cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866v8
title: Data from: Harsh environmental regimes increase the functional significance of intraspecific variation in plant communities

description: The relative importance of intraspecific trait variation (rITV) for
 functional diversity (FD) in plant communities is increasingly apparent,
 but the influence of abiotic factors on the balance between intraspecific
 and interspecific effects in contrasting environments is uncertain. We
 predicted that rITV would increase with environmental harshness
 as a result of decreasing interspecific variation (Inter_FD) and
 concomitant increases in between-population ITV(Intra_FD). We empirically
 tested this prediction in a comparison of rITV for five traits (mature
 plant height, SLA: specific leaf area, leaf dry matter content, and the
 foliar concentrations of nitrogen and phosphorus) characterizing species
 in Tibetan alpine meadow communities from contrasting environmental
 regimes(i.e. valley floor at the base of the ridge, northern- and
 southern-slopes at mid-elevation, and ridge top) on each of three sites
 (ridges). We found that across plots: i) rITV for all five traits
 increased with environmental harshness not only through decreasing
 Inter_FD but also increasing Intra_FD; ii) increases in rITV were mostly
 attributable to declines in soil resources, especially soil phosphorus,
 with lower soil P significantly associated with lower Inter_FD but higher
 Intra_FD for most traits; and iii) although neither Intra_FD nor Inter_FD
 were significantly impacted by species richness for any traits, a higher
 rITV for SLA was significantly associated with low species richness.
DOI: 10.5061/dryad.v6wwpzgs5
title: ‘The last channel’: Vision at the temporal margin of the field

description: The human visual field, on the temporal side, extends to at least 90
 degrees from the line of sight. Using a two-alternative forced-choice
 procedure in which observers are asked to report the direction of motion
 of a Gabor patch, and taking precautions to exclude unconscious eye
 movements in the direction of the stimulus, we show that the limiting
 eccentricity of image-forming vision can be established with precision.
 There are large, but reliable, individual differences in the limiting
 eccentricity. The limiting eccentricity exhibits a dependence on log
 contrast; but it is not reduced when the modulation visible to the rods is
 attenuated, a result compatible with the histological evidence that the
 outermost part of the retina exhibits a high density of cones. Our working
 hypothesis is that only one type of neural channel is present in the far
 periphery of the retina, a channel that responds to temporally modulated
 stimuli of low spatial frequency and that is directionally selective.
description: For a description of how the data were collected and processed,
 please refer to the journal article.
description: A text file ('data_instructions.txt') is provided to
 clarify the contents of the data files ('Experiment1.csv',
 'Experiment2.csv', 'Experiment3.csv').
DOI: 10.25934/pr00012476.0
title: Available datapackage for study 'Alive Church Network: Increasing COVID-19 Testing in Chicago's African American Testing Deserts'

description: This study uses a population-based approach to increase uptake of COVID-19 testing within a highly segregated and underserved African American community in Chicago.
DOI: 10.5061/dryad.tb2rbnzxb
title: Data from: Free-ranging bats alter thermoregulatory behavior in response to reproductive stage, roost type, and weather

description: Heterotherms vary their use of torpor and choice of refugia to deal with
 energetic stresses such as reproductive activity and extreme weather. We
 hypothesized that a temperate-region bat would vary its use of
 heterothermy in response to air temperature but use of torpor would also
 be influenced by reproductive stage and roost choice. To test this
 hypothesis, we collected data on skin temperatures of female Indiana bats
 (Myotis sodalis) carrying temperature-sensitive radiotransmitters during
 the summers of 2013–2015. We also measured internal temperatures and
 external characteristics of roosts used by these bats. We analyzed the
 influence of daytime air temperature, roost canopy closure, roost type,
 and bat reproductive stage, on daily heterothermy index and torpor
 characteristics of 17 bats during 103 full roost days (data collected
 consistently from when a bat entered its roost in the morning to when it
 emerged at night). Our data showed that Indiana bat heterothermy was
 influenced by reproductive stage, roost choice, and weather. Although they
 used torpor, pregnant bats were the least heterothermic (daily
 heterothermy index = 3.3 ± 0.6°C SE), followed by juvenile bats
 (5.6 ± 0.5°C), lactating bats (5.7 ± 0.5°C), and one postlactating bat
 (13.2 ± 1.6°C). Air temperature also influenced heterothermy of pregnant
 bats less than bats of other reproductive stages. Thermoregulatory
 strategies varied on a continuum from use of normothermia in warm roosts
 to use of long and deep bouts of torpor in cool roosts. The
 thermoregulatory strategy used seemed to be determined by potential
 reproductive costs of torpor and energetic consequences of weather.
 Because Indiana bats used different degrees of heterothermy throughout the
 summer maternity season, managers should offer maternity colonies an array
 of refugia to facilitate varying behaviors in response to weather and
 energetic demands.
DOI: 10.15468/dl.d4r7xp
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sepioloidea pacifica",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 61 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002314-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fqz612jq4
title: A molecular view on the escape of lipoplexed DNA from the endosome (no trajectories)

description: The use of non-viral vectors for in vivo gene therapy could drastically
 increase safety, whilst reducing the cost of preparing the vectors. A
 promising approach to non-viral vectors makes use of DNA/cationic liposome
 complexes (lipoplexes) to deliver the genetic material. Here we use
 coarse-grained molecular dynamics simulations to investigate the molecular
 mechanism underlying efficient DNA transfer from lipoplexes. Our
 computational fusion experiments of lipoplexes with endosomal membrane
 models show two distinct modes of transfection: parallel and
 perpendicular. In the parallel fusion pathway, DNA aligns with the
 membrane surface, showing very quick release of genetic material shortly
 after the initial fusion pore is formed. The perpendicular pathway also
 leads to transfection, but release is slower. We further show that the
 composition and size of the lipoplex, as well as the lipid composition of
 the endosomal membrane, have a significant impact on fusion efficiency in
 our models.
description: This dataset contains all initial set-up files as well as PDBs
 and GRO files. Trajectories have been left out but are available on
 requests within reason (this was too much to upload here ~1TB). There is a
 readme which explains the internal folder system.
description: Included filetypes:<br> .ndx<br> .gro<br> .xtc
 (not included but available on request)<br> .tpr<br>
 .mdp The basic set up of all simuations is as
 follows:<br> 1) initial; not always completely used and often copied
 for ease of scripting,<br> therefore names could deviate from what
 was really used in specific cases. In<br> general the initial folder
 is the /scratch folder for generating the intial<br> configurations.
 It also contains a toppar folder which contains the used .itp<br>
 files. However, the .tpr file in de specific simulation folder is the
 actual<br> input file used, the same holds for the mdout.mdp wich
 contains the actual<br> settings used for the run. However, it has
 been included for it sometimes<br> contains useful
 pre-structures.<br> 2) em; basic initial energy
 minimization<br> 3) eq; basic numerical equilibration<br> 4)
 md; initial testing of md settings, this hardly ever contains the real
 simulation data, this is more pre-run to see if there are any
 issues.<br> 5) md_peregrine/md_cartesius; the actual production runs
 performed on the<br> corresponding super computer.
   I you have any question feel free to send an
 email to:<br> bartbruininks@gmail.com and I will try to help you
 out. Cheers and all the best, Bart M
 H Bruininks<br> University of Groningen (2020)
DOI: 10.5061/dryad.np5hqbzq3
title: Interactive Effects of Iron and Temperature on the Growth of Fragilariopsis cylindrus

description: Iron and temperature are important drivers controlling phytoplankton
 growth in the Southern Ocean. Most studies examining phytoplankton
 responses to these variables consider them independently, testing
 responses to changing temperature under constant iron and vice versa.
 Consequently, we lack a phenomenological and mechanistic understanding of
 how concurrent changes in these variables influence primary productivity.
 Here we used a matrix of three temperatures and eight iron levels to
 examine changes in growth rate, photophysiology and size in Fragilariopsis
 cylindrus over four generations. Temperature and iron interactively
 influenced growth; warming decreased iron demand, allowing cells to
 maintain half-maximal growth rate at lower iron concentrations. We also
 observed possible mechanisms underpinning this phenomenon: warming
 increased light-harvesting cross section and reduced cell size, thereby
 increasing light energy availability and iron uptake efficiency. These
 results suggest interactive iron-warming effects could lead to larger
 increases in S.O. phytoplankton growth than those currently predicted by
 marine ecosystem models.
DOI: 10.5061/dryad.18931zct5
title: Study design factors influencing patients’ willingness to participate in clinical research: a randomised vignette-based study

description: Background: High patient participation in clinical research reduces
 selection bias, and ensures the generalisability of study findings. We
 explored study-related factors that may influence patients’ willingness to
 participate in research. Methods: We submitted by mail two vignettes that
 described clinical research studies – a drug trial, and a diagnostic study
 – to patients recently discharged from hospital, and assessed Background:
 High patient participation in clinical research reduces selection bias,
 and ensures the generalisability of study findings. We explored
 study-related factors that may influence patients’ willingness to
 participate in research. Methods: We submitted by mail two vignettes that
 described clinical research studies – a drug trial, and a diagnostic study
 – to patients recently discharged from hospital, and assessed their
 willingness to participate. We used a factorial design to randomly
 allocate three study attributes per vignette: in the drug trial, presumed
 superiority of new drug versus equipoise, public versus industry funding,
 and random versus non-random treatment allocation; in the diagnostic
 study, common versus rare disease, genetic versus protein analysis, and
 automatic reporting of results versus reporting on demand. Results: Of
 2600 patients contacted, 1140 (44%) participated. Globally, willingness to
 participate in a drug trial was lower than in a diagnostic study (44.8%
 vs. 76.2%; P &lt;0.001). In the drug trial, participation was
 significantly higher when the new drug was presented as presumably better
 than the old (vs. equipoise) and when the study was funded by public
 sources (vs. industry), but was not affected by the allocation method.
 None of the factors tested in the diagnostic study was associated with
 participation. Conclusions: Patients were more likely to participate in a
 hypothetical observational diagnostic study than in a hypothetical drug
 trial. Participation in the trial was lower when clinical equipoise was
 expressed, and when the trial was funded by industry. These results
 suggest that some features of study design can influence
 participation.their willingness to participate. We used a factorial design
 to randomly allocate three study attributes per vignette: in the drug
 trial, presumed superiority of new drug versus equipoise, public versus
 industry funding, and random versus non-random treatment allocation; in
 the diagnostic study, common versus rare disease, genetic versus protein
 analysis, and automatic reporting of results versus reporting on demand.
description: Initially, we collected the participant responses in a paper case
 report form (questionnaire). These questionnaires were then recorded
 manually in a database by two independent persons (double entry) using
 pre-formatted variables. The database was finally imported in a STATA
 file.
DOI: 10.5061/dryad.05qfttf0c
title: Data from: Photonic hybrid state entanglement swapping using cat state superpositions

description:   We propose the use of hybrid entanglement in an
 entanglement swapping protocol, as means of distributing a Bell state with
 high fidelity to two parties, Alice and Bob. The hybrid entanglement used
 in this work is described as a discrete variable (Fock state) and a
 continuous variable (cat state superposition) entangled state. We model
 equal and unequal levels of photonic loss between the two propagating
 continuous variable modes, before detecting these states via a projective
 vacuum-one-photon measurement, and the other mode via balanced homodyne
 detection. We investigate homodyne measurement imperfections, and the
 associated success probability of the measurement schemes chosen in this
 protocol.     We show that our
 entanglement swapping scheme is resilient to low levels of photonic
 losses, as well as low levels of averaged unequal losses between the two
 propagating modes, and show an improvement in this loss resilience over
 other hybrid entanglement schemes using coherent state superpositions as
 the propagating modes. Finally, we conclude that our protocol is suitable
 for potential quantum networking applications which require two nodes to
 share entanglement separated over a distance of 5-10 km when used with a
 suitable entanglement purification scheme.
description: The dataset includes mathematica code to generate final density
 matrix of cat state entanglement swapping protocol, including averaged
 unequal photonic losses between both propagating modes. 
 The fidelity plots, and success probability plots, can be
 generated using this code.  Note that to run this code
 to reproduce the data as published in this manuscript, the
 "non-ideal" homodyne measurement variable (\epsilon) should be
 ignored. Therefore \epsilon should be set to 0 in the code. 
 NB - the QDensity Mathematica package (available at: https://library.wolfram.com/infocenter/MathSource/5715/) is required to correctly run this code.
DOI: 10.5061/dryad.xd2547ddk
title: Data from: Biosynthesis of the redox coenzyme F420 in Thermomicrobia involves reduction by standalone nitroreductase superfamily enzymes.

description: Coenzyme F420 is a redox cofactor involved in hydride transfer reactions
 in archaea and bacteria. Since F420-dependent enzymes are attracting
 increasing interest as tools in biocatalysis, F420 biosynthesis is being
 revisited. While it was commonly accepted for long that the
 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was
 recently shown that PEP is incorporated in Actinobacteria and that the
 C-terminal domain of the FbiB protein, a member of the nitroreductase
 superfamily (NTR), converts dehydro-F420 into saturated F420. Outside the
 Actinobacteria, however, the situation is still unclear because FbiB is
 missing in these organisms and enzymes of the NTR family are highly
 diversified. Here, we show by heterologous expression and in-vitro assays
 that standalone NTR enzymes from Thermomicrobia exhibit dehydro-F420
 reductase activity. Metabolome analysis and proteomics studies confirmed
 the proposed biosynthetic pathway in Thermomicrobium roseum. These results
 clarify the biosynthetic route of coenzyme F420 in a class of
 Gram-negative bacteria, redefine functional subgroups of the NTR
 superfamily, and offer an alternative for large-scale production of F420
 in E. coli in the future.
description: Methods are described in the original AEM publication (Braga et
 al., 2020).
description: Data from: "Biosynthesis of the redox coenzyme F420 in
 Thermomicrobia involves reduction by standalone nitroreductase superfamily
 enzymes" This dataset contains 4 archives of LC-MS
 data from 4 different experiments: * Metabolite
 analysis of Thermomicrobium roseum<br> * Nitroreductase - in-vivo
 coexpression in E. coli<br> * Nitroreductase from Thermomicrobium
 roseum - in-vitro assay<br> * Proteomics of Thermomicrobium
 roseum LC-MS data were converted to mzML format before
 upload. All metadata can be found in the original publication.
DOI: 10.25338/b8660d
title: Adaptive changes in color vision from long-term filter usage in anomalous but not normal trichromacy

description: For over 150 years, spectrally selective filters have been proposed to
 improve the vision of observers with color vision deficiencies. About 6%
 of males and &lt;1% of females have anomalies in their gene arrays
 coded on the X chromosome that result in significantly decreased spectral
 separation between their middle- (M-) and long- (L-) wave sensitive cone
 photoreceptors. These shifts alter individuals’ color-matching and
 chromatic discrimination such that they are classified as anomalous
 trichromats. Broad-band spectrally selective filters proposed to improve
 the vision of color-deficient observers principally modify the illuminant
 and are largely ineffective in enhancing discrimination or perception
 because they do not sufficiently change the relative activity of M- and
 L-photoreceptors. Properly tailored notch filters, by contrast, might
 increase the difference of anomalous M- and L-cone signals. Here, we
 evaluated the effects of long-term usage of a commercial filter designed
 for this purpose on luminance and chromatic contrast response, estimated
 with a signal detection-based scaling method. We found that sustained use
 over two weeks was accompanied by increased chromatic contrast response in
 anomalous trichromats. Importantly, these improvements were observed when
 tested without the filters, thereby demonstrating an adaptive visual
 response. Normal observers and a placebo control showed no such changes in
 contrast response. These findings demonstrate a boosted chromatic response
 from exposure to enhanced chromatic contrasts in observers with reduced
 spectral discrimination. They invite the suggestion that modifications of
 photoreceptor signals activate a plastic post-receptoral substrate that
 could potentially be exploited for visual rehabilitation.
DOI: 10.5061/dryad.70rxwdbtw
title: Data from: Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict-containing dioecious forest tree

description: Aim: The historical circumstances promoting the transition from sexual to
 apomictic reproduction in dioecious plant species remains poorly
 understood. Here, we investigated the divergence and demographic history
 of Lindera glauca, a dioecious tree considered to be facultatively
 apomictic in China while comprising only females (obligate apomicts) in
 Japan. Location: East Asia (China and Japan) Methods: Samples from 42
 populations were genotyped using chloroplast DNA and nuclear
 microsatellite (nSSR) loci to assess genetic diversity and structure. The
 nSSR genotypes were also used to detect the mode of reproduction in
 Chinese and Japanese populations, respectively. Approximate Bayesian
 Computation on nSSRs and palaeoclimatic niche models provided further
 insights into the evolutionary and population demographic history.
 Results: Chinese L. glauca was found to harbour both sexual and asexual
 genotypes. Chinese and Japanese L. glauca underwent roughly
 contemporaneous bottlenecks during a mid-Pleistocene glacial period,
 possibly marking the split-time of the island lineage from its mainland
 ancestor. In contrast to Chinese L. glauca, the Japanese lineage
 experienced a massive range contraction during the Last Glacial Maximum
 and postglacial expansions. Main conclusions: While reproductive assurance
 plays an important role in the selection of apomixis in Chinese L. glauca,
 the lack of male plants in Japan likely reflects population demographic
 history driven by (Late) Quaternary climate change. Hence, the present
 study demonstrates a possible link between palaeoclimate change and the
 transition to exclusively apomictic reproduction in a dioecious tree.
description: All 617 samples were genotyped at 19 nSSR loci using primers and
 amplification protocols developed specifically for <i>Lindera glauca
 </i>(Echt, Deemer, Kubisiak, & Nelson, 2006; Edwards
 & Niesenbaum, 2007; Xiong et al., 2016; Zhu, Ding, Yap, &
 Qiu, 2016; see Table S2). Alleles were manually scored and determined
 using genemarker (version 2.2.0; SoftGenetics, State College, PA,
 USA). We performed demographic history analysis based
 on these data using ABC and also provided the R scripts.
 We also provided a file of the Maxent process and the
 results.
description: The original population code has a separate form file.
 The microsatellite genotype for all 617 Lindera glauca samples is
 included in the abc_scripts190326.zip. The ReadMe file
 for R scripts is also included.
DOI: 10.5061/dryad.hmgqnk9cs
title: Accumulation of deleterious mutations in landlocked threespine stickleback populations

description: Colonization of new habitats often reduces population sizes and may result
 in the accumulation of deleterious mutations by genetic drift. Compared to
 the genomic basis for adaptation to new environments, genome-wide analysis
 of deleterious mutations in isolated populations remains limited. In the
 present study, we investigated the accumulation of deleterious mutations
 in five endangered freshwater populations of threespine stickleback
 (Gasterosteus aculeatus) in the central part of the mainland of Japan.
 Using whole genome resequencing data, we first conducted phylogenomic
 analysis and confirmed at least two independent freshwater colonization
 events in the central mainland from ancestral marine ecotypes. Next,
 analyses of single nucleotide polymorphisms (SNPs) showed a substantial
 reduction of heterozygosity in freshwater populations compared to marine
 populations. Reduction in heterozygosity was more apparent at the center
 of each chromosome than the peripheries and on X-chromosomes compared to
 autosomes. Third, bioinformatic analysis of deleterious mutations showed
 increased accumulation of putatively deleterious mutations in the
 landlocked freshwater populations compared to marine populations. For the
 majority of populations examined, the frequencies of putatively
 deleterious mutations were higher on X-chromosomes than on autosomes. The
 inter-population comparison indicated that the majority of putatively
 deleterious mutations may have accumulated independently. Thus, whole
 genome resequencing of endangered populations can help to estimate the
 accumulation of deleterious mutations and inform us of which populations
 are the most severely endangered. Furthermore, analysis of variation among
 chromosomes can give insights into whether any particular chromosomes are
 likely to accumulate deleterious mutations.
description: PROVEAN and SIFT scores of stickleback populations calculated
 using whole genome re-sequence data.