cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18931zctq
title: Convergence, parallelism, and function of extreme parietal callus in diverse groups of Cenozoic Gastropoda

description: We use SEM imaging to examine the shell microstructure of fossil and
 living species in five families of caenogastropods (Strombidae, Volutidae,
 Olividae, Pseudolividae, and Ancillariidae) to determine whether parallel
 or convergent evolution is responsible for the development of a unique
 caenogastropod trait, the extreme parietal callus. The extreme parietal
 callus is defined as a substantial thickening of both the spire callus and
 the callus on the ventral shell surface such that it covers 50% or more of
 the surface. Caenogastropods as a whole construct EPC convergently, using
 a variety of low-density, poorly-organized microstructures that are
 otherwise uncommon in caenogastropod non-callus shell construction. Within
 clades, however, we see evidence for parallelism in decreased regulation
 in both the shell and callus microstructure. Low density and
 poorly-ordered microstructure -- such as used for EPC -- uses less organic
 scaffolding and is less energetically expensive than normal shell
 microstructure. This suggests EPC functions to rapidly and inexpensively
 increase shell thickness and overall body size. Tests of functional
 ecology suggest that EPC might function both to defend against crushing
 predation through increased body size and dissipation of forces while
 aiding in shell orientation of highly-mobile gastropods. These
 interpretations hinge on the current phylogenetic placement of
 caenogastropod families, emphasizing the essential contribution of
 phylogeny when interpreting homoplasy.
description: Scanning Electron Microscopy
DOI: 10.5061/dryad.fj6q573rq
title: Mitochondrial genes from eighteen angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

description: The early diversification of angiosperms is a rapid yet complicated
 process and thus it renders the phylogenetic analyses of early-diverging
 angiosperms much difficulty. Plastid and nuclear phylogenomic studies have
 raised several controversial hypotheses regarding the angiosperm
 phylogeny, whereas mitochondrial genomes have been largely ignored. In
 this study, we newly sequenced mitochondrial genomes from 18 angiosperms
 to fill the sampling gaps in magnoliids, Austrobaileyales, Chloranthales,
 Ceratophyllales, and early-diverging lineages of eudicots and monocots. A
 data matrix of 38 mitochondrial genes from 107 taxa was assembled to
 address this question. Although conflicting phylogenies were recovered in
 this study from different datasets and analytical methods, congruence was
 achieved regarding the deep relationships of several major angiosperm
 lineages: Chloranthales always groups with Ceratophyllales,
 Austrobaileyales is sister to mesangiosperms, and a previously unplaced
 clade—Dilleniales—is consistently resolved as a sister to superasterids.
 Substitutional saturation, GC compositional heterogeneity, and codon-usage
 bias are suggested as common reasons for the noisy signals that impact
 phylogenetic reconstructions, and angiosperm mitochondrial genes seem to
 hardly suffer from these factors. In addition, the 3rd codon positions of
 the mitochondrial genes contained more phylogenetic signals than the 1st
 and 2nd codon positions, which might be responsible for the incongruent
 results recovered among different datasets. Due to the rapid radiation
 process, the relationships among these early lineages are not well
 resolved. Nevertheless, this study based on mitochondrial genomes provides
 additional evidence and alternative hypotheses for the early evolution and
 diversification of angiosperms.
DOI: 10.5061/dryad.9kd51c5dz
title: Exploring the roles of iron and irradiance in dynamics of diatoms and Phaeocystis in the Amundsen Sea continental shelf water

description: The Amundsen Sea continental shelf (ACS) water ecosystem is expected to
 undergo changes since the increasing melt rate of glaciers and decreasing
 sea ice extent by global warming would lead to the mitigation of iron and
 light limitation. We investigated how diatoms and Phaeocystis, two
 dominant taxa, and primary production in the ACS water would respond to
 variations in iron and light availabilities by using a 1-D pelagic
 ecosystem model. In the model, we added sea ice effects that reduce light
 penetration and optimized model parameters for diatoms and Phaeocystis.
 The results from our model showed good agreement with 20-year observations
 of Chl-a as well as the biomass proportion of diatoms and Phaeocystis and
 nutrient distributions during the growing season. Our model experimental
 results suggest that the current moderate iron and high light conditions
 favor the growth of Phaeocystis over diatoms. Moreover, as iron increases,
 the organic carbon exudation by phytoplankton increases more rapidly than
 net primary production (NPP), leading to a decline in phytoplankton
 biomass. On the other hand, irradiance plays a role in controlling NPP in
 terms of photoinhibition which is reduced by increasing iron. Increases in
 both iron and irradiance lead to an advance in the timing of the bloom
 peak (surface Chl-a maximum) due to increases in phytoplankton carbon loss
 and photoinhibition. Our results imply that the dominance of Phaeocystis
 can continue and that the carbon uptake capacity of the ACS in the summer
 seasons might increase given that iron availability will increase with
 future climate change.
DOI: 10.15468/dl.med6uw
title: Occurrence Download

description: A dataset containing 1106767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus, Myocastor coypus)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1106767 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002385-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8pq2
title: The effectiveness of flower strips and hedgerows on pest control, pollination services and crop yield: a quantitative synthesis

description: Floral plantings are promoted to foster ecological intensification of
 agriculture through provisioning of ecosystem services. However, a
 comprehensive assessment of the effectiveness of different floral
 plantings, their characteristics and consequences for crop yield is
 lacking. Here we quantified the impacts of flower strips and hedgerows on
 pest control (18 studies) and pollination services (17 studies) in
 adjacent crops in North America, Europe and New Zealand. Flower strips,
 but not hedgerows, enhanced pest control services in adjacent fields by
 16% on average. However, effects on crop pollination and yield were more
 variable. Our synthesis identifies several important drivers of
 variability in effectiveness of plantings: pollination services declined
 exponentially with distance from plantings, and perennial and older flower
 strips with higher flowering plant diversity enhanced pollination more
 effectively. These findings provide promising pathways to optimize floral
 plantings to more effectively contribute to ecosystem service delivery and
 ecological intensification of agriculture in the future.
description: To identify datasets suitable to address the research questions
 of this quantitative synthesis a search in the ISI Web of Science and
 SCOPUS was performed. To minimise potential publication bias and to
 maximise the number of relevant datasets we also searched for unpublished
 data by contacting potential data holders through researcher networks.
 Data was requested through a standardized data sheet template from dataset
 holders. As different studies used different methods and measures to
 quantify pollination services, pest control services and crop yield, the
 data was standardized prior to statistical analysis using
 <i>z</i>-scores. A mixed effect-modelling approach was used to
 statistically analyse the data. Details on methods of data collection and
 analysis is are given in the material and methods section of the paper,
 and in the Supporting Figure 1 and Supporting Tables 1-5.
description: Meta-data files (ReadMe files) with the information required to
 use this dataset are provided.
DOI: 10.5061/dryad.6m905qfxj
title: Genetic architecture of individual variation in recombination rate on the X-chromosome in cattle

description: Meiotic recombination is an essential biological process that ensures
 proper chromosome segregation and creates genetic diversity. Individual
 variation in global recombination rates has been shown to be heritable in
 several species and variants significantly associated with this trait have
 been identified. Recombination on the sex chromosome has often been
 ignored in these studies although this trait may be particularly
 interesting as it may correspond to a biological process distinct from
 that on autosomes. For instance, recombination in males is restricted to
 the pseudo-autosomal region (PAR). We herein used a large cattle pedigree
 with more than 100,000 genotyped animals to improve the genetic map of the
 X-chromosome and to study the genetic architecture of individual variation
 in recombination rate on the sex-chromosome (XRR). The length of the
 genetic map was 46.4 and 121.2 cM in males and females, respectively, but
 the recombination rate in the PAR was 6 times higher in males. The
 heritability of CO counts on the X-chromosome was comparable to that of
 autosomes in males (0.011) but larger than that of autosomes in females
 (0.024). XRR was highly correlated (0.76) with global recombination rate
 (GRR) in females, suggesting that both traits might be governed by shared
 variants. In agreement, a set of eleven previously identified variants
 associated with GRR had correlated effects on female XRR (0.86). In males,
 XRR and GRR appeared to be distinct traits, although more accurate CO
 counts on the PAR would be valuable to confirm these results.
description: The data set contains CO and CO counts identified on cattle
 genotype data with LINKPHASE3. The CO counts are used
 as phenotypes. A pedigree file is provided to estimate genetic
 parameters. Genotypes at 11 previously variants
 associated with global recombination rate are also available.
 The sex-specific genetic distances between pairs of successive
 markers are also provided.
DOI: 10.5061/dryad.9w0vt4bcd
title: Enhanced Activated Carbon with H2SO4-activation of African Maize Cobs biomass for Supercapacitor electrodes material application

description: The African Maize Cobs (AMC) biomass was converted into activated carbon
 (AC) for electrode materials for supercapacitor application. The
 carbonization was carried out with concentrated sulphuric acid and the
 activation was done in three (3) batches using activation temperatures of
 600, 700 and 800oC. The AC materials were characterized by
 Thermogravimetric analysis (TGA-DSC), N2-adsorption-desorption isotherms,
 Field Emission Scanning Electron Microscopy (FESEM), Fourier Transform
 Infrared Spectroscopy (FTIR), X-Ray Diffraction (XRD), Boehm titration,
 X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy and
 electrochemical analysis (EC). The materials activated were highly
 functionalized with oxygen groups with total acidity of 0.440 –
 0.464mmol/g, basicity of 0.09 – 0.420mmol/g and oxygen percentage
 composition of 22 – 32%. The AC materials were analysed with EC as
 electrode material for supercapacitor devices. The electrode materials
 revealed specific capacitance of; 456.4 F/g with 0.25 A/g giving energy of
 63.39 Wh/kg and Power of 500 W/kg with AC-S-800 material and 6M KOH
 electrolyte using chronopotentiometry technique with potential limitation
description: Using Instrumentation like XRD, EC, XPS
DOI: 10.5061/dryad.sf7m0cg3n
title: Data from: Neurofeedback facilitation enhances post-stroke gait and balance recovery: a randomized trial

description: Objective: To test the hypothesis that supplementary motor area (SMA)
 facilitation with functional near-infrared spectroscopy mediated
 neurofeedback (fNIRS-NFB) augments post-stroke gait and balance recovery
 using the 3-meter-Timed Up-and-Go (TUG) test, we conducted this
 two-center, double-blind, randomized controlled trial involving 54
 Japanese patients. Methods: Patients with subcortical stroke-induced
 mild-to-moderate gait disturbance more than 12 weeks from onset, underwent
 6 sessions of SMA neurofeedback facilitation during gait- and
 balance-related motor imagery using fNIRS-NFB. Participants were randomly
 allocated to intervention (REAL: 28 patients) or placebo (SHAM: 26
 patients) group. In the REAL group, the fNIRS signal contained
 participants’ cortical activation information. Primary outcome was TUG
 improvement, 4 weeks post intervention. Results: The REAL group showed
 greater improvement in the TUG test (12.84 ± 15.07 s, 95% CI: 7.00-18.68)
 than the SHAM group (5.51± 7.64 s, 95% CI: 2.43 – 8.60; group difference
 7.33 s, 95% CI: 0.83 – 13.83; p = 0.028), even after adjusting for
 covariates (group × time interaction; F1.23,61.69 = 4.50, p = 0.030,
 partial η2 = 0.083). Only the REAL group showed significantly increased
 imagery-related SMA activation and enhancement of resting-state
 connectivity between SMA and ventrolateral premotor area. Adverse effects
 associated with fNIRS-mediated neurofeedback intervention were absent.
 Conclusion: SMA facilitation during motor imagery using fNIRS
 neurofeedback may augment post-stroke gait and balance recovery by
 modulating the SMA and its related network. Classification of Evidence:
 This study provides Class III evidence that for patients with gait
 disturbance from subcortical stroke, SMA neurofeedback facilitation
 improves TUG time. (UMIN000010723 at UMIN-CTR
 http://www.umin.ac.jp/english/)
description: This is additional information including protocol, detailed
 methodological procedures, and additional clinical and imaging
 data.
DOI: 10.15468/dl.8w7pcn
title: Occurrence Download

description: A dataset containing 7342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-79.8549 -2.22112,-79.85512 -2.22124,-79.85488 -2.22149,-79.85483 -2.22109,-79.8549 -2.22109,-79.8549 -2.22112))",
 "PublishingCountry is Ecuador"
 ]
}

 The dataset includes 7342 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002436-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vmcvdncqp
title: MVCNN++: CAD model shape classification and retrieval using multi-view convolutional neural networks

description: Deep neural networks have shown promising success towards the
 classification and retrieval tasks for images and text data. While there
 have been several implementations of deep networks in the area of computer
 graphics, these algorithms do not translate easily across different
 datasets, especially for shapes used in product design and manufacturing
 domain. Unlike datasets used in the 3D shape classification and retrieval
 in the computer graphics domain, engineering level description of 3D
 models do not yield themselves to neat distinct classes. The current study
 looks at an improved form of the 3D shape deep learning algorithm for
 classification and retrieval through the use of techniques such as relaxed
 classification, use of prime angled camera angles for capturing feature
 detail and transfer learning for reducing the amount of data and
 processing time needed to train shape recognition algorithms. The proposed
 algorithm (MVCNN++) builds on top of multi-view convolutional neural
 network (MVCNN) algorithm, improving its efficacy for manufacturing part
 classification by enabling use of part metadata, yielding an improvement
 of almost 6% over the original version. With the explosive growth of 3D
 product models available in publicly available repositories, search and
 discovery of relevant models is critical to democratizing access to design
 models.
description: The data is organized in several distinct standard part
 categories - approx 46 classes. Each folder has at least JPEG and STEP
 folder that contain an image and  a .step file of the model. Some folders
 also have an .STL version of it.
DOI: 10.5061/dryad.cjsxksn3n
title: Accelerated reproduction is not an adaptive response to early life adversity in wild baboons

description: In humans and other long-lived species, harsh conditions in early life
 often lead to profound differences in adult life expectancy. In response,
 natural selection is expected to accelerate the timing and pace of
 reproduction in individuals who experience some forms of early life
 adversity. However, the adaptive benefits of reproductive acceleration
 following early adversity remain untested. Here we test a recent version
 of this theory, the internal predictive adaptive response (iPAR) model, by
 assessing for the first time whether accelerating reproduction following
 early life adversity leads to higher lifetime reproductive
 success. We do so by leveraging 48 years of continuous,
 individual-based data from wild female baboons in the Amboseli ecosystem
 in Kenya, including prospective, longitudinal data on early life
 adversity, reproductive pace, and lifetime reproductive success.We find
 that while adversity in early life led to dramatically shorter
 lifespans, individuals who experiencedearly
 adversity didnot accelerate their reproduction compared to those
 who did not experience early adversity. Further, while
 accelerated reproduction predicted increased lifetime reproductive success
 overall, these benefits were not specific to females who experienced early
 life adversity. Instead, females only benefited from reproductive
 acceleration if they also led long lives. Our results call into question
 the theory that accelerated reproduction is an adaptive response to early
 life adversityin baboons and other long-lived species.
description: See the attached ReadMe file for instruction on how to use the
 data files.
DOI: 10.5061/dryad.b8gtht79h
title: nNOS-expressing interneurons control basal and behaviorally evoked arterial dilation in somatosensory cortex of mice

description: Cortical neural activity is coupled to local arterial diameter and blood
 flow. However, which neurons control the dynamics of cerebral arteries is
 not well understood. We dissected the cellular mechanisms controlling the
 basal diameter and evoked dilation in cortical arteries in awake,
 head-fixed mice. Locomotion drove robust arterial dilation, increases in
 gamma band power in the local field potential (LFP), and increases calcium
 signals in pyramidal and neuronal nitric oxide synthase (nNOS)-expressing
 neurons. Chemogenetic or pharmocological modulation of overall neural
 activity up or down caused corresponding increases or decreases in basal
 arterial diameter. Modulation of pyramidal neuron activity alone had
 little effect on basal or evoked arterial dilation, despite pronounced
 changes in the LFP. Modulation of the activity of nNOS-expressing neurons
 drove changes in the basal and evoked arterial diameter without
 corresponding changes in population neural activity.
description: To generate figure, excute
 GenerateFigures_Master_Echagarruga_elife.m in Matlab.  It should be run
 within the directory containing the data folders. Both
 cbrewer and Chronux need to be in the Matlab path for the code to
 run. cbrewer can be downloaded here:
 https://www.mathworks.com/matlabcentral/fileexchange/34087-cbrewer-colorbrewer-schemes-for-matlab Chronux can be downloaded here: http://chronux.org/
DOI: 10.5061/dryad.5x69p8d11
title: Thyroid hormone induces DNA demethylation in Xenopus tadpole brain

description: Thyroid hormone (T3) plays pivotal roles in vertebrate development, acting
 via nuclear receptors (TRs) that regulate gene transcription by promoting
 posttranslational modifications to histones. Methylation of cytosine
 residues in DNA also modulates gene transcription, and our recent finding
 of predominant DNA demethylation in the brain of Xenopus tadpoles at
 metamorphosis, a T3-dependent developmental process, caused us to
 hypothesize that T3 induces these changes in vivo. Treatment of
 pre-metamorphic tadpoles with T3 for 24 or 48 hr increased
 immunoreactivity in several brain regions for the DNA demethylation
 intermediates 5-hydroxymethylcytosine (5-hmC) and 5-carboxylcytosine, and
 the methylcytosine dioxygenase ten-eleven translocation 3 (TET3). Thyroid
 hormone treatment induced locus-specific DNA demethylation in proximity to
 known T3 response elements within the DNA methyltransferase 3a and
 Krüppel-like factor 9 genes, analyzed by 5-hmC immunoprecipitation and
 methylation sensitive restriction enzyme digest.
 Chromatin-immunoprecipitation (ChIP) assay showed that T3 induced TET3
 recruitment to these loci. Furthermore, the mRNAs for several genes
 encoding DNA demethylation enzymes were induced by T3 in a time-dependent
 manner in tadpole brain. A TR ChIP-sequencing experiment identified
 putative TR binding sites at several of these genes, and we provide
 multiple lines of evidence to support that tet2 contains a bona fide T3
 response element. Our findings show that T3 can promote DNA demethylation
 in developing tadpole brain, in part by promoting TET3 recruitment to
 discrete genomic regions, and by inducing genes that encode DNA
 demethylation enzymes.
DOI: 10.5061/dryad.q573n5tgb
title: Drought risk of global terrestrial gross primary productivity in recent 40 years detected by a remote sensing-driven process model

description: Gross primary productivity (GPP) is the largest flux in the global
 terrestrial carbon cycle and affected by multiple factors. In recent
 decades, drought has significantly impacted global terrestrial GPP and
 been projected to occur with increasing frequency and intensity. However,
 the drought risk of global terrestrial GPP has not been well investigated.
 In this study, global terrestrial GPP over the period from 1981 to 2016
 was simulated with the process-based Boreal Ecosystem Productivity
 Simulator (BEPS) model. Then, the drought risk of terrestrial GPP was
 quantified as the product of frequency of drought and reduction of GPP
 caused by drought, which were determined using the standardized
 precipitation evapotranspiration index (SPEI). During the study period,
 the drought risk of terrestrial GPP exhibited detectable spatial
 heterogeneity, high in southeastern United States, most of South America,
 southern Europe, central and eastern Africa, eastern and southeastern
 Asia, and eastern Australia. In these regions, the maximum reduction of
 GPP might be above 30% in drought years relative to that in normal years.
 The drought risk of GPP was low at high latitudes of the Northern
 Hemisphere, in which terrestrial GPP increased slightly in drought years.
 The spatial pattern of the drought risk of GPP simulated by the BEPS model
 was close to that of FLUXCOM GPP, which was scaled from tower observations
 with a machine learning algorithm forced by remote sensing and
 meteorological data. This study advances our understanding on the impact
 of drought on terrestrial GPP over the globe.