scholarly journals A Medicago truncatula Metabolite Atlas Enables the Visualization of Differential Accumulation of Metabolites in Root Tissues

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 238
Author(s):  
Clayton Kranawetter ◽  
Shuai Zeng ◽  
Trupti Joshi ◽  
Lloyd W. Sumner
Keyword(s):  
Medicago Truncatula ◽  
Large Scale ◽  
Spatial Localization ◽  
Plant Roots ◽  
Visualization Tool ◽  
Elongation Zone ◽  
Web Based ◽  
Metabolite Profiles ◽  
Metabolite Accumulation ◽  
Root Tissues

Plant roots are composed of many differentiated tissue types, with each tissue exhibiting differential quantitative and qualitative accumulation of metabolites. The large-scale nontargeted metabolite profiles of these differentiated tissues are complex, which complicates the interpretation and development of hypotheses relative to the biological roles of differentially localized metabolites. Thus, we created a data visualization tool to aid in the visualization and understanding of differential metabolite accumulations in Medicago truncatula roots. This was achieved through the development of the Medicago truncatula Metabolite Atlas based upon an adaptation of the Arabidopsis Electronic Fluorescent Pictograph (eFP) Browser. Medicago truncatula roots were dissected into border cells, root cap, elongation zone, mature root, and root secretions. Each tissue was then analyzed by UHPLC-QTOF-MS and GC-Q-MS. Data were uploaded into a MySQL database and displayed in the Medicago truncatula Metabolite Atlas. The data revealed unique differential spatial localization of many metabolites, some of which are discussed here. Ultimately, the Medicago truncatula Metabolite Atlas compiles metabolite data into a singular, useful, and publicly available web-based tool that enables the visualization and understanding of differential metabolite accumulation and spatial localization.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

Interactive Profiler: An Intuitive, Web-Based Statistical Application in Visualizing Educational and Marketing Databases

2004 ◽  
Vol 29 (2) ◽  
pp. 157-175
Author(s):  
Edward H. Ip ◽  
Phillip Leung ◽  
Joseph Johnson
Keyword(s):  
General Public ◽  
Large Scale ◽  
Visualization Tool ◽  
Educational Progress ◽  
National Assessment ◽  
Web Based ◽  
Design And Implementation ◽  
Statistical Application ◽  
American Students ◽  
Statistical Program

We describe the design and implementation of a web-based statistical program—the Interactive Profiler (IP). The prototypical program, developed in Java, was motivated by the need for the general public to query against data collected from the National Assessment of Educational Progress (NAEP), a large-scale US survey of the academic state of American students. The emphasis of the program requirements is on bringing the NAEP data to a broader and not necessarily technically prepared audience. We show that the IP is an intuitive tool for visualizing students’ profiles. Because the same principles for visualization apply to other databases, in this article we also demonstrate how IP can be used to visualize a large marketing database. Besides NAEP, our statistical visualization tool should be pertinent to other federally maintained databases and large-scale marketing databases.

Using Web-based Testing for Large-Scale Assessment

2013 ◽  
Author(s):  
Laura S. Hamilton ◽  
Stephen P. Klein ◽  
William Lorie
Keyword(s):  
Large Scale ◽  
Web Based ◽  
Large Scale Assessment ◽  
Scale Assessment

Impact of COVID-19 on Nuclear Medicine in Germany, Austria and Switzerland: An International Survey in April 2020

2020 ◽  
Vol 59 (04) ◽  
pp. 294-299 ◽  
Author(s):  
Lutz S. Freudenberg ◽  
Ulf Dittmer ◽  
Ken Herrmann
Keyword(s):  
Nuclear Medicine ◽  
Health Systems ◽  
Personal Protective Equipment ◽  
Large Scale ◽  
Diagnostic Procedures ◽  
Protective Equipment ◽  
Current Crisis ◽  
Web Based ◽  
Public Versus Private ◽  
The Impact

Abstract Introduction Preparations of health systems to accommodate large number of severely ill COVID-19 patients in March/April 2020 has a significant impact on nuclear medicine departments. Materials and Methods A web-based questionnaire was designed to differentiate the impact of the pandemic on inpatient and outpatient nuclear medicine operations and on public versus private health systems, respectively. Questions were addressing the following issues: impact on nuclear medicine diagnostics and therapy, use of recommendations, personal protective equipment, and organizational adaptations. The survey was available for 6 days and closed on April 20, 2020. Results 113 complete responses were recorded. Nearly all participants (97 %) report a decline of nuclear medicine diagnostic procedures. The mean reduction in the last three weeks for PET/CT, scintigraphies of bone, myocardium, lung thyroid, sentinel lymph-node are –14.4 %, –47.2 %, –47.5 %, –40.7 %, –58.4 %, and –25.2 % respectively. Furthermore, 76 % of the participants report a reduction in therapies especially for benign thyroid disease (-41.8 %) and radiosynoviorthesis (–53.8 %) while tumor therapies remained mainly stable. 48 % of the participants report a shortage of personal protective equipment. Conclusions Nuclear medicine services are notably reduced 3 weeks after the SARS-CoV-2 pandemic reached Germany, Austria and Switzerland on a large scale. We must be aware that the current crisis will also have a significant economic impact on the healthcare system. As the survey cannot adapt to daily dynamic changes in priorities, it serves as a first snapshot requiring follow-up studies and comparisons with other countries and regions.

scholarly journals Age impairs mnemonic discrimination of objects more than scenes: A web-based, large-scale approach across the lifespan

Cortex ◽  
2021 ◽  
Vol 137 ◽  
pp. 138-148
Author(s):  
Jeremie Güsten ◽  
Gabriel Ziegler ◽  
Emrah Düzel ◽  
David Berron
Keyword(s):  
Large Scale ◽  
Web Based

scholarly journals Web-based Prostate Visualization Tool

2020 ◽  
Vol 6 (3) ◽  
pp. 563-566
Author(s):  
Cristina Laura Oyarzun ◽  
Katrin Hartwig ◽  
Anna-Sophie Hertlein ◽  
Florian Jung ◽  
Jan Burmeister ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Relevant Information ◽  
Visualization Tool ◽  
Proper Treatment ◽  
Communication Tool ◽  
Web Based ◽  
Tumor Length ◽  
Survival Chance

AbstractProper treatment of prostate cancer is essential to increase the survival chance. In this sense, numerous studies show how important the communication between all stakeholders in the clinic is. This communication is difficult because of the lack of conventions while referring to the location where a biopsy for diagnosis was taken. This becomes even more challenging taking into account that experts of different fields work on the data and have different requirements. In this paper a web-based communication tool is proposed that incorporates a visualization of the prostate divided into 27 segments according to the PI-RADS protocol. The tool provides 2 working modes that consider the requirements of radiologist and pathologist while keeping it consistent. The tool comprises all relevant information given by pathologists and radiologists, such as, severity grades of the disease or tumor length. Everything is visualized using a colour code for better undestanding.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 141-155 ◽  
Author(s):  
H H Yan ◽  
J Mudge ◽  
D-J Kim ◽  
R C Shoemaker ◽  
D R Cook ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Physical Mapping ◽  
Large Scale ◽  
Sequence Similarity ◽  
Artificial Chromosome ◽  
Bac Contig ◽  
Cross Hybridization ◽  
Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

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