cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dp094
title: Data from: Comparison and optimization of hiPSC forebrain cortical differentiation protocols

description: Several protocols have been developed for human induced pluripotent stem
 cell neuronal differentiation. We compare several methods for forebrain
 cortical neuronal differentiation by assessing cell morphology,
 immunostaining and gene expression. We evaluate embryoid aggregate vs.
 monolayer with dual SMAD inhibition differentiation protocols, manual vs.
 AggreWell aggregate formation, plating substrates, neural progenitor cell
 (NPC) isolation methods, NPC maintenance and expansion, and astrocyte
 co-culture. The embryoid aggregate protocol, using a Matrigel substrate,
 consistently generates a high yield and purity of neurons. NPC isolation
 by manual selection, enzymatic rosette selection, or FACS all are
 efficient, but exhibit some differences in resulting cell populations.
 Expansion of NPCs as neural aggregates yields higher cell purity than
 expansion in a monolayer. Finally, co-culture of iPSC-derived neurons with
 astrocytes increases neuronal maturity by day 40. This study directly
 compares commonly employed methods for neuronal differentiation of iPSCs,
 and can be used as a resource for choosing between various differentiation
 protocols.
description: PLOS ONE total
 dataExcel file with all data
 from "Comparison and Optimization of hiPSC Forebrain Cortical
 Differentiation Protocols".
DOI: 10.5061/dryad.dh2hg
title: Data from: Growth affects dispersal success in social mole-rats, but not the duration of philopatry

description: In naked mole-rats (Heterocephalus glaber), some non-breeding males show
 faster growth and are more likely to disperse than others. These
 differences have been suggested to be the result of a specialized
 developmental strategy leading to shorter philopatry and independent
 breeding, as opposed to extended philopatry as non-reproductive helpers.
 However, it is unclear whether fast-growing males disperse sooner than
 slow-growing males. An alternative explanation is that variation in
 quality between individuals causes high-quality individuals to grow
 quickly and maximize dispersal success without reducing philopatry. Here
 we show, that in Damaraland mole-rats (Fukomys damarensis), males that
 subsequently disperse successfully, grow faster than other
 non-reproductive males. This pattern is predicted by both hypotheses and
 does not discriminate between them. However, contrary to the suggestion
 that faster growth represents a developmental specialisation for early
 dispersal, fast-growing and slow-growing males remained equally long in
 their natal groups. Our study provides no evidence for adaptive divergence
 in male development leading either to early dispersal, or extended
 philopatry. Instead of representing specialized dispersers, fast-growing
 males of this species may be high-quality individuals.
description: PublicationDataData of the non-reproductive males with growth rate, body mass, group size, disperser, group ID and sex for each individual.PublicationGrowthDataAnimal ID, group ID, growth rate, body mass, sex and tenure of philopatry (days) for each non-reproductive male.PublicationTimeColonyDataAnima ID, group ID, time of philopatry (days) and disperse (yes-no) for each non-reproductive male.
DOI: 10.5061/dryad.b5335
title: Data from: Applying a biocomplexity approach to modelling farmer decision-making and land-use impacts on wildlife

description: 1. The biocomplexity approach refers to a fully integrated
 social-ecological systems (SES) simulation that represents bidirectional
 feedbacks between social and ecological components. This method is
 essential to accurately assess impacts of economy and policy on SES such
 as agroecosystems, where feedbacks between the drivers and impacts of
 cropping changes need to be simulated. Here we exemplify the biocomplexity
 approach using energy maize, which is becoming an important source of
 bioenergy in Europe, and thus, might cause a significant change in land
 use with knock on-effects on wildlife. 2. The integrated simulation tool
 consisted of a farmer decision making agent-based model fully coupled to
 the Animal Landscape and Man Simulatin System (ALMaSS)an agent-based
 simulation system for predicting impacts of land use on a range of Danish
 wildlife species: the brown hare (Lepus europaeus), the grey partridge
 (Perdix perdix), the skylark (Alauda arvensis), a carabid beetle
 (Bembidion lampros), a linyphiid spider (Erigone atra), and the field vole
 (Microtus agrestis). This was used to assess the impacts of increasing
 demand on energy maize on six animal species. Two types of experimental
 scenarios were evaluated, with and without feedback between the social and
 ecological system. The assessment of species responses was based on
 changes in population size, abundance and occupancy. 3. The response to
 the cultivation of energy maize was negative for three vertebrate species
 (skylark, hare and field vole) and positive for partridge and the two
 invertebrate species. The feedback scenarios showed that the incorporation
 of information from ecological system to the farmer decision making
 affected both a trend in area cultivated with energy maize as well as the
 animal responses. 4. Synthesis and applications. Fully coupling
 agent-based decision making and environmental simulation allows a detailed
 representation and integration of both social and ecological components of
 agricultural systems at proper spatial and temporal scales as well as of
 dynamic feedbacks between the two systems. By employing easy to interpret
 measures of changes in abundance and spatial occupancy of animal species,
 the simulation results could inform and simplify decision-making on
 expected impacts of economy and policy regulations on wildlife.
description: Simulation results
 supporting figures for the paperThis file provides the
 summary of all simulation results used in the paper. All results were
 created using ALMaSS using the input data specified in the papers
 supplementary information.Data for
 upload.xlsx
DOI: 10.5061/dryad.1682
title: Data from: Genetic evidence for high propagule pressure and long-distance dispersal in monk parakeet (Myiopsitta monachus) invasive populations

description: The monk parakeet (Myiopsitta monachus) is a successful invasive species
 that does not exhibit life history traits typically associated with
 colonizing species (e.g., high reproductive rate or long-distance
 dispersal capacity). To investigate this apparent paradox, we examined
 individual and population genetic patterns of microsatellite loci at one
 native and two invasive sites. More specifically, we aimed to evaluate the
 role of propagule pressure, sexual monogamy, and long-distance dispersal
 in monk parakeet invasion success. Our results indicate little loss of
 genetic variation at invasive sites relative to the native site. We also
 found strong evidence for sexual monogamy from patterns of relatedness
 within sites, and no definite cases of extra-pair paternity in either the
 native site sample or the examined invasive site. Taken together, these
 patterns directly and indirectly suggest that high propagule pressure has
 contributed to monk parakeet invasion success. In addition, we found
 evidence for frequent long-distance dispersal at an invasive site (~100km)
 that sharply contrasted with previous estimates of smaller dispersal
 distance made in the native range (~2km), suggesting long-range dispersal
 also contributes to the species' spread within the United States.
 Overall, these results add to a growing body of literature pointing to the
 important role of propagule pressure in determining, and thus predicting,
 invasion success, especially for species whose life history traits are not
 typically associated with invasiveness.
description: Monk parakeet genotype,
 nest membership, age class and sex dataMicrosatellite data, and
 other information on monk parakeets in three sites.myiopalldatabase.xls
DOI: 10.15468/dl.59re95
title: Occurrence Download

description: A dataset containing 270 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Discopodium penninervium",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 270 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000898-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bs79gk5
title: Data from: The plant microbiome and native plant restoration: the example of native mycorrhizal fungi

description: Ecological restoration efforts can increase the diversity and function of
 degraded areas. However, current restoration practices cannot typically
 re-establish the full diversity and species composition of remnant plant
 communities. We present evidence that restoration quality can be improved
 by reintroducing key organisms from the native plant microbiome. In
 particular, root symbionts called arbuscular mycorrhizal fungi are
 critical in shaping grassland communities, but are sensitive to
 anthropogenic disturbance, which may pose a problem for grassland
 restoration. Here we highlight the conceptual motivation and empirical
 evidence evaluating native mycorrhizal fungi, as opposed to commercial
 fungi. Reintroduction of the native microbiome and native mycorrhizal
 fungi improves plant diversity, accelerates succession, and increases the
 establishment of plants that are often missing from restored communities.
 The example of mycorrhizal fungi serves to illustrate the value of a more
 holistic view of plant communities and restoration that embraces the
 intricacies and dynamics of native microbial communities.
description: Data for figures 3, 4,
 5Data
 for figures 3,4, 5Dryad Submission
 2.zip
DOI: 10.5061/dryad.412h3
title: Data from: Historical invasion records can be misleading: genetic evidence for multiple introductions of invasive raccoons (Procyon lotor) in Germany

description: Biological invasions provide excellent study systems to understand
 evolutionary, genetic and ecological processes during range expansions.
 There is strong evidence for positive effects of high propagule pressure
 and the associated higher genetic diversity on invasion success, but some
 species have become invasive despite small founder numbers. The raccoon
 (Procyon lotor) is often considered as a typical example for such a
 successful invasion resulting from a small number of founders. The
 species’ largest non-native population in Germany is commonly assumed to
 stem from a small number of founders and two separate founding events in
 the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20
 microsatellite loci sampled from the invasive range in Western Europe to
 test if these assumptions are correct. Contrary to the expectations,
 different genetic clustering methods detected evidence for at least four
 independent introduction events that gave rise to genetically
 differentiated subpopulations. Further smaller clusters were either
 artifacts or resulted from founder events at the range margin and recent
 release of captive individuals. We also found genetic evidence for
 on-going introductions of individuals. Furthermore a novel randomization
 process was used to determine the potential range of founder population
 size that would suffice to capture all the alleles present in a cluster.
 Our results falsify the assumption that this species has become widespread
 and abundant despite being genetically depauperate and show that
 historical records of species introductions may be misleading.
description: geneticdataFile with individual ID, geographical coordinates, microsatellite genotypes at 20 loci
DOI: 10.5061/dryad.9ts28
title: Data from: Forest management intensity affects aquatic communities in artificial tree holes

description: Forest management could potentially affect organisms in all forest
 habitats. However, aquatic communities in water-filled tree-holes may be
 especially sensitive because of small population sizes, the risk of
 drought and potential dispersal limitation. We set up artificial tree
 holes in forest stands subject to different management intensities in two
 regions in Germany and assessed the influence of local environmental
 properties (tree-hole opening type, tree diameter, water volume and water
 temperature) as well as regional drivers (forest management intensity,
 tree-hole density) on tree-hole insect communities (not considering other
 organisms such as nematodes or rotifers), detritus content, oxygen and
 nutrient concentrations. In addition, we compared data from artificial
 tree holes with data from natural tree holes in the same area to evaluate
 the methodological approach of using tree-hole analogues. We found that
 forest management had strong effects on communities in artificial tree
 holes in both regions and across the season. Abundance and species
 richness declined, community composition shifted and detritus content
 declined with increasing forest management intensity. Environmental
 variables, such as tree-hole density and tree diameter partly explained
 these changes. However, dispersal limitation, indicated by effects of
 tree-hole density, generally showed rather weak impacts on communities.
 Artificial tree holes had higher water temperatures (on average 2°C
 higher) and oxygen concentrations (on average 25% higher) than natural
 tree holes. The abundance of organisms was higher but species richness was
 lower in artificial tree holes. Community composition differed between
 artificial and natural tree holes. Negative management effects were
 detectable in both tree-hole systems, despite their abiotic and biotic
 differences. Our results indicate that forest management has substantial
 and pervasive effects on tree-hole communities and may alter their
 structure and functioning. We furthermore conclude that artificial
 tree-hole analogues represent a useful experimental alternative to test
 effects of changes in forest management on natural communities.
description: Petermann16_artificial
 tree holesPetermann16PLOSONE_data_for_dryad.xlsx
DOI: 10.5061/dryad.8pd38
title: Data from: Pre- and postcopulatory sexual selection favor aggressive, young males in polyandrous groups of red junglefowl

description: A challenge in evolutionary biology is to understand the operation of
 sexual selection on males in polyandrous groups, where sexual selection
 occurs before and after mating. Here, we combine fine-grained behavioural
 information (&gt;41,000 interactions) with molecular parentage data to
 study sexual selection in replicated, age-structured groups of polyandrous
 red junglefowl, Gallus gallus. Male reproductive success was determined by
 the number of females mated (precopulatory sexual selection) and his
 paternity share, which was driven by the polyandry of his female partners
 (postcopulatory sexual selection). Pre- and postcopulatory components of
 male reproductive success covaried positively; males with high mating
 success also had high paternity share. Two male phenotypes affected male
 pre- and postcopulatory performance: average aggressiveness towards rival
 males and age. Aggressive males mated with more females and more often
 with individual females, resulting in higher sexual exclusivity. Younger
 males mated with more females and more often with individual females,
 suffering less intense sperm competition than older males. Older males had
 a lower paternity share even allowing for their limited sexual
 exclusivity, indicating they may produce less competitive ejaculates.
 These results indicate that - in these populations - postcopulatory sexual
 selection reinforces precopulatory sexual selection, consistently
 promoting younger and more aggressive males.
description: Male
 Data1Data for individual male
 red junglefowl. Male reproductive success, mating success, average partner
 fecundity, paternity share and sperm competition intensities. Also
 including male traits (male age, average aggression and remating rate).
 Standardised values within groups are also provided.Male Female
 Data2Sexual network matrices
 for male (rows) and female (columns) red junglefowl in replicate groups.
 Networks are weighted by the number of copulations between male and female
 pairs.Male Male
 Data3Male-male aggression
 networks for replicate groups of red junglefowl. Rows are pairs of male
 red junglefowl. "maleout" is the number of times
 "male1" initiated an aggressive interaction with
 "male2". "malein" is the number of times male2
 initiated an aggressive interaction with
 "male1".
DOI: 10.5061/dryad.f9m8217
title: Data from: Natural language processing and recurrent network models for identifying genomic mutation-associated cancer treatment change from patient progress notes

description: Objectives: Natural language processing (NLP) and machine learning
 approaches were used to build classifiers to identify genomic-related
 treatment changes in the free-text visit progress notes of cancer
 patients. Methods: We obtained 5,889 de-identified progress reports (2,439
 words on average) for 755 cancer patients who have undergone a clinical
 Next Generation Sequencing (NGS) testing in Wake Forest Baptist
 Comprehensive Cancer Center for our data analyses. An NLP system was
 implemented to process the free-text data and extract NGS-related
 information. Three types of recurrent neural network (RNN) namely, gated
 recurrent unit (GRU), long-short term memory (LSTM), and bidirectional
 LSTM (LSTM_Bi) were applied to classify documents to the treatment-change
 and no-treatment-change groups. Further, we compared the performances of
 RNNs to five machine learning algorithms including Naive Bayes (NB),
 K-nearest Neighbor (KNN), Support Vector Machine for classification (SVC),
 Random Forest (RF), and Logistic Regression (LR). Results: Our results
 suggested that, overall, RNNs outperformed traditional machine learning
 algorithms, and LSTM_Bi showed the best performance among the RNNs in
 terms of accuracy, precision, recall, and F1 score. In addition,
 pre-trained word embedding can improve the accuracy of LSTM by 3.4% and
 reduce the training time by more than 60%. Discussion and Conclusion: NLP
 and RNN-based text mining solutions have demonstrated advantages in
 information retrieval and document classification tasks for unstructured
 clinical progress notes.
description: NLP_Report_Process_cleanPython code to process raw clinical report.NonDL_models_cleanPython file used to perform classification with non-RNN models.LSTM_keras_03012018_cleanPython code to perform RNN models.visualizeModels_cleanPython code to create visualizations.
DOI: 10.5061/dryad.bm2cg
title: Data from: Physiological regulation and efﬁcient xylem water transport regulate diurnal water and carbon balances of tropical lianas

description: Tropical lianas deploy most of their leaves towards the top of the forest
 canopy, whereas trees exhibit a more stratified crown. Forest canopies are
 often exposed to hot and windy conditions, and how lianas cope with the
 extremely high transpirational demands under these environments remains
 unknown. We investigated stem hydraulic properties, leaf drought
 tolerance, diurnal changes in leaf and stem water potentials (Ψleaf and
 Ψstem), stomatal conductance (gs), photosynthetic rate, sap flow and stem
 native percentage loss of conductivity (PLC) for four liana species in a
 tropical forest in southwest China. Five co-occurring tree species were
 also selected for comparison. Lianas reached maximal transpiration at a
 relatively lower vapour pressure deficit (&lt;1 kPa) than did
 co-occurring trees, suggesting vigorous photosynthesis during the morning.
 However, liana gs declined markedly over the day, with low gs at midday
 and afternoon. Lianas generally had higher stem sapwood-specific
 conductivity and maximum sap flux density but were less tolerant to
 drought-induced cavitation than were evergreen trees. Both lianas and
 trees lost leaf turgor in the top canopy at midday, but lianas lost leaf
 turgor earlier (∼2 h) than trees. Seven of eight species exhibited midday
 increases in PLC when xylem tensions were released to −0·3 to −0·5 MPa for
 PLC measurements. On average, lianas experienced high PLC (35·9%), along
 with a greater degree of disequilibrium between leaf and stem water
 potentials than trees (ΔΨstem–leaf: 1·37 MPa vs. 0·75 MPa) during the day.
 Earlier stomatal closure and efficient water transport may help lianas
 maintain higher Ψstem than trees despite having similar Ψleaf. Our results
 provide evidence that physiological regulation and efficient water
 transport mediate daily water relations in tropical lianas and may explain
 how lianas operate efficiently in tropical seasonal forests. Further
 studies involving a broader range of species are needed to confirm our
 findings.
description: Data used in all figures
 and Tables.Copy of
 Raw_data-1.xlsx
DOI: 10.5061/dryad.c84f7c4
title: Data from: Song performance is a condition-dependent dynamic trait honestly indicating the quality of paternal care in the Bull-headed Shrike

description: The good parent hypothesis in sexual selection predicts that if females
 can increase their fitness by mating with males who provide high-quality
 parental care, then female preferences for male phenotypes honestly
 indicating the quality of paternal care will evolve. In order to test this
 hypothesis, we investigated correlations between male song, the timing of
 pair formation of males, male feeding rate, and reproductive success, in
 the Bull-headed Shrike Lanius bucephalus (an altricial oscine passerine
 with biparental care). Analysis revealed that although the timing of pair
 formation was not correlated with most song characteristics (e.g.
 repertoire size), male morphological traits (e.g. tail length), or male
 territory size, it was negatively correlated with male singing tempo (i.e.
 the number of notes uttered per second). Those males that sang at higher
 speeds were in better body condition (i.e. body mass standardized by
 tarsus length3 was higher), fed their chicks frequently during the
 nestling period, and raised heavy chicks. These results show that in the
 Bull-headed Shrike male singing tempo is a condition-dependent dynamic
 trait honestly indicating the quality of paternal care, and strongly
 supports the good parent hypothesis.
description: Data from: Song
 performance is a condition-dependent dynamic trait honestly indicating the
 quality of paternal care in the Bull-headed ShrikeNishida_and_Takagi_2018.xlsx
DOI: 10.15468/dl.u35z4e
title: Occurrence Download

description: A dataset containing 3370 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Shortia"
 ]
}

 The dataset includes 3370 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000899-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.