cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hm83f7t
title: Data from: Pollination along an elevational gradient mediated both by floral scent and pollinator compatibility in the fig and fig‐wasp mutualism

description: In the fig (Moraceae) and fig‐wasp (Agaonidae) mutualism, scent is
 believed to be of primary importance in pollinator attraction and
 maintenance of species specificity. Scent divergence between closely
 related Ficus species seems sufficient in promoting reproductive isolation
 through pollinator behaviour, starting the process of speciation. We
 investigated volatile organic compound (VOC) variation from figs in
 several Ficus species endemic to Papua New Guinea. Sister species of
 section Papuacyse and subspecies of Ficus trichocerasa substitute each
 other along the continuously forested Mt. Wilhelm elevational gradient. We
 placed these species in a phylogenetic context to draw conclusions of
 scent divergence between close relatives. In addition, pollinator response
 to VOCs emitted by figs of different species was tested. Volatile profiles
 differed significantly between focal species, although with a varying
 degree of overlap between (sub)species and elevations. Pollinators were
 generally attracted to VOCs emitted only by their hosts except in one case
 where pollinating fig wasps were also attracted to the sister species of
 its host. Wasp morphological traits, however, indicate that it is
 mechanically impossible for this species to oviposit in figs of this
 atypical encounter. Synthesis. This study demonstrates that while scent is
 an effective signal for partner recognition, there are multiple barriers
 which help maintain prepollination isolation in fig and pollinating
 fig‐wasp interactions. Speciation along this elevational gradient is
 reinforced by divergence in key reproductive isolation mechanisms on both
 sides of the mutualism.
description: Wasp y-choice data and
 morphological measurementsThis file includes a
 brief summary of the y-choice experiments plus the raw data, as well as
 morphological measurements of wasps used in this study.behavoiur_morphology.xlsxVolatile data (clean)This is the volatile data after filtering control compounds and samplesPNG_volatiles_clean.csvVolatile data (raw)Raw volatile data before conversion and filteringPNG_volatiles_raw.csvSequence alignment used for the phylogenyfig.phylipVCF file for section Papuacyse used for STRUCTRUEitomicJoE.vcf.txtVCF file for F. trichocerasa used for STRUCTUREtri.vcf
DOI: 10.5061/dryad.4gt710v
title: Data from: Analysing the effect of paddy rice variety on fluorescence characteristics for nitrogen application monitoring

description: Paddy rice is one of the most important cereal crops worldwide, it is a
 significant target to accurately monitor its growth status and
 photosynthetic efficiency. Nitrogen (N) levels is a key factor closely
 related to crop growth. In this study, laser-induced fluorescence (LIF)
 technology combined with multivariate analysis was applied to investigate
 the effect of paddy rice variety on the N fertilizer levels monitoring.
 Principle components analysis was conducted to extract the variables of
 the main fluorescence characteristics to identify N levels. Experimental
 results demonstrated that no nitrogen fertilizer can be completely
 identified for each paddy rice variety. In addition, other N levels can
 also be well classified based on fluorescence characteristics. Then, the
 relationship between the fluorescence ratio (F735/ F685: F735, and F685
 denote the fluorescence intensity at 735nm, 685nm, respectively) and leaf
 N content of different paddy rice varieties was also discussed.
 Experimental results revealed that LIF technology is an effective method
 to monitor N fertilizer and leaf biochemical components of paddy rice.
description: fluore_spectra
DOI: 10.5061/dryad.p6261d6
title: Data from: Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates

description: Nitrogen-containing-bisphosphonates (N-BPs) are widely prescribed to treat
 osteoporosis and other bone-related diseases. Although previous studies
 established that N-BPs function by inhibiting the mevalonate pathway in
 osteoclasts, the mechanism by which N-BPs enter the cytosol from the
 extracellular space to reach their molecular target is not understood.
 Here we implemented a CRISPRi-mediated genome-wide screen and identified
 SLC37A3 (solute carrier family 37 member A3) as a gene required for the
 action of N-BPs in mammalian cells. We observed that SLC37A3 forms a
 complex with ATRAID (all-trans retinoic acid-induced differentiation
 factor), a previously identified genetic target of N-BPs. SLC37A3 and
 ATRAID localize to lysosomes and are required for releasing N-BP molecules
 that have trafficked to lysosomes through fluid-phase endocytosis into the
 cytosol. Our results elucidate the route by which N-BPs are delivered to
 their molecular target, addressing a key aspect of the mechanism of action
 of N-BPs that may have significant clinical relevance.
description: CRISPRi_survival_screen_alendronate_K562Statistical information of all genes targeted in a CRISPRi mediated survival screen performed in human K562 cells using an osteoporosis drug, alendronate, as the selection agent. experimental procedures and statistical analyses are described in the manuscript.ZY_OSHEA_2018_supplementary_data_table_1.xlsxCRISPRi_survival_screen_zoledronate_K562statistical information of all genes targeted in a CRISPRi mediated survival screen performed in human K562 cells using an osteoporosis drug, zoledronate, as the selection agent. experimental procedures and statistical analyses are described in the manuscript.ZY_OSHEA_2018_supplementary_data_table_2.xlsx
DOI: 10.5061/dryad.pq0cs6h
title: Data from: Learning relevance models for patient cohort retrieval

description: OBJECTIVE We explored how judgements provided by physicians can be used to
 learn relevance models that enhance the quality of patient cohorts
 retrieved from Electronic Health Records (EHR) collections. METHODS A very
 large number of features were extracted from patient cohort descriptions
 as well as electronic health record collections. Specifically, we
 investigated retrieving (1) neurology-specific patient cohorts from the
 Temple University Hospital EEG Corpus as well as (2) the more general
 cohorts evaluated in the TREC Medical Records Track (TRECMed) from the
 de-identified hospital records provided by the University of Pittsburgh
 Medical Center. The features informed a Learning Relevance Model (LRM)
 that took advantage of relevance judgements provided by physicians. The
 LRM implements a pairwise learning-to-rank framework, which enables our
 learning patient cohort retrieval (L-PCR) system to learn from physicians’
 feedback. RESULTS AND DISCUSSION We evaluated the L-PCR system against
 state-of-the-art traditional patient cohort retrieval systems, and
 observed a 27% improvement when operating on EEGs and a 53% improvement
 when operating on TRECMed EHRs, showing the promise of the L-PCR system.
 We also performed extensive feature analyses to reveal the most effective
 strategies for representing cohort descriptions as queries, encoding EHRs,
 and measuring relevance. CONCLUSION The learning patient cohort retrieval
 system has significant promise for reliably retrieving patient cohorts
 from EHRs in multiple settings when trained with relevance judgments. When
 provided with additional cohort descriptions, the L-PCR will continue to
 learn, thus offering a potential solution to the performance barriers of
 current cohort retrieval systems.
description: cohortsCohort descriptions used to evaluate and train the L-PCRS system.judgmentsRelevance judgments used to train and evaluate the L-PCRS system.trained_modelsRandom Forest classifiers trained on each dataset, in Lemur's RankLib.jar format.acquiring_the_text_collectionsInstructions for where to find the TUH EEG corpus.
DOI: 10.15468/dl.gsff8d
title: Occurrence Download

description: A dataset containing 7724 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((113.27283 -19.42565,112.3838 -27.34389,114.66988 -36.69381,130.29142 -33.47283,141.08678 -40.36839,143.49986 -44.03594,148.45303 -44.58123,155.43827 -29.68718,152.64417 -21.09365,145.40493 -9.97872,137.27665 -10.60352,127.87833 -9.35271,113.27283 -19.42565))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Carnivora"
 ]
}

 The dataset includes 7724 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001534-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k5d3280
title: Data from: Weather conditions determine attenuation and speed of sound: environmental limitations for monitoring and analysing bat echolocation

description: Echolocating bats are regularly studied to investigate auditory-guided
 behaviours and as important bioindicators. Bioacoustic monitoring methods
 based on echolocation calls are increasingly used for risk assessment and
 to ultimately inform conservation strategies for bats. As echolocation
 calls transmit through the air at the speed of sound, they undergo changes
 due to atmospheric and geometric attenuation. Both the speed of sound and
 atmospheric attenuation, however, are variable and determined by weather
 conditions, particularly temperature and relative humidity. Changing
 weather conditions thus cause variation in analysed call parameters,
 limiting our ability to detect and correctly analyse bat calls. Here, I
 use real-world weather data to exemplify the effect of varying weather
 conditions on the acoustic properties of air. I then present atmospheric
 attenuation and speed of sound for the global range of weather conditions
 and bat call frequencies to show their relative effects. Atmospheric
 attenuation is a non-linear function of call frequency, temperature,
 relative humidity and atmospheric pressure. While atmospheric attenuation
 is strongly positively correlated with call frequency, it is also
 significantly influenced by temperature and relative humidity in a complex
 non-linear fashion. Variable weather conditions thus result in variable
 and unknown effects on the recorded call, affecting estimates of call
 frequency and intensity, particularly for high frequencies.
 Weather-induced variation in speed of sound reaches up to about ±3%, but
 is generally much smaller and only relevant for acoustic localisation
 methods of bats. The frequency- and weather-dependent variation in
 atmospheric attenuation has a three-fold effect on bioacoustic monitoring
 of bats: it limits our capability (1) to monitor bats equally across time,
 space, and species, (2) to correctly measure frequency parameters of bat
 echolocation calls, particularly for high-frequencies, and (3) to
 correctly identify bat species in species-rich assemblies or for sympatric
 species with similar call designs.
description: Goerlitz_2018_ECOL_EVOL_Fig_01_exemplary_dataExemplary weather data and calculated atmospheric attenuation and speed of sound, relating to Figure 1.Goerlitz_2018_ECOL_EVOL_Fig_02_atmospheric_attenuationCalculated atmospheric attenuation as a function of four factores (sound frequency, temperature, relative humidity, air pressure), related to Figure 2.Goerlitz_2018_ECOL_EVOL_Fig_05_weather_data_speed_of_soundCalculated speed of sound as a function of temperature and relative humidity, related to Figure 5 A, B.Goerlitz_2018_ECOL_EVOL_Fig_05_speed_of_sound.xlsGoerlitz_2018_ECOL_EVOL_Fig_05_weather_data_speed_of_soundWeather data of four global areas and calculated speed of sound, related to Figure 5C.
DOI: 10.5061/dryad.3d9r8p1
title: Data from: Contemporary pollen flow as a multiscale process: evidence from the insect-pollinated herb, Pulsatilla vulgaris

description: 1. Understanding the drivers and spatial scale of gene flow is essential
 for the management of species living in fragmented landscapes. In plants,
 contemporary pollen flow is typically modeled as a single spatial process,
 with pollen flow declining exponentially within a short distance of mother
 plants. However, growing evidence suggests that many species do not
 conform to this patterns, often showing an excess of long-distance
 dispersal events or sometimes even multimodality in dispersal kernels.
 This suggests that a single function might be insufficient to capture the
 true complexity of pollination, which in reality is often achieved by
 multiple pollinators that vary in their foraging ranges and interactions
 with the landscape. 2. We reconstructed realized pollen flow and assessed
 pollen immigration for seven populations of the insect-pollinated herb,
 Pulsatilla vulgaris. We quantified the effects of distance, floral
 resources, and landscape composition over multiple spatial scales, and
 tested the hypotheses that within-population pollen flow is related to
 resources and landscape context measured locally, and that
 among-population pollen flow is related to features measured at larger
 spatial scales. 3. We found that pollen flow within populations was more
 likely to occur amongst near neighbours, but that among-population pollen
 flow was random with respect to source populations. We further found that
 local floral density could explain patterns of within-population
 pollination distances and population-level selfing rates, whereas pollen
 immigration rates were best explained by the proportion of forest within a
 radius of 500 m around focal populations. 4. Synthesis. Together our
 results suggest that within- and among-population contemporary pollen flow
 may be governed by different underlying processes possibly related to
 differences in the foraging range and habitat use of bee species that
 contribute to pollination at different scales. This highlights the
 critical need for researchers to take a more pollinator-eyed view of
 contemporary pollen flow in plants by (1) recognizing that within and
 among-population gene flow by pollen may depend on different sets of
 pollinators that respond to features at different spatial scales (2)
 considering additional factors that may alter attractiveness,
 detectability, and accessibility of plants to pollinators beyond the
 effects of distance.
description: 0_rawDataThis folder contains the raw input data and output from COLONY2 paternity analysis1_spatialScalingOfPollenFlowThis folder contains the data and scripts to recreate the simulations of within and among-population pollen flow (Appendix S1)2_pollenFlowPredictorsThis folder contains data and scripts to run all regression models from the paper
DOI: 10.5061/dryad.n08qs2s
title: Data from: The thin(ning) green line? Investigating changes in Kenya’s seagrass coverage

description: Knowledge of seagrass distribution is limited to a few well-studied sites
 and poor where resources are scant (e.g. Africa), hence global estimates
 of seagrass carbon storage are inaccurate. Here, we analysed freely
 available Sentinel-2 and Landsat imagery to quantify contemporary coverage
 and change in seagrass between 1986 and 2016 on Kenya’s coast. Using field
 surveys and independent estimates of historical seagrass, we estimate
 total cover of Kenya’s seagrass to be 317.1 ± 27.2 km2, following losses
 of 0.85% yr-1 since 1986. Losses increased from 0.29% yr-1 in 2000 to
 1.59% yr-1 in 2016, releasing up to 2.17 Tg carbon since 1986. Anecdotal
 evidence suggests fishing pressure is an important cause of loss and is
 likely to intensify in the near future. If these results are
 representative for Africa, global estimates of seagrass extent and loss
 need reconsidering.
description: Supp. Data
 1This
 spreadsheet provides the raw data used in the article, specifically
 relating to seagrass cover, cover change, carbon loss, and mapping
 accuracies. All numbers were calculated in ArcGIS 10.5.Supp. Data
 2Field points associated
 with the ground-truthing survey conducted in 2017. All points are recorded
 in latitude and longitude, and projected in WGS1984. The seagrass column
 represents presence (1) or absence (0).Supp. Data
 3Polygons shapefiles of
 the four seagrass maps; 1986 (LT5), 2000 (LE7), 2016 (LC8), and 2016
 (S2A), provided in zipped file. Each shapefile is projected onto WGS184
 UTM Zone 37S.Supplementary
 InformationThis document provides
 information relating to the aforementioned manuscript. It contains
 information related to the accompanying data files and is provided to
 ensure the results are reproducible.WDH_RylSoc_BioLet_Supp_Info.pdf
DOI: 10.5061/dryad.8js678v
title: Data from: Similarities in temperature-dependent gene expression plasticity across time-scales in threespine stickleback (Gasterosteus aculeatus)

description: Phenotypic plasticity occurs at a variety of time-scales, but little is
 known about the degree to which plastic responses at different time-scales
 are associated with similar underlying molecular processes, which is
 critical for assessing the effects of plasticity on evolutionary
 trajectories. To address this issue, we identified differential gene
 expression in response to developmental temperature in the muscle
 transcriptome of adult threespine stickleback (Gasterosteus aculeatus)
 exposed to 12, 18, and 24 °C until hatch and then held at 18 °C for nine
 months, and compared these results to differential gene expression in
 response to adult thermal acclimation in stickleback developed at 18 °C
 and then acclimated to 5 and 25 °C as adults. Adult thermal acclimation
 affected the expression of 7,940 and 7,015 genes in response to cold and
 warm acclimation, respectively, and 4,851 of these genes responded in both
 treatments. In contrast, the expression of only 33 and 29 genes were
 affected by cold and warm development, respectively. The majority of the
 genes affected by developmental temperature were also affected by adult
 acclimation temperature. Many genes that were differentially expressed as
 a result of adult acclimation were associated with previously identified
 temperature-dependent effects on DNA methylation patterns, suggesting a
 role of epigenetic mechanisms in regulating gene expression plasticity
 during acclimation. Taken together, these results demonstrate similarities
 between the persistent effects of developmental plasticity on gene
 expression and the effects of adult thermal acclimation, emphasizing the
 potential for mechanistic links between plasticity acting at these
 different life stages.
description: Total_Read_Counts_Thermal_AcclimationRNA-seq read count data for muscle tissue of threespine stickleback individuals reared at 18 degrees Celsius from fertilization until adults and then acclimated to 5, 18, or 25 degrees Celsius for four weeks.ATreadcounts.csvTotal_Read_Counts_Developmental_TemperatureRNA-seq read count data for muscle tissue of threespine stickleback individuals reared at either 12, 18, or 24 degrees Celsius from fertilization until hatch. All individuals were then kept at 18 degrees Celsius until muscle tissue samples were taken as adults.DTreadcounts.csvR script for RNA-seq analysis of thermal acclimation read countsR code used for RNA-seq analysis of the thermal acclimation read count data . All read count data files used in this analyses can be found in the additional files associated with this Dryad submission.AccTempRNAseqRscript.txtR script for RNA-seq analysis of developmental temperature read countsR code used for RNA-seq analysis of the developmental temperature read count data . All read count data files used in this analyses can be found in the additional files associated with this Dryad submission.DevTempRNAseqRscript.txt
DOI: 10.5281/zenodo.18389224
title: COMPASS-PTM datasets

description: This is the datasets used in the Paper: "Learning the PTM Code through a Coarse-to-Fine, Mechanism-Aware Framework".
DOI: 10.5281/zenodo.18389225
title: COMPASS-PTM datasets

description: This is the datasets used in the Paper: "Learning the PTM Code through a Coarse-to-Fine, Mechanism-Aware Framework".
DOI: 10.5061/dryad.7687117
title: Data from: Natural regeneration on seismic lines influences movement behaviour of wolves and grizzly bears

description: Across the boreal forest of Canada, habitat disturbance is the ultimate
 cause of caribou (Rangifer tarandus caribou) declines. Habitat restoration
 is a focus of caribou recovery efforts, with a goal to finding ways to
 reduce predator use of disturbances, and caribou-predator encounters. One
 of the most pervasive disturbances within caribou ranges in Alberta,
 Canada are seismic lines cleared for energy exploration. Seismic lines
 facilitate predator movement, and although vegetation on some seismic
 lines is regenerating, it remains unknown whether vegetation regrowth is
 sufficient to alter predator response. We used Light Detection and Ranging
 (LiDAR) data, and GPS locations, to understand how vegetation and other
 attributes of seismic lines influence movements of two predators, wolves
 (Canis lupus) and grizzly bears (Ursus arctos). During winter, wolves
 moved towards seismic lines regardless of vegetation height, while during
 spring wolves moved towards seismic lines with higher vegetation. During
 summer, wolves moved towards seismic lines with lower vegetation and also
 moved faster near seismic lines with vegetation &lt;0.7 m. Seismic
 lines with lower vegetation height were preferred by grizzly bears during
 spring and summer, but there was no relationship between vegetation height
 and grizzly bear movement rates. These results suggest that wolves use
 seismic lines for travel during summer, but during winter wolf movements
 relative to seismic lines could be influenced by factors additional to
 movement efficiency; potentially enhanced access to areas frequented by
 ungulate prey. Grizzly bears may be using seismic lines for movement, but
 could also be using seismic lines as a source of vegetative food or
 ungulate prey. To reduce wolf movement rate, restoration could focus on
 seismic lines with vegetation &lt;1 m in height. However our results
 revealed that seismic lines continue to influence wolf movement behaviour
 decades after they were built, and even at later stages of regeneration.
 Therefore it remains unknown at what stage of natural regeneration, if
 any, wolves cease to respond to seismic lines. To reduce wolf response to
 seismic lines, active restoration tactics like blocking seismic lines and
 tree planting, along with management of alternate prey, could be
 evaluated.
description: Wolf
 denningWolf SSF data in the
 denning seasonWolf
 nomadicWolf SSF data in the
 nomadic seasonWolf
 rendezvousWolf SSF data in the
 rendezvous seasonWolf_rateWolf movement rate dataGB_femalefallFemale grizzly bear SSF data in fallGB_femalespringFemale grizzly bear SSF data in springGB_femalesummerFemale grizzly bear SSF data in summerGB_malefallMale grizzly bear SSF data in fallGB_malespringMale grizzly bear SSF data in springGB_malesummerMale grizzly bear SSF data in summerGBfemale_rateFemale grizzly bear movement rate dataGBmale_rateMale grizzly bear movement rate data