cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.563c25c
title: Phenotypic variability can promote the evolution of adaptive plasticity by reducing the stringency of natural selection

description: Adaptive phenotypic plasticity is a potent but not ubiquitous solution to
 environmental heterogeneity, driving interest in what factors promote and
 limit its evolution. Here a novel computational model representing
 stochastic information flow in development is used to explore evolution
 from a constitutive phenotype to an adaptively plastic response. Results
 show that populations tend to evolve robustness to developmental
 stochasticity, but this evolved robustness limits evolvability;
 specifically, robust genotypes have less ability to evolve adaptive
 plasticity when presented with a mix of both the ancestral environment and
 a new environment. Analytic calculations and computational experiments
 confirm that this constraint occurs when the initial mutational steps
 toward plasticity are pleiotropic, such that mutant fitnesses decline in
 the environment to which their parents are well-adapted. Greater
 phenotypic variability improves evolvability in the model by lessening
 this decline as well as improving the fitness of partial adaptations to
 the new environment. By making initial plastic mutations more palatable to
 natural selection, phenotypic variability can increase the evolvability of
 an innovative, plastic response without improving evolvability to simpler
 challenges such as a shifted optimum in a single environment. Populations
 that evolved robustness by negative feedback between the trait and its
 rate of change show a particularly strong constraining effect on the
 evolvability of plasticity, revealing another mechanism by which
 evolutionary history can limit later innovation. These results document a
 novel mechanism by which weakening selection could actually stimulate the
 evolution of a major innovation.
description: dryad_packageA zip archive containing all code, data files, and analysis scripts.
DOI: 10.5061/dryad.21dd976
title: Data from: Forest structure determines spatial changes in avian community along an elevational gradient in tropical Africa

description: Aim To test if tree species richness and forest structure drive spatial
 variation in avian communities along a tropical elevation gradient and to
 present information about the role of detailed forest parameters. Location
 A 2000-m long elevational gradient of tropical forest on Mt. Cameroon,
 west-central Africa. Taxon Birds and trees. Methods We performed bird
 censuses and vegetation mapping at the same plots across six forested
 sites at elevations of 350, 650, 1,100, 1,500, 1,850, and 2,200 m a.s.l.,
 with 16 plots per elevation. We tested the effects of elevation, forest
 structure and tree diversity on the species richness, functional diversity
 and β-diversity of birds (Bray-Curtis dissimilarity). We used conditional
 inference trees based on random forests (RF) to investigate these
 relationships across all elevation sites as well as within elevations.
 Results Both tree and bird species richness declined monotonically with
 elevation. Vegetation structure correlated with elevation, and all
 vegetation attributes significantly differed among elevations. The RF
 explained 70% of the variance in avian species richness, with the most
 important predictors being elevation, proportion of dead trees, tree
 species richness and herb layer coverage. We found that elevation (and
 shrub layerE2) was a particularly important predictor of avian functional
 diversity. We identified no important predictor of bird species richness
 after standardization within elevations, and the proportion of dead trees
 was the sole important predictor of functional diversity. Within-elevation
 β-diversity in avian community composition was determined by the
 dissimilarity of the tree community and differences in leaf area index,
 solar radiation and spatial distance. The functional dissimilarity was
 best explained by leaf area index. Main conclusions Apart from elevation
 itself, spatial distance even within elevations correlated with
 compositional and functional variation among avian assemblages. Forest
 structural traits can have a significant influence on distribution of
 birds. Thus, gaps in the spatial distribution of species such as along
 elevations might be caused by fine-scale recognition of suitable habitats.
description: Tree species richness at
 census pointsNumber of tree species
 recorded at 16 census points at each of 6 elevations on Mt. Cameroon,
 Central Africa.tree_point_SR_20190707.txtComposition of tree assemblages along elevationSpecies composition of tree assemblages at 6 elevations on Mt. Cameroon, Central Africatree_presence_elevation_20190707.txtBird species richness at census pointsNumber of bird species recorded at 16 census points at each of 6 elevations on Mt. Cameroon, Central Africa.bird_point_SR_20190707.txtComposition of bird assemblages along elevationSpecies composition of bird assemblages at 6 elevations on Mt. Cameroon, Central Africabird_presence_elevation_20190723.txt
DOI: 10.6078/d1jh59
title: NetCDF data from: Numerical investigation of baroclinic channel-shoal interaction in partially stratified estuaries

description: These NetCDF files are the simulation result files for the eleven
 scenarios listed in Table 1 of the manuscript. They are generated using
 a two-dimensional cross-sectional mode of the General Estuarine
 Transport Model (GETM). They include a reference scenario and a
 number of sensitivity scenarios with variation of the longitudinal
 salinity radient, the cross-sectionally averaged tidal velocity magnitude,
 the averaged shoal depth, the slope of the shoal, and the quasi-lateral
 eddy diffusivities. To be specific, scenario 01: reference
 scenario; scenario 02: small longitudinal salinty
 gradient; scenario 03: large longitudinal salinty
 gradient; scenario 04: small tidal velocity; scenario
 05: large tidal velocity; scenario 06: small average shoal
 depth; scenario 07: large average shoal depth; scenario
 08: small shoal slope; scenario 09: large shoal
 slope; scenario 10: small lateral diffusivity; scenario
 11: large lateral diffusivity. To be consistent with the existing
 structure of the code, the cross section of the estuary lies in the x-z
 plane, where x is the across-estuary
 (lateral) direction and z is the
 vertical direction. All gradients in the along-estuary direction
 (y) are assumed to vanish except for the longitudinal barotropic
 and baroclinic pressure gradients. There are four grid points in
 the y direction, with the outter (j=1, 4) set to NaN and the two inner
 ones being independent on j.
DOI: 10.6071/m3t95h
title: Saturated Hydraulic Conductivity Pedotransfer Models

description: This repository contains machine learning-based pedotransfer models that
 predict saturated hydraulic conductivity (Ks). An app with a graphical
 user interface to run these models and other relevant materials including
 R codes used to build and test the models are available at the
 author's GitHub repository:
 https://github.com/saraya209/soil_ksat.  Detailed description of
 this work is available in our paper published in the Journal of Water
 Resources Research: Araya and Ghezzehei (2019).
DOI: 10.6078/d18396
title: EBIT 1

description: Test
DOI: 10.5281/zenodo.18393468
title: IOT TARMOQLARI XAVFSIZLIK PROTOKOLLARINI TADQIQ QILISH

description:  Ushbu maqolada Internet of Things (IoT) tarmoqlarida xavfsizlik protokollarini tadqiq qilish masalalari keng qamrovda o‘rganildi. Tadqiqot doirasida IoT arxitekturasi, qurilmalararo autentifikatsiya va ishonch tizimlari, ma’lumotlarni shifrlash mexanizmlari, kalitlarni boshqarish, yengil kriptografik protokollar, edge computing va blokcheyn texnologiyalarining xavfsizlikka ta’siri tahlil qilindi. Shuningdek, IoT xavfsizligini baholash mezonlari, anomaliyalarni aniqlash va multi-faktorli autentifikatsiya yondashuvlari ko‘rib chiqildi. Tadqiqot natijalari IoT tarmoqlarida samarali xavfsizlikni ta’minlash uchun standartlashtirilgan, moslashuvchan va innovatsion protokollarni joriy etish muhimligini ko‘rsatadi.
DOI: 10.5281/zenodo.18393469
title: IOT TARMOQLARI XAVFSIZLIK PROTOKOLLARINI TADQIQ QILISH

description:  Ushbu maqolada Internet of Things (IoT) tarmoqlarida xavfsizlik protokollarini tadqiq qilish masalalari keng qamrovda o‘rganildi. Tadqiqot doirasida IoT arxitekturasi, qurilmalararo autentifikatsiya va ishonch tizimlari, ma’lumotlarni shifrlash mexanizmlari, kalitlarni boshqarish, yengil kriptografik protokollar, edge computing va blokcheyn texnologiyalarining xavfsizlikka ta’siri tahlil qilindi. Shuningdek, IoT xavfsizligini baholash mezonlari, anomaliyalarni aniqlash va multi-faktorli autentifikatsiya yondashuvlari ko‘rib chiqildi. Tadqiqot natijalari IoT tarmoqlarida samarali xavfsizlikni ta’minlash uchun standartlashtirilgan, moslashuvchan va innovatsion protokollarni joriy etish muhimligini ko‘rsatadi.
DOI: 10.7280/d1z39f
title: Eddy flux measurements and transfer velocities of momentum, water vapor, and sulfur dioxide over the coastal Atlantic ocean

description: This data set contains air/sea eddy covariance fluxes and related data
 measured at the US Army Corps of Engineers Field Research Facility (USACE
 FRF) at Duck, North Carolina.  The goal of this study was to
 determine transfer velocities for momentum, water vapor, and
 sulfur dioxide in order to study the processes controlling air/sea
 deposition of highly soluble gases.  The measurements were made
 during March and April, 2015.
description: The instrumentation and techniques used in collection of this
 data and the methods used in data analysis are documented in Porter et
 al., 2018 and Porter et al. (2019). Porter, J. G., De
 Bruyn, W., & Saltzman, E. S. (2018). Eddy flux measurements of
 sulfur dioxide deposition to the sea surface. <i>Atmospheric
 Chemistry and Physics</i>, <i>18</i>(20), 15291–15305.
 https://doi.org/10.5194/acp-18-15291-2018 Porter, J. G., De Bruyn, W., Miller, S. D. & Saltzman, E. S. (in review).  Air/sea transfer of highly soluble gases over coastal waters. Geophys. Res. Letts.
DOI: 10.7280/d1td4d
title: Acetylene and ethane surface flask measurements from Cape Grim, Australia and South Pole, Antarctica

description: Measurements of the abundance of acetylene and ethane in surface air
 flasks from Cape Grim, Australia (CGO) and South Pole, Antarctica (SPO)
 were made in the Saltzman/Aydin Research Group at the University of
 California, Irvine. The surface flasks are from the the NOAA Halocarbons
 and other Atmospheric Trace Species (HATS) monitoring network shared with
 UC Irvine by Dr. Stephen Montzka to compliment on-going ice core research
 at UC Irvine involving the same trace species. 
description: Surface air samples in glass flasks were collected at South Pole,
 Antarctica and Cape Grim, Australia following the protcol set by the NOAA
 HATS monitoring group: https://www.esrl.noaa.gov/gmd/hats/. The bi-monthly flask air samples were shipped to UC Irvine for analysis with gas chromatography (Agilent 6890 with DB-1 column) and high-resolution mass spectrometry (Waters AutoSpec Ultima in EI+ mode) for the abundance of ethane and acetylene. Details on the UC Irvine analysis system are found in Aydin et al., 2007 JGR. Two air flasks are collected from each sampling date and one of the flasks is analyzed twice, resulting in three measuremetns for each sampling date. 
description: Missing or excluded data are denoted with -999. Mixing ratios are
 repoted in units of pmol mol-1. Errors are also in units of pmol mol-1 and
 represent a one-sigma uncertainity.
DOI: 10.7272/q6rv0kw6
title: Impact of Programming Workshops on Biomedical Reproducibility (IPWBR)

description: The objective of this study was to assess the impact of introductory
 programming workshops on the computational reproducibility of biomedical
 research workflows. This mixed methods study consisted of in-depth
 interviews with 14 biomedical researchers before and after participation
 in an introductory programming workshop. During the interviews,
 participants descreir research workflows and responded to a quantitative
 checklist measuring reproducible behaviors. The interview data was
 analyzed using a thematic analysis approach, and the pre and post workshop
 checklist scores were compared to assess the impact of the workshop on
 computational reproducibility of the researchers’ workflows.
description: A guide to the data is included as the file
 IPWBR_DataOverview
DOI: 10.5061/dryad.1bg1c1f
title: Data from: Enigmatic hook-like structures in Mesozoic ammonites (Scaphitidae)

description: In the last few decades, hook-like structures have been reported in the
 Mesozoic ammonite family Scaphitidae. Despite their exceptional
 preservation and debates about their function, no detailed reconstruction
 of them has yet been made. For the first time, we describe the composition
 and detailed morphology of these structures in the body chambers of six
 specimens of the Campanian ammonite Rhaeboceras halli (Meek and Hayden)
 using high resolution X-ray imaging. The hook-like structures are composed
 of a thin layer of brushite. The base of the hooks is open on one side
 forming an internal cavity, now filled with sediments. The tips of the
 hooks end in one or two cusps or, rarely, none at all. We used geometric
 morphometrics to capture the morphological disparity of the bicuspidate
 morphotypes comprising 98% of the hooks. Principal component analysis
 revealed chirality among the hooks and a cluster analysis (Gaussian
 mixture) recognized five main morphologies. Contrary to previous
 interpretation of these structures, we conclude that they are not radular
 teeth. They are much larger and more variable in size and shape than any
 known ammonite radulae and completely out of proportion with respect to
 the size of the jaw. The chirality, the hook-like shape, and the absence
 of a size relationship between the hooks and the body chambers in which
 they occur, lead us to propose that these hooks could represent elements
 of the brachial crown related to copulatory behavior. If so, these would
 be the first reported remnants of brachial crowns in ammonites.
description: Photographic
 plate.Photographs of the
 studied specimens with hook-like structures preserved. A. AMNH 66448,
 phragmocone (beginning arrowed) and part of the body chamber. B. AMNH
 66350, fragment of the body chamber, ventral view. C. AMNH 66351,
 phragmocone (beginning arrowed) and part of the body chamber. D. AMNH
 66433 fragment of the body chamber with lower jaw (aptychus) preserved
 (arrow). E.AMNH 66434 bodychamber. AMNH 64405 is figured in Figure
 2.Appendix_S1.pdfSynchrotron scanning and Conventional CT scanning parametersAppendix_S2.pdfAMNH 64405 scanning parameters (.pca file)Appendix_S3.pcaTIFF z stack of specimen AMNH-64405Appendix_S4.zip.zipXRD report and curveThe main crystalline phase identified is Brushite. The remaining phases exhibit semi-crystalline characteristics and poor peak shapes, therefore considered estimated phases. The pattern consists of two amorphous regions, from 20-30 deg 2-theta and 40-60 deg 2-theta. The first region is charateristic of amorphous compounds that have longer bonds such as organic compounds. The second is characteristic of metallic or inorganic amorphous materials.Appendix_S5.pdf
DOI: 10.6078/d1zm39
title: Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay

description: Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA
 surveillance pathway that eliminates transcripts with premature
 termination codons. Several studies have tried defined the features
 governing which transcripts are targeted to NMD. However, these approaches
 often rely on inhibiting core NMD factors, which often have roles in
 non-NMD processes within the cell. Based on reports that NMD-targeted
 transcripts are often bound by a single ribosome, we analyzed RNA-Seq data
 from a polysome fractionation experiment (TrIP-Seq) to characterize the
 features of NMD-targeted transcripts in human cells. This approach
 alleviates the need to inhibit the NMD pathway. We found that the EJC
 model, wherein an exon-exon junction located ≥50 nucleotides downstream of
 a stop codon is predicted to elicit NMD, was a powerful predictor of
 transcripts with high abundance in the monosome fraction (bound by a
 single ribosome). This was also true for the presence of an upstream open
 reading frame. In contrast, as 3’ UTR lengths increase, the proportion of
 transcripts that are most abundant monosome fraction does not increase.
 This suggests that either longer 3’ UTRs do not consistently act as potent
 triggers of NMD or that the degradation of these transcripts is
 mechanistically different to other NMD-targeted transcripts. Of the
 ribosome-associated transcripts annotated as “non-coding”, we find that a
 majority are bound by a single ribosome. Many of these transcripts
 increase in response to NMD inhibition, including the oncogenic SHNG15,
 suggesting many might be NMD targets. Finally, we found that retained
 intron transcripts without a premature termination codon are
 over-represented in the monosome fraction, suggesting an alternative
 mechanism is responsible for the low level of translation of these
 transcripts. In summary, our analysis finds that the EJC model is a
 powerful predictor of NMD-targeted transcripts, while the presence of a
 long 3’ UTR is not.
DOI: 10.7291/d13377
title: Interspecific and intra-shell stable isotope variation among the Red Sea giant clams

description: The Gulf of Aqaba is home to three giant clam species with differing
 ecological niches and levels of photosymbiotic activity. Giant clams grow
 a two-layered shell where the outer layer is precipitated in close
 association with photosymbiont-bearing siphonal mantle, and the inner
 layer is grown in association with the light-starved inner mantle. We
 collected 38 shells of the three species (the cosmopolitan Tridacna maxima
 and T. squamosa, as well as the rare endemic T. squamosina), and measured
 carbon and oxygen isotope ratios from inner and outer shell layers, to
 test for differences among species and between the layers of their shells.
 T. squamosina records higher temperatures of shell formation as determined
 by oxygen isotope paleothermometry, consistent with its status as an
 obligately shallow-dwelling species. However, the known negative
 fractionation imparted on tissue carbon isotopes by photosymbiotic algae
 did not produce measurable offsets in the carbonate δ13C values of the
 more symbiotic T. squamosina and T. maxima compared to the more
 heterotrophic T. squamosa. Across all species, outer shell layers recorded
 mean growth temperatures 1.8 °C higher than corresponding inner layers,
 which we propose is a function of the high insolation, low albedo
 microenvironment of the outer mantle, and potentially the activity of the
 symbionts themselves. Population-wide isotopic sampling of reef-dwelling
 bivalve shells can help constrain the ecological niches of rare taxa and
 help reconstruct their internal physiology.
DOI: 10.5061/dryad.m262vd1
title: Data from: HIPK4 is essential for murine spermiogenesis

description: Mammalian spermiogenesis is a remarkable cellular transformation, during
 which round spermatids elongate into chromatin-condensed spermatozoa. The
 signaling pathways that coordinate this process are poorly understood, and
 here we demonstrate that homeodomain-interacting protein kinase 4 (HIPK4)
 is required for sperm head shaping and male fertility in mice. HIPK4 is
 expressed in round and early elongating spermatids. Hipk4 knockout males
 are sterile, exhibiting phenotypes consistent with
 oligoasthenoteratozoospermia. Mutant sperm have reduced oocyte binding and
 are incompetent for in vitro fertilization, but can produce viable
 offspring via intracytoplasmic sperm injection. Ultrastructural analyses
 of HIPK4-null male germ cells reveal defects in the filamentous actin
 (F-actin)-scaffolded acroplaxome during spermatid elongation and abnormal
 head morphologies in mature spermatozoa. We further observe that HIPK4
 overexpression induces branched F-actin structures in cultured
 fibroblasts, supporting a role for this kinase in cytoskeleton remodeling.
 Our findings establish HIPK4 as an essential regulator of spermiogenesis
 and potential target for male contraception.
description: Clariom D
 microarray_HIPK4 null testes Compressed raw data from
 microarray analysis of HIPK4-null testes_Figure 5 - source data
 1   
 MassSpec_HCD_NIH3T3-HIPK4_phospho-enriched Compressed raw mass spectrometry data from the six high-pH reverse-phase elution fractions of pooled phospho-enriched samples from NIH-3T3 cells expressing HIPK4 constructs. Supporting Figure 6 - source data 1   MassSpec_HCD files_NIH3T3-HIPK4_total peptides Compressed raw mass spectrometry data from six high-pH reverse-phase elution fractions of the pooled total peptide samples from NIH-3T3 cells overexpressing HIPK4 constructs. Supporting Figure 6 - source data 1.
DOI: 10.5061/dryad.1536b56
title: Data from: Influence of climate change and post-delisting management on long-term population viability of the conservation-reliant Kirtland’s warbler

description: Rapid global climate change is resulting in novel abiotic and biotic
 conditions and interactions. Identifying management strategies that
 maximize probability of long-term persistence requires an understanding of
 the vulnerability of species to environmental changes. We sought to
 quantify the vulnerability of Kirtland’s Warbler (Setophaga kirtlandii), a
 rare Neotropical migratory songbird that breeds almost exclusively in the
 Lower Peninsula of Michigan and winters in the Bahamian Archipelago, to
 projected environmental changes on the breeding and wintering grounds. We
 developed a population-level simulation model that incorporates the
 influence of annual environmental conditions on the breeding and wintering
 grounds, and parameterized the model using empirical relationships. We
 simulated independent and additive effects of reduced breeding grounds
 habitat quantity and quality, and wintering grounds habitat quality, on
 population viability. Our results indicated the Kirtland’s Warbler
 population is stable under current environmental and management
 conditions. Reduced breeding grounds habitat quantity resulted in
 reductions of the stable population size, but did not cause extinction
 under the scenarios we examined. In contrast, projected large reductions
 in wintering grounds precipitation caused the population to decline, with
 risk of extinction magnified when breeding habitat quantity or quality
 also decreased. Our study indicates that probability of long-term
 persistence for Kirtland’s Warbler will depend on climate change impacts
 to wintering grounds habitat quality, and contributes to the growing
 literature documenting the importance of considering the full annual cycle
 for understanding population dynamics of migratory species.
description: KIWA STELLA
 ModelText file containing the
 code needed to create the KIWA simulation model in STELLA, organized by
 model sector. The habitat module code shows input values for contemporary
 conditions and each environmental change scenario.
DOI: 10.6078/d1p40v
title: As the Wind Blows: The Effects of Long-Term Exposure to Air Pollution on Mortality

description: Replication files for "As the Wind Blows: The Effects of Long-Term
 Exposure to Air Pollution on Mortality", published in the Journal of
 the European Economic Association.