cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1wd8h
title: Methyl halide fluxes from rapeseed (Brassica napus) over its life cycle

description: Rapeseed (Brassica napus) was quantified as one of the
 important terrestrial natural emitters of methyl bromide (CH3Br)
 to the atmosphere. In this study, we planted rapeseed (B. napus
 "Empire") in the field (Oxford Tract, UC Berkeley) and
 measured weekly methyl halide fluxes (CH3Cl, CH3Br and CH3I)
 using static-chamber measurements. The meteorological and physiological
 data, including air tempearture, plant height, leaf area, flowering
 number, biomass were also recorded over the life cycle of
 rapeseed.
description: Methyl halide fluxes were measured by static-chamber methods and
 the concentrations were analyzed by gas chromatography coupled with a mass
 spectrometry (GC/MS; Agilent 6890N/5973, Agilent Technologies, Santa
 Clara, CA).  Air temperature was recorded for every 10 minutes via sensors
 (HOBO U23 Pro v2 Data Logger, Onset Computer Corporation, Bourne, MA). For
 soil chloride and bromide measurements : a known amount (~10g) of soil
 powder was then placed into a centrifuge tube (BD Falcon, Becton,
 Dickinson and Company, Franklin Lakes, NJ) with 35 mL of deionized water
 and then shaken thoroughly for 20 min (Vortex Genie 2 Mixer, Fisher
 Scientific, Hampton, NH) to mix soil and water suspension to extract ions
 into the liquid phase. Afterwards, the mixed slurry was centrifuged for
 approximately 40 minutes at high speed setting to ensure that pellet and
 supernatant are well separated and packed. The aqueous extract was
 filtered with a #5 Whatman filter paper and a Buchner funnel, then being
 analyzed by chloride/bromide ion selective electrodes (Thermo Scientific,
 Waltham, MA).
DOI: 10.5061/dryad.h44j0zph3
title: Seed traits determine species responses to fire under varying soil heating scenarios

description: 1) Many plant species in fire-prone environments maintain persistence
 through fire via soil seedbanks. However, seeds stored within the soil are
 at risk of mortality from elevated soil temperatures during fire. Seeds
 may be protected from fire-temperature impacts by burial, however those
 buried too deeply may germinate but fail to emerge. Thus, successful
 post-fire seed regeneration is contingent upon a trade-off between burial
 depth and survival through fire. 2) We examined the relationships between
 seedling emergence behaviour, seed survival, and soil temperatures during
 fire in 13 native and four non-native woodland species in southwestern
 Australia. We assessed total seedling emergence per depth, maximum
 seedling emergence depth and seedling emergence speed from seeds planted
 at seven depths (0, 1, 2, 3, 4, 5, 7 10 cm). Soil temperatures were
 quantified using distributed temperature sensing in optic fibre (DTS),
 measured continuously between 1 and 10 cm in depth (temperatures were
 subsequently categorised into 1 cm increments for analysis) during five
 experimental fires in beds with fine fuels manipulated between 8–20 t
 ha-1. Using seed survival and emergence success relative to soil
 temperatures, , we determined vulnerability of seedling emergence relative
 to soil temperatures generated by combustion of fuel quantities typically
 observed in woodlands. 3) Maximum depth of emergence varied between
 species from 2 to &gt;10 cm, with a positive linear correlation to
 seed mass. Maximum soil temperatures from the two highest fuel masses
 exceeded seed lethal thresholds (T50 - representing temperatures lethal to
 50% of  seeds) of at least five species. Lethal
 temperatures  exceeded at all potential emergence depths for all
 three grass species, and all four non-native species studied. Of the
 remaining 10 species, temperatures did not exceed the lethal thresholds
 under any of the fuel mass levels tested. We found no relationship between
 lethal temperature thresholds and maximum emergence depth. 4) Our data
 demonstrate that seeds exhibit variation in their response to soil heating
 and capacity to emerge from depth, with three distinct functional
 responses amongst our study species, which enable persistence through, and
 recruitment following, fire. Such variation in species attributes and fuel
 mass may lead to heterogeneity (within fires) or divergent trajectories
 (among fires) in community response under changed fire regime.
description: These data encapulate all data used in the anlaysis, including
 emergence rate data, seed trait data and fire data.
DOI: 10.5061/dryad.k98sf7m40
title: Data from: Female sperm storage mediates postcopulatory costs and benefits of ejaculate anticipatory plasticity in the guppy

description: Males of many species evolved the capability of adjusting their ejaculate
 phenotype in response to social cues to match the expected mating
 conditions. When females store sperm for prolonged time, the expected
 fitness return of plastic adjustments of ejaculate phenotype may depend on
 the interval between mating and fertilization. While, prolonged female
 sperm storage (FSS) increases the opportunity for sperm competition, as a
 consequence of the longer temporal overlapping of ejaculates from several
 males, it may also create variable selective forces on ejaculate
 phenotype, for example by exposing trade-offs between sperm velocity and
 sperm survival. We evaluated the relationship between the plasticity of
 ejaculate quality and FSS in the guppy, Poecilia reticulata, a polyandrous
 livebearing fish in which females store sperm for several months and where
 stored sperm contribute significantly to a male’s lifelong reproductive
 success. In this species, males respond to the perception of future mating
 opportunities by increasing the quantity (number) and quality (swimming
 velocity) of ready-to-use sperm (an anticipatory response called ‘sperm
 priming’). Here we investigated 1) the effect of sperm priming on in-vitro
 sperm viability at stripping and its temporal decline (as estimate of
 sperm survival), and, 2) the in-vitro competitive fertilization success in
 relation to female sperm storage using artificial insemination. As
 expected, sperm-primed males produced more numerous and faster sperm, but
 with a reduced in-vitro sperm viability at stripping and after 4 hours,
 compared to their counterparts. Artificial insemination revealed that the
 small (non-significant) advantage of primed sperm when fertilization
 immediately follows insemination, is reversed when eggs are fertilized by
 female-stored sperm, weeks after insemination. By suggesting a plastic
 trade-off between sperm velocity and viability, these results demonstrate
 that prolonged female sperm storage generates divergent selection
 pressures on ejaculate phenotype.
description: Complete dataset The dataset consists in a
 .xlsx file with 5 sheets where: Fertilization success
 of males with different females, male morphology and colouration, number
 of sperm produced, sperm velocity and sperm viability are
 reported.
DOI: 10.5061/dryad.3n5tb2rdr
title: Data from: Surf and Turf Vision: Patterns and predictors of visual acuity in compound eye evolution

description: Eyes have the flexibility to evolve to meet the ecological demands of
 their users. Relative to camera-type eyes, the fundamental limits
 of optical diffraction in arthropod compound eyes restricts the ability to
 resolve fine detail (visual acuity) to much lower degrees. We tested the
 capacity of several ecological factors to predict arthropod visual acuity,
 while simultaneously controlling for shared phylogenetic
 history. In this study, we have generated the most comprehensive
 review of compound eye visual acuity measurements to date,
 containing 375 species that span six of the major arthropod
 classes. An arthropod phylogeny, made custom to this database, was used to
 develop a phylogenetically-corrected generalized least squares (PGLS)
 linear model to evaluate four ecological factors predicted to underlie
 compound eye visual acuity: environmental light intensity, foraging
 strategy (predator vs. non-predator), horizontal structure of the
 visual scene, and environmental medium (air vs. water). To
 account for optical constraints on acuity related to animal size, body
 length was also included, though this did not show a significant effect in
 any of our models. Rather, the PGLS revealed that the strongest predictors
 of compound eye acuity are described by a combination of environmental
 medium, foraging strategy, and environmental light intensity.
description: Data were collected via a literature review of compound eye
 visual acuity measurements and ecological factor assignments. A
 phylogeny was built custom to the species represented in this database by
 mining sequences from GenBank. 
description: Data provided here are supplemental to the database published in
 our paper. Please see paper for how gene assemblies provided here were
 used to build the tree in "Tree data" folder. All files provided
 in PGLS folder are sufficient to run PGLS code. See code annotations for
 further details.
DOI: 10.5061/dryad.gf1vhhmmb
title: Parasite counts for Corydoras maculifer and Corydoras araguaiaensis

description: The evolutionary impacts of whole genome duplication events are
 still unclear. We collected parasite count data and immune
 gene molecular data for Toll like receptor (TLR) 1 and TLR2 in
 two catfish species; Corydoras maculifer (diploid) and Corydoras
 araguaiaensis (putative allotetraploid). Our aim was to compare parasite
 load and immune gene diversity between these two species. 
description: Samples of the host fish species <em>Corydoras
 maculifer</em> (n= 20) and <em>Corydoras
 araguaiaensis</em> (n=41) were collected from the Rio das Mortes
 drainage of the Araguaia River in Mato Grosso state, Brazil in 2012 and
 2015. All samples were euthanised by anaesthetic overdose and preserved
 individually in 100% ethanol. In addition samples from 2015 were dissected
 in the field; stomach, liver and digestive tract were preserved separately
 in 100% ethanol. Tissues, the external body and body cavity of the host
 fish were then manually screened for parasites using a disecting
 microscope and fiber optic illumination. Parasite count
 and prevalence data are included here along with the r scripts used for
 modeling (GLM) the relationship between host standard length and parasite
 counts.  Immunogenetic data was collected from PCR
 amplified Toll like receptor (TLR) 1 and TLR2, raw sequence data was
 submited to Sequence Read Archive submission: SUB7660075 (individual
 accision numbers included in file uploads). FreeBayes was used to identify
 variants in the immune gene data, corresponding vcf files are inluded in
 these uploads. 
description: These data were used alongside immune gene data sets that have
 been uploaded to Sequence Read Archive (SRA), submission:
 SUB7660075.
DOI: 10.5281/zenodo.15144766
title: Table 1 in Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus

description: Table 1. Definitions of, and abbreviations used for, measurements, mensural ratios, and scale counts.
SymbolDescriptionMeasurementsAHead length from snout to anterior dorsal margin of tympanumBHead width at maximum span of postorbital archCHead depth at midpoint of orbitDHead–neck length from tip of snout to gular foldEBody length from gular fold to cloacaFTail length from cloaca to tip of tailGFacial length from centre of nostril to anterior margin of orbitHSnout length from tip of snout to centre of nostrilTLTotal lengthSVLSnout to vent lengthMensural ratios1Relative tail to body length – F/ SVL10Relative head length to head width – A/B11Relative head length to head height – A/CScale countsSMidbody scale rowsXYDorsal scale rows from posterior margin of tympanic recess to anterior margin of hind limbsTRows of ventral scales from gular fold to anterior margin of hind limbsXRows of dorsal scales from posterior margin of tympanic recess to gular foldmScales around neck at anterior margin of gular foldNRows of ventral scales from tip of snout to gular foldPScales from rictus to rictus across dorsum of headQScales around tail baseRScales around tail counted at 1/3 of tail length from the baseDORNumber of dorsal scale rows from the last occipital scale to a point dorsal to the posterior margin of the cloacaVENVentral scales from the gular fold to the anterior margin of the cloaca
description: Published as part of Weijola, Valter & Kraus, Fred, 2023, Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus, pp. 950 in Journal of Natural History 57 (13 - 16) on page 950, DOI: 10.1080/00222933.2023.2218574, http://zenodo.org/record/8221626
DOI: 10.5281/zenodo.15144767
title: Table 1 in Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus

description: Table 1. Definitions of, and abbreviations used for, measurements, mensural ratios, and scale counts.
SymbolDescriptionMeasurementsAHead length from snout to anterior dorsal margin of tympanumBHead width at maximum span of postorbital archCHead depth at midpoint of orbitDHead–neck length from tip of snout to gular foldEBody length from gular fold to cloacaFTail length from cloaca to tip of tailGFacial length from centre of nostril to anterior margin of orbitHSnout length from tip of snout to centre of nostrilTLTotal lengthSVLSnout to vent lengthMensural ratios1Relative tail to body length – F/ SVL10Relative head length to head width – A/B11Relative head length to head height – A/CScale countsSMidbody scale rowsXYDorsal scale rows from posterior margin of tympanic recess to anterior margin of hind limbsTRows of ventral scales from gular fold to anterior margin of hind limbsXRows of dorsal scales from posterior margin of tympanic recess to gular foldmScales around neck at anterior margin of gular foldNRows of ventral scales from tip of snout to gular foldPScales from rictus to rictus across dorsum of headQScales around tail baseRScales around tail counted at 1/3 of tail length from the baseDORNumber of dorsal scale rows from the last occipital scale to a point dorsal to the posterior margin of the cloacaVENVentral scales from the gular fold to the anterior margin of the cloaca
description: Published as part of Weijola, Valter & Kraus, Fred, 2023, Two new species of monitor lizards (Squamata: Varanus) endemic to the Louisiade and Tanimbar Archipelagos with a key to the subgenus Euprepiosaurus, pp. 950 in Journal of Natural History 57 (13 - 16) on page 950, DOI: 10.1080/00222933.2023.2218574, http://zenodo.org/record/8221626
DOI: 10.5061/dryad.h9w0vt4fw
title: Data from: Hybrid zone barriers comparative data set

description: Many recent studies have addressed the mechanisms operating during the
 early stages of speciation, but surprisingly few studies have tested
 theoretical predictions on the evolution of strong reproductive isolation
 (RI). To help address this gap, we first undertook a quantitative review
 of the hybrid zone literature for flowering plants in relation to
 reproductive barriers. Then, using Populus as an exemplary model group, we
 analysed genome-wide variation for phylogenetic tree topologies in both
 early- and late-stage speciation taxa to determine how these patterns may
 be related to the genomic architecture of RI. Our plant literature survey
 revealed variation in barrier complexity and an association between
 barrier number and introgressive gene flow. Focusing on Populus, our
 genome-wide analysis of tree topologies in speciating poplar taxa points
 to unusually complex genomic architectures of RI, consistent with earlier
 genome-wide association studies. These architectures appear to facilitate
 the ‘escape’ of introgressed genome segments from polygenic barriers even
 with strong RI, thus affecting their relationships with recombination
 rates. Placed within the context of the broader literature, our data
 illustrate how phylogenomic approaches hold great promise for addressing
 the evolution and temporary breakdown of RI during late stages of
 speciation. This article is part of the theme issue ‘Towards the
 completion of speciation: the evolution of reproductive isolation beyond
 the first barriers’.
description: R markdown code for analysis of comparative data requires
 adjustment to working directory.
DOI: 10.5061/dryad.sbcc2fr3w
title: Data from: How qualified immunity fails

description: This Article reports the findings of the largest and most comprehensive
 study to date of the role qualified immunity plays in constitutional
 litigation. Qualified immunity shields government officials from
 constitutional claims for money damages so long as the officials did not
 violate clearly established law. The Supreme Court has described the
 doctrine as incredibly strong—protecting “all but the plainly incompetent
 or those who knowingly violate the law.” Legal scholars and commentators
 describe qualified immunity in equally stark terms, often criticizing the
 doctrine for closing the courthouse doors to plaintiffs whose rights have
 been violated. The Court has repeatedly explained that qualified immunity
 must be as powerful as it is to protect government officials from burdens
 associated with participating in discovery and trial. Yet the Supreme
 Court has relied on no empirical evidence to support its assertion that
 qualified immunity doctrine shields government officials from these
 assumed burdens. This Article is the first to test this foundational
 assumption underlying the Supreme Court’s qualified immunity decisions. I
 reviewed the dockets of 1,183 Section 1983 cases filed against state and
 local law enforcement defendants in five federal court districts over a
 two-year period and measured the frequency with which qualified immunity
 motions were brought by defendants, granted by courts, and dispositive
 before discovery and trial. I found that qualified immunity rarely served
 its intended role as a shield from discovery and trial in these cases.
 Across the five districts in my study, just thirty-eight (3.9%) of the 979
 cases in which qualified immunity could be raised were dismissed on
 qualified immunity grounds. And when one considers all the Section 1983
 cases brought against law enforcement defendants—each of which could
 expose law enforcement officials to burdens associated with discovery and
 trial—just seven (0.6%) were dismissed at the motion to dismiss stage and
 thirty-one (2.6%) were dismissed at summary judgment on qualified immunity
 grounds. My findings enrich our understanding of qualified immunity’s role
 in constitutional litigation, belie expectations about the policy
 interests served by qualified immunity, and show that qualified immunity
 doctrine should be modified to reflect its actual role in constitutional
 litigation.
DOI: 10.5061/dryad.69p8cz8zr
title: Frequency of biologically-defined AD in relation to age, sex, APOEε4 and cognitive impairment in a prospective cohort study

description: Objective:  To assess the frequency of biologically-defined
 Alzheimer’s disease (AD) in relation to age, sex and APOEε4, as well as
 rates of discordance between clinically- and biologically defined AD.
 Methods: We assessed cognitively unimpaired (CU) elderly (n=166),
 amnestic MCI (n=77) and probable AD dementia (n=62) subjects who underwent
 evaluation by dementia specialists and neuropsychologists in addition to
 amyloid-PET with [18F]AZD4694 and tau-PET with [18F]MK6240. Individuals
 were grouped according to their AD biomarker profile. Positive predictive
 value for biologically-defined AD was assessed in relation to clinical
 diagnosis. Frequency of AD biomarker profiles were assessed using logistic
 regressions with odds ratios and 95% CIs. Results: The clinical
 diagnosis of probable AD dementia demonstrated good agreement with
 biologically-defined AD (positive predictive value: 85.2%). 7.88% of CU
 elderly subjects were positive for both amyloid-PET and tau-PET. Frequency
 of biologically-defined AD increased with age (OR: 1.14; p&lt;0.0001)
 and frequency of APOEε4 allele carriers (Single ε4: OR: 3.82;
 p&lt;0.0001; Double ε4: OR: 17.55, p&lt;0.0001). Discussion: While
 we observed strong, but not complete, agreement between clinically-defined
 “probable AD” dementia and biomarker positivity for both amyloid-β and
 tau, we also observed that biologically-defined AD was not rare in CU
 elderly. Abnormal tau-PET was almost exclusively observed in individuals
 with abnormal amyloid-PET. Our results highlight that even in tertiary
 care memory clinics, detailed evaluation by dementia specialists
 systematically underestimates the frequency of biologically-defined AD and
 related entities.
DOI: 10.5061/dryad.9s4mw6md0
title: Data from: Effect of yeast addition on the biogas production performance of a food waste anaerobic digestion system

description: Food waste contains numerous easily degradable components, and anaerobic
 digestion is prone to acidification and instability. This work aimed to
 investigate the effect of adding yeast on biogas production performance,
 when substrate is added after biogas production is reduced. The results
 showed that the daily biogas production increased 520 ml and 550 ml by
 adding 2.0% (VS) of activated yeast on the 12th and 37th day of anaerobic
 digestion, respectively, and the gas production was relatively stable. In
 the control group without yeast, the increase of gas production was
 significantly reduced. After the second addition of substrate and yeast,
 biogas production only increased 60 ml compared with that before the
 addition. After fermentation, the biogas production of yeast group also
 increased by 33.2% compared with the control group. Results of the
 analysis of indicators, such as volatile organic acids, alkalinity, and
 propionic acid, showed that the stability of the anaerobic digestion
 system of the yeast group was higher. Thus, the yeast group is highly
 likely to recover normal gas production when the biogas production is
 reduced, and substrate is added. The results provide a reference for
 experiments on the industrialisation of continuous anaerobic digestion to
 take tolerable measures when the organic load of the feed fluctuates
 dramatically.
DOI: 10.5061/dryad.nvx0k6dpx
title: The fate of Meconopsis species in the Tibeto-Himalayan region under future climate change

description: High-mountain areas such as the Tibeto-Himalayan region (THR) host
 cold-adapted biota expected to be sensitive to anthropogenic climate
 change. Meconopsis is a representative endangered genus confined to alpine
 meadow or subnival habitats in the THR. To obtain occurrence data for
 Meconopsis species found in the THR and adjacent regions, we used records
 from the Chinese Virtual Herbarium (CVH: http://www.cvh.org.cn/), the
 Global Biodiversity Information Facility (GBIF: http://www.gbif.org/), and
 the published literature (He et al., 2019). We only used occurrence data
 collected after 1950, and removed duplicate records found within a
 5-kilometer diameter. Our dataset for ten species of Meconopsis
 are the numbers of records per species ranging from 17 to
 228. For these ten Meconopsis species, we identified potential
 future climate refugia and determined optimal routes for each species to
 disperse to the proposed refugia.  Our results indicate that for
 the ten Meconopsis species the regions with low vulnerability to climate
 change in the THR are the central Qinghai-Tibet Plateau, the Hengduan
 Mountains (HDM), the eastern Himalayas, and the West Qinlin Mountain
 (WQL), and can be considered potential future climate refugia. Under
 future climate change, we found for the ten Meconopsis species potential
 dispersal routes to three of the four identified refugia: the HDM, the
 eastern Himalayas, and the WQL.  Furthermore, climate change may
 affect the threat ranking of Red Listed Species for Meconopsis species, as
 Least Concern species were estimated to become more vulnerable to climate
 change than the only Near Threatened species.