cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbcccr
title: Supplemental information and Data for: Colloidal physics modeling reveals how per-ribosome productivity increases with growth rate in E. coli

description: Faster growing cells must synthesize proteins more quickly. Increased
 ribosome abundance only partly accounts for increases in total protein
 synthesis rates. The productivity of individual ribosomes must increase
 too, almost doubling by an unknown mechanism. Prior models point to
 diffusive transport as a limiting factor but surface a paradox: faster
 growing cells are more crowded, yet crowding slows diffusion. We suspected
 physical crowding, transport, and stoichiometry, considered together,
 might reveal a more nuanced explanation. To investigate, we built a
 first-principles physics-based model of E. coli cytoplasm in
 which Brownian motion and diffusion arise directly from physical
 interactions between individual molecules of finite size, density, and
 physiological abundance. Using our microscopically-detailed model, we
 predict that physical transport of individual ternary complexes accounts
 for ~80% of translation elongation latency. We also find that volumetric
 crowding increases at faster growth even as cytoplasmic mass density
 remains relatively constant. Despite slowed diffusion, we predict that
 improved proximity between ternary complexes and ribosomes wins out,
 illustrating a simple physics-based mechanism for how individual
 elongating ribosomes become more productive. We speculate how crowding
 imposes a physical limit on growth rate and undergirds cellular behavior
 more broadly. Unfitted colloidal-scale modeling offers systems biology a
 complementary “physics engine” for exploring how cellular-scale behaviors
 arise from physical transport and reactions among individual molecules.
description: This dataset includes input parameters and output data for all
 simulations in the associated manuscript. The majority of data was
 produced using Colloidal Smoldyn as described in the associated
 manuscript.
description: This dataset can be used in association with code available on
 github (https://github.com/EndyLab/TranslationDynamics/)
DOI: 10.5061/dryad.cvdncjt5f
title: Data supplement to: Quality control of image sensors using gaseous tritium light sources

description: In the article “Quality Control of Image Sensors using Gaseous Tritium
 Light Sources” (https://doi.org/10.1098/rsta.2021.0130) we propose a
 practical method for radiometrically calibrating cameras using widely
 available gaseous tritium light sources (betalights). This dataset
 includes all the recorded data along with the scripts necessary to
 reproduce the results and figures.
description: The raw data consisting of stacks of calibration images, spectral
 data, and photodiode readings were acquired according to the method
 described in the publication. Tabular data on spectral
 responsivity were manually read from graphical plots that were included in
 the camera brochures or quality control reports. Some
 images may have been converted from one lossless format to lossless tiff
 files in order to read and process the data. Some image sequences may have
 been converted to a 3D stack and vice versa.
description: All processing is done in the .ipynb notebook script (https://doi.org/10.5281/zenodo.5738630). This should be consulted for details about the processing environment and processing steps. The individual steps are commented and figures are saved to an output directory. For convenient viewing, there is also an HTML rendering of the notebook. The "data.zip" archive should be unpacked. When "evaluation_notebook.ipynb" is run, it expects to find the "data" subdirectory. <pre id="codecell4">run_directory/ ├── evaluation_notebook.ipynb └── data/    ├── attenuation_experiment/   └── ... </pre> The notebook uses our publically available "NanoImagingPack" library, available at https://gitlab.com/bionanoimaging/nanoimagingpack/ . Installation instructions are provided there. The package has some additional dependencies that are available from Anaconda. The script was run with code on the following commit: 489080ad8981110f0e1ac043f9952a86827afeb The included readme file describes the individual files in more detail.
DOI: 10.5061/dryad.ksn02v75c
title: Data from: Season rather than habitat affects lynx survival and risk of mortality in the human-dominated landscape of southern Sweden

description: Landscapes are mosaics of habitat associated with different risks and
 resources, including human activities, which can affect individual
 survival in wildlife. Different relationships between habitat
 characteristics and human-caused and natural mortality can result in
 attractive sinks. We used individual-based data from 97 Eurasian lynx
 (Lynx lynx) monitored for 160 exposure years to link adult survival and
 the risk of mortality to home range habitat characteristics in the
 human-dominated landscape of southern Sweden. Human-caused mortality
 dominated mortality causes (24 out of 37 deaths). We did not detect any
 strong effects of habitat characteristics explaining the variation in
 mortality risk in lynx. Although the density of roe deer affects several
 aspects of lynx ecology, we could not detect any effects of roe deer
 density on lynx survival, probably because roe deer density was
 sufficiently high in our study area. Instead, there was a high seasonal
 variation in mortality lynx. Mortality was highest during the hunting
 season for lynx (February 16 – March 31), as well as during autumn and
 winter, probably because lynx poaching occurred opportunistically during
 the hunting season for moose and roe deer. We did not find any indication
 that human activity created attractive sinks for lynx, since there was no
 contrasting pattern between human-caused and natural mortality in terms of
 habitat characteristics. One explanation for the limited influence of the
 home range characteristics may be that lynx in our study died from
 multiple causes (natural causes 35%, legal hunting 27 %, poaching 22 % and
 vehicle collisions 16 %). Therefore, it is less likely that one or a few
 habitat characteristics could explain the risk of mortality at the home
 range scale. There is strong evidence that lynx can coexist with humans in
 multi-use and human-dominated landscapes, even without large protected
 areas, if the management regimes are favourable.
DOI: 10.5061/dryad.pnvx0k6nz
title: Establishment of a fecal DNA quantification technique for rare and cryptic diet constituents in small mammals - raw data

description: DNA-based approaches have highly improved the applicability of dietary
 studies aimed at investigating ecological processes. These studies have
 provided direct insights into, otherwise difficult to measure,
 interactions between species and trophic levels, food web structure and
 ecosystem functioning. However, despite these advances, DNA-based methods
 have been struggling to accurately quantify the whole breadth of diet
 constituents because of methodological biases, such as amplification bias
 and digestive processes. This study is, to our knowledge, the first diet
 study that used droplet digital PCR to quantify diet constituents. We
 manipulated the diet of wild caught wood mice (Apodemus sylvaticus) by
 feeding them with a known amount of small vegetable seeds (onion and
 carrot) and quantified the DNA traces of these diet constituents in fecal
 samples. The sensitivity of the technique combined with the control on the
 experimental design allowed mitigation of methodological bias. We were
 able to accurately determine DNA concentrations of small vegetable seeds
 in the diet of wood mice. Quantification of target DNA demonstrated
 significant differences in DNA content when one vs. five seeds were
 consumed. These differences remained significant when the age, sex, and
 other diet constituents of the mice were altered. Different DNA markers,
 targeting different parts of the chloroplast, influenced onion DNA
 detectability. However, all onion and carrot markers showed higher DNA
 content for higher seed numbers. Overall, the sensitive DNA based approach
 developed in this study allows for minimally-invasive quantification of
 small diet constituents in feces, which would otherwise be undetectable
 with traditional methods.
description: Missing values are denoted as NA.
DOI: 10.5061/dryad.9zw3r22g8
title: Experimental data (Biomass, RGR, LDMC, SLA etc.) of Myriophyllum spicatum and Cabomba caroliniana

description: The synergy between climate change, eutrophication and biological invasion
 is threatening for native submerged plants in many ways. The response of
 submerged plants to these changes is a key factor that determines the
 outcome of biological invasion. In order to explain the invasion
 successes, we investigated the combined effects of climate change and
 eutrophication related environmental factors (temperature, light,
 nutrients) on the hard trait responses of a native and an alien submerged
 species (Myriophyllum spicatum, Cabomba caroliniana) from the same growth
 form. In a factorial design we cultivated the two species in aquaria
 containing low and high nutrient concentrations and incubated at four
 light intensities under two temperature levels. We used invasion related
 four functional traits (relative growth rate, specific leaf area, leaf dry
 matter content, nitrogen to carbon ratio) to measure the environmental
 response of the species. We calculated plasticity indexes to express the
 hard trait differences between species. The alien species C. caroliniana
 showed significantly higher relative growth rate and specific leaf area
 than M. spicatum especially under low light intesity indicating that
 Cabomba is much more shade tolerant. Elevated temperature resulted in
 higher specific leaf area and reduced dry mass content for C. caroliniana
 indicating that Cabomba may have higher invasion success. M. spicatum
 showed significantly higher leaf dry matter content than C. caroliniana.
 Chemical analyses of the plant tissue revealed that although M. spicatum
 showed significantly higher N:C molar ratio, nonetheless the daily
 nitrogen uptake of C. caroliniana was three times faster than that of M.
 spicatum. Results indicated that due to its higher shade tolerance and
 nitrogen uptake capacity, Cabomba has greater invasion success with
 increasing temperature combined with low light levels.
DOI: 10.5061/dryad.z8w9ghxdj
title: Directional selection shifts trait distributions of planted species in dryland restoration

description: 1. The match between species trait values and local abiotic filters can
 restrict community membership. An often-implicit assumption of this
 relationship is that abiotic filters select for a single locally optimal
 strategy, though difficulty in isolating effects of the abiotic
 environment from those of dispersal limitation and biotic interactions has
 resulted in few empirical tests of this assumption. Similar constraints
 have made it difficult to assess whether the type and intensity of abiotic
 filters shift along gradients of environmental harshness, as predicted by
 the stress dominance hypothesis. 2. We planted 9,216 plants of perennial
 grass and forb species that had a range of functional trait values and
 were assigned to a warm, intermediate, or cool temperature tolerance pools
 across eight sites on the Colorado Plateau. We compared the distributions
 of traits of surviving individuals to null distributions to evaluate
 whether there were shifts in trait means and variation. Borrowing from
 phenotypic selection concepts in evolutionary biology, we assessed support
 for stabilizing, directional, and disruptive abiotic filtering of trait
 distributions and whether these types of filtering varied with initial
 species pool. 3. Functional composition was significantly different from
 null distributions for nearly all traits at all sites, with trait
 variation more restricted in harsher abiotic conditions, supporting the
 stress-dominance hypothesis. Contrary to expectations, we primarily found
 evidence for directional selection, which increased in frequency in warm
 species pools while disruptive selection was found more often in cool and
 intermediate species pools. 4. Synthesis: This study provides a controlled
 experimental approach to test the effect of the abiotic environment on
 plant trait filtering. We found that opportunistic strategies allowing for
 rapid water acquisition during favorable periods improved survival at
 warmer sites. Species with these strategies may be expected to benefit
 from increasing aridity and may be selected for active management efforts.
 More generally, the prevalence of directional selection may have important
 implications for dynamic vegetation models that rely on trait
 distributions for translating environmental variation into ecosystem
 processes.
DOI: 10.6084/m9.figshare.30635951.v1
title: Methane emissions

description: The methane emissions of Waliguan and Permian basin region
DOI: 10.25338/b8tp8v
title: Data from "Quantification of major particulate matter species from a single filter type using infrared spectroscopy – Application to a large-scale monitoring network"

description: This data set contains FT-IR data obtained from spectra of PTFE
 filters routinely in IMPROVE network during the time
 period 2015-2017, as well as the corresponding routine IMPROVE
 data for all ( ~160) IMPROVE sites except Korea.  The
 data include PM2.5 aerosol concentrations measurements for organic carbon
 (OC), elemental carbon (EC), total carbon (TC), sulfate, nitrate, silicon,
 aluminum, calcium, titanium, iron, mass and light
 absorption.  The data are in ug/m3. 
  Some samples are excluded based on routine validation criteria
 used by IMPROVE including samples known to be contaminated by a diesel
 generator near the site.  For additional information, refer to
 Debus et al., 2021, submitted.
description: This data was collected from FT-IR spectra of routinely collected
 PTFE samples in the IMPROVE network.  PLS regressions were used to
 calibrate the spectra to routine IMPROVE data from 21 sites to predict
 concentrations at all sites.  The 21 sites were selected based on a
 Gaussian Mixture Model of the spectra. A separate PLS calibration using
 biomass burning samples was used for samples identified as biomass burning
 using spectral features of smoke.
DOI: 10.6084/m9.figshare.30635951
title: Methane emissions

description: The methane emissions of Waliguan and Permian basin region
DOI: 10.5061/dryad.xpnvx0kgz
title: Data from: Modularity and selection of nectar traits in the evolution of the selfing syndrome in Ipomoea lacunosa (Convolvulaceae)

description: Although the evolution of the selfing syndrome often involves reductions
 in floral size, pollen, and nectar, few studies of selfing syndrome
 divergence have examined nectar. We investigate whether nectar traits have
 evolved independently of other floral size traits in the selfing syndrome,
 whether nectar traits diverged due to drift or selection, and the extent
 to which quantitative trait locus (QTL) analyses predict genetic
 correlations. We use F5 recombinant inbred lines (RILs) generated from a
 cross between Ipomoea cordatotriloba and I. lacunosa. We calculate genetic
 correlations to identify evolutionary modules, test whether trait
 divergence was due to selection, identify QTLs, and perform correlation
 analyses to evaluate how well QTL properties reflect genetic correlations.
 Nectar and floral size traits form separate evolutionary modules.
 Selection has acted to reduce nectar traits in the selfing I. lacunosa.
 Genetic correlations predicted from QTL properties are consistent with
 observed genetic correlations. Changes in floral traits associated with
 the selfing syndrome reflect independent evolution of at least two
 evolutionary modules: nectar and floral size traits. We also demonstrate
 directional selection on nectar traits, which is likely independent of
 selection on floral size traits. Our study also supports the expected
 mechanistic link between QTL properties and genetic correlations.
description: We crossed <em>Ipomoea
 cordatotriloba </em>by <em>Ipomoea lacunosa</em> and
 generated a F2 mapping population; F2 individuals were selfed by single
 seed decent to the F5 generation. Nectaries were collected while
 phenotyping for nectar volume and nectar sugar concentration and stored in
 RNA later and in the -20 freezer. They were subsequently imaged using a
 Leica MZFLIII stereomicroscope set at 1X magnification and connected to a
 4D HD digital microscope camera from Microscope Systems, Inc.
 (https://microscope-systems.com/).
description: # Data from: Modularity and selection of nectar traits in the evolution of
 the selfing syndrome in *Ipomoea lacunosa* (Convolvulaceae)
 [https://doi.org/10.5061/dryad.xpnvx0kgz](https://doi.org/10.5061/dryad.xpnvx0kgz) ## Nectary images Images used for measuring/estimating nectary size are included in this dataset. File naming:\ IMGxxxxx.JPG\ mIMGxxxxx.tif where xxxxx is the number of the image, .JPG is the raw file, and .tif is the modified file with points selected using FIJI. All scripts and additional information for converting the points into distances and associating the photos with the individual flower can be found in [https://github.com/itliao/IpomoeaNectarQTL/blob/main/Phenotypic_Datasets/NectarySize/](https://github.com/itliao/IpomoeaNectarQTL/blob/main/Phenotypic_Datasets/NectarySize/)
DOI: 10.5061/dryad.15dv41nzk
title: Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)

description: Hybridization with introduced or invasive species is a major threat and
 driver of population declines in native salmonids. The rainbow trout
 (Oncorhynchus mykiss, RBT) has been widely introduced globally and
 represents an important invasive species, often establishing entrenched
 naturalized populations. The cutthroat trout (Oncorhynchus clarkii, CT), a
 close congener, is particularly susceptible to competition and
 hybridization from RBT introductions which has led to range-wide
 population declines and loss of CT genetic variation. The Lahontan CT (O.
 c. henshawi, LCT) whose historic distribution included the Lake Tahoe
 basin, was extirpated by the 1940s due to overfishing and introduction of
 nonnative salmonids, including now naturalized RBT. Here, we characterize
 genetic variation of RBT in a subset of Lake Tahoe tributaries to assess
 potential homing of RBT to streams for spawning, thereby informing LCT
 reintroduction. Diploid reproductively viable RBT were stocked annually
 into Lake Tahoe from the late 1800s until the mid-2000s by California and
 Nevada fish and wildlife agencies, planting the same commonly raised
 hatchery strains over time. Since 2007, triploid RBT comprise the bulk of
 RBT planted. Despite extensive dispersal from stocking locations, our
 analyses revealed variation in population differentiation among
 tributaries, with individuals from spatially proximate streams clustering
 across multiple population genetic analyses. Although subtle, we detected
 evidence for genetic differentiation among tributaries from the southern,
 western, and northern regions, including surprising structure involving a
 single tributary. These results illustrate the extent of differentiation
 within and among streams and could inform possibilities for and
 implications of RBT removal and LCT reintroduction.
DOI: 10.5061/dryad.2280gb5t9
title: UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction

description: The genus Cryptopone Emery contains 25 species of litter
 and soil ants, 5 of which occur in the
 Americas. Cryptoponegilva occurs in the southeastern
 U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon
 biogeographic disjunction observed most often in plants. We used
 phylogenomic data from ultraconserved elements (UCEs), as well as
 mitogenomes and legacy markers, to investigate phylogenetic relationships,
 species boundaries, and divergence dates among New
 World Cryptopone. Species delimitation was conducted using a
 standard approach and then tested using model-based molecular methods
 (SNAPP,  BPP, SODA, and bPTP). We found
 that Cryptopone as currently constituted is
 polyphyletic, and that all the South American species belong
 to Wadeura Weber, a separate genus unrelated
 to Cryptopone. A single clade of
 true Cryptopone occurs in the Americas, restricted to
 North and Central America. This clade is composed of four species that
 originated ~4.2 million years ago. One species from the mountains of
 Guatemala is sister to the other three, favoring a vicariance hypothesis
 of diversification. The taxonomy of the New
 World Cryptoponeand Wadeura are revised.
 Taxonomic changes are: Wadeura Weber
 is resurrected, with new combinations W.
 guianensisWeber, W. holmgreni (Wheeler), and W.
 pauli (Fernandes & Delabie); C.
 guatemalensis (Forel) (rev. stat.) is raised to species, and
 includes C. obsoleta (Menozzi) (syn. nov.). The
 following new species are described: Cryptopone
 gilvagrande, C. gilvatumida, and Wadeura
 holmgrenita. Cryptopone hartwigi is transferred
 to Fisheropone (n. comb.). Cryptopone
 mirabilis (Mackay & Mackay 2010) is a junior synonym
 of Centromyrmex brachycola (Roger) (syn. nov.).
DOI: 10.5061/dryad.f7m0cfxxs
title: Moonlight influence on quality of nestlings of scops owls depends on paternal coloration

description: The moon might favour the maintenance of colour polymorphism via
 disruptive selection if the different colour variants performed
 differently in terms of prey capture under different moonlight levels.
 Moonlight, however, may affect prey capture as a by side effect of its
 influence on prey behaviours. Here we combine data of parental
 provisioning and owlets' quality with one ex-situ study of
 grasshoppers' activity to test whether Eurasian scops owls
 (Otus scops) with different plumage colour and their prey are differently
 affected by moonlight. Food provisioning increased from new- to full-moon.
 However, the effect of moonlight on owlet mass gain and immune response
 depended on paternal coloration. On the one hand, body mass gain of
 nestlings of the greyest fathers increased from nights with new- to
 full-moon, whereas it did not change with moonlight for the brownest
 fathers. On the other hand, PHA response of nestlings of the brownest
 fathers increased with high moonlight levels during the first week of
 life, whereas it did not change with moonlight levels for the greyest
 fathers. Grasshoppers were more active at new moon than at full or waning
 moon. Our study provides supporting evidence that moonlight influences the
 behaviour of both scops owls and its prey and suggests that fluctuations
 in environmental conditions can modulate the advantages of morphs. These
 results are important because they provide a general insight into a little
 appreciated mechanism for the maintenance of colour polymorphism in
 natural populations based on the interactive effect of different
 environmental factors.