cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c2fqz6158
title: Data from: The ovipositor actuation mechanism of a parasitic wasp and its functional implications

description: Parasitic wasps use specialized needle-like structures­­—ovipositors—to
 drill in substrates to reach hidden hosts. The external ovipositor
 (terebra) consists of three interconnected, sliding elements (valvulae)
 which are moved reciprocally during insertion. This presumably reduces the
 required pushing force on the terebra and limits the risk of damage whilst
 probing. Although this is an important mechanism, it is still not
 completely understood how the actuation of the valvulae is achieved, and
 it has only been studied with the ovipositor in rest position.
 Additionally, very little is known about the magnitude of the forces
 generated during probing. We used synchrotron X-ray microtomography to
 reconstruct the actuation mechanism of the parasitic wasp Diachasmimorpha
 longicaudata (Braconidae) in four distinct phases of the probing cycle. We
 show that only the paired first valvulae of the terebra move
 independently, while the second valvula moves with the metasoma
 (‘abdomen’). The first valvula movements are initiated by rotation of one
 chitin plate (first valvifer) with respect to another such plate (second
 valvifer). This is achieved indirectly by muscles connecting the
 non-rotating second valvifer and the abdominal ninth tergite. Unlike
 previously reported, we found muscle fibres running inside the terebra,
 although their function remains unclear. The estimated maximal forces that
 can be exerted by the first valvulae are small (protraction 1.19
 mN and retraction 0.874 mN), which reduces the risk of buckling
 but are sufficient for successful probing. The small net forces of the
 valvulae on the substrate may still lead to buckling of the terebra; we
 show that the sheaths surrounding the valvulae prevent this by effectively
 increasing the diameter and second moment of area of the terebra. Our
 findings improve the comprehension of hymenopteran probing mechanisms, the
 function of the associated muscles, and the forces and damage limiting
 mechanism that are involved in drilling a slender terebra into a
 substrate.
description: For the methodology, please refer to our
 paper: http://dx.doi.org/10.1111/joa.13216.
description: The files contain surface meshes (.ply) of the ovipositor
 apparatus of the parasitic wasp <em>Diachasmimorpha
 longicaudata</em>, which can be opened for example by using the free
 software Meshlab (www.meshlab.net).    File names: [<b>position</b>]_[<b>valvula alignment</b> (if position = probing)]_[<b>M</b> (muscle)/<b>S</b> (sclerites)]_[<b>abbreviated name structure</b>].ply e.g. <i>ProbingPosition_Aligned_S_1vlf-1vlv.ply</i> is the file with the 1<sup>st</sup> valvula and valvifer of the aligned probing ovipositor base.
DOI: 10.5061/dryad.vt4b8gtpc
title: Data from: Ecological speciation in European whitefish is driven by a large‐gaped predator

description: Lake‐dwelling fish that form species pairs/flocks characterized by body
 size divergence are important model systems for speciation research.
 Although several sources of divergent selection have been identified in
 these systems, their importance for driving the speciation process remains
 elusive. A major problem is that in retrospect, we cannot distinguish
 selection pressures that initiated divergence from those acting later in
 the process. To address this issue, we studied the initial stages of
 speciation in European whitefish (Coregonus lavaretus) using data from 358
 populations of varying age (26–10,000 years). We find that whitefish
 speciation is driven by a large‐growing predator, the northern pike (Esox
 lucius). Pike initiates divergence by causing a largely plastic
 differentiation into benthic giants and pelagic dwarfs: ecotypes that will
 subsequently develop partial reproductive isolation and heritable
 differences in gill raker number. Using an eco‐evolutionary model, we
 demonstrate how pike's habitat specificity and large gape size are
 critical for imposing a between‐habitat trade‐off, causing prey to mature
 in a safer place or at a safer size. Thereby, we propose a novel mechanism
 for how predators may cause dwarf/giant speciation in lake‐dwelling fish
 species.
description: The data has been collected using interviews with local fishers
 and gillnet sampling. A description of the data and our analyses can be
 found in each sheet of the uploaded excel file.
description: A description of the data and our analyses can be found in each
 sheet of the uploaded excel file.
DOI: 10.5061/dryad.mcvdncjxn
title: Data from: Pest control potential of adjacent agri-environment schemes varies with crop type and is shaped by landscape context and within-field position

description: Increasing natural pest control in agricultural fields is an important aim
 of ecological intensification. Combined effects of landscape context and
 local placement of agri-environmental schemes on natural pest control and
 within field distance functions of natural pest control agents have rarely
 been addressed but might affect the distribution of biocontrol providers.
 Importantly, it is currently unknown whether ecosystem services provided
 by adjacent agri-environmental schemes (AES) are consistent for different
 crop types during crop rotation. In this study, we assessed whether crop
 rotation from oilseed rape to cereals altered within-field distance
 functions of ground dwelling predators from adjacent agri-environmental
 fields along a gradient in landscape context. Additionally we recorded
 crop pests, predation rates, parasitoids as well as crop yields on a total
 of 30 study sites. Distance functions varied between trophic levels:
 Carabid richness decreased while densities of carabid beetles, staphylinid
 beetles as well as crop yields increased towards the field centres.
 Distance functions of parasitoids and pests were modulated by the amount
 of semi-natural habitat in the surrounding landscape, while the effects of
 adjacent AES were limited. Distance decay functions found for ground
 dwelling predators in oilseed rape in the previous year were not always
 present in cereals. Increasing distance to the field edge also increased
 effects of crop rotation on carabid beetle assemblages, indicating a
 source habitat function of field edges. Synthesis and applications.
 Distance functions of natural pest control are not universal and the
 effects of agri-environmental schemes (AES) in different adjacent crops
 during crop rotation vary and depends on ecological contrasts. A network
 of semi-natural habitats and spatially optimised AES habitats can benefit
 pest control in agricultural landscapes, but constraints as a result of
 crop type need to be addressed by annually targeted, spatially shifting
 AES schemes for different crops.
description: Abbreviations and units used in the dataset:
 Distance is measured in meteres from the field edge.
 SR = species richness (total) AD = Activity
 density (measured as specimens per day of recording)
 Predation rates vary between 0 and 1 with 0 being 0% predation, 1
 being 100% predation. Yield is measured in TKW
 (thousand kernel weight aka the weight of 1000 kernels in dt (1/10
 t)). Areas are measured in ha (1ha =
 10000m²). Semi-natural habitat (SNH) is measured in %
 of a 1 km radius around the study site.
DOI: 10.5061/dryad.59zw3r24h
title: Colony-age-dependent variation in cuticular hydrocarbon profiles in subterranean termite colonies

description: Cuticular hydrocarbons (CHCs) have, in insects, important physiological
 and ecological functions, such as protection against desiccation and as
 semiochemicals in eusocial taxa, including termites. CHCs are, in
 termites, known to vary qualitatively and/or quantitatively among species,
 populations, or seasons. Changes to hydrocarbon profile composition have
 been linked to varying degrees of aggression between termite colonies,
 although the variability of results among studies suggests that additional
 factors might have been involved. One source of variability may be colony
 age; however, this factor has never been investigated. We studied
 caste-specific patterns of CHC profiles in Coptotermes gestroi colonies of
 four different age classes (6, 18, 30, and 42 months). The CHC profiles
 were variable among castes in the youngest colonies, but progressively
 converged with increasing colony age. Young colonies had a less-defined
 CHC identity compared to older ones, which likely obscures the colony’s
 ability to detect non-nestmates. Our data suggest that there is no
 selective pressure on an early-defined colony CHC profile, potentially
 allowing incipient colonies to merge non-agonistically with competing
 conspecifics as an indirect result. 
description: 4 age classes of termite colonies were samples for
 Brood (eggs/larvae), Workers, Kings, and Queens 
 Compounds were eluted in hexane.  
 GC-MS outputs identified using retention time, CHC
 standards, NIST mass spectral library, and known <em>C.
 gestroi</em> profile (Chouvenc et al. 2017) 
 Poor matches were discarded from outputs
 Area under the peak integrated for total
 raw abundance for each compound 
 Cumulative overall abundance for the 13 CHC compounds of interest
 was used to determine the relative abundance of each CHC for all
 samples
DOI: 10.5061/dryad.wstqjq2hk
title: Data from: Omnivorous ants are less carnivorous and more protein-limited in exotic plantations

description: 1. Diets of species are crucial in determining how they influence food
 webs and community structures, and how their populations are regulated by
 different bottom-up processes. Omnivores are able to adjust their diet
 flexibly according to environmental conditions, such that their impacts on
 food webs and communities, and the macronutrients constraining their
 population, can be plastic. In particular, omnivore diets are known to be
 influenced by prey availability, which exhibit high spatial and temporal
 variation. 2. To examine the plasticity of diet and macronutrient
 limitation in omnivores, we compared trophic positions, macronutrient
 preferences and food exploitation rates of omnivorous ants in
 invertebrate-rich (secondary forests) and invertebrate-poor (Lophostemon
 confertus plantations) habitats. We hypothesized that omnivorous ants
 would have lower trophic positions, enhanced protein-limitation and
 reduced food exploitation rates in L. confertus plantations relative to
 secondary forests. 3. We performed cafeteria experiments to examine
 changes in macronutrient limitation and food exploitation rates. We also
 sampled ants and conducted stable isotope analyses to investigate dietary
 shifts between these habitats. 4. We found that conspecific ants were less
 carnivorous and had higher preferences for protein-rich food in L.
 confertus plantations compared to secondary forests. However, ant
 assemblages did not exhibit increased preferences for protein-rich food in
 L. confertus plantations. At the species-level, food exploitation rates
 varied idiosyncratically between habitats. At the assemblage-level, food
 exploitation rates were significantly reduced in L. confertus plantations.
 5. Our results reveal that plantation establishments alter the diet and
 foraging behavior of omnivorous ants. Such changes suggest that omnivorous
 ants in plantations will have reduced top-down impacts on prey communities
 but also see an increased importance of protein as a bottom-up force in
 constraining omnivore population sizes.
description: The data were collected via cafeteria experiments and stable
 isotope analyses.
description: Please find the readme.txt file for details.
DOI: 10.5061/dryad.0k6djh9x2
title: Data from: Can ancestry and morphology be used as surrogates for species niche relationships?

description: Species interactions are difficult to quantify, and, consequently, many
 studies have used species traits and phylogeny as proxies under an
 assumption of niche conservatism (i.e., closely related and
 morphologically similar species should have similar niches). However, few
 studies have investigated whether niches actually are conserved within and
 across diverse communities. Here, we tested the degree to which
 phylogenetic relatedness and morphological similarity predict diets and
 stable isotopic ratios (δ15N and δ13C), two common descriptors of the
 trophic niche, in fish assemblages of two small streams in the Neotropics.
 We also tested the strength of the association between isotopic ratios and
 diet composition and found significant correlations implying that isotopic
 signals reveal trophic structure despite error associated with estimates
 of trophic enrichment and variation associated with tissue preservation,
 metabolism, and other factors affecting isotopic ratios. Morphological
 traits yielded a significant phylogenetic signal, and both morphological
 traits and phylogeny were correlated with diet composition, with
 morphological traits being a stronger predictor. We infer that
 functionally relevant morphological traits of fish can be used to infer
 trophic niches for certain kinds of questions and analyses when trophic
 data are lacking. However, we highlight that using phylogenetic and
 morphological data in combination with dietary and/or isotopic data can
 improve resolution of assemblage trophic structure and niche
 diversification.
DOI: 10.5061/dryad.4f4qrfj8g
title: The implications of interrelated assumptions on estimates of divergence times and rates of diversification

description: Phylogenies are increasingly being used as a basis to provide insight into
 macroevolutionary history. Here, we use simulation experiments and
 empirical analyses to evaluate methods that use phylogenies as a basis to
 make estimates of divergence times and rates of diversification. This is
 the first study to present a comprehensive assessment of the key variables
 that underpin analyses in this field – including substitution rates,
 speciation rates, and extinction, plus character sampling and taxon
 sampling. We show that in unrealistically simplistic cases (where
 substitution rates and speciation rates are constant, and where there is
 no extinction), increased character and taxon sampling lead to more
 accurate and precise parameter estimates. By contrast, in more complex but
 realistic cases (where substitution rates, speciation rates, and
 extinction rates vary), gains in accuracy and precision from increased
 character and taxon sampling are far more limited. The lack of accuracy
 and precision even occurs when using methods that are designed to account
 for more complex cases, such as relaxed clocks, fossil calibrations, and
 models that allow speciation rates and extinction rates to vary. The
 problem also persists when analysing genomic scale datasets. These results
 suggest two interrelated problems that occur when the processes that
 generated the data are more complex. First, methodological assumptions are
 more likely to be violated. Second, limitations in the information content
 of the data become more important.
DOI: 10.5061/dryad.xsj3tx9bs
title: Data from: Neurologic manifestations in an infant with COVID-19

description: Currently, there are over 1.9 million confirmed cases of Coronavirus
 disease 2019 (COVID-19) globally with over 590,000 cases in the United
 States.1 The number of COVID-19 positive children in the United
 States is unknown. A report summarizing 72,314 COVID-19 cases from the
 Chinese Center for Disease Control and Prevention noted 416 COVID-19
 positive children under 10.2 An observational study at Wuhan
 Children's Hospital noted 31 COVID-19 positive children under 1 year
 with the youngest confirmed case in a 1 day old.3 Cases were
 largely characterized by upper respiratory tract infection or pneumonia,
 fever, cough and pharyngeal erythema.3 Concomitant neurologic
 problems have been reported amongst COVID-19 positive adult patients.
description: Sequencing on the Illumina NextSeq 550 platform
 (Illumina, San Diego, CA, USA) resulted in 159,204,153 (150 bp) single end
 reads. The reads were adapter trimmed and filtered based on the average
 quality scores, presence of indeterminate nucleotides and homopolymeric
 regions. Host background levels were determined by mapping filtered reads
 against human reference database using Bowtie2 mapper (v 2.2.9 (1)). The
 host-subtracted reads were de-novo assembled using MIRA (4.0 (2))
 assembler. Contigs and unique singletons aligned against GenBank
 nucleotide database using Megablast tool from NCBI. Sequences with poor or
 no homology from Megablast were screened with BLASTX against the viral
 GenBank protein database. The filtered reads were mapped to the
 coronavirus and rhinovirus strains identified from blast.
 1) Langmead B, Salzberg S. Fast gapped-read alignment
 with Bowtie 2. Nature Methods. 2012, 9:357-359. 2)
 Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace
 signals and additional sequence information. Comput Sci Biol
 99:45–56
description: We are providing Zipped FASTq file for each of the following
 sample after human host-substraction and quality check.
   
 Original ID CII ID Species Sample Type Barcode IPS-553 COVID-AS Human Anal swab G5 IPS-554 COVID-BS Human nasopharyngeal swab G7 IPS-555 COVID-CSF Human CSF G9 IPS-556 COVID-SERUM Human Serum G11 IPS-557 COVID-PLASMA Human Plasma H1
DOI: 10.5281/zenodo.18395274
title: A CORPUS-BASED ERROR ANALYSIS OF WRITTEN ESSAYS BY UZBEK ENGLISH LEARNERS

description: This study reports a corpus-based error analysis (EA) of 25 short written essays produced by Uzbek learners of English as a foreign language (EFL) under a CEFR-aligned Task 1 prompt (functional writing). Following the EA procedure described in Kutlimuratova’s (2021) corpus-based methodology, all identifiable errors were classified and quantified using a synthesized 13-tag scheme adapted from Divsar and Heydari’s (2017) IELTS learner-corpus coding model. The scheme is theoretically grounded in (i) Chuang and Nesi’s (2006) hierarchical error coding, (ii) Dagneaux et al.’s (1998) computer-aided error analysis approach, and (iii) Hou’s (2016) ten-category system for learner writing. Descriptive statistics show 211 errors in total (M = 8.44 errors per essay, range = 1–16). Verb-related errors (V) were the most frequent (n = 40, 19.0%), followed by article errors (A) and sentence structure errors (SS) (n = 23 each, 10.9%). Spelling (S) and deletion (D) errors were also prominent (n = 19 each, 9.0%), and confusing/unclear statements (CU) accounted for 18 instances (8.5%). Findings are discussed in relation to Uzbek learners’ developing interlanguage and the genre demands of short functional writing, and pedagogical implications are proposed for form-focused instruction, corpus-informed materials, and targeted feedback.
DOI: 10.5281/zenodo.18395275
title: A CORPUS-BASED ERROR ANALYSIS OF WRITTEN ESSAYS BY UZBEK ENGLISH LEARNERS

description: This study reports a corpus-based error analysis (EA) of 25 short written essays produced by Uzbek learners of English as a foreign language (EFL) under a CEFR-aligned Task 1 prompt (functional writing). Following the EA procedure described in Kutlimuratova’s (2021) corpus-based methodology, all identifiable errors were classified and quantified using a synthesized 13-tag scheme adapted from Divsar and Heydari’s (2017) IELTS learner-corpus coding model. The scheme is theoretically grounded in (i) Chuang and Nesi’s (2006) hierarchical error coding, (ii) Dagneaux et al.’s (1998) computer-aided error analysis approach, and (iii) Hou’s (2016) ten-category system for learner writing. Descriptive statistics show 211 errors in total (M = 8.44 errors per essay, range = 1–16). Verb-related errors (V) were the most frequent (n = 40, 19.0%), followed by article errors (A) and sentence structure errors (SS) (n = 23 each, 10.9%). Spelling (S) and deletion (D) errors were also prominent (n = 19 each, 9.0%), and confusing/unclear statements (CU) accounted for 18 instances (8.5%). Findings are discussed in relation to Uzbek learners’ developing interlanguage and the genre demands of short functional writing, and pedagogical implications are proposed for form-focused instruction, corpus-informed materials, and targeted feedback.
DOI: 10.5061/dryad.h44j0zpgp
title: Software code for simulations and analyses concerning the calculation of canopy stomatal conductance at eddy covariance sites

description: These software codes compare different methods of calculating canopy
 stomatal conductance based on eddy covariance measurements of the latent
 heat flux. The R code "CanopyGsErrorSim.R" simulates
 true and measured canopy stomatal conductance and assesses errors when
 using the various methods. The Igor Pro code
 "AmeriFluxHo1gsCalc.ipf" calculates canopy stomatal conductance
 by the various methods based on real data from the Howland Forest
 as reported in the Ameriflux eddy covariance site data archive
 (Hollinger, D.: AmeriFlux US-Ho1 Howland Forest (main tower),
 doi:10.17190/AMF/1246061, 1996-.).
DOI: 10.25349/d91s49
title: Quantifying climate change impacts to City of Santa Barbara water supplies

description: Climate change affects water supply through changes in precipitation,
 temperature, and evapotranspiration. The City of Santa Barbara’s water
 supply relies largely on water held in Lake Cachuma and Gibraltar
 Reservoir, located in the upper Santa Ynez River watershed. Quantifying
 climate change impacts to this watershed is critical to planning for
 future water supply. This project modeled the potential impacts of climate
 change on the Santa Ynez River watershed out to 2058 using the Soil and
 Water Assessment Tool. The model was calibrated using meteorological and
 streamflow data for the upper Santa Ynez River watershed. Future
 streamflow was then simulated for the high-emissions scenario (RCP 8.5)
 using five global climate models which produce a range of possible futures
 for California. The simulated streamflow was evaluated to estimate a range
 of future upper Santa Ynez River watershed inflows to Lake Cachuma under
 the different climate simulations. The results of the drought model
 simulation indicate: (1) a projected decrease of approximately 40% in
 average streamflow and (2) a decrease in the contribution of the upper
 Santa Ynez River watershed to Lake Cachuma by as much as a factor of 2
 compared to the historical baseline. Compared to the historical baseline,
 the other four climate conditions that were simulated produced changes in
 average streamflow, from -20% to +20%, and upper Santa Ynez River
 watershed contributions to Lake Cachuma, from 0% to +20%. The results from
 the simulations will inform the City of Santa Barbara’s water supply
 planning out to 2050.
description: This dataset was produced by collecting data from public
 agencies, including the City of Santa Barbara, County of Santa Barbara,
 California Department of Forestry and Fire, Cal-Adapt, National Oceanic
 and Atmospheric Administration, and United States Geological Survey. In
 addition, a Soil and Water Assessment Tool (SWAT) model was created and
 run using Cal-Adapt climate model temperature and projection data to
 obtain streamflow projections for the upper Santa Ynez River watershed for
 the years leading up to 2058. The outputs of this model are also included
 in this dataset. The raw, unmanipulated files are denoted with a prefix of
 “RAW_”. The data was processed and examined using R.  
description: There is a metadata spreadsheet that lists each data file by
 name, the source of the file, and explains the contents of the
 file.
DOI: 10.15468/dl.7q8ayq
title: Occurrence Download

description: A dataset containing 133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Scleromystax macropterus"
 ]
}

 The dataset includes 133 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002359-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.