cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bk3j9kdfx
title: ReviewR: A light-weight and extensible tool for manual review of clinical records

description: Objectives: Manual record review is a crucial step for electronic health
 record (EHR)-based research, but it has poor workflows and is error prone.
 We sought to build a tool that provides a unified environment for data
 review and chart abstraction data entry. Materials and methods: ReviewR is
 an open-source R Shiny application that can be deployed on a single
 machine or made available to multiple users. It supports multiple data
 models and database systems, and integrates with the REDCap API for
 storing abstraction results. Results: We describe two real-world uses and
 extensions of ReviewR. Since its release in April 2021 as a package on
 CRAN it has been downloaded 2,204 times. Discussion and conclusion:
 ReviewR provides an easily accessible review interface for clinical data
 warehouses. Its modular, extensible, and open source nature afford future
 expansion by other researchers. 
description: These data are the results of double chart review of the same
 patients using either Epic Hyperspace or the tool developed in the
 manuscript, ReviewR. Half of the charts reviewed were first completed in
 ReviewR then Hyperspace, the other half were reviewed in Hyperspace then
 ReviewR. Three items were extracted - if the patient ever had a brain
 aneurysm, if the patient ever had a subarachnoid hemorrhage (SAH), and if
 they had an SAH whether it was from an aneurysm (vs say
 trauma).
DOI: 10.5061/dryad.f1vhhmh0p
title: Nestling begging calls resemble maternal vocal signatures when mothers call slowly to embryos

description: Vocal production learning (the capacity to learn to produce vocalizations)
 is a multi-dimensional trait that involves different learning
 mechanisms during different temporal and socio-ecological
 contexts. A key outstanding question is whether vocal production
 learning begins during the embryonic stage and whether mothers play an
 active role in this through pupil-directed vocalization
 behaviors. We examined variation in vocal copy similarity (an
 indicator of learning) in eight species from the songbird family
 Maluridae, using comparative and experimental approaches. We found that:
 (1) incubating females from all species vocalized inside the nest and
 produced call types including a signature ‘B element’ that was
 structurally similar to their nestlings’ begging call; (2) in a prenatal
 playback experiment using superb fairywrens (Malurus cyaneus), embryos
 showed a stronger heart rate response to playbacks of the B
 element than to another call element (A); and (3) mothers that
 produced slower calls had offspring with greater similarity between their
 begging call and the mother’s B element vocalization. We conclude
 that malurid mothers display behaviors concordant with pupil-directed
 vocalizations and may actively influence their offspring’s early-life
 through sound learning shaped by maternal call tempo. 
description: We placed microphones near the nests of eight species of
 Maluridae to record incubating female in-nest calls. Across species, we
 identified up to four element types and in all species, every female
 produced a signature B element. We calculated female element rate as the
 number of elements per s. We recorded the chicks' B element begging
 calls after hatching and used spectrographic cross-correlation analysis to
 compare vocal copy similarity between the mother's B element and the
 offspring's B element. We used an experimental approach in superb
 fairywrens and broadcast calls with different numbers of A and B elements,
 and measured embryo response to calls with different numbers of A and B
 elements using change in heart rate as the response variable.
DOI: 10.5061/dryad.pnvx0k6r0
title: Putative signals of generalist plant species adaptation to local pollinator communities and abiotic factors

description: The reproductive success of flowering plants with generalized pollination
 systems is influenced by the interactions with a diverse pollinator
 community and abiotic factors. However, knowledge about the adaptative
 potential of plants to complex ecological networks and the underlying
 genetic mechanisms is still limited. Based on a pool-sequencing approach
 of 21 natural populations of Brassica incana in Southern Italy, we
 combined a genome-environmental association analysis with a genome scan
 for signals of population genomic differentiation to discover genetic
 variants associated with ecological variation. We identified genomic
 regions putatively involved in the adaptation of B. incana to the identity
 of local pollinator functional categories and pollinator community
 composition. Interestingly, we observed several shared candidate genes
 associated with long-tongue bees, soil texture, and temperature variation.
 We established a genomic map of potential generalist flowering plant local
 adaptation to complex biotic interactions, and the importance of
 considering multiple environmental factors to describe the adaptive
 landscape of plant populations.
DOI: 10.5061/dryad.cjsxksn8g
title: A biogeographical approach to characterising the climatic, physical and geomorphic niche of the most widely distributed mangrove species, Avicennia marina

description: Aim: Mangroves are coastal ecosystems exposed to terrestrial, marine,
 geomorphic and climatic forcings operating in concert, making the mangrove
 niche hard to define, as evidenced by extremely poor restoration outcomes.
 We have developed a set of high-resolution species distribution models and
 interpreted the variables that have the largest impact on the niche of
 Avicennia marina, the most globally widespread mangrove species, to
 comprehensively detail the forcings driving habitat suitability. Location:
 Australia. Time period: 1970–2020. Major taxa studied: Avicennia marina
 (Forssk.) Vierh. Methods: We modelled the suitable habitat for A. marina
 in Australia using the maxent method incorporating 38 environmental
 variables and the Global Mangrove Watch baseline for the presence records.
 Using k-means grouping we identified sub-regions where similar suites of
 environmental variables influence habitat suitability, while also
 identifying biogeographical commonalities among the sub-regions. To better
 understand the low realisation of the fundamental niche we analysed the
 other land covers occupying the niche. Results: A. marina in Australia
 occupies six different environmental sub-regions. Maxent distribution
 models accurately predicted the presence of A. marina in each
 subpopulation (AUC &gt; 0.9). A. marina’s presence in all sub-regions
 was strongly determined by its proximity to freshwater. Precipitation and
 temperature extreme values were more important than average values in
 predicting the species' presence. The species requires low-energy
 coastlines with high solar radiation. The suitable areas are primarily
 shared with salt marshes, seagrass and buildings or cleared land. Main
 conclusions: Our results offer a baseline for the suitable area of A.
 marina’s presence that includes a range of environmental conditions, A.
 marina currently occupies &lt;50% of its suitable habitat and there is
 scope for restoration with significant ecosystem service gains. The six
 different sub-regions in Australia map to known phylogenetically distinct
 populations indicating genetic plasticity in response to region-specific
 climatic conditions.
description: This dataset contains a markdown notebook that can be opened in
 RStudio.  The variables used in the code are provided
 as .csv files and also as .tif files.
DOI: 10.5061/dryad.0zpc86719
title: Jumping out of trouble: Evidence for a cognitive map in guppies (Poecilia reticulata)

description: Spatial cognitive abilities allow individuals to remember the location of
 resources such as food patches, predator hide-outs, or shelters. Animals
 typically incorporate learnt spatial information or use external
 environmental cues to navigate their surroundings. A spectacular example
 of how some fishes move is through aerial jumping. For instance, fish that
 are trapped within isolated pools, cut off from the main body of water
 during dry periods, may jump over obstacles and direct their jumps to
 return to safe locations. However, what information such as re-orientation
 behaviour during jumping is based on remains enigmatic. Here we combine a
 lab and field experiment to test if guppies (Poecilia reticulata)
 incorporate learnt spatial information and external environmental cues
 (visual and auditory) to determine where to jump. In a spatial memory
 assay we found that guppies were more likely to jump towards deeper areas,
 hence incorporating past spatial information to jump to safety. In a
 matched vs. mismatched spatial cue experiment in the field, we found that
 animals only showed directed jumping when visual and auditory cues
 matched. We show that in unfamiliar entrapments guppies direct their jumps
 by combining visual and auditory cues, while in familiar entrapments they
 use a cognitive map. We hence conclude that jumping behaviour is a
 goal-directed behaviour, guided by different sources of information and
 involving important spatial cognitive skills.
description: Data collected as described in the methods section of
 "Jumping out of trouble: Evidence for a cognitive map in guppies
 (<em>Poecilia reticulata</em>)".
description: Please refer to ReadMe file. Data are in .xlsx format. Code for
 analyses was performed in R.
DOI: 10.5061/dryad.2bvq83bt7
title: The role of a synanthropic bird in the nest niche expansion of a secondary cavity-nester to man-made structures

description: Species with similar ecological characters often compete with each other;
 however, a species may also facilitate the survival or reproduction of
 another ecologically similar species although such interaction is rarely
 documented in birds. Here we reported a facilitative species interaction
 between Asian house martins (Delichon dasypus) and russet sparrows (Passer
 cinnamomeus), both passerines using closed nests, in a montane farming
 area of Taiwan. We found that Asian house martins constructed dome-shaped
 nests in human houses that provided additional nest sites for russet
 sparrows, secondary cavity-nesters with greatly declining populations in
 Taiwan. Russet sparrows that used house martin nests had reproductive
 success comparable to those that used artificial nest boxes. However,
 Asian house martins avoided reclaiming sparrow-used nests, which reduced
 their available nest sites. Interestingly, our results imply that man-made
 structures may be used as a conservation tool to improve the breeding of
 the endangered russet sparrows via this facilitative interaction.
description: We checked the nests of Asian
 house martins in the mornings using an endoscope. We recorded the status
 of the nests (occupied by russet sparrows or Asian house martins) and the
 numbers and developmental stages of eggs and chicks in each brood. The
 survey was done at regular intervals in 2020 and 2021 (once every 3-4 days
 in 2020 and daily in 2021) and at irregular intervals in 2019.  We defined
 the developmental stage of “fledging” as: 1) one chick that was at least
 12-days old was found in the nest (Yang et al. 2012), and 2) an empty nest
 with no chick carcass nearby, suggesting the chicks had successfully
 fledged rather than being predated.
description: The dataset files can be opened by Excel.  The datasets files
 were used to generated Fig.2 and 3 of the paper entitled "The role of
 a synanthropic bird in the nest niche expansion of a secondary
 cavity-nester to man-made structures".
DOI: 10.5061/dryad.sn02v6x74
title: Simulation data from: Dynamics of immune memory and learning in bacterial communities

description: From bacteria to humans, adaptive immune systems provide learned memories
 of past infections. Despite their vast biological differences, adaptive
 immunity shares features from microbes to vertebrates such as emergent
 immune diversity, long-term coexistence of hosts and pathogens, and
 fitness pressures from evolving pathogens and adapting hosts, yet there is
 no conceptual model that addresses all of these together. To address these
 questions, we propose and solve a simple phenomenological model of
 CRISPR-based adaptive immunity in microbes. We show that in coexisting
 phage and bacteria populations, immune diversity in both populations
 emerges spontaneously and in tandem, that bacteria track phage evolution
 with a context-dependent lag, and that high levels of diversity are
 paradoxically linked to low overall CRISPR immunity. We define average
 immunity, an important summary parameter predicted by our model, and use
 it to perform synthetic time-shift analyses on available experimental data
 to reveal different modalities of coevolution. Finally, immune
 cross-reactivity in our model leads to qualitatively different states of
 evolutionary dynamics, including an influenza-like traveling wave regime
 that resembles a similar state in models of vertebrate adaptive immunity.
 Our results show that CRISPR immunity provides a tractable model, both
 theoretically and experimentally, to understand general features of
 adaptive immunity.
description: This data was simulated using a custom python script to model a
 community of bacteria and phages interacting with CRISPR adaptive
 immunity. Each simulation uses the tau-leaping method to approximate the
 Gillespie stochastic simulation algorithm. The base simulation script is
 the same for all simulations with modifications to different
 parameters.
description: Simulation files are stored as plain text files. An intermediate
 processing file is included for each simulation that stores the simulation
 results in a compressed scipy sparse array (*.npz). Each individual
 simulation folder contains the Python script used to generate the
 simulation results.
DOI: 10.5061/dryad.8cz8w9gtv
title: Phenotypic changes of beak dimensions in urban birds of Switzerland

description: Humans’ large influence on the environment has constructed many new
 ecological niches, such as in urban areas. Phenotypic changes, including
 morphological ones related to human influence are known from a small
 number of bird species. The amount of change in a given time period, i.e.,
 the rate of change, may vary. Rates of change (both evolutionary and
 through phenotypic plasticity) are reportedly rapid in human-influenced
 settings, although this is disputed. We present new data on changes in
 beak dimensions and rates of change over historical time periods in four
 urban bird species (Common Chaffinch, European Greenfinch, Eurasian
 Blackbird, House Sparrow) from three Swiss cities (Basel, Bern, Geneva).
 Our study shows that beak dimensions have changed little in most
 investigated urban bird populations over the past century. Only in Genevan
 Blackbirds there was evidence for an increase in beak length over the past
 65 years; Bernese Chaffinches appear to be trending toward a decrease in
 beak width over the past 55 years. Rates of change in our sample in
 comparison with literature records showed that compared to populations
 less influenced by humans, urban evolutionary rates appear to be similar.
 Although in accordance with previous findings about other urban bird
 species, our study exemplifies the difficulty to find universal patterns
 in tempo and mode of phenotypic evolution in urban areas, even when
 considering the same taxa. Our data contribute to the expanding field of
 urban evolutionary biology, which is particularly important regarding the
 growing urban habitats worldwide.
description: Measurement data were collected from museum collections of bird
 skins from four bird species. Three different beak dimensions were
 measured. 
description: The data can be opened with Microsoft Office
DOI: 10.5061/dryad.3tx95x6jz
title: Evolutionary divergence in phenotypic plasticity shapes brain size variation between coexisting sunfish ecotypes

description: Mechanisms that generate brain size variation and the consequences of such
 variation on ecological performance are poorly understood in most natural
 animal populations. We use a reciprocal-transplant common garden
 experiment and foraging performance trials to test for brain size
 plasticity and the functional consequences of brain size variation in
 Pumpkinseed sunfish (Lepomis gibbosus) ecotypes that have diverged between
 nearshore littoral and offshore pelagic lake habitats. Different
 age-classes of wild-caught juveniles from both habitats were exposed for
 six months to treatments that mimicked littoral and pelagic foraging.
 Plastic responses in oral jaw size suggested that treatments mimicked
 natural habitat-specific foraging conditions. Plastic brain size responses
 to foraging manipulations differed between ecotypes, as only pelagic
 sourced fish showed brain size plasticity. Only pelagic juveniles under 1
 year-old expressed this plastic response, suggesting that plastic brain
 size responses decline with age and so may be irreversible. Finally,
 larger brain size was associated with enhanced foraging performance on
 live benthic but not pelagic prey, providing the first experimental
 evidence of a relationship between brain size and prey-specific foraging
 performance in fishes. The recent post-glacial origin of these ecotypes
 suggests that brain size plasticity can rapidly evolve and diverge in fish
 under contrasting ecological conditions.
DOI: 10.5061/dryad.zcrjdfngf
title: Data for: Russian honey bee genotype identification through enhanced marker panel set

description: Russian honey bees (RHB) are a breeding population developed by USDA-ARS
 as an effort to provide Varroa-resistant honey bees to beekeepers. The
 selection strategy for this breeding population was the first in honey
 bees to incorporate genetic stock identification (GSI). The original GSI
 approach has been in use for over a decade, and though effective, novel
 technologies and analytical approaches recently developed provide an
 opportunity for improvement. Here we outline a novel genotyping assay that
 capitalizes on the markers used in the GSI as well as novel loci recently
 identified in a whole genome pooled study of commercial honey bee stocks.
 Our approach utilizes a microfluidic platform and machine learning
 analyses to arrive at an accurate, high throughput assay. This novel
 approach provides an improved tool that can be readily incorporated into
 breeding decisions towards healthier more productive bees.
description: Four files are provided here: 1) Genotypes and
 sample metadata obtained from a Fluidigm 96.96 Dynamic ArrayTM
 characterizing RHB population. This data set forms the core sample set for
 the updated genotype stock identification approach outlined in the
 reference article. 2) An R script detailing the process
 by which to access and process (1) to arrive at a reproduction of the
 model used in the referenced study. 3 & 4)
 Output tuning and model files specific to the referenced study provided
 for scrutiny and contrasts.
description: Open source R and RStudio are the only required software to
 access data.
DOI: 10.5061/dryad.xgxd254k8
title: Arms-race and fluctuating-selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1

description: Experimental evolution studies have examined coevolutionary
 dynamics between bacteria and lytic phages, where two models for
 antagonistic coevolution dominate: arms-race dynamics (ARD) and
 fluctuating-selection dynamics (FSD). Here, we tested the ability for
 Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in
 the laboratory; whether ARD versus FSD coevolution occurred; and how
 coevolution affected a predicted phenotypic trade-off between phage
 resistance and antibiotic sensitivity. We used a unique “deep” sampling
 design, where 96 bacterial clones per passage were obtained from the three
 replicate coevolving communities. Next, we examined phenotypic changes in
 growth ability, susceptibility to phage attack, and resistance against
 antibiotics. Results confirmed that the bacteria and phages coexisted
 throughout the study with one community undergoing ARD while the other two
 showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated
 the anticipated trade-off. Whole genome sequencing revealed that treatment
 populations of bacteria accrued more de novo mutations, relative to a
 control bacterial population. Additionally, coevolved bacteria presented
 mutations in genes for biosynthesis of flagella, type-IV pilus and
 lipopolysaccharide, with three mutations fixing contemporaneously with the
 occurrence of the phenotypic trade-off in the ARD-coevolved bacteria. Our
 study demonstrates that both ARD and FSD coevolution outcomes are possible
 in a single interacting bacteria-phage system, and that occurrence of
 predicted phage-driven evolutionary trade-offs may depend on the genetics
 underlying evolution of phage-resistance in bacteria. These results are
 relevant for the ongoing development of lytic phages, such as OMKO1, in
 personalized treatment of human patients, as an alternative to
 antibiotics.
DOI: 10.5061/dryad.s1rn8pkbv
title: Yellowstone Upper Basin Geyser binary eruption data (April 2007- October 2008; revised)

description: Binary eruption data for 10 Geysers (Beehive, Castle, Depression, Dome,
 Grand, Lion, Little Squirt, Old Faithful, Plate, and Plume) over 19
 consecutive months (April 2007- October 2008) at a sampling interval of 6
 minutes.
description: Geyser eruptions were monitored using sensors that record
 temperature in outflow channels. Temperature data was mapped to binary
 (1/0) time series, with ones indicating an eruption. Eruptions were
 characterized by a rapid, short increase in temperature (typically
 temperature peaks above 50°C, implemented using Python's peakutils
 function). To minimize false positive eruptions in the temperature
 records, we relied on an independent observation-based dataset consisting
 of IBE assessments from collocated temperature sensors deployed by GOSA to
 specify a minimum distance between temperature peaks for each
 geyser.
description: # Yellowstone Upper Basin Geyser Binary Eruption Data (April 2007- October
 2008; revised)
 [https://doi.org/10.5061/dryad.s1rn8pkbv](https://doi.org/10.5061/dryad.s1rn8pkbv) ## Description of the data and file structure Yellowstone Upper Basin Geyser Binary Eruption Data (April 2007- October 2008) This database contains binary eruption data for 10 Geysers (Beehive, Castle, Depression, Dome, Grand, Lion, Little Squirt, Old Faithful, Plate, and Plume) over 19 consecutive months (April 2007- October 2008) at a sampling interval of 6 minutes. The data are all contained in one CSV file where each row represents a time and each column represents a geyser. Geysers are abbreviated as follows: * BE: Beehive * CA: Castle * DE: Depression * DO: Dome * GR: Grand * LN: Lion * LS: Little Squirt * OF: Old Faithful * PT: Plate * PM: Plume ## Code/Software The code used to analyze these data are accessible via the Supplementary Information of the published research article associated with this dataset (DOI: [10.1029/2021JB023749).](https://doi.org/10.1029/2021JB023749)