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opencc-by-4.0May 2023View details →

Discrete Feature Representations of CHO Reaction Mechanisms as Quasireaction Subgraphs

This data set contains 194778 quasireaction subgraphs extracted from CHO transition networks with 2-6 non-hydrogen atoms (CxHyOz, 2 <= x + z <= 6). The complete table of subgraphs (including file locations) is in CHO-6-atoms-subgraphs.csv file. The subgraphs are in GraphML format (http://graphml.graphdrawing.org) and are compressed using bzip2. All subgraphs are undirected and unweighted. The reactant and product nodes (initial and final) are labeled in the "type" node attribute. The nodes are represented as multi-molecule SMILES strings. The edges are labeled by the reaction rules in SMARTS representation. The forward and backward reading of the SMARTS string should be considered equivalent. The generation and analysis of this data set is described in D. Rappoport, Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models, 2023, submitted. Preprint at ChemrXiv, DOI: 10.26434/chemrxiv-2023-wltcr Simulation parameters - CHO networks constructed using polar bond break/bond formation rule set for CHO. - High-energy nodes were excluded using the following rules:   (i) more than 3 rings, (ii) triple and allene bonds in rings, (iii) double bonds at   bridge atoms,(iv) double bonds in fused 3-membered rings. - Neutral nodes were defined as containing only neutral molecules. - Shortest path lengths were determined for all pairs of neutral nodes. - Pairs of neutral nodes with shortest-path length > 8 were excluded. - Additionally, pairs of neutral nodes connected only by shortest paths passing through   additional neutral nodes (reducible paths) were excluded. For background and additional details, see paper above.

opencc-zeroMay 2023View details →

Scripts and sample information for: Molecular mechanisms of Eda-mediated adaptation to freshwater in threespine stickleback

A main goal of evolutionary biology is to understand the genetic basis of adaptive evolution. Although the genes that underlie some adaptive phenotypes are now known, the molecular pathways and regulatory mechanisms mediating the phenotypic effects of those genes often remain a black box. Unveiling this black box is necessary to fully understand the genetic basis of adaptive phenotypes, and to understand why particular genes might be used during phenotypic evolution. Here, we investigated which genes and regulatory mechanisms are mediating the phenotypic effects of the Eda haplotype, a locus responsible for the loss of lateral plates and changes in the sensory lateral line of freshwater threespine stickleback (Gasterosteus aculeatus) populations. Using a combination of RNAseq and a cross design that isolated the Eda haplotype on a fixed genomic background, we found that the Eda haplotype affects both gene expression and alternative splicing of genes related to bone development, neuronal development and immunity. These include genes in conserved pathways, like the BMP, netrin and bradykinin signalling pathways, known to play a role in these biological processes. Furthermore, we found that differentially expressed and differentially spliced genes had different levels of connectivity and expression, suggesting that these factors might influence which regulatory mechanisms are used during phenotypic evolution. Taken together, these results provide a better understanding of the mechanisms mediating the effects of an important adaptive locus in stickleback and suggest that alternative splicing could be an important regulatory mechanism mediating adaptive phenotypes.

opencc-zeroMay 2023View details →

Data for: Wall fracturing versus mechanical instability as competing intrusion mechanisms of dikes: Insights from laboratory experiments

Igneous dike intrusion is a primary crust-forming process. Understanding its governing mechanism is very crucial for studies related to the lithosphere. We performed liquid injection experiments in the laboratory with two new crust analog model materials, i) ultrasound transmission gel (USTG) and gel wax. To conduct a properly scaled model experiment, we test their rheology using an Anton Paar M302e rheometer. The measured rheological data were presented in this present data repository. We identified three mechanisms from our laboratory studies: a) fracturing, b) interfacial instability, and c) hybrid, i.e., a combination of both. These three mechanisms give rise to distinct 3D geometries. To quantitatively analyze their geometric shapes, we performed fractal, aspect ratio, and skewness-kurtosis analysis. The procedure and the data collected during the analysis were also presented in the current data repository.

Proposed catalytic mechanism of mAMCase.

This directory contains all files required to analyze the proposed catalytic mechanism of mouse AMCase at pH 2.0 and 6.5 presented in Figure 6 in the manuscript <a href="https://www.biorxiv.org/content/10.1101/2023.06.03.542675">Díaz et al. (2023)</a>. Structure models were analyzed using PyMOL. Figures were compiled using PerkinElmer ChemDraw and Adobe Illustrator. Files included in this directory:     Figures - contains ChemDraw file for the proposed catalytic mechanism schematic, PNGs of each step of the proposed catalytic mechanism at pH 2.0 and 6.5, and a GIF of the entire proposed catalytic mechanism at pH 2.0 and 6.5.   PyMOL - contains all structure models, PyMOL script, and PyMOL session used to generate Figure 6.   Contact: Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com

Experimental investigation of the effects of particle shape and friction on the mechanics of granular media

This dataset corresponds to the raw data and experimental measurements of the PhD thesis "Experimental investigation of the effects of particle shape and friction on the mechanics of granular media" of Gustavo Pinzón (2023, Université Grenoble Alpes), available at: <a href="https://hal.science/tel-04202827v1">https://hal.science/tel-04202827v1</a>. The experiments correspond to a drained triaxial compression test of cylindrical granular specimens, a common  testing procedure used in soil mechanics to characterise the mechanical response of a specimen under deviatoric loading. Each specimen is 140mm in height and 70mm in diameter, and is composed of more than 20000 ellipsoidal particles of a given aspect ratio and interparticle friction. The dataset comprises the test of six specimens, as a result of the combination of 3 particles shapes (Flat, Medium, and Rounded) and 2 values of interparticle friction (Rough and Smooth). A naming system for the specimens is adopted to reflect the morphology of the composing particles (e.g., the test EFR correspond to the specimen with Flat and Rough particles). Further details on the experimental methods are found in Ch. 2 of the thesis. The compression tests are performed inside the x-ray scanner of Laboratoire 3SR in Grenoble (France), where the specimens are scanned each 0.5% of axial shortening, at an isotropic voxel size of 100 micrometer per pixel. The obtained radiographies are reconstructed using a Filtered Back Projection algorithm, using the software given by the x-ray cabin manufacturer (RX Solutions, France). The series of obtained 16-bit greyscale 3D images are processed with the open source software <a href="https://spam-project.gitlab.io/spam/index.html">spam</a>, version 0.6.2. The coordinate system of all the images is ZYX, where Z corresponds to compression direction. Further details on the image analysis techniques are found in Ch. 3 of the thesis.Additional greyscale images, raw projections, and x-ray tomography files are available upon request. For visualisation purposes, the 3D images in .tif format can be opened using <a href="https://imagej.net/software/fiji/">Fiji</a>.

The Relationship Between Different Python Argument-Passing Mechanisms and Fixes: An Empirical Study

Replication package for the paper: The Relationship Between Different Python Argument-Passing Mechanisms and Fixes -- An Empirical Study

opencc-zeroJun 2023View details →

Mechanisms of simultaneous linear and nonlinear computations at the mammalian cone photoreceptor synapse

Neurons enhance their computational power by combining linear and nonlinear transformations in extended dendritic trees. Rich, spatially distributed processing is rarely associated with individual synapses, but the cone photoreceptor synapse may be an exception. Graded voltages temporally modulate vesicle fusion at a cone's ~20 ribbon active zones. The transmitter then flows into a common, glia-free volume where bipolar cell dendrites are organized by type in successive tiers. Using super-resolution microscopy and tracking vesicle fusion and postsynaptic response at the quantal level in the thirteen-lined ground squirrel, Ictidomys tridecemlineatus, we show that certain bipolar cell types respond to individual fusion events in the stream while other types respond to degrees of locally coincident events, creating a gradient across tiers that are increasingly nonlinear. Nonlinearities emerge from a combination of factors specific to each bipolar cell type including diffusion distance, contact number, receptor affinity, and proximity to transporters. Complex computations related to feature detection begin within the first visual synapse.

Source data for "Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing"

Source data for "Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing"  The data is organized by Figure and associated Supp Figure(s). A README file is included in each figure folder to explain the files. (note: Data is included for Figs2-7 and SuppFigs 2-8. Fig.1 and SuppFig.1 did not have any associated data matrices, so there is no upload for them here).  Briefly, the single molecule data is included in several different formats, all generated from single-molecule TIRF-microscopy video files using Matlab: Integrated trace files "traces" include integrated fluorescence intensity at individual DNA molecules over a 20 minute reaction. Background-corrected trace files normalize the integrated fluorescence intensity to a local-average background, as described in the Methods section of the paper-- these are used for EFRET calculations. "Intervals" files include the start, end time, and duration of protein-DNA interactions and were generated from the trace files and the raw videos using the Imscroll program (available at: https://github.com/gelles-brandeis/CoSMoS_Analysis). EFRET vectors are concatenated vectors of the EFRET vs time values of all protein-DNA interactions in the experiment-- these are used to generate EFRET heat maps.  Matlab analysis scripts used in the paper are uploaded in a separate folder "ALA_scripts_used_final". Several of these scripts reference custom Matlab functions from the Gelles lab which are available here: https://github.com/gelles-brandeis/jganalyze and should be downloaded along with my attached scripts file.  note: Raw single-molecule video files have not been uploaded here due to large sizes, but can be provided upon request.

opencc-zeroJun 2023View details →

Data from: Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria

Prosocial behavior is ubiquitous despite the relative fitness costs carried by cooperative individuals. However, the stability of cooperation in populations is fragile, and often maintained through enforcement. We propose that homologous recombination provides such a mechanism in bacteria. Using an agent-based model of recombination in a population of bacteria playing a public goods game, we demonstrate how changes in recombination rate affect the proportion of cooperating cells. In our model, recombination converts cells to a different strategy, either freeloading (cheaters) or cooperation, based on the strategies of neighboring cells and the recombination rate. Increasing the recombination rate expands the parameter space in which cooperators dominate freeloaders. However, increasing the recombination rate alone is neither sufficient nor necessary. Intermediate benefits of cooperation, lower population viscosity, and higher population size can promote cooperation in a population of cheater strains. Our findings demonstrate how recombination influences the persistence of cooperative behavior in bacteria.

Microscopic View of the iRGD Peptide Binding Mechanism

Input and trajectory files used to obtain an atomistic picture of the  folding and mechanism of binding of the iRGD peptide to RGD integrin receptors.

opencc-by-4.0Jul 2023View details →

Membrane interaction and mechanism of LC3 lipidation machinery in autophagy raw GUV data

Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.

opencc-zeroJul 2023View details →

Multiple mechanisms contribute to isolation-by-environment in the redheaded pine sawfly, Neodiprion lecontei

Isolation by environment (IBE) is a population genomic pattern that arises when ecological barriers reduce gene flow between populations. Although current evidence suggests IBE is common in nature, few studies have evaluated the underlying mechanisms that generate IBE patterns. In this study, we evaluate five proposed mechanisms of IBE (natural selection against immigrants, sexual selection against immigrants, selection against hybrids, biased dispersal, environment-based phenological differences) that may give rise to host-associated differentiation within a sympatric population of the redheaded pine sawfly, Neodiprion lecontei, a species for which IBE has previously been detected. We first characterize the three pine species used by N. lecontei at the site, finding morphological and chemical differences among the hosts that could generate divergent selection on sawfly host-use traits. Next, using morphometrics and ddRAD sequencing, we detect modest phenotypic and genetic differentiation among sawflies originating from different pines that is consistent with recent, in situ divergence. Finally, via a series of laboratory assays – including assessments of larval performance on different hosts, adult mate and host preferences, hybrid fitness, and adult eclosion timing – we find evidence that multiple mechanisms contribute to IBE in N. lecontei. Overall, our results suggest IBE can emerge quickly, possibly due to multiple mechanisms acting in concert to reduce migration between different environments.

opencc-by-4.0Jul 2023View details →

From Electron Tomography of Dislocations to Field Dislocation Mechanics: application to olivine

Aligned and numerically filtered tilt-series of the PoEM9 specimen (double-tilt sample-holder + weak-beam dark-field conditions + precession angle = 0.1°+ objective aperture = 20 micron): Tilted-series 1: Projection angles from -48° to 52° every 2° (from image 01.tif to 51.tif) Tilted-series 5: Projection angles from -56° to 50° every 2° (from image 01.tif to 54.tif)

Supplementary Files and Data of 'Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond'

Live birth (viviparity) has arisen repeatedly and independently among animals. We sequenced the genome and transcriptome of the viviparous Pacific beetle-mimic cockroach and performed comparative analyses with two other viviparous insect lineages, tsetse flies and aphids, to unravel the basis underlying the transition to viviparity in insects. We identified pathways undergoing adaptive evolution for insects, involved in uro-genital remodeling, tracheal system, heart development, and nutrient metabolism. Transcriptomic analysis in the cockroach and tsetse viviparity reveals that uterine remodeling and nutrient production are increased and the immune response is altered during pregnancy, facilitating structural and physiological changes to accommodate and nourish the progeny. These patterns of convergent evolution of viviparity among insects, together with similar adaptive mechanisms identified among vertebrates, highlight that the transition to viviparity requires changes in uro-genital remodeling, enhanced tracheal and heart development (corresponding to angiogenesis in vertebrates), nutrient metabolism, and shifted immunity in all animal systems.

Mechanical Shaker Experiments: Amsterdam Study into the Properties of Wearable Accelerometers (ASPWA)

Mechanical Shaker Experiments: Amsterdam Study into the Properties of Wearable Accelerometers (ASPWA) A description of the data files in this archive can be found in: 20230816_Documentation-raw-folder-structure.pdf If you have a question: <ol> <li>use the search functionality <a href="https://github.com/wadpac/mechanicalshakerexperiments/issues">here</a> to see if someone already experienced the same issue;</li> <li>if your search did not yield any relevant results, please start a new conversation.</li> </ol>

Disgust and Politics: Investigating the Causal Mechanism Between Pathogen-Avoidance and Conservatism

Data for the bachelor thesis of L. Y. Kogelheide. (.csv format) FEE_FEE are answers from the disgust sensitivity questionnaire Path are answers for the Disgust Image Set - Experimental Condition No_Path are answers for the Disgust Image Set - Control Condition Traditionalism_T are answers for the traditionalism questionnaire SDO_SDO are answers for the social dominance orientation questionnaire HC is honesty check

Data from: Correlation of Microstructure and Local Mechanical Properties Along Build Direction for Multi-layer Friction Surfacing of Aluminum Alloys

This dataset contains the data for the publication " Correlation of Microstructure and Local Mechanical Properties Along Build Direction for Multi-layer Friction Surfacing of Aluminum Alloys".

opencc-zeroAug 2023View details →

Computational mechanisms underlying latent value updating of unchosen actions

Current studies suggest that individuals estimate the value of their choices based on observed feedback. Here, we ask whether individuals also update the value of their unchosen actions, even when the associated feedback remains unknown. One hundred and seventy-eight individuals completed a multi-armed bandit task, making choices to gain rewards. We found robust evidence suggesting latent value updating of unchosen actions based on the chosen action's outcome. Computational modeling results suggested that this effect is mainly explained by a value updating mechanism whereby individuals integrate the outcome history for choosing an option with that of rejecting the alternative. Properties of the deliberation (i.e., duration/difficulty) did not moderate the latent value updating of unchosen actions, suggesting that memory traces generated during deliberation might take a smaller role in this specific phenomenon than previously thought. We discuss the mechanisms facilitating credit assignment to unchosen actions and their implications for human decision-making.

Why The Perfectly Symmetric Cobalt-Pentapyridyl Loses the H2 Production Challenge: Theoretical Insight into Reaction Mechanism and Reduction Free Energies

Abstract Researchers have extensively investigated photo-catalytic water reduction utilizing Cobalt-based catalysts with poly-pyridyl ligands. While catalysts exhibiting distorted poly-pyridyl ligand demonstrate higher H2 production yields, those with ideal octahedral coordination display poor performance. This outcome suggests the crucial role of ligand framework in catalytic activity, yet reasons behind the disparity in H2 production rates for catalysts with octahedral geometries remain unclear. We theoretically examined the water reduction mechanism of Co-based poly-pyridyl catalyst, CoPy5, having perfect octahedral coordination. We clarified the effect of octahedral coordination by utilizing each intermediate step of ECEC mechanism. We determined spin states, solvent response, electronic structures, and reduction free energies. CoPy5 with perfect octahedral coordination, alongside its distorted counterparts, exhibit similar spin states as the reaction progresses through each intermediate step. However, the first reduction free energy obtained for the CoPy5 is slightly higher than that of its distorted counterparts. Following the second protonation, resulting H2 molecule experiences limited diffusion from the Co center due to the compact structure of the CoPy5, which blocks the Co center for the next H2 production cycle. Catalysts having distorted octahedral geometries facilitate fast removal of H2 into the solvent. Thus, the reaction center becomes immediately available for subsequent H2 production. Computational Details AIMD simulations have been performed for modeling intermediate states of the ECEC mechanisms of H2 production through water splitting. Open source CP2K simulation package have been used in all simulations. PBE density functional in general gradient approximation (GGA) formalism was employed for the AIMD simulations. Goedecker-Teter-Hutter (GTH) potentials were applied for the estimation of core electron interactions with the valence shell and nucleus. Valence electrons were modeled explicitly and valence shells of Co, N, C, O and H contain 17, 5, 4, 6 and 1 electrons, respectively. DZVP-MOLOPT basis set was used for all atomic kinds. For auxiliary plane wave basis set, a cutoff of 400 Ry was utilized. Dispersion interactions were taken into consideration by applying Vydrov and Van Voorhis vdW density functional, in the revised form (rVV10). Periodic boundary conditions and spin polarization were always applied. For the CoPy5 complex, AIMD simulations were carried out in a box defined as cubic with explicit water environment. The CoPy5 catalyst was first solvated in 215 water molecules and the simulation volume was relaxed by performing AIMD simulations for approximately 20 ps in the isothermal-isobaric ensemble (NPT). Cubic simulation box volume was determined as 6163.28  ̊A3. Following the determination of the simulation box size, each intermediate step were modeled by applying AIMD simulations in the canonical ensemble (NVT) for approximately 20 ps. Time step was set to 0.5 fs. Canonical sampling through velocity rescaling (CSVR) thermostat with a time constant of 100 fs was applied in order to keep the simulation temperature at 300 K. Please see the corresponding article for more details.

Illuminating the mechanism and allosteric behavior of NanoLuc luciferase

NanoLuc, a superior β-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques were combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Binding to the allosteric site prevents simultaneous binding to the catalytic site, and vice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin which then react with O 2 via a radical charge-transfer mechanism, and it also protonates the resulting excited amide product to form a light- emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, is fine-tuning the blue color emitter to secure a high emission intensity. This information is critical to engineering the next- generation of ultrasensitive bioluminescent reporters.