A knowledgebase system to enhance scientific discovery: Telemakus

BACKGROUND: With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged. METHODS: Case study. RESULTS: The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports. CONCLUSION: Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.     

Evaluation of a large healthy lifestyle program: informing program implementation and scale-up in the prevention of obesity

Background

The Healthy Lifestyle Program for women (HeLP-her) is a low-intensity, self-management program which has demonstrated efficacy in preventing excess weight gain in women. However, little is known about the implementation, reach, and sustainability of low-intensity prevention programs in rural settings, where risk for obesity in women is higher than urban settings. We aimed to evaluate a low-intensity healthy lifestyle program delivered to women in a rural setting to inform development of effective community prevention programs.

Methods

A mixed method hybrid implementation and evaluation study, guided by the RE-AIM framework (addressing the Reach, Effectiveness, Adoption, Implementation, and Maintenance), was undertaken. Data collection tools included anthropometric measures, program checklists, questionnaires, and semi-structured interviews with participants and local stakeholders. The RE-AIM self-audit tool was applied to assess evaluation rigor.

Results

Six hundred and forty-nine women from 41 relatively socio-economic disadvantaged communities in Australia participated: mean age 39.6 years (±SD 6.7) and body mass index of 28.8 kg/m² (±SD 6.9). A between-group weight difference of ?0.92 kg (95% CI ?1.67 to ?0.16) showed program effectiveness. Reach was broad across 41 towns with 62% of participants reporting influencing some of the health behaviors of their families. Strong implementation fidelity was achieved with good retention rates at 1 year (76%) and high participant satisfaction (82% of participants willing to recommend this program). Over 300 multi-level community partnerships were established supporting high adoption. Stakeholders reported potential capacity to implement and sustain the prevention program in resource poor rural settings, due to the low-intensity design and minimal resources required.

Conclusions

Our comprehensive RE-AIM evaluation demonstrates that an evidence-based obesity prevention program can be successfully implemented in real-world settings. The program achieved broad reach, effectiveness, and satisfaction at the community and stakeholder level, revealing potential for program sustainability. The evaluation addressed implementation knowledge gaps to support future obesity prevention program scale-up.

Trial registration

Australian and New Zealand Clinical Trial Registry ACTRN 12612000115831 [http://www.anzctr.org.au/].

     

BeingAliveLanguage: Visualizing soil information from a design perspective to enhance multidisciplinary communication

Soil forms the foundation for biotic and abiotic activities that shape landscapes over time. Effective communication and understanding of soil profiles, contents, and interactions with other systems such as vegetation and climate are crucial for multidisciplinary research and projects involving soil. A robust, comprehensible, and extendable visualization system is required to enhance communication across diverse disciplines, including landscape architecture, agronomy, and ecology.This paper introduces the BeingAliveLanguage, an innovative, extensible visualization system for soil-centric information within a multidisciplinary communication framework. The system employs a fractal-based visual language to effectively convey vital soil information to professionals in various fields engaged in architecture, landscape design, and urban planning projects. The corresponding software, developed as a plugin for the Rhino-Grasshopper CAD environment, allows users to automatically generate easily understandable soil-centered diagrams using a node-based programming language. Designed to enhance communication in landscape, geoscience, and agriculture-related fields, the system provides critical information to support the design and decision-making process. We showcase the system’s efficacy through two extensions and by utilizing the tool in multiple real-world projects.     

Grassland to shrubland state transitions enhance carbon sequestration in the northern Chihuahuan Desert

The replacement of native C₄‐dominated grassland by C₃‐dominated shrubland is considered an ecological state transition where different ecological communities can exist under similar environmental conditions. These state transitions are occurring globally, and may be exacerbated by climate change. One consequence of the global increase in woody vegetation may be enhanced ecosystem carbon sequestration, although the responses of arid and semiarid ecosystems may be highly variable. During a drier than average period from 2007 to 2011 in the northern Chihuahuan Desert, we found established shrubland to sequester 49 g C m^?2 yr^?1 on average, while nearby native C₄ grassland was a net source of 31 g C m^?2 yr^?1 over this same period. Differences in C exchange between these ecosystems were pronounced – grassland had similar productivity compared to shrubland but experienced higher C efflux via ecosystem respiration, while shrubland was a consistent C sink because of a longer growing season and lower ecosystem respiration. At daily timescales, rates of carbon exchange were more sensitive to soil moisture variation in grassland than shrubland, such that grassland had a net uptake of C when wet but lost C when dry. Thus, even under unfavorable, drier than average climate conditions, the state transition from grassland to shrubland resulted in a substantial increase in terrestrial C sequestration. These results illustrate the inherent tradeoffs in quantifying ecosystem services that result from ecological state transitions, such as shrub encroachment. In this case, the deleterious changes to ecosystem services often linked to grassland to shrubland state transitions may at least be partially offset by increased ecosystem carbon sequestration.     

Development and implementation of a database system to manage a large-scale mouse ENU-mutagenesis program

A mouse ENU-mutagenesis program at RIKEN GSC has been initiated to conduct a large-scale, genome-wide, early- and late-onset phenotypic screen of mutant mice. We screened about a hundred mice every week with a comprehensive set of phenotype assays including behavioral tests based on a modified SHIRPA protocol, blood tests (both clinical biochemical testing and hemogram), and measurement of locomotor activity in their home cages. To manage the entire program, we developed a client/server architecture database system and named it MUSDB (Mutagenesis Universal Support DataBase). It manages mouse husbandry, mating protocols, procedures for ENU injection and phenotypic screens, phenotype inheritance tests, preservation of sperm and organs, and other materials generated during the program. We have implemented MUSDB in quite a large-scale system that includes 150 client computers. It has, helped reduce typographical errors and provided simple and efficient operation via its front-end user interface. It significantly contributed to the communication within and between workgroups in the program and in the accumulation of various phenotypic and inheritance data.     

Application of discrete choice experiments to enhance stakeholder engagement as a strategy for advancing implementation: a systematic review

Background

One of the key strategies to successful implementation of effective health-related interventions is targeting improvements in stakeholder engagement. The discrete choice experiment (DCE) is a stated preference technique for eliciting individual preferences over hypothetical alternative scenarios that is increasingly being used in health-related applications. DCEs are a dynamic approach to systematically measure health preferences which can be applied in enhancing stakeholder engagement. However, a knowledge gap exists in characterizing the extent to which DCEs are used in implementation science.

Methods

We conducted a systematic literature search (up to December 2016) of the English literature to identify and describe the use of DCEs in engaging stakeholders as an implementation strategy. We searched the following electronic databases: MEDLINE, Econlit, PsychINFO, and the CINAHL using mesh terms. Studies were categorized according to application type, stakeholder(s), healthcare setting, and implementation outcome.

Results

Seventy-five publications were selected for analysis in this systematic review. Studies were categorized by application type: (1) characterizing demand for therapies and treatment technologies (n?=?32), (2) comparing implementation strategies (n?=?22), (3) incentivizing workforce participation (n?=?11), and (4) prioritizing interventions (n?=?10). Stakeholders included providers (n?=?27), patients (n?=?25), caregivers (n?=?5), and administrators (n?=?2). The remaining studies (n?=?16) engaged multiple stakeholders (i.e., combination of patients, caregivers, providers, and/or administrators). The following implementation outcomes were discussed: acceptability (n?=?75), appropriateness (n?=?34), adoption (n?=?19), feasibility (n?=?16), and fidelity (n?=?3).

Conclusions

The number of DCE studies engaging stakeholders as an implementation strategy has been increasing over the past decade. As DCEs are more widely used as a healthcare assessment tool, there is a wide range of applications for them in stakeholder engagement. The DCE approach could serve as a tool for engaging stakeholders in implementation science.

     

高中生物学课程应提高基本科学素养要求

高中生物学课程改革应注意提高基本科学素养要求,一是要增进对科学知识的理解,构建更合理的知识体系：二是要增进对科学过程和方法的理解,重视模型方法和数学方法在探究中的运用;三是要增进对科学,技术,社会三者关系的理解。突出科技意识增养和系统分析能力的发展。     

Implementing the LifeSkills Training drug prevention program: factors related to implementation fidelity

Background

Organizational context plays a central role in shaping the use of research by healthcare professionals. The largest group of professionals employed in healthcare organizations is nurses, putting them in a position to influence patient and system outcomes significantly. However, investigators have often limited their study on the determinants of research use to individual factors over organizational or contextual factors.

Methods

The purpose of this study was to examine the determinants of research use among nurses working in acute care hospitals, with an emphasis on identifying contextual determinants of research use. A comparative ethnographic case study design was used to examine seven patient care units (two adult and five pediatric units) in four hospitals in two Canadian provinces (Ontario and Alberta). Data were collected over a six-month period by means of quantitative and qualitative approaches using an array of instruments and extensive fieldwork. The patient care unit was the unit of analysis. Drawing on the quantitative data and using correspondence analysis, relationships between various factors were mapped using the coefficient of variation.

Results

Units with the highest mean research utilization scores clustered together on factors such as nurse critical thinking dispositions, unit culture (as measured by work creativity, work efficiency, questioning behavior, co-worker support, and the importance nurses place on access to continuing education), environmental complexity (as measured by changing patient acuity and re-sequencing of work), and nurses' attitudes towards research. Units with moderate research utilization clustered on organizational support, belief suspension, and intent to use research. Higher nursing workloads and lack of people support clustered more closely to units with the lowest research utilization scores.

Conclusion

Modifiable characteristics of organizational context at the patient care unit level influences research utilization by nurses. These findings have implications for patient care unit structures and offer beginning direction for the development of interventions to enhance research use by nurses.     

培育基础医学微生物学专业研究生人文素养和科学素养方式

微生物学是基础医学和生物学的重要基础学科,微生物学专业培养的研究生是微生物领域科学研究和教学的高级后备人才,随着基础医学的发展,对微生物学专业研究人员的人文素养和科学素养要求越来越高,本专业研究生全面发展培育方式的改革,已成为高等医学教育改革的重要课题。本研究针对基础医学微生物专业研究生培养的现状,根据基础医学微生物学专业研究生的特点,着重探讨其人文素养和科学素养培育方式的改革,为培养具有优良的科研能力、科学素养、健全人格的人才提供一定的思路。     

Developing and maintaining a surgical research program: surgical suite design

When building or renovating a laboratory animal facility, one must consider the requirements of the surgery program. The authors outline the critical considerations for designing a large-animal surgical suite.     

Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design

Key message

We enhance power and accuracy of QTL mapping in multiple related families, by clustering the founders of the families on their local genomic similarity.

Abstract

MCQTL is a linkage mapping software application that allows the joint QTL mapping of multiple related families. In its current implementation, QTLs are modeled with one or two parameters for each parent that is a founder of the multi-cross design. The higher the number of parents, the higher the number of model parameters which can impact the power and the accuracy of the mapping. We propose to make use of the availability of denser and denser genotyping information on the founders to lessen the number of MCQTL parameters and thus boost the QTL discovery. We developed clusthaplo, an R package (http://cran.r-project.org/web/packages/clusthaplo/index.html), which aims to cluster haplotypes using a genomic similarity that reflects the probability of sharing the same ancestral allele. Computed in a sliding window along the genome and followed by a clustering method, the genomic similarity allows the local clustering of the parent haplotypes. Our assumption is that the haplotypes belonging to the same class transmit the same ancestral allele. So their putative QTL allelic effects can be modeled with the same parameter, leading to a parsimonious model, that is plugged in MCQTL. Intensive simulations using three maize data sets showed the significant gain in power and in accuracy of the QTL mapping with the ancestral allele model compared to the classical MCQTL model. MCQTL_LD (clusthaplo outputs plug in MCQTL) is a versatile and powerful tool for QTL mapping in multiple related families that makes use of linkage and linkage disequilibrium (web site http://carlit.toulouse.inra.fr/MCQTL/).     

Madeline 2.0 PDE: a new program for local and web-based pedigree drawing

The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. For complex pedigrees, we use a hybrid algorithm in which consanguinous loops are drawn as cyclic graphs whenever possible, but we resort to acyclic graphs when matings can no longer be connected without line crossings. A similar hybrid approach is used to avoid line crossings for matings between distant descendants of different founding groups. Written in object-oriented C++ and released under the GNU General Public License (GPL), Madeline 2.0 PDE reads input files specified on the command line and generates pedigree drawings without user interaction. Pedigree output in scalable vector graphics (SVG) format can be viewed in browsers with native SVG rendering support or in vector graphics editors. We provide an easy-to-use public web service, which is experimental and still under development. Availability: http://kellogg.umich.edu/madeline.     

Toward implementation of a regional quality assurance program in cytopathology: the Hong Kong experience

OBJECTIVE: To develop a local quality assurance program in cytopathology based on circulation of patient specimens on glass slides, with limited resources. STUDY DESIGN: A working group was set up for design and running of the program. Participation is on a laboratory basis. The scope and frequency of testing are defined. Well-documented cases (including gynecologic, nongynecologic and fine needle aspiration cytology) with commonly encountered diagnoses are collected. Consensus concerning the diagnosis, interpretive menu and scoring system is sought before the actual slide circulations using express mail. After returning their answers to the program organizer, the participating laboratories receive immediate feedback on their scores, with reference answers, explanatory notes, "whole-mount" images of glass slides and cumulative responses of peer laboratories for on-site checking. At the end of each year, an electronic file containing representative photomicrographs of all cases examined is provided to individual laboratories for their permanent records and training purposes. RESULTS: The program was launched in mid-2003. There were 24 and 27 participating laboratories from Hong Kong (and Macau) in 2003 and 2004, respectively. To date, >150 well-documented cytology cases are available in the slide pool and ready for circulation. As the revenue is mainly to cover the expenses of express mail, the program can be carried out at a relatively low cost. CONCLUSION: In order to have any cytology quality assurance program accepted by local laboratories, it has to be fair and practical. Strict confidentiality needs to be observed throughout the process. This program emphasizes both performance assessment and educational value. Adequate representation from experienced local cytology workers, detailed documentation support from authorities and assistance from dedicated staff are essential to the success of any external proficiency testing scheme. Regular review and evaluation are also necessary for continuous improvement. The Hong Kong experience can serve as an example of running a glass slide-based cytology quality assurance program in a small region with limited resources.