A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In interpreting such results, two tasks are crucial: clustering of redundant motifs, and attributing the motifs to transcription factors by retrieval of similar motifs from previously characterized motif libraries. Both tasks inherently involve motif comparison. Here we present a novel method for comparing and merging motifs, based on Bayesian probabilistic principles. This method takes into account both the similarity in positional nucleotide distributions of the two motifs and their dissimilarity to the background distribution. We demonstrate the use of the new comparison method as a basis for motif clustering and retrieval procedures, and compare it to several commonly used alternatives. Our results show that the new method outperforms other available methods in accuracy and sensitivity. We incorporated the resulting motif clustering and retrieval procedures in a large-scale automated pipeline for analyzing DNA motifs. This pipeline integrates the results of various DNA motif discovery algorithms and automatically merges redundant motifs from multiple training sets into a coherent annotated library of motifs. Application of this pipeline to recent genome-wide transcription factor location data in S. cerevisiae successfully identified DNA motifs in a manner that is as good as semi-automated analysis reported in the literature. Moreover, we show how this analysis elucidates the mechanisms of condition-specific preferences of transcription factors

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km² resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e., offset) between in-situ soil temperature measurements, based on time series from over 1200 1-km² pixels (summarized from 8500 unique temperature sensors) across all the world’s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in-situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Prevention of Cardiovascular Diseases in Community Settings and Primary Health Care: A Pre-Implementation Contextual Analysis Using the Consolidated Framework for Implementation Research

Cardiovascular diseases are the world’s leading cause of mortality, with a high burden especially among vulnerable populations. Interventions for primary prevention need to be further implemented in community and primary health care settings. Context is critically important to understand potential implementation determinants. Therefore, we explored stakeholders’ views on the evidence-based SPICES program (EBSP); a multicomponent intervention for the primary prevention of cardiovascular disease, to inform its implementation. In this qualitative study, we conducted interviews and focus groups with 24 key stakeholders, 10 general practitioners, 9 practice nurses, and 13 lay community partners. We used adaptive framework analysis. The Consolidated Framework for Implementation Research guided our data collection, analysis, and reporting. The EBSP was valued as an opportunity to improve risk awareness and health behavior, especially in vulnerable populations. Its relative advantage, evidence-based design, adaptability to the needs and resources of target communities, and the alignment with policy evolutions and local mission and vision, were seen as important facilitators for its implementation. Concerns remain around legal and structural characteristics and intervention complexity. Our results highlight context dimensions that need to be considered and tailored to primary care and community needs and capacities when planning EBSP implementation in real life settings

Primary prevention of cardiovascular diseases in Belgian primary health care : development and implementation of a comprehensive intervention program in general practice and community settings in Antwerp

Abstract: Cardiovascular diseases (CVD) are the world\u2019s leading cause of morbidity and mortality, placing a disproportionately higher burden in populations with a low socio-economic status. Nearly 75% of premature CVD deaths are preventable. Healthy lifestyle behaviour is important in the prevention of CVD and its modifiable risk factors. However, a critical research-practice gap remains on the implementation of structured preventive interventions. Horizon 2020 funded \u2018Scaling-up Packages of Interventions for cardiovascular disease prevention in selected sites in Europe and sub-Saharan Africa\u2019 (SPICES) project aimed to implement a multicomponent intervention package in different contexts. This PhD outlines part of the SPICES project activities. The general objective of this thesis was to develop and implement a comprehensive intervention program for the primary prevention of CVD in primary health care (PHC) and community settings in Belgium. This implementation research project applied principles of participatory action research and mixed-methods evaluation, using the Consolidated Framework for Implementation Research and RE-AIM. During the implementation process, we conducted exploratory qualitative research, systematic literature review, contextual analysis, multi-method intervention development and contextualization, and formative process evaluation of the implementation. Our research activities showed that to reach vulnerable populations for prevention and to maximize intervention effectivity, programs should be delivered by multi- or interdisciplinary teams in PHC and community settings. However, the current link between PHC and the community is unclear. Moreover, Belgian general practice is urging for well-defined task descriptions for interprofessional collaboration and systematic support for the sustainable integration of practice nurses. The SPICES program consisted of two main components: 1) a CVD risk profiling component using the Non-Laboratory INTERHEART Risk Score, and 2) a coaching component including behaviour change strategies and motivational interviewing. Contextualization was necessary to overcome identified barriers. Our evaluation demonstrated the high potential of general practice and existing community organizations for preventive interventions. Prioritizing prevention, stakeholder engagement, compatibility with existing systems, upskilling competence profiles, supportive financial and regulatory frameworks, and a strong PHC-community link, were identified as crucial factors to increase implementation success and sustainability of prevention programs. Our findings urge healthcare systems to move towards a community health model integrating health and social care to strengthen health promotion and cardiovascular disease prevention efforts. This requires aligning policy, legislative and financial systems with the current and future challenges of PHC. Furthermore, collective efforts are needed across sectors to improve health in all communities, including vulnerable populations

Voice Your Opinion!: Young Voters’ Usage and Perceptions of a Text-Based, Voice-Based and Text-Voice Combined Conversational Agent Voting Advice Application (CAVAA)

Conversational Agent Voting Advice Applications (CAVAAs) are chatbot-based information retrieval systems for citizens who aim to inform themselves about the political issues at stake in times of political elections. Previous studies investigating these relatively young tools primarily focused on the effects of CAVAAs that include a text-based chatbot. In order to further optimize their design, current research compared the effects of CAVAAs with a text, voice, and combined chatbot. In an experimental lab study among young voters (N = 60) these three modalities have been compared on usage measures (the amount of information retrieved from the chatbot, and miscommunication), evaluation measures (ease of use, usefulness, and enjoyment), and political measures (perceived and factual political knowledge). Results show that the three CAVAA modalities score equally high on political measures and the perception of enjoyment. At the same time, the textual and combined CAVAA outperform the voice CAVAA on several aspects: the voice CAVAA received lower ease of use and usefulness scores, respondents requested less additional information, and they experienced more miscommunication when interacting with the voice chatbot. Analyses of the usage data also indicate that in the combined condition users hardly use the voiceoption and instead almost exclusively rely on text-functionalities like clicking on suggestion buttons. This seems to suggest that using voice is too much of an effort for CAVAA users; we therefore recommend the usage of text-bots in this specific usage context