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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: Bernhardt, Boris C.; Fadaie, Fatemeh; Liu, Min; Caldairou, Benoit; +6 Authors

    OBJECTIVE. To assess whether HS severity is mirrored at the level of large-scale networks. METHODS. We studied preoperative high-resolution anatomical and diffusion-weighted MRI of 44 TLE patients with histopathological diagnosis of HS (n=25; TLE-HS) and isolated gliosis (n=19; TLE-G), and 25 healthy controls. Hippocampal measurements included surface-based subfield mapping of atrophy and T2 hyperintensity indexing cell loss and gliosis, respectively. Whole-brain connectomes were generated via diffusion tractography and examined using graph theory along with a novel network control theory paradigm which simulates functional dynamics from structural network data. RESULTS. Compared to controls, we observed markedly increased path length and decreased clustering in TLE-HS compared to controls, indicating lower global and local network efficiency, while TLE-G showed only subtle alterations. Similarly, network controllability was lower in TLE-HS only, suggesting limited range of functional dynamics. Hippocampal imaging markers were positively associated with macroscale network alterations, particularly in ipsilateral CA1-3. Systematic assessment across several networks revealed maximal changes in the hippocampal circuity. Findings were consistent when correcting for cortical thickness, suggesting independence from grey matter atrophy. CONCLUSIONS. Severe HS is associated with marked remodeling of connectome topology and structurally-governed functional dynamics in TLE, as opposed to isolated gliosis which has negligible effects. Cell loss, particularly in CA1-3, may exert a cascading effect on brain-wide connectomes, underlining coupled disease processes across multiple scales. Data_phen_conn_dryadPhenotypic information and mean connectome feature data for Bernhardt et al. (2019) Temporal lobe epilepsy: hippocampal pathology modulates white matter connectome topology and controllability. Neurology

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    DANS-EASY
    Dataset . 2019
    Data sources: B2FIND
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    ZENODO; NARCIS; DRYAD
    Dataset . 2019
    License: CC 0
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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
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      DANS-EASY
      Dataset . 2019
      Data sources: B2FIND
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      ZENODO; NARCIS; DRYAD
      Dataset . 2019
      License: CC 0
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    Authors: Campitelli, Laura F.; Yellan, Isaac; Albu, Mihai; Barazandeh, Marjan; +3 Authors

    Web Supplementary Files Web Supplementary File 1 - FASTA files containing full-length reconstruction input sequences: full_length_reconstruction_input_sequence_fastas.zip Web Supplementary File 2 - FASTA files containing Muscle alignments of the full-length reconstruction input sequences. full_length_reconstruction_input_sequence_alns.zip Web Supplementary File 3 - FASTA file of full-length reconstructed sequences: full_length_reconstructions.fa Web Supplementary File 4 - Table of full-length reconstruction statistics: full_length_reconstruction_stats.csv Web Supplementary File 5 - FASTA files containing ORF reconstruction input sequences: orf_fastas.zip Web Supplementary File 6 - FASTA files containing Macse alignments of the ORF reconstruction input sequences: ORF_reconstruction_input_sequence_alns.zip Web Supplementary File 7 - Table of ORF reconstruction statistics: ORF_reconstructions.fa Web Supplementary File 8 - Table of ORF reconstruction statistics: ORF_reconstruction_stats.csv Web Supplementary File 9 - Table of Composite Sequences: bestfl_selection_fixed_CS_seqs.csv Web Supplementary File 10 - Database of gold standards: L1_goldstandards.csv Data Underlying Figures RepeatMasker scans of hg38 and ancestral genomes: anc_gen_RM_out_files.zip Figure 4 4A Source alignment of 54 composite sequences: 220121_dropped12+L1ME3A_muscle.nt.afa Tree produced using the alignment and FastTree: 220121_dropped12+L1ME3A.tree 4B Source alignment of 67 Dfam L1 subfamily 3’ end models: 200123_dfam_3ends.fa.muscle.aln Tree produced using the alignment: 200123_dfam_3ends.fa.muscle.aln.tree Figure 5 KZFP-TE enrichment p-values (from Barazandeh et al 2018): TE_KZFP_enrichment_pvals.xlsx KZFP-TE top 500 peak overlap (from Barazandeh et al 2018): top500_peak_overlap.xlsx Figure 6 RepeatMasker .out file for the Composite Sequence custom library queried against hg38: CS_RM_hg38.fa.out.gz Figure S2 RepeatMasker scan .out file of hg38 (CG corrected Kimura Divergence values are in last column): hg38+KimDiv_RM.out RepeatMasker scan .out file of the Progressive Cactus eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Progressive_Cactus_Euth+KimDiv_RM.out RepeatMasker scan .out file of the Ancestors 1.1 eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Ancestors_Euth+KimDiv_RM.out Figure S5 RepeatMasker scan .out files for Progressive Cactus simian and primate reconstructed ancestral genomes: progCactus_RM_outfiles.zip S5A FASTA files containing Cactus genome-derived reconstructed sequences equivalent to the L1MA2, L1MA4, and L1MD1-3 best full-length sequences: progCactus_reconstruction_bestFL_equivalents.zip S5B FASTA files containing Muscle alignments of Cactus genome-derived full-length reconstruction input sequences: progCactus_reconstruction_input_sequence_alns.zip Figure S6 S6A Results of Conserved Domain scans of Cactus genome-derived full-length reconstructed sequences: CD_search_results_short_nms.txt S6B-D Character posterior probabilities of “best” full-length reconstructed sequences: best_fl_post_probs.zip Figure S7 S7B-C Results of Conserved Domain scans of translated initial full-length reconstructed sequences: initial_recons_all_3frametrans_CD-search.txt Results of Conserved Domain scans of translated reconstructed ORFs: recons_ORF1-2_all_3frametrans_CD-search.csv Figure S15 S15A Source alignment of 67 composite sequences: bestfl_selection_fixed_CS_seqs_muscle.nt.afa Tree produced using the alignment: bestfl_selection_fixed_CS_seqs_muscle.nt.afa.tree S15B-E Source Muscle alignments for phylogenetic trees of reconstructed sequence components: ORF2: ORF2_keep54_muscle.nt.afa 5’ UTR: 5utr_keep54_muscle.nt.afa ORF1: ORF1_keep54_muscle.nt.afa 3’ UTR: 3utr_keep54_muscle.nt.afa Trees produced using above alignments: ORF2: ORF2_keep54_muscle.nt.afa.tree 5’ UTR: 5utr_keep54_muscle.nt.afa.tree ORF1: ORF1_keep54_muscle.nt.afa.tree 3’ UTR: 3utr_keep54_muscle.nt.afa.tree Figure S17 Unfiltered BLAST results of Composite Sequences queried against hg38: CS_hg38_blastn.csv.zip BED file of L1 instances annotated using BLAST pipeline: BLAST_L1_hits.bed

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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Dataset . 2022
      License: CC BY
      Data sources: Datacite
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    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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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
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    Authors: Wallin, Mitchell T.; Culpepper, William J.; Campbell, Jonathan D.; Nelson, Lorene M.; +11 Authors

    Objective: To generate a national multiple sclerosis (MS) prevalence estimate for the United States by applying a validated algorithm to multiple administrative health claims (AHC) datasets. Methods: A validated algorithm was applied to private, military, and public AHC datasets to identify adult cases of MS between 2008 and 2010. In each dataset, we determined the 3-year cumulative prevalence overall and stratified by age, sex, and census region. We applied insurance-specific and stratum-specific estimates to the 2010 US Census data and pooled the findings to calculate the 2010 prevalence of MS in the United States cumulated over 3 years. We also estimated the 2010 prevalence cumulated over 10 years using 2 models and extrapolated our estimate to 2017. Results: The estimated 2010 prevalence of MS in the US adult population cumulated over 10 years was 309.2 per 100,000 (95% confidence interval [CI] 308.1–310.1), representing 727,344 cases. During the same time period, the MS prevalence was 450.1 per 100,000 (95% CI 448.1–451.6) for women and 159.7 (95% CI 158.7–160.6) for men (female:male ratio 2.8). The estimated 2010 prevalence of MS was highest in the 55- to 64-year age group. A US north-south decreasing prevalence gradient was identified. The estimated MS prevalence is also presented for 2017. Conclusion: The estimated US national MS prevalence for 2010 is the highest reported to date and provides evidence that the north-south gradient persists. Our rigorous algorithm-based approach to estimating prevalence is efficient and has the potential to be used for other chronic neurologic conditions. Prev of MS in the US-E-Appendix-Feb-19-2018

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    DANS-EASY
    Dataset . 2019
    Data sources: B2FIND
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    ZENODO; NARCIS; DRYAD
    Dataset . 2019
    License: CC 0
    Borealis
    Dataset . 2021
    Data sources: Datacite
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      DANS-EASY
      Dataset . 2019
      Data sources: B2FIND
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      ZENODO; NARCIS; DRYAD
      Dataset . 2019
      License: CC 0
      Borealis
      Dataset . 2021
      Data sources: Datacite
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    Authors: Williams, Rebecca J.; Tse, Tony; DiPiazza, Katelyn; Zarin, Deborah A.;

    Background: Clinical trials that end prematurely (or “terminate”) raise financial, ethical, and scientific concerns. The extent to which the results of such trials are disseminated and the reasons for termination have not been well characterized. Methods and Findings: A cross-sectional, descriptive study of terminated clinical trials posted on the ClinicalTrials.gov results database as of February 2013 was conducted. The main outcomes were to characterize the availability of primary outcome data on ClinicalTrials.gov and in the published literature and to identify the reasons for trial termination. Approximately 12% of trials with results posted on the ClinicalTrials.gov results database (905/7,646) were terminated. Most trials were terminated for reasons other than accumulated data from the trial (68%; 619/905), with an insufficient rate of accrual being the lead reason for termination among these trials (57%; 350/619). Of the remaining trials, 21% (193/905) were terminated based on data from the trial (findings of efficacy or toxicity) and 10% (93/905) did not specify a reason. Overall, data for a primary outcome measure were available on ClinicalTrials.gov and in the published literature for 72% (648/905) and 22% (198/905) of trials, respectively. Primary outcome data were reported on the ClinicalTrials.gov results database and in the published literature more frequently (91% and 46%, respectively) when the decision to terminate was based on data from the trial. Conclusions: Trials terminate for a variety of reasons, not all of which reflect failures in the process or an inability to achieve the intended goals. Primary outcome data were reported most often when termination was based on data from the trial. Further research is needed to identify best practices for disseminating the experience and data resulting from terminated trials in order to help ensure maximal societal benefit from the investments of trial participants and others involved with the study. DATA_Terminated Trials in ClinicalTrialsgov Results Database (19 Feb 2013)CSV data file containing data retrieved from the ClinicalTrials.gov registry and results database on February 19, 2013. Additional details are available in the ReadMe file.

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    DANS-EASY
    Dataset . 2015
    Data sources: B2FIND
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    DRYAD; ZENODO; NARCIS
    Dataset . 2015
    License: CC 0
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      DANS-EASY
      Dataset . 2015
      Data sources: B2FIND
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      DRYAD; ZENODO; NARCIS
      Dataset . 2015
      License: CC 0
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    Authors: Rashid, Asim J.; Yan, Chen; Mercaldo, Valentina; Hsiang, Hwa-Lin; +9 Authors

    Collections of cells called engrams are thought to represent memories. Although there has been progress in identifying and manipulating single engrams, little is known about how multiple engrams interact to influence memory. In lateral amygdala (LA), neurons with increased excitability during training outcompete their neighbors for allocation to an engram. We examined whether competition based on neuronal excitability also governs the interaction between engrams. Mice received two distinct fear conditioning events separated by different intervals. LA neuron excitability was optogenetically manipulated and revealed a transient competitive process that integrates memories for events occurring closely in time (coallocating overlapping populations of neurons to both engrams) and separates memories for events occurring at distal times (disallocating nonoverlapping populations to each engram). Rashid et al Science 2016- Data for Figs 1-4, S1-S9Excel file with all data presented in manuscript (each sheet corresponds to specific figures as indicated).Rashid et al Science 2016.xlsx

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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: Mielke, Alexander; Preis, Anna; Samuni, Liran; Gogarten, Jan; +2 Authors

    Living in permanent social groups forces animals to make decisions about when, how and with whom to interact, requiring decisions to be made that integrate multiple sources of information. Changing social environments can influence this decision-making process by constraining choice or altering the likelihood of a positive outcome. Here, we conceptualised grooming as a choice situation where an individual chooses one of a number of potential partners. Studying two wild populations of sympatric primate species, sooty mangabeys (Cercocebus atys atys) and Western chimpanzees (Pan troglodytes verus), we tested what properties of potential partners influenced grooming decisions, including their relative value based on available alternatives and the social relationships of potential partners with bystanders who could observe the outcome of the decision. Across 1,529 decision events, multiple partner attributes (e.g. dominance ranks, social relationship quality, reproductive state, partner sex) influenced choice. Individuals preferred to initiate grooming with partners of similar global rank, but this effect was driven by a bias towards partners with a high rank compared to other locally available options. Individuals also avoided grooming partners who had strong social relationships with at least one bystander. Results indicated flexible decision-making in grooming interactions in both species, based on a partner’s value given the local social environment. Viewing partner choice as a value-based decision-making process allows researchers to compare how different species solve similar social problems. Data Model1Data for Models 1-1 and 1-2Data Model2Data for Models 2-1 and 2-2Script Model 1 and 2Scripts necessary to analyse Models 1 and 2

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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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      Dataset . 2018
      Data sources: B2FIND
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      Dataset . 2018
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    Authors: Urbanus, Malene L.; Quaile, Andrew T.; Stogios, Peter J.; Morar, Mariya; +13 Authors

    Query strain identities and corresponding screening set.In order to obtain an IDTS-wide genetic interaction map, we modified the automated, high-density replica plating approaches previously developed for analyzing S. cerevisiae double mutants through Synthetic Genetic Array (SGA) analysis (Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368). Instead of looking at double mutants, however, we used yeast genetics to systematically assess the effects of Legionella effector co-expression on yeast growth. Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/) (Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L (2013) SGAtools: One-stop analysis and visualization of array-based genetic interaction screens. Nucleic acids research 41: W591-596). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This spreadsheet lists all query strains and links them to one or more specific analysis set.Array_set_annotation.xlsSGA output for analysis sets 1-10.Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 1-10.UrbanusMSB_SGA.zipUrbanus_SGA_1-10.zipSGA output for analysis sets 11-20.Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 11-20.Urbanus_SGA_11-20.zipSGA output for analysis sets 21-30.Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 21-30.Urbanus_SGA_21-30.zipSGA output for analysis sets 31-37.Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 31-37.Urbanus_SGA_31-37.zip Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional interaction. We used Saccharomyces cerevisiae, an established proxy for the eukaryotic host, to query > 108,000 pairwise genetic interactions between two compatible expression libraries of ~330 L. pneumophila‐translocated substrates. While capturing all known examples of effector–effector suppression, we identify fourteen novel translocated substrates that suppress the activity of other bacterial effectors and one pair with synergistic activities. In at least nine instances, this regulation is direct—a hallmark of an emerging class of proteins called metaeffectors, or “effectors of effectors”. Through detailed structural and functional analysis, we show that metaeffector activity derives from a diverse range of mechanisms, shapes evolution, and can be used to reveal important aspects of each cognate effector's function. Metaeffectors, along with other, indirect, forms of effector–effector modulation, may be a common feature of many intracellular pathogens—with unrealized potential to inform our understanding of how pathogens regulate their interactions with the host cell.

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    Dataset . 2016
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      Dataset . 2016
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    Authors: Leger, Michelle M.; Kolisko, Martin; Kamikawa, Ryoma; Stairs, Courtney W.; +13 Authors

    Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed. Here, we present a large-scale comparative transcriptomic study of MROs across a major eukaryotic group, Metamonada, examining lineage-specific gain and loss of metabolic functions in the MROs of Trichomonas, Giardia, Spironucleus and their free-living relatives. Our analyses uncover a complex history of ATP production machinery in diplomonads such as Giardia, and their closest relative, Dysnectes; and a correlation between the glycine cleavage machinery and lifestyles. Our data further suggest the existence of a previously undescribed biochemical class of MRO that generates hydrogen but is incapable of ATP synthesis. Protein alignmentsAlignments of organellar proteinsmito_alignments.zipPhylogenomic datasetSingle gene alignments used for phylogenomic analysisPhylogenomic.zipData SourcesFasta files with assembled transcriptomes of Carpediemonas-like organismsAssemblies.zip

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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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      Dataset . 2017
      Data sources: B2FIND
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    Authors: Zaremba, Jeffrey D.; Diamantopoulou, Anastasia; Danielson, Nathan B.; Grosmark, Andres D.; +6 Authors

    Behavior dataData recorded during mouse in vivo imaging and behavior sessions. Data saved as Python pickle files containing a dictionary of arrays of timestamped mouse behavior recordings and stimulus presentaitons. Data includes licking activity, treadmill position, and contextual stimuli presentation times. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.behavior.zipExperiment metadataExperiment metadata xml files containing a record of experimental parameters and links the locations of imaging and behavior data for a given experiment. Data recorded during mouse in vivo imaging and behavior sessions. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.metadata.zipPlace cell enrichment model dataContains place cell data recorded during in vivo calcium imaging sessions of our goal-oriented learning task, as well as enrichment model parameters fit to the data, and saved simulations of the place cell enrichment model. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.enrichment_model.zipImaging Data - Part 1Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.001Imaging Data - Part 2Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.002Imaging Data - Part 3Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.003Imaging Data - Part 4Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.004Imaging Data - Part 5Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.005Imaging Data - Part 6Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.006Imaging Data - Part 7Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.007Imaging Data - Part 8Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.008Imaging Data - Part 9Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.009Imaging Data - Part 10Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.010Imaging Data - Part 11Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.011Imaging Data - Part 12Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.012Imaging Data - Part 13Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.013Imaging Data - Part 14Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.014Imaging Data - Part 15Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.015Imaging Data - Part 16Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.imaging.zip.016 Hippocampal place cells represent the cellular substrate of episodic memory. Place cell ensembles reorganize to support learning but must also maintain stable representations to facilitate memory recall. Despite extensive research, the learning-related role of place cell dynamics in health and disease remains elusive. Using chronic two-photon Ca2+ imaging in hippocampal area CA1 of wild-type and Df(16)A+/− mice, an animal model of 22q11.2 deletion syndrome, one of the most common genetic risk factors for cognitive dysfunction and schizophrenia, we found that goal-oriented learning in wild-type mice was supported by stable spatial maps and robust remapping of place fields toward the goal location. Df(16)A+/− mice showed a significant learning deficit accompanied by reduced spatial map stability and the absence of goal-directed place cell reorganization. These results expand our understanding of the hippocampal ensemble dynamics supporting cognitive flexibility and demonstrate their importance in a model of 22q11.2-associated cognitive dysfunction.

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    Dataset . 2017
    Data sources: B2FIND
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    NARCIS; DRYAD; ZENODO
    Dataset . 2018
    License: CC 0
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      Dataset . 2017
      Data sources: B2FIND
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      NARCIS; DRYAD; ZENODO
      Dataset . 2018
      License: CC 0
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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: Bernhardt, Boris C.; Fadaie, Fatemeh; Liu, Min; Caldairou, Benoit; +6 Authors

    OBJECTIVE. To assess whether HS severity is mirrored at the level of large-scale networks. METHODS. We studied preoperative high-resolution anatomical and diffusion-weighted MRI of 44 TLE patients with histopathological diagnosis of HS (n=25; TLE-HS) and isolated gliosis (n=19; TLE-G), and 25 healthy controls. Hippocampal measurements included surface-based subfield mapping of atrophy and T2 hyperintensity indexing cell loss and gliosis, respectively. Whole-brain connectomes were generated via diffusion tractography and examined using graph theory along with a novel network control theory paradigm which simulates functional dynamics from structural network data. RESULTS. Compared to controls, we observed markedly increased path length and decreased clustering in TLE-HS compared to controls, indicating lower global and local network efficiency, while TLE-G showed only subtle alterations. Similarly, network controllability was lower in TLE-HS only, suggesting limited range of functional dynamics. Hippocampal imaging markers were positively associated with macroscale network alterations, particularly in ipsilateral CA1-3. Systematic assessment across several networks revealed maximal changes in the hippocampal circuity. Findings were consistent when correcting for cortical thickness, suggesting independence from grey matter atrophy. CONCLUSIONS. Severe HS is associated with marked remodeling of connectome topology and structurally-governed functional dynamics in TLE, as opposed to isolated gliosis which has negligible effects. Cell loss, particularly in CA1-3, may exert a cascading effect on brain-wide connectomes, underlining coupled disease processes across multiple scales. Data_phen_conn_dryadPhenotypic information and mean connectome feature data for Bernhardt et al. (2019) Temporal lobe epilepsy: hippocampal pathology modulates white matter connectome topology and controllability. Neurology

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    DANS-EASY
    Dataset . 2019
    Data sources: B2FIND
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    ZENODO; NARCIS; DRYAD
    Dataset . 2019
    License: CC 0
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      DANS-EASY
      Dataset . 2019
      Data sources: B2FIND
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      ZENODO; NARCIS; DRYAD
      Dataset . 2019
      License: CC 0
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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: Campitelli, Laura F.; Yellan, Isaac; Albu, Mihai; Barazandeh, Marjan; +3 Authors

    Web Supplementary Files Web Supplementary File 1 - FASTA files containing full-length reconstruction input sequences: full_length_reconstruction_input_sequence_fastas.zip Web Supplementary File 2 - FASTA files containing Muscle alignments of the full-length reconstruction input sequences. full_length_reconstruction_input_sequence_alns.zip Web Supplementary File 3 - FASTA file of full-length reconstructed sequences: full_length_reconstructions.fa Web Supplementary File 4 - Table of full-length reconstruction statistics: full_length_reconstruction_stats.csv Web Supplementary File 5 - FASTA files containing ORF reconstruction input sequences: orf_fastas.zip Web Supplementary File 6 - FASTA files containing Macse alignments of the ORF reconstruction input sequences: ORF_reconstruction_input_sequence_alns.zip Web Supplementary File 7 - Table of ORF reconstruction statistics: ORF_reconstructions.fa Web Supplementary File 8 - Table of ORF reconstruction statistics: ORF_reconstruction_stats.csv Web Supplementary File 9 - Table of Composite Sequences: bestfl_selection_fixed_CS_seqs.csv Web Supplementary File 10 - Database of gold standards: L1_goldstandards.csv Data Underlying Figures RepeatMasker scans of hg38 and ancestral genomes: anc_gen_RM_out_files.zip Figure 4 4A Source alignment of 54 composite sequences: 220121_dropped12+L1ME3A_muscle.nt.afa Tree produced using the alignment and FastTree: 220121_dropped12+L1ME3A.tree 4B Source alignment of 67 Dfam L1 subfamily 3’ end models: 200123_dfam_3ends.fa.muscle.aln Tree produced using the alignment: 200123_dfam_3ends.fa.muscle.aln.tree Figure 5 KZFP-TE enrichment p-values (from Barazandeh et al 2018): TE_KZFP_enrichment_pvals.xlsx KZFP-TE top 500 peak overlap (from Barazandeh et al 2018): top500_peak_overlap.xlsx Figure 6 RepeatMasker .out file for the Composite Sequence custom library queried against hg38: CS_RM_hg38.fa.out.gz Figure S2 RepeatMasker scan .out file of hg38 (CG corrected Kimura Divergence values are in last column): hg38+KimDiv_RM.out RepeatMasker scan .out file of the Progressive Cactus eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Progressive_Cactus_Euth+KimDiv_RM.out RepeatMasker scan .out file of the Ancestors 1.1 eutherian ancestral genome (CG corrected Kimura Divergence values are in last column): Ancestors_Euth+KimDiv_RM.out Figure S5 RepeatMasker scan .out files for Progressive Cactus simian and primate reconstructed ancestral genomes: progCactus_RM_outfiles.zip S5A FASTA files containing Cactus genome-derived reconstructed sequences equivalent to the L1MA2, L1MA4, and L1MD1-3 best full-length sequences: progCactus_reconstruction_bestFL_equivalents.zip S5B FASTA files containing Muscle alignments of Cactus genome-derived full-length reconstruction input sequences: progCactus_reconstruction_input_sequence_alns.zip Figure S6 S6A Results of Conserved Domain scans of Cactus genome-derived full-length reconstructed sequences: CD_search_results_short_nms.txt S6B-D Character posterior probabilities of “best” full-length reconstructed sequences: best_fl_post_probs.zip Figure S7 S7B-C Results of Conserved Domain scans of translated initial full-length reconstructed sequences: initial_recons_all_3frametrans_CD-search.txt Results of Conserved Domain scans of translated reconstructed ORFs: recons_ORF1-2_all_3frametrans_CD-search.csv Figure S15 S15A Source alignment of 67 composite sequences: bestfl_selection_fixed_CS_seqs_muscle.nt.afa Tree produced using the alignment: bestfl_selection_fixed_CS_seqs_muscle.nt.afa.tree S15B-E Source Muscle alignments for phylogenetic trees of reconstructed sequence components: ORF2: ORF2_keep54_muscle.nt.afa 5’ UTR: 5utr_keep54_muscle.nt.afa ORF1: ORF1_keep54_muscle.nt.afa 3’ UTR: 3utr_keep54_muscle.nt.afa Trees produced using above alignments: ORF2: ORF2_keep54_muscle.nt.afa.tree 5’ UTR: 5utr_keep54_muscle.nt.afa.tree ORF1: ORF1_keep54_muscle.nt.afa.tree 3’ UTR: 3utr_keep54_muscle.nt.afa.tree Figure S17 Unfiltered BLAST results of Composite Sequences queried against hg38: CS_hg38_blastn.csv.zip BED file of L1 instances annotated using BLAST pipeline: BLAST_L1_hits.bed

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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Dataset . 2022
      License: CC BY
      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: 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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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2014
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