     

Can social research paradigms justify the diversity of approaches to social life cycle assessment?

Purpose

The present paper aims to offer an explanation for the diversity of methodological approaches proposed up to the present for social life cycle assessment (sLCA), tracking down its roots in the cultural and scientific heritage of social sciences and especially management sciences. A second aim is to shift the current debate on methodologies to an epistemological level, presenting the first results of an ongoing critical review about which underlying paradigms have been applied in sLCA literature.

Methods

This paper moves from the hypothesis that the diversity of positions in philosophy of science and the “multiparadigmatic” character of social sciences have had repercussions on sLCA literature since its beginnings, probably in an unconscious manner. Therefore, a discriminating reflection on the scientific and disciplinary inheritance that can represent the roots of sLCA has been conducted. The philosophy of science and the role of different research paradigms in social sciences have been deepened to provide an overview of the main elements of a paradigm (in terms of ontology, epistemology, and methodology). Finally, a brief but critical review of 133 selected scientific contributions on sLCA has been conducted to highlight which paradigms have been applied in sLCA studies.

Results and discussion

Recognizing that boundaries between paradigms are subtle and that researchers are rarely conscious of which paradigm underpins their works, a distinction between the interpretivist and post-positivist approaches used by the studies has been carried out on the basis of a text analysis conducted by identifying the main “literal” criteria. From an initial population of 209 studies, we excluded those concerning reviews of sLCA literature and those with selected criteria that were insufficient to catch the epistemological viewpoint of the authors. Among the remaining papers (133), 73 % has been ascribed to the group of interpretivism-oriented paradigms and only 24 % could be ascribed to the post-positivist one; the remaining 3 % is represented by studies with both characteristics. This data deserves some attention because, since the beginnings of sLCA methodologies, most sLCA publications explicitly suggest having the same underlying perspectives as environmental life cycle assessment (eLCA).

Conclusions

In light of the reflections carried out, we argue that it is important, before going into methodological questioning issues, to be aware of which paradigm is underlying. Indeed, in this phase of sLCA development, scholars should go beyond the simple methodological debate and recognize the “multilayered” nature of social phenomena and the multiparadigmatic characteristics of social and management sciences.

     

From correlation to causation: analysis of metabolomics data using systems biology approaches

Introduction

Metabolomics is a well-established tool in systems biology, especially in the top–down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches.

Objectives

This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods.

Methods

We review the most recent applications of systems biology tools in the field of metabolomics, such as network inference and analysis, metabolic modelling and pathways analysis.

Results

We offer an ample overview of systems biology tools that can be applied to address metabolomics problems. The characteristics and application results of these tools are discussed also in a comparative manner.

Conclusions

Systems biology-enhanced analysis of metabolomics data can provide insights into the molecular mechanisms originating the observed metabolic profiles and enhance the scientific impact of metabolomics studies.