This study addresses a debate on the nature of gamma (>30Hz) oscillations in language generation and structuring from a top-down vs. bottom-up chunking approach. Working within the framework of recent oscillatory models for syntax, we argue that a time-frequency analysis of electroencephalography at crucial points of recursions in bi-clausal wh-movement is probative of the role of gramma oscillations in the creation of referential dependencies nested into wh-dependencies, accounting for aspects of the expressive power of language.
The study proposes that gamma oscillations in frontotemporal circuitry create syntax-semantics objects in contrast with slow-rhythm entrainment of gamma oscillations tracking semantic fitness in bottom-up chunking. We show gamma power effects associated with aspects of anaphoric relations established in syntax vs. discourse during the processing of bi-clausal filler-gap dependencies. Despite equal semantic fitness across conditions for noun phrase modifiers (Mods) and noun complements (Comps), Mod-Comp modulations of ERPDs linked to anaphoric relations with early vs. late antecedents arose in referential processing aligned with gap positions, suggesting the gamma-based implementation of referential relations is induced by the re-representations of pronouns in complex filler-gap dependencies.
Cortical 𝛾-Oscillations Implement Basic Language Operations: Evidence from Electroencephalography in Anaphora During English Filler-gap Dependency Processing
Spectroscopy data were collected on a BioTek Synergy H1 plate reader, then exported to and analyzed in Excel. 3D charts used in the manuscript were generated with OriginPro. Microscopy images are in proprietary .nd2 format of Nikon Elements software. .nd2 files were opened and processed with ImageJ. Gels were imaged on a BioRad Chemidoc.
Laughlin, P. M.; Young, K.; Gonzalez-Guiterrez, G.; Wang, J. C.-Y.,; Zlotnick, A. A narrow ratio of nucleic acid to SARS-CoV-2 N-protein enables phase separation. 2024.
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Raw data for "A narrow ratio of nucleic acid to SARS-CoV-2 N-protein enables phase separation"
We discuss event-related power differences (ERPDs) in low- and broadband-γ oscillations as the edge of embedded clauses is processed in wh-dependencies such as Which decision regarding/about him/her did Paul say that Lydie rejected without hesitation? in native and nonnative French speakers. The experimental conditions manipulated whether pronouns appeared in modifiers (Mods) or in noun complements (Comps) and whether they matched or mismatched a matrix-clause subject in gender. Across native and nonnative speakers, we found that anaphora-linked ERPDs for Mods vs. Comps in evoked power first arose in low γ and then in broadband γ. Therefore, referential elements first seem to be retrieved from working memory by narrowband processes in low-γ and then referential identification seems to be computed in broadband-γ output. Interactions between discourse- and syntax-based referential processes for the Mods vs. Comps in these ERPDs furthermore suggest that multidomain γ-range processing enables a range of elementary operations for discourse and semantic interpretation. We argue that a multidomain mechanism enabling operations conditioned by the syntactic and semantic nature of the elements processed interacts with local brain microcircuits representing features and feature sets that have been established in first- or second-language acquisition, accounting for a single language epistemology for native and nonnative language.
This zip file contains WAV-audio files and annotations. The recordings were produced using a digital audio recorder (ZOOM H6) and can be listened to using any sound software that can play WAV-audio files. The annotations can be viewed and edited by the ELAN software packages. ELAN ( https://tla.mpi.nl/tools/tla-tools/elan/) is a professional tool for the creation of complex annotations of video and audio resources. Download the dataset using the link below.
Download the software applications and data used for the 2017 Student Cluster Competition by clicking the URLs below: Model for Prediction Across Scales (MPAS); Born seismic imaging tool; MrBayes program for Bayesian inference and model choice; LAMMPS molecular dynamics (MD) code. Note that download times may vary.
Accompanying dataset to the protocol published in Methods in Molecular Biology. Click on the PURL link below in the "External Files" section to download the dataset.
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Title:
Bioinformatics Analysis of Top-Down Mass Spectrometry Data
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D. MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 3/2 100 3/2 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size. Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
Supporting datasets for drill-down topic modeling workflow described in "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library." PLOS ONE. https://doi.org/10.1371/journal.pone.0184188
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Supporting Data for "Multi-level computational methods for interdisciplinary research in the HathiTrust Digital Library"
The evigene_corn2016 archive package contains a complete, reconstructed gene set of Zea mays, corn plant, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Title:
Genes of Zea mays, corn plant reconstructed with EvidentialGene
The evigene_wasp_nasvit2012 archive package contains a complete, reconstructed gene set of Nasonia vitripennis, jewel wasp, produced with EvidentialGene methods. This file set includes gene sequences, annotations, analyses and summary documents.
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Genes of Nasonia vitripennis, jewel wasp reconstructed with EvidentialGene
The two major components of this supplement are packaged as two separate UNIX tar files available through links below. The two tar file names are:
(1) ModelConstructionDetails.tar - this contains the pdf file with the text (file name SupplementText.pdf) describing the technical details of how the 3D model was constructed. The package also contains a directory called Figures that contain five interactive figures. The SupplementText.pdf file contains links to these files that will resolve only if the files are left in that directory. There is also a small README text file to make the set of files more self contained.
(2) DataSupplement.tar - this is the package of data files that form the data supplement. The organization of the files in the package and file descriptions are described in the pdf file with the name DataSupplementDescription.pdf. That file can also be accessed directly from the link below.
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Electronic Supplement to “A Unified Three-dimensional Model of the Lithospheric Structure at the Subduction Corner in Southeast Alaska: Summary Results from STEEP”
Initial Jetstream Featured image. Based on Ubuntu 14.04.3 Development Patched up to date as of 3/28/16 Base Ubuntu 14.04.3 + Xfce + Xfce-goodies, firefox, icon sets and themes
