An inferential spatiotemporal approach for knowledge synthesis to identify trends in public health research.

Background: Decisions follow patterns that are introduced by human perception. Research and development (R&D) are influenced by these patterns. Furthermore, R&D publications can represent repetitive attempts to solve similar, or the same problems. Literature reviews serve as an important tool for identifying these trends, but they are time consuming. The time commitment of a literature review can be reduced by using a sample of research. This will allow an infinite population of research to be generalized. Additionally, spatiotemporal analysis is most appropriate for fields that follow time and geographic trends, such as public health. Also, using research locations to perform this analysis potentially captures the social return of R&D, as knowledge gained. As a result, an inferential spatiotemporal methodological framework is introduced to quickly identify research trends using public health research. This was applied to a childhood Pb exposure case study. Methods: A body of more than 1000 childhood elevated blood lead (Pb) level (EBLL) research articles were used to extract publication years, research locations, and subtopics. These publications were grouped into research locations (i.e., U.S. states where research was conducted; not publication location) and averaged over years published (i.e., 29 years). Binary indicator variables were derived using the subtopics extracted and the periods identified in time trend analyses. Explanatory variables were used to conduct hypothesis testing. Significant variables were used to generalize the population of the annual average EBLL articles written per state. Results: The range of the annual average of EBLL research articles by state was 0-1.7 articles, with a mean of 0.3 articles. Thirty-eight explanatory variables suggested a significant effect on research article production. These included temporal, sociodemographic, education, structure age, environmental, and economic variables. The strongest effect on research production for U.S. states came from the number of structures built before 1950. A predictive model was selected to generalize the population of articles using time-periods 1990-95, environmental subtopic, and structures built before 1950. The locations with the most research production for this topic were California and New York. The locations with the least research production for this topic were Alaska, Hawaii, Nevada, Wyoming, North Dakota, South Dakota, Mississippi, Delaware, and New Hampshire. Conclusion: If the trend for R&D is to make fast decisions, more human bias will be introduced into the decision-making process. Analytical tools that enable researchers to identify trends and ask more questions about their field will mitigate these biases. This hypothesis testing and predictive modeling methodology provide researchers and other decision makers with analytical tools they can use to quickly identify research trends and narrow their field of research. Additionally, this analysis potentially captures the impact of discovered ideas, as a social return spillover, for this topic.

Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement.

Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort's fingerprint genomic sites. The FPFinder was developed based on the term frequency-inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future.

Low availability of functional seed trait data from the tropics could negatively affect global macroecological studies, predictive models and plant conservation.

BACKGROUND: Plant seeds have many traits that influence ecological functions, ex situ conservation, restoration success and their sustainable use. Several seed traits are known to vary significantly between tropical and temperate regions. Here we present three additional traits for which existing data indicate differences between geographical zones. We discuss evidence for geographical bias in availability of data for these traits, as well as the negative consequences of this bias. SCOPE: We reviewed the literature on seed desiccation sensitivity studies that compare predictive models to experimental data and show how a lack of data on populations and species from tropical regions could reduce the predictive power of global models. In addition, we compiled existing data on relative embryo size and post-dispersal embryo growth and found that relative embryo size was significantly larger, and embryo growth limited, in tropical species. The available data showed strong biases towards non-tropical species and certain families, indicating that these biases need to be corrected to perform truly global analyses. Furthermore, we argue that the low number of seed germination studies on tropical high-mountain species makes it difficult to compare across geographical regions and predict the effects of climate change in these highly specialized tropical ecosystems. In particular, we show that seed traits of geographically restricted páramo species have been studied less than those of more widely distributed species, with most publications unavailable in English or in the peer-reviewed literature. CONCLUSIONS: The low availability of functional seed trait data from populations and species in the tropics can have negative consequences for macroecological studies, predictive models and their application to plant conservation. We propose that global analyses of seed traits with evidence for geographical variation prioritize generation of new data from tropical regions as well as multi-lingual searches of both the grey- and peer-reviewed literature in order to fill geographical and taxonomic gaps.

COVID-19 pandemic drives changes in participation in citizen science project "City Nature Challenge" in Tokyo.

The COVID-19 pandemic has changed the way large citizen science events can be carried out-reducing gatherings of large groups and shifting toward individual, small-group, and online participation. This paper aims to describe changes in participant engagement in the City Nature Challenge (CNC) in Tokyo. The CNC is a four-day international event held in April to document biodiversity in cities using an online citizen science platform, iNaturalist. To assess the impact of COVID-19, we compared the number of participants, observations, species, and identification rates in 2019 (pre-pandemic) and 2020 (during the pandemic). We also used cluster analysis to elucidate participation patterns, and we assessed changes in the geographical distribution of observation sites. The results showed: (1) the number of participants and observations decreased by 63% and 68%, respectively; however, the number of species was almost the same in the two years, and the identification rate increased 154% in 2020 relative to 2019. (2) The most enthusiastic participants contributed in similar amounts in 2019 and 2020, but participation by less enthusiastic volunteers drastically declined. (3) The spatial distribution of observation sites changed from cluster-like to scattered. Understanding participant engagement during the pandemic could help to improve data quality, reduce geographical bias in observations, maintain records, and recruit more users in future years. Online citizen science could provide opportunities for many citizens to get outside and participate in conservation science during and after the pandemic.

The geographic bias of mammal studies: a comparison of a half a century of research on Palearctic and Neotropical mammals / El sesgo geográfico en el estudio de los mamíferos: comparación de medio siglo de investigación sobre mamíferos paleárticos y neotropicales

Abstract Introduction: There are no studies that specifically compare research output of Palearctic and Neotropical mammalogy; such comparison would be useful for informed decisions in conservation and management. Objective: To compare the scientific documents and citations about Palearctic and Neotropical mammals over half a century. Methods: We compared 50 years (1970-2019) of documents on 60 medium and large-sized (heavier than 1 kg) mammal species, in Scopus and the Web of Science (WoS) Core Collection, considering number of documents and four citation indicators at the species level (h-index, citation rate, total citations, and citations per year). Results: We retrieved 13 274 documents in Scopus and 12 913 in WoS. We found that Palearctic mammals have 3.77 times more documents than Neotropical species in Scopus (3.91 times in WoS), and that the documents recorded 5.95 more total citations in Scopus (6.93 times more in WoS). Palearctic documents also record more yearly citations and a higher h-index in both Scopus and WoS. Scopus retrieved more articles for Neotropical species (2 782 vs. 2 631 in WoS) and had more citations (28 120 vs. 24 977 in WoS); differences for the citation indicators between regions were marker in WoS. The h-index and total citations are greatly affected by how many studies are published, i.e. the region with more production is the one with higher values. The Neotropical articles showed a greater growth rate in the last decade, decreasing the gap between both regions. Conclusion: There is a regional bias in WoS and Scopus, which retrieve more articles and citations about Palearctic mammals than about Neotropical mammals; this bias is worse in WoS and means that an urgent increase in indexed research about Neotropical species is needed to be on par with Palearctic research.

Resumen Introducción: No existen estudios que comparen, específicamente, la investigación de la mastozoología paleártica con la neotropical; pero tales comparaciones serían útiles para tomar decisiones informadas en conservación y manejo. Objetivo: Comparar los documentos científicos sobre mamíferos paleárticos y neotropicales, y su impacto en citas, durante medio siglo. Métodos: Comparamos 50 años (1970-2019) de documentos sobre 60 especies de mamíferos de tamaño mediano y grande (más de 1 kg), en Scopus y la colección principal del Web of Science (WoS), considerando el número de documentos y cuatro indicadores de citas a nivel de especie (índice h, tasa de citas, total de citas y citas por año). Resultados: Recuperamos 13 274 documentos en Scopus y 12 913 en WoS, y encontramos que los mamíferos paleárticos tienen 3.77 veces más documentos que las especies neotropicales en Scopus (3.91 veces en WoS), y que los documentos registran 5.95 más citas totales en Scopus (6.93 veces más en WoS). Los documentos paleárticos también registran más citas anuales y un índice h más alto, tanto en Scopus como en WoS. Scopus recuperó más artículos para especies neotropicales (2 782 vs. 2 631 en WoS) y tuvo más citas (28 120 vs. 24 977 en WoS). Las diferencias para los indicadores de citas entre regiones fueron más marcadas en WoS. El índice h y el total de citas se ven muy afectados por la cantidad de estudios publicados, es decir, la región con más producción será la que tenga indicadores más altos. Los artículos neotropicales mostraron una mayor tasa de crecimiento en la última década, disminuyendo la brecha entre ambas regiones. Conclusión: Existe un sesgo regional en WoS y Scopus, que recuperan más artículos y citas sobre mamíferos paleárticos que sobre mamíferos neotropicales; este sesgo es peor en WoS y significa que se necesita un aumento urgente en la investigación indexada sobre especies neotropicales para estar al nivel de la investigación paleártica.

Does Geographical Bias Impact the Match for General Surgery Residents?

OBJECTIVE: As the competitiveness of applicants for general surgery residency grows, it is becoming challenging for programs to differentiate qualified candidates with a genuine interest in matching at their institution. The purpose of this study was to examine geographic trends in the general surgery match in order to elicit regional biases and optimize applicant interview selection strategies. DESIGN: In this single-center retrospective study, geographical information regarding birth place, college, medical school, and final match institution for general surgery residency applicants was examined. SETTING: This study was set at the University of Cincinnati College of Medicine. PARTICIPANTS: All general surgery residency applicants interviewing at our institution between 2015-2017 were included. METHODS: Academic variables and geographical information were collected for all applicants in the cohort. Statistical analyses were performed using chi-square and logistic regression techniques to determine any association between geography and match outcomes. RESULTS: Of 198 applicants included in the analysis, approximately 25% matched at an institution located in the same state as their medical school. Total 75% of applicants matched at a residency program located less than 640 miles away from either their birth place, college, or medical school, while only 15% matched at an institution located over 1000 miles away and 4% matched over 2000 miles away. When examining applicant characteristics, there were no significant differences in gender, clerkship grade, United States Medical Licensing Exam scores, Alpha Omega Alpha Honor Society membership, or quality of recommendation letters between applicants who matched in the lowest and highest quartiles of distance to final residency program location. CONCLUSIONS: A significant proportion of general surgery applicants matched at institutions located in a region near either their birth place, college, or medical school. Given the limited number of interviews able to be offered by institutions and the associated opportunity costs, general surgery programs should consider regional biases when evaluating residency applicants.

Contrasting effects of temperature and precipitation change on amphibian phenology, abundance and performance.

Climate change is determining a generalized phenological advancement, and amphibians are among the taxa showing the strongest phenological responsiveness to warming temperatures. Amphibians are strongly influenced by climate change, but we do not have a clear picture of how climate influences important parameters of amphibian populations, such as abundance, survival, breeding success and morphology. Furthermore, the relative impact of temperature and precipitation change remains underappreciated. We used Bayesian meta-analysis and meta-regression to quantify the impact of temperature and precipitation change on amphibian phenology, abundance, individual features and performance. We obtained effect sizes from studies performed in five continents. Temperature increase was the major driver of phenological advancement, while the impact of precipitation on phenology was weak. Conversely, population dynamics was mostly determined by precipitation: negative trends were associated with drying regimes. The impact of precipitation on abundance was particularly strong in tropical areas, while the importance of temperature was feeble. Both temperature and precipitation influenced parameters representing breeding performance, morphology, developmental rate and survival, but the response was highly heterogeneous among species. For instance, warming temperature increased body size in some species, and decreased size in others. Similarly, rainy periods increased survival of some species and reduced the survival of others. Our study showed contrasting impacts of temperature and precipitation changes on amphibian populations. Both climatic parameters strongly influenced amphibian performance, but temperature was the major determinant of the phenological changes, while precipitation had the major role on population dynamics, with alarming declines associated with drying trends.

Inadequate use and regulation of interventions against publication bias decreases their effectiveness: a systematic review.

OBJECTIVES: To determine the effectiveness of interventions designed to prevent or reduce publication and related biases. STUDY DESIGN AND SETTING: We searched multiple databases and performed manual searches using terms related to publication bias and known interventions against publication bias. We dually reviewed citations and assessed risk of bias. We synthesized results by intervention and outcomes measured and graded the quality of the evidence (QoE). RESULTS: We located 38 eligible studies. The use of prospective trial registries (PTR) has increased since 2005 (seven studies, moderate QoE); however, positive outcome-reporting bias is prevalent (14 studies, low QoE), and information in nonmandatory fields is vague (10 studies, low QoE). Disclosure of financial conflict of interest (CoI) is inadequate (five studies, low QoE). Blinding peer reviewers may reduce geographical bias (two studies, very low QoE), and open-access publishing does not discriminate against authors from low-income countries (two studies, very low QoE). CONCLUSION: The use of PTR and CoI disclosures is increasing; however, the adequacy of their use requires improvement. The effect of open-access publication and blinding of peer reviewers on publication bias is unclear, as is the effect of other interventions such as electronic publication and authors' rights to publish their results.