A Productive Scholar's Guide to Respectful, Responsible Inquiry During the COVID-19 Pandemic: Moving Forward

As a result of the COVID-19 pandemic of 2020, schools across the country have pivoted to providing a range of instructional opportunities including remote, hybrid, and modified in-person options with a commitment to keeping our society safe and supporting our nations' youth in continuing their education. One byproduct of this most challenging situation has been the interruption of scientific inquiry in many fields, including educational research. Using a framework of self-leadership, in this feature article, we provide reflections to guide discussion among scholars involved in school-based research during and after the COVID-19 pandemic. Based on lessons learned in our own mentee-mentor relationships and from our collective experiences, the purpose of this article is to offer considerations primarily for early-career scholars, but also to engage dialogue among mid- and late-career scholars to promote school-based inquiry in this defining moment in history, at a time when educators are concerned with mitigating learning loss. We focus on (a) revisiting and refining programmatic lines of inquiry, (b) crafting articles to disseminate lessons learned from research conducted to date-including those with lost time points, (c) retooling in a focused area of inquiry (e.g., methodology), (d) conceptualizing future studies featuring procedures that do-and do not-allow for interpersonal contact, and (e) appreciating and acknowledging individuals who have facilitated inquiry. We conclude with a note of encouragement and call to action for future educational research.

The methodological quality and clinical applicability of meta-analyses on probiotics in 2020: A cross-sectional study

Systematic reviews with meta-analyses (SR/MA) are frequently conducted to investigate clinical efficacy of probiotics. However, only rigorously prepared analyses can serve as the highest level of evidence for a specified research question. We have aimed to determine (1) what is the methodological quality of recent SR/MA conducted to assess the efficacy of probiotics; (2) whether the results of SR/MA have a clinical application; and (3) what are factors associated with better quality and applicability of the SR/MA. We systematically searched 4 databases for SR/MA on the probiotics efficacy published in 2020 (PROSPERO CRD42020222716). The AMSTAR 2 tool and pre-defined authors' criteria were used to evaluate methodological quality and clinical applicability, respectively. A total of 114 SR/MA were appraised. In the case of 88 papers (77%), the overall confidence in the results was rated as "critically low". The most prevalent flaws were lack of list of excluded studies with justification (79.8%), lack of study protocol (60.5%), and problems with appropriate results combination(54.4%). A declaration of conduction a probiotic efficacy SR/MA could have been misleading in case of 18 studies that included also synbiotics, paraprobiotics, and prebiotics trials in analyses. Only 14 SR/MA provided results that can be apply in clinical practice. Higher journal impact factor and European affiliation of the 1st and corresponding authors were most consistently associated with higher odds of AMSTAR 2 items fulfillments. Based on our findings, SR/MA of probiotics trials cannot be treated as the highest level of evidence without a careful evaluation of their methodological validity.

Mapping the discursive dimensions of the reproducibility crisis: A mixed methods analysis

To those involved in discussions about rigor, reproducibility, and replication in science, conversation about the "reproducibility crisis" appear ill-structured. Seemingly very different issues concerning the purity of reagents, accessibility of computational code, or misaligned incentives in academic research writ large are all collected up under this label. Prior work has attempted to address this problem by creating analytical definitions of reproducibility. We take a novel empirical, mixed methods approach to understanding variation in reproducibility discussions, using a combination of grounded theory and correspondence analysis to examine how a variety of authors narrate the story of the reproducibility crisis. Contrary to expectations, this analysis demonstrates that there is a clear thematic core to reproducibility discussions, centered on the incentive structure of science, the transparency of methods and data, and the need to reform academic publishing. However, we also identify three clusters of discussion that are distinct from the main body of articles: one focused on reagents, another on statistical methods, and a final cluster focused on the heterogeneity of the natural world. Although there are discursive differences between scientific and popular articles, we find no strong differences in how scientists and journalists write about the reproducibility crisis. Our findings demonstrate the value of using qualitative methods to identify the bounds and features of reproducibility discourse, and identify distinct vocabularies and constituencies that reformers should engage with to promote change.

An Estimation of the Retraction Gap Across Neurosurgery-A Crevice or a Chasm?

BACKGROUND

The incidence of retractions has been increasing steadily, in direct proportion to the volume of scientific literature. Retraction of published articles depends on the visibility of journals and on postpublication scrutiny of published articles by peers. The possibility thus exists that not all compromised ("retractable") articles are detected and retracted from the less-visible journals. The proportion of "retractable" articles and its converse, the proportion of published articles in each journal that are likely to be "true" (PTP), have not been estimated hitherto.

METHODS

Three journal sets were created: pure neurosurgery journals (NS-P), the neurosurgery component of multidisciplinary journals (NS-MD), and high-impact clinical journals (HICJs). We described a new metric (the retraction gap [RGap]), defined as the proportion of retractable articles in journals that have not been retracted. We computed the expected number of retractable articles, RGap, and PTP for each journal, and compared these metrics across groups.

RESULTS

Fifty-three NS-P journals, 10 NS-MD journals, and 63 HICJs were included in the analysis. The estimated number of retractable articles was 31 times the actual number of retractions in NS-P journals, 6 times higher in the NS-MD journals, and 26 times higher for the HICJs. The RGap was 96.7% for the NS-P group, 83.5% for the NS-MD group, and 96.2% for the HICJs. The PTP was 99.3% in the NS-P group, 99.2% in the NS-MD group, and 98.6% in the HICJs.

CONCLUSIONS

Neurosurgery as a discipline had a higher RGap but also a higher PTP than the other 2 groups.

Triaging ethical issues in the coronavirus pandemic: how to prioritize bioethics research during public health emergencies

Much of the ethical discourse concerning the coronavirus pandemic has focused on the allocation of scarce resources, be it potentially beneficial new treatments, ventilators, intensive care beds, or oxygen. Somewhat ironically, the more important ethical issues may lie elsewhere, just as the more important medical issues do not concern intensive care or treatment for COVID-19 patients, but rather the diversion towards these modes of care at the expense of non-Covid patients and treatment. In this article I explore how ethicists can and should prioritize which ethical issues to deal with, and develop a method of triage for identification and prioritization of ethical issues both in the next public health emergency and in bioethics more widely.

Systems Exercise Genetics Research Design Standards

It is clear, based on a deep scientific literature base, that genetic and genomic factors play significant roles in determining a wide range of sport and exercise characteristics including exercise endurance capacity, strength, daily physical activity levels, and trainability of both endurance and strength. Although the research field of exercise systems genetics has rapidly expanded over the past two decades, many researchers publishing in this field are not extensively trained in molecular biology or genomics techniques, sometimes creating gaps in generating high-quality and cutting-edge research for publication. As current or former Associate Editors for Medicine and Science in Sports and Exercise that have handled the majority of exercise genetics articles for Medicine and Science in Sports and Exercise in the past 15 yr, we have observed a large number of scientific manuscripts submitted for publication review that have exhibited significant flaws preventing their publication; flaws that often directly stem from a lack of knowledge regarding the "state-of-the-art" methods and accepted literature base that is rapidly changing as the field evolves. The purpose of this commentary is to provide researchers-especially those coming from a nongenetics background attempting to publish in the exercise system genetics area-with recommendations regarding best-practice research standards and data analysis in the field of exercise systems genetics, to strengthen the overall literature in this important and evolving field of research.

On measuring agreement with numerically bounded linguistic probability schemes: A re-analysis of data from Wintle, Fraser, Wills, Nicholson, and Fidler (2019)

Across a wide range of domains, experts make probabilistic judgments under conditions of uncertainty to support decision-making. These judgments are often conveyed using linguistic expressions (e.g., x is likely). Seeking to foster shared understanding of these expressions between senders and receivers, the US intelligence community implemented a communication standard that prescribes a set of probability terms and assigns each term an equivalent numerical probability range. In an earlier PLOS ONE article, [1] tested whether access to the standard improves shared understanding and also explored the efficacy of various enhanced presentation formats. Notably, they found that embedding numeric equivalents in text (e.g., x is likely [55–80%]) substantially outperformed the status-quo approach in terms of the percentage overlap between participants’ interpretations of linguistic probabilities (defined in terms of the numeric range equivalents they provided for each term) and the numeric ranges in the standard. These results have important prescriptive implications, yet Wintle et al.’s percentage overlap measure of agreement may be viewed as unfairly punitive because it penalizes individuals for being more precise than the stipulated guidelines even when the individuals’ interpretations fall perfectly within the stipulated ranges. Arguably, subjects’ within-range precision is a positive attribute and should not be penalized in scoring interpretive agreement. Accordingly, in the present article, we reanalyzed Wintle et al.’s data using an alternative measure of percentage overlap that does not penalize in-range precision. Using the alternative measure, we find that percentage overlap is substantially elevated across conditions. More importantly, however, the effects of presentation format and probability level are highly consistent with the original study. By removing the ambiguity caused by Wintle et al.’s unduly punitive measure of agreement, these findings buttress Wintle et al.’s original claim that the methods currently used by intelligence organizations are ineffective at coordinating the meaning of uncertainty expressions between intelligence producers and intelligence consumers. Future studies examining agreement between senders and receivers are also encouraged to reflect carefully on the most appropriate measures of agreement to employ in their experiments and to explicate the bases for their methodological choices.

Shaping our worldviews: a conversation about and of theory

This paper introduces a new column in the Journal for the exploration of and reflection on the roles and articulations of theory in the health professions education sciences. This introduction provides initial orientation to concepts such as theory as worldview, theory linked to empiricism and paradigm, and theory and reflexivity. The authors invite scholars to submit papers that explore the role of theory in HPE scholarship, that propose new and adapted theoretical positions, and that critique the many theories that might be brought to bear to address questions in the field.

Tackling the void: the importance of addressing absences in the field of health professions education research

Many processes and practices in the field of health professions education have been based more on tradition and assumption than on evidence and theory. As the field matures, researchers are increasingly seeking evidence to support various teaching and assessment methods. However, there is a tendency to focus on a limited set of topics, leaving other areas under-examined and limiting our understanding of the field. By explicitly examining areas that are undescribed, i.e. absences in the literature, researchers and scholars have the potential to enrich our practice and our field's understanding of what counts as legitimate research. Using the theoretical framework of Bourdieu's concept of field, we conducted an instrumental case study of three published research projects that each had a finding of absence. We examined each case individually, and then analyzed across cases. Our dataset included published papers, peer-review feedback, and reflective notes. Each of the cases interrogated a different form of absence: absence of content, absence of research, and absence of evidence. While the typology suggests that each absence was different, there were similarities across cases in terms of challenges in 'proving' the reality of the absence and some disbelief or discomfort with accepting the findings as rigorous and/or legitimate. Absence research has potential to add to our theoretical and methodological approaches to the field. This type of research is potentially an exciting and productive new way for scholars to shed light on aspects of health professions education that have received limited attention to date.

A CTSA One Health Alliance guidance on institutional review of veterinary clinical studies

Harmonized institutional processes and reviewer training are vital to maintain integrity and ethical rigor of the veterinary clinical research pipeline and are a prerequisite to future work that might establish centralized or single-site ethical and regulatory review to ease initiation of multi-center studies. Funded by a CTSA One Health Alliance (COHA) pilot award, a diverse working group of veterinary clinicians and institutional representatives was convened in February 2020 to develop a guidance document detailing broadly agreed upon practices for ethical review and approval of veterinary clinical studies conducted in the United States.The working group defined key areas of need for consensus, developed a set of associated guidelines, and circulated these for review by COHA's fifteen member institutions. Six focus areas were identified by the working group and included vital items of protocol review, composition of the review committee, post-approval monitoring and adverse event reporting, consideration of special circumstances such as satellite sites and the use of healthy veterinary subjects in research, and the informed consent process.This document outlines a broadly agreed-upon framework through which to approach vital items associated with veterinary clinical study protocol review and approval. These approaches represent current best practice in the review and approval of veterinary clinical studies, and can serve as a guidance for veterinary clinician-scientists and regulatory experts, to ensure robust and ethically conducted studies that can contribute to the advancement of both animal and human health.

Defining Core Competencies for Epidemiologists in Academic Settings to Tackle Tomorrow's Health Research Challenges: A Structured, Multinational Effort

Only a few efforts have been made to define core competencies for epidemiologists working in academic settings. Here we describe a multinational effort to define competencies for epidemiologists, who are increasingly facing emerging and potentially disruptive technological and societal health trends in academic research. During a 1.5-year period (2017–2019), we followed an iterative process that aimed to be inclusive and multinational to reflect the various perspectives of a diverse group of epidemiologists. Competencies were developed by a consortium in a consensus-oriented process that spanned 3 main activities: 2 in-person interactive meetings held in Amsterdam, the Netherlands, and Zurich, Switzerland, and an online survey. In total, 93 meeting participants from 16 countries and 173 respondents from 19 countries contributed to the development of 31 competencies. These 31 competencies included 14 on “developing a scientific question” and “study planning,” 12 on “study conduct and analysis,” 3 on “overarching competencies,” and 2 on “communication and translation.” The process described here provides a consensus-based framework for defining and adapting the field. It should initiate a continuous process of thinking about competencies and the implications for teaching epidemiology to ensure that epidemiologists working in academic settings are well prepared for today’s and tomorrow’s health research.

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

A Market Shaping Approach for the Biopharmaceutical Industry: Governing Innovation Towards the Public Interest

Enhancing research and development and ensuring equitable pricing and access to cutting-edge treatments are both vital to a biopharmaceutical innovation system that works in the public interest. However, despite delivering numerous therapeutic advances, the existing system suffers from major problems: a lack of directionality to meet key needs, inefficient collaboration, high prices that fail to reflect the public contribution, and an overly-financialized business model.

The ethics of innovation for Alzheimer's disease: the risk of overstating evidence for metabolic enhancement protocols

Medical practice is ideally based on robust, relevant research. However, the lack of disease-modifying treatments for Alzheimer's disease has motivated "innovative practice" to improve patients' well-being despite insufficient evidence for the regular use of such interventions in health systems treating millions of patients. Innovative or new non-validated practice poses at least three distinct ethical questions: first, about the responsible application of new non-validated practice to individual patients (clinical ethics); second, about the way in which data from new non-validated practice are communicated via the scientific and lay press (scientific communication ethics); and third, about the prospect of making new non-validated interventions widely available before more definitive testing (public health ethics). We argue that the authors of metabolic enhancement protocols for Alzheimer's disease have overstated the evidence in favor of these interventions within the scientific and lay press, failing to communicate weaknesses in their data and uncertainty about their conclusions. Such unmeasured language may create false hope, cause financial harm, undermine informed consent, and frustrate the production of generalizable knowledge necessary to face the societal problems posed by this devastating disease. We therefore offer more stringent guidelines for responsible innovation in the treatment of Alzheimer's disease.

Islands and archipelagos: Reconciling programmatic vs. opportunistic research in health professions education

None

The carnage of substandard research during the COVID-19 pandemic: a call for quality

Worldwide there are currently over 1200 research studies being performed on the topic of COVID-19. Many of these involve children and adults over age 65 years. There are also numerous studies testing investigational vaccines on healthy volunteers. No research team is exempt from the pressures and speed at which COVID-19 research is occurring. And this can increase the risk of honest error as well as misconduct. To date, 33 papers have been identified as unsuitable for public use and either retracted, withdrawn, or noted with concern. Asia is the source of most of these manuscripts (n=19; 57.6%) with China the largest Asian subgroup (n=11; 57.9%). This paper explores these findings and offers guidance for responsible research practice during pandemics.

Mice with humanized-lungs and immune system - an idealized model for COVID-19 and other respiratory illness

Lack of an appropriate animal model to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for COVID-19 pandemic disease, represents a significant hurdle in the process of understanding disease biology and evaluating therapeutic and preventive candidates. It is time for public health agencies to revisit regulation on transplantation of human pluripotent stem cells for the possibility of the development of a humanized mice model with a humanized lung.

Publication rates of research projects of an internal funding program of a university medical center in Germany: A retrospective study (2004-2013)

Objectives

Non-publication and publication bias are topics of considerable importance to the scientific community. These issues may limit progress toward the 3R principle for animal research, promote waste of public resources, and generate biased interpretations of clinical outcomes. To investigate current publishing practices and to gain some understanding of the extent to which research results are reported, we examined publication rates of research projects that were approved within an internal funding program of the Faculty of Medicine at a university medical center in Germany, which is exemplary for comparable research funding programs for the promotion of young researchers in Germany and Europe.

Methods

We analyzed the complete set (n = 363) of research projects that were supported by an internal funding program between 2004 and 2013. We divided the projects into four different proposal types that included those that required an ethics vote, those that included an animal proposal, those that included both requirements, and those that included neither requirement.

Results

We found that 65% of the internally funded research projects resulted in at least one peer-reviewed publication; this increased to 73% if other research contributions were considered, including abstracts, book and congress contributions, scientific posters, and presentations. There were no significant differences with respect to publication rates based on (a) the clinic/institute of the applicant, (b) project duration, (c) scope of funding or (d) proposal type.

Conclusion

To the best of our knowledge, this is the first study to explore publication rates associated with early-career medical research funding. As >70% of the projects ultimately generated some form of publication, the program was overall effective toward this goal; however, non-publication of research results is still prevalent. Further research will explore the reasons underlying non-publication. We hope to use these findings to develop strategies that encourage publication of research results.

A survey of research quality in core facilities

Core facilities are an effective way of making expensive experimental equipment available to a large number of researchers, and are thus well placed to contribute to efforts to promote good research practices. Here we report the results of a survey that asked core facilities in Europe about their approaches to the promotion of good research practices, and about their interactions with users from the first contact to the publication of the results. Based on 253 responses we identified four ways that good research practices could be encouraged: (i) motivating users to follow the advice and procedures for best research practice; (ii) providing clear guidance on data-management practices; (iii) improving communication along the whole research process; and (iv) clearly defining the responsibilities of each party.

Correlates related to follow-up in a community engagement program in North Central Florida

AIMS

This analysis identifies the correlates of 60- and 120-day telephone-based study follow-ups among community-dwelling adults in North Central Florida.

METHODS

Six thousand three hundred and forty participants were recruited by Community Health Workers from the University of Florida's community engagement program with a face-to-face baseline and two phone follow-ups assessing indicators of health.

RESULTS

Physical disability versus none (adjusted odds ratio [aOR], 1.5; 95% confidence interval [CI], 1.2─1.9), high trust in research versus none (aOR, 1.5; 95% CI, 1.1─2.1), history of research participation versus none (aOR, 1.6; 95% CI, 1.3─2.0), having health insurance versus none (aOR, 1.4; 95% CI, 1.1─1.7), interest in research participation versus none (aOR, 1.8; 95% CI, 1.3─2.7), and no drug use versus drug use (aOR, 0.5; 95% CI, 0.3─0.9) significantly predicted completion of follow-up.

CONCLUSIONS

Health and social factors such as disability, insurance, history of and interest in research, trust and no drug use significantly predicted completing two follow-ups. These findings can facilitate efforts to minimize attrition in the research enterprise.