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1,197 results for “FLEXIBILITY”
Processed results supporting MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics
<p>Search results supporting the manuscript "MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics". Processed PSM, ion, peptide, and protein tables for each search are provided, sorted by figure within the zip file. FragPipe workflows with parameters are also provided for all searches. </p>
Internal Normal Mode Analysis applied to RNA flexibility and conformational changes
<p>We investigated the capability of internal normal modes to reproduce RNA dynamics and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified rep- resentation of RNA structure and its potential energy. In this study, we considered three main data sets to investigate different aspects : i) one based on single-stranded RNA molecules for which all-atom MD simulations were computed; ii) one based on the available structures belonged to a specific Rfam family; iii) one based on the transition from unbound to bound RNA.</p> <p><strong>In each folder</strong></p> <p><em>modes.dat</em>: results obtained by iNMA (frequency and normal modes)</p> <p><em>das1.dat</em>: conversion from internal to cartesian normal modes</p> <p>Each file <em>name_enm.pdb</em> refers to a PDB structure with a CG representation (RNA three-bead model).</p> <p><strong>Dataset 1</strong>: d1.zip</p> <p>For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis, the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub> and some scripts.</p> <p>Matlab and python scripts: </p> <p><em>analysis_pca.py</em>: to extract the different principal components</p> <p><em>analysis_PCA.m</em>: to compute overlap and cumative overlap in each folder</p> <p><em>analysis_complete_new.m</em>: to summarize the results</p> <p><strong>Dataset 2</strong>: d2.zip</p> <p>For this dataset, we provide the structure ensemble for Rfam family and the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub>and some scripts.</p> <p>PDB files:</p> <p><em>allensemble.pdb</em>: ensemble of PDB structures for a given Rfam family</p> <p><em>allensemble_enm.pdb</em>: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model)</p> <p><em>allensemble_enm_new.pdb</em>: ensemble of PDB structures for a given Rfam family with the same number of atoms for each model converted to CG representation (RNA three-bead model)</p> <p><em>model.pdb</em>: reference PDB structure</p> <p><em>model_enm.pdb</em>: reference PDB structure converted to CG representation (RNA three-bead model)</p> <p>Matlab script: </p> <p><em>pca_xray_anal.m</em>: PCA analysis, overlap, cumulative overlap, rmsip and plots</p> <p><strong>Dataset 3</strong>: d3.zip</p> <p>PDB structure:</p> <p><em>bound.pdb</em>: bound structure</p> <p><em>unbound.pdb</em>: unbound structure</p> <p><em>diff.dat</em>: difference between bound and unbound structure after superimposition </p> <p>RMSD<em>n </em>with n a number: the first column represents <span class="math-tex">\(\sqrt{\beta/2}\)</span></p> <p>Matlab script:</p> <p><em>rmsd_anal.m</em>: analysis best mode based on RMSD</p> <p><strong>Application to the CrPV-IRES</strong>: IRES.zip</p> <p>PDB structures:</p> <p> <em>IRES_cg.pdb</em>: Coarse-grain structure based on the PDB ID 5IT9</p> <p><em>b_end001_01_70.pdb</em>, <em>b_end001_01_80.pdb, b_end001_01_90.pdb</em>: Example of modified structures using the first lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p> <p><em>b_end002_03_50.pdb</em>, <em>b_end002_03_60.pdb, b_end002_03_70.pdb</em>: Example of modified structures using the third lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p>
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
<p>The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p> </p>
Mechanism of rotenone binding to respiratory complex I depends on ligand flexibility
<p>Snapshots from MD simulations (with umbrella sampling and metadynamics) of<br> respiratory complex I. Only subunits ND1, NDUFS2 and NDUFS7 (with the membrane spanning N-terminus<br> truncated) and rotenone are shown in binding mode (see Fig. 2 of main paper): </p> <p>1) ROT1: configurations/rot1.pdb<br> 2) pre-redox: configurations/rot1.5.pdb<br> 3) ROT2: configurations/rot2.pdb</p> <p>Force-field and topology files in GROMACS format:</p> <p>4) Bonded parameters: parameters/rotenoids_ffBonded.itp<br> 5) Rotenone: parameters/rot.itp<br> 6) Dehydrated derivative: parameters/dehyd_rot.itp</p>
Artifacts for the 2023 Trends in Functional Programming Publication: Versatile and Flexible Modelling of the RISC-V Instruction Set Architecture
<p>This dataset contains the artifacts for the performance evaluation conducted in the publication <em>Versatile and Flexible Modelling of the RISC-V Instruction Set Architecture</em> which will be published in the proceedings of the 2023 <em>Trends in Functional Programming</em> conference. The provided artifacts contain a <a href="https://docker.io">Docker</a> container for executing <a href="https://embench.org">Embench</a> benchmarks with LibRISCV, RISC-V VP, Grift and Forvis. A pre-built version of the container is included.</p>
Flexible use of visual and acoustic cues during roost finding in Spix's disc-winged bat Thyroptera tricolor
<p>The ability of an animal to detect environmental cues is crucial for its survival and fitness. In bats, sound certainly plays a significant role in the search for food, spatial navigation, and social communication. Yet, the efficiency of a bat's echolocation could be limited by atmospheric attenuation and background clutter. In this context, sound can be complemented by other sensory modalities, like smell or vision. Spix's disc-winged bat (<em>Thyroptera tricolor</em>) uses acoustic cues from other group members to locate the roost (tubular unfurled leaves of plants in the order Zingiberales). Our research focused on how individuals find a roost that has not been yet occupied, considering the urge to find a suitable leaf approximately every day, during nighttime or in daylight. We observed the process of roost finding in <em>T. tricolor</em> in a flight cage, manipulating the audio/visual sensory input available for each trial. A broadband noise was broadcast in order to mask echolocation, while experiments conducted at night significantly reduced the amount of light. We measured the time needed to locate the roost under these different conditions. Results show that with limited visual and acoustic cues, search time increases significantly. In contrast, bats seemed capable of using acoustic and visual cues in a similarly efficient manner, since roost search showed no strong differences in duration when bats could use only sound, only vision, or both senses at the same time. Our results show that non-acoustic inputs can still be an important source of information for finding critical resources in bats.</p>
Data for: Evidence for a maintenance cost for birds maintaining highly flexible basal, but not summit, metabolic rates
<p>Reversible phenotypic flexibility allows organisms to better match phenotypes to prevailing environmental conditions and may produce fitness benefits. Costs and constraints of phenotypic flexibility may limit the capacity for flexible responses but are not well understood or documented. Costs could include expenses associated with maintaining the flexible system or with generating the flexible response. One potential cost of maintaining a flexible system is an energetic cost reflected in the basal metabolic rate (BMR), with elevated BMR in individuals with more flexible metabolic responses. We accessed data from thermal acclimation studies of birds where BMR and/or M<sub>sum</sub> (maximum cold-induced metabolic rate) were measured before and after acclimation, as a measure of metabolic flexibility, to test the hypothesis that flexibility in BMR (ΔBMR), M<sub>sum</sub> (ΔM<sub>sum</sub>), or metabolic scope (M<sub>sum</sub> – BMR; ΔScope) is positively correlated with BMR. When temperature treatments lasted at least three weeks, three of six species showed significant positive correlations between ΔBMR and BMR, one species showed a significant negative correlation, and two species showed no significant correlation. ΔM<sub>sum</sub> and BMR were not significantly correlated for any species and ΔScope and BMR were significantly positively correlated for only one species. These data suggest that support costs exist for maintaining high BMR flexibility for some bird species, but high flexibility in M<sub>sum</sub> or metabolic scope does not generally incur elevated maintenance costs. </p>
openENTRANCE - Case Study 3 - Need for flexibility - Storage - version 21062023
<p>This dataset partially comprises the main results of case study 3 of the openENTRANCE project. Additionally, input data related to the power generation system and renewables profiles are included in the dataset.</p>
Dataset to Study Flexibility Service Providers' Gaming Potential and its Impact on TSO-DSO Coordinated Markets
<p>We publish the dataset and nomenclature table used to study the Flexibility Service Providers’ Gaming Potential and its Impact on TSO-DSO Coordinated Markets (paper published in the 2023 SEST conference).</p> <p>The dataset is composed by an interconnected system consisting of the IEEE 14-bus (TN) transmission network connected to two distribution networks: the Matpower systems 69-bus (DN_69), and 141-bus (DN_141). All systems topology and some parameters are based on the corresponding cases in Matpower [1]. Injections and loads of the nodes are adapted to create an anticipated negative imbalance (total load surpassing total generation) in the interconnected system, resolved by upward flexibility. In addition, the lines’ upper limits are adjusted to create anticipated congestion in the networks. The interconnected system is fully represented in "Network.xlsx".<br>Upward and downward flexibility bids are randomly generated and allocated to the nodes. Their quantities are aligned with the nodes’ base injection/load and their marginal values are in the range [10, 26] euro/MW for downward, and marginal costs in the range [30, 73] euro/MW for upward, totaling 536 bids. </p> <p>4 bids lists are available in this dataset, to allow the strategic behavior analysis with different levels of liquidity:</p> <p>- In the list of bids "case 0", all 536 bids are present.</p> <p>- In the list of bids "case 1", 40% of bids in the transmission list are deleted (distribution bids are the same as in case 0).</p> <p>- In the list of bids "case 2", 98% of the bids in the distribution bids are deleted (transmission bids are the same as in case 0).</p> <p>- In the list of bids "case 3", only bids needed to solve distribution systems congestions are kept (all the others are deleted) (transmission bids are the same as in case 0).</p> <p>Source of the systems' topology:</p> <p>[1] R. D. Zimmerman, C. E. Murillo-Sanchez, and R. J. Thomas, “Mat-power: Steady-state operations, planning, and analysis tools for power systems research and education,” IEEE Transactions on power systems, vol. 26, no. 1, pp. 12–19, 2010.</p> <p>Please notice that this dataset does not replace the information provided by Matpower related to the aforementioned systems. It rather uses those systems topology and some of their parameters to build a case study to investigate TSO-DSO coordination market models for the procurement of flexibility. For the full description of these systems, please visit: <a href="https://matpower.org/">MATPOWER – Free, open-source tools for electric power system simulation and optimization</a>.</p>
Policy Review Data and Outcomes on Local Flexibility Markets Operation
<p>This is a collaborative work with several researcher involved from the PARITY project.</p> <p>We conducted research on the different PARITY offerings, attempting to bring evidence-based recommendations arising from the whole PARITY project process. The conducted survey and workshop helped us to deliver the PARITY policy review data that could enable relevant stakeholders (including the EC and national regulatory authorities) to understand the complications and the actions needed to facilitate a wide, sustainable, fair and future proof uptake of local flexibility markets in Europe</p>
Datasets for "Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents"
<p>Datasets used in the manuscript titled, "<strong>Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents</strong>" are uploaded here. </p> <p><strong>Brightfield and fluorescent stained images of brain tissue used for Fig. 5(a):</strong></p> <p>Malt3-20190624_Region 009_DAPI.png</p> <p>Malt3-20190624_Region 009_qCy5.png</p> <p>Malt3-20190624_Region 009_qFITC.png</p> <p>Malt3-20190624_Region 009_qTexasRed.png</p> <p>Malt3_BF20190628_Region 001.png</p> <p><strong>Fluorescent image of brain with embedded CFETs:</strong></p> <p>MALT2_Rat_100um_MOR1_x500_TSA_AF488.jpg</p> <p>Rat_100um_MOR1_x500_TSA.czi</p> <p><strong>In vivo dopamine recording data for Fig. 3:</strong></p> <p>ratarrays822_163.mat</p> <p>ratarrays822_57.mat</p>
CAD-based Assembly Sequence Planning for Increased Operational Flexibility Dataset
<p>Operational flexibility represents the ability to adapt to changes in production or assembly<br> processes. It is a crucial aspect of assembly sequence planning for a dynamic environment (such as<br> large-scale assembly systems). The choice of graph model, such as precedence graph or AND/OR<br> graph, can significantly impact operational flexibility. The state-of-the-art research has demonstrated<br> the utility of precedence graphs and AND/OR graphs for flexible assembly lines.<br> However, AND/OR graphs offer the potential for even greater operational flexibility but with a higher<br> computational cost. Further research is still needed on the detailed effects of precedence graphs and<br> AND/OR graphs on operational flexibility and the limits for their application to large-scale assemblies.<br> The trade-offs between different models and their impact on operational flexibility and computational<br> costs is observed.</p> <p><br> <strong>1st underlying research question: </strong>Which graph model, derived from CAD-based assembly-by-<br> disassembly, can increase the operational flexibility in integrated assembly sequence planning and job<br> scheduling problems?</p> <p><br> A hypothesis is formulated to answer this research question, which will be used to design an experiment<br> and be tested.</p> <p><br> <strong>Hypothesis 1: </strong>The AND/OR graph can be utilized to improve the operational flexibility in comparison<br> to the precedence graph.</p>
PyPSA-PL: Limited flexibility of the Polish power system
<p>This record contains all the scripts and data from the PyPSA-PL modelling exercise that supported the report:</p> <ul> <li>Kubiczek P. (2023). Praca w podstawie. Modelowanie kosztów niskiej elastyczności polskiego systemu<br> elektroenergetycznego. Instrat Policy Paper 04/2023. <a href="https://www.instrat.pl/praca-w-podstawie">https://www.instrat.pl/praca-w-podstawie</a></li> </ul> <p>The record structure is based on the PyPSA-PL repository <a href="https://github.com/instrat-pl/pypsa-pl">https://github.com/instrat-pl/pypsa-pl</a> (v2.0 with changes).</p>
PAM-Flexible Genome Editing with an Engineered Chimeric Cas9
<p>CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN PAM preference, with the N-terminus of Sc++, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse NNN PAMs and disease-related loci for potential therapeutic applications. In total, the unique approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.</p>
Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture
<p><span>Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in <em>Arabidopsis</em> found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.</span></p>
Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
<p>Ensembles of models predicted by AlphaFold for the proteins C3 (Complement component 3), luciferase and QBP (glutamine-binding periplasmic protein). Models interpolated between two conformations of C3, and luciferase are also included. This dataset is cited in the following paper: https://www.biorxiv.org/content/10.1101/2023.09.11.557128v1</p>
Data: Double Task Switching: an investigation into the effects of similarity and task-rule congruency on cognitive flexibility in the context of mental fatigue
<p>This is the data that was collected for the Double Task Switching Experiment (Hinss, Brock & Roy 2023). The File contains the behavioral as well as the subjective data of all participants.</p> <p><br> Some details:<br> Switch<br> 1= repetition trial<br> 2= internal switch<br> 3= external switch</p> <p>Task<br> 1= Low/High<br> 2= Even/Odd<br> 3= Vertical/Horizontal<br> 4= Cold/Hot</p> <p>Language (of instructions)<br> 0= French<br> 1= English</p> <p>Congruency<br> 1= Neutral<br> 2= Internally incongruent<br> 3= Externally incongruent<br> 4= Double incongruent<br> 5= Internally congruent<br> 6= Externally congruent<br> 7= Double congruent</p> <p>Correct<br> 1= Correct Response<br> 0= Error</p> <p>Hit<br> 0= Correct response on letter S<br> 1= Correct response on letter L</p> <p>Response<br> 0= Participants response on letter S<br> 1= Participants response on letter L</p> <p>EDI (Edinburgh Handedness questionnaire)</p> <p>MaryA1: What time did you settle in for the night?<br> MaryA2: What time did you fall asleep last night?<br> MaryA3: What time did you wake up this morning?<br> MaryA4: What time did you get up this morning?<br> MaryB1: How was your sleep<br> MaryB2: How many times did you wake up last night ?<br> MaryB3: How many hours did you sleep last night?<br> MaryB4: How many hours did you sleep during the day yesterday?<br> MaryB5: How well did you sleep last night?<br> MaryC1: If you didn't sleep well, what was the problem? (e.g., restless, etc.)<br> MaryD1: How much caffine/theine did you consume today ( in cups of coffee) ?<br> MaryD2: How much caffeine/theine would you usually have consumed at this time of the day ( in cups of coffee)?</p> <p> </p> <p>For any further questions, please refer to the full journal paper (<a href="https://doi.org/10.1371/journal.pone.0279021">https://doi.org/10.1371/journal.pone.0279021</a>).</p> <p>For publications, please cite as:</p> <p>Hinss MF, Brock AM, Roy RN (2023) The double task-switching protocol: An investigation into the effects of similarity and conflict on cognitive flexibility in the context of mental fatigue. PLOS ONE 18(2): e0279021. <a href="https://doi.org/10.1371/journal.pone.0279021">https://doi.org/10.1371/journal.pone.0279021</a><br> </p>
"CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data" datasets
<p>Datasets from the article:</p> <p><strong>CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data </strong></p> <p>by Franck Simon, Maria Colomba Comes, Tiziana Tocci, Louise Dupuis, Vincent Cabeli, Nikita Lagrange, Arianna Mencattini, Maria Carla Parrini, Eugenio Martinelli, Hervé Isambert.</p> <p> </p> <p>The <strong>original videos</strong> are uploaded as: "20161230.zip", "20170105.rar", "Video_2017_0517.zip".</p> <p><strong>Details </strong>for each <strong>experiment </strong>can be found in: "Experiments' details.zip".</p> <p>The <strong>ROIs </strong>(ROI: Region of Interest) are uploaded as .tif files in: "EXTRACTED ROIs.zip".</p> <p>The <strong>MATLAB data</strong> is uploaded in "MATLAB_DATA.rar" and includes: the cancer cells' trajectories (subfolder: "TUMOR TRAJECTORIES"), the immune cells' trajectories (subfolder: "IMMUNE TRAJECTORIES"), the ROIs videos as .mat files for the detection of cells (subfolder: "ROI MAT"), the ROIs further cropped for the extraction of shape descriptors (folder: "ROI_TU MAT"). The ROIs videos .mat files included in the last two subfolders are stopped after their apoptosis has been detected.</p>
Dataset for the publication: Flexible copper: exploring capacity-based energy demand flexibility in the industry
<p>This file contains the inputs for the study (currently under review) "Flexible copper: exploring capacity-based energy demand flexibility in the industry"</p>
A Study to Evaluate the Efficacy, Safety, and Tolerability of Flexible Doses of Intranasal Esketamine Plus an Oral Antidepressant in Adult Participants With Treatment-resistant Depression
ClinicalTrials.gov study NCT02418585. IPD Sharing: Not stated. Countries: 5. Publications: 16.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.