scholarly journals KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

2020 ◽  
Author(s):  
Keywan Hassani-Pak ◽  
Ajit Singh ◽  
Marco Brandizi ◽  
Joseph Hearnshaw ◽  
Sandeep Amberkar ◽  
...  
Keyword(s):  
Biological Networks ◽  
Complex Traits ◽  
Gene Discovery ◽  
Biological Properties ◽  
Comprehensive Approach ◽  
Biological Research ◽  
Evidence Based ◽  
Extensive Literature ◽  
Supporting Evidence ◽  
Knowledge Graphs

ABSTRACTGenerating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We have developed a comprehensive approach to guide this technically challenging data integration task and to make knowledge discovery and hypotheses generation easier for plant and crop researchers. KnetMiner can digest large volumes of scientific literature and biological research to find and visualise links between the genetic and biological properties of complex traits and diseases. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. We have developed KnetMiner knowledge graphs and applications for a range of species including plants, crops and pathogens. KnetMiner is the first open-source gene discovery platform that can leverage genome-scale knowledge graphs, generate evidence-based biological networks and be deployed for any species with a sequenced genome. KnetMiner is available at http://knetminer.org.

scholarly journals KnetMiner: a comprehensive approach for supporting evidence‐based gene discovery and complex trait analysis across species

2021 ◽  
Author(s):  
Keywan Hassani‐Pak ◽  
Ajit Singh ◽  
Marco Brandizi ◽  
Joseph Hearnshaw ◽  
Jeremy D. Parsons ◽  
...  
Keyword(s):  
Gene Discovery ◽  
Complex Trait ◽  
Comprehensive Approach ◽  
Evidence Based ◽  
Supporting Evidence ◽  
Trait Analysis

Abstraction: An alternative neurocognitive account of recognition, prediction, and decision making

2020 ◽  
Vol 43 ◽  
Author(s):  
Valerie F. Reyna ◽  
David A. Broniatowski
Keyword(s):  
Decision Making ◽  
Software Engineering ◽  
Systems Engineering ◽  
Evidence Based ◽  
Extensive Literature ◽  
Trace Theory ◽  
Fuzzy Trace Theory ◽  
Abstract Representations ◽  
Technical Systems

Abstract Gilead et al. offer a thoughtful and much-needed treatment of abstraction. However, it fails to build on an extensive literature on abstraction, representational diversity, neurocognition, and psychopathology that provides important constraints and alternative evidence-based conceptions. We draw on conceptions in software engineering, socio-technical systems engineering, and a neurocognitive theory with abstract representations of gist at its core, fuzzy-trace theory.

Developing an Evidence-Based Clinical Decision-Support System to Enhance Prosthetic Prescription

2021 ◽  
Vol 10 (1) ◽  
pp. 121-125
Author(s):  
Pratima Saravanan ◽  
Jessica Menold
Keyword(s):  
Decision Making ◽  
Decision Support ◽  
Decision Support System ◽  
Gait Analysis ◽  
Support System ◽  
Patient Specific ◽  
Evidence Based ◽  
Extensive Literature ◽  
Analysis Tool ◽  
Care Providers

With the rapid increase in the global amputee population, there is a clear need to assist amputee care providers with their decision-making during the prosthetic prescription process. To achieve this, an evidence-based decision support system that encompasses existing literature, current decision-making strategies employed by amputee care providers and patient-specific factors is proposed. Based on an extensive literature review combined with natural language processing and expert survey, the factors influencing the current decision-making of amputee care providers in prosthetic prescription were identified. Following that, the decision-making strategies employed by expert and novice prosthetists were captured and analyzed. Finally, a fundamental understanding of the effect gait analysis has on the decision-making strategies of prosthetists was studied. Findings from this work lay the foundation for developing a real-time decision support system integrated with a portable gait analysis tool to enhance prescription processes. This is critical in the low-income countries where there is a scarcity of amputee care providers and resources for an appropriate prescription.

Translating Evidence-Based Interventions Into Practice

2011 ◽  
Vol 12 (6_suppl_1) ◽  
pp. 9S-19S ◽  
Author(s):  
Meera Viswanathan ◽  
Linda Lux ◽  
Kathleen N. Lohr ◽  
Tammeka Swinson Evans ◽  
Lucia Rojas Smith ◽  
...  
Keyword(s):  
Health Care Providers ◽  
System Integration ◽  
Pediatric Asthma ◽  
Evidence Based ◽  
Extensive Literature ◽  
Care Providers ◽  
Planning Period ◽  
Community Based ◽  
Asthma Morbidity ◽  
Effective Interventions

Pediatric asthma is a multifactorial disease, requiring complex, interrelated interventions addressing children, families, schools, and communities. The Merck Childhood Asthma Network, Inc. (MCAN) is a nonprofit organization that provides support to translate evidence-based interventions from research to practice. MCAN developed the rationale and vision for the program through a phased approach, including an extensive literature review, stakeholder engagement, and evaluation of funding gaps. The analysis pointed to the need to identify pediatric asthma interventions implemented in urban U.S. settings that have demonstrated efficacy and materials for replication and to translate the interventions into wider practice. In addition to this overall MCAN objective, specific goals included service and system integration through linkages among health care providers, schools, community-based organizations, patients, parents, and other caregivers. MCAN selected sites based on demonstrated ability to implement effective interventions and to address multiple contexts of pediatric asthma prevention and management. Selected MCAN program sites were mature institutions or organizations with significant infrastructure, existing funding, and the ability to provide services without requiring a lengthy planning period. Program sites were located in communities with high asthma morbidity and intended to integrate new elements into existing programs to create comprehensive care approaches.

Evidence-based guidelines for acute stabilization and management of neonates with persistent pulmonary hypertension of the newborn

2021 ◽  
Author(s):  
Molly K Ball ◽  
Ruth Seabrook ◽  
Elizabeth M Bonachea ◽  
Bernadette Chen ◽  
Omid Fathi ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Neonatal Intensive Care ◽  
Best Practice ◽  
Clinical Care ◽  
Persistent Pulmonary Hypertension ◽  
High Morbidity ◽  
Evidence Based ◽  
Extensive Literature ◽  
Disciplinary Expertise ◽  
Evidence Based Guidelines

Persistent pulmonary hypertension of the newborn, or PPHN, represents a challenging condition associated with high morbidity and mortality. Management is complicated by complex pathophysiology and limited neonatal specific evidence-based literature, leading to a lack of universal contemporary clinical guidelines for the care of these patients. To address this need and to provide consistent high-quality clinical care for this challenging population in our neonatal intensive care unit, we sought to develop a comprehensive clinical guideline for the acute stabilization and management of neonates with PPHN. Utilizing cross-disciplinary expertise and incorporating an extensive literature search to guide best practice, we present an approachable, pragmatic, and clinically relevant guide for the bedside management of acute PPHN.

scholarly journals Antibiotic Use in Hand Surgery: Surgeon Decision Making and Adherence to Available Evidence

Hand ◽  
2018 ◽  
Vol 15 (4) ◽  
pp. 534-541 ◽  
Author(s):  
John C. Dunn ◽  
Kenneth R. Means ◽  
Sameer Desale ◽  
Aviram M. Giladi
Keyword(s):  
Antibiotic Prophylaxis ◽  
Hand Surgery ◽  
Antibiotic Use ◽  
Demographic Variables ◽  
Fisher Exact Test ◽  
Evidence Based ◽  
Supporting Evidence ◽  
Exact Test ◽  
Preoperative Antibiotic Prophylaxis ◽  
Group 1

Background: There are no clearly defined guidelines from hand surgical societies regarding preoperative antibiotic prophylaxis. Many hand surgeons continue to routinely use preoperative prophylaxis with limited supporting evidence. This study aimed to determine for which scenarios surgeons give antibiotics, the reasons for administration, and whether these decisions are evidence-based. Methods: An anonymous 25-question survey was e-mailed to the 921-member American Society for Surgery of the Hand listserv. We collected demographic information; participants were asked whether they would administer antibiotics in a number of surgical scenarios and for what reasons. Respondents were broken into 3 groups based on when they said they would administer antibiotics: Group 1 (40 respondents) would give antibiotics in the case of short cases, healthy patients, without hardware; group 2 (9 respondents) would not give antibiotics in any scenario; and group 3 (129 respondents) would give antibiotics situationally. The Fisher exact test compared demographic variables, frequency of use, and indications of antibiotic prophylaxis. Results: Of the 921 recipients, 178 (19%) responded. Demographic variables did not correlate with the antibiotic use group. Operative case time >60 minutes, medical comorbidity, and pinning each increased antibiotic use. Group 1 respondents were more likely to admit that their practice was not evidence-based (74.4%) and that they gave antibiotics for medical-legal concern (75%). Twenty-two percent of respondents reported seeing a complication from routine prophylaxis, including Clostridium difficile infection. Conclusions: Antibiotics are still given unnecessarily before hand surgery, most often for medical-legal concern. Clear guidelines for preoperative antibiotic use may help reduce excessive and potentially inappropriate treatment and provide medical-legal support.

Supporting Evidence-Based Design

2010 ◽  
pp. 151-165 ◽  
Author(s):  
Ricardo Codinhoto ◽  
Bronwyn Platten ◽  
Patricia Tzortzopoulos ◽  
Mike Kagioglou
Keyword(s):  
Evidence Based ◽  
Supporting Evidence
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