cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f8c0c8h
title: Data from: The role of climate, water and biotic interactions in shaping biodiversity patterns in arid environments across spatial scales

description: Aim: Desert ecosystems, with their harsh environmental conditions, hold
 the key to understanding the responses of biodiversity to climate change.
 As desert community structure is influenced by processes acting at
 different spatial scales, studies combining multiple scales are essential
 for understanding the conservation requirements of desert biota. We
 investigated the role of environmental variables and biotic interactions
 in shaping broad and fine-scale patterns of diversity and distribution of
 bats in arid environments to understand how the expansion of nondesert
 species can affect the long-term conservation of desert biodiversity.
 Location: Levant, Eastern Mediterranean. Methods: We combine species
 distribution modelling and niche overlap statistics with a statistical
 model selection approach to integrate interspecific interactions into
 broadscale distribution models and fine-scale analysis of ecological
 requirements. We focus on competition between desert bats and mesic
 species that recently expanded their distribution into arid environment
 following anthropogenic land-use changes. Results: We show that both
 climate and water availability limit bat distributions and diversity
 across spatial scales. The broadscale distribution of bats was determined
 by proximity to water and high temperatures, although the latter did not
 affect the distribution of mesic species. At the fine-scale, high levels
 of bat activity and diversity were associated with increased water
 availability and warmer periods. Desert species were strongly associated
 with warmer and drier desert types. Range and niche overlap were high
 among potential competitors, but coexistence was facilitated through
 fine-scale spatial partitioning of water resources. Main conclusions:
 Adaptations to drier and warmer conditions allow desert-obligate species
 to prevail in more arid environments. However, this competitive advantage
 may disappear as anthropogenic activities encroach further into desert
 habitats. We conclude that reduced water availability in arid environments
 under future climate change projections pose a major threat to desert
 wildlife because it can affect survival and reproductive success and may
 increase competition over remaining water resources.
description: Razgour2018_DDI_GLMM_R_scriptsR scripts for running the GLMMs for the fine-scale analysis of the effect of water body characteristics on bat activity, species richness and the activity of the three potentially competing Pipistrellus species.Razgour2018_DDI_Maxent_model_outputsSpecies distribution modelling (Maxent) outputs for all desert bats.
DOI: 10.5061/dryad.248g184
title: Data from: Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants

description: This study exploits time, the relatively unexplored fourth dimension of
 gene regulatory networks (GRNs), to learn the temporal transcriptional
 logic underlying dynamic nitrogen (N) signaling in plants. Our
 “just-in-time” analysis of time-series transcriptome data uncovered a
 temporal cascade of cis elements underlying dynamic N signaling. To infer
 transcription factor (TF)-target edges in a GRN, we applied a time-based
 machine learning method to 2,174 dynamic N-responsive genes. We
 experimentally determined a network precision cutoff, using TF-regulated
 genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to
 “prune” the network to 155 TFs and 608 targets. This network precision was
 reconfirmed using genome-wide TF-target regulation data for four
 additional TFs (TGA1, HHO5/6, and PHL1) not used in network pruning. These
 higher-confidence edges in the GRN were further filtered by independent
 TF-target binding data, used to calculate a TF “N-specificity” index. This
 refined GRN identifies the temporal relationship of known/validated
 regulators of N signaling (NLP7/8, TGA1/4, NAC4, HRS1, and LBD37/38/39)
 and 146 additional regulators. Six TFs—CRF4, SNZ, CDF1, HHO5/6, and
 PHL1—validated herein regulate a significant number of genes in the
 dynamic N response, targeting 54% of N-uptake/assimilation pathway genes.
 Phenotypically, inducible overexpression of CRF4 in planta regulates genes
 resulting in altered biomass, root development, and 15NO3− uptake,
 specifically under low-N conditions. This dynamic N-signaling GRN now
 provides the temporal “transcriptional logic” for 155 candidate TFs to
 improve nitrogen use efficiency with potential agricultural applications.
 Broadly, these time-based approaches can uncover the temporal
 transcriptional logic for any biological response system in biology,
 agriculture, or medicine. External links: 1. DFG:
 http://cs.nyu.edu/~mirowski/pub/GRN_Krouk_Mirowski_GenomeBiology.zip, 2.
 GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97500
description: Shoot_NxTime_genePlotsGene expression plots for all N-responsive genes in shoots.Root_NxTime_genePlotsGene expression plots of all N-responsive genes in RootsDE_SplineR script for identifying differential gene expression in response to N-supply.ShootRawCountsRaw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from shoot samples.RootRawCountsRaw counts of total RNA-Seq reads aligned to each gene model in the Arabidopsis thaliana genome (TAIR10 version). These counts are from the RNA-Seq libraries constructed from root samples.Plotting DEgenesR script to create gene expression plots from the normalized counts.DEgene_Plots.RPlot DataData files needed to generate the gene expression plots.PlotData.tar
DOI: 10.5281/zenodo.18351122
title: INRIM_Brand1_10F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18351123
title: INRIM_Brand1_10F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 10F SC sample 4 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.qq934j2
title: Data from: Mapping movement, mood, motivation, and mentation in the subthalamic nucleus

description: The anatomical connections of the subthalamic nucleus (STN) have driven
 hypotheses about its functional anatomy, including the hypothesis that the
 precise anatomical location of STN deep brain stimulation (DBS)
 contributes to the variability of motor and non-motor responses across
 Parkinson disease (PD) patients. We previously tested that hypothesis
 using a three-dimensional (3D) statistical method to interpret the acute
 effects of unilateral DBS at each patient’s clinically optimized DBS
 settings and active contact. Here we report a similar analysis from a new
 study in which DBS parameters were standardized and DBS locations were
 chosen blind to clinical response. In 74 individuals with PD and STN DBS,
 STN contacts were selected near the dorsal and ventral border of the STN
 contralateral to the more affected side of the body. Participants were
 tested off PD medications in each of 3 unilateral DBS conditions (ventral
 STN DBS, dorsal STN DBS and DBS off) for acute effects on mood, apathy,
 working memory, response inhibition and motor function. Voltage,
 frequency, and pulse width were standardized, and participants and raters
 were blind to condition. In a categorical analysis, both dorsal and
 ventral STN DBS improved mean motor function without affecting cognitive
 measures. Ventral STN DBS induced greater improvement in rigidity and
 anxiety than dorsal STN DBS. In the 3D analysis, contact location was
 significant for body hypokinesia, rigidity, and resting tremor, with the
 greatest improvement occurring with DBS in dorsal STN and zona incerta.
 The 3D results provide new, direct functional evidence for the
 anatomically-derived model of STN, in which motor function is best
 represented in dorsal STN. However, our data suggest that functional
 segregation between motor and non-motor areas of the STN is limited, since
 locations that induced improvements in motor function and mood overlapped
 substantially.
description: Images and text files
 for the above publicationThis is a 7-zip
 (https://www.7-zip.org/) containing the files described in the README
 file. These files include the atlas-space location of all active contacts,
 the changes in UPDRS, cognitive and visual analog scale measures with
 stimulation at each contact, and the statistical images described in the
 manuscript, in NIFTI format.Gourisankar_2018_data.7z
DOI: 10.5061/dryad.11rf64v
title: Data from: Mammal communities are larger and more diverse in moderately developed areas

description: Developed areas are thought to have low species diversity, low animal
 abundance, few native predators, and thus low resilience and ecological
 function. Working with citizen scientist volunteers to survey mammals at
 1427 sites across two development gradients
 (wild-rural-exurban-suburban-urban) and four plot types (large forests,
 small forest fragments, open areas and residential yards) in the eastern
 US, we show that developed areas actually had significantly higher or
 statistically similar mammalian occupancy, relative abundance, richness
 and diversity compared to wild areas. However, although some animals can
 thrive in suburbia, conservation of wild areas and preservation of green
 space within cities are needed to protect sensitive species and to give
 all species the chance to adapt and persist in the Anthropocene.
description: Raw detection data from
 camera trapsEach row represents a
 detection of a species from camera traps set in Raleigh, NC, USA and
 Washington, DC, USA between 2012 and 2016.Raw_Data.xlsx
DOI: 10.5061/dryad.n102b1s
title: Data from: Rising temperatures, molting phenology and epizootic shell disease in the American lobster

description: Phenological mismatch, maladaptive changes in phenology resulting from
 altered timing of environmental cues, is an increasing concern in many
 ecological systems, yet its effects on disease are poorly characterized.
 American lobster (Homarus americanus) is declining at its southern
 geographic limit. Rising seawater temperatures are associated with
 seasonal outbreaks of epizootic shell disease (ESD), which peaks in
 prevalence in the fall. We used a 34-year mark-recapture dataset to
 investigate relationships between temperature, molting phenology, and ESD
 in Long Island Sound, where temperatures are increasing at 0.4 °C per
 decade. Our analyses support the hypothesis that phenological mismatch is
 linked to the epidemiology of ESD. Warming spring temperatures are
 correlated with earlier spring molting. Lobsters lose diseased cuticle by
 molting, and early molting increases the intermolt period in the summer,
 when disease prevalence is increasing to a fall peak. In juvenile and
 adult male lobsters, September ESD prevalence was correlated with early
 molting, while October ESD prevalence was correlated with summer seawater
 temperature. This suggests that temperature-induced molting phenology
 affects the timing of the onset of ESD, but, later in the summer, this
 signal is swamped by the stronger signal of summer temperatures, which we
 hypothesize are associated with an increased rate of new infections.
 October ESD prevalence was ~80% in years with hot summers, and ~30% in
 years with cooler summers. Yearly survival of diseased lobsters is
 &lt;50% that of healthy lobsters. Thus, population impacts of ESD are
 expected to increase with increasing seawater temperatures.
description: Seawater temperatures
 East LIS 1976-2015See README for
 metadataMillstone_lobster
 1982-2015.csvCatch per unit effort
 dataSee README file for
 metadataLobster_CPUE.csvTagged lobster dataSee README file for metadatalobster_all_tagged.txtREADMEDescriptions of data and code associated with this publication.A1 Millstone temperature trends 1976-2015Exploratory analysis of seawater temperature trendsA2 Average molting, prevalence and CPUE 1999-2015Exploratory analyses of lobster dataA3 H1 Spring molting phenology is altered by temperatureTest of hypothesis 1A4 H2 Spring molting reduces risk of ESDTest of hypothesis 2A5 H3 ESD induces moltingTest of hypothesis 3A6 H4 ESD Prevalence in Sept and Oct Juveniles and Adult MalesTest of hypothesis 4
DOI: 10.5061/dryad.mk69rg6
title: Data from: Spatiotemporal distribution and environmental drivers of Barley yellow dwarf virus and vector abundance in Kansas

description: Several aphid species transmit barley yellow dwarf, a globally destructive
 disease caused by viruses that infect cereal grain crops. Data from
 &gt;400 samples collected across Kansas wheat fields in 2014 and 2015
 were used to develop spatio-temporal models predicting the extent to which
 landcover, temperature and precipitation affect spring aphid vector
 abundance and presence of individuals carrying Barley yellow dwarf virus
 (BYDV). The distribution of Rhopalosiphum padi abundance was not
 correlated with climate or landcover, but Sitobion avenae abundance was
 positively correlated to fall temperature and negatively correlated to
 spring temperature and precipitation. The abundance of Schizaphis graminum
 was negatively correlated with fall precipitation and winter temperature.
 The incidence of viruliferous (+BYDV) R. padi was positively correlated
 with fall precipitation but negatively correlated with winter
 precipitation. In contrast, the probability of +BYDV S. avenae was
 unaffected by precipitation but was positively correlated with average
 fall temperatures and distance to nearest forest or shrubland. R. padi and
 S. avenae were more prevalent at Eastern sample sites where ground cover
 is more grassland than cropland, suggesting that grassland may provide
 over-summering sites for vectors and pose a risk as potential BYDV
 reservoirs. Nevertheless, land cover patterns were not strongly associated
 with differences in abundance or probability that viruliferous aphids were
 present.
description: Field samples with
 covariatesField samples from
 Kansas of Rhopalosiphum padi, Schizaphis graminum, Sitobion avena, and
 Barley yellow dwarf virus with covariates.all-data-with-covariates.csvall covariates for predictionsSpatio-temporal covariates used to make predictive maps across the state of Kansas.all-covariates-for-predictions.csv
DOI: 10.5061/dryad.1717129
title: Data from: Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts

description: The advent of molecular data has transformed the science of organizing and
 studying life on Earth. Genetics-based evidence provides fundamental
 insights into the diversity, ecology, and origins of many biological
 systems, including the mutualisms between metazoan hosts and their
 micro-algal partners. A well-known example is the dinoflagellate
 endosymbionts (“zooxanthellae”) that power the growth of stony corals and
 coral reef ecosystems. Once assumed to encompass a single panmictic
 species, genetic evidence has revealed a divergent and rich diversity
 within the zooxanthella genus Symbiodinium. Despite decades of reporting
 on the significance of this diversity, the formal systematics of these
 eukaryotic microbes have not kept pace, and a major revision is long
 overdue. With the consideration of molecular, morphological,
 physiological, and ecological data, we propose that evolutionarily
 divergent Symbiodinium “clades” are equivalent to genera in the family
 Symbiodiniaceae, and we provide formal descriptions for seven of them.
 Additionally, we recalibrate the molecular clock for the group and amend
 the date for the earliest diversification of this family to the middle of
 the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive
 radiation of analogs to modern shallow-water stony corals during the
 Jurassic Period and connects the rise of these symbiotic dinoflagellates
 with the emergence and evolutionary success of reef-building corals. This
 improved framework acknowledges the Symbiodiniaceae’s long evolutionary
 history while filling a pronounced taxonomic gap. Its adoption will
 facilitate scientific dialog and future research on the physiology,
 ecology, and evolution of these important micro-algae.
description: LSU rDNA nexus
 fileLSU rDNA nexus file
 containing sequence alignments of partial Large Ribosomal Subunit (LSU)
 from 76 species representing 36 genera and 7 orders of Dinophyceae, in
 addition to the Symbiodiniaceae.CurrentBiology_LSU_dinoflagellate_Orders.nexuscytochrome b nexus fileNexus file containing sequence alignments of the mitochondrial cytochrome b (cob) from 48 species representing 29 genera and 7orders of Dinophyceae, in addition to the Symbiodiniaceae.CurrentBiology_cob_Dinoflagellate_Orders.nexusSuessialies LSU nexus fileNexus file containing sequence alignments of partial Large Ribosomal Subunit (LSU) from 33 species representing 15 genera in the order Suessiales, used to generate Figure 4.CurrentBiology_Suessialies_LSU_v3.nexusSuessiales Beast2Beast2 xml input file used to generate Figure 1.Suessiales_Beast_input_file_Figure 1.xmlBEAST2_log_fileBeast2 output log file containing statistical data and rate of nucleotide evolution calculated for Figure 1.Suessialies_BEAST_1.logCurrentBiology_Fig2_morphology_data_and_r_codeMorphology-related data (cell size) and R code to recreate Figure 2a.CurrentBiology_Fig3_genetic_data_and_r_codeGenetics-related data (distance and proportion of orthologs) and R code to recreate Figure 3.
DOI: 10.5061/dryad.g082q0b
title: Data from: Exploring the potential pharmacodynamic material basis and pharmacologic mechanism of the Fufang-Xialian-Capsule in chronic atrophic gastritis by network pharmacology approach based on the components absorbed into the blood

description: In this study, a new network pharmacology approach based on the components
 absorbed into the blood was utilized to investigate the pharmacodynamic
 material basis and the pharmacologic mechanism of the
 Fufang-Xialian-Capsule (FXL) in treating chronic atrophic gastritis (CAG).
 Initially, we confirmed the components absorbed into the blood by
 ultra-high-performance liquid chromatography coupled with quadrupole
 time-of-flight mass spectrometry. Then, the network approach, which was
 based on the results of components absorbed into the blood, was utilized
 to analyze the pharmacodynamic material basis and the pharmacologic
 mechanism of FXL on treating CAG. As a result, 22 absorbed components were
 found in the rat’s plasma. Given the results of the absorption analysis of
 the components, 8 pathways associated with CAG development were found. The
 targets linked to these pathways are the drug targets of FXL in CAG
 treatment. The components associated with these targets are the potential
 pharmacodynamic material basis and exert synergy in regulating pathways
 during CAG treatment.
description: Absorbed into
 bloodThe chromatorgraphy of
 the components absorbed into bloodAbsorbed into blood
 2The
 chromatorgraphy of the components absorbed into blood
DOI: 10.5061/dryad.pv3rc1m
title: Data from: Seasonal dynamics of spatial distribution and overlap between Northeast Arctic cod (Gadus morhua) and capelin (Mallotus villosus) in the Barents Sea

description: The trophic link between cod (Gadus sp.) and capelin (Mallotus sp.) is
 important in many panarctic ecosystems. Since the early 2000s, the
 Northeast Arctic cod stock (G. morhua) in the Barents Sea has increased
 greatly, and the sea has been exceptionally warm. Such changes have
 potentially large effects on species distributions and overlap, which in
 turn could affect the strength of species interactions. Due to its high
 latitude location, the Barents Sea has strong seasonal variation in
 physical conditions and interactions. To study drivers of variation in
 cod-capelin overlap, we use data from two annual surveys run in winter and
 in autumn of 2004-2015. We first model winter and autumn spatial
 distributions of mature and immature cod and capelin. We then calculate
 overlap from model predictions on a grid with similar spatial resolution
 as the survey data. Our approach allowed us to interpret changes in
 overlap as species-specific effects of stock size and temperature, while
 accounting for sampling variation due to sampling time and depth. We found
 that during winter both species expanded their distribution in response to
 increased stock sizes, but how strongly and where the expansion occurred
 varied. The effect of temperature on distributions varied in space, and
 differed for cod and capelin and for different components of the two
 species. The results for autumn were clearer and more consistent. Both
 species expanded their distribution areas as their stock sizes increased.
 A positive effect of temperature was found in the north-eastern Barents
 Sea, where temperatures were lowest at the start of the study. Overlap
 increased and shifted north-eastwards during the study period and remained
 high despite a decline in the capelin stock. The increased overlap during
 autumn could mainly be attributed to the shift in cod distribution with
 increased cod stock biomass.
description: Ecosystem survey
 2004-2015Field-collected data on
 cod and capelin distribution from the Norwegian parts of the ecosystem
 survey 2004-2015. For details see README file.Norwegian part of ecosystem
 survey cod-capelin 2004-2015.txtWinter survey
 2004-2015Field-collected data on
 cod and capelin distribution from the Norwegian parts of the winter survey
 2004-2015. For details see README file.Norwegian part of winter survey
 cod-capelin 2004-2015.txt
DOI: 10.5061/dryad.t308jh7
title: Data from: Seasonality, alarm pheromone and serotonin: insights on the neurobiology of honeybee defence from winter bees

description: Honeybees maintain their colony throughout the cold winters, a strategy
 that enables them to make the most of early spring flowers. During this
 period, their activity is mostly limited to thermoregulation, while
 foraging and brood rearing are stopped. Less is known about seasonal
 changes to the essential task of defending the colony against intruders,
 which is regulated by the sting alarm pheromone. We studied the stinging
 responsiveness of winter bees exposed to this scent or a control
 (solvent). Surprisingly winter bees, while maintaining their
 responsiveness in control conditions, did not increase stinging frequency
 in response to the alarm pheromone. This was not due to the bees not
 perceiving the pheromone, as shown by calcium-imaging of the antennal
 lobes. Since the alarm pheromone is thought to act through an increase in
 brain serotonin levels, ultimately causing heightened defensiveness, we
 checked if serotonin treatments would affect the stinging behaviour of
 winter bees. Indeed, treated winter bees became more inclined to sting.
 Thus, we postulate that loss of responsiveness to the sting alarm
 pheromone is based on a partial or total disruption of the mechanism
 converting alarm pheromone perception into high serotonin levels in winter
 bees.
description: BehaviourRaw data for behavioural experiments (corresponding to Figure 1)ImagingRaw data for imaging results (Figure 2)