Project description:Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying the tumor microenvironment of two data sets: 10× Visium samples from a cohort of melanoma metastasis and NanoString CosMx fields of vision from a cohort of Merkel cell carcinoma samples. These results support the ability of spatialGE to identify spatial gene expression patterns that provide valuable insights into the tumor microenvironment and highlight its utility in democratizing ST data analysis for the wider scientific community.
Project description:The COVID-19 pandemic stimulated the interest of scientists, decision makers and the general public in short-term mortality fluctuations caused by epidemics and other natural or man-made disasters. To address this interest and provide a basis for further research, in May 2020, the Short-term Mortality Fluctuations data series was launched as a new section of the Human Mortality Database. At present, this unique data resource provides weekly mortality death counts and rates by age and sex for 38 countries and regions. The main objective of this paper is to detail the web-based application for visualizing and analyzing the excess mortality based on the Short-term Mortality Fluctuation data series. The application yields a visual representation of the database that enhances the understanding of the underlying data. Besides, it enables the users to explore data on weekly mortality and excess mortality across years and countries. The contribution of this paper is twofold. First, to describe a visualization tool that aims to facilitate research on short-term mortality fluctuations. Second, to provide a comprehensive open-source software solution for demographic data to encourage data holders to promote their datasets in a visual framework.
Project description:ObjectivesTo assess age, period, and birth cohort effects and patterns of obesity-attributable mortality in Czech Republic, Finland, France, Germany, Hungary, Italy, Poland, and the UK (UK).MethodsWe obtained obesity prevalence and all-cause mortality data by age (20-79), sex and country for 1990-2012. We applied Clayton and Schifflers' age-period-cohort approach to obesity-attributable mortality rates (OAMRs).ResultsBetween 1990 and 2012, obesity prevalence increased and age-standardised OAMRs declined, although not uniformly. The nonlinear birth cohort effects contributed significantly (p < 0.01) to obesity-attributable mortality trends in all populations, except in Czech Republic, Finland, and among German women, and Polish men. Their contribution was greater than 25% in UK and among French women, and larger than that of the nonlinear period effects. In the UK, mortality rate ratios (MRRs) increased among the cohorts born after 1950. In other populations with significant birth cohort effects, MRRs increased among the 1935-1960 cohorts and decreased thereafter.ConclusionsGiven its potential effects on obesity-attributable mortality, the cohort dimension should not be ignored and calls for interventions early in life next to actions targeting broader societal changes.
Project description:The Sting Report is a versatile web-based application for extraction and presentation of detailed information about any individual amino acid of a protein structure stored in the STING Database. The extracted information is presented as a series of GIF images and tables, containing the values of up to 125 sequence/structure/function descriptors/parameters. The GIF images are generated by the Gold STING modules. The HTML page resulting from the STING Report query can be printed and, most importantly, it can be composed and visualized on a computer platform with an elementary configuration. Using the STING Report, a user can generate a collection of customized reports for amino acids of specific interest. Such a collection comes as an ideal match for a demand for the rapid and detailed consultation and documentation of data about structure/function. The inclusion of information generated with STING Report in a research report or even a textbook, allows for the increased density of its contents. STING Report is freely accessible within the Gold STING Suite at http://www.cbi.cnptia.embrapa.br, http://www.es.embnet.org/SMS/, http://gibk26.bse.kyutech.ac.jp/SMS/ and http://trantor.bioc.columbia.edu/SMS (option: STING Report).
Project description:ImportanceThere are wide disparities in neonatal mortality rates (NMRs, deaths <28 days of life after live birth per 1000 live births) between countries in Europe, indicating potential for improvement. Comparing country-specific patterns of births and deaths with countries with low mortality rates can facilitate the development of effective intervention strategies.ObjectiveTo investigate how these disparities are associated with the distribution of gestational age (GA) and GA-specific mortality rates.Design, setting, and participantsThis was a cross-sectional study of all live births in 14 participating European countries using routine data compiled by the Euro-Peristat Network. Live births with a GA of 22 weeks or higher from 2015 to 2020 were included. Data were analyzed from May to October 2023.ExposuresGA at birth.Main outcomes and measuresThe study investigated excess neonatal mortality, defined as a rate difference relative to the pooled rate in the 3 countries with the lowest NMRs (Norway, Sweden, and Finland; hereafter termed the top 3). The Kitagawa method was used to divide this excess into the proportion explained by the GA distribution of births and by GA-specific mortality rates. A sensitivity analysis was conducted among births 24 weeks' GA or greater.ResultsThere were 35 094 neonatal deaths among 15 123 428 live births for an overall NMR of 2.32 per 1000. The pooled NMR in the top 3 was 1.44 per 1000 (1937 of 1 342 528). Excess neonatal mortality compared with the top 3 ranged from 0.17 per 1000 in the Czech Republic to 1.82 per 1000 in Romania. Excess deaths were predominantly concentrated among births less than 28 weeks' GA (57.6% overall). Full-term births represented 22.7% of the excess deaths in Belgium, 17.8% in France, 40.6% in Romania and 17.3% in the United Kingdom. Heterogeneous patterns were observed when partitioning excess mortality into the proportion associated with the GA distribution vs GA-specific mortality. For example, these proportions were 9.2% and 90.8% in France, 58.4% and 41.6% in the United Kingdom, and 92.9% and 7.1% in Austria, respectively. These associations remained stable after removing births under 24 weeks' GA in most, but not all, countries.Conclusions and relevanceThis cohort study of 14 European countries found wide NMR disparities with varying patterns by GA. This knowledge is important for developing effective strategies to reduce neonatal mortality.
Project description:The number of online data repositories is growing and they are becoming increasingly difficult to navigate. Data are scattered among different repositories, or hidden on personal or institutional servers. To access data, users must search extensively and rely on site-specific tools. These hurdles substantially inhibit data findability and accessibility; in particular, those in the long tail of data. We developed an open source web application, Spatial Data Hub, that is a geospatial data index, connected to remote Internet sources. It allows simultaneous display and comparison of disparate datasets on a single map. It aims to promote all data equally and provide the flexibility to connect to any storage system, effectively making long-tail datasets as visible as those in large, established repositories. Its low barrier of entry allows scientists and organizations to easily add data throughout the research process; enhancing transparency, openness and reproducibility. This flexibility and functionality makes Spatial Data Hub a novel platform for researchers to promote their work, develop new hypotheses and create new collaborations.
Project description:The objective was to examine changes in temporal trends in suicide mortality in 26 Western countries by retrospective trend analysis of the WHO mortality database on causes of deaths. From 1990 to 2010, there was a median reduction in suicide mortality of 22.7%, ranging from a 46% reduction in Estonia to a 26.2% increase in Romania. Suicide mortality decreased by ≥ 20% in 15 countries, and the reduction tended to be greater in countries with higher mortality in 1990. In most of the central European countries mortality strongly declined. The median changes in the age groups were -25.3% (range -62.9% to 72.6%) in people aged 15-24 years, -36.9% (-60.5% to 32.4%) in 25-34 years, -3.6% (-57.1% to 92%) in 35-54 years, -12.2% (-37% to 65,7%) in 55-74 years and -16.1% (-54.5% to 166.7%) in ≥ 75 years. Suicide prevention programs in youths and in the elderly seem to be effective (at least in females for the elderly) and efforts should be pursued in this way. However, suicide mortality of the people aged 35-54 years has increased in half of the studied countries between 1990 and 2010. Public policies should further orientate their efforts toward this population.
Project description:Summary:The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training. Availability and implementation:Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics. Contact:katherinejh@ufl.edu or remizallot@ufl.edu. Supplementary information:Supplementary data are available at Bioinformatics online.
Project description:Web-based data analysis and visualization tools are mostly designed for specific purposes, such as the analysis of data from whole transcriptome RNA sequencing or single-cell RNA sequencing. However, generic tools designed for the analysis of common laboratory data for noncomputational scientists are also needed. The importance of such web-based tools is emphasized by the continuing increases in the sample capacity of conventional laboratory tools such as quantitative PCR, flow cytometry or ELISA instruments. We present a web-based application FaDA, developed with the R Shiny package that provides users with the ability to perform statistical group comparisons, including parametric and nonparametric tests, with multiple testing corrections suitable for most standard wet-laboratory analyses. FaDA provides data visualizations such as heatmaps, principal component analysis (PCA) plots, correlograms and receiver operating curves (ROCs). Calculations are performed through the R language. The FaDA application provides a free and intuitive interface that allows biologists without bioinformatic skill to easily and quickly perform common laboratory data analyses. The application is freely accessible at https://shiny-bird.univ-nantes.fr/app/Fada.
Project description:IntroductionPulmonary embolism (PE) has not been accounted for as a cause of death contributing to cause-specific mortality in global reports.MethodsWe analyzed global PE-related mortality by focusing on the latest year available for each member state in the World Health Organization (WHO) mortality database, which provides age-sex-specific aggregated mortality data transmitted by national authorities for each underlying cause of death. PE-related deaths were defined by International Classification of Diseases, Tenth Revision codes for acute PE or nonfatal manifestations of venous thromboembolism (VTE). The 2001 WHO standard population served for standardization.ResultsWe obtained data from 123 countries covering a total population of 2 602 561 422. Overall, 50 (40.6%) were European, 39 (31.7%) American, 13 (10.6%) Eastern Mediterranean, 13 (10.6%) Western Pacific, 3 (2.4%) Southeast Asian, and 2 (1.6%) African. Of 116 countries classifiable according to population income, 57 (49.1%) were high income, 42 (36.2%) upper-middle income, 14 (12.1%) lower-middle income, and 3 (2.6%) low income. A total of 18 726 382 deaths were recorded, of which 86 930 (0.46%) were attributed to PE. PE-related mortality rate increased with age in most countries. The reporting of PE-related deaths was heterogeneous, with an age-standardized mortality rate ranging from 0 to 24 deaths per 100 000 population-years. Income status only partially explained this heterogeneity.ConclusionsReporting of PE-related mortality in official national vital registration was characterized by extreme heterogeneity across countries. These findings mandate enhanced efforts toward systematic and uniform coverage of PE-related mortality and provides a case for full recognition of PE and VTE as a primary cause of death.