cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ht76hdrdz
title: Why do insects shut their spiracles? A meta-analytic evaluation of the adaptive hypotheses of discontinuous gas exchange in insects

description: The earliest description of the discontinuous gas exchange cycle (DGC) in
 lepidopterous insects supported the role played by the spiracles and
 tracheal system in modulating the release of carbon dioxide. Further
 understanding led to the idea that the adaptive significance of regulated
 opening and closure of the spiracles is to reduce water loss (hygric
 hypothesis) and facilitate gaseous exchange in hyperoxia/hypoxia (chthonic
 hypothesis). With technological advances, other insect orders were
 investigated and the hygric and chthonic hypotheses were questioned. To
 allow for broad-scale comparison and conclusion, we conducted a
 meta-analysis to evaluate the merit of both postulated hypotheses that
 included 46 insect species in 24 families across nine orders. We also
 quantified the percent change in metabolic rates per ºC change of
 temperature during DGC. DGC was shown to reduce water loss (-3.27 ± 0.88;
 estimate ± 95% confidence limits [95% CI]; P &lt; 0.0001) in insects.
 However, DGC does not favor gaseous exchange in hyperoxia (0.21 ± 0.25
 [estimate ± 95% CI]; P = 0.12) nor hypoxia, but was shown to favor gaseous
 exchange in normoxia (0.27 ± 0.26 [estimate ± 95% CI]; P = 0.04). After
 accounting for variation associated with authorship, order phylogeny,
 family, and species, a phylogenetic model reflected that metabolic rate
 exhibited a significant, non-zero increase of 8.13% (± 3.48 95% CI; P
 &lt; 0.0001) per ºC increase in temperature. These data represent the
 first meta-analytic attempt to resolve the controversies surrounding the
 merit of adaptive hypotheses in insects.
description: Literature searches were conducted in the English language on 10
 January 2020. Searches were conducted using the Web of Science and PubMed
 with the following terms: “gas patterns*”, “discontinuous gas exchange”,
 “DGC*”, “DGE”, “cuticular water loss”, “respiratory water loss”, and “gas
 exchange patterns”. The title and abstract for each paper (in both search
 engines) were screened for relevancy. Duplicates and papers that were not
 DGC or DGE specific were removed. A study was selected if it satisfied the
 inclusion criteria for at least one objective.
DOI: 10.5061/dryad.qnk98sffv
title: Data from: Ambient nitrogen deposition drives plant-diversity decline by nitrogen accumulation in a closed grassland ecosystem

description: Atmospheric nitrogen (N) deposition, climatic variables and anthropogenic
 management affect grassland-ecosystem stability by driving changes in
 plant community and loss of plant diversity. Determination of their
 influences on plant composition and diversity is essential for predicting
 ecosystem response to future global changes and for making policies of
 sustainable grassland management. We evaluated the relative contributions
 of atmospheric N deposition, climatic variables and grassland management
 to plant diversity and N accumulation by temporally monitoring the changes
 in plant community and N status in a temperate grassland ecosystem.
 Ambient low-level N deposition combined with long-term grassland enclosure
 led to increases in aboveground biomass and abundance of grasses and
 sedges, and decreases in those of forbs. The dominant species of perennial
 forbs and grasses also displayed divergence in their biomass and abundance
 over time. Nitrogen deposition made greater contributions to the divergent
 changes in perennial forbs and grasses. However, air temperature and
 precipitation fluctuations mainly contributed to the annual fluctuations
 in annual and biennial species. Long-term enclosure aggravated the
 cumulative effects of soil inorganic N on plant-diversity loss, while
 mowing had opposite effects on the N accumulation. Synthesis and
 applications. Ambient low-level N deposition can drive loss of plant
 diversity due to N accumulation in grassland ecosystem under long-time
 enclosure. Therefore, appropriate grassland management, such as rationally
 grazing and/or mowing, may be effective practices in terms of maintenance
 of plant biodiversity under the scenario of enhanced atmospheric N
 deposition.
DOI: 10.5061/dryad.3bk3j9kj9
title: Adaptation and competition in deteriorating environments

description: Evolution might rescue populations from extinction in changing
 environments. Using experimental evolution with microalgae, we
 investigated if competition influences adaptation to an abiotic stressor,
 and vice versa, if adaptation to abiotic change influences competition. In
 a first set of experiments, we propagated monocultures of five species
 with and without increasing salt stress for ~180 generations. When assayed
 in monoculture, two of the five species showed signatures of adaptation,
 that is, lines with a history of salt stress had higher population growth
 rates at high salt than lines without prior exposure to salt. When assayed
 in mixtures of species, however, only one of these two species had
 increased population size at high salt, indicating that competition can
 alter how adaptation to abiotic change influences population dynamics. In
 a second experiment, we cultivated two species in monocultures and in
 pairs, with and without increasing salt. While we found no effect of
 competition on adaptation to salt, our experiment revealed that
 evolutionary responses to salt can influence competition. Specifically,
 one of the two species had reduced competitive ability in the no-salt
 environment after long-term exposure to salt stress. Collectively, our
 results highlight the complex interplay of adaptation to abiotic change
 and competitive interactions.
DOI: 10.5061/dryad.2jm63xsnw
title: New sphenodontian (Reptilia: Lepidosauria) from a novel Late Triassic palaeobiota in western North America sheds light on the earliest radiation of herbivorous lepidosaurs

description: Herbivory is a common ecological function among extant lepidosaurs, but
 little is known about the origin of this feeding strategy within
 Lepidosauria. Here we describe a sphenodontian (Lepidosauria) from the
 Late Triassic of western North America, Trullidens purgatorii n. gen. n.
 sp. that reveals new aspects of the earliest radiation of herbivorous
 lepidosaurs. This taxon is represented by an isolated lower jaw with
 robust structure bearing transversely widened dentition and extensive wear
 facets, suggesting a masticatory apparatus specialized for herbivory. An
 unusual ‘incisor-like’ tooth is present at the anterior end of the jaw; a
 unique feature among lepidosaurs, this tooth is convergent with the
 incisors of extant rodents and lagomorphs. Phylogenetic analyses supports
 the placement of this taxon within opisthodontian sphenodontians, a group
 sharing derived cranio-dental morphologies specialized for herbivory. The
 new taxon was recovered in a recently discovered and unnamed series of
 Upper Triassic strata in southeastern Colorado, USA, exposed in Canyons
 incised by the Purgatoire River and its tributaries. These strata comprise
 a dominantly red-bed sequence of conglomerates, sandstones, and siltstones
 deposited in a fluvio-lacustrine setting, preserving a Late Triassic biota
 of invertebrate and vertebrate ichnofossils, plant macrofossils, bony
 fish, temnospondyl amphibians, and reptiles. We use aetosaur osteoderms as
 biostratigraphic links to the nearby Chinle Formation of Arizona, USA,
 establishing a middle Norian age for these strata. The presence of an
 opisthodontian from western equatorial Pangaea in the Norian Stage reveals
 a near-global radiation of this clade across the Pangaean supercontinent
 during the Late Triassic.
DOI: 10.5061/dryad.dv41ns1x9
title: Perception of speaker sincerity in complex social interactions by cochlear implant users

description: Understanding insincere language, for example sarcasm and teasing, is a
 fundamental element of communication and crucial for maintaining social
 relationships. This can be a challenging task for cochlear implant users
 (CIs) who receive degraded suprasegmental information important for
 perceiving a speaker’s attitude. We measured perception of speaker
 sincerity (literal positive, literal negative, sarcasm, and teasing) in 16
 adults with CIs using an established video inventory. Participants were
 presented with audio-only and audio-visual social interactions between two
 people with and without supporting verbal context. They were instructed to
 describe the content of the conversation and answer whether the speakers
 meant what they said. Results showed that subjects could not always
 identify speaker sincerity, even when the content of the conversation was
 perfectly understood. This deficit was greater for perceiving insincere
 relative to sincere utterances. Performance improved when additional
 visual cues or verbal context cues were provided. Subjects who were better
 at perceiving the content of the interactions in the audio-only condition
 benefited more from having additional visual cues for judging the
 speaker’s sincerity, suggesting that the two modalities compete for
 cognitive recourses. Percentage scores for understanding the content also
 did not correlate with that for extracting speaker sincerity, suggesting
 that what was said vs. how it was said were perceived using unrelated
 segmental versus suprasegmental cues. Our results further showed that
 subjects who had access to lower-order resolved harmonic information
 provided by a hearing aids in the contralateral ear identified speaker
 sincerity better than those who used implants alone. The results suggest
 that measuring speech recognition alone in CI users do not fully describe
 the outcome and our findings stress the importance of measuring social
 communication functions in people with CIs.
DOI: 10.5061/dryad.m63xsj41d
title: Data from: Motifier: an IgOme profiler based on peptide-motifs using machine learning

description: Antibodies provide a comprehensive record of the encounters with threats
 and insults to the immune system. The ability to examine the repertoire of
 antibodies in serum and discover those that best represent “discriminating
 features” characteristic of various clinical situations, is potentially
 very useful. Recently, phage display technologies combined with
 Next-Generation Sequencing (NGS) produced a powerful experimental
 methodology, coined “Deep-Panning”, in which the spectrum of serum
 antibodies is probed. In order to extract meaningful biological insights
 from the tens of millions of affinity-selected peptides generated by
 Deep-Panning, advanced bioinformatics algorithms are a must. In this
 study, we describe Motifier, a computational pipeline comprised
 of a set of algorithms that systematically generates discriminatory
 peptide motifs based on the affinity-selected peptides identified by
 Deep-Panning. These motifs are shown to effectively characterize antibody
 binding activities and through the implementation of machine-learning
 protocols are shown to accurately classify complex antibody mixtures
 representing various biological conditions.
description: The file called Exp12.fastq contains the NGS data obtained from
 the mAbs experiment. The file called Exp22.fastq
 contains the NGS data obtained from the HIV experiment.
DOI: 10.5061/dryad.jh9w0vt9w
title: Expression of Mst89B and CG31287 is needed for effective sperm storage and egg fertilization in Drosophila

description: In Drosophila, male reproductive fitness can be affected by any number of
 processes, ranging from development of gametes, transfer to and storage of
 mature sperm within the female sperm storage organs, and utilization of
 sperm for fertilization. We have previously identified the 89B cytogenetic
 map position of D. melanogaster as a hub for genes that effect male
 paternity success when disturbed. Here, we used RNA interference to test
 11 genes that are highly expressed in the testes and located within the
 89B region for their role in sperm competition and male fecundity when
 their expression is perturbed. Testes-specific knockdown (KD) of bor and
 CSN5 resulted in complete sterility, whereas KD of CG31287, Manf and
 Mst89B, showed a breakdown in sperm competitive success when second to
 mate (P2 &lt; 0.5) and reduced fecundity in single matings. The low
 fecundity of Manf KD is explained by a significant reduction in the amount
 of mature sperm produced. KD of Mst89B and CG31287 does not affect sperm
 production, sperm transfer into the female bursa or storage within 30 min
 after mating. Instead, a significant reduction of sperm in female storage
 is observed 24 h after mating. Egg hatchability 24 h after mating is also
 drasti-cally reduced for females mated to Mst89B or CG31287 KD males, and
 this reduction parallels the decrease in fecundity. We show that normal
 germ-line expression of Mst89B and CG31287 is needed for effective sperm
 usage and egg fertilization.
DOI: 10.5061/dryad.msbcc2fxd
title: Light pollution affects West Nile virus exposure risk across Florida

description: Emerging infectious diseases (EIDs) present global health threats, and
 their emergences are often linked to anthropogenic change. Artificial
 light at night (ALAN) is one form of anthropogenic change that spans
 beyond urban boundaries and may be relevant to EIDs through its influence
 on behavior and physiology of hosts and/or vectors. Although West Nile
 virus (WNV) emergence has been described as peri-urban, we hypothesized
 that exposure risk could also be influenced by ALAN in particular, which
 is testable by comparing the effects of ALAN on prevalence while
 controlling for other aspects of urbanization. By modeling WNV exposure
 among sentinel chickens in Florida, we found strong support for a
 nonlinear relationship between ALAN and WNV exposure risk in chickens with
 peak WNV risk occurring at low ALAN levels. Although our goal was not to
 discern how ALAN affected WNV relative to other factors, effects of ALAN
 on WNV exposure were stronger than other known drivers of risk (i.e.,
 impervious surface, human population density). Ambient temperature in the
 month prior to sampling, but no other considered variables, strongly
 influenced WNV risk. These results indicate that ALAN may contribute to
 spatiotemporal changes in WNV risk, justifying future investigations of
 ALAN on other vector-borne parasites.
DOI: 10.5061/dryad.pzgmsbck6
title: Supplementary data for: Abducens nerve palsy with ipsilateral excessive eye tearing attributed to internal carotid artery sympathetic plexus schwannoma

description: A 65-year-old man developed subacute horizontal diplopia due to
 left-abducens nerve (AN) palsy and excessive left-eye tearing. Brain-MRI
 revealed a hyperintense T2-lesion with an elongated course within the
 left-carotid canal, presenting homogenous contrast-enhancement (Figure-1).
 The imaging findings were characteristic for an internal-carotid-artery
 sympathetic plexus (ICSP) schwannoma compressing the left-AN. Subsequent
 irritation of the deep petrosal nerve originating directly from ICSP and
 continuing as the vidian nerve may have led to the lacrimal gland edema
 and excessive left-eye tearing (Figure-2). ICSP schwannoma represents an
 uncommon cause of AN palsy that may also manifest with excessive
 ipsilateral-eye tearing due to vidian nerve involvement.
DOI: 10.5061/dryad.4tmpg4f8r
title: Ex Vivo MRI in Frontotemporal Lobar Degeneration

description: Ex vivo MRI of 7 human hemispheres, acquired at 7 T using multi-echo
 gradient recalled echo imaging. Details of these samples are presented in
 the associated manuscript.
description: Samples were placed in Fomblin (California Vacuum Technology; Freemont, CA), a proton-free fluid with volume magnetic susceptibility close to that of tissue. Samples were enclosed in either custom-build cylindrical holders or plastic bags, and then left to rest for at least two days to allow air bubbles to escape from the tissue. Depending on their size, samples were scanned using either a custom-built small solenoid coil or a custom-modified quadrature birdcage (Varian, Palo Alto, CA, USA) coil. These transmit/receive coils were attached to a two-channel transmit-receive adapter (Stark Contrast, Erlangen, Germany). The smallest coil was chosen that could hold each sample, tuned/matched by hand, and then placed into our whole-body 7 T scanner (MAGNETOM Terra, Siemens Healthineers, Erlangen, Germany) using plastic shims under the coils to position the sample near isocenter. MRI data were acquired with a 3D-encoded, 8-echo gradient-recalled echo (GRE) sequence with non-selective RF pulses. To maintain readout polarity and minimize distortions due to field inhomogeneity, each readout was followed by a flyback rephrasing gradient. The final echo was followed by an additional completely rephrased readout to measure frequency drifts. Each line of k-space was acquired with multiple averages sequentially before advancing to the next phase-encode step. Common parameters for the sequence were: 280 µm isotropic resolution, 25° flip angle, 60 ms repetition time (TR), minimum echo time (TE) 3.48 ms, echo spacing 6.62 ms, bandwidth 400 Hz/px. The field of view was adapted to each sample, and subsequently TRs and TEs were slightly modified based on the necessary readout duration. Total scan times were 8-10 hours for each sample. Images were reconstructed using the vendor’s on-scanner reconstruction software which automatically corrected the global frequency drift, combined the signal averages in k-space, and produced magnitude images for each echo.
description: Image data is in DICOM format, organized with per-patient
 directories. Imaging data dimensions are described in the DICOM data
 headers. Details of the patients' clinical and demographic
 information is included in the associated manuscript.
DOI: 10.15468/dl.9eybzr
title: Occurrence Download

description: A dataset containing 1088 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cleidion javanicum"
 ]
}

 The dataset includes 1088 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002771-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zpc866t7q
title: Far Eastern Curlew and Whimbrel prefer flying low: wind support and good visibility appear only secondary factors in determining migratory flight altitude

description: Background: In-flight conditions are hypothesized to influence the timing
 and success of long-distance migration. Wind assistance and thermal uplift
 are thought to reduce the energetic costs of flight, humidity, air
 pressure and temperature may affect the migrants’ water balance, and
 clouds may impede navigation. Recent advances in animal-borne
 long-distance tracking enable evaluating the importance of these factors
 in determining animals’ flight altitude. Methods: Here we determine the
 effects of wind, humidity, temperature, cloud cover, and altitude (as
 proxy for climbing costs and air pressure) on flight altitude selection of
 two long-distance migratory shorebirds, far eastern curlew (Numenius
 madagascariensis) and whimbrel (Numenius phaeopus). To reveal the
 predominant drivers of flight altitude selection during migration we
 compared the atmospheric conditions at the altitude the birds were found
 flying with conditions elsewhere in the air column using conditional
 logistic mixed effect models. Results: Our results demonstrate that
 despite occasional high-altitude migrations (up to 5,550 m above ground
 level), our study species typically forego flying at high altitudes,
 limiting climbing costs and potentially alleviating water loss and
 facilitating navigation. While mainly migrating at low altitude, the birds
 also preferred flying with wind support to likely reduce flight costs, and
 avoided clouds, which would help navigation and reduce the risks from
 adverse weather. Conclusions: We conclude that the primary determinant of
 avian migrant’s flight altitude selection is a preference for low altitude
 with wind support as an important secondary factor. Our approach and
 findings can assist in predicting climate change effects on migration and
 in mitigating bird strikes with air traffic, wind farms, power lines, and
 other human-made structures.
DOI: 10.5061/dryad.34tmpg4jh
title: Data and R code from: GC-MS analysis of murine oestrous odours

description: For female mammals, communicating the timing of ovulation is essential for
 successful reproduction. Urinary volatile organic compounds (VOCs) play a
 key role in intraspecific communication among many mammals. Using
 laboratory mice as a model species, we investigated urinary VOCs across
 the oestrous cycle. We monitored the oestrous stage through daily vaginal
 cytology assessment and analysed urinary VOCs using headspace gas
 chromatography-mass spectrometry (GC-MS), testing the utility of portable
 GC-MS against the more robust benchtop device. We detected 65 VOCs from 40
 samples stored in VOC traps and analysed on a benchtop GC-MS and 15 VOCs
 from 90 samples extracted by solid-phase microextraction (SPME) and
 analysed on a portable GC-MS. Only three of the identified compounds were
 found in common between the two techniques. Urine collected from the
 fertile stages of the oestrous cycle had increased quantities of a few
 notable VOCs (3,4-dehydro-exo-brevicomin, butanoic acid,
 pent-1-ene/cyclopentane, 1,2,3-/1,2,4-trimethylbenzene, heptadecane,
 dioctyl ether, dodecan-1-ol and 2-ethylhexyl salicylate), compared to
 urine collected from non-fertile stages. However, we did not find
 differences in the Bray-Curtis chemical dissimilarity indices among
 oestrous stages. It is possible that the variation in urine VOCs
 concentration at play during the oestrous cycle was too subtle to be
 detected by our analytical methods. Overall, the use of the VOC traps
 combined with benchtop GC-MS was more successful than SPME combined with
 portable GC-MS in capturing and identifying murine urinary VOCs.
 Nonetheless, portable GC-MS systems have the potential for some in situ
 applications since they allow for the immediate interpretation of results,
 especially at remote field sites.
description: Using laboratory mice as a model species, we investigated urinary
 VOCs across the oestrous cycle. We monitored the oestrous stage through
 daily vaginal cytology assessment and analysed urinary VOCs using
 headspace gas chromatography-mass spectrometry (GC-MS), testing the
 utility of portable GC-MS against the more robust benchtop
 device.