cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.236j7
title: Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

description: The spatial organization of genomes is non-random, cell-type specific, and
 has been linked to cellular function. The investigation of spatial
 organization has traditionally relied extensively on fluorescence
 microscopy. The validity of the imaging methods used to probe spatial
 genome organization often depends on the accuracy and precision of
 distance measurements. Imaging-based measurements may either use 2
 dimensional datasets or 3D datasets which include the z-axis information
 in image stacks. Here we compare the suitability of 2D vs 3D distance
 measurements in the analysis of various features of spatial genome
 organization. We find in general good agreement between 2D and 3D analysis
 with higher convergence of measurements as the interrogated distance
 increases, especially in flat cells. Overall, 3D distance measurements are
 more accurate than 2D distances, but are also more susceptible to noise.
 In particular, z-stacks are prone to error due to imaging properties such
 as limited resolution along the z-axis and optical aberrations, and we
 also find significant deviations from unimodal distance distributions
 caused by low sampling frequency in z. These deviations are ameliorated by
 significantly higher sampling frequency in the z-direction. We conclude
 that 2D distances are preferred for comparative analyses between cells,
 but 3D distances are preferred when comparing to theoretical models in
 large samples of cells. In general and for practical purposes, 2D distance
 measurements are preferable for many applications of analysis of spatial
 genome organization.
description: READMESpot Position
 MeasurementsTables including the
 Acapella output (spot positions) and the R-calculated spot-to-spot
 distances by experiment.SpotPositionMeasurements.zipAcapella Scripts and ParametersAcapella scripts and parameter files used to analyze image files and generate spot positionsAcapellaScriptsAndParameters.zipRmd ScriptsR markdown scripts used to calculate distances from Acapella output spot positions and perform subsequent analysesRmdScripts.zipBC_160524_1000 imagesImages from acquisition BC_160524 with 1 micron z-slicesBC_160524_1000.zipBC_160525_300 imagesImages from BC_160525 experiment with 300 nm z-slicesBC_160525_300.zipBC_160531_300 imagesImages from BC_160531 acquisition with 300 nm z-slicesBC_160531_300.zipBC_160614_300 imagesImages from BC_160614 acquisition with a 300 nm z-slicesBC_160614_300.zip
DOI: 10.5061/dryad.j2t92
title: Data from: Towards the automatic classification of avian flight calls for bioacoustic monitoring

description: Automatic classification of animal vocalizations has great potential to
 enhance the monitoring of species movements and behaviors. This is
 particularly true for monitoring nocturnal bird migration, where automated
 classification of migrants’ flight calls could yield new biological
 insights and conservation applications for birds that vocalize during
 migration. In this paper we investigate the automatic classification of
 bird species from flight calls, and in particular the relationship between
 two different problem formulations commonly found in the literature:
 classifying a short clip containing one of a fixed set of known species
 (N-class problem) and the continuous monitoring problem, the latter of
 which is relevant to migration monitoring. We implemented a
 state-of-the-art audio classification model based on unsupervised feature
 learning and evaluated it on three novel datasets, one for studying the
 N-class problem including over 5000 flight calls from 43 different
 species, and two realistic datasets for studying the monitoring scenario
 comprising hundreds of thousands of audio clips that were compiled by
 means of remote acoustic sensors deployed in the field during two
 migration seasons. We show that the model achieves high accuracy when
 classifying a clip to one of N known species, even for a large number of
 species. In contrast, the model does not perform as well in the continuous
 monitoring case. Through a detailed error analysis (that included full
 expert review of false positives and negatives) we show the model is
 confounded by varying background noise conditions and previously unseen
 vocalizations. We also show that the model needs to be parameterized and
 benchmarked differently for the continuous monitoring scenario. Finally,
 we show that despite the reduced performance, given the right conditions
 the model can still characterize the migration pattern of a specific
 species. The paper concludes with directions for future research.
description: CLO-43SDCLO-WTSPCLO-SWTHCLO-43SD-AUDIOCLO-WTSP-AUDIOCLO-SWTH-AUDIO
DOI: 10.6084/m9.figshare.31160266
title: Climate Change–Driven Projections of Suitable Habitat for <i>Phleum pratense</i> across China

description: In the context of global climate change, clarifying the effects of climatic factors on the potential distribution of forage grass species is of critical importance for grassland development and ecological management. In this study, <i>Phleum pratense</i> was selected as the focal species, and an ensemble species distribution modeling framework was constructed using the Biomod2 platform. After excluding highly correlated environmental variables, 17 ecologically meaningful predictors were retained to project the potential habitat suitability patterns of <i>P. pratense</i> and their future dynamics. The results indicate that the ensemble model achieved high predictive accuracy. Annual mean UV-B radiation, mean temperature of the driest quarter, and precipitation of the coldest quarter were identified as the primary climatic factors shaping the potential distribution of <i>P. pratense</i>. Under current climatic conditions, highly suitable habitats occupy a relatively limited and fragmented area, whereas low- and moderately suitable habitats are predominant. Under future climate scenarios, increasing emission levels are associated with an overall contraction of moderately and highly suitable areas, accompanied by a continuous expansion of unsuitable habitats. In addition, the centroid of highly suitable habitats is projected to shift northwestward. These findings suggest that climate change may substantially alter the potential suitable range of <i>P. pratense</i> by modifying key climatic gradients and stress-period conditions. This study provides a scientific basis for the utilization of <i>P. pratense</i> germplasm resources and the sustainable development of plateau grassland systems.
DOI: 10.6084/m9.figshare.31160266.v2
title: Climate Change–Driven Projections of Suitable Habitat for <i>Phleum pratense</i> across China

description: In the context of global climate change, clarifying the effects of climatic factors on the potential distribution of forage grass species is of critical importance for grassland development and ecological management. In this study, <i>Phleum pratense</i> was selected as the focal species, and an ensemble species distribution modeling framework was constructed using the Biomod2 platform. After excluding highly correlated environmental variables, 17 ecologically meaningful predictors were retained to project the potential habitat suitability patterns of <i>P. pratense</i> and their future dynamics. The results indicate that the ensemble model achieved high predictive accuracy. Annual mean UV-B radiation, mean temperature of the driest quarter, and precipitation of the coldest quarter were identified as the primary climatic factors shaping the potential distribution of <i>P. pratense</i>. Under current climatic conditions, highly suitable habitats occupy a relatively limited and fragmented area, whereas low- and moderately suitable habitats are predominant. Under future climate scenarios, increasing emission levels are associated with an overall contraction of moderately and highly suitable areas, accompanied by a continuous expansion of unsuitable habitats. In addition, the centroid of highly suitable habitats is projected to shift northwestward. These findings suggest that climate change may substantially alter the potential suitable range of <i>P. pratense</i> by modifying key climatic gradients and stress-period conditions. This study provides a scientific basis for the utilization of <i>P. pratense</i> germplasm resources and the sustainable development of plateau grassland systems.
DOI: 10.6084/m9.figshare.31160266.v1
title: Climate Change–Driven Projections of Suitable Habitat for <i>Phleum pratense</i> across China

description: In the context of global climate change, clarifying the effects of climatic factors on the potential distribution of forage grass species is of critical importance for grassland development and ecological management. In this study, <i>Phleum pratense</i> was selected as the focal species, and an ensemble species distribution modeling framework was constructed using the Biomod2 platform. After excluding highly correlated environmental variables, 17 ecologically meaningful predictors were retained to project the potential habitat suitability patterns of <i>P. pratense</i> and their future dynamics. The results indicate that the ensemble model achieved high predictive accuracy. Annual mean UV-B radiation, mean temperature of the driest quarter, and precipitation of the coldest quarter were identified as the primary climatic factors shaping the potential distribution of <i>P. pratense</i>. Under current climatic conditions, highly suitable habitats occupy a relatively limited and fragmented area, whereas low- and moderately suitable habitats are predominant. Under future climate scenarios, increasing emission levels are associated with an overall contraction of moderately and highly suitable areas, accompanied by a continuous expansion of unsuitable habitats. In addition, the centroid of highly suitable habitats is projected to shift northwestward. These findings suggest that climate change may substantially alter the potential suitable range of <i>P. pratense</i> by modifying key climatic gradients and stress-period conditions. This study provides a scientific basis for the utilization of <i>P. pratense</i> germplasm resources and the sustainable development of plateau grassland systems.
DOI: 10.5281/zenodo.18391293
title: SuperDARN data in netCDF format (2006-Jan)

description: 2006-Jan SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6632899
title: SuperDARN data in netCDF format (2006-Jan)

description: 2006-Jan SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.8kn8c
title: Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them

description: Custom genotyping arrays provide a flexible and accurate means of
 genotyping single nucleotide polymorphisms (SNPs) in a large number of
 individuals of essentially any organism. However, validation rates,
 defined as the proportion of putative SNPs that are verified to be
 polymorphic in a population, are often very low. A number of potential
 causes of assay failure have been identified, but none have been explored
 systematically. In particular, as SNPs are often developed from
 transcriptomes, parameters relating to the genomic context are rarely
 taken into account. Here, we assembled a draft Antarctic fur seal
 (Arctocephalus gazella) genome (assembly size: 2.41Gb; scaffold/contig
 N50: 3.1Mb/27.5kb). We then used this resource to map the probe sequences
 of 144 putative SNPs genotyped in 480 individuals. The number of
 probe-to-genome mappings and alignment length together explained almost a
 third of the variation in validation success, indicating that sequence
 uniqueness and proximity to intron-exon boundaries play an important role.
 The same pattern was found after mapping the probe sequences to the Walrus
 and Weddell seal genomes, suggesting that the genomes of species divergent
 by as much as 23 million years can hold information relevant to SNP
 validation outcomes. Additionally, re-analysis of genotyping data from
 seven previous studies found the same two variables to be significantly
 associated with SNP validation success across a variety of taxa. Finally,
 our study reveals considerable scope for validation rates to be improved,
 either by simply filtering for SNPs whose flanking sequences align
 uniquely and completely to a reference genome, or through predictive
 modeling.
description: submission.assembly.ArcGaz001_AP3.fastaDraft fur seal genome v1.0Seal_assay_SNPs.csvList of pre-validated fur seal SNPs plus variables used for modeling SNP validation success.crossvalidation.RR script to perform the k-fold cross-validation.
DOI: 10.5061/dryad.32tm1k4
title: Data from: Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

description: Although Plasmodium vivax is responsible for the majority of malaria
 infections outside Africa, little is known about its evolution and pathway
 to humans. Its closest genetic relative, Plasmodium vivax-like, was
 discovered in African great apes and is hypothesized to have given rise to
 P. vivax in humans. To unravel the evolutionary history and adaptation of
 P. vivax to different host environments, we generated using long and short
 read sequence technologies two new P. vivax-like reference genomes and 9
 additional P. vivax-like genotypes. Analyses show that the genomes of P.
 vivax and P. vivax-like are highly similar and co-linear within the core
 regions. Phylogenetic analyses clearly show that P. vivax-like parasites
 form a genetically distinct clade from P. vivax. Concerning the relative
 divergence dating, we show that the evolution of P. vivax in humans did
 not occur at the same time as the other agents of human malaria, thus
 suggesting that the transfer of Plasmodium parasites to humans happened
 several times independently over the history of the Homo genus. We further
 identify several key genes that exhibit signatures of positive selection
 exclusively in the human P. vivax parasites. Interestingly, two of these
 genes have been identified to also be under positive selection in the
 other main human malaria agent, Plasmodium falciparum, thus suggesting
 their key role in the evolution of the ability of these parasites to
 infect humans or their anthropophilic vectors. We finally demonstrate that
 some gene families important for red blood cell (RBC) invasion (a key step
 of the life cycle of these parasites) have undergone lineage-specific
 evolution in the human parasite (e.g. Reticulocyte Binding Proteins).
description: S1FigData_PvlkRAFdataset_1 samples Pvl01 to Pvl06This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl01 to Pvl06. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_1.zipS1FigData_PvlkRAFdataset_2 samples Pvl07 to Pvl09This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl07 to Pvl09. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_2.zipS1FigData_PvlkRAFdataset_3 samples Pvl10 and Pvl11This archive contains the vcf files listing all the high quality positions kept to draw the reference allele frequency distribution for samples Pvl10 and Pvl11. Please see the Materials and methods section for a detailed description.S1FigData_PvlkRAFdataset_3.zipPvivaxlikeGenomes.tarThe Pvl_genomeData folder contains the data of two genomes of Plasmodium vivax-like parasites (Pvl01 and Pvl06). Further information is included in the README within "PvivaxlikeGenomes.tar.gz"
DOI: 10.5061/dryad.hn8gp
title: Data from: ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system

description: Numerous biological systems oscillate over time or space. Despite these
 oscillators’ importance, data from an oscillatory system is problematic
 for existing methods of regularized supervised learning. We present
 ZeitZeiger, a method to predict a periodic variable (e.g. time of day)
 from a high-dimensional observation. ZeitZeiger learns a sparse
 representation of the variation associated with the periodic variable in
 the training observations, then uses maximum-likelihood to make a
 prediction for a test observation. We applied ZeitZeiger to a
 comprehensive dataset of genome-wide gene expression from the mammalian
 circadian oscillator. Using the expression of 13 genes, ZeitZeiger
 predicted circadian time (internal time of day) in each of 12 mouse organs
 to within ∼1 h, resulting in a multi-organ predictor of circadian time.
 Compared to the state-of-the-art approach, ZeitZeiger was faster, more
 accurate and used fewer genes. We then validated the multi-organ predictor
 on 20 additional datasets comprising nearly 800 samples. Our results
 suggest that ZeitZeiger not only makes accurate predictions, but also
 gives insight into the behavior and structure of the oscillator from which
 the data originated. As our ability to collect high-dimensional data from
 various biological oscillators increases, ZeitZeiger should enhance
 efforts to convert these data to knowledge.
description: Data, code, and results
 used in the paper.The zip file contains
 all gene expression data, metadata, R code, and results, and can be used
 to reproduce all the figures in the paper. See the readme.txt for
 instructions.zeitzeiger_mouse.zip
DOI: 10.5061/dryad.155kb26
title: Data from: Intraspecific trait variation increases species diversity in a trait-based grassland model

description: Intraspecific trait variation (ITV) is thought to play a significant role
 in community assembly, but the magnitude and direction of its influence
 are not well understood. Although it may be critical to better explain
 population persistence, species interactions, and therefore biodiversity
 patterns, manipulating ITV in experiments is challenging. We therefore
 incorporated ITV into a trait- and individual-based model of grassland
 community assembly by adding variation to the plants’ functional traits,
 which then drive life-history trade-offs. Varying the amount of ITV in the
 simulation, we examine its influence on pairwise-coexistence and then on
 the species diversity in communities of different initial sizes. We find
 that ITV increases the ability of the weakest species to invade most, but
 that this effect does not scale to the community level, where the primary
 effect of ITV is to increase the persistence and abundance of the
 competitively-average species. Diversity of the initial community is also
 of critical importance in determining ITV’s efficacy; above a threshold of
 interspecific diversity, ITV does not increase diversity further. For
 communities below this threshold, ITV mainly helps to increase diversity
 in those communities that would otherwise be low-diversity. These findings
 suggest that ITV actively maintains diversity by helping the species on
 the margins of persistence, but mostly in habitats of relatively low alpha
 and beta diversity.
description: IBC-grassSimulated datasets and their corresponding analyses (deriving the paper's graphs) from IBC-grass. Please note that the file paths in each script must be set, pointing to both the Util.R script (some utility functions each analysis script uses) as well as to the .Rda data files themselves.CrawfordEtAl_2018_IBC-grass.zip