cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pv40d2r
title: Data from: A dataset of egg size and shape from more than 6,700 insect species

description: Offspring size is a fundamental trait in disparate biological fields of
 study. This trait can be measured as the size of plant seeds, animal eggs,
 or live young, and it influences ecological interactions, organism
 fitness, maternal investment, and embryonic development. Although multiple
 evolutionary processes have been predicted to drive the evolution of
 offspring size, the phylogenetic distribution of this trait remains poorly
 understood, due to the difficulty of reliably collecting and comparing
 offspring size data from many species. Here we present a database of
 10,449 morphological descriptions of insect eggs, with records for 6,706
 unique insect species and representatives from every extant hexapod order.
 The dataset includes eggs whose volumes span more than eight orders of
 magnitude. We created this database by partially automating the extraction
 of egg traits from the primary literature. In the process, we overcame
 challenges associated with large-scale phenotyping by designing and
 employing custom bioinformatic solutions to common problems. We matched
 the taxa in this database to the currently accepted scientific names in
 taxonomic and genetic databases, which will facilitate the use of this
 data for testing the pressing evolutionary hypotheses in offspring size
 evolution.
description: Egg
 DatasetA tab delimited dataset
 of insect egg shape and size from the published literature, including
 additional variables (e.g. volume, aspect ratio) calculated from data in
 egg_dataset_raw_values.tsv. See publication methods for details on how
 final values were calculated.egg_dataset.tsvEgg Dataset (Raw Values)A tab delimited dataset of insect egg shape and size from the published literature, reporting the values as recorded (e.g. original published taxonomic name, text description of maximum and minimum egg length). See publication for details and on how data was collected.egg_dataset_raw_values.tsvBibliography Egg Dataset (BibTeX format)A bibtex file of sources cited in the egg dataset. References listed here can be matched to entries in the egg dataset by their unique bibliographic identifier (e.g. Iwata1958).bibliography_egg_dataset.bibBibliography Egg Dataset (PDF format)A formatted bibliography of sources cited in the egg dataset.bibliography_egg_dataset.pdf
DOI: 10.5061/dryad.1f62752
title: Data from: Stem-group fossils of Symphrasinae shed light on early evolution of Mantispidae (Insecta, Neuroptera)

description: New genera and species mantid lacewings of Symphrasinae (Neuroptera,
 Mantispidae), Archaeosymphrasis pennyi gen. et sp. nov. and
 Habrosymphrasis xiai gen. et sp. nov., are described from mid-Cretaceous
 Myanmar amber, representing the oldest fossil record of the subfamily.
 Phylogenetic analysis recovered the new genera as stem-group Symphrasinae,
 sister to the rest of the subfamily. These new amber taxa illuminate the
 evolutionary history of Symphrasinae, as well as insights into their
 historical biogeography. They also provide new evidence for divergence
 time estimates of extant mantispid subfamilies.
description: matrixcharacter
 list
DOI: 10.5061/dryad.14hq8cd
title: Data from: Flow imaging microscopy as a novel tool for high-throughput evaluation of elastin-like polymer coacervates

description: Biological and bioinspired polymer microparticles have broad biomedical
 and industrial applications, including drug delivery, tissue engineering,
 surface modification, environmental remediation, imaging, and sensing.
 Full realization of the potential of biopolymer microparticles will
 require methods for rigorous characterization of particle sizes,
 morphologies, and dynamics, so that researchers may correlate particle
 characteristics with synthesis methods and desired functions. Toward this
 end, we evaluated biopolymer microparticles using flow imaging microscopy.
 This technology is widely used in the biopharmaceutical industry but is
 not yet well-known among the materials community. Our polymer, a
 genetically engineered elastin-like polypeptide (ELP), self-assembles into
 micron-scale coacervates. We performed flow imaging of ELP coacervates
 using two different instruments, one with a lower size limit of
 approximately 2 microns, the other with a lower size limit of
 approximately 300 nanometers. We validated flow imaging results by
 comparison with dynamic light scattering and atomic force microscopy
 analyses. We explored the effects of various solvent conditions on ELP
 coacervate size, morphology, and behavior, such as the dispersion of
 single particles versus aggregates. We found that flow imaging is a
 superior tool for rapid and thorough particle analysis of ELP coacervates
 in solution. We anticipate that researchers studying many types of
 microscale protein or polymer assemblies will be interested in flow
 imaging as a tool for quantitative, solution-based characterization.
description: I40 ELP DNA sequencing
 dataThe files in this folder
 are the sequencing results received from Eurofins Genomics for the I40
 POE-W plasmid.fcI40_LMERMB_DNA.zipI40 ELP DLS data and analysisThe files in this folder were used to generate Fig 2.fcI40_LMERMB_DLS.zipI40 ELP AFM dataIGOR Pro binary wave file containing AFM data used to generate Fig 3.fcI40_LMERMB_AFM_X180709I40H2O0004.ibw.zipI40 ELP FlowCam filters and classification filesfcI40_LMERMB_FlowCamFiltersClassification.zipI40 ELP data analysis and graphics - OriginUnicode-compliant Origin 2018 project file containing all data analysis and graphing for this studyfcI40_LMERMB_OriginAnalysis.opjuI40 ELP FlowCam in waterfcI40_LMERMB_FlowCam_Water.zipI40 ELP FlowCam in high salt non-reducing conditionsfcI40_LMERMB_FlowCamHighSaltNon-Reducing.zipI40 ELP FlowCam in high salt reducing conditionsfcI40_LMERMB_FlowCamHighSaltReducing.zipI40 ELP FlowCam in water - Nano Run 208-24-2018-I40-Water-Run#2 2.zipI40 ELP FlowCam in water - Nano Run 308-24-2018-I40-Water-Run#3 2.zipI40 ELP FlowCam in water - Nano Run 408-24-2018-I40-Water-Run#4 2.zipREADMEDescription of all directories and files contained in this data package.
DOI: 10.5061/dryad.630mg39
title: Data from: Insular and anterior cingulate cortex deep stimulation for central neuropathic pain: disassembling the percept of pain

description: Objective: To compare the analgesic effects of stimulation of the anterior
 cingulate cortex (ACC) or the posterior superior insula (PSI) against sham
 deep (d) repetitive (r) transcranial magnetic stimulation (TMS) in
 patients with central neuropathic pain (CNP) after stroke or spinal cord
 injury in a randomized, double-blinded, sham-controlled, 3-arm parallel
 study. Methods: Participants were randomly allocated into the active
 PSI-rTMS, ACC-rTMS, sham-PSI-rTMS, or sham-ACC-rTMS arms. Stimulations
 were performed for 12 weeks, and a comprehensive clinical and pain
 assessment, psychophysics, and cortical excitability measurements were
 performed at baseline and during treatment. The main outcome of the study
 was pain intensity (numeric rating scale [NRS]) after the last stimulation
 session. Results: Ninety-eight patients (age 55.02 ± 12.13 years)
 completed the study. NRS score was not significantly different between
 groups at the end of the study. Active rTMS treatments had no significant
 effects on pain interference with daily activities, pain dimensions,
 neuropathic pain symptoms, mood, medication use, cortical excitability
 measurements, or quality of life. Heat pain threshold was significantly
 increased after treatment in the PSI-dTMS group from baseline (1.58, 95%
 confidence interval [CI] 0.09–3.06]) compared to sham-dTMS (−1.02, 95% CI
 −2.10 to 0.04, p = 0.014), and ACC-dTMS caused a significant decrease in
 anxiety scores (−2.96, 95% CI −4.1 to −1.7]) compared to sham-dTMS (−0.78,
 95% CI −1.9 to 0.3; p = 0.018). Conclusions: ACC- and PSI-dTMS were not
 different from sham-dTMS for pain relief in CNP despite a significant
 antinociceptive effect after insular stimulation and anxiolytic effects of
 ACC-dTMS. These results showed that the different dimensions of pain can
 be modulated in humans noninvasively by directly stimulating deeper SNC
 cortical structures without necessarily affecting clinical pain per se.
description: Supplementary
 files_R1_30112018Supplementary
 file
DOI: 10.5061/dryad.c392v5q
title: Data from: X-linked myotubular myopathy: a prospective international natural history study

description: Objectives: As X-linked myotubular myopathy (XLMTM) is a rare
 neuromuscular disease caused by mutations in the MTM1 gene with a large
 phenotypic heterogeneity, to ensure clinical trial readiness, it was
 mandatory to better quantify disease burden and determine best outcomes
 measures. Methods: We designed an international prospective and
 longitudinal natural history study in patients with XLMTM and assessed
 muscle strength and motor and respiratory functions over the first year of
 follow-up. The humoral immunity against adeno-associated virus serotype 8
 was also monitored. Results: Forty-five male patients aged 3.5 months to
 56.8 years were enrolled between May 2014 and May 2017. Thirteen patients
 had a mild phenotype (no ventilation support), seven had an intermediate
 phenotype (ventilation support less than 12 hours a day), and twenty-five
 had a severe phenotype (ventilation support equal to or greater than 12
 hours a day). Most strength and motor function assessments could be
 performed even in very weak patients. MFM32 total score, grip and pinch
 strengths, and FVC, FEV1 and PCF measures discriminated the three groups
 of patients. Disease history revealed motor milestone loss in several
 patients. Longitudinal data on 37 patients shown a MFM32 total score
 significantly decreased by 2%. Of the 38 patients evaluated, anti-AAV8
 neutralizing activity was detected in 26% with two patients having an
 inhibitory titer &gt;1:10. Conclusions: Our data confirm that XLMTM is
 slowly progressive for male survivors regardless of their phenotype and
 provide outcome validation and natural history data that can support
 clinical development in this population. NCT02057705.
description: Quality of
 lifeQuality of life based on
 the PROMIS® systemNatHis-MTM_art-Neurol-Figure-e1.pdf
DOI: 10.5061/dryad.1t38n12
title: Data from: Evolution and plasticity of thermal performance: An analysis of variation in thermal tolerance and fitness in 22 Drosophila species

description: The thermal biology of ectotherms is often used to infer species’
 responses to changes in temperature. It is often proposed that temperate
 species are more cold-tolerant, less heat-tolerant, more plastic, have
 broader thermal performance curves (TPCs), and lower optimal temperatures,
 when compared to tropical species; however, relatively little empirical
 work has investigated these expectations. Here we measure thermal
 tolerance limits and thermal performance of the fitness components
 viability, developmental speed, and fecundity at seven temperatures in 22
 species of Drosophila reared at a common temperature. For 10 of these
 species, we also measured thermal tolerance and thermal performance
 following developmental acclimation to three additional temperatures.
 Using these data, we test several fundamental hypotheses about the
 evolution and plasticity of heat and cold resistance and thermal
 performance. We find that cold (and to a lesser degree heat) tolerance
 varied between the species in a predictable pattern. This confirms the
 marked effect of evolutionary adaptation and acclimation on thermal
 tolerance. However, contrary to expectation, find that the breadth of
 thermal performance in fitness traits were similar in temperate,
 widespread and tropical species and we also find that the plasticity of
 TPCs is constrained. These data support the idea that thermal tolerance
 limits have evolved in response to extreme environmental conditions that
 limits species persistence whereas the temperature range for optimal
 thermal performance is likely under selection by the temperatures that
 prevail during the more benign seasons. Further, it calls to question the
 utility of TPCs in inferring ecological adaptation. We conclude that the
 thermal performance of fitness traits in Drosophila species are temporally
 and spatially stable and that thermal tolerance varies considerably across
 latitudes.
description: SupplementaryDataTopt
DOI: 10.15468/25vq9q
title: NEON Biorepository Mammal Collection (Vouchers [Standard Sampling])

description: Small mammals collected during NEON live-trapping events.
Sampling

3-8 mammal trapping grids per site

3 are designated pathogen grids (3 nights per bout)
Rest are designated diversity grids (1 night per bout)


Number of bouts/year dependant on site type

Core sites: ~6 bouts/year
Gradient sites: ~4 bouts/year
Sampling aligned with lunar cycle (within &plusmn;10 days of new moon)



Methods

Live capture using Sherman box traps (10 &times; 10 grids, 10 m spacing)
Traps opened over night and closed during the day
Individuals vouchered if found deceased or require euthanasia, otherwise processed and released

Preservation

Received as whole frozen specimens
Prepared either as study skins with skulls (or full skeletons) or in 70-95% ethanol
Standard mammalian measurements taken (in mm; total length, tail length, hind foot length, ear length; and in g: mass)
Endo- and ectoparasites removed and archived
DOI: 10.5061/dryad.3b025hh
title: Data from: An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity

description: A rapid increase of new nanomaterial products poses new challenges for
 their risk assessment. Current traditional methods for estimating
 potential adverse health effect of nanomaterials (NMs) are complex, time
 consuming and expensive. In order to develop new prediction tests for
 nanotoxicity evaluation, a systems biology approach and data from
 high-throughput omics experiments can be used. We present a computational
 approach that combines reverse engineering techniques, network analysis
 and pathway enrichment analysis for inferring the transcriptional
 regulation landscape and its functional interpretation. To illustrate this
 approach, we used published transcriptomic data derived from mice lung
 tissue exposed to carbon nanotubes (NM-401 and NRCWE-26). Because fibrosis
 is the most common adverse effect of these NMs, we included in our
 analysis the data for bleomycin (BLM) treatment, which is a well-known
 fibrosis inducer. We inferred gene regulatory networks for each NM and BLM
 to capture functional hierarchical regulatory structures between genes and
 their regulators. Despite the different nature of the lung injury caused
 by nanoparticles and BLM, we identified several conserved core regulators
 for all agents. We reason that these regulators can be considered as early
 predictors of toxic responses after NMs exposure. This integrative
 approach, which refines traditional methods of transcriptomic analysis,
 can be useful for prioritization of potential core regulators and
 generation of new hypothesis about mechanisms of nanoparticles toxicity.
description: Supplementary file
 1Inferred GRNs in
 cytoscape file formatSupplementary file
 2KEGG
 pathway analysis of differentially expressed genes from GRN
 modulesSupplementary file
 3List
 of fibrosis markers from CTDSupplementary file
 4Balance of Myc and
 Mxd1Supplementary file
 5Connectivity patterns
 for TFsSupplementary file
 6Venn
 diagrams for sets of genes connected with selected TFs for the NM-401,
 NRCWE-26 and BLM GRNs
DOI: 10.5517/ccdc.csd.cc10gxft
title: CCDC 937856: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10gxgv
title: CCDC 937857: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10gxhw
title: CCDC 937858: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10gxjx
title: CCDC 937859: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.6c642t3
title: Data from: Effects of single and repeated drought on soil microarthropods in a semi-arid ecosystem depend more on timing and duration than drought severity

description: Soil moisture is one of the most important factors affecting soil biota.
 In arid and semi-arid ecosystems, soil mesofauna is adapted to temporary
 drought events, but, until now, we have had a limited understanding of the
 impacts of the different magnitudes and frequencies of drought predicted
 to occur according to future climate change scenarios. The present study
 focuses on how springtails and mites respond to simulated repeated drought
 events of different magnitudes in a field experiment in a Hungarian
 semi-arid sand steppe. Changes in soil arthropod activities were monitored
 with soil trapping over two years in a sandy soil. In the first year
 (2014), we applied an extreme drought pretreatment, and in the consecutive
 year, we applied less devastating treatments (severe drought, moderate
 drought, water addition) to these sites. In the first year, the extreme
 drought pretreatment tended to have a negative effect (either
 significantly or not significantly) on the capture of all Collembola
 groups, whereas all mite groups increased in activity density. However, in
 the consecutive year, between the extreme drought and control treatments,
 we only detected differences in soil microbial biomass. In the cases of
 severe drought, moderate drought and water addition, we did not find
 considerable changes across the microarthropods, except in the case of
 epedaphic Collembola. In the cases of the water addition and drought
 treatments, the duration and timing of the manipulation seemed to be more
 important for soil mesofauna than their severity (i.e., the level of soil
 moisture decrease). We suggest that in these extreme habitats, soil
 mesofauna are able to survive extreme conditions, and their populations
 recover rapidly, but they may not be able to cope with very long drought
 periods.
description: EXDATA_nflorianRaw data file, from the field manipulation
DOI: 10.5517/ccdc.csd.cc10gxky
title: CCDC 937860: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10gxlz
title: CCDC 937861: Experimental Crystal Structure Determination

description: Related Article: Almudena I. Gallego, Oscar Castillo, Felix Zamora, Salome Delgado
|2013|RSC Advances|3|18406|doi:10.1039/c3ra43319f
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10kmfm
title: CCDC 940460: Experimental Crystal Structure Determination

description: Related Article: Dani Vallejo-Sanchez, Garikoitz Beobide, Oscar Castillo, Monica Lanchas|2013|Eur.J.Inorg.Chem.|2013|5592|doi:10.1002/ejic.201300649
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10kmgn
title: CCDC 940461: Experimental Crystal Structure Determination

description: Related Article: Dani Vallejo-Sanchez, Garikoitz Beobide, Oscar Castillo, Monica Lanchas|2013|Eur.J.Inorg.Chem.|2013|5592|doi:10.1002/ejic.201300649
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10kmhp
title: CCDC 940462: Experimental Crystal Structure Determination

description: Related Article: Dani Vallejo-Sanchez, Garikoitz Beobide, Oscar Castillo, Monica Lanchas|2013|Eur.J.Inorg.Chem.|2013|5592|doi:10.1002/ejic.201300649
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10kmjq
title: CCDC 940463: Experimental Crystal Structure Determination

description: Related Article: Dani Vallejo-Sanchez, Garikoitz Beobide, Oscar Castillo, Monica Lanchas|2013|Eur.J.Inorg.Chem.|2013|5592|doi:10.1002/ejic.201300649
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.