Statistical Analysis Must Improve to Address the Reproducibility Crisis: The ACcess to Transparent Statistics (ACTS) Call to Action.

The ACcess to Transparent Statistics (ACTS) call to action assembles four measures that are rapidly achievable by journals and funding agencies to enhance the quality of statistical reporting. The ACTS call to action is an appeal for concrete actions from institutions that should spearhead the battle for reproducibility.

Sex bias and omission in neuroscience research is influenced by research model and journal, but not reported NIH funding.

Neuroscience research has historically demonstrated sex bias that favors male over female research subjects, as well as sex omission, which is the lack of reporting sex. Here we analyzed the status of sex bias and omission in neuroscience research published across six different journals in 2017. Regarding sex omission, 16% of articles did not report sex. Regarding sex bias, 52% of neuroscience articles reported using both males and females, albeit only 15% of articles using both males and females reported assessing sex as an experimental variable. Overrepresentation of the sole use of males compared to females persisted (26% versus 5%, respectively). Sex bias and omission differed across research models, but not by reported NIH funding status. Sex omission differed across journals. These findings represent the latest information regarding the complex status of sex in neuroscience research and illustrate the continued need for thoughtful and informed action to enhance scientific discovery.

Hallmarks of a new era in mitochondrial biochemistry.

Stemming from the pioneering studies of bioenergetics in the 1950s, 1960s, and 1970s, mitochondria have become ingrained in the collective psyche of scientists as the "powerhouses" of the cell. While this remains a worthy moniker, more recent efforts have revealed that these organelles are home to a vast array of metabolic and signaling processes and possess a proteomic landscape that is both highly varied and largely uncharted. As mitochondrial dysfunction is increasingly being implicated in a spectrum of human diseases, it is imperative that we construct a more complete framework of these organelles by systematically defining the functions of their component parts. Powerful new approaches in biochemistry and systems biology are helping to fill in the gaps.

Female Authorship in Radiology: Trends in the Past Decade in CARJ.

PURPOSE: To identify trends in female authorship in the Canadian Association of Radiologists Journal (CARJ) from 2010 to 2019. METHODS: We retrieved papers published in the CARJ over a 10-year period, and retrospectively reviewed 602 articles. All articles except editorials and advertisements were included. We categorized the names of the first and last position authors as female or male and excluded articles that had at least one author of which gender was not known. We compared the trends in the first and last position authors of the articles from 2010 to 2019. For statistical analysis, logistic regression was performed with reported odds ratios (ORs), and a P value of <.05 was defined as statistically significant. RESULTS: Five hundred thirteen articles met inclusion criteria. Among them, 23 articles with a single author were classified as having only a first author. 39.8% (204/513) of first authors were female and 26.9% (132/490) of last authors were female. There has been an overall temporal increase in the odds of both the first and last author being female in CARJ publications (OR: 1.11, P = .034). Similarly, the odds a CARJ publication's first author being female increased over time (OR: 1.07, P = .033). Female last author did not predict female first author (OR: 1.48, P = .056). There was no association identified between female last author and year of publication (OR: 1.04, P = .225). CONCLUSION: There has been an overall increase in engagement of female authorship in CARJ.

Mind the gap: Gendered publication trends in oncology.

BACKGROUND: Investigating scientific publication trends in the field of oncology may highlight opportunities for improved representation, mentorship, collaboration, and advancement for women. METHODS: We conducted a bibliometric analysis of Annals of Surgical Oncology; Cancer; International Journal of Radiation Oncology, Biology, Physics (IJROBP); JAMA Oncology; and Journal of Clinical Oncology in 1990, 2000, 2010, and 2017. Full name and degree credentials per author role (ie, first or senior author), article type, publication year, and citation metrics were collected. First names were used to identify author gender. RESULTS: Across 9189 articles, female representation rose between 1990 and 2017 (first authors: 17.7% in 1990, 36.6% in 2017; senior authors: 11.7% in 1990, 28.5% in 2017). For the 50 most cited articles per year, women comprised a smaller percent of first (26.5%) and senior (19.9%) authors. The average citation count was higher for male first (44.8 per article) and senior (47.1) authors compared to female first (39.7) and senior (44.1) authors. With male senior authors, the first author was more likely male (71.4% male; 25.0% female); with female senior authors, first authors were 50.2% male and 47.6% female. IJROBP had the lowest total female representation among first (25.1%) and senior (16.7%) authors. Women had more MDs with Masters degrees, whereas men held more MDs only and more MDs with PhDs. CONCLUSION: Despite positive trends, substantial gendered differences in oncology publications persist. Fostering more women in oncology research will benefit female representation at many levels of academia and improve productivity, collaboration, and recruitment, especially in technical fields such as radiation and surgical oncology.

A century of Hereditas: from local publication to international journal.

BACKGROUND: The Mendelian Society of Lund launched Hereditas in 1920. The purpose of this article is to give an overview of Hereditas's hundred-year existence, focusing on the conditions for a learned society to publish a scientific journal, and the journal's importance for the publication and dissemination of genetic research. The article focuses on the historical development of the journal and analyses how the content and orientation of research published in Hereditas have changed over the years. METHODS: The historical study is based on the collation and interpretation of archival material, mainly held in the Mendelian Society's archive, which includes the Hereditas archive. The bibliometric analyses are based on bibliographic metadata from Web of Science (WoS). Together with descriptive statistics, co-citation analyses were performed by using BibExcel, in combination with the clustering and visualisation tool VOSviewer. Journals with articles citing Hereditas articles were identified as a complement to the co-citation analyses. RESULTS: The history of the journal falls into three main periods: a local period, 1920-1959, when Hereditas was primarily intended for Swedish geneticists; a Scandinavian period, 1960-1988, when Hereditas was the official journal of the Scandinavian Association of Geneticists; and an international period from 1989 onwards. The original decision that Hereditas should cover genetic research with no particular specialisation was retained throughout. Its publications demonstrate the continuing presence of genetic research on plants and animals, albeit with a shifting focus, while human genetics emerged slowly and reached its peak in the period 1960-1988. CONCLUSION: In the hundred years of Hereditas's existence, the publishing landscape has changed dramatically, including a far greater number of specialist journals, changes to the academic merit system, new commercial models for publishing, and digitalisation. Over the years, the journal's survival has therefore been dependent on the strong commitment of its owners and an ability to adapt to changing conditions.

Systematic mapping of organophosphate contaminant (OPC) research trends between 1990 and 2018.

Since the addition of polybrominated diphenyls and organochlorine pesticides (OCPs) to the world banned list, toxic organophosphate contaminants (OPCs) such as organophosphate flame retardants and organophosphate pesticides have been, respectively, used as substitutes. These chemicals are reported to be more toxic than their halogenated counterparts. It is rare to find a study that focuses on visualising the publication trends of these chemical classes. In this study, we employed a bibliometric model to systematically map research activities between 1990 and 2018 using OPC articles retrieved from the WoS and Scopus databases. A total of 1090 articles were retrieved from the hybrid databases with an article/author and author/article ratio of 0.33 and 3.02, respectively. Articles on OPC studies were positively correlated with the number of years (r2 = 0.96; y = 0.23x2 - 3.82x + 27.90) suggesting an increase in the number of articles on this subject in future. The USA ranked first in terms of articles (n = 245) and citations (n = 12,922) followed by China and India (203 and 89 articles, respectively). Articles from China and the USA had strong collaboration with other countries. Research priorities and top author keywords included pesticides (n = 112), organophosphate (n = 83) and acetylcholinesterase (n = 60) and were also well represented in keywords-plus. Developed countries had higher outputs compared to developing countries. It was observed that from our thematic literature classifications, human toxicity, ecotoxicological impacts, and environmental monitoring of OPCs were of greater importance to scholars, thus indicating the direction of future research. Futuristic studies need to foster partnership with policymakers, journalists, consultants, farmers, artisans and community workers on OPC research. This will not only enhance scientific communication and community engagement but will also increase the awareness of these pollutants to the general public.

Badges to Acknowledge Open Practices: A Simple, Low-Cost, Effective Method for Increasing Transparency.

Beginning January 2014, Psychological Science gave authors the opportunity to signal open data and materials if they qualified for badges that accompanied published articles. Before badges, less than 3% of Psychological Science articles reported open data. After badges, 23% reported open data, with an accelerating trend; 39% reported open data in the first half of 2015, an increase of more than an order of magnitude from baseline. There was no change over time in the low rates of data sharing among comparison journals. Moreover, reporting openness does not guarantee openness. When badges were earned, reportedly available data were more likely to be actually available, correct, usable, and complete than when badges were not earned. Open materials also increased to a weaker degree, and there was more variability among comparison journals. Badges are simple, effective signals to promote open practices and improve preservation of data and materials by using independent repositories.

Assessments of Metals in Coastal Environments: State of Art.

This study is an overview of the assessments of metal contamination in coastal environments for the past five decades. Research articles with evaluations in sediments and biota were quantified and had their content visited for the registry of (1) the source of metals (anthropogenic or natural), (2) assessed country/territory, (3) groups of organisms assessed, (4) trophic transfer evaluation, (5) spatio-temporal variations, and (6) metals evaluated. We found an increase in the number of assessments over the years, mainly from 2014. The majority of the assessments pointed to anthropogenic sources of metals. The United States, the United Kingdom, and China were the most assessed countries. "Mollusks" was the most assessed group of organisms, and only 17% of all sampled studies identified any trophic relation, although there has been an increase since 2013. Spatial variations were more frequent than spatio-temporal and temporal variations alone. Cadmium, copper, zinc, and lead were the top metals evaluated in both sediment and biota. We believe that these are all valuable information for researchers and policy makers interested in the topic.

Genetic approach towards a vaccine against malaria.

Malaria is a major concern for international health authorities. Millions of people contract it every year in the world due to a parasite of the Plasmodium genus. Due to the complexity of the parasite biology and genetics, there is currently no vaccine against the disease. However, due to the great resistance both to the medicines and to the insecticides used to combat the disease, it has become essential to obtain a vaccine as the necessary tool to prevent transmission and eliminate the disease. The bibliometric data indicate that interest in vaccines has been growing steadily since the 1980s. But nowadays, a powerful tool is used: the Plasmodium genome. This allows us to improve the fight against the disease. Knowing the sequences of the genes that favor the appearance of drug resistance, or those that encode for proteins with greater antigenic response, is a tool that can become fundamental. This article reviews the state of the art on vaccines and genetics, in the fight against malaria, and analyzes the fixed photo that the worldwide research on the disease poses.

Publication Rate of Avian Medicine Conference Abstracts and Influencing Factors: 2011-2015.

International conferences on avian medicine and surgery aim to disseminate scientific and evidence-based information in the form of oral presentations and posters. Most manuscripts presented are printed in the conference proceedings as abstracts. Subsequent publication in a scientific peer-reviewed journal is the natural outcome of the research cycle, although studies have shown that the vast majority of conference abstracts are not published. The purpose of this study was to explore 1) the fate of abstracts presented in avian conferences (Association of Avian Veterinarians, European Association of Avian Veterinarians, International Conference on Avian Herpetological and Exotic Mammal Medicine) in the years 2011-2015, 2) assess the publication rate in peer-reviewed journals, 3) describe the time course of subsequent publication, and 4) identify factors associated with increased likelihood of publication. The results showed that 24% of conference abstracts were published within the next 2 years. Depending on the statistical model used, several factors were identified as associated with increased publication rate. North American papers seem to publish with more frequency (univariate model), while European papers had the opposite trend (multivariable model). Likewise, experimental studies were more prone to being published overall (univariate model), whereas retrospective observational studies had a lower rate of publication (multivariable model). Increasing the number of authors was also associated with increased publication rate. Most publications were published in the Journal of Avian Medicine and Surgery, which tends to suggest that this journal is the main journal of the specialty. Some parameters highlighted in this study may assist conference attendees to assess the likelihood of later publication.

The impact of physician burnout on clinical and academic productivity of gynecologic oncologists: A decision analysis.

OBJECTIVE: Physician burnout is associated with mental illness, alcohol abuse, and job dissatisfaction. Our objective was to estimate the impact of burnout on productivity of gynecologic oncologists during the first half of their career. METHODS: A decision model evaluated the impact of burnout on total relative value (RVU) production during the first 15years of practice for gynecologic oncologists entering the workforce from 2011 to 2015. The SGO practice survey provided physician demographics and mean annual RVUs. Published data were used to estimate probability of burnout for male and female gynecologic oncologists, and the impact of depression, alcohol abuse, and early retirement. Academic productivity was defined as annual PubMed publications since finishing fellowship. RESULTS: Without burnout, RVU production for the cohort of 250 gynecologic oncologists was 26.2 million (M) RVUs over 15years. With burnout, RVU production decreased by 1.6 M (5.9% decrease). Disproportionate rates of burnout among females resulted in 1.1 M lost RVUs for females vs. 488 K for males. Academic production without burnout was estimated at 9277 publications for the cohort. Burnout resulted in 1383 estimated fewer publications over 15years (14.9%). CONCLUSIONS: The impact of burnout on clinical and academic productivity is substantial across all specialties. As health care systems struggle with human resource shortages, this study highlights the need for effective burnout prevention and wellness programs for gynecologic oncologists. Unless significant resources are designated to wellness programs, burnout will increasingly affect the care of our patients and the advancement of our field.

Presenting data in such a fashion that they can be used by other scientists.

Data always have an experimental uncertainty, i.e. error limits within which the value is very likely to be found. Although the use of statistics is common as is the use of least squares it remains uncommon to see reported the covariance between parameters for an equation to which data have been fitted. This means that a reader cannot properly calculate the error in an extrapolated or interpolated value. Even when the uncertainties in the least squares parameters are reported, errors calculated without the covariance are often too large and almost always different from the correct values calculated using the full formula. This report will demonstrate the importance of covariance in several examples. Systematic errors are also touched on; solubilities of highly hydrophobic and highly insoluble compounds are very difficult to measure for reasons not widely enough appreciated. Aggregation leading to suspended nanodroplets or nanocrystals can lead to spuriously high apparent solubilities. Another class of systematic errors comes from using an equation which is too simple for a desired extrapolation to a value of interest. The magnitude of this possible error is presented for a number of cases. Extrapolation can lead to a value of some use even though it is very uncertain, but expected uncertainty should be pointed out. Recommendations for good publishing practice are proposed for both authors and editors.

Do citation trends reflect epidemiologic patterns? Assessing MRSA, emerging and re-emerging pathogens, 1963-2014.

BACKGROUND: A rapid rise in PubMed citations on methicillin-resistant Staphylococcus aureus (MRSA) occurred after 2000, but the relationship of trends in citation to epidemiologic trends for infectious disease is not known. METHODS: We queried PubMed(R), for citations to the following: MRSA, HIV/AIDS, Staphylococcus aureus, severe acute respiratory syndrome, Lyme disease, avian influenza, West Nile virus, Chikungunya, Ebola virus and Middle Eastern respiratory syndrome. Incidence or mortality data were tabulated. RESULTS: We identified 560,225 citations in 1963-2014. There were two distinct qualitative citation patterns. Type I pathogens showed a decade of initial exponential growth. Type II pathogens showed a sudden spike in citations in a year or two, followed by a relative decline. MRSA most closely resembled a Type I pathogen. CONCLUSIONS: The Type I pattern pathogens had varied trends in disease incidence in the years following the exponential growth and subsequent decline in the number of citations. Their differing epidemiologic patterns did not correlate with their pattern of citations. We conclude that citation trends on MRSA cannot be used to determine past epidemiologic trends and also that the citation trend for MRSA in 1995-2011 most closely resembled that for HIV in 1981-1998.

A small field for fertile science: the low visibility of reproductive science in high impact journals.

PURPOSE: Our success as a field and as individuals in reproductive science and medicine relies on our ability to produce high quality work that has broad visibility and impact. A common metric for assessing such success is the quantity of publications that are published in journals with high impact factors. It is unclear, however, how frequently work related to reproductive science and medicine actually appears in what are considered the highest impact journals. METHODS: To address this gap in knowledge, we first determined how the field of reproductive biology in general compared to other research areas in terms of composite journal impact factor. Second, using a targeted search approach in the PubMed database, we examined the relationship between a journal's impact factor and the number of reproductive research articles published per journal issue. RESULTS: We found that compared to other major scientific disciplines, our field lacks journals with impact factors above 4. In addition, primary original research articles on reproduction-irrespective of male or female search terms-do not appear often in high impact journals. Instead, there is an increased percentage of secondary reproductive literature in high impact journals compared to topic-specific journals of lower impact. CONCLUSIONS: There are likely several explanations for why reproductive science and medicine has low visibility, including the field's small relative size, its lack of a specific disease and associated strong advocacy, and its surrounding social, ethical, and political unease. Nevertheless, there are concrete actions we can take to minimize the role of impact factor in our evaluation while simultaneously increasing influence through global awareness of the importance and need for reproductive research.