cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kwh70rz3g
title: Additional data: Submillimetre mechanistic designs of termite-built structures

description: Termites inhabit complex underground mounds of intricate stigmergic
 labyrinthine designs with multiple functions as nursery, food storage, and
 refuge, while maintaining a homeostatic microclimate. Past research
 studied termite building activities rather than the actual material
 structure. Yet, prior to understanding how multi-functionality shaped
 termite building, a thorough grasp of submillimetre mechanistic
 architecture of mounds is required. Here, we identify
 for Nasutitermes exitiosus via granulometry and Fourier
 transform infrared spectroscopy analysis, preferential particle sizes
 related to coarse silts and unknown mixtures of organic/ inorganic
 components. High-resolution micro-computed X-ray tomography and
 microindentation tests reveal wall patterns of filigree laminated layers
 and sub-millimetre porosity wrapped around a coarse-grained inner
 scaffold. The scaffold geometry, which is designed of a lignin-based
 composite and densely biocementitious stercoral mortar, resembles that of
 trabecula cancellous bones. Fractal dimension estimates indicate
 multi-scaled porosity, important for enhanced evaporative cooling and
 structural stability. The indentation moduli increase from the outer to
 the inner wall parts to values higher than those found in loose clays and
 which exceed locally the properties of anthropogenic cementitious
 materials. Termites engineer intricately layered biocementitious
 composites of high elasticity. The multiple-scales and porosity of the
 structure indicate a potential to pioneer bio-architected lightweight and
 high-strength materials.
description: Granulometry study, FTIR, density calculations and data of
 microindentation; description of data use and all other data see
 Electronic Supplementary Materials (ESM) 
description: See paper and ESM; see readme file and follow instructions in
 main paper. Software used Drishti
 https://github.com/nci/drishti/wiki
DOI: 10.5061/dryad.3n5tb2rh6
title: Small‐scale genetic structure and mating patterns in an extensive sessile oak forest (Quercus petraea (Matt.) Liebl.)

description: Oaks (Quercus) are major components of temperate forest ecosystems in the
 Northern Hemisphere where they form intermediate or climax communities.
 Sessile oak (Quercus petraea) forests represent the climax vegetation in
 eastern Germany and western Poland. Here, sessile oak forms pure stands or
 occurs intermixed with Scots Pine (Pinus sylvestris). A large body of
 research is available on gene flow, reproduction dynamics, and genetic
 structure in fragmented landscapes and mixed populations. At the same
 time, our knowledge regarding large, contiguous and monospecific
 populations is considerably less well developed. Our study is an attempt
 to further develop our understanding of the reproduction ecology of
 sessile oak as an ecologically and economically important forest tree by
 analyzing mating patterns and genetic structure within adult trees and
 seedlings originating from one or two reproduction events in an extensive,
 naturally regenerating sessile oak forest. We detected positive spatial
 genetic structure up to 30 meters between adult trees and up to 40 meters
 between seedlings. Seed dispersal distances averaged 8.4 meters. Pollen
 dispersal distances averaged 22.6 meters. In both cases, the largest
 proportion of the dispersal occurred over short distances. Dispersal over
 longer distances was more common for pollen but also appeared regularly
 for seeds. The reproductive success of individual trees was highly skewed.
 Only 41 percent of all adult trees produced any offspring while the
 majority did not participate in reproduction. Among those trees that
 contributed to the analyzed seedling sample, 80 percent contributed 1-3
 gametes. Only 20 percent of all parent trees contributed four or more
 gametes. However, these relatively few most fertile trees contributed 51
 percent of all gametes within the seedling sample. Our study demonstrates
 that extensive, apparently homogenous oak forests are far from uniform on
 the genetic level. On the contrary, they form highly complex mosaics of
 remarkably small local neighborhoods. This counterbalances the levelling
 effect of long-distance dispersal and may increase the species’ adaptive
 potential. Incorporating these dynamics in the management, conservation
 and restoration of oak forests can support the conservation of forest
 genetic diversity and assist those forests in coping with environmental
 change.
DOI: 10.5061/dryad.fn2z34tt8
title: Hygroscopic growth and size distribution data for: In situ measurements of human cough aerosol hygroscopicity

description: The airborne dynamics of respiratory droplets, and the transmission routes
 of pathogens embedded within them, are governed primarily by the
 diameter of the particles. These particles are composed of the
 fluid which lines the respiratory tract, and is primarily mucins and
 salts, which will interact with the atmosphere and evaporate to
 reach an equilibrium diameter. Measuring organic volume
 fraction (OVF) of cough aerosol has proved challenging due to
 large variability and low material volume produced after
 coughing. Here, the diametric hygroscopic growth factors (GF) of the cough
 aerosol produced by healthy participants were measured in situ
 using a rotating aerosol suspension chamber and a humidification
 tandem differential mobility analyser. Using hygroscopicity models, it
 was estimated that the average OVF in the evaporated cough
 aerosol was 0.88±0.07 and the average GF at 90% relative humidity
 (RH) was 1.31±0.03. To reach equilibrium in dry air the droplets will
 reduce in diameter by a factor of approximately 2.8 with an
 evaporation factor of 0.36±0.05. Hysteresis was observed in cough
 aerosol at RH = ~35% and RH = ~65% for efflorescence and
 deliquescence, respectively, and may depend on the OVF. The same
 behaviour and GF was observed in nebulised bovine bronchoalveolar
 lavage fluid.
description: The data was collected by having human participants voluntarily
 cough into a sealed and particle-free rotating drum. The cough aerosol
 hygroscopic growth was then measured using a humidity ramp in a
 humidification tandem differential mobility analyser (H-TDMA) in both
 hydration and dehydration modes. The size distributions of the
 participant's cough aerosol was also measured using a scanning
 mobility particle sizer (SMPS). The data was
 preprocessed to be used with the TDMAinv algorithm, and the hygroscopic
 growth data presented in the manuscript is presented here (.mat) and are
 the resulting data extracted from the Igor experiments. Additionally, the
 SMPS data (size distribution) for all participants is presented here
 (.txt) as exported data from Aerosol Instrument Manager (AIM).
description: The data reported in the manuscript consist of the following
 tables in the .mat files: data_LR_deli, data_HR_deli, data_LR_effl,
 data_HR_effl. The data here (.mat) are compatible with MATLAB, and the
 variables of interest are RetrGFvolAVG (hygroscopic growth factor) and
 RHdma2Avg (RH at which the GF is measured). The readme
 file (Groth_2021_hygro_readme.txt) contains more information relating to
 usage of the data.
DOI: 10.5061/dryad.gxd2547kx
title: Muscle fiber size, myonuclear domain, and fat mass phenotypes in pre-migratory snow buntings

description: In long-distance migrants, preparation for migration is typically
 associated with increases in fat and body mass, and with an enlargement of
 pectoralis muscle mass that likely improves flight performance. Although
 changes in muscle mass or size have been well described in migratory
 birds, potential changes in muscle ultrastructure during this transition
 still deserves scrutiny. Using outdoor captive snow buntings
 (Plectrophenax nivalis n = 15) measured during their transition into a
 spring migratory phenotype as a model system, we studied changes in
 pectoralis muscle ultrastructure and predicted that muscle fiber diameter
 could increase in parallel with the gain in body mass. We also expected
 that larger fibers could either recruit satellite cells to
 support cellular maintenance and protein turnover, increase myonuclear
 domain (cytoplasm per nuclei) with the potential increase for protein
 turnover load per myonucleus, or existing myonuclei could undergo
 endoreduplication. Buntings increased body mass by 46% within a month,
 largely due to a &gt; 6-fold increase in body fat. However, this
 increase in body mass was also associated with a 36% increase in muscle
 fiber diameter. Both pectoralis muscle mass (r2 = 0.57-0.77) and fiber
 diameter (r2 = 0.32) correlated with total body mass, without any change
 in the number of nuclei per fiber. Consequently, variation in myonuclear
 domain (i.e. the amount of cytoplasm per nucleus), was also positively
 associated with body mass (r2 = 0.51). Therefore, buntings preparing for
 migration may experience an increase in muscle contraction force due to
 larger muscle fibers, but this is also coupled with increases in
 myonuclear domain, which may force these cells to increase protein
 production to safeguard satellite cells.
DOI: 10.5061/dryad.wpzgmsbn2
title: Exposure to artificial light at night alters innate immune response in wild great tit nestlings

description: The large-scale impact of urbanization on wildlife is rather well
 documented; however, the mechanisms underlying the effects of
 urban environments on animal physiology and behaviour are still poorly
 understood. Here, we focused on one major urban pollutant - artificial
 light at night (ALAN) - and its effects on the capacity to mount an innate
 immune response in wild great tit (Parus major) nestlings. Exposure to
 ALAN alters circadian rhythms of physiological processes, by disrupting
 the nocturnal production of the hormone melatonin. Nestlings were exposed
 to a light source emitting 3 lux for seven consecutive nights.
 Subsequently, nestlings were immune-challenged with a lipopolysaccharide
 injection, and we measured haptoglobin and nitric oxide levels pre- and
 post-injection. Both haptoglobin and nitric oxide are important markers
 for innate immune function. We found that ALAN exposure altered the innate
 immune response, with nestlings exposed to ALAN having lower haptoglobin
 and higher nitric oxide levels after the immune-challenge compared to
 dark-night nestlings. Unexpectedly, nitric oxide levels were overall,
 lower after the immune-challenge than before. These effects were probabbly
 mediated by melatonin, as ALAN-treated birds had on average 49%
 lower melatonin levels than the dark-night birds. ALAN exposure did not
 have any clear effects on nestling growth. This study provides a potential
 physiological mechanism underlying the documented differences in immune
 function between urban and rural birds observed in other studies.
 Moreover, it gives evidence that ALAN exposure affects nestling
 physiology, potentially causing long-term effects on physiology and
 behaviour, which ultimately can affect their fitness.
DOI: 10.5061/dryad.g1jwstqqv
title: A phase-separated nuclear GBPL circuit controls immunity in plants

description: Liquid-liquid phase separation (LLPS) has emerged as a central paradigm
 for understanding how membrane-less organelles compartmentalize diverse
 cellular activities in eukaryotes. Here, we identified a new superfamily
 of plant Guanylate-Binding Protein-Like GTPases (GBPLs) that assemble
 LLPS-driven condensates within the nucleus to protect against infection
 and autoimmunity. In Arabidopsis thaliana, two family members - GBPL1 and
 GBPL3 - undergo phase transition behavior to control transcriptional
 responses as part of an allosteric switch triggered by exposure to biotic
 stress. GBPL1, a pseudoGTPase, sequesters catalytically-active GBPL3 under
 basal conditions but is displaced by GBPL3 LLPS when it enters the nucleus
 following immune cues to drive formation of unique membrane-less
 organelles termed GDACs (GBPL Defense-Activated Condensates) that we
 visualized by in situ cryo-electron tomography. Within these mesoscale
 GDAC structures, native GBPL3 directly bound defense gene promoters and
 recruited specific transcriptional coactivators of the Mediator complex
 plus RNA Pol II machinery to massively reprogram host gene expression for
 disease resistance. Together, our study identifies a new GBPL circuit that
 reinforces the biological importance of phase-separated condensates, in
 this case, as indispensable players in plant defense.
DOI: 10.5061/dryad.gtht76hm4
title: Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone

description: The exploration of hybrid zones and the intergenomic conflicts exposed
 through hybridization provide windows into the processes of divergence and
 speciation. Sex chromosomes and mitonuclear incompatibilities have strong
 associations with the genetics of hybrid dysfunction. In ZW
 sex-determining systems, maternal co-inheritance of the mitochondrial and
 W chromosomes immediately exposes incompatibilities between these maternal
 contributions of one species and the Z chromosome of another. We analyze
 mitochondrial and Z chromosome admixture in the long-tailed finch
 (Poephila acuticauda) of Australia, where hybridizing subspecies differ
 prominently in Z chromosome genotype and in bill color, yet the respective
 centers of geographic admixture for these two traits are offset by 350 km.
 We report two well-defined mitochondrial clades that diverged ~0.5 Mya.
 Mitochondrial contact is geographically co-located within a hybrid zone of
 Z chromosome admixture and is displaced from bill color admixture by
 nearly 400 km. Consistent with Haldane’s rule expectations, hybrid zone
 females are significantly less likely than males to carry an admixed Z
 chromosome or have mismatched Z-mitochondrial genotypes. Furthermore,
 there are significantly fewer than expected mitonuclear mismatches in
 hybrid zone females and paternal backcross males. Results suggest a
 potential for mitonuclear/sex chromosome incompatibilities in the
 emergence of reproductive isolation in this system.
DOI: 10.5061/dryad.2z34tmpmb
title: Economic evaluation of sea-level rise adaptation strongly influenced by hydrodynamic feedbacks: Dataset 1

description: Coastal communities rely on levees and seawalls as critical protection
 against sea-level rise; in the U.S. alone, $300 billion in shoreline
 armoring costs are forecast by 2100. But despite the local flood risk
 reduction benefits, these structures can exacerbate flooding and
 associated damages along other parts of the shoreline—particularly in
 coastal bays and estuaries, where nearly 500 million people globally are
 at risk from sea-level rise. The magnitude and spatial distribution of the
 economic impact of this dynamic, however, are poorly understood. Here we
 combine hydrodynamic and economic models to assess the extent of both
 local and regional flooding and damages expected from a range of shoreline
 protection and sea-level rise scenarios in San Francisco Bay, California.
 We find that protection of individual shoreline segments (5-75 km) can
 increase flooding in other areas by as much as 36 million cubic
 meters and damages by $723 million for a single flood event, and
 in some cases can even cause regional flood damages that exceed the local
 damages prevented from protection. We also demonstrate that strategic
 flooding of certain shoreline segments, such as those with gradually
 sloping baylands and space for water storage, can help alleviate flooding
 and damages along other stretches of the coastline. By matching the scale
 of the economic assessment to the scale of the threat, we reveal the
 previously uncounted costs associated with uncoordinated adaptation
 actions and demonstrate that a regional planning perspective is essential
 for reducing shared risk and wisely spending adaptation resources in
 coastal bays. This dataset is associated with a github
 repository https://github.com/rmgriffin/OLU-flood-externalities
 This dataset is part of a two record data repository associated with the
 paper "Economic evaluation of sea-level rise adaptation strongly
 influenced by hydrodynamic feedbacks." This is part one.
description: Please see Dryad dataset DOI: 10.5061/dryad.g79cnp5pt for part 2
 of the data for this article containing flood depth rasters for 150cm and
 200cm of sea level rise.
DOI: 10.5061/dryad.rxwdbrv85
title: Aurora kinase A is essential for meiosis in mouse oocytes

description: The Aurora protein kinases are well-established regulators of spindle
 building and chromosome segregation in mitotic and meiotic cells. In mouse
 oocytes, there is significant Aurora kinase A (AURKA) compensatory
 abilities when the other Aurora kinase homologs are deleted. Whether the
 other homologs, AURKB or AURKC can compensate for loss of AURKA is not
 known. Using a conditional mouse oocyte knockout model, we demonstrate
 that this compensation is not reciprocal because female oocyte-specific
 knockout mice are sterile and their oocytes fail to complete meiosis I. In
 determining the AURKA-specific functions, we demonstrate that its first
 meiotic requirement is to activate Polo-like kinase 1 at microtubule
 organizing centers (MTOCs; meiotic spindle poles). This activation induces
 fragmentation of the MTOCs, a step essential for building a bipolar
 spindle. The next step that requires AURKA is building the liquid-like
 spindle domain that involves TACC3. Finally, we find that AURKA is also
 required for anaphase I onset to trigger cohesin cleavage in an APC/C
 independent manner. We conclude that AURKA has multiple functions
 essential to completing MI that are distinct from AURKB and AURKC.
description: Data was obtained by image analysis of confocal or light sheet
 microscopy
DOI: 10.5061/dryad.m905qfv13
title: Data from: Cortico-Fugal regulation of predictive coding

description: Sensory systems must account for both contextual factors and prior
 experience to adaptively engage with the dynamic external environment. In
 the central auditory system, neurons modulate their responses to sounds
 based on statistical context. These response modulations can be understood
 through a hierarchical predictive coding lens: responses to repeated
 stimuli are progressively decreased, in a process known as repetition
 suppression, whereas unexpected stimuli produce a prediction error signal.
 Prediction error incrementally increases along the auditory hierarchy from
 the inferior colliculus (IC) to the auditory cortex (AC), suggesting that
 these regions may engage in hierarchical predictive coding. A potential
 substrate for top-down predictive cues is the massive set of descending
 projections from the auditory cortex to subcortical structures. To assess
 the role of these projections in predictive coding, we optogenetically
 suppressed the auditory cortico-collicular feedback in awake mice while
 recording responses from IC neurons to stimuli designed to test prediction
 error and repetition suppression. Suppression of the cortico-collicular
 pathway led to a decrease in prediction error in IC. Repetition
 suppression was unaffected by cortico-collicular inactivation, suggesting
 that this metric may reflect fatigue of bottom-up sensory inputs rather
 than predictive processing. We also discovered populations of IC neurons
 that exhibit repetition enhancement, an increase in firing with stimulus
 repetition, and error suppression, a stronger response to a tone in a
 predictable rather than unpredictable context. Cortico-collicular
 suppression led to a decrease in repetition enhancement in the central
 nucleus and a reduction in error suppression in shell regions of IC. These
 changes in predictive coding metrics arose from bidirectional modulations
 in the response to the standard and deviant contexts, such that neurons in
 IC responded more similarly to each context in the absence of cortical
 input. Our results demonstrate that the auditory cortex provides cues
 about the statistical context of sound to subcortical brain regions via
 direct feedback, regulating processing of both prediction and repetition.
DOI: 10.5061/dryad.s7h44j16f
title: A facilitation between large herbivores and ants accelerates litter decomposition by modifying soil micro-environmental conditions

description: 1. Large herbivores and insects commonly coexist and play important
 functional roles in grassland ecosystems. The interactive effects of these
 two animal groups in shaping ecosystem processes and functioning are
 poorly understood. In a semi-arid grassland of northeastern China, we
 previously found a reciprocal facilitation between large herbivores
 (cattle; Bos tarurs) and ants: cattle grazing led to a two-fold increase
 in ant mound abundance compared with ungrazed sites, while the presence of
 ant mounds, in turn, increased the foraging of cattle during the peak of
 the growing season. 2. Here, by using a large-scale, 4-year (2010-2013)
 manipulative experiment, we further investigated how such a facilitation
 between large herbivores and ants can affect a key ecosystem process,
 litter decomposition. Using a set of small-scale reciprocal translocation
 litterbag experiments, we separated the effects of litter quality and soil
 micro-environmental factors altered by cattle and ants on litter
 decomposition rates. 3. A significant interaction between the experimental
 factors cattle grazing and ant presence showed that litter decomposition
 rate was at the highest levels when both cattle and ants were present,
 with only a small impact when each was present on its own.
 Mechanistically, cattle and ants exerted limited effects on litter quality
 (litter C:N ratio). However, these animals greatly altered soil
 micro-environments by increasing soil N availability, which in turn
 increased soil microbial biomass and accelerated decomposition process. 4.
 Synthesis. Our results demonstrate how positive interactions between two
 groups of animals, large herbivores and ants, can affect decomposition
 rates, with important consequences for ecosystem carbon and nutrient
 cycling. Large herbivores, either domestic or wild, often coexist and
 interact with a diverse of other fauna in terrestrial ecosystems.
 Assessing their interactive effects will help us to better understand
 their role in shaping ecosystem processes and functioning with important
 management implications.