Find research datasets worth reusing

opencc-by-4.0Nov 2022View details →

Data from: Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons

This dataset is originally used in: I. Silva Barreto, M. Pierantoni, M. Hammerman, E. Törnquist, S. Le Cann, A. Diaz, J. Engqvist, M. Liebi, P. Eliasson, H. Isaksson, Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons, Matrix Biology (2022), doi:https://doi.org/10.1016/j.matbio.2022.11.006 Abstract: The specific viscoelastic mechanical properties of Achilles tendons are highly dependent on the structural characteristics of collagen at and between all hierarchical levels. Research has been conducted on the deformation mechanisms of positional tendons and single fibrils, but knowledge about the coupling between the whole tendon and nanoscale deformation mechanisms of more commonly injured energy-storing tendons, such as Achilles tendons, remains sparse. By exploiting the highly periodic arrangement of tendons at the nanoscale, in situ loading of rat Achilles tendons during small-angle X-ray scattering acquisition was used to investigate the collagen structural response during load to rupture, cyclic loading and stress relaxation. The fibril strain was substantially lower than the applied tissue strain. The fibrils strained linearly in the elastic region of the tissue, but also exhibited viscoelastic properties, such as an increased stretchability and recovery during cyclic loading and fibril strain relaxation during tissue stress relaxation. We demonstrate that the changes in the width of the collagen reflections could be attributed to strain heterogeneity and not changes in size of the coherently diffracting domains. Fibril strain heterogeneity increased with applied loads and after the toe region, fibrils also became increasingly disordered. Additionally, a thorough evaluation of radiation damage was performed. In conclusion, this study clearly displays the simultaneous structural response and adaption of the collagen fibrils to the applied tissue loads and provide novel information about the transition of loads between length scales in the Achilles tendon. Any queries related to the data set or the publication may be directed to Hanna Isaksson by email (hanna.isaksson@bme.lth.se).

opencc-zeroDec 2021View details →

Morphological data from: Strong species structure but weak geographical structure in demersal Lake Victoria cichlids

Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably less than 20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation-by-distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow.

opencc-by-4.0Aug 2022View details →

Data deposition for "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins"

The deposited data for the publication "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins". Data contains folder and sub-folders for the raw data, Main excel sheet named as "MasterTable_FRET-Challenge-Protein-Dynamics_Nat_Meth_Agam et al" has most of the data used in the publication. Another excel sheets "Data List for FIgures for Agam et al_revised" and "Data List for Supplmentary FIgures for Agam et al_revised" have the information regarding the Figure-wise data description and where the respective data locates.

opencc-by-4.0Dec 2022View details →

Mode structure reconstruction by detected and undetected light: data sets

Data sets related to the multimode optical field reconstructions reported in manuscript <a href="https://arxiv.org/abs/2212.13873v1">arXiv:2212.13873v1</a>

opencc-by-4.0Dec 2022View details →

raw data for a manuscript submitted to Materials and Structures Journal

raw data for a manuscript submitted to Materials and Structures Journal. Includes: coating thickness, jointly with economic and environmental calculations

opencc-by-4.0Jul 2022View details →

Data for: Reconstructing Cosmological Initial Conditions from Late-Time Structure with Convolutional Neural Networks

Trained models and evaluation data for the revised submitted paper "Reconstructing Cosmological Initial Conditions from Late-Time Structure with Convolutional Neural Networks," Christopher J. Shallue & Daniel J. Eisenstein (2022)

opencc-zeroJan 2023View details →

Data for: Oligonucleotide mapping via mass spectrometry to enable comprehensive primary structure characterization of an mRNA vaccine against SARS-CoV-2

Oligonucleotide mapping via liquid chromatography mass spectrometry mass spectrometry (LC-MS/MS) was recently developed to support development of Comirnaty®, the world's first commercial mRNA vaccine which immunizes against the SARS-CoV-2 virus. Analogous to peptide mapping of therapeutic protein modalities, oligonucleotide mapping described here provides direct primary structure characterization of mRNA, through enzymatic digestion, accurate mass determinations, and optimized collisionally-induced fragmentation. Sample preparation for oligonucleotide mapping is a rapid, one-pot, one-enzyme digestion. The digest is analyzed via LC-MS/MS with an extended gradient and resulting data analysis employs semi-automated software. In a single method, oligonucleotide mapping readouts include a highly reproducible and completely annotated UV chromatogram with >98% sequence coverage and a microheterogeneity assessment of 5´ terminus capping and 3´ terminus poly(A) tail length. Oligonucleotide mapping was pivotal to ensure the quality, safety, and efficacy of mRNA vaccines by providing: confirmation of construct identity and primary structure and assessment of product comparability following manufacturing process changes. More broadly, this technique may be used to directly interrogate the primary structure of RNA molecules in general.

Mn3O4 Structure Data

Atomistic structure data for Mn3O4 related to the work titled "Flexible Nanogenerators based on Flexoelectricity-Boosted Triboelectricity in Few-Layered Hausmannite."

Quasi-Newton methods for partitioned simulation of fluid-structure interaction reviewed in the generalized Broyden framework: code and data

These files accompany the publicationN. Delaissé, T. Demeester, R. Haelterman and J. Degroote. Quasi-Newton methods for partitioned simulation of fluid-structure interaction reviewed in the generalized Broyden framework. Archives of Computational Methods in Engineering, Vol. 30, 3271-3300, 2023. doi: <a href="https://doi.org/10.1007/s11831-023-09907-y">10.1007/s11831-023-09907-y</a>In this work, the performance of multiple quasi-Newton methods are compared in terms of memory requirements and computational time. The results are generated for the well-known flexible tube example case, using the open-source code <a href="http://github.com/pyfsi/coconut">CoCoNuT</a>. This code, developed at Ghent University, is Python-based and has the capability to couple existing solvers, both open-source and commercial solvers.This archive consists of the following files.<ul><li>coconut.tar.gz: the specific CoCoNuT version used (sep-2022), including the Python flow and structure solvers for the flexible tube and modifications for monitoring memory requirements</li><li>compare_coupling_algorithms.tar.gz: the scripts to set up the cases and perform the calculations and post-processing</li><li>results.tar.gz: the generated result data</li></ul>For requirements to run CoCoNuT, refer to the <a href="http://pyfsi.github.io/coconut/">documentation</a>. Additionally, the Python package guppy3 is required for monitoring the memory use. In this work the data were generated with Andaconda3-2022.05 and the package guppy3-3.1.2.Before running the provided scripts, make sure the parent directory of the "coconut" folder is added to the PYTHONPATH. The calculations can be started with "python run.py". For the cases which names contain "_m" followed by a number, e.g. "_m100", the number refers to the number of discretization points on the interface. The cases with suffix "_c" are distinct from those without, as they don't perform the time consuming memory monitoring and are therefore used for measuring computational time.

opencc-by-4.0Feb 2023View details →

Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"

MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the  OxlT-out directory.

opencc-zeroJan 2023View details →

Data from: Phylogenetic structure of the extinction and biotic factors explaining differential survival of terrestrial notosuchians at the Cretaceous-Palaeogene crisis

Although the clade Crocodylomorpha is represented by few extant species (Crocodylia), it has a rich fossil record. Hundreds of species adapted to terrestrial, semi-aquatic and marine environments, have existed over more than 200 million years. Numerous studies have attempted to characterize the factors driving the diversification and extinction events of Crocodylomorpha, resulting in ambiguous and even contradictory conclusions, which points to the need for phylogenetically and temporally smaller-scaled studies. Here, we focus on differential survival at the Cretaceous-Palaeogene crisis of Notosuchia, a diverse clade of mostly terrestrial Crocodylomorpha that achieved great diversity during the Cretaceous. More precisely, we tested the effect of body size and palaeotemperatures on notosuchian survival probability during the K-Pg crisis as well as the effect of diet on the evolution of their body size. We find that Notosuchia showed an evolutionary trend towards larger body sizes through time, associated with a shift from an omnivorous to a carnivorous diet. This may explain why sebecids were the only notosuchians to survive the K-Pg crisis. We also corroborate conclusions of previous studies that detected a Lagerstätten effect occurring in the Adamantina Formation (Upper Cretaceous, Brazil, Bauru Group). This work confirms the value of more finely-scaled macroevolutionary studies for understanding the history of a rich and complex group such as Crocodylomorpha.

Data from: Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success

Data: Plant-pollinator interactions, pollinator body size (inter-tegular distance, ITD) and plant reproductive success (number of seeds produced). Data collected by Christie J. Webber. Data collected in 14 experimental flowering plant patches during December 2012–February 2013. Patches were located in a 105 hectare sheep farm pasture in Oxford, North Canterbury, New Zealand (43°19'21"S 172°12'25"E). Files: <ul> <li>Data_S1: contains plant-pollinator interactions sampled and pollinator inter-tegular distance (ITD). Data_S1 columns: patch ID where the interaction was recorded, plant species, pollinator ITD (mm), and pollinator family, genus and species.</li> <li>Data_S2: contains the number of seeds produced by each of the five flowers of each plant individual from each plant species on each patch. Data_S2 columns: patch ID where the measurement was taken, plant species, plant number (individual sampled), number of seeds.</li> </ul> Dataset used in "Scale-dependent effects of landscape structure on pollinator traits, species interactions and pollination success" by G. Peralta, C.J. Webber, G.L.W. Perry, D.B. Stouffer, D.P. Vázquez and J.M. Tylianakis.

MCL-1 promiscuity and the structural resilience of its binding partners - DATA

Data supporting: "MCL-1 promiscuity and the structural resilience of its binding partners"; Journal of Chemical Physics (JCP); 2023.

Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos

Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyze geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.

ConforMine Molecular Dynamics Data: Conformational Variability, Secondary Structure Propensities and Molecular Dynamics Simulations

<pre>This dataset contains all the data used to calculate Conformational Variability (ConVa) and Conformational Propensities as well as to train ConforMine. Each directory one level below this document contains another readme for further explanation on the contained data. The following information can be found in this dataset: </pre> <ul> <li>ConforMine_MD_training_sequences.fasta: FASTA file with the amino acid sequences of all used proteins.</li> <li>simulations (directory): Contains all the raw data derived from the MD simulations.</li> <li>ConforMine_training_MD_dihedrals (directory): Contains .xvg files with the dihedral angles of each amino acid at each step of the MD simulation.</li> <li>ConforMine_training_data_conformational_variability (directory): Contains the Conformational Variability values for all amino acids. Each file contains all ConVa values for a whole protein. The data is provided in .csv and .npy format.</li> <li>ConforMine_training_data_conformational_propensities (directory): Contains the Conformational Propensities values for all amino acids. Each file contains all propensities for a whole protein. The data is provided in .csv and .npy format.</li> </ul>

Data for: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA

Productive transcriptional elongation of many cellular and viral mRNAs requires transcriptional factors to extract pTEFb from the 7SK snRNP by modulating the association between the HEXIM protein and the 7SK snRNA. Here we report the structure of the HEXIM arginine-rich motif in complex with the apical stemloop-1 of 7SK (7SK-SL1apical) and detail how the HIV transcriptional regulator Tat from various subtypes overcome the structural constraints required to displace HEXIM. While most interactions between 7SK and HEXIM and Tat are similar, critical differences exist that guide function. First, the conformational plasticity of 7SK enables the formation of three different base pair configurations at a critical remodeling site, which allows for the modulation required for HEXIM binding and its subsequent displacement by Tat. Furthermore, the specific sequence variations observed in various Tat subtypes all converge on remodeling 7SK at this region. Second, we show that HEXIM primes its own displacement by causing specific local destabilization upon binding — a feature that is then exploited by Tat to bind 7SK more efficiently. Overall, our study details the molecular environment presented by HEXIM and uncovers a destabilization-driven displacement strategy that increases the conformational sampling of 7SK-snRNP, which may allow diverse transcriptional factors to competitively regulate pTEFb.

opencc-by-4.0Feb 2023View details →

Supporting data for: Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics

This repository contains supporting data and code for the paper titled "Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics" by Bernadette Mohr, Diego van der Mast, and Tristan Bereau.

Data for: The influence of vegetation structure on secondary diaspore dispersal by wind

The role of vegetation structure in relation to wind speed and diaspore attributes on secondary diaspore dispersal by wind has not been empirically studied. Here, we investigated secondary dispersal by wind of diaspores placed in 12 different kinds of vegetation and bare land. The experiments were conducted in a wind tunnel using a range of wind speeds and diaspores that differed in mass and kind of appendages. The explanations of wind speed, diaspore attributes, vegetation coverage, life-form, vertical pattern and horizontal pattern for diaspore dispersal capacity were 6.67~10.40%, 16.13~20.53%, 6.227~24.64%, 0.10%, 0.74%, and 0.10%, respectively. Compared with wind speed and diaspore attributes, vegetation coverage contributed the most to diaspore dispersal capacity when vegetation coverage was low (<10% in our study). However, but with a high (10-30%) coverage, vegetation coverage was the least influential factor in secondary diaspore dispersal by wind. Vegetation coverage significantly interacted with vegetation life-form, horizontal pattern and vertical pattern on affecting diaspore dispersal capacity. Thus, the most influential factor determining secondary diaspore dispersal by wind is vegetation coverage.

opencc-by-4.0Feb 2021View details →

Data for cryo-EM structure refinement with density-guided simulations

Data accompanying prepared manuscript to describe novel density-guided simulation algorithms.