cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.89v53
title: Data from: Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux

description: We report the sequencing of seven genomes from two haloarchaeal genera,
 Haloferax and Haloarcula. Ease of cultivation and the existence of
 well-developed genetic and biochemical tools for several diverse
 haloarchaeal species make haloarchaea a model group for the study of
 archaeal biology. The unique physiological properties of these organisms
 also make them good candidates for novel enzyme discovery for
 biotechnological applications. Seven genomes were sequenced to
 ~20×coverage and assembled to an average of 50 contigs (range 5 scaffolds
 - 168 contigs). Comparisons of protein-coding gene compliments revealed
 large-scale differences in COG functional group enrichment between these
 genera. Analysis of genes encoding machinery for DNA metabolism reveals
 genera-specific expansions of the general transcription factor TATA
 binding protein as well as a history of extensive duplication and
 horizontal transfer of the proliferating cell nuclear antigen. Insights
 gained from this study emphasize the importance of haloarchaea for
 investigation of archaeal biology.
description: RAST_AnnotationsRAST-generated annotations for all genomes included in the analyses in this manuscript.Raw_sequence_readsFragment libraries were constructed for eight species of the family Halobacteriacea, three from the genus Haloarcula (Har. californiae, Har. sinaiiensis, Har. vallismortis) and five from the genus Haloferax (Hfx. denitrificans, Hfx. mediterranei, Hfx. mucosum, Hfx. sulfurifontis, and Hfx. volcanii), and sequenced on a single GS FLX Titanium run following standard protocols (454 Life Sciences - http://454.com/). Hfx. volcanii was included as a sequencing control, as its genome had been completed previously [19]. Additionally, for Har. sinaiiensis and Hfx. mediterranei, 8 Kb pair-end libraries were constructed and the terminal 100 bp of each end was sequenced, according to standard protocols. The paired-end information and any trimming information are specified using annotation strings on the description line of the reads. Reads were assembled using the Genome Sequencer De Novo assembler (454 Life Sciences - http://www.my454.com/).
DOI: 10.5281/zenodo.18377538
title: Dataset: elasticity-circlehollow-m1

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377539
title: Dataset: elasticity-circlehollow-m1

description: This dataset is part of a collection.
DOI: 10.5061/dryad.f12cg
title: Data from: The replication of Frataxin gene is assured by activation of dormant origins in the presence of a GAA-repeat expansion

description: It is well known that DNA replication affects the stability of several
 trinucleotide repeats, but whether replication profiles of human loci
 carrying an expanded repeat differ from those of normal alleles is poorly
 understood in the endogenous context. We investigated this issue using
 cell lines from Friedreich’s ataxia patients, homozygous for a GAA-repeat
 expansion in intron 1 of the Frataxin gene. By interphase, FISH we found
 that in comparison to the normal Frataxin sequence the replication of
 expanded alleles is slowed or delayed. According to molecular combing,
 origins never fired within the normal Frataxin allele. In contrast, in
 mutant alleles dormant origins are recruited within the gene, causing a
 switch of the prevalent fork direction through the expanded repeat.
 Furthermore, a global modification of the replication profile, involving
 origin choice and a differential distribution of unidirectional forks, was
 observed in the surrounding 850 kb region. These data provide a wide-view
 of the interplay of events occurring during replication of genes carrying
 an expanded repeat.
description: Replication profile of
 Frataxin locus in FRDA GM15850 cellsFRDA_GM15850.zipReplication profile of Frataxin locus in FRDA_GM16227 cellsFRDA_GM16227.zipReplication profile of Frataxin locus in control_GM15851 cellsControl_GM15851.zipReplication profile of Frataxin locus in control_H691 cellsControl_H691.zip
DOI: 10.5281/zenodo.18377675
title: Dataset: elasticity-squarehollow-m1

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377676
title: Dataset: elasticity-squarehollow-m1

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377691
title: Dataset: elasticity-boomcircletri-m1

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377692
title: Dataset: elasticity-boomcircletri-m1

description: This dataset is part of a collection.
DOI: 10.5061/dryad.tv5v1v26
title: Data from: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

description: Haptophytes are a key phylum of marine protists, including ~300 described
 morphospecies and 80 morphogenera. We used 454 pyrosequencing on large
 subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from
 size-fractioned plankton samples collected in the Bay of Naples. One
 group-specific primer set targeting the LSU rDNA D1/D2 region was designed
 to amplify Haptophyte sequences from nucleic acid extracts (total DNA or
 RNA) of two size fractions (0.8–3 or 3–20 μm) and two sampling depths
 [subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads
 were identified using a database covering the entire Haptophyta diversity
 currently sequenced. Our data set revealed several hundreds of Haptophyte
 clusters. However, most of these clusters could not be linked to
 taxonomically known sequences: considering OTUs97% (clusters build at a
 sequence identity level of 97%) on our global data set, less than 1% of
 the reads clustered with sequences from cultures, and less than 12%
 clustered with reference sequences obtained previously from cloning and
 Sanger sequencing of environmental samples. Thus, we highlighted a large
 uncharacterized environmental genetic diversity, which clearly shows that
 currently cultivated species poorly reflect the actual diversity present
 in the natural environment. Haptophyte community appeared to be
 significantly structured according to the depth. The highest diversity and
 evenness were obtained in samples from the DCM, and samples from the large
 size fraction (3–20 μm) taken at the DCM shared a lower proportion of
 common OTUs97% with the other samples. Reads from the species Chrysoculter
 romboideus were notably found at the DCM, while they could be detected at
 the subsurface. The highest proportion of totally unknown OTUs97% was
 collected at the DCM in the smallest size fraction (0.8–3 μm). Overall,
 this study emphasized several technical and theoretical barriers inherent
 to the exploration of the large and largely unknown diversity of
 unicellular eukaryotes.
description: 454
 DatasetFull metagenomic dataset
 for this study, generated by a 454 FLX sequencer. More details on samples
 available in this file are given in the ReadMe.txt
 file.hapto.GS6QRMN04.sff454table_sequencing_HaptoTable describing Multiplex Indexing Barcodes and primers used in the 454 datasetHapto_baseref_LSUReference Haptophyte sequences used in this study.
DOI: 10.5281/zenodo.18377698
title: Dataset: elasticity-circlehollow-m2

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377699
title: Dataset: elasticity-circlehollow-m2

description: This dataset is part of a collection.
DOI: 10.5061/dryad.8kd16
title: Data from: Cranial biomechanics underpins high sauropod diversity in resource-poor environments

description: High megaherbivore species richness is documented in both fossil and
 contemporary ecosystems despite their high individual energy requirements.
 An extreme example of this is the Late Jurassic Morrison Formation, which
 was dominated by sauropod dinosaurs, the largest known terrestrial
 vertebrates. High sauropod diversity within the resource-limited Morrison
 is paradoxical, but might be explicable through sophisticated resource
 partitioning. This hypothesis was tested through finite-element analysis
 of the crania of the Morrison taxa Camarasaurus andDiplodocus. Results
 demonstrate divergent specialization, with Camarasaurus capable of
 exerting and accommodating greater bite forces thanDiplodocus, permitting
 consumption of harder food items. Analysis of craniodental biomechanical
 characters taken from 35 sauropod taxa demonstrates a functional dichotomy
 in terms of bite force, cranial robustness and occlusal relationships
 yielding two polyphyletic functional ‘grades’. Morrison taxa are widely
 distributed within and between these two morphotypes, reflecting
 distinctive foraging specializations that formed a biomechanical basis for
 niche partitioning between them. This partitioning, coupled with benefits
 associated with large body size, would have enabled the high sauropod
 diversities present in the Morrison Formation. Further, this provides
 insight into the mechanisms responsible for supporting the high
 diversities of large megaherbivores observed in other Mesozoic and
 Cenozoic communities, particularly those occurring in resource-limited
 environments.
description: Camarasaurus_skullA surface file of the skull and jaw model of Camarasaurus lentus created for this study
DOI: 10.5281/zenodo.18377705
title: Dataset: elasticity-squarehollow-m2

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377706
title: Dataset: elasticity-squarehollow-m2

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377713
title: Dataset: elasticity-boomcircletri-m2

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377714
title: Dataset: elasticity-boomcircletri-m2

description: This dataset is part of a collection.
DOI: 10.5061/dryad.dn45c
title: Data from: Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias

description: Studies of insect assemblages are suited to the simultaneous DNA-based
 identification of multiple taxa known as metabarcoding. To obtain accurate
 estimates of diversity, metabarcoding markers ideally possess appropriate
 taxonomic coverage to avoid PCR-amplification bias, as well as sufficient
 sequence divergence to resolve species. We used in silico PCR to compare
 the taxonomic coverage and resolution of newly designed insect
 metabarcodes (targeting 16S) with that of existing markers (16S and COI)
 and then compared their efficiency in vitro. Existing metabarcoding
 primers amplified in silico less than 75% of insect species with complete
 mitochondrial genomes available, whereas new primers targeting 16S
 provided greater than 90% coverage. Furthermore, metabarcodes targeting
 COI appeared to introduce taxonomic PCR-amplification bias, typically
 amplifying a greater percentage of Lepidoptera and Diptera species, while
 failing to amplify certain orders in silico. To test whether bias
 predicted in silico was observed in vitro, we created an artificial DNA
 blend containing equal amounts of DNA from 14 species, representing 11
 different insect orders and one arachnid. We PCR-amplified the blend using
 five primers sets, targeting either COI or 16S, with high-throughput
 amplicon sequencing yielding more than 6 million reads. In vitro results
 typically corresponded to in silico PCR predictions, with newly designed
 16S primers detecting 11 insect taxa present, thus providing equivalent or
 better taxonomic coverage than COI metabarcodes. Our results demonstrate
 that in silico PCR is a useful tool for predicting taxonomic bias in mixed
 template PCR, and that researchers should be wary of potential bias when
 selecting metabarcoding markers.
description: Reference_sequencesReference DNA sequences for each taxon in the artificial DNA blend used to test the five metabarcoding markers. Sequences were downloaded from GenBank or generated by Sanger or high-throughput sequencing.Enviro metabarcodes for insects PGM dataIon Torrent PGM sequencing reads (FASTQ format) separated by barcode according to marker and PCR protocol (pub - published protocol, 45 - standardised protocol).Enviro metabarcodes for insects PGM demultiplexed reads.zip
DOI: 10.15468/dl.fj74py
title: Occurrence Download

description: A dataset containing 2877 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Distribution of marine forests based on citizen science"
 ]
}

 The dataset includes 2877 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000365-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8310n
title: Data from: Estimation of inhalation flow profile using audio-based methods to assess inhaler medication adherence

description: Asthma and chronic obstructive pulmonary disease (COPD) patients are
 required to inhale forcefully and deeply to receive medication when using
 a dry powder inhaler (DPI). There is a clinical need to objectively
 monitor the inhalation flow profile of DPIs in order to remotely monitor
 patient inhalation technique. Audio-based methods have been previously
 employed to accurately estimate flow parameters such as the peak
 inspiratory flow rate of inhalations, however, these methods required
 multiple calibration inhalation audio recordings. In this study, an
 audio-based method is presented that accurately estimates inhalation flow
 profile using only one calibration inhalation audio recording. Twenty
 healthy participants were asked to perform 15 inhalations through a
 placebo Ellipta™ DPI at a range of inspiratory flow rates. Inhalation flow
 signals were recorded using a pneumotachograph spirometer while inhalation
 audio signals were recorded simultaneously using the Inhaler Compliance
 Assessment device attached to the inhaler. The acoustic (amplitude)
 envelope was estimated from each inhalation audio signal. Using only one
 recording, linear and power law regression models were employed to
 determine which model best described the relationship between the
 inhalation acoustic envelope and flow signal. Each model was then employed
 to estimate the flow signals of the remaining 14 inhalation audio
 recordings. This process repeated until each of the 15 recordings were
 employed to calibrate single models while testing on the remaining 14
 recordings. It was observed that power law models generated the highest
 average flow estimation accuracy across all participants (90.89±0.9% for
 power law models and 76.63±2.38% for linear models). The method also
 generated sufficient accuracy in estimating inhalation parameters such as
 peak inspiratory flow rate and inspiratory capacity within the presence of
 noise. Estimating inhaler inhalation flow profiles using audio based
 methods may be clinically beneficial for inhaler technique training and
 the remote monitoring of patient adherence.
description: Taylor et al - Inhaler
 inhalation audio and flow dataThe .mat file contains
 data in the form of a 287x4 cell matrix. Each row corresponds to a
 different inhaler inhalation recording. Column 1 contains the anonymized
 participant numbers, Column 2 contains the inspiratory flow range group to
 which each recording belongs to. Details of this labeling is given in the
 manuscript. Column 3 contains the inhalation flow signals and Column 4
 contains the acoustic envelope signals from the inhalation audio
 recordings. Signals are low pass filtered below 4Hz. Moving average filter
 not applied to acoustic envelope signals until after flow
 estimation.TAYLOR_INHALER_AUDIO_FLOW_DATA.mat
DOI: 10.5281/zenodo.18377722
title: Dataset: elasticity-circlehollow-m3

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377723
title: Dataset: elasticity-circlehollow-m3

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377726
title: Dataset: elasticity-squarehollow-m3

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377727
title: Dataset: elasticity-squarehollow-m3

description: This dataset is part of a collection.
DOI: 10.5061/dryad.5j8p8
title: Data from: Inflorescence and flower development in Musa velutina H. Wendl. & Drude (Musaceae), with a consideration of developmental variability, restricted phyllotactic direction, and hand initiation

description: Premise of research. Inflorescence and flower structure in the Musaceae is
 unique in the Zingiberales. The inflorescence lacks the obvious cincinnus
 structure that characterizes the order, and the flowers are unisexual.
 Previous studies were conducted using cultivated varieties and were
 carried out with sectioned material, which does not permit accurate
 developmental descriptions. Developmental study of a wild species with
 modern methods addresses these shortcomings and provides more accurate
 descriptions. Methodology. Young inflorescences and flowers were collected
 from botanical gardens in Hawaii and Australia and critical-point dried
 for observation with a scanning electron microscope. Pivotal results. All
 shoots and inflorescences have sinistrorse (left-handed) phyllotaxy, and
 the sequence of flower initiation is usually correlated with this pattern.
 Initiation begins on the cathodic side of the hand (opposite the direction
 of phyllotactic rise) and progresses anodically (in the direction of
 phyllotactic rise). Within this general pattern, the sequence of flower
 initiation is variable, even within the same inflorescence. Five patterns
 of initiation are reported, with additional variation within each pattern.
 Both male and female flowers have similar early developmental patterns but
 diverge at the time of petal/inner androecial formation. In male flowers
 the anterior side of the flower develops slightly ahead of the posterior,
 while in female flowers the posterior side develops slightly ahead of the
 anterior. While consistently present in the material analyzed here, these
 differences are not apparent at the time of gynoecial initiation or in the
 mature flowers. Conclusions. The banana inflorescence is another example
 of how higher-level phyllotactic patterns can influence the sequence of
 organ initiation at lower levels. Despite variability in the sequence of
 flower initiation in a hand, the best interpretation of the hand remains a
 cincinnus. Variability in inflorescence and floral development is rarely
 reported and may be more common than currently supposed.
description: Musa velutina flower
 development, SEMMusa_velutina_flower_development_SEM.zip
DOI: 10.5281/zenodo.18377756
title: Dataset: elasticity-boomcircletri-m3

description: This dataset is part of a collection.
DOI: 10.5281/zenodo.18377757
title: Dataset: elasticity-boomcircletri-m3

description: This dataset is part of a collection.
DOI: 10.5061/dryad.kt24554
title: Data from: Immune genes are hotspots of shared positive selection across birds and mammals

description: Consistent patterns of positive selection in functionally similar genes
 can suggest a common selective pressure across a group of species. We use
 alignments of orthologous protein-coding genes from 39 species of birds to
 estimate parameters related to positive selection for 11,000 genes
 conserved across birds. We show that functional pathways related to the
 immune system, recombination, lipid metabolism, and phototransduction are
 enriched for positively selected genes. By comparing our results with
 mammalian data, we find a significant enrichment for positively selected
 genes shared between taxa, and that these shared selected genes are
 enriched for viral immune pathways. Using pathogen-challenge transcriptome
 data, we show that genes up-regulated in response to pathogens are also
 enriched for positively selected genes. Together, our results suggest that
 pathogens, particularly viruses, consistently target the same genes across
 divergent clades, and that these genes are hotspots of host-pathogen
 conflict over deep evolutionary time.
description: Alignments used for
 comparative genomicsMultiple species
 alignment for each HOG. NCBI gene IDs for HOGs can be found in
 R_data_and_scripts/02_output_annotated_data/raw_results_sptrees_all_annotations.csv from zipped R_data_and_scripts file.comparative_genomics_hog_alignments.zipR Scripts and Data FilesAll selection scan and differential expression results (PAML results, HyPhy results, Sleuth results), and all scripts for subsequent analyses. There are seven modules that include and R script, directory with any necessary input data, and directory with any output files. The scripts do the following: 1. process all PAML and HyPhy output into analysis-ready formats. 2. Annotate all HOGs with NCBI and Ensembl gene IDs. 3. General dataset statistic calculations 4. Bird KEGG pathway enrichment analyses. 5. Comparisons of bird and mammal selection scan results 6. Clustering and analysis of bird aBS-REL results. 7. Transcriptome analyses for both birds and mammals.R_data_and_scripts.zip
DOI: 10.5061/dryad.ft7dj
title: Data from: Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness

description: The concept of robustness in biology has gained much attention recently,
 but a mechanistic understanding of how genetic networks regulate
 phenotypic variation has remained elusive. One approach to understand the
 genetic architecture of variability has been to analyze dispensable gene
 deletions in model organisms; however, the most important genes cannot be
 deleted. Here, we have utilized two systems in yeast whereby essential
 genes have been altered to reduce expression. Using high‐throughput
 microscopy and image analysis, we have characterized a large number of
 morphological phenotypes, and their associated variation, for the majority
 of essential genes in yeast. Our results indicate that phenotypic
 robustness is more highly dependent upon the expression of essential genes
 than on the presence of dispensable genes. Morphological robustness
 appears to be a general property of a genotype that is closely related to
 pleiotropy. While the fitness profile across a range of expression levels
 is idiosyncratic to each gene, the global pattern indicates that there is
 a window in which phenotypic variation can be released before fitness
 effects are observable.
description: CalMorph.pooled.raw.data.RfileThis file contains an R object summarizing all data collected in this study.
DOI: 10.5061/dryad.d0779mb
title: Data from: Visualization of currents in neural models with similar behavior and different conductance densities

description: Conductance-based models of neural activity produce large amounts of data
 that can be hard to visualize and interpret. We introduce visualization
 methods to display the dynamics of the ionic currents and to display the
 models' response to perturbations. To visualize the currents'
 dynamics we compute the percent contribution of each current and display
 them over time using stacked-area plots. The waveform of the membrane
 potential and the contribution of each current change as the models are
 perturbed. To represent these changes over a range of the perturbation
 control parameter, we compute and display the distributions of these
 waveforms. We illustrate these procedures in six examples of bursting
 model neurons with similar activity but that differ as much as 3-fold in
 their conductance densities. These visualization methods provide heuristic
 insight into why individual neurons or networks with similar behavior can
 respond widely differently to perturbations.
description: Alonso_and_Marder_visualization_code_and_numerical_dataThere are 4 folders in the zip file. Each folder has an independent set of scripts that are useful to (a) reproduce the exact figures in the manuscript (b) wrap in other projects. See README file for specifics.