scholarly journals The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Aaron Trautman ◽  
Richard Linchangco ◽  
Rachel Walstead ◽  
Jeremy J. Jay ◽  
Cory Brouwer
Keyword(s):  
Health Outcomes ◽  
Human Health ◽  
Fruits And Vegetables ◽  
Graph Database ◽  
Breeding Programs ◽  
Plant Products ◽  
Link Type ◽  
User Friendly ◽  
Bodily Condition

Abstract Objective Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary. Results We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant $$\rightarrow$$ → plant product $$\rightarrow$$ → human gene $$\rightarrow$$ → pathways $$\rightarrow$$ → indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github (https://github.com/atrautm1/ABCkb) along with basic directions for building the knowledgebase and a browsable interface is available (https://abckb.charlotte.edu).

scholarly journals The Aliment to Bodily Condition knowledgebase (ABCkb): A database connecting plants and human health

2021 ◽  
Author(s):  
Aaron Trautman ◽  
Richard Linchangco ◽  
Rachel Walstead ◽  
Jeremy J Jay ◽  
Cory Brouwer
Keyword(s):  
Health Outcomes ◽  
Human Health ◽  
Fruits And Vegetables ◽  
Human Gene ◽  
Graph Database ◽  
Breeding Programs ◽  
Plant Products ◽  
User Friendly ◽  
Bodily Condition

Objective: Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary. Results: We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant → plant product → human gene → pathways → indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github (https://github.com/atrautm1/ABCkb) along with basic directions for building the knowledgebase.

scholarly journals The Impact of a Produce Prescription Programme on Healthy Food Purchasing and Diabetes-Related Health Outcomes

2021 ◽  
pp. 1-24
Author(s):  
Julian Xie ◽  
Ashley Price ◽  
Neal Curran ◽  
Truls Østbye
Keyword(s):  
Health Outcomes ◽  
Fruits And Vegetables ◽  
Healthy Food ◽  
Grocery Store ◽  
Diabetes Control ◽  
Food Purchasing ◽  
Significant Relationships ◽  
Expenditure Share ◽  
The Impact

Abstract Objective: To evaluate a Produce Prescription Programme’s utilisation, and its effects on healthy food purchasing and diabetes control among participants with type 2 diabetes. Design: Prospective cohort study using participants’ electronic health records (EHR) and food transaction data. Participants were categorized as “Frequent Spenders” and “Sometimes Spenders” based on utilisation frequency. Multivariate regressions assessed utilisation predictors; and programme effects on fruit/vegetable purchasing (spending, expenditure share, variety) and on diabetes-related outcomes (HbA1c, BMI, blood pressure). Setting: Patients enrolled by clinics in Durham, North Carolina, USA. Participants received $40 monthly for fruits and vegetables at a grocery store chain. Subjects: 699 food-insecure participants (353 with diabetes). Results: Being female and older was associated with higher programme utilisation; hospitalisations were negatively associated with programme utilisation. Frequent Spender status was associated with $8.77 more in fruit/vegetable spending (p < 0.001), 3.3% increase in expenditure share (p = 0.007), and variety increase of 2.52 fruits and vegetables (p < 0.001). For $10 of Produce Prescription Dollars spent, there was an $8.00 increase in fruit/vegetable spending (p < 0.001), 4.1% increase in expenditure share, and variety increase of 2.3 fruits/vegetables (p < 0.001). For the 353 participants with diabetes, there were no statistically significant relationships between programme utilisation and diabetes control. Conclusions: Programme utilisation was associated with healthier food purchasing, but the relatively short study period and modest intervention prevent making conclusions about health outcomes. Produce Prescription Programmes can increase healthy food purchasing among food-insecure people, which may improve chronic disease care.

Pedigree and Pedigree Import Wizard

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552g-553
Author(s):  
Shahrokh Khandizadeh
Keyword(s):  
Additional Data ◽  
File Format ◽  
Fruit Crops ◽  
Operating Environment ◽  
Agronomic Characteristics ◽  
Link Type ◽  
Plant Characteristics ◽  
User Friendly

Pedigree for Windows is a user-friendly program that allows the user to trace agronomic characteristics, draw pedigrees, and view images of several fruit crops, including more than 1400 apple, 800 strawberry, 800 almond, 100 blackberry, 80 blueberry, 790 pear, 200 raspberry examples. Pedigree Import Wizard®© for Windows is an add-on software for users who are interested in importing their research or breeding data records of fruit, flower, and plant characteristics and any related images into Pedigree for Windows. Pedigree for Windows and Pedigree Import Wizard have been designed so that a user familiar with the Windows operating environment should have little need to refer to the documentation provided with the program. Pedigree Import Wizard uses a comma-separated value (csv) file format under the MS Excel environment. This option allows the user to add or import additional data to the existing database that are already stored in other software such as Lotus, Excel, Access, QuattroPro, WordPerfect, and MS Word tables, etc., as long as they work under the Windows environment. A free demo version of Pedigree and Pedigree Import Wizard for Windows is available from http://www.pgris.com.

Outcomes of a digitally delivered, culturally-sensitive behaviour change platform for BAME adults with type 2 diabetes: 1 year health and engagement outcomes (Preprint)

2020 ◽  
Author(s):  
Charlotte Summers
Keyword(s):  
Type 2 Diabetes ◽  
Body Weight ◽  
Health Outcomes ◽  
Behavioural Change ◽  
Culturally Sensitive ◽  
Lifestyle Changes ◽  
Haemoglobin A1c ◽  
Central Asian ◽  
Increased Risk

BACKGROUND People from Black, Asian and Minority Ethnic (BAME) groups are known to have an increased risk of developing type 2 diabetes and face greater barriers to accessing healthcare resources compared to their “white British” counterparts. The main mediators of lifestyle behavioural change are gender, generation, geography, genes, God/religion, and gaps in knowledge and economic resources. Dietary and cultural practices of these individuals significantly vary according to gender, generation, geographical origin and religion. Recognition of these factors and implementing culturally sensitive interventions for type 2 diabetes prevention and management is essential in increasing knowledge of healthy eating, engagement in physical activity and improving health outcomes in BAME communities. Few health apps are tailored for BAME populations, and BAME communities are considered hard-to-reach. OBJECTIVE Our objective was to establish whether the Low Carb Program is a viable scalable solution that can be used as an effective tailored type 2 diabetes intervention for BAME communities. We hypothesized that by taking into account cultural sensitivities, providing the platform in native languages and personalising the platform in accordance with known barriers to health disparities including gender, generation, dietary preferences and religion, the app would engage BAME communities and improve type 2 diabetes related health outcomes. METHODS The study used a quasi-experimental research design comprised of an open-label, single-arm, pre-post intervention using a sample of convenience. All 705 adults with type 2 diabetes who had activated their referral to the Low Carb Program as a result of an NHS consultation between September 2018 and March 2019 were followed for a period of 12 months; mean age 54.61 (SD 16.69) years; 58.2% (410/705) women; 45.1% (318/705) white, 28.5% (201/705) Indian/Pakistani/Bangladeshi/Other Central Asian, 10.8% (76/705) Arab, 6.2% (44/705) Mixed/Multiple ethnic groups, 6% (43/705) black, 1.8% (13/705) other, (7/705) 1% Chinese/Japanese/Other East Asian. Mean starting glycated haemoglobin A1c (HbA1c) 7.99% (SD 2.05%); mean body weight 88.96kg (SD 23.25kg). RESULTS Of the 705 study participants, 513 (72.76%) had completed the Low Carb Program at 12 months. There were statistically significant reductions in body weight and HbA1c in white, Indian/Pakistani/Bangladeshi/Other Central Asian, Arabic and black participants with the most significant differences in the Indian/Pakistani/Bangladeshi/Other Central Asian population HbA1c -1.18% (SD 1.49%) and weight 8.03kg (SD 10.65kg). 82.9% of all participants (419/705) of all participants lost at least 5% of their body weight. CONCLUSIONS Offering the culturally tailored Low Carb Program that empowers members to make dietary and lifestyle changes to different BAME groups is an effective and engaging tool in the management of type 2 diabetes. Most importantly, BAME populations in particular people from Indian/Pakistani/Bangladeshi and Arabic groups who achieve better health outcomes than their white counterparts.

scholarly journals Examining the impact of mental disease on type 2 diabetes outcomes: results from the EpiChron Cohort

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
I Guerrero Fernández de Alba ◽  
A Gimeno-Miguel ◽  
B Poblador Plou ◽  
K Bliek Bueno ◽  
J Carmona Pirez ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Substance Abuse ◽  
Early Detection ◽  
Health Outcomes ◽  
Emergency Room ◽  
Mental Disease ◽  
Emergency Room Visits ◽  
Mental Diseases ◽  
The Impact

Abstract Background Type 2 diabetes mellitus (T2D) is often accompanied by other chronic diseases, including mental diseases (MD). This work aimed at studying MD prevalence in T2D patients and analyse its impact on T2D health outcomes. Methods Retrospective, observational study of individuals of the EpiChron Cohort aged 18 and over with prevalent T2D at baseline (2011) in Aragón, Spain (n = 63,365). Participants were categorized by the existence or absence of MD, defined as the presence of depression, anxiety, schizophrenia or substance abuse. MD prevalence was calculated, and a logistic regression model was performed to analyse the likelihood of the four studied health outcomes (4-year all-cause mortality, all-cause hospitalization, T2D-hospitalization, and emergency room visits) based on the presence of each type of MD, after adjusting by age, sex and number of comorbidities. Results Mental diseases were observed in 19% of T2D patients, with depression being the most frequent condition, especially in women (20.7% vs. 7.57%). Mortality risk was significantly higher in patients with MD (odds ratio -OR- 1.24; 95% confidence interval -CI- 1.16-1.31), especially in those with substance abuse (OR 2.18; 95% CI 1.84-2.57) and schizophrenia (OR 1.82; 95% CI 1.50-2.21). The presence of MD also increased the risk of T2D-hospitalization (OR 1.51; 95% CI 1.18-1.93), emergency room visits (OR 1.26; 95% CI 1.21-1.32) and all-cause hospitalization (OR 1.16; 95% CI 1.10-1.23). Conclusions The high prevalence of MD among T2D patients, and its association with health outcomes, underscores the importance of providing integrated, person-centred care and early detection of comorbid mental diseases in T2D patients to improve disease management and health outcomes. Key messages Comprehensive care of T2D should include specific strategies for prevention, early detection, and management of comorbidities, especially mental disorders, in order to reduce their impact on health. Substance abuse was the mental disease with the highest risk of T2D-hospitalization, emergency room visits and all-cause hospitalization.

scholarly journals Advantages of using graph databases to explore chromatin conformation capture experiments

2021 ◽  
Vol 22 (S2) ◽  
Author(s):  
Daniele D’Agostino ◽  
Pietro Liò ◽  
Marco Aldinucci ◽  
Ivan Merelli
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Graph Database ◽  
Graph Databases ◽  
Sources Of Information ◽  
Chromosome Conformation ◽  
Wide Scale ◽  
User Friendly ◽  
Different Cell Types

Abstract Background High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be advantageous to describe the complex topology achieved by the DNA in the nucleus of eukaryotic cells. Methods Here we discuss the use of a graph database for storing and analysing data achieved by performing Hi-C experiments. The main issue is the size of the produced data and, working with a graph-based representation, the consequent necessity of adequately managing a large number of edges (contacts) connecting nodes (genes), which represents the sources of information. For this, currently available graph visualisation tools and libraries fall short with Hi-C data. The use of graph databases, instead, supports both the analysis and the visualisation of the spatial pattern present in Hi-C data, in particular for comparing different experiments or for re-mapping omics data in a space-aware context efficiently. In particular, the possibility of describing graphs through statistical indicators and, even more, the capability of correlating them through statistical distributions allows highlighting similarities and differences among different Hi-C experiments, in different cell conditions or different cell types. Results These concepts have been implemented in NeoHiC, an open-source and user-friendly web application for the progressive visualisation and analysis of Hi-C networks based on the use of the Neo4j graph database (version 3.5). Conclusion With the accumulation of more experiments, the tool will provide invaluable support to compare neighbours of genes across experiments and conditions, helping in highlighting changes in functional domains and identifying new co-organised genomic compartments.

scholarly journals Response of Pea Varieties to Damage Degree of Pea Weevil,Bruchus pisorumL.

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Ivelina Mitkova Nikolova
Keyword(s):  
Crop Yields ◽  
Egg Laying ◽  
Breeding Programs ◽  
Good Opportunity ◽  
Damage Degree ◽  
Field Germination ◽  
Type 3 ◽  
Emergence Hole

A study was conducted to determine the response of five pea varieties (Pisum sativumL.) to damage degree ofBruchus pisorum: Glyans, Modus, Kamerton, and Svit (Ukrainian cultivars) and Pleven 4 (Bulgarian cultivar). The seeds were classified into three types: healthy seeds (type 1), damaged seeds with parasitoid emergence hole (type 2), and damaged seeds with bruchid emergence hole (type 3) and they were sown. It was found that the weight of 1000 seeds did not affect the field germination of the pea varieties. Healthy and damaged seeds with parasitoid emergence holes (first and second seed types) provide a very good opportunity for growth and development while plants from damaged seeds with bruchid emergence holes had poor germination and vigor and low productivity. These seeds cannot provide the creation of well-garnished seeding and stable crop yields. Among tested varieties, the Ukrainian variety Glyans had considerably higher seed weight, field germination, and index germination and weak egg-laying activity ofB. pisorumcompared to others. Use of spring pea cultivars that are weakly preferred by the pea weevil in breeding programs would reduce losses due to pea weevil and provide an environmentally safer option to its control.

scholarly journals Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes

2014 ◽  
Vol 38 (1) ◽  
pp. 1-40 ◽  
Author(s):  
Valerie J. Harwood ◽  
Christopher Staley ◽  
Brian D. Badgley ◽  
Kim Borges ◽  
Asja Korajkic
Keyword(s):  
Health Outcomes ◽  
Human Health ◽  
Fecal Contamination ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Environmental Waters
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