cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rbnzs7kc
title: Soil engineering by ants facilitates plant compensation for large herbivore removal of aboveground biomass

description: The interplay between top-down and bottom-up processes determines
 ecosystem productivity. Yet, the factors that mediate the balance between
 these opposing forces remain poorly understood. Furthering this challenge,
 complex and often cryptic factors like ecosystem engineering and
 trait-mediated interactions may play major roles in mediating the outcomes
 of top-down and bottom-up interactions. In semi-arid grasslands of
 northeastern China, we conducted a large-scale, three-year experiment to
 evaluate how soil engineering by ants and plasticity in
 plants independently and jointly influenced the top-down effects
 of grazing by a ubiquitous herbivore (cattle) on aboveground
 standing biomass of the dominant perennial grass, Leymus chinensis.
 Herbivory had strong top-down effects, reducing L. chinensis AB
 by 25% relative to baseline levels without cattle or ants. In contrast,
 soil engineering by ants facilitated weak bottom-up effects in the absence
 of herbivory. However, in the presence of herbivory, soil engineering
 effects were strong enough to fully offset herbivore removal of
 aboveground biomass. This outcome was mediated by L. chinensis’s
 plasticity in reallocating growth from below- to aboveground biomass, a
 result linked to additive effects of engineers and herbivores increasing
 soil N availability and engineering effects improving soil structure. Soil
 engineering increased soil N by 12%, promoting aboveground biomass.
 Herbivores increased soil N by 13% via defecation, but this increase
 failed to offset their reductions in aboveground biomass in isolation.
 However, when combined, engineers and herbivores increased soil N by 26%
 and engineers improved soil bulk density, facilitating L.
 chinensis to shift resource allocations from below- to
 aboveground biomass sufficiently to fully offset herbivore suppression of
 aboveground biomass. Our results demonstrate that soil engineering and
 trait-mediated effects of plant plasticity can strongly mediate the
 outcome of top-down and bottom-up interactions. These cryptic but perhaps
 ubiquitous processes may help to explain the long-debated phenomenon of
 plant compensatory responses to large grazers.
DOI: 10.5061/dryad.c59zw3r4s
title: Data from: Global pattern and drivers of nitrogen saturation threshold of grassland productivity

description: Ecosystem productivity usually exhibits first increase and then saturated
 response to increasing nitrogen (N) additions, yet the broad-scale pattern
 and potential drivers of the N saturation threshold are little
 investigated. By synthesizing N addition experiments with at least four
 N-input levels from the global grasslands, we applied the
 quadratic-plus-plateau model to fit the aboveground net primary
 productivity (ANPP)－N rate relationship, and estimated the saturation
 threshold for N rate (critical N rate, NCR) and maximum ANPP (ANPPmax)
 from the inflection point where ANPP no longer statistically increased
 with N rate for individual experiments. Based on these estimations, we
 investigated the spatial pattern and driving factors of NCR and ANPPmax.
 The mean NCR and ANPPmax were 15.0 and 477.0 g m-2 year-1, respectively,
 but varied greatly across single-site experiments. Management strategies
 (e.g., biomass harvest, different N forms and addition frequency)
 minimally influenced both parameters. Structural equation models
 demonstrated that the spatial difference in NCR and ANPPmax were mainly
 explained by aridity index, and soil carbon (C)/N ratio availability also
 predicted the variation in NCR. Given that grasslands are important not
 only for the trend and variability of the land C sink but also for the
 maintenance of pasture yield, the pattern and controls of NCR and ANPPmax,
 as revealed by the current study, are crucial for constructing robust
 predictions of C sink capacity and improving N fertilizer management in
 grasslands.
DOI: 10.5061/dryad.4tmpg4f70
title: The sequences of the lignolitic enzymes from an Aspergillus sp.

description: Ligninolytic enzymes including laccase (Lac), manganese peroxidase (Mnp),
 and lignin peroxidase (Lip) have attracted much attention in the
 degradation of contaminants. Amino acid sequence of the Lac, Mnp and Lip
 were showed from Aspergillus sp. TS-A.
description: <i>Aspergillus</i> sp. TS-A were cultivated in
 czapek–dox medium. After 48 hours, the mycelium were collected by
 filtration and ground. DNA fragments were obtained with a fungal gDNA
 extraction kit. Snapgene was used to translate it into amino acid
 sequence.
DOI: 10.5061/dryad.7pvmcvdqr
title: Effects of future climate on coral-coral competition

description: As carbon dioxide (CO 2 ) levels increase, coral reefs and other marine
 systems will be affected by the joint stressors of ocean acidification
 (OA) and warming. The effects of these two stressors on coral physiology
 are relatively well studied, but their impact on biotic interactions
 between corals are poorly understood. While coral-coral interactions are
 less common on modern reefs, it is important to document the nature of
 these interactions to better inform restoration strategies in the face of
 climate change. Using a mesocosm study, we evaluated whether the combined
 effects of ocean acidification and warming alter the competitive
 interactions between the common coral Porites astreoides and two other
 mounding corals ( Montastraea cavernosa or Orbicella faveolata ) common in
 the Caribbean. After 7 days of direct contact, P. astreoides suppressed
 the photosynthetic potential of M. cavernosa by 100% in areas of contact
 under both present (~28.5°C and ~400 μatm p CO 2 ) and predicted future
 (~30.0°C and ~1000 μatm p CO 2 ) conditions. In contrast, under present
 conditions M. cavernosa reduced the photosynthetic potential of P.
 astreoides by only 38% in areas of contact, while under future conditions
 reduction was 100%.  A similar pattern occurred between P.
 astreoides and O. faveolata at day 7 post contact, but by day 14, each
 coral had reduced the photosynthetic potential of the other by 100% at the
 point of contact, and O. faveolata was generating larger lesions on P.
 astreoides than the reverse.  In the absence of competition, OA
 and warming did not affect the photosynthetic potential of any coral.
 These results suggest that OA and warming can alter the severity of
 initial coral-coral interactions, with potential cascading effects due to
 corals serving as foundation species on coral reefs.
description: This dataset comes from a tank experiment. Data was collected
 using PAM flourometry and photography. Photos were processed in Image J.
 Data was analyzed in R.
description: The second experiment ran twice as long as the first experiment,
 so there are more data points. Some alkalinity samples were lost in the
 process due to issues with the titrator.
DOI: 10.5061/dryad.5qfttdz2m
title: Strong stabilizing selection on timing of germination in a Mediterranean population of Arabidopsis thaliana

description: Premise Timing of germination can strongly influence plant fitness by
 affecting seedling survival and by having cascading effects on later
 life-history traits. In seasonal environments, the period favorable for
 seedling establishment and growth is limited, and timing of germination is
 likely to be under stabilizing selection because of conflicting selection
 through survival and fecundity. Moreover, optimal germination time may
 vary among genotypes because of inherent differences in later life-history
 traits.   Methods To examine how germination time affects
 survival, fecundity and the relative fitness of two genotypes differing in
 time to first flower, we conducted a field experiment in an Italian
 population of the winter annual Arabidopsis thaliana, in which seedling
 establishment occurs mainly in November. We transplanted seedlings of the
 local genotype and of a Swedish genotype monthly from August to December
 and monitored survival and fecundity.   Key Results Only
 seedlings transplanted in November and December survived until
 reproduction, and fitness of the November cohort was 35 times higher than
 that of the December cohort, indicating strong stabilizing selection.
 There was no evidence of conflicting selection: seedling survival, adult
 survival and fecundity were all highest in the November cohort. Moreover,
 the relative fitness of the two genotypes did not differ significantly
 between cohorts.   Conclusions The very narrow window of
 opportunity for seedling establishment was related to rapid seasonal
 changes in soil moisture and temperature, suggesting that rate of seasonal
 change is an important aspect to consider for understanding
 spatio-temporal variation in selection on phenological traits.
DOI: 10.15468/dl.wf9vyd
title: Occurrence Download

description: A dataset containing 781 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Baudouinia fluggeiformis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 781 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002425-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b87c9v
title: Data from: Efficacy of masks and face coverings in controlling aerosol particle emission from expiratory activities

description: The dataset provided here is associated with the
 work "Efficacy of masks and face coverings in controlling
 aerosol particle emission from expiratory activities," by Asadi et
 al. This includes measurements made of the influence of different
 types of face coverings (surgical masks, both vented and unvented N95
 respirators, and homemade fabric and paper towel masks) on the
 emission of micron-scale aerosols from various expiratory
 activities (coughing, breathing, speaking). 
description: Participants were asked to perform various expiratory activities
 (breathing, speaking, coughing, jaw movement) while wearing no mask or a
 mask or face covering (surgical masks, vented and unvented N95
 respirators, homemade paper towel or one or two-layer cotton masks). Study
 participants performed these activities in front of a funnel connected to
 an aerodynamic particle sizer (APS), which measured the size-dependent
 aerosol concentration. Size-dependent concentrations were measured every
 1-second during the activities. Additionally, the intensity and duration
 of the talking and coughing activities were measured using a calibrated
 microphone. The APS was located in a HEPA-filtered laminar flow hood to
 reduce background counts to near zero. Further details are provided in the
 associated manuscript (Asadi et al., to be submitted) or dissertation
 chapter (Asadi et al., 2020b). There were 11 participants total.
 Provided here for each participant/mask type/expiratory activity
 are two files: (i) a text (.txt) file containing the
 tab-delimited exported files from the APS. Particle sizes are in microns;
 the smallest size includes all particles measured below that size.
 Particle counts are given for each size every second. 
 (ii) a .wav file containing the microphone signals (in volts)
 recorded during the activity. These files are provided for only the
 talking and coughing activities.  All files have the
 naming structure FX_YYYY_ZZZZ or MX_YYYY_ZZZZ, where X is the participant
 number (1-11) YYYY is the designator for each mask type (KN95, N95, No =
 no mask, SLP = single-layer paper towel, Surg = surgical, UDLT =
 double-layer homemade cloth, SDLT = single-layer homemade cloth), and ZZZZ
 is the activity (Talk, Jaw, Cough, Breath).  Files are
 additionally provided for experiments where the masks were folded and
 rubbed against themselves to characterize particle shedding. These files
 have the names Rub_YYYY, where YYYY is again the mask type. 
 Data were processed using Matlab. The data are available as a
 single zip file for download. All personal identifiers have been
 removed.
DOI: 10.7272/q61v5c64
title: Evaluation of Person Centered-Care During Family Planning Services at Public Facilities in India

description: This data is from a larger 5 year project on person-centered quality for
 delivery, family planning, and abortion in both India and Kenya. This is
 the baseline data evaluating Person Centered Care during Family Planning
 services at Public Facilities in Uttar Pradesh, India.
description: This data forms a part of a case-control pair of surveys of
 clients of family planning counselling guidance from local community
 health workers in Uttar Pradesh, India.  This survey was collected
 immediately following the clients' first encounter with the community
 workers.
DOI: 10.5061/dryad.cvdncjt1w
title: An investigation on the effect of high energy storage anchor on surrounding rock conditions

description: High pre-tension bolt is an effective strata control technique and is the
 key to ensure the stability of anchorage and roadway. Based on the
 performances of high energy storage tension rock bolts in different rock
 properties, this study proposed a constitutive model to describe the
 energy balance of anchor under uniaxial compression. UDEC was used to
 simulate the behaviour of anchor in coal under uniaxial compression and
 the results were analysed to study the rock mechanical properties, degree
 of damage and energy evolution. Simulation results showed that tension
 rock bolts can improve the mechanical properties and energy storage
 capacities of anchor. The energy evolution was divided into three stages:
 i) the external work was stored in the form of elastic strain energy (Ue)
 in the anchor prior to the yielding strength; ii) the elastic strain
 energy reached its maximum near the peak strength; iii) Energy was
 dissipated from fracture friction (Wf ), plastic deformation (Wp) and
 acoustic emission (Ur) during post-peak stage. The installation of tension
 rock bolts was more suitable for medium hard rock (e.g. sandy mudstone),
 whereas it was not effective for hard rock (e.g. sandstone).
DOI: 10.5061/dryad.d51c5b00g
title: Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change

description: All code and simulation data necessary to repeat the analysis described in
 "Insights from Fisher’s geometric model on the likelihood of
 speciation under different histories of environmental change."
DOI: 10.5061/dryad.rbnzs7h8m
title: Data from: The Cumulative Indel Model: fast and accurate statistical evolutionary alignment

description: Sequence alignment is essential for phylogenetic and molecular evolution
 inference, as well as in many other areas of bioinformatics and
 evolutionary biology. Inaccurate alignments can lead to severe biases in
 most downstream statistical analyses. Statistical alignment based on
 probabilistic models of sequence evolution addresses these issues by
 replacing heuristic score functions with evolutionary model-based
 probabilities. However, score-based aligners and fixed-alignment
 phylogenetic approaches are still more prevalent than methods based on
 evolutionary indel models, mostly due to computational convenience. Here,
 I present new techniques for improving the accuracy and speed of
 statistical evolutionary alignment. The "cumulative indel model"
 approximates realistic evolutionary indel dynamics using differential
 equations. "Adaptive banding" reduces the computational demand
 of most alignment algorithms without requiring prior knowledge of
 divergence levels or pseudo-optimal alignments. Using simulations, I show
 that these methods lead to fast and accurate pairwise alignment inference.
 Also, I show that it is possible, with these methods, to align and infer
 evolutionary parameters from a single long synteny block (approximately
 530kbp) between the human and chimp genomes. The cumulative indel model
 and adaptive banding can therefore improve the performance of alignment
 and phylogenetic methods.
description: The code for this project can be found at
 https://bitbucket.org/nicofmay/cumulativeindel/ .
DOI: 10.5061/dryad.gf1vhhmm8
title: Life history data for longer-lived tropical songbirds reduce breeding activity as they buffer impacts of drought

description: Droughts are expected to increase in frequency and severity with climate
 change. Population impacts of such harsh environmental events are
 theorized to vary with life history strategies among species. However,
 existing demographic models generally do not consider behavioral
 plasticity that may modify the impact of harsh events. Here we show that
 tropical songbirds in the New and Old World reduced reproduction during
 drought, with greater reductions in species with higher average long-term
 survival. Large reductions in reproduction by longer-lived species were
 associated with higher survival during drought than pre-drought years in
 Malaysia, whereas shorter-lived species maintained reproduction and
 survival decreased. Behavioral strategies of longer-lived, but not
 shorter-lived, species mitigated the effect of increasing drought
 frequency on long-term population growth. Behavioral plasticity can buffer
 the impact of climate change on populations of some species, and
 differences in plasticity among species related to their life histories
 are critical for predicting population trajectories.
description: see methods in paper
DOI: 10.5061/dryad.d51c5b00h
title: Data from: Emigrating together but not establishing together: A cockroach rides ants and leaves

description: Symbionts of ant colonies can hitchhike on winged ant reproductives
 (alates) during colony nuptial flights. Attaphila fungicola Wheeler, a
 miniature cockroach that lives in the nests of Texas leaf-cutter ants
 (Atta texana Buckley), hitchhikes on female alates (winged queens).
 Hitchhiking roaches are presumably vertically transmitted from leaf-cutter
 parent colony to daughter colony, remaining with female alates as they
 transition into foundresses (workerless queens); however, foundresses have
 limited resources and high mortality rates. Rather than remaining with
 foundresses likely to die (vertical transmission), roaches might abandon
 them during dispersal to infect higher quality later stages of colony
 development (female alate-vectored transmission). In field experiments, I
 find evidence for female alate-vectored transmission, and discover roaches
 use a second hitchhiking step, riding foraged plant material, to infect
 established colonies. This work reveals a novel relationship between host
 dispersal and symbiont transmission, and shows colony development can be
 an important selection pressure on transmission.
description: This data was collected in the field with direct observations
 recorded in field journals.  All observations are described in more detail
 in the Methods and Results section of the manuscript, "Emigrating
 together but not establishing together: A cockroach rides ants and
 leaves."
description: As a natural history paper, observations and their resulting data
 are described in more detail in the Methods and Results section of the
 manuscript itself.
DOI: 10.5061/dryad.tb2rbnzxm
title: Data from: eIF4E S209 phosphorylation licenses myc- and stress-driven oncogenesis

description: Mutational activation of Wnt/Myc and RAS signaling promotes colorectal
 cancer (CRC) development and deregulates translation. Phosphorylation of
 the cap binding protein eIF4E (Serine 209) is commonly elevated in cancer
 such as CRC yet dispensable for normal development. To better understand
 an oncogenic role of eIF4ES209, we generated eIF4E (S209A/+) heterozygous
 knockin (4EKI) HCT 116 human colorectal cancer (CRC) cells. 4EKI had
 little or no effect on total eIF4E levels, cap binding or global
 translation, while markedly reduced HCT 116 cell growth in spheroids and
 mice. 4EKI strongly inhibited Myc and ATF4 translation, the integrated
 Stress Response (ISR)-dependent glutamine metabolic signature, AKT
 activation and proliferation in vivo. p-eIF4E was found to be
 highly elevated in CRC precursor lesions in mouse and human.
 4EKI inhibited polyposis in APC+/min mice by suppressing Myc
 protein and AKT activation. Furthermore, mutant KRAS cooperated with
 p-eIF4E and Myc to promote ISR-dependent glutamine addition in various CRC
 cell lines, which was characterized by increased cell death,
 transcriptomic heterogeneity and immune suppression upon deprivation.
 These findings demonstrate a critical role of eIF4ES209-dependent
 translation in Myc and stress-driven oncogenesis and as a potential
 therapeutic vulnerability.
description: Gene expression data generated via cDNA microarray using
 Affymetrix Human Genome U133 Plus 2.0 array.
DOI: 10.5061/dryad.n5tb2rbsv
title: Data for: Phantom rivers filter birds and bats by acoustic niche

description: Natural sensory environments, despite strong potential for structuring
 systems, have been neglected in ecological theory. Here, we test the
 hypothesis that intense natural acoustic environments shape animal
 distributions and behavior by broadcasting whitewater river noise in
 montane riparian zones for two summers. We find that both birds and bats
 avoid areas with high sound levels, while birds avoid frequencies that
 overlap with birdsong, and bats avoid higher frequencies more generally.
 Behaviorally, intense sound levels decrease foraging in birds, whereas
 bats appear to switch hunting strategies from passive listening to aerial
 hawking as sound levels increase. Natural acoustic environments are an
 underappreciated niche axis, a conclusion that serves to escalate the
 urgency of mitigating human-created noise.
description: See supplementary materials within manuscript.
description: Check the README.Rmd file
DOI: 10.5061/dryad.tb2rbnzxn
title: Evidence that male sea lamprey increase pheromone release after perceiving a competitor: raw data, R-code, R analyses

description: Sexual signals evolve via selective pressures arising from male-male
 competition and female choice, including those originating from unintended
 receivers that detect the signal. For example, males can acquire
 information from other males signaling to females and alter their own
 signal. Relative to visual and acoustic signals, less is known about how
 such communication networks influence chemical signaling among animals. In
 sea lamprey (Petromyzon marinus), chemical communication system is
 essential for reproduction, offering a useful system to study a pheromone
 communication network that includes signalers and both intended and
 unintended receivers. Male sea lamprey aggregate on spawning grounds where
 individuals build nests and signal to females using sex pheromones. We
 examined how exposure to a major component of the male pheromone,
 3keto-petromyzonol sulfate (3kPZS), influenced male pheromone signaling,
 and whether females had a preference for males that altered their signal.
 Exposure to 3kPZS, at a concentration of 5x10-10 M, simulated the presence
 of other male(s) and led to increased 3kPZS release rates within 10 min,
 followed by a return to baseline levels within 30 min. Exposure also led
 to increases in hepatic synthesis and circulatory transport of pheromone
 components. In behavioral assays, females preferred the odor of males that
 had been exposed to 3kPZS; therefore, males likely benefit from
 upregulating 3kPZS release after detecting competition for mates. Here, we
 define how a specific pheromone component influences chemical signaling
 during intrasexual competition, and show a rare example of how changes in
 chemical signaling strategies resulting from male competition may
 influence mate choice.
description: See methods in manuscript