232 Works

Path sampling simulations reveal how the Q61L mutation restricts the dynamics of KRas

Jocelyne Vreede, Sander Roet & David Swenson
The GTPase KRas is a signaling protein in networks for cell differentiation, growth, and division. KRas mutations can prolong activation of these networks, resulting in tumor formation. When active, KRas tightly binds GTP. Several oncogenic mutations affect the conversion between this rigid state and inactive, more flexible states. Detailed understanding of these transitions may provide valuable insights into how mutations affect KRas. Path sampling simulations, which focus on transitions, show KRas visiting several states, which...

Path sampling simulations reveal how the Q61L mutation restricts the dynamics of KRas

Jocelyne Vreede, Sander Roet & David Swenson
The GTPase KRas is a signaling protein in networks for cell differentiation, growth, and division. KRas mutations can prolong activation of these networks, resulting in tumor formation. When active, KRas tightly binds GTP. Several oncogenic mutations affect the conversion between this rigid state and inactive, more flexible states. Detailed understanding of these transitions may provide valuable insights into how mutations affect KRas. Path sampling simulations, which focus on transitions, show KRas visiting several states, which...

Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L

J. Vreede, Sander Roet & David Swenson
This is the data and scripts to reproduce the kras data, after unpakcing all tar files. 1. Install the conda environment "kras.env" 2. pip install openpathsampling to commit 78382fce67f99f4d160c01673d5553affebb2437 (also listed in the comment at the top of kras.env)3. Make sure that you set the shell environment variables needed for the OpenMM platform you intend to use. 4. Go into the directory you want to simulate. 5. Alter the "make_engine" function in the .py file...

Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L

J. Vreede, Sander Roet & David Swenson
This is the data and scripts to reproduce the kras data, after unpakcing all tar files. 1. Install the conda environment "kras.env" 2. pip install openpathsampling to commit 78382fce67f99f4d160c01673d5553affebb2437 (also listed in the comment at the top of kras.env)3. Make sure that you set the shell environment variables needed for the OpenMM platform you intend to use. 4. Go into the directory you want to simulate. 5. Alter the "make_engine" function in the .py file...

Mother-Specific Signature in the Maternal Transcriptome Composition of Mature,Unfertilized Zebrafish Eggs

J. Rauwerda & Timo M. Breit
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize...

Mother-Specific Signature in the Maternal Transcriptome Composition of Mature,Unfertilized Zebrafish Eggs

J. Rauwerda & Timo M. Breit
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize...

Image sequence of bird migration Netherlands, Germany and Belgium (2017-10-18)

B. Kranstauber, Willem Bouten, Hidde Leijnse, Berend-Christiaan Wijers, Liesbeth Verlinden, Judy Z. Shamoun-Baranes & Adriaan M. Dokter
Example of vertically integrated bird density for different time slices through the night of 18-19 October 2017 over the Netherlands, Germany and Belgium

Image sequence of bird migration Netherlands and Belgium (2016-10-3)

B. Kranstauber, Willem Bouten, Hidde Leijnse, Berend-Christiaan Wijers, Liesbeth Verlinden, Judy Z. Shamoun-Baranes & Adriaan M. Dokter
Example of vertically integrated bird density for different time slices through the night of 3-4 October 2016 over the Netherlands and Belgium

Image sequence of bird migration Netherlands, Germany and Belgium (2017-10-18)

B. Kranstauber, Willem Bouten, Hidde Leijnse, Berend-Christiaan Wijers, Liesbeth Verlinden, Judy Z. Shamoun-Baranes & Adriaan M. Dokter
Example of vertically integrated bird density for different time slices through the night of 18-19 October 2017 over the Netherlands, Germany and Belgium

Image sequence of bird migration Netherlands and Belgium (2016-10-3)

B. Kranstauber, Willem Bouten, Hidde Leijnse, Berend-Christiaan Wijers, Liesbeth Verlinden, Judy Z. Shamoun-Baranes & Adriaan M. Dokter
Example of vertically integrated bird density for different time slices through the night of 3-4 October 2016 over the Netherlands and Belgium

Image sequence of bird migration Netherlands, Germany and Belgium (2017-10-18)

B. Kranstauber, Willem Bouten, Hidde Leijnse, Berend-Christiaan Wijers, Liesbeth Verlinden, Judy Z. Shamoun-Baranes & Adriaan M. Dokter
Example of vertically integrated bird density for different time slices through the night of 18-19 October 2017 over the Netherlands, Germany and Belgium

Differential receptor use of Enterovirus D-68 strains in human airway epithelial cultures

Adithya Sridhar, Eveliina Karelehto, Jim Baggen, Lonneke Van Der Linden, Adam Meijer, Frank J. M Van Kuppeveld, Dasja Pajkrt & Katja C. Wolthers
Abstract submitted for positive strand meeting 2019. File available on request.

The Credibility Gap in CSR Reporting (CREDGAP)

I.J. Lock & Peter Seele
This collection includes data from the research project "The “Credibility Gap” in CSR Reporting: Analyzing Contents and Stakeholders’ Perceptions of CSR Reports from 11 European Countries" funded by the Swiss National Science Foundation (SNSF) under grant no. 150296 from 01.03.2014 - 31.10.2017.The research project analyzes the credibility of CSR reports of European companies according to the “credibility gap” by formalizing and quantifying Habermas’ four validity claims and applying them to CSR reports and “expert stakeholder’s’”...

JHC 2014

G.J. De Bruijn
Contains raw and computer data that were used in De Bruijn G-J, Budding J. Temporal consequences, message framing, and consideration of future consequences: Persuasion effects on adult fruit intake intention and resolve. Journal of Health Communication. 2016;21:944-953.

I.Lock_STRING_CODEBOOK_SAMPLE_Explicating Relationships_Systematic Review

I.J. Lock
This file is the appendix to the article "Explicating Communicative Organization-Stakeholder Relationships in the Digital Age: A Systematic Review and Research Agenda." published in Public Relations Review. It contains the search string of the systematic review, the applied codebook, and the list of references included in the analysis.

The Credibility Gap in CSR Reporting (CREDGAP)

I.J. Lock & Peter Seele
This collection includes data from the research project "The “Credibility Gap” in CSR Reporting: Analyzing Contents and Stakeholders’ Perceptions of CSR Reports from 11 European Countries" funded by the Swiss National Science Foundation (SNSF) under grant no. 150296 from 01.03.2014 - 31.10.2017.The research project analyzes the credibility of CSR reports of European companies according to the “credibility gap” by formalizing and quantifying Habermas’ four validity claims and applying them to CSR reports and “expert stakeholder’s’”...

Test item

Adithya Sridhar & J.G. Daams
Test file

16S rRNA gene amplicon sequence data soda sediments

C.D. Vavourakis
Pre-processed amplicon Pyrotag sequence files (quality & length trimmed, adaptor sequences & primers removed, dereplicated) targeting the V4-V6 region of the 16S rRNA gene obtained from hypersaline soda lake sediments in the Kulunda Steppe (Siberia, Russia).

I.Lock_DATASET_Explicating Relationships_Systematic Review

I.J. Lock
Excel file containing data form a qualitative content analysis, the codebook is attached as well as the research diary. The variables are mostly categorical (binary) or open text entries. Three scale items (coder ratings) are also included. The data set also contains the comments coders made during coding and analysis.

Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

S. Yang
The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes...

Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

S. Yang
The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes...

Data for health app usage BCT and UG integration

G.J. De Bruijn
These data are for the publication on health app usage in Dutch adults (collected May 2018) using BCT and UG concepts

Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

S. Yang
The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes...

Data for health app usage BCT and UG integration

G.J. De Bruijn
These data are for the publication on health app usage in Dutch adults (collected May 2018) using BCT and UG concepts

Dataset for Yang et al. Lithology and climate-controlled soil aggregate-size distribution and organic carbon stability in the Peruvian Andes, SOIL, 2020.

S. Yang
Dataset 3A: It is the dataset of soil organic carbon stocks of the total soil profile and assessed to the depths from 10 to 60 cm. Soil samples were collected from 12 sampling plots based the combination of two contrasting bedrocks (limestone vs. acid rock) and two precipitation levels (wet vs. dry), having 3 replicates for each combination.
Dataset 3B: It is the dataset of the distributions of fraction weight, SOC contents and N contents of...

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