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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carrasco, Andres; Brown, Trecia A.; Lomber, Stephen G.;

    Assemblies of vertically connected neurons in the cerebral cortex form information processing units (columns) that participate in the distribution and segregation of sensory signals. Despite well-accepted models of columnar architecture, functional mechanisms of inter-laminar communication remain poorly understood. Hence, the purpose of the present investigation was to examine the effects of sensory information features on columnar response properties. Using acute recording techniques, extracellular response activity was collected from the right hemisphere of eight mature cats (felis catus). Recordings were conducted with multichannel electrodes that permitted the simultaneous acquisition of neuronal activity within primary auditory cortex columns. Neuronal responses to simple (pure tones), complex (noise burst and frequency modulated sweeps), and ecologically relevant (con-specific vocalizations) acoustic signals were measured. Collectively, the present investigation demonstrates that despite consistencies in neuronal tuning (characteristic frequency), irregularities in discharge activity between neurons of individual A1 columns increase as a function of spectral (signal complexity) and temporal (duration) acoustic variations. Multi-unit responses to acoustic signals within A1 columnsThe data set consists of eight multi-unit electrophysiology experiments located within a single .zip file. Acoustic feature (signal type and duration) are in subfolders where data rasters for each recording session conducted can be found. Columns represent time and rows trial number. Data is presented as Matlab files.DRYAD.zip

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Henry, Molly J.; Herrmann, Bjorn; Grahn, Jessica A.;

    Entrainment of neural oscillations on multiple time scales is important for the perception of speech. Musical rhythms, and in particular the perception of a regular beat in musical rhythms, is also likely to rely on entrainment of neural oscillations. One recently proposed approach to studying beat perception in the context of neural entrainment and resonance (the “frequency-tagging” approach) has received an enthusiastic response from the scientific community. A specific version of the approach involves comparing frequency-domain representations of acoustic rhythm stimuli to the frequency-domain representations of neural responses to those rhythms (measured by electroencephalography, EEG). The relative amplitudes at specific EEG frequencies are compared to the relative amplitudes at the same stimulus frequencies, and enhancements at beat-related frequencies in the EEG signal are interpreted as reflecting an internal representation of the beat. Here, we show that frequency-domain representations of rhythms are sensitive to the acoustic features of the tones making up the rhythms (tone duration, onset/offset ramp duration); in fact, relative amplitudes at beat-related frequencies can be completely reversed by manipulating tone acoustics. Crucially, we show that changes to these acoustic tone features, and in turn changes to the frequency-domain representations of rhythms, do not affect beat perception. Instead, beat perception depends on the pattern of onsets (i.e., whether a rhythm has a simple or complex metrical structure). Moreover, we show that beat perception can differ for rhythms that have numerically identical frequency-domain representations. Thus, frequency-domain representations of rhythms are dissociable from beat perception. For this reason, we suggest caution in interpreting direct comparisons of rhythms and brain signals in the frequency domain. Instead, we suggest that combining EEG measurements of neural signals with creative behavioral paradigms is of more benefit to our understanding of beat perception. single participant behavioral data files.mat files for single participants. README.txt file in each zipped folder describes columnsdryad_data.zip

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Kasper, Claudia; Hebert, Francois Olivier; Aubin-Horth, Nadia; Taborsky, Barbara;

    Juveniles of the cooperatively-breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ('cleaners') or consistently abstain from helping ('non-cleaners'). These phenotypes are not based on heritable genetic differences. Instead they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and non-cleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (i) expression differences between cleaners and non-cleaners in the control, (ii) changes in gene expression induced by the opportunity, and (iii) differences in plasticity of gene expression between cleaners and non-cleaners. Control cleaners and non-cleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and non-cleaners had three up-regulated genes in common, which were implicated in neuroplasticity, hormonal signalling, and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner-specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were down-regulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity, and that only cleaners responded by down-regulating developmental genes. Read count matrix and treatment information on individualsRead count matrix from RNA-seq experiment of two distinct helper types in the cooperatively breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2 full-factorial design of cleaners and non-cleaners in control and opportunity. 38,2425 genes expressed in the telencephalon 45 min after the onset of the cooperation opportunity.data_Kasper_cichlid_helping_transcriptome.xlsx

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODO; NARCIS; DRYA...arrow_drop_down
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    ZENODO; NARCIS; DRYAD
    Dataset . 2018
    License: CC 0
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2018
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODO; NARCIS; DRYA...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO; NARCIS; DRYAD
      Dataset . 2018
      License: CC 0
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2018
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Piwowar, Heather A.; Vision, Todd J.; Whitlock, Michael C.;

    PubMed Central reuse of GEO datasets deposited in 2007This is the raw data behind the analysis. It contains one row for every mention of a 2007 GEO dataset in PubMed Central. Each row identifies the mentioned GEO dataset, the PubMed Central article that mentions the dataset's accession number, whether the authors of the dataset and the attributing article overlap, and whether this is considered an instance of third-party data reuse.PMC_reuse_of_2007_GEO_datasets.csvAggregate Table DataAggregate table data behind the figures and results in the README associated with the main dataset. Includes Baseline metrics used for extrapolating PubMed Central (PMC) results to PubMed, Number of mentions of a 2007 GEO dataset by authors who submitted the dataset, and Number of mentions of a dataset by authors who DID NOT submit the dataset across 2007-2010.tables.csv Funding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.

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    DANS-EASY
    Dataset . 2011
    Data sources: B2FIND
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    DRYAD; ZENODO; NARCIS
    Dataset . 2011
    License: CC 0
    Borealis
    Dataset . 2021
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2011
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DRYAD; ZENODO; NARCIS
      Dataset . 2011
      License: CC 0
      Borealis
      Dataset . 2021
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: O'Connor, Constance M.; Marsh-Rollo, Susan E.; Aubin-Horth, Nadia; Balshine, Sigal;

    Comparative studies have revealed that vasopressin-oxytocin pathways are associated with both pair bonding and grouping behaviour. However, the relationship between pair bonding and grouping behaviourremains unclear.In this study,our aim was to identify whether two species that differ in grouping behaviourdisplay a corresponding difference in their pair bonds, and in the underlying vasopressin-oxytocinhormonal pathways. Using two species of cichlid fishes, the highly social Neolamprologuspulcher and the non-social Telmatochromis temporalis, we measuredproximity of pairs during pair bond formation, and then measured social behaviors (proximity, aggression, submission,affiliation)and brain gene expression of isotocin and arginine vasotocin (the teleost homologues of oxytocin and vasopressin, respectively), as well as their receptors, after a temporary separation and subsequent reunion of the bonded pairs. Pairs of the social species spent more time in close proximity relative to the non-social species. Rates of aggression increased in both species following the separation and reunion treatment, relative to controls that were not separated.Overall, whole brain expression of isotocin was higher in the social species relative to the non-social species, and correlated with proximity, submission, and affiliation, but only in the social species. Our results suggest that both a social and a non-social cichlid species have similar behavioural responses to a temporary separation from a mate, and we found no differencein the brain gene expression of measured hormones and receptors based on our separation-reunion treatment. However, our results highlight the importance of isotocin in mediating submissive and affiliativebehaviourin cichlid fishes, and demonstrate thatisotocinhas species-specific correlations with socially relevantbehaviours. Cichlid pair bonding IT AVT dataRT-qPCR values and behavioral scores

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; NARCIS; Feder...arrow_drop_down
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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; NARCIS; Feder...arrow_drop_down
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      Dataset . 2016
      Data sources: B2FIND
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    Authors: Azócar, Guillermo; Brenning, Alexander; Bodin, Xavier;

    The Permafrost Favorability Index (PFI) map for the Chilean Semi-Arid Andes (29°S-32°S) indicates where permafrost is likely to occur (resolution 30 m x 30 m). The predicted favorability of permafrost occurrence ranges between 0 and 1, where high PFI values indicate most favorable environmental conditions for permafrost existence and low values indicates that permafrost will be present in exceptional circumstances with favorable local conditions. Conditions highly favorable to permafrost presence (PFI > 0.75) are predicted for 1051 km² of mountain terrain, or 2.7 % of the total area of the watersheds studied. Favorable conditions are expected to occur in 2636 km², or 6.8% of the area. Especially the Elqui and Huasco watersheds in the northern half of the study area where a substantial surface portion (11.8 % each) was considered to be favorable for permafrost presence, while predicted favorable areas in the southern Limarí and Choapa watersheds are mostly limited to specific sub-watersheds. Supplement to: Azócar, Guillermo; Brenning, Alexander; Bodin, Xavier (2016): Permafrost Distribution Modeling in the Semi-Arid Chilean Andes. The Cryosphere, 11, 877-890 Raster files are saved in SAGA format (.sgrd) and vector file as Shapefile. All data are projected in WGS84 UTM 19 South.

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    PANGAEA
    Dataset . 2016
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2016
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nachmani, Omri; Coutinho, Jonathan; Khan, Aarlenne Z.; Lefèvre, Philippe; +1 Authors

    For foveated animals, visual tracking of moving stimuli requires the synergy between saccades and smooth pursuit eye movements. Deciding to trigger a catch-up saccade during pursuit influences the quality of visual input. This decision is a trade-off between tolerating sustained position error when no saccade is triggered or a transient loss of vision during the saccade due to saccadic suppression. Although catch-up saccades have been extensively investigated, it remains unclear how the trigger decision is made by the brain. de Brouwer et al (2002) demonstrated that catch-up saccades were less likely to occur when the expected time to foveate a target using pursuit alone is between 40 and 180ms into the future, referred to as the smooth zone. However, this descriptive result lacks a mechanistic explanation for how the trigger decision is made. More recently, we proposed a decision model (Coutinho et al., 2018) that relies on a probabilistic estimation of predicted position error (PEpred) during visual tracking. To test the model predictions, we investigated how human participants combined predicted position error, retinal slip, and the uncertainty in those estimates to make trigger decisions. We found a significant effect of the pre-saccadic magnitude of PEpred on trigger time and occurrence of catch-up saccades. To test the role of uncertainty, we blurred the moving target which led to longer and more variable saccade trigger times and more smooth pursuit trials, consistent with model predictions. As predicted by our model, large PEpred (>10deg) produced early saccades regardless of the level of uncertainty while saccades preceded by small PEpred (<10deg) were significantly modulated by high uncertainty. Our model also predicted increased signal dependent noise as retinal slip increases, which resulted in longer saccade trigger times and more smooth trials. In conclusion, the data supports our hypothesized role of PEpred in deciding when to trigger a catch-up saccade during smooth pursuit while taking into account uncertainty in sensory estimates. RawRaw double-step ramp eye-tracking data of 15 subjects from EyeLink 1000 and Matlab.LabeledS1-S5Labeled data file for subjects 1-5LabeledS7-S11Labeled data for subjects 7-11LabeledS12-S16Labeled data for subjects 12-16Data Collection Log

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    Authors: Combrisson, Etienne; Vallat, Raphael; Eichenlaub, Jean-Baptiste; O'Reilly, Christian; +4 Authors

    We introduce Sleep, a new Python open-source graphical user interface (GUI) dedicated to visualization, scoring and analyses of sleep data. Among its most prominent features are: (1) Dynamic display of polysomnographic data, spectrogram, hypnogram and topographic maps with several customizable parameters, (2) Implementation of several automatic detection of sleep features such as spindles, K-complexes, slow waves, and rapid eye movements (REM), (3) Implementation of practical signal processing tools such as re-referencing or filtering, and (4) Display of main descriptive statistics including publication-ready tables and figures. The software package supports loading and reading raw EEG data from standard file formats such as European Data Format, in addition to a range of commercial data formats. Most importantly, Sleep is built on top of the VisPy library, which provides GPU-based fast and high-level visualization. As a result, it is capable of efficiently handling and displaying large sleep datasets. Sleep is freely available (http://visbrain.org/sleep) and comes with sample datasets and an extensive documentation. Novel functionalities will continue to be added and open-science community efforts are expected to enhance the capacities of this module.

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    Frontiers in Neuroinformatics
    2017 . Peer-reviewed
    Data sources: Frontiers
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      Frontiers in Neuroinformatics
      2017 . Peer-reviewed
      Data sources: Frontiers
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    Authors: Robles-Rubio, Carlos Alejandro; Bertolizio, Gianluca; Brown, Karen A.; Kearney, Robert E.;

    Infants recovering from anesthesia are at risk of life threatening Postoperative Apnea (POA). POA events are rare, and so the study of POA requires the analysis of long cardiorespiratory records. Manual scoring is the preferred method of analysis for these data, but it is limited by low intra- and inter-scorer repeatability. Furthermore, recommended scoring rules do not provide a comprehensive description of the respiratory patterns. This work describes a set of manual scoring tools that address these limitations. These tools include: (i) a set of definitions and scoring rules for 6 mutually exclusive, unique patterns that fully characterize infant respiratory inductive plethysmography (RIP) signals; (ii) RIPScore, a graphical, manual scoring software to apply these rules to infant data; (iii) a library of data segments representing each of the 6 patterns; (iv) a fully automated, interactive formal training protocol to standardize the analysis and establish intra- and inter-scorer repeatability; and (v) a quality control method to monitor scorer ongoing performance over time. To evaluate these tools, three scorers from varied backgrounds were recruited and trained to reach a performance level similar to that of an expert. These scorers used RIPScore to analyze data from infants at risk of POA in two separate, independent instances. Scorers performed with high accuracy and consistency, analyzed data efficiently, had very good intra- and inter-scorer repeatability, and exhibited only minor confusion between patterns. These results indicate that our tools represent an excellent method for the analysis of respiratory patterns in long data records. Although the tools were developed for the study of POA, their use extends to any study of respiratory patterns using RIP (e.g., sleep apnea, extubation readiness). Moreover, by establishing and monitoring scorer repeatability, our tools enable the analysis of large data sets by multiple scorers, which is essential for longitudinal and multicenter studies. Original and pre-processed data, and analysis resultsData acquired from infants at risk of Postoperative Apnea (in MATLAB *.mat format). Also, results of the analysis of these data by 4 scorers using the RIPScore manual scoring tool.StudyData.zip

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    Dataset . 2015
    Data sources: B2FIND
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      Dataset . 2015
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Harel, Yann; Cyr, André; Boyle, Julie; Pinsard, Basile; +7 Authors

    {"references": ["Harel et al., (2023). Open design and validation of a reproducible videogame controller for MRI and MEG."]} Full documentation and files required to build the CNeuromod controller.

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    ZENODO
    PhysicalObject . 2023
    License: CC BY
    Data sources: Datacite
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    ZENODO
    PhysicalObject . 2023
    License: CC BY
    Data sources: ZENODO
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      ZENODO
      PhysicalObject . 2023
      License: CC BY
      Data sources: Datacite
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      ZENODO
      PhysicalObject . 2023
      License: CC BY
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carrasco, Andres; Brown, Trecia A.; Lomber, Stephen G.;

    Assemblies of vertically connected neurons in the cerebral cortex form information processing units (columns) that participate in the distribution and segregation of sensory signals. Despite well-accepted models of columnar architecture, functional mechanisms of inter-laminar communication remain poorly understood. Hence, the purpose of the present investigation was to examine the effects of sensory information features on columnar response properties. Using acute recording techniques, extracellular response activity was collected from the right hemisphere of eight mature cats (felis catus). Recordings were conducted with multichannel electrodes that permitted the simultaneous acquisition of neuronal activity within primary auditory cortex columns. Neuronal responses to simple (pure tones), complex (noise burst and frequency modulated sweeps), and ecologically relevant (con-specific vocalizations) acoustic signals were measured. Collectively, the present investigation demonstrates that despite consistencies in neuronal tuning (characteristic frequency), irregularities in discharge activity between neurons of individual A1 columns increase as a function of spectral (signal complexity) and temporal (duration) acoustic variations. Multi-unit responses to acoustic signals within A1 columnsThe data set consists of eight multi-unit electrophysiology experiments located within a single .zip file. Acoustic feature (signal type and duration) are in subfolders where data rasters for each recording session conducted can be found. Columns represent time and rows trial number. Data is presented as Matlab files.DRYAD.zip

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    Dataset . 2014
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Henry, Molly J.; Herrmann, Bjorn; Grahn, Jessica A.;

    Entrainment of neural oscillations on multiple time scales is important for the perception of speech. Musical rhythms, and in particular the perception of a regular beat in musical rhythms, is also likely to rely on entrainment of neural oscillations. One recently proposed approach to studying beat perception in the context of neural entrainment and resonance (the “frequency-tagging” approach) has received an enthusiastic response from the scientific community. A specific version of the approach involves comparing frequency-domain representations of acoustic rhythm stimuli to the frequency-domain representations of neural responses to those rhythms (measured by electroencephalography, EEG). The relative amplitudes at specific EEG frequencies are compared to the relative amplitudes at the same stimulus frequencies, and enhancements at beat-related frequencies in the EEG signal are interpreted as reflecting an internal representation of the beat. Here, we show that frequency-domain representations of rhythms are sensitive to the acoustic features of the tones making up the rhythms (tone duration, onset/offset ramp duration); in fact, relative amplitudes at beat-related frequencies can be completely reversed by manipulating tone acoustics. Crucially, we show that changes to these acoustic tone features, and in turn changes to the frequency-domain representations of rhythms, do not affect beat perception. Instead, beat perception depends on the pattern of onsets (i.e., whether a rhythm has a simple or complex metrical structure). Moreover, we show that beat perception can differ for rhythms that have numerically identical frequency-domain representations. Thus, frequency-domain representations of rhythms are dissociable from beat perception. For this reason, we suggest caution in interpreting direct comparisons of rhythms and brain signals in the frequency domain. Instead, we suggest that combining EEG measurements of neural signals with creative behavioral paradigms is of more benefit to our understanding of beat perception. single participant behavioral data files.mat files for single participants. README.txt file in each zipped folder describes columnsdryad_data.zip

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    Dataset . 2017
    Data sources: B2FIND
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      Dataset . 2017
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Kasper, Claudia; Hebert, Francois Olivier; Aubin-Horth, Nadia; Taborsky, Barbara;

    Juveniles of the cooperatively-breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ('cleaners') or consistently abstain from helping ('non-cleaners'). These phenotypes are not based on heritable genetic differences. Instead they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and non-cleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (i) expression differences between cleaners and non-cleaners in the control, (ii) changes in gene expression induced by the opportunity, and (iii) differences in plasticity of gene expression between cleaners and non-cleaners. Control cleaners and non-cleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and non-cleaners had three up-regulated genes in common, which were implicated in neuroplasticity, hormonal signalling, and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner-specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were down-regulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity, and that only cleaners responded by down-regulating developmental genes. Read count matrix and treatment information on individualsRead count matrix from RNA-seq experiment of two distinct helper types in the cooperatively breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2 full-factorial design of cleaners and non-cleaners in control and opportunity. 38,2425 genes expressed in the telencephalon 45 min after the onset of the cooperation opportunity.data_Kasper_cichlid_helping_transcriptome.xlsx

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    ZENODO; NARCIS; DRYAD
    Dataset . 2018
    License: CC 0
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    DANS-EASY
    Dataset . 2018
    Data sources: B2FIND
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      ZENODO; NARCIS; DRYAD
      Dataset . 2018
      License: CC 0
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      DANS-EASY
      Dataset . 2018
      Data sources: B2FIND
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    Authors: Piwowar, Heather A.; Vision, Todd J.; Whitlock, Michael C.;

    PubMed Central reuse of GEO datasets deposited in 2007This is the raw data behind the analysis. It contains one row for every mention of a 2007 GEO dataset in PubMed Central. Each row identifies the mentioned GEO dataset, the PubMed Central article that mentions the dataset's accession number, whether the authors of the dataset and the attributing article overlap, and whether this is considered an instance of third-party data reuse.PMC_reuse_of_2007_GEO_datasets.csvAggregate Table DataAggregate table data behind the figures and results in the README associated with the main dataset. Includes Baseline metrics used for extrapolating PubMed Central (PMC) results to PubMed, Number of mentions of a 2007 GEO dataset by authors who submitted the dataset, and Number of mentions of a dataset by authors who DID NOT submit the dataset across 2007-2010.tables.csv Funding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.

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    DANS-EASY
    Dataset . 2011
    Data sources: B2FIND
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    DRYAD; ZENODO; NARCIS
    Dataset . 2011
    License: CC 0
    Borealis
    Dataset . 2021
    Data sources: Datacite
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      DANS-EASY
      Dataset . 2011
      Data sources: B2FIND
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      DRYAD; ZENODO; NARCIS
      Dataset . 2011
      License: CC 0
      Borealis
      Dataset . 2021
      Data sources: Datacite
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    Authors: O'Connor, Constance M.; Marsh-Rollo, Susan E.; Aubin-Horth, Nadia; Balshine, Sigal;

    Comparative studies have revealed that vasopressin-oxytocin pathways are associated with both pair bonding and grouping behaviour. However, the relationship between pair bonding and grouping behaviourremains unclear.In this study,our aim was to identify whether two species that differ in grouping behaviourdisplay a corresponding difference in their pair bonds, and in the underlying vasopressin-oxytocinhormonal pathways. Using two species of cichlid fishes, the highly social Neolamprologuspulcher and the non-social Telmatochromis temporalis, we measuredproximity of pairs during pair bond formation, and then measured social behaviors (proximity, aggression, submission,affiliation)and brain gene expression of isotocin and arginine vasotocin (the teleost homologues of oxytocin and vasopressin, respectively), as well as their receptors, after a temporary separation and subsequent reunion of the bonded pairs. Pairs of the social species spent more time in close proximity relative to the non-social species. Rates of aggression increased in both species following the separation and reunion treatment, relative to controls that were not separated.Overall, whole brain expression of isotocin was higher in the social species relative to the non-social species, and correlated with proximity, submission, and affiliation, but only in the social species. Our results suggest that both a social and a non-social cichlid species have similar behavioural responses to a temporary separation from a mate, and we found no differencein the brain gene expression of measured hormones and receptors based on our separation-reunion treatment. However, our results highlight the importance of isotocin in mediating submissive and affiliativebehaviourin cichlid fishes, and demonstrate thatisotocinhas species-specific correlations with socially relevantbehaviours. Cichlid pair bonding IT AVT dataRT-qPCR values and behavioral scores

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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    Authors: Azócar, Guillermo; Brenning, Alexander; Bodin, Xavier;

    The Permafrost Favorability Index (PFI) map for the Chilean Semi-Arid Andes (29°S-32°S) indicates where permafrost is likely to occur (resolution 30 m x 30 m). The predicted favorability of permafrost occurrence ranges between 0 and 1, where high PFI values indicate most favorable environmental conditions for permafrost existence and low values indicates that permafrost will be present in exceptional circumstances with favorable local conditions. Conditions highly favorable to permafrost presence (PFI > 0.75) are predicted for 1051 km² of mountain terrain, or 2.7 % of the total area of the watersheds studied. Favorable conditions are expected to occur in 2636 km², or 6.8% of the area. Especially the Elqui and Huasco watersheds in the northern half of the study area where a substantial surface portion (11.8 % each) was considered to be favorable for permafrost presence, while predicted favorable areas in the southern Limarí and Choapa watersheds are mostly limited to specific sub-watersheds. Supplement to: Azócar, Guillermo; Brenning, Alexander; Bodin, Xavier (2016): Permafrost Distribution Modeling in the Semi-Arid Chilean Andes. The Cryosphere, 11, 877-890 Raster files are saved in SAGA format (.sgrd) and vector file as Shapefile. All data are projected in WGS84 UTM 19 South.

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