Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Morphological colour adaptation during development: Involvement of Growth Hormone Receptor 1

Morphological background adaptation is both an endocrine and a nervous response, involving changes in the amount of chromatophores and pigment concentration. However, if this adaptation takes place at early developmental stages is largely unknown. Somatolactin (SL) is a pituitary hormone present in fish, which has been associated to skin pigmentation. Moreover, growth hormone receptor type 1 (ghr1) has been suggested to be the SL receptor and was associated to background adaptation in adults. In this context, the aim of this work was to evaluate the ontogeny of morphological adaptation to background and the participation of ghr1 in this process. We found in larval stages of Cichlasoma dimerus that the number of head melanophores and ir-SL pituitary cells were increased in individuals reared in black backgrounds compared to fish grown in white tanks. In medaka (Oryzias latipes) larval stages a similar response was observed that is altered by a ghr1 biallelic mutations using CRISPR/cas9. Interestingly, melanophore and leucophore numbers are highly associated. Furthermore, we found that somatic growth is reduced in ghr1 biallelic mutant medaka, establishing the dual function of this growth hormone receptor. Taken together, these results show that morphological background adaptation is present at early stages during development and that is dependent upon ghr1 unless during this period.Fil: Delgadin, Tomás Horacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental. Laboratorio de Embriología Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Castañeda Cortes, Diana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Sacks, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Breccia, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Fernandino, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Vissio, Paula Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental. Laboratorio de Embriología Animal; Argentin

Public support for healthy supermarket initiatives focused on product placement: a multi-country cross-sectional analysis of the 2018 International Food Policy Study

BACKGROUND: Food retail environments have an influential role in shaping purchasing behavior and could contribute to improving dietary patterns at a population level. However, little is known about the level of public support for different types of initiatives to encourage healthy food choices in supermarkets, and whether this varies across countries or context. The current study aimed to explore the level of support for three potential supermarket initiatives focused on product placement across five countries, and factors that may influence this support. METHODS: A total of 22,264 adults from Australia, Canada, Mexico, the United Kingdom and the United States (US) provided information on support for three supermarket initiatives related to product placement (targeting product positioning: ‘checkouts with only healthy products’, ‘fewer end-of-aisle displays containing unhealthy foods or soft drinks’ or availability: ‘more shelf space for fresh and healthier foods’) as part of the online 2018 International Food Policy Study. The proportion of respondents that supported each initiative was assessed across countries, and multivariable logistic regression analyses were conducted to evaluate the influence of sociodemographic factors on support. RESULTS: The initiative that received the highest support was ‘more shelf space for fresh and healthier foods’: 72.0% [95% CI 71.3–72.7], whereas ‘checkouts with only healthy products’ received the lowest support: 48.6% [95% CI 47.8–49.4]. The level of support differed between countries (p < 0.001 for all initiatives), with the US generally showing the lowest support and Mexico the highest. Noteworthy, in the overall sample, there was not much opposition to any of the initiatives (2.5–14.2%), whereas there was a large proportion of neutral responses (25.5–37.2%). Respondents who were older, female, highly educated, and those who reported having more nutrition knowledge tended to be more supportive, with several differences between countries and initiatives. CONCLUSIONS: Most people in the assessed five countries showed a generally high level of support for three placement initiatives in supermarkets to encourage healthy food choices. Support varied by type of initiative (i.e., product positioning or availability) and was influenced by several factors related to country context and sociodemographic characteristics. This evidence could prompt and guide retailers and policy makers to take stronger action to promote healthy food choices in stores. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12966-021-01149-0

Meat-Reduced Dietary Practices and Efforts in 5 Countries: Analysis of Cross-Sectional Surveys in 2018 and 2019.

BACKGROUND: Diets that reduce reliance on animal-source foods are recommended in some contexts. OBJECTIVES: This study aimed to compare proportions of respondents who reported following meat-reduced dietary practices (i.e., vegetarian, vegan, or pescatarian diets) and/or making efforts to reduce animal-source foods, and to examine sociodemographic correlates across 5 countries. METHODS: Online surveys were conducted in November and December 2018 and 2019 with 41,607 adults from Australia (n = 7926), Canada (n = 8031), Mexico (n = 8110), the United Kingdom (n = 9129), and the United States (n = 8411) as part of the International Food Policy Study. Respondents were asked whether they would describe themselves as vegetarian, vegan, or pescatarian, and whether they had made efforts to consume less red meat, less of all meats, or less dairy in the past year. Logistic regressions examined differences in the likelihood of each behavior between countries and sociodemographic subgroups. RESULTS: Approximately 1 in 10 respondents reported following a vegetarian, vegan, or pescatarian diet, ranging from 8.6% (Canada) to 11.7% (UK). In the past 12 months, the proportions of respondents who reported efforts to consume less red meat ranged from 34.5% (Australia) to 44.4% (Mexico), less of all meats ranged from 27.9% (US) to 35.2% (Mexico), and to consume less dairy ranged from 20.6% (UK) to 41.3% (Mexico). Respondents were more likely to report efforts to consume less animal-source products in 2019 compared to 2018 in most countries. Sociodemographic patterns varied by country; in general, women, those with higher education levels, and those in minority ethnic groups were more likely to report following meat-reduced dietary practices or efforts to consume fewer animal-source products. CONCLUSIONS: Nearly half of respondents reported following a meat-reduced diet or efforts to reduce animal-source products, with differences between countries and population subgroups. Population-level approaches and policies that support meat reduction may further reduce consumption of animal-source products.Funding for the International Food Policy Study was provided by a Canadian Institutes of Health Research (CIHR) Project Grant (PJT-162167), with additional support from Health Canada, the Public Health Agency of Canada (PHAC), and a CIHR-PHAC Applied Public Health Chair (DH). MW is supported with funding for a research programme in the MRC Epidemiology Unit, University of Cambridge, UK (MRC grant number: MC/UU/00006/7)

O aprendizado da utilização da substituição sensorial visuo-tátil por pessoas com deficiência visual: primeiras experiências e estratégias metodológicas The learning of the use of the tactile-vision sensory substitution by people with visual disability: first experiences and methodological strategies

O sistema de substituição tátil-visual (TVSS) é uma tecnologia assistiva criada para ajudar deficientes visuais a perceberem aspectos visuais de seu ambiente através do tato e contribuir para sua inclusão social. Para melhor entender o processo de aprendizagem dessa tecnologia, quatro participantes cegos foram treinados com o Brainport®, a última versão do TVSS, onde imagens visuais transformadas são exploradas pela língua. O artigo objetiva de investigar o estágio inicial desse processo de aprendizagem, em termos tanto do desempenho dos participantes quanto da qualidade de sua experiência. O treinamento, conduzido de acordo com um método clínico-pedagógico, produziu dados em terceira pessoa e em primeira pessoa. Os dados foram obtidos através de registros de desempenho e de entrevistas de explicitação. Os resultados mostram que as maiores dificuldades surgidas foram relativas ao acoplamento sensório-motor, aos movimentos do corpo e da cabeça e à dissonância entre as expectativas e a qualidade da experiência perceptiva.<br>The tactile-vision-substitution-system (TVSS) is an assistive technology designed to aid the visually impaired in perceiving visual aspects of their environment located beyond touch. In order to better understand the learning process of that assistive aid, we trained four blind participants with the Brainport®, the last version of the TVSS, where the transformed visual images are explored by the tongue. More specifically, this article aims to investigate the initial stage of this learning process, in terms both of participants' performance and their qualitative experience. The training, conducted according to the clinical-pedagogic method, produced data both from the first-person and the third-person point of view. Data were gathered through records of participants' performance and explanation interviews. Results show that the main difficulties arising during the process concerned sensory-motor coupling, body and head movement, and the gap between actual and expected quality of the perceptual experience