cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mcvdnck4r
title: Data for study on the permeability of biogeographic barriers to marine species on the east and west coasts of North America

description: Aim: We assess the role of contemporary oceanography and species traits in
 shaping observed patterns of biogeography over broad spatial scales.
 Location: Our study domain covers the east and west coasts of North
 America, from 30° to 73° on the east coast and 33° to 73° on the west
 coast. Time Period: Hydrodynamic models use climatological fields from
 1990 to 2015 on the east coast, and 1993 to 2018 on the west coast. Major
 Taxa Studied: Model simulations represent larval dispersal for generalized
 benthic invertebrate species distributed in the subtidal zone from 10 m to
 100 m depth, with planktonic larval durations ranging from 21–60 days.
 Methods: We conducted a literature review to identify major biogeographic
 barriers along the east and west coasts of North America, and then
 assessed the permeability of these barriers to larval dispersal using
 Lagrangian Particle Tracking. We ran a series of simulations in which we
 varied the suitable habitat distribution, planktonic larval duration, and
 spawning seasonality of simulated larvae (i.e. particles) to assess the
 role of species traits on biogeography. Results: Our results showed a
 strong alignment of observed biogeographic barriers with larval dispersal
 patterns, with high variation in barrier permeability depending on the
 traits of the species considered. The location of suitable habitat and the
 season during which particle release occurred were the biological traits
 that drove much of the variation in barrier permeability among simulations
 on both coasts. Main Conclusions: Our results indicate an important role
 of contemporary oceanographic and geographic features in determining the
 biogeography of species whose primary dispersal is during larval stages,
 suggesting that climate change is likely to alter patterns of species
 biogeography. Our results also demonstrate that species traits play a
 strong role in determining the location and strength of biogeographic
 barriers.
description: Data are connectivity matricies between coastal zones defined
 from literature data identifying the location of biogeographic barriers.
 Connectivity matrices were generated from model simulations of larval
 dispersal of coastal benthic species using Lagrangian Particle Track
 modelling. Simulations include particles with three sets of generalized
 initial habitat distributions defined by bathymetric depth and distance
 from shore (10m and 5km, 30m 20km, and 100m 50km), and were run and
 processed for three planktonic larval durations (21, 30, and 60 days).
 Simulations were run for 6 months per year, with the seasonality of
 particle release in each zone defined by a generalized spawning
 seasonality assigned to each zone based on temperature conditions. See the
 manuscript for more detail on the methods used to generate
 matrices.
DOI: 10.5061/dryad.1zcrjdfws
title: Experimental ectoparasite removal has a sex-specific effect on nestling telomere length

description: Parasites are a strong selective force that can influence fitness-related
 traits. The length of chromosome-capping telomeres can be used to assess
 the long-term costs of parasitism, as telomere loss accelerates in
 response to environmental stressors and often precedes poorer survival
 prospects. Here, we explored the sex-specific effects of ectoparasite
 removal on morphology and telomere length in nestling tree swallows
 (Tachycineta bicolor). To do so, we experimentally removed blowfly
 (Protocalliphora spp.) larvae from nests using Permethrin, a
 broad-spectrum insecticide. Compared to water-treated controls,
 insecticide treatment of nests had a sex-biased effect on blood telomere
 length: ectoparasite removal resulted in significantly longer telomeres in
 males but not females. While this treatment did not influence nestling
 body mass, it was associated with reduced feather development regardless
 of sex. This may reflect a relaxed pressure to fledge quickly in the
 absence of parasites, or alternatively, could be a negative side effect of
 permethrin on morphology. Exploring robust sex-specific telomere dynamics
 in response to early-life environmental pressures such as parasitism will
 shed light on sexual dimorphism in adult life histories and ageing.
DOI: 10.5061/dryad.b5mkkwhhg
title: Do plant-soil feedbacks promote coexistence in a sagebrush steppe?

description: Recent studies have shown the potential for negative plant-soil feedbacks
 (PSFs) to promote stable coexistence but have not quantified the
 stabilizing effect relative to other coexistence mechanisms. We conducted
 a field experiment to test the role of PSFs in stabilizing coexistence
 among four dominant sagebrush steppe species that appear to coexist
 stably, based on previous work with observational data and models. We then
 integrated the effects of PSF treatments on focal species across
 germination, survival, and first-year growth. To contribute to stable
 coexistence, soil microbes should have host-specific effects that result
 in negative feedbacks. Over two replicated growing seasons, our
 experiments consistently showed that soil microbes have negative effects
 on plant growth, but these effects were rarely host-specific. The uncommon
 host-specific effects were mostly positive at the germination stage and
 negative for growth. Integrated effects of PSF across early life-stage
 vital rates showed that PSF-mediated self-limitation occasionally had
 large effects on projected plant biomass but occurred inconsistently
 between years. Our results suggest that while microbially-mediated PSF may
 not be a common mechanism of coexistence in this community, it may still
 affect the relative abundance of dominant plant species via changes in
 host fitness. Our work also serves as a blueprint for future
 investigations that aim to identify underlying processes and test
 alternative mechanisms to explain important patterns in community ecology.
DOI: 10.5281/zenodo.18361346
title: Data related to paper "Stochastic ion emission perturbation mechanisms in atom probe tomography: Linking simulations to experiment"

description: The generated raw simulation data related to paper "Stochastic ion emission perturbation mechanisms in atom probe tomography: Linking simulations to experiment". The instructions for use are included in the README-file.
DOI: 10.5281/zenodo.18361347
title: Data related to paper "Stochastic ion emission perturbation mechanisms in atom probe tomography: Linking simulations to experiment"

description: The generated raw simulation data related to paper "Stochastic ion emission perturbation mechanisms in atom probe tomography: Linking simulations to experiment". The instructions for use are included in the README-file.
DOI: 10.5061/dryad.0k6djhb48
title: Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation

description: A long-standing goal in the field of polyploid biology has been the
 derivation of mathematical models of gamete mode formation. These models
 form the basis of statistical inference and evolutionary theory. Here, we
 present 3-locus models of gamete mode formation in autotetraploids without
 and with preferential cross-over formation. The three loci are assumed to
 occur on one arm of the same chromosome. For preferential cross-over
 formation, one of the three loci affects the tendency for sets of sister
 chromatids to pair and therefore affects rates of recombination. The
 models are derived such that the process of double reduction is a function
 of rates of synaptic partner switches and recombination, as opposed to
 being independent of these processes. We assume potentially one synaptic
 partner switch per meiosis. We also assume the coefficient of coincidence
 is one, such that cross-over events are independent, given a set of
 cross-over rates. Illustrative cases are examined demonstrating
 differences in the gamete mode probabilities without and with preferential
 cross-over formation. Lastly, we explore the accuracy of maximum
 likelihood estimates of the probability of synaptic partner switches and
 preferential cross-over formation when the locus controlling preferences
 is at a proximal, middle or distal location on the chromosome arm. All
 Supplementary Information is available at
 https://github.com/ckgriswold/3-locus-autotetraploid-meiosis.
DOI: 10.5061/dryad.2280gb5x2
title: Data from: Diversification of the ruminant skull along an evolutionary line of least resistance

description: Clarifying how microevolutionary processes scale to macroevolutionary
 patterns is a fundamental goal in evolutionary biology, but these
 analyses, requiring comparative datasets of population-level variation,
 are limited. By analyzing a previously published dataset of 2859 ruminant
 crania, we find that variation within and between ruminant species is
 biased by a highly conserved mammalian-wide allometric pattern, CREA
 (CR-aniofacial E-volutionary A-llometry), where larger species have
 proportionally longer faces. Species with higher morphological integration
 and species more biased towards CREA have diverged farther from their
 ancestors, and Ruminantia as a clade diversified farther than expected in
 the direction of CREA. Our analyses indicate that CREA acts as an
 evolutionary ‘line of least resistance’ and facilitates morphological
 diversification due to its alignment with the browser-grazer continuum.
 Taken together, our results demonstrate that constraints at the
 population-level can produce highly directional patterns of phenotypic
 evolution at the macroevolutionary scale. Further research is needed to
 explore how CREA has been exploited in other mammalian clades.
description: The raw landmark data was retrieved from a previous publication
 (Haber 2016, https://doi.org/10.5061/dryad.1vm38) and processed in R ('processing_data.R' script). 
description: This data package includes the necessary R scripts and data to
 reproduce results presented in the manuscript. The R script
 "processing_data.R" contains the code needed to clean and
 wrangle the raw landmark data and ecological data into formats suitable
 for analysis, "ruminant_functions_Nov22.R" contains the custom
 scripts written in order to run the analyses and plot the data. The
 different "FigureX...R" scripts contain the code needed to
 replicate the different figures and analyses in the manuscript. The
 'data' folder contains the data needed for all figures and
 analysis. The 'app' folder contains the R scripts supporting the
 interactive morphospaces as a Shiny dashboard.
DOI: 10.5281/zenodo.10810148
title: Data Part 2: Megascale tomography of a quantum detector

description: This contains the outcome matrix and the input state matrix, which are used to reconstruct the positive operator valued measures (POVMs) of the detector. The three POVM matrices based on reconstructions with no smoothing, standard next-neighbor smoothing and long-range smoothing as well as the POVMs based on the analytical model are included as well.

Wigner function data based on the long-range smoothing and the analytical model POVMs are also included.

The raw measurement data that is the basis of this processed data can be found here: https://doi.org/10.5281/zenodo.10803758
description: Funded by the European Union (ERC, QuESADILLA, 101042399). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The authors gratefully acknowledge the computing time provided to them on the high-performance computer Noctua 2 at the NHR Center PC2. These are funded by the Federal Ministry of Education and Research, and the state governments participate on the basis of the resolutions of the GWK for the national high-performance computing at universities (www.nhr-verein.de/unsere-partner).
DOI: 10.5281/zenodo.10810149
title: Data Part 2: Megascale tomography of a quantum detector

description: This contains the outcome matrix and the input state matrix, which are used to reconstruct the positive operator valued measures (POVMs) of the detector. The three POVM matrices based on reconstructions with no smoothing, standard next-neighbor smoothing and long-range smoothing as well as the POVMs based on the analytical model are included as well.

Wigner function data based on the long-range smoothing and the analytical model POVMs are also included.

The raw measurement data that is the basis of this processed data can be found here: https://doi.org/10.5281/zenodo.10803758
description: Funded by the European Union (ERC, QuESADILLA, 101042399). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.The authors gratefully acknowledge the computing time provided to them on the high-performance computer Noctua 2 at the NHR Center PC2. These are funded by the Federal Ministry of Education and Research, and the state governments participate on the basis of the resolutions of the GWK for the national high-performance computing at universities (www.nhr-verein.de/unsere-partner).
DOI: 10.5061/dryad.2280gb5x3
title: Electrophysiological data from five species of Xenopus

description: Across phyla, species-specific vocalizations are used by males to attract
 females. Functional analyses of the neural circuitry underlying behavior
 have been difficult, particularly in vertebrates. However, using an ex
 vivo brain preparation that produces fictive vocalizations, we previously
 identified anatomically distinct fast and slow central pattern generators
 (CPGs) that drive the fast and slow clicks of male courtship calls in male
 African clawed frogs, Xenopus laevis. To gain insight into the evolution
 of neural circuits underlying courtship calls, we extended this approach
 to four additional species. Here, we show that although the exact rate and
 duration of the clicks are unique to each species, fast and slow CPGs
 identified in male X. laevis are conserved across species. Further, we
 show that the development of fast CPGs depends on testosterone in a
 species-specific manner: testosterone facilitates the development of fast
 CPGs in a species with a courtship call containing fast clicks, but not in
 a species with a courtship call made entirely of slow clicks. Finally, we
 showed that, unlike other vestigial neural circuits that remain latent,
 the fast CPGs are not inherited by all species; rather, they are possessed
 only by the species that produce fast clicks. The results suggest that
 species-specific calls of the genus Xenopus have evolved by utilizing
 conserved fast or slow CPGs that are broadly tuned to generate fast or
 slow trains of clicks, the development of which appear to be regulated by
 a strategic expression of testosterone receptors in the brain of each
 species.  
description: Electrophysiological data collected using ClampEx was analyzed to
 determine CAP/click rates, latency, and number. For some data,
 cross-correlation coefficients were calculated, and the time at which the
 maximum CCC was obtained was determined to be the lag time. PSD was
 calculated using Clampfit and averaged across individuals.
DOI: 10.5061/dryad.5mkkwh79k
title: Data from: HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes

description: The mature HIV-1 capsid is stabilized by host and viral determinants. The
 capsid protein CA binds to the cellular metabolites inositol
 hexakisphosphate (IP6) and its precursor inositol (1, 3, 4, 5, 6)
 pentakisphosphate (IP5) to stabilize the mature capsid. In target cells,
 capsid destabilization by the antiviral compounds lenacapavir and PF74
 reveals an HIV-1 infectivity defect due to IP5/IP6 (IP5/6)
 depletion.  To test whether intrinsic HIV-1 capsid stability and/
 or host factor binding determines HIV-1 insensitivity to IP5/6 depletion,
 a panel of CA mutants was assayed for infection of IP5/6-depleted T cells
 and wildtype cells.  Four CA mutants with unstable capsids
 exhibited dependence on host IP5/6 for infection and reverse transcription
 (RTN).  Adaptation of one such mutant, Q219A, by spread in
 culture resulted in Vpu truncation and a capsid three-fold interface
 mutation, T200I.  T200I increased intrinsic capsid stability as
 determined by in vitro uncoating of purified cores and partially reversed
 the IP5/6-dependence in target cells for each of the four CA mutants.
 T200I further rescued the changes to lenacapavir sensitivity associated
 with the parental mutation. The premature dissolution of the capsid caused
 by the IP5/6-dependent mutations imparted a unique defect in integration
 targeting that was rescued by T200I.  Collectively, these results
 demonstrate that T200I restored other capsid functions after RTN for the
 panel of mutants. Thus, the hyperstable T200I mutation stabilized the
 instability defects imparted by the parental IP5/6-dependent CA mutation.
 The contribution of Vpu truncation to mutant adaptation was linked to
 BST-2 antagonization, suggesting that cell-to-cell transfer promoted
 replication of the mutants.  We conclude that interactions at the
 three-fold interface are adaptable, key mediators of capsid stability in
 target cells and are able to antagonize even severe capsid instability to
 promote infection.
description: Please use Microsoft Excel or Open Office equivalent.  All other
 files can be opened with a text editor.
DOI: 10.21223/p3/ooq73n
title: Dataset for: Advanced clones of group LBHT cycle 1, population B (LBHT) in Comas-Peru

description: In anticipation of the effects of global warming on potato cultivation in both tropical and subtropical environments. Since 2004, efforts have turned to the development of a new group in Population B with improved adaptation to warm environments, resistance to late blight and virus, mid-season maturity (90 day growing period under short day length conditions), adaptation to mid elevations, low glycoalkaloids content, along with economically important traits such as high tuber yield, quality for table and industry. And so group LBHT of population B was developed, denominated LBHT because of its late blight and heat tolerance. All trials were conducted in randomized complete block design (RCBD) with 2-4 replicates or in simple lattice design at Comas, located at 2400 to 2788 masl in Junin situated in the Central mountain ranges in Peru The trials were established at Comas due to high disease pressure of late blight, disease endemic, highly favorable for disease development and severity during the rainy periods in these areas from 2006 to 2007.
DOI: 10.25338/b8m06b
title: Exploring impact of federal tax credit on decision to lease or purchase a PEV

description: Using a sample of approximately 7,000 California PEV drivers recruited
 from California Clean Vehicle Rebate Program applicants, two logistic
 regression models are specified to analyze responses by PEV lessees and
 purchasers to the question of what they would do in the absence of the
 federal tax credit. Possible responses include: Purchase/lease the same
 PEV, switch to a different PEV, switch to a conventional or hybrid
 (non-plug in) vehicle, or do not acquire a vehicle at all. Several key
 insights are found; higher discounts from the tax credit increase the
 probability of lessees indicating they would not lease a PEV at all. For
 purchasers, in addition to not purchasing any vehicle at all, the
 probability of purchasing a conventional vehicle, or another PEV also
 increase. These findings could have implications for California’s ability
 to reach its ZEV milestones and are important to consider due to recent
 changes to the US federal tax credit. Our findings indicate that many PEV
 adopters would likely not adopt their PEV without the tax credit,
 potentially more so for leased compared to purchased vehicles. There are
 also unique results for lessees related to the impact of home ownership;
 renters are more likely than homeowners to lease a conventional vehicle
 than a PEV in the absence of the tax credit. This finding contributes to
 the literature which finds homeowners to be more likely to adopt a PEV
 than renters, emphasizing the importance of access to at-home charging for
 PEV adoption. These results show how incentives may be more influential
 for adoption decisions in the PEV lease market is, and the factors which
 are associated with consumers’ PEV adoption behavior in the absence of the
 federal tax credit.
description: We use results from a cohort survey of electric vehicle owners in
 California conducted in 2019. The respondents of the survey are sampled
 from the pool of California Clean Vehicle Rebate Project (CVRP)
 recipients, a rebate program for purchasers and leasers of electric
 vehicles within California. The CVRP is administered by the Center for
 Sustainable Energy & California Air Resources Board, who have an
 agreement with the University to provide contacts (e-mail) for
 solicitation for the purposes of disseminating and gathering respondents
 for the survey. Altogether, phase 5 include 7,078 respondents, all of whom
 have applied for the CVRP rebate following the purchase or lease of a
 PEV.
description: Excel
DOI: 10.5061/dryad.5qfttdz9n
title: Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model

description: Cancer cells bypass cell death by changing the expression of the BCL-2
 family of proteins, which are apoptotic pathway regulators. Upregulation
 of pro-survival BCL-2 proteins or downregulation of cell death effectors
 BAX and BAK interferes with the initiation of the intrinsic apoptotic
 pathway. In normal cells, apoptosis can occur through pro-apoptotic
 BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins.
 When cancer cells over-express pro-survival BCL-2 proteins, a potential
 remedy is the sequestration of these pro-survival proteins through a class
 of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic
 groove of pro-survival BCL-2 proteins. To improve the design of these BH3
 mimetics, the packing interface between BH3 domain ligands and
 pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to
 identify the amino acid residues responsible for interaction affinity and
 specificity. A Knob-Socket analysis organizes all the residues in a
 binding interface into simple 4 residue units: 3-residue sockets defining
 surfaces on a protein that pack a 4th residue knob from the other
 protein. In this way, the position and composition of the knobs packing
 into sockets across the BH3/BCL-2 interface can be classified. A
 Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal
 multiple conserved binding patterns across protein paralogs. Conserved
 knob residues such as a Gly, Leu, Ala and Glu most likely define binding
 specificity in the BH3/BCL-2 interface, whereas other residues such as
 Asp, Asn, and Val are important for forming surface sockets that bind
 these knobs. These findings can be used to inform the design of BH3
 mimetics that are specific to pro-survival BCL-2 proteins for cancer
 therapeutics.
description: Protein structure files were obtained from the Protein Data Bank.
 These files were cleaned for a single domain with a ligand as well as
 completeness. The files were then processed throught the Knob-Socket
 Analysis to produce the data files.