scholarly journals SorghumBase: a web-based portal for sorghum genetic information and community advancement

Planta ◽  
2022 ◽  
Vol 255 (2) ◽  
Author(s):  
Nicholas Gladman ◽  
Andrew Olson ◽  
Sharon Wei ◽  
Kapeel Chougule ◽  
Zhenyuan Lu ◽  
...  
Keyword(s):  
Resource Sharing ◽  
Content Management ◽  
Research Community ◽  
Data Types ◽  
Training Materials ◽  
Wide Range ◽  
Variant Information ◽  
Data Collation ◽  
Genome Assemblies ◽  
User Friendly

Abstract Main conclusion SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal (https://www.sorghumbase.org), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.

scholarly journals A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2298
Author(s):  
Manosh Kumar Biswas ◽  
Dhima Biswas ◽  
Mita Bagchi ◽  
Ganjun Yi ◽  
Guiming Deng
Keyword(s):  
Draft Genome ◽  
Genome Survey ◽  
Plant Mirna ◽  
Wide Range ◽  
Intergenic Regions ◽  
Mirna Evolution ◽  
Taxonomic Groups ◽  
Genome Assemblies ◽  
User Friendly ◽  
Simple Sequence

Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.

scholarly journals FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

2020 ◽  
Vol 49 (D1) ◽  
pp. D892-D898
Author(s):  
Imad Abugessaisa ◽  
Jordan A Ramilowski ◽  
Marina Lizio ◽  
Jesicca Severin ◽  
Akira Hasegawa ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Research Community ◽  
Dermal Fibroblasts ◽  
Data Types ◽  
Web Interfaces ◽  
Web Resource ◽  
Non Coding Rna ◽  
Mammalian Genomes ◽  
Non Coding Rnas ◽  
Genome Assemblies

Abstract The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

scholarly journals TreeGenes: A Forest Tree Genome Database

2008 ◽  
Vol 2008 ◽  
pp. 1-7 ◽  
Author(s):  
Jill L. Wegrzyn ◽  
Jennifer M. Lee ◽  
Brandon R. Tearse ◽  
David B. Neale
Keyword(s):  
Data Retrieval ◽  
Forest Tree ◽  
Research Community ◽  
Genetic Maps ◽  
Data Types ◽  
Genome Database ◽  
Access Points ◽  
Web Resource ◽  
Wide Range ◽  
Visualization Tools

The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

scholarly journals Carbon Nanotube Films for Energy Applications

Energies ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1890
Author(s):  
Monika Rdest ◽  
Dawid Janas
Keyword(s):  
Carbon Nanotube ◽  
Mechanical Energy ◽  
Research Community ◽  
Thermal Interface Materials ◽  
Thermal Interface ◽  
Conductive Coatings ◽  
Storage Devices ◽  
Energy Applications ◽  
Wide Range ◽  
Interface Materials

This perspective article describes the application opportunities of carbon nanotube (CNT) films for the energy sector. Up to date progress in this regard is illustrated with representative examples of a wide range of energy management and transformation studies employing CNT ensembles. Firstly, this paper features an overview of how such macroscopic networks from nanocarbon can be produced. Then, the capabilities for their application in specific energy-related scenarios are described. Among the highlighted cases are conductive coatings, charge storage devices, thermal interface materials, and actuators. The selected examples demonstrate how electrical, thermal, radiant, and mechanical energy can be converted from one form to another using such formulations based on CNTs. The article is concluded with a future outlook, which anticipates the next steps which the research community will take to bring these concepts closer to implementation.

scholarly journals Using Satellite Data for CBRN (Chemical, Biological, Radiological, and Nuclear) Threat Detection, Monitoring, and Modelling

2021 ◽  
Author(s):  
Gary Sutlieff ◽  
Lucy Berthoud ◽  
Mark Stinchcombe
Keyword(s):  
Satellite Data ◽  
Meteorological Data ◽  
Atmospheric Composition ◽  
Chemical Detection ◽  
List Type ◽  
Data Types ◽  
Wide Range ◽  
Future Technologies ◽  
The Impact ◽  
Near Future

Abstract CBRN (Chemical, Biological, Radiological, and Nuclear) threats are becoming more prevalent, as more entities gain access to modern weapons and industrial technologies and chemicals. This has produced a need for improvements to modelling, detection, and monitoring of these events. While there are currently no dedicated satellites for CBRN purposes, there are a wide range of possibilities for satellite data to contribute to this field, from atmospheric composition and chemical detection to cloud cover, land mapping, and surface property measurements. This study looks at currently available satellite data, including meteorological data such as wind and cloud profiles, surface properties like temperature and humidity, chemical detection, and sounding. Results of this survey revealed several gaps in the available data, particularly concerning biological and radiological detection. The results also suggest that publicly available satellite data largely does not meet the requirements of spatial resolution, coverage, and latency that CBRN detection requires, outside of providing terrain use and building height data for constructing models. Lastly, the study evaluates upcoming instruments, platforms, and satellite technologies to gauge the impact these developments will have in the near future. Improvements in spatial and temporal resolution as well as latency are already becoming possible, and new instruments will fill in the gaps in detection by imaging a wider range of chemicals and other agents and by collecting new data types. This study shows that with developments coming within the next decade, satellites should begin to provide valuable augmentations to CBRN event detection and monitoring. Article Highlights There is a wide range of existing satellite data in fields that are of interest to CBRN detection and monitoring. The data is mostly of insufficient quality (resolution or latency) for the demanding requirements of CBRN modelling for incident control. Future technologies and platforms will improve resolution and latency, making satellite data more viable in the CBRN management field

scholarly journals Technology-enhanced and game based learning for children with special needs: a systematic mapping study

2021 ◽  
Author(s):  
Jose A. Gallud ◽  
Monica Carreño ◽  
Ricardo Tesoriero ◽  
Andrés Sandoval ◽  
María D. Lozano ◽  
...  
Keyword(s):  
Special Needs ◽  
State Of The Art ◽  
Research Community ◽  
Systematic Mapping Study ◽  
Children With Special Needs ◽  
Game Based Learning ◽  
Mapping Study ◽  
Systematic Mapping ◽  
Wide Range ◽  
Research Questions

AbstractTechnology-based education of children with special needs has become the focus of many research works in recent years. The wide range of different disabilities that are encompassed by the term “special needs”, together with the educational requirements of the children affected, represent an enormous multidisciplinary challenge for the research community. In this article, we present a systematic literature review of technology-enhanced and game-based learning systems and methods applied on children with special needs. The article analyzes the state-of-the-art of the research in this field by selecting a group of primary studies and answering a set of research questions. Although there are some previous systematic reviews, it is still not clear what the best tools, games or academic subjects (with technology-enhanced, game-based learning) are, out of those that have obtained good results with children with special needs. The 18 articles selected (carefully filtered out of 614 contributions) have been used to reveal the most frequent disabilities, the different technologies used in the prototypes, the number of learning subjects, and the kind of learning games used. The article also summarizes research opportunities identified in the primary studies.

scholarly journals Product formalisms for measures on spaces with binary tree structures: representation, visualization, and multiscale noise

2020 ◽  
Vol 8 ◽  
Author(s):  
Devasis Bassu ◽  
Peter W. Jones ◽  
Linda Ness ◽  
David Shallcross
Keyword(s):  
Data Science ◽  
Theoretical Foundation ◽  
Continuous Functions ◽  
Noise Model ◽  
Data Types ◽  
Data Set ◽  
Tree Structures ◽  
Simple Concept ◽  
Wide Range ◽  
Computer Scientists

Abstract In this paper, we present a theoretical foundation for a representation of a data set as a measure in a very large hierarchically parametrized family of positive measures, whose parameters can be computed explicitly (rather than estimated by optimization), and illustrate its applicability to a wide range of data types. The preprocessing step then consists of representing data sets as simple measures. The theoretical foundation consists of a dyadic product formula representation lemma, and a visualization theorem. We also define an additive multiscale noise model that can be used to sample from dyadic measures and a more general multiplicative multiscale noise model that can be used to perturb continuous functions, Borel measures, and dyadic measures. The first two results are based on theorems in [15, 3, 1]. The representation uses the very simple concept of a dyadic tree and hence is widely applicable, easily understood, and easily computed. Since the data sample is represented as a measure, subsequent analysis can exploit statistical and measure theoretic concepts and theories. Because the representation uses the very simple concept of a dyadic tree defined on the universe of a data set, and the parameters are simply and explicitly computable and easily interpretable and visualizable, we hope that this approach will be broadly useful to mathematicians, statisticians, and computer scientists who are intrigued by or involved in data science, including its mathematical foundations.

The Management of Teaching in Online and Blended Learning Applied in the Project “Modern Competences of Academic Teachers – the Key to Modern Higher Education Institutions” – Acronym MOCAT

2021 ◽  
Vol 29 (4) ◽  
pp. 390-401
Author(s):  
Roxana Stefanescu ◽  
◽  
Mariana Iatagan ◽  
Cristian Uta
Keyword(s):  
Higher Education ◽  
Blended Learning ◽  
Online Courses ◽  
Higher Education Institutions ◽  
Teaching Methodology ◽  
Teaching Competencies ◽  
Training Materials ◽  
Wide Range ◽  
Academic Teachers ◽  
Academic Teacher

The management of teaching is connected and could be increased by using a wide range of different methods especially when we refer to Online and Blended learning. In the first part, the paper is aiming at reviewing the literature regarding the concepts and benefits of Online and Blended learning. Based on this considerations, 8 partner universities from 8 countries jointly developed the Project “Modern competences of academic teachers – the key to modern Higher Education Institutions (HEI)” – Acronym MOCAT. The paper underlines the goals and achievements of the MOCAT project that proposes a conceptual process to increase the management performance in teaching. The paper shows in an organized manner the main deficiencies that are altering the teaching competencies of academic teachers and in connection with this, the project offers solutions to improve the methodological competency of the teachers regarding the development and use of modern approaches. The outcomes of the project consist in the development and implementation of a Multicultural Model of an Academic Teacher Competencies and in 10 online courses that represent modern training materials in the field of teaching methodology. In the end are exposed the way the results of the project can be evaluated in time as well as the anticipated effects of the project implementation.

The Intelligent Design of the Gear Reducer

2012 ◽  
Vol 522 ◽  
pp. 823-827
Author(s):  
Jian Jiang Fang ◽  
Wen Jun Qi
Keyword(s):  
Intelligent Design ◽  
Object Oriented ◽  
Data Access ◽  
Mechanical Transmission ◽  
Design Efficiency ◽  
Integrated Technology ◽  
Gear Drive ◽  
Object Oriented Technology ◽  
Wide Range ◽  
User Friendly

The gear drive is the wide range of applications and is particularly important as a form of mechanical transmission, but the design process requires large amounts of data access and computation. In the paper, computer integrated technology and object-oriented technology is used to research and develop the intelligent design of Straight gear reducer system with user-friendly interactive platform, easy to use, high design efficiency and reliable data.

scholarly journals Principles of reusability of XML-based enterprise documents

2010 ◽  
Vol 58 (6) ◽  
pp. 295-302
Author(s):  
Roman Malo
Keyword(s):  
Main Idea ◽  
Content Management ◽  
Document Management ◽  
Management Systems ◽  
Data Types ◽  
Software Infrastructure ◽  
Basic Principles ◽  
Xml Databases ◽  
Extensible Markup ◽  
Partial Redundancy

XML (Extensible Markup Language) represents one of flexible platforms for processing enterprise documents. Its simple syntax and powerful software infrastructure for processing this type of documents is a guarantee for high interoperability of individual documents. XML is today one of technologies influencing all aspects of ICT area.In the paper questions and basic principles of reusing XML-based documents are described in the field of enterprise documents. If we use XML databases or XML data types for storing these types of documents then partial redundancy could be expected due to possible documents’ similarity. This similarity can be found especially in documents’ structure and also in documents’ content and its elimination is necessary part of data optimization.The main idea of the paper is focused to possibilities how to think about dividing complex XML docu­ments into independent fragments that can be used as standalone documents and how to process them.Conclusions could be applied within software tools working with XML-based structured data and documents as document management systems or content management systems.

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