scholarly journals XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into Data

2019 ◽  
Author(s):  
Jordan A. Berg ◽  
Jonathan R. Belyeu ◽  
Jeffrey T. Morgan ◽  
Yeyun Ouyang ◽  
Alex J. Bott ◽  
...  
Keyword(s):  
Best Practices ◽  
Protein Translation ◽  
Ribosome Profiling ◽  
Translation Regulation ◽  
Computational Tools ◽  
Current State ◽  
Reference Implementation ◽  
Computational Analyses ◽  
Profiling Analysis ◽  
Insight Into

AbstractRibosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak. We introduce XPRESSyourself, an analytical toolkit that eliminates barriers and bottlenecks associated with this specialized data type by filling gaps in the computational toolset for both experts and non-experts of ribosome profiling. XPRESSyourself automates and standardizes analysis procedures, decreasing time-to-discovery and increasing reproducibility. This toolkit acts as a reference implementation of current best practices in ribosome profiling analysis. We demonstrate this toolkit’s performance on publicly available ribosome profiling data by rapidly identifying hypothetical mechanisms related to neurodegenerative phenotypes and neuroprotective mechanisms of the small-molecule ISRIB during acute cellular stress. XPRESSyourself brings robust, rapid analysis of ribosome-profiling data to a broad and ever-expanding audience and will lead to more reproducible and accessible measurements of translation regulation. XPRESSyourself software is perpetually open-source under the GPL-3.0 license and is hosted at https://github.com/XPRESSyourself, where users can access additional documentation and report software issues.

scholarly journals RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints

2015 ◽  
Author(s):  
Yi Zhong ◽  
Theofanis Karaletsos ◽  
Philipp Drewe ◽  
Vipin Thankam T Sreedharan ◽  
David Kuo ◽  
...  
Keyword(s):  
Linear Models ◽  
Protein Translation ◽  
Ribosome Profiling ◽  
Translation Regulation ◽  
Analysis Tool ◽  
Translation Efficiency ◽  
Case Control Studies ◽  
Statistical Framework ◽  
Experimental Treatments ◽  
Over Dispersion

Motivation: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed. Results: We present a statistical framework and analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy. Availability: Source code and documentation are available at http://github.com/ratschlab/ribodiff. Supplementary Material can be found at http://bioweb.me/ribo.

scholarly journals XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data

2020 ◽  
Vol 16 (1) ◽  
pp. e1007625 ◽  
Author(s):  
Jordan A. Berg ◽  
Jonathan R. Belyeu ◽  
Jeffrey T. Morgan ◽  
Yeyun Ouyang ◽  
Alex J. Bott ◽  
...  
Keyword(s):  
Ribosome Profiling ◽  
Computational Analyses ◽  
Insight Into

PROFESSIONAL TRAINING OF ELECTRONICS ENGINEERS: APPLYING US EXPERICENCE TO UKRAINAN HIGHER EDUCATION INSTITUTIONS

2020 ◽  
pp. 80-85
Author(s):  
Olha Pavlenko
Keyword(s):  
Higher Education ◽  
Education Research ◽  
Best Practices ◽  
Cost Reduction ◽  
Professional Training ◽  
Higher Education Institutions ◽  
Academic Staff ◽  
Research And Innovation ◽  
Current State

The article discusses the current state of professional training of engineers, in particular, electronics engineers in Ukrainian higher education institutions (HEIs) and explores best practices from US HEIs. The research outlines the features of professional training of electronics engineers and recent changes in Ukrainian HEIs. Such challenges for Ukrainian HEIs as lack of collaboration between higher education and science with industry, R&D cost reduction for HEIs, and downsizing the research and academic staff, the disparity between the available quality of human capital training and the demanded are addressed. The study attempts to identify successful practices of US HEIs professional training of engineers in order to suggest potential improvements in education, research, and innovation for training electronics engineers in Ukraine.

Insight into the formation of H-bonds propagating the monomeric zinc complexes of a tridentate reduced Schiff base to form an infinite chain

CrystEngComm ◽  
2021 ◽  
Author(s):  
Mainak Karmakar ◽  
Antonio Frontera ◽  
Shouvik Chattopadhyay
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Dft Calculations ◽  
Zinc Complexes ◽  
Infinite Chain ◽  
State Structure ◽  
Computational Tools ◽  
Solid State Structure ◽  
Reduced Schiff Base ◽  
Insight Into

The formation of an infinite 1D assembly is governed by the H-bonding interactions in the solid state structure of the two zinc complexes. It has been analyzed energetically using DFT calculations and several computational tools.

scholarly journals The European Green Capital Award—Is It a Dream or Reality for Belgrade (Serbia)?

2021 ◽  
Vol 13 (11) ◽  
pp. 6182
Author(s):  
Marijana Pantić ◽  
Saša Milijić
Keyword(s):  
Urban Transformation ◽  
The Other ◽  
Transmission Of Knowledge ◽  
Current State ◽  
Transitional Countries ◽  
Great Hope ◽  
Environmentally Responsible ◽  
Potential Benefits ◽  
The City ◽  
Insight Into

An agreement of cooperation and transmission of knowledge regarding the nomination for the European Green Capital Award (EGCA) was signed between the mayors of Belgrade and Ljubljana (EGCA 2016 winner) in September 2018. The candidacy of Belgrade was finally realized in October 2019. Great hope was placed in this endeavour because internationally recognized awards, such as the EGCA, represent enormous capital for both the city and the state. The EGCA requires serious preparation and significant fulfilment of preconditions. Many economically strong and environmentally responsible cities competed for the award, but did not win. On the other hand, the capital of Serbia does not appear to be an obvious winning candidate, especially as it is differentiated from the previous winners by being a non-EU city and by the fact that it is still undergoing an intense urban transformation, characteristic of transitional countries. Therefore, the main aim of this article is to present a review of the current state of Belgrade’s environmental qualities and its comparison with the EGCA criteria and with Grenoble as one of the winning competitors. The article gives a full overview of the EGCA requirements with certain details on required indicators, gives relevant insight into the procedure, which could be of use for any future candidacy, and discusses potential benefits for winners, losers and repeat candidacies.

Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa

2015 ◽  
Vol 35 (3) ◽  
pp. 561-571 ◽  
Author(s):  
Wenxian Liu ◽  
Zhengshe Zhang ◽  
Shuangyan Chen ◽  
Lichao Ma ◽  
Hucheng Wang ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Global Transcriptome ◽  
Profiling Analysis ◽  
Insight Into

scholarly journals Challenges for Change Agents. Best Practices at the University Library of Freie Universität Berlin

ABI-Technik ◽  
2020 ◽  
Vol 40 (4) ◽  
pp. 357-364
Author(s):  
Martin Lee ◽  
Christina Riesenweber
Keyword(s):  
Best Practices ◽  
Change Agents ◽  
Large Change ◽  
University Library ◽  
The Future ◽  
The University ◽  
Insight Into

AbstractThe authors of this article have been managing a large change project at the university library of Freie Universität Berlin since January 2019. At the time of writing this in the summer of 2020, the project is about halfway completed. With this text, we would like to give some insight into our work and the challenges we faced, thereby starting conversations with similar undertakings in the future.

¿¿Nueva narrativa? Entrevista con David Toscana

2002 ◽  
Vol 18 (2) ◽  
pp. 351-362
Author(s):  
Pablo A. J. Brescia ◽  
Scott M. Bennett
Keyword(s):  
Latin American ◽  
The Past ◽  
Current State ◽  
Latin American Narrative ◽  
Boom Latinoamericano ◽  
The 1960S ◽  
Time Frames ◽  
Insight Into

This interview with Mexican writer David Toscana ponders the current state of both Mexican and Latin American narrative and serves as an insight into his own works. Toscana's statements about the recurring themes in his narrative (failure, loneliness, characters put to the test, and a tendency to play with different time frames, especially in his novels) help illustrate some of the characteristics of his fiction, which, according to various critics, is one of the most promising today in Mexico. Also noteworthy are his comments about the tendency of writers from his generation (born in the 1960s and later) to reject the legacy of the "boom" writers. Toscana's own interest is to revisit history and tradition by constructing a different voice and a different vision, a new way of seeing and hearing both the past and the present. Esta entrevista con el escritor mexicano David Toscana trata de explorar el estado actual de la narrativa mexicana y latinoamericana, améén de servir como una aproximacióón a la incipiente obra de este autor. Las respuestas de Toscana sobre los temas recurrentes en su literatura (el fracaso, la soledad, los personajes sometidos a pruebas y una tendencia a proponer diferentes marcos temporales, especialmente en sus novelas) subrayan algunos rasgos de su ficcióón, la cual, segúún la críítica especializada, es una de las máás prometedoras en el panorama mexicano de hoy. De especial interéés son los comentarios de Toscana sobre la tendencia de los escritores de su generacióón a rechazar el legado del "boom" latinoamericano. Toscana reacciona contra ese rechazo y propone una voz personal que vuelva a la historia y a la tradicióón y plantee una nueva manera de ver el pasado y el presente de Mééxico.

scholarly journals The Synthesis Map Is a Multidimensional Educational Tool That Provides Insight into Students’ Mental Models and Promotes Students’ Synthetic Knowledge Generation

2015 ◽  
Vol 14 (2) ◽  
pp. ar14 ◽  
Author(s):  
Ryan A. Ortega ◽  
Cynthia J. Brame
Keyword(s):  
Best Practices ◽  
Concept Mapping ◽  
Student Understanding ◽  
Knowledge Structures ◽  
Cognitive Domain ◽  
Knowledge Generation ◽  
Natural Evolution ◽  
Student Work ◽  
Presentation Software ◽  
Insight Into

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi’s zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms.

Sign in / Sign up

Export Citation Format

Share Document