cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31165975.v1
title: Additional file 3 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 3: Supplementary data 3. KEGG pathway reconstruction for the kinases in the F. hepatica kinome.
DOI: 10.6084/m9.figshare.31165978
title: Additional file 4 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 4: Supplementary data 4. Protein kinase homologs in F. hepatica and S. mansoni predicted by the phylogenetic tree in Fig. 2.
DOI: 10.6084/m9.figshare.31165978.v1
title: Additional file 4 of Curation of the Fasciola hepatica kinome as a resource for drug target discovery

description: Additional file 4: Supplementary data 4. Protein kinase homologs in F. hepatica and S. mansoni predicted by the phylogenetic tree in Fig. 2.
DOI: 10.5061/dryad.zpc866t8c
title: Contributing countries, centers and center coordinators

description: Objective: To test the hypothesis that intravenous thrombolysis (IVT)
 treatment prior to endovascular thrombectomy (EVT) is associated with
 better outcomes in patients with anterior circulation large artery
 occlusion (LAO) stroke, we examined a large real-world database, the
 SITS-International Stroke Thrombectomy Register (SITS-ISTR). Methods: We
 identified centers recording ³10 consecutive patients in the SITS-ISTR,
 with at least 70% available modified Rankin Scale (mRS) scores at 3 months
 during 2014-19. We defined LAO as intracranial internal carotid artery,
 first and second segment of middle cerebral artery and first segment of
 anterior cerebral artery. Main outcomes were functional independence (mRS
 0-2) and death at 3 months and symptomatic intracranial hemorrhage (SICH)
 per modified SITS-MOST. We performed propensity score matched (PSM) and
 multivariable logistic regression analyses. Results: Of 6350 patients from
 42 centers, 3944 (62.1%) received IVT. IVT+EVT treated patients had less
 frequent atrial fibrillation, ongoing anticoagulation, previous stroke,
 heart failure and pre-stroke disability. PSM analysis showed that IVT+EVT
 patients had a higher rate of functional independence than EVT alone
 patients (46.4% vs. 40.3%, p&lt;0.001) and a lower rate of death at 3
 months (20.3% vs. 23.3%, p=0.035). SICH rates (3.5% vs. 3.0%, p= 0.42)
 were similar in both groups. Multivariate adjustment yielded results
 consistent with PSM. Interpretation: Pretreatment with IVT was associated
 with favorable outcomes in EVT-treated LAO stroke in the SITS Thrombectomy
 Registry. These findings, while indicative of international routine
 clinical practice, are limited by observational design, unmeasured
 confounding and possible residual confounding by indication.
 Classification of Evidence: This study provides Class II evidence that IVT
 prior to EVT increases the probability of functional independence at 3
 months compared to EVT alone.
DOI: 10.5061/dryad.d51c5b036
title: Flatfish exon-capture

description: This dataset contains alignments used to study phylogenetic relationships
 of flatfishes based on exon-capture data. The samples in this dataset
 represent 89 species: 86 flatfishes and 3 outgroup Carangidae. 57 samples
 were extracted and assembled from tissues collected for this project,
 while 39 were sourced from previously assembled data that were prepared as
 part of the FishLife project. For this study we targeted 4,434 markers
 developed by Jiang et al. (2019) for capture efficiency in ray-finned
 fishes (Actinopterygii). Library preparation followed the protocol from Li
 et al. (2013) involving a double capture method used to increase
 concentrations of hybridized DNA. Raw reads were assembled into
 loci using the Assexon bioinformatics pipeline (Yuan et al. 2020).
 Assembled exons were aligned on amino acids using MAFFT (Katoh et al.,
 2002), then translated back to codon-based alignment using a custom perl
 script mafft_aln.pl, and poorly aligned markers were removed. These
 aligned data represent the unfiltered dataset in the associated study,
 which was further processed into subsets based on missing data,
 clocklikeness, nucleotide composition, and evolutionary rate.
description: For 57 samples processed for the study: DNA was extracted using
 the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). RNA baits and
 gene-capture reagents were supplied by the Arbor Biosciences myBaits
 Hybridization Capture Kit. Target-capture hybridizations were done
 according to the myBaits Manual v.4.01 specifications, with baits diluted
 down as to use only 0.5μL per capture. Sequencing was performed by the
 University of Delaware Sequencing and Genotyping Center on two lanes of
 Illumina HiSeq 2500 System using paired-end 150 bp reads. The Assexon
 pipeline used to assemble reads into loci used the following
 dependencies: TrimGalore (Krüger 2012), String Graph Assembler (Simpson
 and Durbin 2012), Exonerate (Slater and Birney, 2005), MAFFT (Katoh et
 al., 2002).
DOI: 10.5061/dryad.6hdr7sr0x
title: Nitrogen-fixing trees increase soil nitrous oxide emissions: A meta-analysis

description: Nitrogen-fixing trees are an important nitrogen source to terrestrial
 ecosystems. While they can fuel primary production and drive carbon
 dioxide sequestration, they can also potentially stimulate soil emissions
 of nitrous oxide, a potent greenhouse gas. However, studies on the
 influence of nitrogen-fixing trees on soil nitrous oxide emissions have
 not been quantitatively synthesised. Here, we show in a meta-analysis that
 nitrogen-fixing trees more than double soil nitrous oxide emissions
 relative to non-fixing trees and soils. If planted in reforestation
 projects at the global scale, nitrogen-fixing trees could increase global
 soil nitrous oxide emissions from natural terrestrial ecosystems by up to
 4.1%, offsetting climate change mitigation via reforestation by up to
 4.4%.
DOI: 10.6084/m9.figshare.31165994
title: Additional file 2 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 2: Morphology statistics. Gene expression analysis statistics. PCA gene expression analysis statistics. Log Fold Change for differential gene expression analysis. Alpha diversity. Beta diversity
DOI: 10.6084/m9.figshare.31165994.v1
title: Additional file 2 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 2: Morphology statistics. Gene expression analysis statistics. PCA gene expression analysis statistics. Log Fold Change for differential gene expression analysis. Alpha diversity. Beta diversity
DOI: 10.6084/m9.figshare.31165997
title: Additional file 3 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 3: Parental morphological measurements, including weight, total body length, condition index, and fat content, for both males and females across all treatment groups. Offspring morphological measurements of 5 individuals per family, including weight, total body length, condition index, and fat content, right after birth
DOI: 10.6084/m9.figshare.31165997.v1
title: Additional file 3 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 3: Parental morphological measurements, including weight, total body length, condition index, and fat content, for both males and females across all treatment groups. Offspring morphological measurements of 5 individuals per family, including weight, total body length, condition index, and fat content, right after birth
DOI: 10.6084/m9.figshare.31166000
title: Additional file 4 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 4: Information on the primers used for the Fluidigm analysis. Efficiency results calculated from the dilution series. Primer efficiency range between 0.8 and 1.2 are acceptable
DOI: 10.6084/m9.figshare.31166000.v1
title: Additional file 4 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 4: Information on the primers used for the Fluidigm analysis. Efficiency results calculated from the dilution series. Primer efficiency range between 0.8 and 1.2 are acceptable
DOI: 10.6084/m9.figshare.31166003
title: Additional file 5 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 5: Raw Fluidigm Ct values organized with samples in rowsand columns for gene names and metadata, including Family, Sex, Treatment Group, and Plate Run
DOI: 10.6084/m9.figshare.31166003.v1
title: Additional file 5 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 5: Raw Fluidigm Ct values organized with samples in rowsand columns for gene names and metadata, including Family, Sex, Treatment Group, and Plate Run
DOI: 10.6084/m9.figshare.31166006
title: Additional file 6 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 6: 16S rRNA sequencing count data at the genus level, used for downstream analysis
DOI: 10.6084/m9.figshare.31166006.v1
title: Additional file 6 of Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle)

description: Additional file 6: 16S rRNA sequencing count data at the genus level, used for downstream analysis
DOI: 10.5061/dryad.3n5tb2rhk
title: The past, present, and future of herbivore impacts on savanna vegetation

description: 1) Herbivory is a key process structuring vegetation in savannas,
 especially in Africa where large mammal herbivore communities remain
 intact. Exclusion experiments consistently show that herbivores impact
 savanna vegetation, but effect size variation has resisted explanation,
 limiting our understanding of the past, present, and future roles of
 herbivory in savanna ecosystems. 2) Synthesis of vegetation responses to
 herbivore exclusion shows that herbivory decreased grass abundance by
 57.0% and tree abundance by 30.6% across African savannas. 3) The
 magnitude of herbivore exclusion effects scaled with herbivore abundance:
 more grazing herbivores resulted in larger grass responses and more
 browsing herbivores in larger tree responses. However, existing
 experiments are concentrated in semi-arid savannas (400-800 mm rainfall)
 and soils data are mostly lacking, which makes disentangling environmental
 constraints a challenge and priority for future research. 4) Observed
 herbivore impacts were ~ 2.1× larger than existing estimates modeled based
 on consumption. Wildlife metabolic rates may be higher than are usually
 used for estimating consumption, which offers one clear avenue for
 reconciling estimated herbivore consumption with observed herbivore
 impacts. Plant-soil feedbacks, plant community composition, and the
 phenological or demographic timing of herbivory may also influence
 vegetation productivity, thereby magnifying herbivore impacts. 5) Because
 herbivore abundance so closely predicts vegetation impact, changes in
 herbivore abundance through time are likely predictive of the past and
 future of their impacts. Grazer diversity in Africa has declined from its
 peak 1 million years ago and wild grazer abundance has declined
 historically, suggesting that grazing likely had larger impacts in the
 past than it does today. 6) Current wildlife impacts are dominated by
 small-bodied mixed feeders, which will likely continue into the future,
 but the magnitude of top-down control may also depend on changing climate,
 fire, and atmospheric CO2. 7) Synthesis. Herbivore biomass determines the
 magnitude of their impacts on savanna vegetation, with effect sizes based
 on direct observation that potentially outstrip existing modeled estimates
 across African savannas. Findings suggest substantial ecosystem impacts of
 herbivory and allow us to generate evidence-based hypotheses of the past
 and future impacts of herbivores on savanna vegetation. --
DOI: 10.5061/dryad.3j9kd51hv
title: Data of: Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts

description: These files are results obtained inImputation-free reconstructions of
 three-dimensional chromosome architectures in human diploid single-cells
 using allele-specified contactsby Yoshito Hirata, Arisa H. Oda, Chie
 Motono, Masanori Shiro & Kunihiro Ohta. There are 33 files for the
 corresponding each reconstruction of three-dimensional chromosomone
 structuresfor each cell.There are 3D structures for 15 GM cells and 18
 PBMC cells, which are obtained from the single cell Hi-C
 data of Tan et al. Science (2018). For each file, there
 are 6 columns:The first column corresponds to the allele (0: maternal, 1:
 paternal)The second column corresponds to the chromosome (1-22:
 chromosome's number, 23: X, 24: Y)The third column corrsponds to the
 base point.The fourth column, the fifth column and the sixth column
 correspond to x-, y-, and z-axes of our reconstruction.
description: First, the single cell Hi-C data of Tan et al. (2018) have been
 downloaded from through GEO Series accession number
 GSE117876 at www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117876.  Then, we applied the proposed recurrence plot-based method here to reconstruct 3D chromosome structures of 33 cells (15 GM cells and 18 PBMC cells). The resulting 3D chromosome structures are deposited here.
description: Each file represents the 3D chromosome structure for each
 cell. For each file, there are 6 columns to represent
 3D structure:<br>The first column corresponds to the allele (0:
 maternal, 1: paternal)<br>The second column corresponds to the
 chromosome (1-22: chromosome's number, 23: X, 24: Y)<br>The
 third column corrsponds to the base point.<br>The fourth column, the
 fifth column and the sixth column correspond to x-, y-, and z-axes of our
 reconstruction.
DOI: 10.6084/m9.figshare.31166018
title: Additional file 2 of Clinical and genetic analyses of 17 Chinese patients with glycogen storage disease type IXc

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.31166018.v1
title: Additional file 2 of Clinical and genetic analyses of 17 Chinese patients with glycogen storage disease type IXc

description: Supplementary Material 2
DOI: 10.5061/dryad.n02v6wwwz
title: Win-Stay-Lose-Shift as a self-confirming equilibrium in the iterated prisoner's dilemma

description: Evolutionary game theory assumes that players replicate a highly scored
 player's strategy through genetic inheritance. However, when learning
 occurs culturally, it is often difficult to recognize
 someone's strategy just by observing the behaviour. In this
 work, we consider players with memory-one stochastic strategies in the
 iterated prisoner's dilemma, with an assumption that they cannot
 directly access each other's strategy but only observe the actual
 moves for a certain number of rounds. Based on the observation, the
 observer has to infer the resident strategy in a Bayesian way and
 chooses his or her own strategy accordingly. By examining
 the best-response relations, we argue that players can escape
 from full defection into a cooperative equilibrium supported by
 Win-Stay-Lose-Shift in a self-confirming manner, provided that the cost of
 cooperation is low and the observational learning supplies sufficiently
 large uncertainty.
DOI: 10.5061/dryad.h18931zks
title: African apes data set

description: Aim: Modelling African great ape distribution has until now focused on
 current or past conditions, whilst future scenarios remain scarcely
 explored. Using an ensemble forecasting approach, we predicted changes in
 taxon-specific distribution under future scenarios of climate, land-use
 and human populations for 1) areas outside protected areas (PAs) only
 (assuming complete management effectiveness of PAs), 2) the entire study
 region, and 3) interspecies range overlap. Location: Tropical Africa
 Methods: We compiled occurrence data (n=5,203) on African apes from the
 IUCN A.P.E.S. database and extracted relevant climate-, habitat-, and
 human-related predictors representing current and future (2050) conditions
 to predict taxon-specific range change under a best- and a worst-case
 scenario, using ensemble forecasting. Results: The predictive performance
 of the models varied across taxa. Synergistic interactions between
 predictors are shaping African ape distribution, particularly
 human-related variables. On average across taxa, a range decline of 50% is
 expected outside PAs under the best scenario if no dispersal occurs (61%
 in worst scenario). Otherwise, an 85% range reduction is predicted to
 occur across study regions (94% worst). However, range gains are predicted
 outside PAs if dispersal occurs (52% best, 21% worst), with a slight
 increase in gains expected across study regions (66% best, 24% worst).
 Moreover, more than half of range losses and gains are predicted to occur
 outside PAs where interspecific ranges overlap. Main Conclusions: Massive
 range decline is expected by 2050, but range gain is uncertain as African
 apes will not be able to occupy these new areas immediately due to their
 limited dispersal capacity, migration lag and ecological constraints.
 Given that most future range changes are predicted outside PAs, Africa’s
 current PA network is likely to be insufficient for preserving suitable
 habitats and maintaining connected ape populations. Thus, conservation
 planners urgently need to integrate land-use planning and climate change
 mitigation measures at all decision-making levels both in range countries
 and abroad.
description: This data set represents released data from the APES
 Database <b>(</b><b>http://apesportal.eva.mpg.de</b>) under restricted policies and user agreement. This data set was made available for the purpose of this paper and all data owners should be contacted whenever the data set is used for other purposes including reports, book sections, articles, conference papers, theses, dissertations, or other publications (see information about the co-authors in the paper or contact the main author).
DOI: 10.6084/m9.figshare.31166024
title: Additional file 1 of A pangenome insight into the genome divergence and flower color diversity among Rhododendron species

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.31166024.v1
title: Additional file 1 of A pangenome insight into the genome divergence and flower color diversity among Rhododendron species

description: Supplementary Material 1.
DOI: 10.5061/dryad.tqjq2bvzx
title: A Tasquinomod-loaded dopamine-modified pH sensitive hydrogel is effective at inhibiting the proliferation of KRAS mutant lung cancer cells

description: Hydrogels can maintain a high local drug concentration during treatments
 and may be useful to local targeting diseased areas. We propose a pH
 sensitive hydrogel consisting of polyvinylpyrrolidone (PVP) and chitosan
 as a new treatment method for KRAS mutant lung cancer. Addition of
 dopamine improved the drug loading and release effects of this hydrogel.
 We demonstrate that Tasquinimod-loading of this dopamine-modified pH
 sensitive hydrogel is more effective than Tasquinimod alone for inhibiting
 the proliferation of KRAS mutant lung cancer cells. Combina-tion of
 conventional drugs with hydrogels may thus provide a new treatment
 modality for lung cancer.
description: The data was collected directly during the experiment and
 processed by GraphPad Prism and Origin Graph.
description: We uploaded all reusable files and original data, which can be
 processed in GraphPad Prism and Origin Graph to achieve the results we
 presented.
DOI: 10.5061/dryad.tx95x69xr
title: Measuring resilience and resistance in aging and Alzheimer disease using residual methods: A systematic review and meta-analysis

description: Objective: There is currently a lack of consensus on how to optimally
 define and measure resistance and resilience in brain and cognitive aging.
 Residual methods use residuals from regression analysis to quantify the
 capacity to avoid (resistance) or cope (resilience) “better or worse than
 expected” given a certain level of risk or cerebral damage. We reviewed
 the rapidly-growing literature on residual methods in the context of aging
 and Alzheimer’s disease (AD), and performed meta-analyses to investigate
 associations of residual-method based resilience and resistance measures
 with longitudinal cognitive and clinical outcomes. Methods: A systematic
 literature search of PubMed and Web-of-Science databases (consulted until
 March 2020) and subsequent screening led to 54 studies fulfilling
 eligibility criteria, including 10 studies suitable for the meta-analyses.
 Results: We identified articles using residual methods aimed at
 quantifying resistance (n=33), cognitive resilience (n=23) and brain
 resilience (n=2). Critical examination of the literature revealed that
 there is considerable methodological variability in how the residual
 measures were derived and validated. Despite methodological differences
 across studies, meta-analytic assessments showed significant associations
 of levels of resistance (HR[95%CI]=1.12[1.07-1.17], p&lt;0.0001) and
 levels of resilience (HR[95%CI]=0.46[0.32-0.68], p&lt;0.001) with risk
 of progression to dementia/AD. Resilience was also associated with rate of
 cognitive decline (β[95%CI]=0.05[0.01-0.08], p&lt;0.01). Conclusion:
 This review and meta-analysis supports the usefulness of residual methods
 as appropriate measures of resilience and resistance, as they capture
 clinically meaningful information in aging and AD. More rigorous
 methodological standardization is needed, however, to increase
 comparability across studies and, ultimately, application in clinical
 practice.
DOI: 10.5061/dryad.fqz612jsc
title: Knowledge on microbiome and dysbiosis science in medical sciences students

description: Background: The emerging science of the human microbiome examines the
 microbial composition and diversity of the human body. Concurrent evidence
 has shown that each body system’s microbiome is unique in nature and that
 the gut microbiome seems to master the other microbiota that colonise the
 human body. Disturbance of microbiome diversity has been shown to be
 associated with a wide spectrum of diseases, such as obesity, diabetes
 mellitus, asthma, and autism, which highlights beneficial bacteria
 supplementation as a potential therapeutic measure. Consequently, the
 current paper examined the knowledge of final-year students and interns in
 three health track majors. Methods: A survey comprising 34 questions
 covering three main topics was designed, validated, and distributed to
 students to assess knowledge on the human microbiome, dysbiosis, and
 management of a disordered microbiome. Result: Overall knowledge of the
 microbial composition of the human body was adequate in the three tested
 majors; however, knowledge on dysbiosis and management of impaired
 microbiome was significantly low. Conclusion: Knowledge of
 microbiome-dysbiosis sciences is necessary, and our findings demonstrate
 the need to address this emerging science as a learning outcome that is
 implemented in all microbiology courses taught to the three investigated
 programs.
description: A set of questions surveyed through QuestionPro.