Reproducibility Of Research Results Research Articles

Development of Certified Reference Material Solutions for Phytochemicals in Ginger and Kava.

Dietary supplements derived from botanicals are commonly consumed and investigated in biomedical studies for their potential health benefits. Accurate identification and quantification of key chemical constituents from botanical ingredients is necessary for consistent product preparations and reproducible research results. Manufacturers need quantitative reference materials of the chemical constituents of interest to verify the content of ingredients and products. The rigor and reproducibility of biomedical research is enhanced through thorough characterization of the interventions used in mechanistic, clinical, and safety investigations. Quantitative reference materials enable reliable product quality assessments and reproducible research results. Solution-based certified reference material (CRM) mixes were developed as calibrants for phytochemicals in Ginger and Kava. The Kava CRM contained yangonin, desmethoxyyangonin, dihydrokavain, DL-kavain, methysticin, dihydromethysticin, flavokawain A, flavokawain B, and flavokawain C. The Ginger CRM contained 6-gingerol, 8-gingerol, 10-gingerol, 6-shogaol, 8-shogaol, and 10-shogaol. Each phytochemical was sourced as an isolated compound and assigned a purity factor by a mass balance approach accounting for residual impurities. The solution standard mixes were formulated by gravimetric addition of each phytochemical incorporating the purity factor and diluting with acetonitrile to the target concentrations of 500 µg/mL for the gingerols and shogaols, 250 µg/mL for the kavalactones and 25 µg/mL for the flavokawains. The concentration accuracy of each component in the solution mixes was analytically verified by HPLC-UV assay comparison to an independently prepared calibration solution. Each component in the Ginger and Kava CRMs were within 5% and 7% of the target concentrations, respectively. Homogeneous Kava and Ginger phytochemical solution mixes were produced with accurate constituent concentrations and demonstrated good stability over two years. These solution mixes were launched as commercially available CRMs. These mixes can be used as accurate concentration stock solutions to prepare calibrators and controls for botanical dietary supplement product testing and standardization.

Open Science and the impact of Open Access, Open Data, and FAIR publishing principles on data-driven academic research: Towards ever more transparent, accessible, and reproducible academic output?

Contemporary evidence-informed policy-making (EIPM) and societies require openly accessible high-quality knowledge as input into transparent and accountable decision-making and informed societal action. Open Science1 supports this requirement. As both enablers and logical consequences of the paradigm of Open Science, the ideas of Open Access, Open Data, and FAIR publishing principles revolutionise how academic research needs to be conceptualised, conducted, disseminated, published, and used. This ‘academic openness quartet’ is especially relevant for the ways in which research data are created, annotated, curated, managed, shared, reproduced, (re-)used, and further developed in academia. Greater accessibility of scientific output and scholarly data also aims at increasing the transparency and reproducibility of research results and the quality of research itself. In the applied ‘academic openness quartet’ perspective, they also function as remedies for academic malaises, like missing replicability of results or secrecy around research data. Against this backdrop, the present article offers a conceptual discussion on the four academic openness paradigms, their meanings, interrelations, as well as potential benefits and challenges arising from their application in data-driven research.

Comprehensive Colony Health Management and Emerging Pathogens of the Annual Killifish Species Nothobranchius furzeri.

The Leibniz Institute on Aging has maintained killifish colonies for over 15 y. Our veterinarians, scientists, and animal technicians developed a fish health scoring system and routine colony health surveillance program for our colonies. Over a 4-y period, health data from the African turquoise killifish Nothobranchius furzeri colony were systematically collected and analyzed. The fish health assessment system facilitated categorization of clinical signs and differentiation of fish with mild clinical signs from fish that required euthanasia. This report provides new information on clinical signs and conditions that may occur in young and aged N. furzeri. To be comprehensive, a colony health surveillance program incorporates animal health at both the individual and the population levels. The quarterly routine health monitoring program identified Mycobacterium spp. as the most common agent in our facility and identified the killifish pathogen (Loma acerinae) for the first time. Taken together, these findings demonstrate the importance of a comprehensive colony health management system in a fish research facility. By improving the health and welfare of fish used for research, the scientific community will benefit from less variable and more reliably reproducible research results.

Revisiting Schistosoma mansoni Micro-Exon Gene (MEG) Protein Family: A Tour into Conserved Motifs and Annotation.

Genome sequencing of the human parasite Schistosoma mansoni revealed an interesting gene superfamily, called micro-exon gene (meg), that encodes secreted MEG proteins. The genes are composed of short exons (3-81 base pairs) regularly interspersed with long introns (up to 5 kbp). This article recollects 35 S. mansoni specific meg genes that are distributed over 7 autosomes and one pair of sex chromosomes and that code for at least 87 verified MEG proteins. We used various bioinformatics tools to produce an optimal alignment and propose a phylogenetic analysis. This work highlighted intriguing conserved patterns/motifs in the sequences of the highly variable MEG proteins. Based on the analyses, we were able to classify the verified MEG proteins into two subfamilies and to hypothesize their duplication and colonization of all the chromosomes. Together with motif identification, we also proposed to revisit MEGs' common names and annotation in order to avoid duplication, to help the reproducibility of research results and to avoid possible misunderstandings.

Research Data Management and Data Sharing for Reproducible Research-Results of a Community Survey of the German National Research Data Infrastructure Initiative Neuroscience.

Science is changing: the volume and complexity of data are increasing, the number of studies is growing and the goal of achieving reproducible results requires new solutions for scientific data management. In the field of neuroscience, the German National Research Data Infrastructure (NFDI-Neuro) initiative aims to develop sustainable solutions for research data management (RDM). To obtain an understanding of the present RDM situation in the neuroscience community, NFDI-Neuro conducted a comprehensive survey among the neuroscience community. Here, we report and analyze the results of the survey. We focused the survey and our analysis on current needs, challenges, and opinions about RDM. The German neuroscience community perceives barriers with respect to RDM and data sharing mainly linked to (1) lack of data and metadata standards, (2) lack of community adopted provenance tracking methods, (3) lack of secure and privacy preserving research infrastructure for sensitive data, (4) lack of RDM literacy, and (5) lack of resources (time, personnel, money) for proper RDM. However, an overwhelming majority of community members (91%) indicated that they would be willing to share their data with other researchers and are interested to increase their RDM skills. Taking advantage of this willingness and overcoming the existing barriers requires the systematic development of standards, tools, and infrastructure, the provision of training, education, and support, as well as additional resources for RDM to the research community and a constant dialogue with relevant stakeholders including policy makers to leverage of a culture change through adapted incentivization and regulation.

Hubzero: Community Growth for Four Science Gateways Supporting Open Science

The research landscape has become increasingly interdisciplinary and complex with novel hardware, software, data, and lab instruments. Reproducibility of research results, the usability of tools, and sharing of methods are all crucial for timely collaboration for research and teaching. Hubzero is a widely used science gateway framework designed to support online communities with efficient sharing and publication processes. The paper discusses the growth of communities for the four science gateways nanoHUB, MyGeoHub, QUBEShub, and HubICL using the Hubzero Platform to foster open science and tackling education with a diverse set of approaches and target communities.

Standard operating procedures for the collection, processing, and storage of oral biospecimens at the Korea Oral Biobank Network.

The Korea Oral Biobank Network (KOBN) was established in 2021 as a branch of the Korea Biobank Network under the Korea Centers for Disease Control and Prevention to provide infrastructure for the collection, management, storage, and utilization of human bioresources from the oral cavity and associated clinical data for basic research and clinical studies. To address the need for the unification of the biobanking process, the KOBN organized the concept review for all the processes. The KOBN established standard operating procedures for the collection, processing, and storage of oral samples. The importance of collecting high-quality bioresources to generate accurate and reproducible research results has always been emphasized. A standardized procedure is a basic prerequisite for implementing comprehensive quality management of biological resources and accurate data production.

ASSESSMENT OF LABORATORY ANIMAL FUNCTIONAL STATUS: MODERN METHODOLOGICAL APPROACHES FOR CONDUCTING BIOMEDICAL RESEARCH

Aim: to outline modern scientific approaches for evaluating the functional condition of small laboratory animals in experimental research. Materials and Methods: Scientific publications on the rules of using laboratory animals in scientific experiments, testing, educational process have been studied. The bioethical norms and principles of animal care and use of material for medical, veterinary and biological profiles were also studied, for example modern methodological approaches for conducting biomedical research, since it is the responsibility of the scientist to achieve reproducible research results using the minimum number of laboratory animals. Conclusions: The main conditions for their implementation and effectiveness include: adherence to the “Ethical Code” published by the International Council for Medical Scientific Organizations in the early 1980s, the principles of the European Convention for the Protection of Vertebrate Animals Used for Experimental and Other Scientific Purposes (Strasbourg, 18 March 1986), and Directive 2010/63/EU adopted on 22 September 2010; the use of advanced and modern diagnostic equipment that enables low-invasive yet highly informative research on small laboratory animals; conducting comprehensive, multi-level studies on an optimal number of animals in laboratories that meet international standards.

Biobanking potential for biomedical research in endocrinology

Biobanking is an actively developing scientific area that provides tools for conducting biomedical research, increasing the reliability and reproducibility of their results. In endocrinology, more and more attention is paid to the study of molecular and genetic markers of diseases for the selection of new points of influence in treatment, the development of targeted therapy and a strategy for personalized prevention. This approach is designed to solve the problems of endocrine disorders, their complications, causing significant damage to the individual and he population health, and reduce the financial burden of chronic endocrine disorders. To increase the reliability and reproducibility of research results, requirements for working with biological material should be strictly complied. The use of biobanking will increase the validity of data obtained in clinical trials in endocrinology. There are successful examples of Russian and foreign studies using the capabilities of biobanks aimed at studying diabetes, polycystic ovary syndrome, adenomas and other endocrine disorders. The article discusses the prospects for partnership with biobanks in the framework of endocrinology research. The purpose of this review is to analyze the literature to systematize knowledge for application of biobanking in biomedical research in the field of endocrinology.

EiC Editorial – Advancing Reproducibility in Parallel and Distributed Systems Research

, the TPDS Reproducibility Initiative [2][3] has being exploring postpublication peer review of code associated with published articles for a few years. Authors who have published in TPDS can make their published article more reproducible and earn a reproducibility badge by submitting their associated code for post-publication peer review. To date, this pilot has largely focused on two badges: 1. Code Available: The code, including any associated data and documentation, provided by the authors is reasonable and complete and can potentially be used to support reproducibility of the published results. 2. Code Reviewed: The code, including any associated data and documentation, provided by the authors is reasonable and complete, runs to produce the outputs described, and can support reproducibility of the published results. While TPDS’ goal has always been to include badges for reproducing research results using the code and/or data provided, the nature of research in parallel and distributed systems covered by TPDS makes it challenging to evaluate code and data challenging for reproducibility. This is because such an evaluation may require access to specific hardware, system architectures and scales, OS configurations, and so on, which may not be feasible or practical. vel system/middleware services, is typically infeasible. Consequently, TPDS has piloted an alternate approach where members of the community can submit short, supplemental ‘critique’ papers that present their experiences in reproducing published results using the artifacts, and/or evaluations or experiences with published artifacts. These supplemental paper submissions are reviewed and, if accepted, are linked to the original publication and are citable, serving to help validate the reproducibility of the original publication. This approach was first implemented in a special section guest edited by Stephen Lien Harrell and Beth Plale and consisting of a primary paper and 6 critique papers that reproduce the results of the primary paper. This special section continues this effort, building on the SC20 Student Cluster Competition, which was part of the SC20 conference. It consists of 9 critique papers that reproduce the results of the primary paper.

Promoting and Enabling Reproducible Data Science Through a Reproducibility Challenge

The reproducibility of research results is the basic requirement for the reliability of scientific discovery, yet it is hard to achieve. Whereas funding agencies, scientific journals, and professional societies are developing guidelines, requirements, and incentives, and researchers are developing tools and processes, the role of a university in promoting and enabling reproducible research has been unclear. In this report, we describe the Reproducibility Challenge that we organized at the University of Michigan to promote reproducible research in data science and Artificial Intelligence (AI). We observed that most researchers focused on nuts-and-bolts reproducibility issues relevant to their own research. Many teams were building their own reproducibility protocols and software for lack of any available options off the shelf. If we could help them with this, they would have preferred to adopt rather than build anew. We argue that universities—their data science centers and research support units—have a critical role to play in promoting “actionable reproducibility” (Goeva et al., 2020) through creating and validating tools and processes, and subsequently enabling and encouraging their adoption.

AURORA, a multi-sensor dataset for robotic ocean exploration

The current maturity of autonomous underwater vehicles (AUVs) has made their deployment practical and cost-effective, such that many scientific, industrial and military applications now include AUV operations. However, the logistical difficulties and high costs of operating at sea are still critical limiting factors in further technology development, the benchmarking of new techniques and the reproducibility of research results. To overcome this problem, this paper presents a freely available dataset suitable to test control, navigation, sensor processing algorithms and others tasks. This dataset combines AUV navigation data, sidescan sonar, multibeam echosounder data and seafloor camera image data, and associated sensor acquisition metadata to provide a detailed characterisation of surveys carried out by the National Oceanography Centre (NOC) in the Greater Haig Fras Marine Conservation Zone (MCZ) of the U.K in 2015.

The identification and the quantitative determination of loratadine by the HPLC method

Aim. To develop the unified method of the HPLC analysis of loratadine, which can allow obtaining reliable and reproducible results of the studies of pharmaceuticals and biological matrices for monitoring the treatment effectiveness.Materials and methods. The HPLC analysis was performed on a “Milichrome A-02” microcolumn liquid chromatograph under the following conditions: a reversed-phase variant, 2 × 75 mm column filled with a non-polar sorbent Prontosil 120-5 C18 AQ, 5 μm; the mobile phase in the mode of a linear gradient – from eluent А (5 % of acetonitrile and 95  % of a buffer solution) to eluent B (100 % of acetonitrile) for 40 min. The flow rate of the mobile phase was 100 μL/min; the injection volume was 4 μL. The multichannel detection of the substance was carried out using an UV-detector at 210, 220, 230, 240, 250, 260, 280 and 300 nm; the optimal value of the column temperature was 37 – 40 °С, and the pump pressure was 2.8 – 3.2 MPa.Results and discussion. As a result of the studies performed, the retention parameters of loratadine and spectral relationships were determined using the unified HPLC method. This made it possible to include the results obtained in the database for the identification of antihistamines in the therapeutic monitoring of the treatment with an individual drug or in the complex treatment of allergic reactions. The development of the quantitative determination of loratadine by HPLC on model solutions using various concentrations of the drug was carried out. The content of loratadine was determined by the equation S = 1.14 × 10-3C – 0.50 × 10-4; the correlation coefficient was 0.9998. It was found that the relative standard deviation RSD did not exceed 0.93 % when analyzing loratadine in the model solutions by HPLC.Conclusions. The identification and the quantitative determination of loratadine by the unified HPLC method have been conducted. The method allows obtaining reliable and reproducible research results. The results of the studies can be recommended for implementation in the practice of forensic bureaus, toxicological centers, and clinical laboratories.

Pre-registration: Weighing costs and benefits for researchers

In the past decade, the social and behavioral sciences underwent a methodological revolution, offering practical prescriptions for improving the replicability and reproducibility of research results. One key to reforming science is a simple and scalable practice: pre-registration. Pre-registration constitutes pre-specifying an analysis plan prior to data collection. A growing chorus of articles discusses the prescriptive, field-wide benefits of pre-registration. To increase adoption, however, scientists need to know who currently pre-registers and understand perceived barriers to doing so. Thus, we weigh costs and benefits of pre-registration. Our survey of researchers reveals generational differences in who pre-registers and uncertainty regarding how pre-registration benefits individual researchers. We leverage these data to directly address researchers’ uncertainty by clarifying why pre-registration improves the research process itself. Finally, we discuss how to pre-register and compare available resources. The present work examines the who, why, and how of pre-registration in order to weigh the costs and benefits of pre-registration to researchers and motivate continued adoption.

A community-led initiative for training in reproducible research.

Open and reproducible research practices increase the reusability and impact of scientific research. The reproducibility of research results is influenced by many factors, most of which can be addressed by improved education and training. Here we describe how workshops developed by the Reproducibility for Everyone (R4E) initiative can be customized to provide researchers at all career stages and across most disciplines with education and training in reproducible research practices. The R4E initiative, which is led by volunteers, has reached more than 3000 researchers worldwide to date, and all workshop materials, including accompanying resources, are available under a CC-BY 4.0 license at https://www.repro4everyone.org/.

Nanocellulose characterization challenges

Despite the extraordinary properties of nanocellulose (NC), as confirmed through two decades of exhaustive research, addressing an array of potential applications, the NC market is still far from reaching its full potential. Among the main causes is the lack of process-adapted measuring tools capable of characterizing NC, at acceptable speed and reliability, to meet the industrial demands in a cost-effective way. Therefore, reliable characterization methodologies of NC and new standards are of paramount importance in ensuring reproducible research results and quality control specifications for present and future NC products and applications. Furthermore, the successful industrial use of NC products depends on critical parameters that are still being identified and studied. This review paper aims to identify some of the current drawbacks and limitations in NC characterization that hinder their commercial deployment. Moreover, important challenges related to characterization and new opportunities for future research in this field are addressed.

Limits of reproducibility and hydrodynamic noise in atmospheric regional modelling

Reproducibility of research results is a fundamental quality criterion in science; thus, computer architecture effects on simulation results must be determined. Here, we investigate whether an ensemble of runs of a regional climate model with the same code on different computer platforms generates the same sequences of similar and dissimilar weather streams when noise is seeded using different initial states of the atmosphere. Both ensembles were produced using a regional climate model named COSMO-CLM5.0 model with ERA-Interim forcing. Divergent phase timing was dependent on the dynamic state of the atmosphere and was not affected by noise seeded by changing computers or initial model state variations. Bitwise reproducibility of numerical results is possible with such models only if everything is fixed (i.e., computer, compiler, chosen options, boundary values, and initial conditions) and the order of mathematical operations is unchanged between program runs; otherwise, at best, statistically identical simulation results can be expected.

Using Jupyter for Reproducible Scientific Workflows

Literate computing has emerged as an important tool for computational studies and open science, with growing folklore of best practices. In this work, we report two case studies-one in computational magnetism and another in computational mathematics-where domain-specific software was exposed to the Jupyter environment. This enables high level control of simulations and computation, interactive exploration of computational results, batch processing on HPC resources, and reproducible workflow documentation in Jupyter notebooks. In the first study, Ubermag drives existing computational micromagnetics software through a domain-specific language embedded in Python. In the second study, a dedicated Jupyter kernel interfaces with the GAP system for computational discrete algebra and its dedicated programming language. In light of these case studies, we discuss the benefits of this approach, including progress toward more reproducible and reusable research results and outputs, notably through the use of infrastructure such as JupyterHub and Binder.

Considering Registered Reports at C&RL

In January 2020, I presented at the Librarians Building Momentum for Reproducibility virtual conference. The theme of the presentation was preregistration and registered reports and their role in reproducibility of research results. The presentation was twofold in that it provided background information on these themes and then advocated for the adoption of a registered reports submission track in Library and Information Science journals. I asked attendees to notify me if they wanted to learn more and to join me in contacting LIS journals to advocate for this model. The first journal that we targeted was College & Research Libraries. We drafted a letter that was sent to editor Wendi Arant Kaspar who discussed the topic with the editorial board and ultimately asked me to write a guest editorial for C&RL.

Identification and quantitative determination of clonidine by HPLC method

The aim of this work is identification and quantification of clonidine hydrochloride by a unified HPLC method, which allows to obtain reliable and reproducible research results.Materials and methods. HPLC analysis was carried out on a microcolumn liquid chromatograph Milichrome A-02 in conditions: reversed-phase variant, column with non-polar sorbent Prontosil 120-5 C18 AQ, 5 μm; mobile phase in the mode of linear gradient – from eluent А (5 % acetonitrile and 95 % buffer solution) to eluent B (100 % acetonitrile) as during 40 min. The flow rate of the mobile phase has been formed 100 μl/min, injection volume – 4 μl. Multichannel detection of the substance was carried out using a UV detector at 210, 220, 230, 240, 250, 260, 280 and 300 nm; the optimal value of column temperature – 37 - 40°С and pressure of pump – 2.8 – 3.2 MPa.Results and its discussion. As a result of studies using a unified HPLC method, were obtained the retention parameters of clonidine hydrochloride and spectral relationships, which made it possible to include the results obtained in the database for the identification of antihypertensive drugs in the therapeutic monitoring of treatment with an individual drug, or comprehensive treatment of diseases of the cardiovascular system. The development of the quantitative determination of clonidine hydrochloride by HPLC on model solutions using various concentrations of the drug was carried out. The content of clonidine hydrochloride was determined according to the equation S = 0.5 · 10-4 C + 1.8 · 10-3; the correlation coefficient was 0.9964. It is established that the relative uncertainty of the average result did not exceed +2.12 % when HPLC analysing of clonidine hydrochloride in model solutions.Conclusions. Identification and quantification of clonidine hydrochloride by a unified HPLC method, which allows to obtain reliable and reproducible research results were conducted. The results of research by a unified HPLC method can be recommended for implementation in the practice of forensic bureaus, toxicological centers, clinical laboratories for the study of drugs in biological objects