cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2ch4ns2
title: Data from: Climate-dependent variation in cold tolerance of weedy rice and rice mediated by OsICE1 promoter methylation

description: The mechanisms by which weedy rice (Oryza sativa f. spontanea) has adapted
 to endure low-temperature stress in northern latitudes remain unresolved.
 In this study, we assessed cold tolerance of 100 rice varieties and 100
 co-occurring weedy rice populations, which were sampled across a broad
 range of climates in China. A parallel pattern of latitude-dependent
 variation in cold tolerance was detected in cultivated rice and weedy
 rice. At the molecular level, differential cold tolerance was strongly
 correlated with relative expression levels of CBF cold response pathway
 genes and with methylation levels in the promoter region of OsICE1, a
 regulator of this pathway. Among all methylated cytosine sites of the
 OsICE1 promoter, levels of CHG and CHH methylation were found to be
 significantly correlated with cold tolerance among accessions.
 Furthermore, within many of the collection locales, weedy rice shared
 identical or near-identical OsICE1 methylation patterns with co-occurring
 cultivated rice. These findings provide new insights on the possible roles
 that methylation variation in the OsICE1 promoter may play in cold
 tolerance, and they suggest that weedy rice can rapidly acquire cold
 tolerance via methylation patterns that are shared with co-occurring rice
 cultivars.  
description: DNA methylation
 sequences   Cold tolerance-By
 LXY.rar qRT-PCR
  
 
 Cold tolerance-By
 LXY   
 Cold tolerance-By
 HYH   
 photosynthetic
 parameters-1   
 photosynthetic
 parameters-2
DOI: 10.5061/dryad.v5h2fd7
title: Data from: Amyloid and cerebrovascular burden divergently influence brain functional network changes over time

description: Objective: To examine the effects of baseline Alzheimer’s disease and
 cerebrovascular disease markers on longitudinal default mode network (DMN)
 and executive control network (ECN) functional connectivity (FC) changes
 in mild cognitive impairment (MCI) patients. Methods: We studied 30
 amnestic (aMCI) and 55 subcortical vascular MCI (svMCI) patients with
 baseline Pittsburgh Compound B (PiB)–positron emission tomography (PET)
 scans and longitudinal magnetic resonance imaging (MRI) scans.
 Participants were followed up clinically with annual MR imaging for up to
 four years (aMCI: 26 with two time-points, 4 with three time-points;
 svMCI: 13 with two time-points, 16 with three time-points, 26 with four
 time-points). Results: Amyloid-β burden was associated with longitudinal
 DMN FC declines, while cerebrovascular burden was associated with
 longitudinal ECN FC changes. When patients were divided into PiB+ and PiB-
 groups, PiB+ patients showed longitudinal DMN FC declines, while svMCI
 patients showed longitudinal ECN FC increases. Direct comparisons between
 the two groups without mixed pathology (aMCI PiB+ and svMCI PiB-)
 recapitulated this divergent pattern: aMCI PiB+ patients showed steeper
 longitudinal DMN FC declines, while svMCI PiB- patients showed steeper
 longitudinal ECN FC increases. Finally, using baseline PiB uptake and
 lacune numbers as continuous variables, baseline PiB uptake showed inverse
 U-shape associations with longitudinal DMN FC changes in both MCI
 subtypes, while baseline lacune numbers showed both mainly inverse-U shape
 relationships with longitudinal ECN FC changes in svMCI patients.
 Conclusions: Our findings underscore the divergent effects of amyloid-β
 and cerebrovascular burden on longitudinal FC changes in the DMN and ECN
 in the pre-dementia stage, which reflect the underlying pathology and may
 be used to track early changes in Alzheimer’s disease and cerebrovascular
 disease.
description: Supplemental
 dataSupplemental
 dataSupplementalData.docx
DOI: 10.5061/dryad.t389h81
title: Data from: GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments

description: Molecular sequence data that have evolved under the influence of
 heterotachous evolutionary processes are known to mislead phylogenetic
 inference. We introduce the General Heterogeneous evolution On a Single
 Topology (GHOST) model of sequence evolution, implemented under a
 maximum-likelihood framework in the phylogenetic program IQ-TREE
 (http://www.iqtree.org). Simulations show that using the GHOST model,
 IQ-TREE can accurately recover the tree topology, branch lengths, and
 substitution model parameters from heterotachously evolved sequences. We
 investigate the performance of the GHOST model on empirical data by
 sampling phylogenomic alignments of varying lengths from a plastome
 alignment. We then carry out inference under the GHOST model on a
 phylogenomic data set composed of 248 genes from 16 taxa, where we find
 the GHOST model concurs with the currently accepted view, placing turtles
 as a sister lineage of archosaurs, in contrast to results obtained using
 traditional variable rates-across-sites models. Finally, we apply the
 model to a data set composed of a sodium channel gene of 11 fish taxa,
 finding that the GHOST model is able to elucidate a subtle component of
 the historical signal, linked to the previously established convergent
 evolution of the electric organ in two geographically distinct lineages of
 electric fish. We compare inference under the GHOST model to partitioning
 by codon position and show that, owing to the minimization of model
 constraints, the GHOST model offers unique biological insights when
 applied to empirical data.
description: Electric fish
 alignment electricFish.fa
 
 Turtle
 dataset Chiari_amnios248genes_nt.nex Supplementary Figures and Tables manuscript_GHOST_SB_4thRevision_Supplement.pdf 12-taxon simulations Class 1 tree 12-taxon simulations Class 1 tree file in Newick format t12SimsSpecific.tree1 12-taxon simulations Class 2 tree 12-taxon simulations Class 2 tree file in Newick format t12SimsSpecific.tree2
DOI: 10.5061/dryad.2cs8d7f
title: Data from: Antibiotics as chemical warfare across multiple taxonomic domains and trophic levels

description: Bacteria and fungi secrete antibiotics to suppress and kill other
 microbes, but can these compounds be agents of competition against
 macroorganisms? We explore how one competitive tactic, antibiotic
 production, can structure the composition and function of brown food webs.
 This aspect of warfare between microbes and invertebrates is particularly
 important today as antibiotics are introduced into ecosystems via
 anthropogenic activities, but the ecological implications of these
 introductions are largely unknown. We hypothesized that antimicrobial
 compounds act as agents of competition against invertebrate and microbial
 competitors. Using field-like mesocosms, we tested how antifungal and
 antibacterial compounds influence microbes, invertebrates, and
 decomposition in the brown food web. Both antibiotics changed prokaryotic
 microbial community composition, but only the antibacterial changed
 invertebrate composition. Antibacterials reduced the abundance of
 invertebrate detritivores by 34%. However, the addition of antimicrobials
 did not ramify up the food web as predator abundances were unaffected.
 Decomposition rates did not change. Our results show that antibiotic
 compounds could be an effective weapon for microbes to compete against
 both microbial and invertebrate competitors. In the context of human
 introductions, the detrimental effects of antibiotics on invertebrate
 communities indicates that the scope of this anthropogenic disturbance is
 much greater than previously expected.
description: Invertebrate_Abundance_Data This file contains the raw data and associated metadata for all invertebrate abundance counts.   weighted_unifrac_dm Prokaryotic Unifrac Distance Matrix used for PERMANOVA analyses.   Prokaryotic_NMDS_File Prokaryotic NMDS scores and associated metadata. NMDS_File.csv Microbial BIOM File otu_table_meso_only.biom SurvivalAnalysis_ProcB R code for survival analysis and plotting.   MesocosmInvertCode R code for invertebrate analyses.   QiimeCodeForSequences Qiime code for generating biom table and initial analyses.   MillipedeIsopod_Survival_RawData Raw data for the survival analysis of isopods and millipedes.
DOI: 10.5061/dryad.851d6k5
title: Genetic diversity, structure, and demography of Pandanus boninensis(Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands

description: Pandanus boninensis, endemic to the Ogasawara Islands, Japan, is
 distributed on both the older Bonin and younger Volcano Islands. In this
 study, we conducted population genetic analyses of P. boninensis on these
 islands to examine the population diversity and structure across old and
 young islands, to assess potential differences in population demography
 with island age, and to collect any evidence of migration between old and
 young islands. We found that the genetic diversity of expressed sequence
 tag (EST)–based microsatellite (SSR) markers, the nucleotide diversity of
 nuclear DNA sequences, and the haplotype diversity of chloroplast DNA on
 young islands were lower than those on old islands. Clustering analyses of
 EST-SSR indicated that populations on old islands were strongly diverged
 from those on young islands. Approximate Bayesian computation analysis of
 EST-SSR suggested that population expansion occurred on old islands while
 population reduction occurred on young islands. We also found evidence of
 migration among old islands (mostly from south to north), while it appears
 that there have been very few migration events between old and young
 islands. These differences could be due to the fact that young islands
 tend to be geographically isolated and support smaller populations that
 began a shorter time ago from limited founders. The P. boninensis
 populations on the Volcano Islands are interesting from an evolutionary
 perspective as they constitute a classic example of the early stages of
 progressive colonization on oceanic islands with small effective
 population sizes and low genetic diversity.
description: Setsuko_et
 _al_Pandanus_boninensis_EST-SSRs_GENOTYPEGenotypes of 944
 individuals of Pandanus boninensis at 14 EST-SSRs.P.boninensisDryad.xlsx
description: Leaf samples of 944 individuals of
 <i>Pandanus boninensis</i> were collected from 34 populations
 from 20 islands of the Mukojima, Chichijima, Hahajima, and Volcano
 Islands. Genotypes for 944 individuals were determined using 14 EST-SSRs
 (Pb_0084, Pb_0195, Pb_0400, Pb_0760, Pb_0880, Pb_0979, Pb_1138, Pb_1142,
 Pb_1425, Pb_1733, Pb_2057, Pb_3598, Pb_3868, and Pb_4444) developed for
 <i>P. boninensis</i> (Setsuko <i>et al</i>.,
 2012).
DOI: 10.5061/dryad.r852n88
title: Data from: Brokering the core and the periphery: creative success and collaboration networks in the film industry

description: In collaboration-based creative industries, such as film production,
 creators in the network core enjoy prestige and legitimacy that are key
 for creative success. However, core creators are challenged to maintain
 diverse access to new ideas or alternative views that often emerge from
 the network periphery. In this paper, we demonstrate that creators in the
 network core can increase the probability of their creative success by
 brokering peripheral collaborators to the core. The argument is tested on
 a dynamic collaboration network of movie creators constructed from a
 unique dataset of Hungarian feature films for the 1990-2009 period. We
 propose a new way to capture brokers’ role in core/periphery networks and
 provide evidence that being in the core and at the same time bridging
 between the core and the periphery of the network significantly increases
 the likelihood of award winning.
description: creators_movies_1975_2010.csv Bipartite network dataset used to construct evolving networks of movie creators. Variables:<br> 'film_id': anonymised IDs of Hungarian feature films produced between 1975-2010<br> 'year': year of production<br> 'creator_id': anonymised creators of movies (such as cinematographers, directors, editors, producers, writers) award_winners.csv Subset of creators_movies_1975_2010.csv, where each award winning individual individual is marked by a dummy. Note that individuals could get an award for individual performance or for the best picture. Variables:<br> 'film_id': anonymised IDs of Hungarian feature films produced between 1975-2010<br> 'year': year of production<br> 'creator_id': anonymised creators of movies with an award at the given years' Hungarian Film Week (such as cinematographers, directors, editors, producers, writers)
DOI: 10.5061/dryad.v4455hc
title: Data from: Systematic review on barriers and enablers for access to diabetic retinopathy screening services in different income settings

description: Background: Diabetic retinopathy (DR) can lead to visual impairment and
 blindness if not detected and treated in time. Knowing the
 barriers/enablers in advance in contrasting different country income
 settings may accelerate development of a successful DR screening (DRS)
 program. This would be especially applicable in the low-income settings
 with the rising prevalence of DR. Objectives: The aim of this systematic
 review is to identify and contrast the barriers/enablers to DRS for
 different contexts using both consumers i.e., people with diabetes (PwDM)
 and provider perspectives and system level factors in different country
 income settings. Methods: We searched MEDLINE, Embase, CENTRAL in the
 Cochrane Library from the databases start date to December 2018. We
 included the studies reported on barriers and enablers to access DRS
 services based at health care facilities. We categorised and synthesized
 themes related to the consumers (individuals), providers and the health
 systems (environment) as main dimensions according to the constructs of
 social cognitive theory, supported by the quantitative measures i.e., odds
 ratios as reported by each of the study authors. Main Results: We included
 77 studies primarily describing the barriers and enablers. Most of the
 studies were from high income settings (72.7%, 56/77) and cross sectional
 in design (76.6%, 59/77). From the perspectives of consumers, lack of
 knowledge, attitude, awareness and motivation were identified as major
 barriers. The enablers were fear of blindness, proximity of screening
 facility, experiences of vision loss and being concerned of eye
 complications. In providers’ perspectives, lack of skilled human
 resources, training programs, infrastructure of retinal imaging and cost
 of services were the main barriers. Higher odds of uptake of DRS services
 was observed when PwDM were provided health education (odds ratio (OR)
 4.3) and having knowledge on DR (OR range 1.3-19.7). Conclusion: Knowing
 the barriers to access DRS is a pre-requisite in development of a
 successful screening program. The awareness, knowledge and attitude of the
 consumers, availability of skilled human resources and infrastructure
 emerged as the major barriers to access to DRS in any income setting.
description: Systematic Rw
 Barriers_V1.14_MasterCopy_Dec_2018_PLOS 1Systematic review
 primary data extraction file
DOI: 10.5061/dryad.tv06pt2
title: Data from: Clinical EEG slowing correlates with delirium severity and predicts poor clinical outcomes

description: Objective To determine which findings on routine clinical EEGs correlate
 with delirium severity across various presentations, and to determine
 whether EEG findings independently predict important clinical outcomes.
 Methods We prospectively studied a cohort of non-intubated inpatients
 undergoing EEG for evaluation of altered mental status. Patients were
 assessed for delirium within one hour of EEG using the 3-Minute Diagnostic
 Interview for Confusion Assessment Method (3D-CAM) and 3D-CAM severity
 score (3D-CAM-S). EEGs were interpreted clinically by neurophysiologists,
 and reports were reviewed to identify features such as theta or delta
 slowing and triphasic waves. Generalized linear models were used to
 quantify associations between EEG findings, delirium, and clinical
 outcomes, including length of stay, Glasgow Outcome Scale scores, and
 mortality. Results We evaluated 200 patients (median age 60 years, IQR
 48.5-72); 121 (60.5%) met delirium criteria. The EEG finding most strongly
 associated with delirium presence was a composite of generalized theta or
 delta slowing (OR 10.3, 95% CI 5.3-20.1). The prevalence of slowing
 correlated not only with overall delirium severity (R2 = 0.907), but also
 with the severity of each feature assessed by CAM-based delirium
 algorithms. Slowing was common in delirium even with normal arousal. EEG
 slowing was associated with longer hospitalizations, worse functional
 outcomes, and increased mortality, even after adjusting for delirium
 presence or severity. Conclusions Generalized slowing on routine clinical
 EEG strongly correlates with delirium and may be a valuable biomarker for
 delirium severity. Additionally, generalized EEG slowing should trigger
 elevated concern for the prognosis of patients with altered mental status.
description: SupplementSupplementary Tables and Figures for "Clinical EEG Slowing Correlates with Delirium Severity and Predicts Poor Clinical Outcomes"DeliriumEEG_Neurology_Supplement.pdf
DOI: 10.5061/dryad.kf0mp49
title: Data from: Effect of graphene on rate capability of spinel LTO as an anode material for Li-ion battery

description: Spinel structured Li4Ti5O12 (LTO) is one of the most promising candidate
 anode material for Li-ion battery known as zero strain material, it has
 poor intrinsic electronic properties. In order to enhance it, graphene was
 used as additive. The LTO and graphene composites were synthesized by
 reduction process of graphene oxide via hydrothermal treatment. The
 powders were characterized by X-Ray diffraction (XRD), Infrared
 spectroscopy (FT-IR). For the galvanostatic discharge and charge
 measurements were performed at room temperature against Li/Li+ metal
 electrode.
description: Data
 availabilityThe data include raw
 files of XRD, IR results, figures and data ploted in
 origin.
DOI: 10.5061/dryad.qn3287b
title: Data from: The epileptology of alternating hemiplegia of childhood

description: Objective: Report our experience and investigate five original hypotheses:
 1) Multiple types of epileptic seizures occur in Alternating Hemiplegia of
 Childhood (AHC) and these can be the initial presentation. 2) Epileptiform
 abnormalities often appear well after clinical seizures. 3) Non-epileptic
 reduced awareness spells (RAS) occur frequently. 4) Epilepsy is commonly
 drug resistant but may respond to vagal nerve stimulation (VNS). 5) Status
 epilepticus (SE) is common and is usually refractory and recurrent.
 Methods: Analyze a cohort of 51 consecutive AHC patients. Results: 1)
 Seizure types: 32/51 had epilepsy: Eighteen focal seizures, frontal more
 frequently than temporal, then posterior. Eleven had primary generalized
 seizures (tonic-clonic, myoclonic, and/or absence). Epileptic seizures
 preceded other AHC paroxysmal events in eight (lag: 5.63±6.55 months;
 p=0.0365). 2) EEG: In 7/32, initial EEGs were normal with the first
 epileptiform EEG lagging behind by 3.53±4.65 years (p=0.0484). RAS
 occurred equally in epilepsy (16/32) and non-epilepsy patients (10/19,
 p=1.0). 28/28 video-EEG captured RAS showed no concomitant EEG changes. 4)
 Therapies: Nineteen (59%) were drug resistant. VNS resulted in &gt;50%
 reduction in seizures in 5/6 (p&lt;0.04). 5) SE: Twelve (38%) had SE
 (9/12 multiple episodes), refractory/super-refractory in all
 (p&lt;0.001). 4/12 had regression after SE. Significance: Epilepsy in
 AHC can be focal or generalized. Epileptic seizures may be the first
 paroxysmal symptom. EEG may only become epileptiform on follow-up.
 Epilepsy, though frequently drug resistant, can respond to VNS. RAS are
 frequent and non-epileptic. SE often recurs and is, usually,
 refractory/super-refractory. Our observations are consistent with current
 data on AHC-ATP1A3 pathophysiology.
description: Appendix
 E-1Appendix
 E-2Appendix
 E-3Appendix
 E-4Suplementary Figure
 E-1Supplementary Table
 E-1Supplementary Table
 E-2
DOI: 10.5061/dryad.f83kt85
title: Data from: Structured inhibitory activity dynamics in new virtual environments

description: Inhibition plays a powerful role in regulating network excitation and
 plasticity; however, the activity of defined interneuron types during
 spatial exploration remain poorly understood. Using two-photon calcium
 imaging, we recorded hippocampal CA1 somatostatin- and
 parvalbumin-expressing interneurons as mice performed a goal-directed
 spatial navigation task in new visual virtual reality (VR) contexts.
 Activity in both interneuron classes was strongly suppressed but recovered
 as animals learned to adapt the previously learned task to the new spatial
 context. Surprisingly, although there was a range of activity suppression
 across the population, individual somatostatin-expressing interneurons
 showed consistent levels of activity modulation across exposure to
 multiple novel environments, suggesting context-independent, stable
 network roles during spatial exploration. This work reveals
 population-level temporally dynamic interneuron activity in new
 environments, within which each interneuron shows stable and consistent
 activity modulation.
description: SOM_Remap1Activity traces from representative recording of SOM-ints over 5 days of remapping in New world with behavioral data.SOM_Remap2Activity traces from representative recording of SOM-ints over 5 days of remapping in New world with behavioral data.SOM_NoTaskActivity traces from representative recording of SOM-ints over 5 days of exposure to “No Task” with behavioral data.SOM_Re_GLMActivity traces from representative recording of SOM-ints over 5 days of remapping with GLM modeled traces and behavioral data included.