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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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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doi: 10.5061/dryad.s5587
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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pmid: 30457571
pmc: PMC6244184
Alzheimer's disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/.
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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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doi: 10.5061/dryad.v5403
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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doi: 10.5061/dryad.5tp75
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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handle: 11375/21211 , 11375/20839
Canadian Institutes of Health Research and McMaster University's Labarge Optimal Aging Initiative
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Promoting uptake of research findings is an objective common to those who fund, produce and publish health services and policy research. Open access (OA) is one method being employed to maximize impact. OA articles are online, free to access and use. This paper contributes to growing body of research exploring the “OA advantage” by employing an article-level analysis comparing citation rates for articles drawn from the same, purposively selected journals. We used a two-stage analytic approach designed to test whether OA is associated with (1) likelihood that an article is cited at all and (2) total number citations that an article receives, conditional on being cited at least once. Adjusting for potential confounders: number of authors, time since publication, journal, and article subject, we found that OA archived articles were 60% more likely to be cited at least once, and, once cited, were cited 29% more than non-OA articles.
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This paper addresses indicators of the performance of the Vancouver human health biotechnology cluster.
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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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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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doi: 10.5061/dryad.s5587
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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citations | 1 | |
popularity | Average | |
influence | Average | |
impulse | Average |
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pmid: 30457571
pmc: PMC6244184
Alzheimer's disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/.
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citations | 47 | |
popularity | Top 10% | |
influence | Top 10% | |