cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf4f363
title: Data from: A causal role for the precuneus in network-wide theta and gamma oscillatory activity during complex memory retrieval

description: Complex memory of personal events is thought to depend on coordinated
 reinstatement of cortical representations by the medial temporal lobes
 (MTL). MTL-cortical theta and gamma coupling is believed to mediate such
 coordination, but which cortical structures are critical for retrieval and
 how they influence oscillatory coupling is unclear. We used
 magnetoencephalography (MEG) combined with continuous theta burst
 stimulation (cTBS) to (i) clarify the roles of theta and gamma
 oscillations in network-wide communication during naturalistic memory
 retrieval, and (ii) understand the causal relationship between cortical
 network nodes and oscillatory communication. Retrieval was associated with
 MTL-posterior neocortical theta phase coupling and theta-gamma
 phase-amplitude coupling relative to a rest period. Precuneus cTBS altered
 MTL-neocortical communication by modulating theta and gamma oscillatory
 coupling. These findings provide a mechanistic account for MTL-cortical
 com munication and demonstrate that the precuneus is a critical cortical
 node of oscillatory activity, coordinating cross-regional interactions
 that drive remembering.
description: ScriptsPhase coupling and phase-amplitude coupling scripts7405_dataPreprocessed MEG datasets and anatomical data7405.rar8007_dataPreprocessed MEG datasets and anatomical data8007.rar8395_dataPreprocessed MEG datasets and anatomical data8395.rar9193_dataPreprocessed MEG datasets and anatomical data9193.rar10615_dataPreprocessed MEG datasets and anatomical data10615.rar11130_dataPreprocessed MEG datasets and anatomical data11130.rar11480_dataPreprocessed MEG datasets and anatomical data11480.rar11674_dataPreprocessed MEG datasets and anatomical data11674.rar12084_dataPreprocessed MEG datasets and anatomical data12084.rar12546_dataPreprocessed MEG datasets and anatomical data12546.rar12590_dataPreprocessed MEG datasets and anatomical data12590.rar12728_dataPreprocessed MEG datasets and anatomical data12728.rar12750_dataPreprocessed MEG datasets and anatomical data12750.rar13112_dataPreprocessed MEG datasets and anatomical data13112.rar13863_dataPreprocessed MEG datasets and anatomical data13863.rar13907_dataPreprocessed MEG datasets and anatomical data13907.rar13910_dataPreprocessed MEG datasets and anatomical data13910.rar13999_dataPreprocessed MEG datasets and anatomical data13999.rar14005_dataPreprocessed MEG datasets and anatomical data14005.rar14134_dataPreprocessed MEG datasets and anatomical data14134.rar14744_dataPreprocessed MEG datasets and anatomical data14744.rar14771_dataPreprocessed MEG datasets and anatomical data14771.rar14851_dataPreprocessed MEG datasets and anatomical data14851.rarREADME
DOI: 10.5061/dryad.v9f16
title: Data from: Large-scale functional networks identified from resting-state EEG using spatial ICA

description: Several methods have been applied to EEG or MEG signals to detect
 functional networks. In recent works using MEG/EEG and fMRI data, temporal
 ICA analysis has been used to extract spatial maps of resting-state
 networks with or without an atlas-based parcellation of the cortex. Since
 the links between the fMRI signal and the electromagnetic signals are not
 fully established, and to avoid any bias, we examined whether EEG alone
 was able to derive the spatial distribution and temporal characteristics
 of functional networks. To do so, we propose a two-step original method:
 1) An individual multi-frequency data analysis including EEG-based source
 localisation and spatial independent component analysis, which allowed us
 to characterize the resting-state networks. 2) A group-level analysis
 involving a hierarchical clustering procedure to identify reproducible
 large-scale networks across the population. Compared with large-scale
 resting-state networks obtained with fMRI, the proposed EEG-based analysis
 revealed smaller independent networks thanks to the high temporal
 resolution of EEG, hence hierarchical organization of networks. The
 comparison showed a substantial overlap between EEG and fMRI networks in
 motor, premotor, sensory, frontal, and parietal areas. However, there were
 mismatches between EEG-based and fMRI-based networks in temporal areas,
 presumably resulting from a poor sensitivity of fMRI in these regions or
 artefacts in the EEG signals. The proposed method opens the way for
 studying the high temporal dynamics of networks at the source level thanks
 to the high temporal resolution of EEG. It would then become possible to
 study detailed measures of the dynamics of connectivity.
description: EEG resting state
 dataData used in paper
 "Large-scale Functional Networks Indentified from Resting-state EEG
 Using Spatial ICA" data_EEG: raw data on 64 electrodes - 1 run per
 subject - the last 300 seconds were used in this paper - (BrainAmps
 system) xxx.eeg &gt;&gt;&gt; EEG binary xxx.vhdr &gt;&gt;&gt; EEG header
 xxx.vrmk &gt;&gt;&gt; EEG markers polhemus.pol &gt;&gt;&gt; polhemus file
 - electrodes localizationdata_PONE-D-15-33632.tgz
DOI: 10.35079/hbm532.mlpc.335
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.35079/hbm437.trhx.348
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.5mr8v1v
title: Data from: Debugging diversity – a pan‐continental exploration of the potential of terrestrial blood‐feeding leeches as a vertebrate monitoring tool

description: The use of environmental DNA (eDNA) has become an applicable non-invasive
 tool with which to obtain information about biodiversity. A sub-discipline
 of eDNA is iDNA (invertebrate-derived DNA), where genetic material
 ingested by invertebrates is used to characterise the biodiversity of the
 species that served as hosts. While promising, these techniques are still
 in their infancy, as they have only been explored on limited numbers of
 samples from only a single or a few different locations. In this study, we
 investigate the suitability of iDNA extracted from more than 3,000
 haematophagous terrestrial leeches as a tool for detecting a wide range of
 terrestrial vertebrates across five different geographical regions on
 three different continents. These regions cover almost the full
 geographical range of haematophagous terrestrial leeches, thus
 representing all parts of the world where this method might apply. We
 identify host taxa through metabarcoding coupled with high-throughput
 sequencing on Illumina and IonTorrent sequencing platforms to decrease
 economic costs and workload and thereby make the approach attractive for
 practitioners in conservation management. We identified hosts in four
 different taxonomic vertebrate classes: mammals, birds, reptiles, and
 amphibians, belonging to at least 42 different taxonomic families. We find
 that vertebrate blood ingested by haematophagous terrestrial leeches
 throughout their distribution is a viable source of DNA with which to
 examine a wide range of vertebrates. Thus, this study provides encouraging
 support for the potential of haematophagous terrestrial leeches as a tool
 for detecting and monitoring terrestrial vertebrate biodiversity.
description: Australia_PSinfo_12sAustralia_PSinfo_16sAustralia_TagsPeninsularMalaysia_PSinfoAsiaMadagascar_Tags_16sLaosVietnamDS1_PSinfoLaosVietnamDS1_Pool1_merged.fastqLaosVietnamDS1_Pool2_mergedLaosVietnamDS1_Pool3_mergedLaosVietnamDS1_Pool4_mergedLaosVietnamDS1_Pool5_mergedLaosVietnamDS1_Pool6_mergedLaosVietnamDS1_Pool7_mergedLaosVietnamDS1_Pool8_mergedLaosVietnamDS1_Pool9_mergedLaosVietnamDS1_Pool10_mergedLaosVietnamDS1_Pool11_mergedLaosVietnamDS1_Pool12_mergedLaosVietnamDS2_mergedLaosVietnamDS2_PSinfoMadagascar_Pool1_mergedMadagascar_Pool2_mergedMadagascar_Pool3_mergedMadagascar_Pool4_mergedMadagascar_PSinfoMalaysianBorneoDS1_Pool1_mergedMalaysianBorneoDS1_Pool2_mergedMalaysianBorneoDS1_PSinfoMalaysianBorneoDS2_Pool1_mergedMalaysianBorneoDS2_Pool2_mergedMalaysianBorneoDS2_PSinfoPeninsularMalaysia_mergedAustralia_Pool1_mergedAustralia_Pool2_mergedAustralia_Pool3_merged
DOI: 10.57830/2316691
title: 2025 Estuarine Nutrient Enrichment Tier-2 Seagrass Monitoring Data Package

description: Residential, agricultural, and urban expansion in the Northeast has resulted in an increase in anthropogenic nutrient loading to the region’s coastal zone. Estuaries can generally assimilate some degree of enrichment without major ecological ramifications, but excessive nutrient inputs typically lead to dense blooms of phytoplankton and fast-growing macroalgae and loss of seagrasses. Protecting the ecological integrity of park estuaries depends on implementing a scientifically-based monitoring program that is capable of diagnosing local causes of nutrient enrichment, detecting changes in nutrient loads, and determining if nutrient inputs are near to exceeding thresholds that would result in shifts in ecosystem structure and function. The current database includes data from NCBN's Tier 2 seagrass sampling protocol for 2006 to 2025 at Cape Cod National Seashore and Fire Island National Seashore.
DOI: 10.5061/dryad.jp917
title: Data from: Building the graph of medicine from millions of clinical narratives

description: Electronic health records (EHR) represent a rich and relatively untapped
 resource for characterizing the true nature of clinical practice and for
 quantifying the degree of inter-relatedness of medical entities such as
 drugs, diseases, procedures and devices. We provide a unique set of
 co-occurrence matrices, quantifying the pairwise mentions of 3 million
 terms mapped onto 1 million clinical concepts, calculated from the raw
 text of 20 million clinical notes spanning 19 years of data.
 Co-frequencies were computed by means of a parallelized annotation,
 hashing, and counting pipeline that was applied over clinical notes from
 Stanford Hospitals and Clinics. The co-occurrence matrix quantifies the
 relatedness among medical concepts which can serve as the basis for many
 statistical tests, and can be used to directly compute Bayesian
 conditional probabilities, association rules, as well as a range of test
 statistics such as relative risks and odds ratios. This dataset can be
 leveraged to quantitatively assess comorbidity, drug-drug, and
 drug-disease patterns for a range of clinical, epidemiological, and
 financial applications.
description: 1_Cofrequency_Counts.tar.gzSee ReadMe.txt2_Singleton_Frequency_Counts.tar.gzSee ReadMe.txt provided with "1_Cofrequency_Counts.tar.gz"3_ID_Mappings.tar.gzSee ReadMe.txt provided with "1_Cofrequency_Counts.tar.gz"4_Scripts.tar.gzSee ReadMe.txt provided with "1_Cofrequency_Counts.tar.gz"
DOI: 10.35079/hbm945.gdlq.497
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.35079/hbm976.gpfk.798
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.ss6c9
title: Data from: RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

description: Molecular ecologists seek to genotype hundreds to thousands of loci from
 hundreds to thousands of individuals at minimal cost per sample. Current
 methods, such as restriction site associated DNA sequencing (RADseq) and
 sequence capture, are constrained by costs associated with inefficient use
 of sequencing data and sample preparation. Here, we introduce RADcap, an
 approach that combines the major benefits of RADseq (low cost with
 specific start positions) with those of sequence capture (repeatable
 sequencing of specific loci) to significantly increase efficiency and
 reduce costs relative to current approaches. RADcap uses a new version of
 dual-digest RADseq (3RAD) to identify candidate SNP loci for capture bait
 design, and subsequently uses custom sequence capture baits to
 consistently enrich candidate SNP loci across many individuals. We
 combined this approach with a new library preparation method for
 identifying and removing PCR duplicates from 3RAD libraries, which allows
 researchers to process RADseq data using traditional pipelines, and we
 tested the RADcap method by genotyping sets of 96 to 384 Wisteria plants.
 Our results demonstrate that our RADcap method: (1) methodologically
 reduces (to &lt;5%) and allows computational removal of PCR duplicate
 reads from data; (2) achieves 80-90% reads-on-target in 11 of 12
 enrichments; (3) returns consistent coverage (≥4x) across &gt;90% of
 individuals at up to 99.8% of the targeted loci; (4) produces consistently
 high occupancy matrices of genotypes across hundreds of individuals; and
 (5) costs significantly less than current approaches.
description: RADcap_optimized_Plate5,
 read 2RADcap_optimized_Plate5.2.fq.gzRADcap_optimized_Plate5, Read 1RADcap_optimized_Plate5.1.fq.gzRADcap_Low_Template_Plate1, Read 2RADcap_Low_Template_Plate1.2.fq.gzRADcap_Low_Template_Plate1, Read 1RADcap_Low_Template_Plate1.1.fq.gzRADcap_5cycle_Plate4, Read 2RADcap_5cycle_Plate4.2.fq.gzRADcap_5cycle_Plate4, Read 1RADcap_5cycle_Plate4.1.fq.gzRADcap_5cycle_Plate3, Read 2RADcap_5cycle_Plate3.2.fq.gzRADcap_5cycle_Plate3, Read 1RADcap_5cycle_Plate3.1.fq.gzRADcap_5cycle_Plate2, Read 2RADcap_5cycle_Plate2.2.fq.gzRADcap_5cycle_Plate2, Read 1RADcap_5cycle_Plate2.1.fq.gzRADcap_5cycle_Plate1, Read 2RADcap_5cycle_Plate1.2.fq.gzRADcap_1cycle_Plate1, Read 1RADcap_1cycle_Plate1.1.fq.gz3RAD_SizeSelect_Plate5, Read 13RAD_SizeSelect_Plate5.1.fq.gz3RAD_SizeSelect_Plate5, Read 23RAD_SizeSelect_Plate5.2.fq.gzRADcap_5cycle_Plate1, Read 1RADcap_5cycle_Plate1.1.fq.gzRADcap_1cycle_Plate1, Read 2RADcap_1cycle_Plate1.2.fq.gzRADcap_1cycle_Plate2, Read 1RADcap_1cycle_Plate2.1.fq.gzRADcap_1cycle_Plate2, Read 2RADcap_1cycle_Plate2.2.fq.gzRADcap_1cycle_Plate3, Read 1RADcap_1cycle_Plate3.1.fq.gzRADcap_1cycle_Plate3, Read 2RADcap_1cycle_Plate3.2.fq.gzRADcap_1cycle_Plate4, Read 1RADcap_1cycle_Plate4.1.fq.gzRADcap_1cycle_Plate4, Read 2RADcap_1cycle_Plate4.2.fq.gzPassing and filtered SNP VCF files for all treatmentsPassing_and_filtered_SNP_VCF_files.zip
DOI: 10.5061/dryad.96b0h
title: Data from: Homology-aware phylogenomics at gigabase scales

description: Obstacles to inferring species trees from whole genome data sets range
 from algorithmic and data management challenges to the wholesale
 discordance in evolutionary history found in different parts of a genome.
 Recent work that builds trees directly from genomes by parsing them into
 sets of small k-mer strings holds promise to streamline and simplify these
 efforts, but existing approaches do not account well for gene tree
 discordance. We describe a “seed and extend” protocol that finds nearly
 exact matching sets of orthologous k-mers and extends them to construct
 data sets that can properly account for genomic heterogeneity. Exploiting
 an efficient suffix array data structure, sets of whole genomes can be
 parsed and converted into phylogenetic data matrices rapidly, with
 contiguous blocks of k-mers from the same chromosome, gene, or scaffold
 concatenated as needed. Phylogenetic trees constructed from highly curated
 rice genome data and a diverse set of six other eukaryotic whole genome,
 transcriptome, and organellar genome data sets recovered trees nearly
 identical to published phylogenomic analyses, in a small fraction of the
 time, and requiring many fewer parameter choices. Our method’s ability to
 retain local homology information was demonstrated by using it to
 characterize gene tree discordance across the rice genome, and by its
 robustness to the high rate of interchromosomal gene transfer found in
 several rice species.
description: Supplementary Tables and
 FiguresThis file contains
 Supplementary Table 1 and Supplementary Figures 1-8.SI.SB.pdfData archiveA gzipped tarred archive that contains the raw data, logfiles, supermatrices, etc.that were needed in the paper and its appendix. Please see the README file for details on this (very large) archive.SANDERSON_ETAL_HAKMER_DATA.tar.gz
DOI: 10.35079/hbm547.sscc.469
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.8b83gn8
title: Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host

description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin
 of amphibians, and has caused severe declines and extinctions of
 amphibians globally. In this study, we investigate the interaction between
 Bd and the bacterial skin microbiome of the endangered Sierra Nevada
 yellow-legged frog, Rana sierrae, using both culture-dependent and
 culture-independent methods. Samples were collected from two populations
 of R. sierrae that likely underwent Bd epizootics in the past, but that
 continue to persist with Bd in an enzootic disease state, and we address
 the hypothesis that such “persistent” populations are aided by mutualistic
 skin microbes. Our 16S rRNA metabarcoding data reveal that the skin
 microbiome of highly infected juvenile frogs is characterized by
 significantly reduced species richness and evenness, and by strikingly
 lower variation between individuals, compared to juveniles and adults with
 lower infection levels. Over 90% of DNA sequences from the skin microbiome
 of highly infected frogs were derived from bacteria in a single order,
 Burkholderiales, compared to just 54% in frogs with lower infection
 levels. In a culture-dependent Bd-inhibition assay, the bacterial
 metabolites we evaluated all inhibited the growth of Bd. Together, these
 results illustrate the disruptive effects of Bd infection on host skin
 microbial community structure and dynamics, and suggest possible avenues
 for the development of anti-Bd probiotic treatments.
description: 2018 Ellison Molecular
 Ecology Rana sierrae skin microbiome Illumina sequencesMetabarcoding sequences
 generated using an Illumina MiSeq. Paired-end reads have been joined and
 demultiplexed using QIIME (this file is equivalent to the
 "seqs.fna" file generated by the QIIME script
 "multiple_split_libraries_fastq.py").2018_Ellison_Rsierrae_microbiome_Illumina_sequences.fna2018 Ellison Molecular Ecology Rana sierrae Bd resultsBd results (qPCR) and associated metadata for all Rana sierrae included in the study.2018_Ellison_Rsierrae_Bd_results.csv2018 Ellison Molecular Ecology Rana sierrae microbiome QIIME mapping fileMapping file containing sample metadata for all microbiome samples included in the study. Used to analyze microbial communities in QIIME.2018_Ellison_Rsierrae_microbiome_mapping_file.csv2018 Ellison Molecular Ecology Rana sierrae CFS inhibition trial resultsResults for the cell-free supernatant inhibition trials conducted using bacteria isolated from the skin of Rana sierrae.2018_Ellison_Rsierrae_CFS_inhibition_results.csv2018 Ellison Molecular Ecology Rana sierrae CFS inhibition sequencesFASTA file containing DNA sequences for the bacterial isolates included in the cell-free supernatant inhibition trials.2018_Ellison_Rsierrae_CFS_inhibition_sequences.txt
DOI: 10.35079/hbm822.pdkv.262
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.rd70f
title: Data from: Acquisition of germ plasm accelerates vertebrate evolution.

description: Primordial germ cell (PGC) specification occurs either by induction from
 pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated
 by germ plasm (preformation). Among vertebrates, epigenesis is basal,
 whereas germ plasm has evolved convergently across lineages and is
 associated with greater speciation. We compared protein-coding sequences
 of vertebrate species that employ preformation with their sister taxa that
 use epigenesis and demonstrate that genes evolve more rapidly in species
 containing germ plasm. Furthermore, differences in rates of evolution
 appear to cause phylogenetic incongruence in protein-coding sequence
 comparisons between vertebrate taxa. Our results support the hypothesis
 that germ plasm liberates constraints on somatic development and that
 enhanced evolvability drives the evolution of germ plasm.
description: Scripts for
 AnalysesThis file contains the
 instructions for generating the appropriate mySQL databases and the
 scripts required to process this data and recreate the analyses described
 in Evans et al.Scripts.tar.gzAlignment FilesThis file contains the folder system storing the alignments (*.nex) and Maximum-Likelihood tree files (*_tree.tre) for the sequences presented in Evans et al. Each file is named according to the seq_number information as in the database basic_db.sql (also contained within this DataDryad submission). Each alignment contains only the sequence from the first two codon positions as reported in Evans et. al.Alignment_files.tar.gzmySQL Database including dataThis file contains a mySQL database including all the data used in Evans et al. It is in the same format as the database which can be created using the files available in the Scripts package associated with this datadryad package.basic_db.sql
DOI: 10.35079/hbm439.kzvb.477
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.6s39h64
title: Data from: Selective visual representation of letters and words in the left ventral occipito-temporal cortex with intracerebral recordings

description: We report a comprehensive cartography of selective responses to visual
 letters and words in the human ventral occipito-temporal cortex (VOTC)
 with direct neural recordings, clarifying key aspects of the neural basis
 of reading. Intracerebral recordings were performed in a large group of
 patients (n = 37) presented with visual words inserted periodically in
 rapid sequences of pseudofonts, nonwords, or pseudowords, enabling
 classification of responses at three levels of word processing: letter,
 prelexical, and lexical. While letter selective responses are found in
 much of the VOTC, with a higher proportion in left posterior regions,
 prelexical/lexical responses are confined to the middle and anterior
 sections of the left fusiform gyrus. This region overlaps with and extends
 more anteriorly than the visual word form area typically identified with
 functional magnetic resonance imaging. In this region, prelexical
 responses provide evidence for populations of neurons sensitive to the
 statistical regularity of letter combinations independently of lexical
 responses to familiar words. Despite extensive sampling in anterior
 ventral temporal regions, there is no hierarchical organization between
 prelexical and lexical responses in the left fusiform gyrus. Overall,
 distinct word processing levels depend on neural populations that are
 spatially intermingled rather than organized according to a strict
 posteroanterior hierarchy in the left VOTC.
description: Lochy_et_al_PNAS_2018_P001-P012Data for participants 1 to 12 + read_me file and directory with stimuli used in the experiment.Lochy_et_al_PNAS_2018_P013-P024Data for participants 13 to 24Lochy_et_al_PNAS_2018_P025-P037Dat for participants 25 to 37
DOI: 10.35079/hbm277.qfsz.695
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female