cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jsxksn08x
title: PacBio IsoSeq reference transcriptomes for Pinus taeda L.

description: Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f.
 sp. fusiforme, is the most damaging disease affecting economically
 important pine species in the southeast United States. In this report, we
 detail the genomic localization and sequence-level discovery of candidate
 race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus
 taeda L. Two full-sib families, each with ~1000 progeny, were challenged
 with a complex inoculum consisting of over 150 pathogen isolates.
 High-density linkage mapping revealed three QTL distributed on two linkage
 groups. The two QTL on linkage group 2 were additive with respect to their
 effects on the probability of disease outcome. All three QTL were
 validated using a population of 2057 cloned pine genotypes in a
 six-year-old multi-environmental field trial. As a complement to the QTL
 mapping approach, bulked  segregant RNAseq analysis revealed a
 small number of candidate nucleotide binding leucine rich repeat genes
 harboring SNP significantly associated with disease resistance. The
 results of this study demonstrate that single qualitative resistance genes
 can confer effective resistance against genetically diverse mixtures of an
 endemic pathogen.
description: Reference transcriptomes for both families were produced using
 the standard <b>isoseq3</b> pipeline implemented in SMRTLink
 v.7.0 from PacBio. Consensus sequences were generated from the ‘pooled’
 and the ‘size-selected’ fractions of each family. The
 <i>ccs</i> command-line application was used to generate
 circular consensus sequences (CCS) from the
 <i>subreads.bam</i> files, using a minimum length of 100bp.
 The circular consensus sequences were then clustered using the isoseq3
 <i>cluste</i>r command-line application, and final error
 correction was performed via the isoseq3 <i>polish</i> tool.
 Reference transcriptomes for each family were produced by concatenating
 the polished high-quality transcript sequences from both fractions. The
 reference transcriptome for family E4 contained 38634 contigs with a
 contig N50 of 4236bp and a total length of 115,867,422 bp. For family E9,
 there were 42881 contigs with an N50 of 3967 bp and a total length of
 133,843,719 bp.<br> <br> No trimming or other post-hoc data
 manipulation of the sequences were performed. All contigs are presented as
 full-length sequences which were the primary output of the isoseq3
 pipeline.
description: The raw 'subreads.bam' files used to produce the
 transcriptomes via the Isoseq3 pipeline was deposited on NCBI under
 accession number PRJNA719490<br> <br> No trimming or other
 post-hoc data manipulation of the sequences were performed. All contigs
 are presented as full-length sequences which were the primary output of
 the isoseq3 pipeline. Sequence ID's are consistent with the ID's
 posted in Supplementary Table 3 of the manuscript.
DOI: 10.5281/zenodo.18396905
title: Effect of impactor oblateness on the formation of lunar simple craters

description: This dataset includes:(1) iSALE-2D model input files for simple crater formation process, including asteroid.inp and material.inp (in Crater Formation.zip);(2) iSALE-2D model input files for impact-induced melt volume estimation, including asteroid.inp and material.inp (in Impact Melt.zip);(3) iSALE-2D model input files for rubble-pile asteroid impacts and tests for impactor properties, including asteroid.inp and material.inp (in Rubble Pile Impacts.zip);(4) Appendix videos A1 and A2
DOI: 10.5281/zenodo.18396906
title: Effect of impactor oblateness on the formation of lunar simple craters

description: This dataset includes:(1) iSALE-2D model input files for simple crater formation process, including asteroid.inp and material.inp (in Crater Formation.zip);(2) iSALE-2D model input files for impact-induced melt volume estimation, including asteroid.inp and material.inp (in Impact Melt.zip);(3) iSALE-2D model input files for rubble-pile asteroid impacts and tests for impactor properties, including asteroid.inp and material.inp (in Rubble Pile Impacts.zip);(4) Appendix videos A1 and A2
DOI: 10.5061/dryad.wwpzgmsjq
title: Assessing the effectiveness of a forest Habitat Conservation Plan for a threatened seabird, the marbled murrelet

description: Habitat Conservation Plans (HCPs) commonly facilitate habitat conservation
 on private land in the United States, yet the effectiveness of individual
 HCPs is rarely evaluated. Here, we assess the effectiveness of a
 high-profile HCP created by a lumber company to protect old-growth forest
 used for breeding by Marbled Murrelets (Brachyramphus marmoratus) on
 private land. We used 17 years of HCP-monitoring data to compare trends in
 murrelet occupancy and inland counts between private HCP areas and public
 reference areas over time. Based on occupancy models applied to
 audio-visual survey data, average occupancy was higher in public reference
 areas (0.85; 85% CI: 0.79-0.90) than in private HCP areas (0.46; 85% CI:
 0.38-0.54). Numerically, trends in occupancy were slightly positive in
 public areas (λ=1.01; 85% CI: 0.94-1.08) and slightly negative in private
 areas (λ=0.97; 85% CI: 0.87-1.06), but confidence intervals did not
 preclude stable occupancy on both ownerships. Based on generalized linear
 mixed models applied to inland radar survey data, murrelet counts in
 private HCP areas (LS mean=8.7; 85% CI: 6.2-12.2) were lower than those in
 public reference areas (LS mean=14.8; 85% CI: 10.1-21.7), but confidence
 intervals overlapped. Murrelet counts declined by 12-17% annually on both
 ownerships over the study period based on the top model, but a closely
 competing interactive model suggested more rapid declines in public
 reference (14-20%) than in private HCP (10-15%) areas. Both models
 indicated that murrelet counts were negatively related to sea surface
 temperature, suggesting that warm ocean conditions negatively affect
 murrelet breeding effort. Collectively, these results suggest that while
 HCP habitat may be lower quality than public reference areas, the HCP has
 likely not exacerbated ongoing declines of murrelets in the region. This
 work highlights the importance of including reference areas when
 evaluating conservation policies. 
description: These datasets were collected using audiovisual and radar surveys
 on land owned by the Humboldt Redwood Company in Humboldt County,
 California, USA. Audiovisual survey data were analyzed using dynamic
 occupancy modeling in Program Presence. and radar survey data were
 analyzed using Generalized Linear Mixed Models in the R Statistical
 Environment (package 'lme4') to produce a manuscript accepted
 for publication by Ornithological Applications. 
description: The readme file contains information about the data within each
 spreadsheet including variable explanations.
DOI: 10.5061/dryad.b2rbnzsf4
title: Generalized LDPC codes for ultra reliable low latency communication in 5G and beyond

description: Fifth-generation (5G) systems aim to increase the capacity of existing
 mobile networks by a factor of 1000, supporting an extremely high user
 density, as well as numerous device- to-device and machine communications.
 Ultra Reliable Low Latency Communication (URLLC) constitutes one of the
 critical operating regimes in 5G, since it will enable low-cost and
 power-efficient anywhere and anytime signalling services 
 Generalized low-density parity-check (GLDPC) codes, where single
 parity-check constraints on the code bits are replaced with generalized
 constraints (an arbitrary linear code), are a promising class of codes for
 low-latency communication. We have constructed quasi-cyclic GLDPC codes,
 where the proportion of generalized constraints is determined by an
 asymptotic analysis. We have analyzed the complexity and performance of
 the message passing decoder with various update rules (including standard
 full-precision sum-product and min-sum algorithms) and quantization
 schemes for a GLDPC code over the additive white Gaussian noise (AWGN)
 channel and determined a constraint-to-variable update rule based on the
 specific codewords of the component codes. This data set includes the
 simulated GLDPC code constructions and the block error rate performance,
 which is shown to outperform a variety of state- of-the-art code and
 decoder designs with suitable lengths and rates for the 5G ultra-reliable
 low-latency communication regime over an AWGN channel with quadrature PSK
 modulation.
description: Monte Carlo
 methods for computer simulations were performed with the belief
 propagation decoding algorithm on a binary input additive white Gaussian
 noise (AWGN) channel with QPSK modulation. 
description: File Usage notes
 IEEE_ACCESS_2018 The Data scripts are .tex files intended to be opened with LaTex editor. These files can alternatively be opened in a text editor and contain the data produced by our experiments. The Parity-check matrices can be opened in MATLAB, or open source alternative such as Octave. The matrices were used to generate the data from our experiments in the associated manuscript. The text files give a description of the construction. GLOBECOM_2020 The Data scripts are .tex files intended to be opened with LaTex editor. These files can alternatively be opened in a text editor and contain the data produced by our experiments. The Parity-check matrices can be opened in MATLAB, or open source alternative such as Octave. The matrices were used to generate the data in the associated manuscript. The text files give a description of the construction.
DOI: 10.5061/dryad.83bk3j9r5
title: Tissue-type specific accumulation of the plastoglobular proteome, transcriptional networks and plastoglobular functions

description: Plastoglobules (PGs) are dynamic protein-lipid micro-compartments in
 plastids enriched for isoprenoid-derived metabolites. Chloroplast PGs
 support formation, remodeling and controlled dismantling of thylakoids
 during developmental transitions and environmental responses. However, the
 specific molecular functions of most PG proteins are still poorly
 understood. This review harnesses recent co-mRNA expression data from
 combined microarray and RNAseq information in ATTED-II on an updated
 inventory of 34 PG proteins, as well as proteomics data across 30
 Arabidopsis tissue types from ATHENA. Hierarchical clustering based on
 relative abundance for the PG proteins across non-photosynthetic and
 photosynthetic tissue types showed their coordinated protein accumulation
 across Arabidopsis parts, tissue types, development and senescence.
 Evaluation of mRNA-based forced networks at different coefficient
 thresholds identified a central hub with seven PG proteins and four
 peripheral modules.  Enrichment of specific nuclear transcription
 factors (e.g. Golden2-like) and support for cross-talk between PGs and the
 plastid gene expression was observed, and specific ABC1 kinases appear
 part of a light signaling network. Examples of other specific findings are
 that FBN7b is involved with upstream steps of tetrapyrrole biosynthesis
 and that ABC1K9 is involved in starch metabolism. This review provides new
 insights in PG protein functions and an improved framework for
 experimental studies.
description: Data mining from public repositories and literature.
DOI: 10.5061/dryad.nk98sf7sv
title: Key words related to public engagement with science by Society of Freshwater Science journals and conference sessions (1997-2019)

description: Data set that was used to determine the frequency each of 4 key words
 (public engagement, education, outreach, or science communication) in the
 title or abstract of published papers in Freshwater Science (formerly the
 Journal of the North American Benthological Society) and oral
 presentations (talks) at the annual Society for Freshwater Science
 meetings from 1997 to 2019. Does not include any data on talks for
 2013-2014 because they were not published during those years.
description: The dataset was
 collected by reviewing abstracts in the journal Freshwater Science
 (formerly the Journal of North American Benthological Society [JNABS])
 from 1997 to 2019 as well as searching abstracts from oral presentations
 at the SFS Annual Meeting (available online for 1997–2012 and 2015–2019 at
 https://sfsannualmeeting.org/SearchAll.cfm) for key words (public
 engagement, science communication, education, outreach) related to PES.
 The dataset was processed by inputting the data collected from our search
 (i.e., year, type of work, keyword, and number of times the keyword
 appeared in that type of work during the specified year) into a .csv file
 using Microsoft Excel. R was used (https://www.r-project.org/) and its
 accompanying package ggplot2 (https://ggplot2.tidyverse.org/) to plot the
 data.
DOI: 10.6071/m39106
title: On the social and cognitive dimensions of wicked environmental problems characterized by conceptual and solution uncertainty

description: We develop a quantitative framework for understanding the class of wicked
 problems that emerge at the intersections of “natural”, social, and
 technological complex systems. Wicked problems reflect our incomplete
 understanding of interdependent global systems and the systemic risk they
 pose; such problems escape solutions because they are often ill-defined,
 and thus misidentified and under-appreciated by communities of
 problem-solvers. While there are well-documented benefits to tackling
 boundary-crossing problems from various viewpoints, the integration of
 diverse approaches can nevertheless contribute confusion around the
 collective understanding of the core concepts and feasible solutions. We
 explore this paradox by analyzing the development of both scholarly and
 topical communities within three wicked problems: deforestation, invasive
 species, and wildlife trade. We posit that saturation in the dynamics of
 social and cognitive diversity growth is an indicator of reduced
 uncertainty in the evolution of the comprehensive knowledge trajectory
 emerging around each wicked problem. Informed by comprehensive
 bibliometric data capturing both social and cognitive dimensions of each
 problem domain, we thereby develop a framework that assesses the stability
 of knowledge trajectory dynamics as an indicator of wickedness associated
 with conceptual and solution uncertainty. As such, our results identify
 wildlife trade as a wicked problem that may be difficult to address given
 recent instability in its knowledge trajectory.
DOI: 10.5061/dryad.4qrfj6q9c
title: Body size determines the thermal coupling between insects and plant surfaces

description: 1. Most studies in global change biology predict biological impacts of
 warming from information on macroclimates. Most organisms, however, live
 in microhabitats with physical conditions which are decoupled to varying
 degrees from those in macroclimates depending partly on organism body
 size. 2. Small ectotherms of a few millimetres in length live deep in
 surface boundary layers such that their heat budgets are dominated by
 different processes compared to larger ectotherms, whose bodies emerge
 from surface boundary layers. We therefore hypothesized that the body size
 relative to surface boundary layer thickness generates different patterns
 of body temperature variation for organisms in the same nominal habitats.
 3. We tested this hypothesis in a community of arthropods living on a
 subalpine plant by combining physical models to acquire high-resolution
 time series of operative temperatures, thermal imaging to assess the
 strength of coupling between physical models or arthropod bodies and
 surrounding leaf temperatures, and a cross-scale approach to infer the
 temperature distributions available to small ectotherms. 4. The size of
 the physical model strongly influenced operative temperature dynamics: the
 bigger, the warmer. Small models were just a few degrees warmer than leaf
 surfaces whereas large models deviated from leaf temperature by
 &gt;10°C. 5. We found similar patterns of body temperature of
 naturally occurring arthropods. Temperatures of small insects closely
 tracked leaf surface temperatures even in full sun, whereas larger insects
 were warmer than leaf surfaces. 6. At the whole plant scale, the thermal
 diversity of leaf surfaces was high, especially in the sun, typically
 generating a range of microclimatic temperatures (for small insects) of
 &gt;10 °C. Larger insects instead could move between shaded and sunny
 portions of the whole plant to vary body temperatures by a larger extent.
 7. The bulk of animal biodiversity consists of small terrestrial
 arthropods, the majority of which are associated with plant surfaces at
 some point in their life cycles. The distribution of body sizes determines
 how much thermal diversity is available for behavioural thermoregulation,
 thereby contributing to their potential response to climate change.
DOI: 10.5061/dryad.sqv9s4n3s
title: Dataset of wild spotted hyenas from 3 clans in the Serengeti National Park

description: Host immune defenses are important components of host-parasite
 interactions that affect the outcome of infection and may have fitness
 consequences for hosts when increased allocation of resources to immune
 responses undermines other essential life processes. Research on
 host-parasite interactions in large free-ranging wild mammals is currently
 hampered by a lack of verified non-invasive assays. We successfully
 adapted existing assays to measure innate and adaptive immune responses
 produced by the gastrointestinal mucosa in spotted hyena (Crocuta crocuta)
 faeces, including enzyme-linked immunosorbent assays (ELISAs), to quantify
 faecal immunoglobulins (total IgA, total IgG) and total faecal O-linked
 oligosaccharides (mucin). We investigated the effect of infection load by
 an energetically costly hookworm (Ancylostoma), parasite richness, host
 age, sex, year of sampling and clan membership on immune responses and
 asked whether high investment in immune responses during early life
 affects longevity in individually known spotted hyenas in the Serengeti
 National Park, Tanzania. Faecal concentrations of IgA, IgG and mucin
 increased with Ancylostoma egg load and were higher in juveniles than in
 adults. Females had higher mucin concentrations than males. Juvenile
 females had higher IgG concentrations than juvenile males whereas adult
 females had lower IgG concentrations than males. High IgA concentrations
 during the first year of life was linked to reduced longevity after
 controlling for age at sampling and Ancylostoma egg load. Our study
 demonstrates that the use of non-invasive methods can increase knowledge
 on the complex relationship between gastrointestinal parasites and host
 local immune responses in wild large mammals and reveal fitness-relevant
 effects of these responses.
description: All methods used to produce this dataset have been described in
 detail in the research article.
description: Age= 1: juvenile; 3: adult Sex= 1: male; 2:
 female age = age at sampling
 age_death = age of death Rich_a = Number of
 parasite taxa present other than Ancylostoma IMDSx =
 Sample scores of axis x of the immune profile Non-metric Multidimensional
 Scaling (NMS) PMDSx = Sample scores of axis x of the
 parasite community Non-metric Multidimensional Scaling (NMS)
DOI: 10.5061/dryad.4xgxd258x
title: Data from: Late Cretaceous European theropod palaeobiodiversity, palaeobiogeography and the intra-Maastrichtian faunal turnover: new contributions from the Iberian fossil site of Laño

description: A total of 227 theropod teeth have so far been recovered from the late
 Campanian Laño site (northern Iberian Peninsula). The teeth were studied
 for their qualitative and quantitative features. From the theropod sample
 found at Laño, seven morphotypes attributed to five taxa are identified: a
 medium to large abelisaurid (Arcovenator sp.) and four small
 coelurosaurians (Dromaeosauridae indet., Paraves indet., cf. Paronychodon
 sp. and cf. Richardoestesia sp.). Together with the ground bird
 Gargantuavis and a possible ornithomimosaur, the theropod fauna of Laño
 might be composed of two medium- to large-sized non-avian theropods, four
 small-bodied non-avian theropods and a large terrestrial bird. This makes
 the Laño site the richest and most diverse latest Cretaceous theropod site
 of Europe. Furthermore, the Laño site and the Late Cretaceous localities
 of Europe that have yielded theropod remains suggest that the medium- to
 large-sized theropods were abelisaurids or indeterminate theropods. The
 small theropods are more abundant, diverse and represented by different
 dromaeosaurids, Paronychodon, Richardoestesia, or related forms,
 troodontids and, probably, by other paravians. Among birds,
 enantiornithines, gargantuaviids and ornithurines are also common in the
 European Late Cretaceous sites. The theropod assemblage of Laño, together
 with the taxa of other Late Cretaceous sites, supports the idea that
 several theropod dispersal events took place during the Cretaceous. This
 resulted in a mixture of European endemic, Asiamerican and Gondwanan
 forms. This study also supports the hypothesis that the
 intra-Maastrichtian faunal turnover that occurred in the Ibero-Armorican
 landmass seems to have had no effect on theropods.
description: The dataset of the theropod teeth measurements was built by
 measuring the teeth recovered from the Laño site (northern Iberia) and by
 collecting data from other already published datasets cited on the
 documents. For the documents that gather the theropod
 record of Europe during the Turonian-Maastrichtian, the data was collected
 from former published articles as well as this work. Furthermore, in some
 cases, this record has been reassigned to other taxa in this
 work.
description: Appendix A. Theropod teeth dataset used for the statistical
 analyses and discriminant analysis. Appendix B.
 Theropod record and sites from the Turonian-Maastrichtian of
 Europe. Appendix C. Theropod record from the
 Turonian-Maastrichtian deposits of Europe.