scholarly journals Exploring biomedical ontology mappings with graph theory methods

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2990 ◽  
Author(s):  
Simon Kocbek ◽  
Jin-Dong Kim
Keyword(s):  
Graph Theory ◽  
Biomedical Ontology ◽  
Data Consistency ◽  
Mapping Data ◽  
Time Points ◽  
Modularity Analysis ◽  
Analyse Data ◽  
Ontology Reuse ◽  
Core Ontologies ◽  
Over Time

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. Methods We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. Results With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

scholarly journals Exploring biomedical ontology mappings with graph theory methods

2017 ◽  
Author(s):  
Simon Kocbek ◽  
Jin-Dong Kim
Keyword(s):  
Graph Theory ◽  
Biomedical Ontology ◽  
Data Consistency ◽  
Mapping Data ◽  
Time Points ◽  
Modularity Analysis ◽  
Analyse Data ◽  
Ontology Reuse ◽  
Core Ontologies ◽  
Over Time

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. Methods We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. Results With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

scholarly journals Exploring biomedical ontology mappings with graph theory methods

2017 ◽  
Author(s):  
Simon Kocbek ◽  
Jin-Dong Kim
Keyword(s):  
Graph Theory ◽  
Biomedical Ontology ◽  
Data Consistency ◽  
Mapping Data ◽  
Time Points ◽  
Modularity Analysis ◽  
Analyse Data ◽  
Ontology Reuse ◽  
Core Ontologies ◽  
Over Time

Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. Methods We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. Results With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

Measuring Agency Change Across the Domain of Hypnosis

2019 ◽  
Author(s):  
Vince Polito ◽  
Amanda Barnier ◽  
Erik Woody
Keyword(s):  
Rating Scale ◽  
Sense Of Agency ◽  
Pass Rates ◽  
Current Experiment ◽  
Multidimensional Construct ◽  
Time Points ◽  
Hypnotic Induction ◽  
Different Types ◽  
Over Time ◽  
Postexperimental Inquiry

Building on Hilgard’s (1965) classic work, the domain of hypnosis has been conceptualised by Barnier, Dienes, and Mitchell (2008) as comprising three levels: (1) classic hypnotic items, (2) responding between and within items, and (3) state and trait. The current experiment investigates sense of agency across each of these three levels. Forty-six high hypnotisable participants completed an ideomotor (arm levitation), a challenge (arm rigidity) and a cognitive (anosmia) item either following a hypnotic induction (hypnosis condition) or without a hypnotic induction (wake condition). In a postexperimental inquiry, participants rated their feelings of control at three time points for each item: during the suggestion, test and cancellation phases. They also completed the Sense of Agency Rating Scale (Polito, Barnier, & Woody, 2013) for each item. Pass rates, control ratings, and agency scores fluctuated across the different types of items and for the three phases of each item; also, control ratings and agency scores often differed across participants who passed versus failed each item. Interestingly, whereas a hypnotic induction influenced the likelihood of passing items, it had no direct effect on agentive experiences. These results suggest that altered sense of agency is not a unidimensional or static quality “switched on” by hypnotic induction, but a dynamic multidimensional construct that varies across items, over time and according to whether individuals pass or fail suggestions.

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

scholarly journals Levels of physical activity in four domains and affective wellbeing before and during the Covid-19 pandemic

2021 ◽  
Vol 79 (1) ◽  
Author(s):  
Eliane S. Engels ◽  
Michael Mutz ◽  
Yolanda Demetriou ◽  
Anne K. Reimers
Keyword(s):  
Mental Health ◽  
Physical Activity ◽  
Protective Factor ◽  
Total Sample ◽  
Poor Mental Health ◽  
German Population ◽  
Time Points ◽  
Sport And Exercise ◽  
Over Time ◽  
Time Point

Abstract Background Latest studies indicated that the general mental health level is low during the pandemic. Probably, this deterioration of the mental health situation is partly due to declines in physical activity. The aim of this study was to investigate differences in and the association between affective wellbeing and levels of different domains of physical activity at three time points before and during the pandemic. Method We used a nationwide online panel with a trend data design encompassing a total sample of N = 3517, representing the German population (> 14 years). Four different activity domains (sport and exercise, light outdoor activity, housework/gardening, active travel) and affective wellbeing (positive and negative affect) were assessed at three time points before and during the Covid-19 pandemic (October 2019, March 2020, October 2020). Results Multivariate analyses of variance (MANOVA) indicate differences regarding affective wellbeing over the three time points with the lowest values at the second time point. Levels of activity in the four domains differed significantly over time with the strongest decrease for sport and exercise from the first to the second time point. Partial correlations indicated that the relationships between sport and exercise and positive affect were most consistent over time. Conclusions Overall, our findings suggest that physical activity plays a particularly important role in the pandemic period as a protective factor against poor mental health. Especially sports and exercise seem to be supportive and should be encouraged, e.g. by providing additional support in finding adequate outdoor, home-based or digital substitutes.

scholarly journals 152. Applying A Difference-in-Difference Analysis to Assess Effect of Antimicrobial Stewardship Strategies on Changes in Antimicrobial Use

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S86-S86
Author(s):  
Ann F Chou ◽  
Yue Zhang ◽  
Makoto M Jones ◽  
Christopher J Graber ◽  
Matthew B Goetz ◽  
...  
Keyword(s):  
Antimicrobial Stewardship ◽  
Clinical Pharmacist ◽  
Antibiotic Use ◽  
Feedback Mechanism ◽  
Health Care Facilities ◽  
Antimicrobial Use ◽  
Time Points ◽  
The Difference ◽  
The Impact ◽  
Over Time

Abstract Background About 30–50% of inpatient antimicrobial therapy is sub-optimal. Health care facilities have utilized various antimicrobial stewardship (AS) strategies to optimize appropriate antimicrobial use, improve health outcomes, and promote patient safety. However, little evidence exists to assess relationships between AS strategies and antimicrobial use. This study examined the impact of changes in AS strategies on antimicrobial use over time. Methods This study used data from the Veterans Affairs (VA) Healthcare Analysis & Informatics Group (HAIG) AS survey, administered at 130 VA facilities in 2012 and 2015, and antimicrobial utilization from VA Corporate Data Warehouse. Four AS strategies were examined: having an AS team, feedback mechanism on antimicrobial use, infectious diseases (ID) attending physicians, and clinical pharmacist on wards. Change in AS strategies were computed by taking the difference in the presence of a given strategy in a facility between 2012–2015. The outcome was the difference between antimicrobial use per 1000 patient days in 2012–2013 and 2015–2016. Employing multiple regression analysis, changes in antimicrobial use was estimated as a function of changes in AS strategies, controlling for ID human resources in and organizational complexity. Results Of the 4 strategies, only change in availability of AS teams had an impact on antimicrobial use. Compared to facilities with no AS teams at both time points, antibiotic use decreased by 63.9 uses per 1000 patient days in facilities that did not have a AS team in 2012 but implemented one in 2015 (p=0.0183). Facilities that had an AS team at both time points decreased use by 62.2 per 1000 patient days (p=0.0324). Conclusion The findings showed that AS teams reduced inpatient antibiotic use over time. While changes in having feedback on antimicrobial use and clinical pharmacist on wards showed reduced antimicrobial use between 2012–2015, the differences were not statistically significant. These strategies may already be a part of a comprehensive AS program and employed by AS teams. In further development of stewardship programs within healthcare organizations, the association between AS teams and antibiotic use should inform program design and implementation. Disclosures All Authors: No reported disclosures

T3 Are Burns a Chronic Condition: Examining Physical and Mental Functioning up to 20 Years After Injury

2021 ◽  
Vol 42 (Supplement_1) ◽  
pp. S2-S3
Author(s):  
Callie Abouzeid ◽  
Audrey E Wolfe ◽  
Gretchen J Carrougher ◽  
Nicole S Gibran ◽  
Radha K Holavanahalli ◽  
...  
Keyword(s):  
Mental Health ◽  
Hospital Stay ◽  
National Database ◽  
Time Points ◽  
Patient Reported ◽  
Burn Survivors ◽  
Population Demographic ◽  
The Impact ◽  
Over Time

Abstract Introduction Burn survivors often face many long-term physical and psychological symptoms associated with their injury. To date, however, few studies have examined the impact of burn injuries on quality of life beyond 2 years post-injury. The purpose of this study is to examine the physical and mental well-being of burn survivors up to 20 years after injury. Methods Data from the Burn Model System National Database (1997–2020) were analyzed. Patient-reported outcome measures were collected at discharge with a recall of preinjury status, and then at 5, 10, 15, and 20 years after injury. Outcomes examined were the Physical Component Summary (PCS) and Mental Component Summary (MCS) of the Short Form-12. Trajectories were developed using linear mixed methods model with repeated measures of PCS and MCS scores over time and controlling for demographic and clinical variables. The model fitted score trajectory was generated with 95% confidence intervals to demonstrate score changes over time and associations with covariates. Results The study population included 420 adult burn survivors with a mean age of 42.4 years. The population was mainly male (66%) and white (76.4%) with a mean burn size of 21.5% and length of hospital stay of 31.3 days. Higher PCS scores were associated with follow-up time points closer to injury, shorter hospital stay, and younger age. Similarly, higher MCS scores were associated with earlier follow-up time points, shorter hospital stay, female gender, and non-perineal burns. MCS trajectories are demonstrated in the Figure. Conclusions Burn survivors’ physical and mental health worsened over time. Such a trend is different from previous reported results for mental health in the general population. Demographic and clinical predictors of recovery over time are identified.

scholarly journals Back in Time for Breakfast: An Analysis of the Changing Breakfast Cereal Aisle

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 489
Author(s):  
Emilie Croisier ◽  
Jaimee Hughes ◽  
Stephanie Duncombe ◽  
Sara Grafenauer
Keyword(s):  
Dietary Fibre ◽  
Saturated Fat ◽  
Health Claims ◽  
Whole Grain ◽  
Breakfast Cereal ◽  
Full Data ◽  
Data Set ◽  
Time Points ◽  
Total Fat ◽  
Over Time

Breakfast cereal improves overall diet quality yet is under constant scrutiny with assertions that the category has not improved over time. This study aimed to comprehensively analyse the category of breakfast cereals, the nutritional values, and health claims across eight distinct sub-categories at four time points (2013, 2015, 2018, and 2020). An audit of products from four major supermarkets in metropolitan Sydney (Aldi, Coles, IGA, and Woolworths) collected ingredient lists, nutrition information, claims and Health Star Rating (HSR) for biscuits and bites; brans; bubbles, puffs, and flakes; granola and clusters; hot cereal flavoured; hot cereal plain; muesli; breakfast biscuits. The median (IQR) were calculated for energy, protein, fat, saturated fat, carbohydrate, sugars, dietary fibre, and sodium for comparisons over time points by nutrient. Data from 2013 was compared with 2020 (by sub-category and then for a sub-section of common products available at each time point). Product numbers between 2013 (n = 283) and 2020 (n = 543) almost doubled, led by granola and clusters. Whole grain cereals ≥ 8 g/serve made up 67% of products (↑114%). While there were positive changes in nutrient composition over time within the full data set, the most notable changes were in the nutrition composition of cereals marketed as the same product in both years (n = 134); with decreases in mean carbohydrate (2%), sugar (10%) and sodium (16%) (p < 0.000), while protein and total fat increased significantly (p = 0.036; p = 0.021). Claims regarding Dietary Fibre and Whole Grain doubled since 2013. Analysis of sub-categories of breakfast cereal assisted in identifying some changes over time, but products common to both timeframes provided a clearer analysis of change within the breakfast category, following introduction of HSR. Whole grain products were lower in the two target nutrients, sodium and sugars, and well-chosen products represent a better choice within this category.

scholarly journals Knee Muscle Strength Recovery in the Early Period After ACL Reconstruction

2014 ◽  
Vol 2 (11_suppl3) ◽  
pp. 2325967114S0014
Author(s):  
Gulcan Harput ◽  
Hasan Erkan Kılınc ◽  
Hamza Özer ◽  
Gül Baltacı ◽  
Carl G. Mattacola
Keyword(s):  
Acl Reconstruction ◽  
Early Period ◽  
Quadriceps Strength ◽  
Isometric Strength ◽  
Time Points ◽  
Hamstring Muscles ◽  
Significant Difference ◽  
Isometric Torque ◽  
Over Time ◽  
Time Point

Objectives: The aim of this study was to investigate quadriceps and hamstrings isometric strength at 4, 8 and 12 week time points following ACL Reconstruction (ACLR) and to document the strength changes of these muscles over time. The primary hypothesis was that there would be significant increases in quadriceps and hamstring muscle strengths between the 4th, 8th and 12th weeks following ACLR. The secondary hypothesis was that the quadriceps index would be higher than hamstring index at 12th week after ACLR. Methods: Thirty patients (Mean ± SD [age, 29.1±2.3yrs; weight, 77.3±13.2kg; height, 172.1±7.1cm; BMI, 21.2±3.5kg/m2, time to surgery: 7.1±7.2 months]) who underwent ACLR with Hamstring Tendon Autograft (HTG) were enrolled in this study. The isometric strength of quadriceps and hamstring muscles was measured on an isokinetic dynamometer at 60° knee flexion angle at 4th, 8th and 12th weeks after surgery. The recovery of quadriceps and hamstring muscles strength following rehabilitation was expressed as a Quadriceps Index (QI) and Hamstring Index (HI) and calculated with the following formula:[(maximum voluntary isometric torque of the involved limb / maximum voluntary isometric torque by uninvolved limb) × 100]. Torque output of the involved and uninvolved limbs and quadriceps and hamstring indexes were used for the statistical analysis. A repeated measures of ANOVA was used to determine the strength changes of quadriceps and hamstrings over time. Results: Quadriceps and Hamstrings strengths significantly increased over time for both involved (Quadriceps: F (2,46)=58.3, p<0.001, Hamstring: F (2,46)=35.7, p<0.001) and uninvolved limb (Quadriceps: F(2,46)=17.9, p<0.001, Hamstring: F(2,46)=56.9, p=0.001 ). Quadriceps strength was higher at 12th week when compared to the 8 and 4 week time points for the involved limb (p<0.001), and it was higher at 8th week when compared to 4 week time point for the involved limb (p<0.001). For the uninvolved limb, quadriceps strength was also higher at 12th week when compared to the 8 (p=0.02) and 4 week time point (p<0.001), and higher at 8 week when compared to the 4 week time point (p=0.02). Hamstring strength was higher at 12 week when compared to the 8 and 4 week time points (p<0.001) and it was higher at 8 week when compared to 4 week time point for the involved limb (p<0.001). For the uninvolved limb hamstring strength was also higher at 12 week when compared to 4 week time point (p=0.01). There was no significant difference between the 4 and 8 week time points (p>0.05) or between the 8 and 12 week time points (p=0.07). Quadriceps and hamstring indexes significantly changed from 4th weeks (QI:57.9, HI:54.4 ) to 8th weeks (QI:78.8, HI:69.9 ) and from 8th weeks to 12th weeks (QI:82, HI:75.7 ) (p<0.001); however, there was no difference between indexes at the 12-week time point (p=0.17). Conclusion: Isometric strength of quadriceps and hamstring muscles for the involved and uninvolved limb increased during the early period of ACLR. The results of this study could be a baseline for clinicians while prescribing a rehabilitation protocol for ACLR patients with HTG to better appreciate expected strength changes of the muscles in the early phase.

Comparing Student Attitudes to Spreadsheet and Advanced Statistical Packages

2020 ◽  
pp. 009862832097726
Author(s):  
Angela R. Surrusco ◽  
Zachary J. Kunicki ◽  
Sarah L. DiPerri ◽  
Marie C. Tate ◽  
Megan M. Risi ◽  
...  
Keyword(s):  
Student Attitudes ◽  
Quantitative Methods ◽  
Student Attitude ◽  
Methods Course ◽  
Microsoft Excel ◽  
Time Points ◽  
Over Time

The statistical package chosen to aid in teaching quantitative methods is at the instructor’s discretion, but little research has investigated student attitude toward these different packages. This study compared Google Sheets, a spreadsheet package similar to Microsoft Excel, and a traditional package, SPSS, to determine which of the two programs students preferred to use. One hundred and thirty-nine students enrolled in a quantitative methods course completed surveys at the middle and end of the semester during Spring 2016 and Fall 2016. The results suggested Google Sheets was preferred to SPSS at both time points, and attitudes toward Google Sheets improved over time. Further research could investigate the perspectives of students in other levels of experience with statistics and other statistical packages.

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