Integration of USDA Food Classification System and Food Composition Database for Image-Based Dietary Assessment among Individuals Using Insulin

New imaging technologies to identify food can reduce the reporting burden of participants but heavily rely on the quality of the food image databases to which they are linked to accurately identify food images. The objective of this study was to develop methods to create a food image database based on the most commonly consumed U.S. foods and those contributing the most to energy. The objective included using a systematic classification structure for foods based on the standardized United States Department of Agriculture (USDA) What We Eat in America (WWEIA) food classification system that can ultimately be used to link food images to a nutrition composition database, the USDA Food and Nutrient Database for Dietary Studies (FNDDS). The food image database was built using images mined from the web that were fitted with bounding boxes, identified, annotated, and then organized according to classifications aligning with USDA WWEIA. The images were classified by food category and subcategory and then assigned a corresponding USDA food code within the USDA's FNDDS in order to systematically organize the food images and facilitate a linkage to nutrient composition. The resulting food image database can be used in food identification and dietary assessment.

The Viscum album Gene Space database

The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on 'Benchmarking Universal Single-Copy Orthologs' (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).

LppDB - a Comprehensive Database for Lipopeptide based drugs: Exploring potential drug discovery aspects

AIM

Lipopeptides are amphiphilic compounds consisting of a cyclic peptide attached to a fatty acid side chain. These are found with various medicinal properties ranging from broad-spectrum antimicrobial to anticancer properties.

INTRODUCTION

Elaborated studies on the therapeutic properties of peptides are hindered due to a lack of databases specifically dedicated to such classes of compounds where all the medicinal information of compounds is collectively studied in one place, which can accelerate the future scope of research on peptidolipidic compounds.

METHOD

The chemical information was retrieved from the PubChem compound database, and their metabolism information was generated through Swiss ADME. The application information about their particular pathways was obtained from different kinds of literature.

RESULTS

A python script was developed to extract the information about lipopeptides from a CSV file, and the information was stored in MySQL Database. The database contains information for 70 lipopeptides and their biochemical information, structure, chemical and physical properties, information on industrial and medicinal applications, functions and references for lipopeptides.

CONCLUSION

The development of web-based database applications allows the data stored in the database to be accessed and viewed publicly.

Development of a Probiotics Practice E-Reference Database for Health Care Professionals

PURPOSE

Currently available references provide evidence on the efficacy of probiotics strains but exclude product-specific information, making it challenging for health care professionals (HCPs) to provide consumers with suitable recommendations on probiotics. An online probiotics e-reference database was developed to assist HCPs in delivering evidence-based recommendations on probiotics to consumers. The usability and applicability of the database in health care practice were evaluated.

METHODS

Information on the efficacy of probiotics and probiotic products was collated using a PubMed literature search, and from local pharmacies and online supplement stores. A web database was compiled using various programming scripts and uploaded onto a web server. The database was beta-tested using an online self-administered questionnaire for community-based pharmacists, and responses were analyzed using descriptive statistics.

FINDINGS

The database comprised 584 clinical study excerpts, 449 probiotic products, and 1879 unique product-study links. Users can search for suitable probiotics based on their indication profile or for a specific probiotic product. Information provided includes the probiotic constituents, dosage regimen, and indications of the product, with supporting clinical evidence. Overall, all participants of the beta-test indicated that they were satisfied with the database and were willing to use it again (both, 13 participants [100%]). In addition, all participants indicated that they found the database intuitive to use and smooth functioning, without inconsistencies (both, 13 [100%]). The majority also indicated that they found the information provided to be clear, comprehensive, and useful in health care practice (12 [92.3%] each).

IMPLICATIONS

The probiotics e-reference database is an integrated resource that is user-friendly, and provides HCPs with ready access to clear and comprehensive information on probiotic products and clinical studies, so that HCPs can provide consumers with relevant and evidence-based recommendations on probiotics.

A Novel Multispecies Toxicokinetic Modeling Approach in Support of Chemical Risk Assessment

Standardized laboratory tests with a limited number of model species are a key component of chemical risk assessments. These surrogate species cannot represent the entire diversity of native species, but there are practical and ethical objections against testing chemicals in a large variety of species. In previous research, we have developed a multispecies toxicokinetic model to extrapolate chemical bioconcentration across species by combining single-species physiologically based toxicokinetic (PBTK) models. This "top-down" approach was limited, however, by the availability of fully parameterized single-species models. Here, we present a "bottom-up" multispecies PBTK model based on available data from 69 freshwater fishes found in Canada. Monte Carlo-like simulations were performed using statistical distributions of model parameters derived from these data to predict steady-state bioconcentration factors (BCFs) for a set of well-studied chemicals. The distributions of predicted BCFs for 1,4-dichlorobenzene and dichlorodiphenyltrichloroethane largely overlapped those of empirical data, although a tendency existed toward overestimation of measured values. When expressed as means, predicted BCFs for 26 of 34 chemicals (82%) deviated by less than 10-fold from measured data, indicating an accuracy similar to that of previously published single-species models. This new model potentially enables more environmentally relevant predictions of bioconcentration in support of chemical risk assessments.

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e. NicotianaCyc as well as six species-specific databases for Nicotiana tabacum TN90, N. tabacum K326, Nicotiana benthamiana, N. sylvestris, N. tomentosiformis and N. attenuata. New pathways were created through the extraction, examination and verification of related data from the literature and the aid of external database guided by an expert-led curation process. Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway for cholesterol in plants. The current content of our databases comprises 266 pathways and 36 superpathways in SolanaCyc and 143 pathways plus 21 superpathways in NicotianaCyc, manually curated and validated specifically for the Solanaceae family and Nicotiana genus, respectively. The curated data have been propagated to the respective Nicotiana-specific databases, which resulted in the enrichment and more accurate presentation of their metabolic networks. The quality and coverage in those databases have been compared with related external databases and discussed in terms of literature support and metabolic content.

Seventy Years of RN Effectiveness: A Database Development Project to Inform Best Practice

BACKGROUND

The appropriate nursing staff mix is imperative to the provision of quality care. Nurse staffing levels and staff mix vary from country to country, as well as between care settings. Understanding how staffing skill mix impacts patient, organizational, and financial outcomes is critical in order to allow policymakers and clinicians to make evidence-informed staffing decisions.

AIMS

This paper reports on the methodology for creation of an electronic database of studies exploring the effectiveness of Registered Nurses (RNs) on clinical and patient outcomes, organizational and nurse outcomes, and financial outcomes.

METHODS

Comprehensive literature searches were conducted in four electronic databases. Inclusion criteria for the database included studies published from 1946 to 2016, peer-reviewed international literature, and studies focused on RNs in all health-care disciplines, settings, and sectors. Masters-prepared nurse researchers conducted title and abstract screening and relevance review to determine eligibility of studies for the database. High-level analysis was conducted to determine key outcomes and the frequency at which they appeared within the database.

RESULTS

Of the initial 90,352 records, a total of 626 abstracts were included within the database. Studies were organized into three groups corresponding to clinical and patient outcomes, organizational and nurse-related outcomes, and financial outcomes. Organizational and nurse-related outcomes represented the largest category in the database with 282 studies, followed by clinical and patient outcomes with 244 studies, and lastly financial outcomes, which included 124 studies.

LINKING EVIDENCE TO ACTION

The comprehensive database of evidence for RN effectiveness is freely available at https://rnao.ca/bpg/initiatives/RNEffectiveness. The database will serve as a resource for the Registered Nurses' Association of Ontario, as well as a tool for researchers, clinicians, and policymakers for making evidence-informed staffing decisions.

Development of a Web-based repository for sharing biomedical terminology from systematic review searches: a case study

Requests for comprehensive searches, such as searches to support systematic reviews, seem to be evolving into routine practice in the health sciences library environment. Collecting terminology for these searches is often a time-consuming process. This case study reports on the development of a searchable Web-based repository, MedTerm Search Assist, as a means for librarians to share biomedical terminology from systematic review searches.