VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.

Dexmedetomidine for Sedation During Pediatric Noninvasive Ventilation.

BACKGROUND: Noninvasive ventilation (NIV) facilitates management of acute respiratory failure without intubation. Many pediatric patients cannot tolerate the discomfort associated with noninvasive support and require sedation with agents that may decrease respiratory drive. Dexmedetomidine does not decrease respiratory drive, and we hypothesized that its use would increase tolerance of noninvasive respiratory support without increasing risk for intubation. METHODS: A retrospective chart review was performed of all subjects at least 3 months of age with acute respiratory failure requiring NIV who were admitted to the pediatric ICU at a children's hospital for a 3-y period from 2015-2018. Subjects were stratified to those receiving continuous dexmedetomidine versus those not receiving sedation. Medical history was reviewed for developmental delay (DD) or intellectual disability (ID) as well as basic demographic information. To control the association between these variables with both dexmedetomidine use and intubation, augmented inverse probability weighting was utilized to establish equivalent baselines between the dexmedetomidine and no-sedation groups. Primary outcome was intubation rate within 6 h of initiation of dexmedetomidine infusion or NIV. RESULTS: Based on the strong association between age and dexmedetomidine use, a statistical model including subjects > age 5 was not able to be generated, and these subjects were excluded from final analysis. One-hundred eight subjects were included in the final statistical analysis, with 60 receiving dexmedetomidine and 48 receiving no sedation. Dexmedetomidine was effective at reducing agitation, with no difference noted in intubation rate at 6 h between subjects receiving dexmedetomidine versus no sedation (13.1 vs 12.4%). CONCLUSIONS: Dexmedetomidine may allow tolerance of NIV in acute respiratory failure without increasing risk for intubation, especially in preschool age patients and those with DD or ID. A larger study involving multiple centers would help support our conclusions.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms.

VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.

MIReAD, a minimum information standard for reporting arthropod abundance data.

Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the "FAIR," (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.

Ethical implications of medical crowdfunding: the case of Charlie Gard.

Patients are increasingly turning to medical crowdfunding as a way to cover their healthcare costs. In the case of Charlie Gard, an infant born with encephalomyopathic mitochondrial DNA depletion syndrome, crowdfunding was used to finance experimental nucleoside therapy. Although this treatment was not provided in the end, we will argue that the success of the Gard family's crowdfunding campaign reveals a number of potential ethical concerns. First, this case shows that crowdfunding can change the way in which communal healthcare resources are allocated. Second, within the UK's National Health Service, healthcare is ostensibly not a market resource; thus, permitting crowdfunding introduces market norms that could commodify healthcare. Third, pressures inherent to receiving funds from external parties may threaten the ability of patients-cum-recipients to voluntarily consent to treatment. We conclude that while crowdfunding itself is not unethical, its use can have unforeseen consequences that may influence conceptions of healthcare and how it is delivered.

Tracking of obesity-related behaviours from childhood to adulthood: A systematic review.

Obesity in childhood carries a wide range of physical, psychological and social disbenefits and also increases the risk of adult obesity with its well-recognised, enhanced risk of several common complex diseases as well as adverse socioeconomic and psychosocial sequelae. Understanding the tracking of the two key modifiable behaviours, food consumption and physical activity, between childhood and adulthood may illuminate the childhood determinants of adult obesity and contribute to the development of effective interventions. We performed a systematic review of the available literature on tracking of both physical activity and of dietary intake between childhood and adulthood by searching MEDLINE, EMBASE, CINAHL, PSYCInfo, Google and Google Scholar. For inclusion, studies had to report baseline measurements when the children were less than, or equal to, 18 years and to report follow-up for at least 5 years to any age over 18 years. After removal of duplicates, 9625 search hits were screened by title and/or abstract and 79 potentially relevant papers were identified and full papers obtained. In total 39 papers were included in this analysis. Of these, 11 papers (from 5 studies) reported data on tracking of diet from childhood to adulthood and 28 papers (from 16 studies) reported data on tracking of physical activity or inactivity. Despite the diversity of study design and measurement methodology, we found evidence of tracking of both physical activity and of diet between childhood and adulthood with estimates of strength of tracking of a similar order for both behaviours. Because of the inherent methodological difficulties in quantifying habitual behaviour, it is likely that the reported estimates of strength of tracking under-estimate the true degree of tracking. The evidence of tracking reported here may give greater impetus to the development of interventions aimed to prevent the persistence of obesity from childhood into adulthood and its attendant adverse socioeconomic, psychosocial and health sequelae.

MRI estimation of total renal volume demonstrates significant association with healthy donor weight.

PURPOSE: The purpose of this study was to correlate total renal volume (TRV) calculations, obtained through the voxel-count method and ellipsoid formula with various physical characteristics. MATERIALS AND METHODS: MRI reports and physical examination from 210 healthy kidney donors (420 kidneys), on whom renal volumes were obtained using the voxel-count method, were retrospectively reviewed. These values along with ones obtained through a more traditional method (ellipsoid formula) were correlated with subject height, body weight, body mass index (BMI), and age. RESULTS: TRV correlated strongly with body weight (r=0.7) and to a lesser degree with height, age, or BMI (r=0.5, -0.2, 0.3, respectively). The left kidney volume was greater than the right, on average (p<0.001). The ellipsoid formula method over-estimated renal volume by 17% on average which was significant (p<0.001). CONCLUSIONS: Body weight was the physical characteristic which demonstrated the strongest correlation with renal volume in healthy subjects. Given this finding, a formula was derived for estimating the TRV for a given patient based on the his or her weight: TRV = 2.96 x weight (kg) + 113+/-64.

Comparison of methods to estimate non-milk extrinsic sugars and their application to sugars in the diet of young adolescents.

Consistent information on the non-milk extrinsic sugars (NMES) content of foods and the NMES intake by the population is required in order to allow comparisons between dietary surveys. A critical appraisal of methods of NMES estimation was conducted to investigate whether the different published methods for estimating the NMES content of foods lead to significantly different values for the dietary intake of NMES by children and to consider the relative practicality of each method. NMES values of foods were calculated using three different published descriptions of methods of NMES estimation, and the values were compared within food groups. Dietary intake values for English children aged 11-12 years were calculated using each method and compared in terms of overall NMES intake and the contribution of different food groups to NMES intake. There was no significant difference in the dietary intake of NMES in children between the method used in the National Diet and Nutrition Surveys (NDNS) (81.9 g/d; 95 % CI 79.0, 84.7) and a method developed by the Human Nutrition Research Centre (84.3 g/d; 95 % CI 81.4, 87.2) at Newcastle University, UK, although the latter gave slightly higher values. An earlier method used by the Ministry of Agriculture, Food and Fisheries gave significantly higher values than the other two methods (102.5 g/d; 95 % CI 99.3, 105.6; P<0.05). The method used in the NDNS surveys and the method used by the Human Nutrition Research Centre at Newcastle University are both thorough and detailed methods that give consistent results. However, the method used in the NDNS surveys was more straightforward to apply in practice and is the best method for a single uniform approach to the estimation of NMES.