cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v15dv41sg
title: Data From: An artificial habitat increases the reproductive fitness of a range-shifting species within a newly colonized ecosystem

description: When a range-shifting species colonizes an ecosystem it has not previously
 inhabited, it may experience suboptimal conditions that challenge its
 continued persistence and expansion. Some impacts may be partially
 mitigated by artificial habitat analogues: artificial habitats that more
 closely resemble a species’ historic ecosystem than the surrounding
 habitat. If conditions provided by such habitats increase reproductive
 success, they could be vital to the expansion and persistence of
 range-shifting species. We investigated the reproduction of the mangrove
 tree crab Aratus pisonii in its historic mangrove habitat, the suboptimal
 colonized salt marsh ecosystem, and on docks within the marsh, an
 artificial mangrove analogue. Crabs were assessed for offspring production
 and quality, as well as measures of maternal investment and egg quality.
 Aratus pisonii found on docks produced more eggs, more eggs per unit
 energy investment, and higher quality larvae than conspecifics in the
 surrounding salt marsh. Yet, crabs in the mangrove produced the highest
 quality larvae. Egg lipids suggest these different reproductive outcomes
 result from disparities in the quality of diet-driven maternal
 investments, particularly key fatty acids. This study suggests habitat
 analogues may increase the reproductive fitness of range-shifting species
 allowing more rapid expansion into, and better persistence in, colonized
 ecosystems.
description: <strong>Clutch Size Data: </strong>Clutch sizes
 of <em>Aratus pisonii</em> collected from mangrove, salt
 marsh, and dock habitats. <strong>Egg Enery
 Data:</strong> Energy content
 of <em>Aratus pisoni</em><em>i </em> eggs
 collected from mangrove, salt marsh, and dock habitats.
 <strong>Egg Fatty Acids Data:</strong> Concentrations
 of fatty acids extracted from <em>Aratus pisonii </em>eggs
 collected from mangrove, salt marsh, and dock habitats.
 <strong>Egg Glycogen and Gross Lipid Concentration
 Data:</strong> Concentrations of glycogen and gross lipids extracted
 from <em>Aratus pisonii</em> eggs collected from mangrove,
 salt marsh, and dock habitats.
 <strong>Gonadosomatic Index Data:</strong> Relative
 energetic investment into reproduction, as gonadosomatic index, of
 <i>Aratus pisonii </i>collected from mangrove, salt marsh, and
 dock habitats. <strong>Larval Size
 Data:</strong> Larval size, as dry mass at hatching, of
 larval <em>Aratus pisonii</em> hatched from eggs collected in
 mangrove, salt marsh, and dock habitats. Dataset includes morphological
 data of maternal crabs from whcih eggs were collected.
 <strong>Larval Survival Data: </strong>Larval
 survival, as starvation resistance, of larval <em>Aratus
 pisonii</em> hatched from eggs collected in mangrove, salt marsh,
 and dock habitats. Dataset includes morphological data of maternal crabs
 from whcih eggs were collected.
DOI: 10.6075/j01n823h
title: Maui 2015-02 (Expedition) - Maui (Island) - Raw Images. In Long-term Coral Reef Monitoring Across Leeward Maui

description: In February of 2015 the Smith Lab visited Maui to collect large-area imagery as part of the Maui 2015-02 expedition. The imagery collected here are resurveys of permanent sites established during the Maui 2014-07 expedition as part of the Smith Lab Maui large-area imagery timeseries. For each site, a preview image and the raw digital images used to create composite large-area image products of the underwater sites have been made available. A general description of the methods used to acquire the images can be found in a README.txt file for each site. Site specific metadata can be found within a METADATA.txt file for each site.
DOI: 10.15468/dl.pdd3ur
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus calidus",
 "Year 1900-2026"
 ]
}

 The dataset includes 215 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002141-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tmpg4f4vb
title: Effects of capsular tension ring on surgical outcomes of premium intraocular lens in patients with suspected zonular weakness

description: Purpose: To assess the influence of capsular tension ring (CTR) on
 surgical outcomes of toric and multifocal intraocular lenses (IOLs) in
 eyes at high risk of zonular instability. Methods: Fifty-five eyes of 43
 patients who had undergone phacoemulsification and IOL implantation were
 included in the analysis. They had some risk of zonular weakness, such as
 pseudoexfoliation, shallow anterior chamber, high myopia, and
 phacodonesis, or were judged to have unstable zonules during surgery.
 Toric IOL was implanted in 9 eyes with CTR and 22 eyes without CTR, while
 multifocal IOL was used in 9 eyes with CTR and 15 eyes without CTR.
 Manifest refraction, refractive astigmatism, visual acuity, and degree of
 IOL decentration and tilt measured using swept-source anterior segment
 optical coherence tomography were analyzed. Axis misalignment of toric
 IOLs were also evaluated. Results: In toric IOLs, co-implantation of CTR
 significantly reduced decentration and axis misalignment of IOL, resulting
 in better uncorrected and corrected visual acuity after surgery. In
 multifocal IOLs, combined use of CTR significantly prevented IOL tilt,
 leading to better intermediate visual acuity. Spherical equivalent and
 residual astigmatism were not significantly affected by the use of CTR.
 Conclusions: CTR reduces decentration and axis misalignment of toric IOL
 and tilt of multifocal IOL, achieving improvement of postoperative visual
 function in eyes with suspected zonular instability.
DOI: 10.6075/j0s46sxv
title: Maui 2024-07 (Expedition) - Maui (Island) - Raw Images. In Long-term Coral Reef Monitoring Across Leeward Maui

description: In July of 2024 the Smith Lab visited Maui to collect large-area imagery as part of the Maui 2024-07 expedition. The imagery collected here are resurveys of permanent sites established during the Maui 2014-07 expedition as part of the Smith Lab Maui large-area imagery timeseries, and several new sites were added near Lahaina to document impacts from the 2023 West Maui wildfires. The team also collaborated with the Hawaii Division of Aquatic Resources to image several transects that have been maintained by the State since the early 2000s as part of the Hawaii Coral Reef Assessment and Monitoring Program (CRAMP). For each site, a preview image and the raw digital images used to create composite large-area image products of the underwater sites have been made available. A general description of the methods used to acquire the images can be found in a README.txt file for each site. Site specific metadata can be found within a METADATA.txt file for each site.
DOI: 10.15468/dl.jb8nzp
title: Occurrence Download

description: A dataset containing 323725 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Aedes aegypti, Culex quinquefasciatus, Culex tarsalis, Culex pipiens, Anopheles quadrimaculatus, Anopheles freeborni)",
 "Year 1981-2017"
 ]
}

 The dataset includes 323725 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002059-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kwh70rz0g
title: Diagnosis of prion diseases by RT-QuIC results in improved surveillance

description: Objective:  We present the National Prion Disease Pathology
 Surveillance Center’s (NPDPSC) experience using cerebrospinal fluid (CSF)
 real time quaking induced conversion (RT-QuIC) as a diagnostic test,
 examine factors associated with false negative RT-QuIC results, and
 investigate RT-QuIC’s impact on prion disease surveillance. 
   Methods:  Between May 2015-April 2018, the NPDPSC
 received 10,498 CSF specimens that were included in the
 study.   Sensitivity and specificity analyses were
 performed using 567 autopsy verified cases.  Prion
 disease type, demographic characteristics, specimen color, and time
 variables were examined for association with RT-QuIC results. 
 The effect of including positive RT-QuIC cases in prion disease
 surveillance was examined.   Results: The diagnostic
 sensitivity and specificity of RT-QuIC across all prion diseases was 90.3%
 and 98.5%, respectively.  Diagnostic sensitivity was
 lower for fatal familial insomnia, Gerstmann-Sträussler-Scheinker disease,
 sporadic fatal insomnia, variably protease sensitive prionopathy, and the
 VV1 and MM2 subtypes of sCJD.  Individuals with prion
 disease and negative RT-QuIC results were younger, had elevated tau
 levels, and non-elevated 14-3-3 levels compared to RT-QuIC positive cases.
 Sensitivity was high throughout the disease course.  Some cases
 that initially tested RT-QuIC negative had a subsequent specimen test
 positive.  Including positive RT-QuIC cases in
 surveillance statistics increased laboratory-based case ascertainment of
 prion disease by 90% over autopsy alone.   
 Conclusions: RT-QuIC has high sensitivity and specificity for
 diagnosing prion diseases.  Sensitivity limitations are
 associated with prion disease type, age, and related CSF diagnostic
 results. RT-QuIC greatly improves laboratory-based prion disease
 ascertainment for surveillance purposes.    
 Classification of Evidence:  This study provides Class III
 evidence that 2nd generation real time quaking-induced conversion
 (RT-QuIC) identifies prion disease with sensitivity of 90.3% and
 specificity of 98.5%, among patients being screened for these diseases due
 to concerning symptoms. 
description: Using STARD guidelines
DOI: 10.5061/dryad.f4qrfj6sd
title: Wavelet filters for automated recognition of birdsong in long-time field recordings

description: 1. Ecoacoustics has the potential to provide a large amount of information
 about the abundance of many animal species at a relatively low cost.
 Acoustic recording units are widely used in field data collection, but the
 facilities to reliably process the data recorded -- recognising calls that
 are relatively infrequent, and often significantly degraded by noise and
 distance to the microphone -- are not well developed yet. 2. We propose a
 call detection method for continuous field recordings that can be trained
 quickly and easily on new species, and degrades gracefully with increased
 noise or distance from the microphone. The method is based on the
 reconstruction of the sound from a subset of the wavelet nodes (elements
 in the wavelet packet decomposition tree). It is intended as a
 preprocessing filter, therefore we aim to minimise false negatives: false
 positives can be removed in subsequent processing, but missed calls will
 not be looked at again. 3. We compare our method to standard call
 detection methods, and also to machine learning methods (using as input
 features either wavelet energies or Mel-Frequency Cepstral Coefficients
 (MFCC)) on real-world noisy field recordings of six bird species. The
 results show that our method has higher recall (proportion detected) than
 the alternative methods: 87% with 85% specificity on &gt;53 hrs of
 test data, resulting in an 80% reduction in the amount of data that needed
 further verification. It detected &gt;60% of calls that were extremely
 faint (far away), even with high background noise. 4. This preprocessing
 method is available in our AviaNZ bioacoustic analysis program and enables
 the user to significantly reduce the amount of subsequent processing
 required (whether manual or automatic) to analyse continuous field
 recordings collected by spatially and temporally large-scale monitoring of
 animal species. It can be trained to recognise new species without
 difficulty, and if several species are sought simultaneously, filters can
 be run in parallel.
description: These are the annotated acoustic datasets of five species used in
 the paper: brown kiwi (Apteryx mantelli), morepork (Ninox
 novaeseelandiae), kakapo (Strigops habroptilus), fantail (Rhipidura
 fuliginosa), and saddleback (Philesturnus rufusater). Each dataset
 includes the sound (.wav) and annotation files (.data; AviaNZ format). The
 recordings were mainly collected using omnidirectional acoustic
 recorders from the New Zealand Department of Conservation (DOC) while some
 recordings were made using SM2 recorders. The data was collected from
 variety of locations accorss New Zealand.
DOI: 10.5061/dryad.fqz612jpk
title: Long-term deepened snow cover alters litter layer turnover rate in temperate steppes

description: 1. The turnover of litter layer is a biogeochemical process fundamental to
 carbon and nutrient cycling, influencing seed germination, species
 coexisting, and carbon storage. Winter snow depth is undergoing increasing
 trend in Northern China, which has been shown to alter litter
 decomposition rate of individual species. However, it remains unknown how
 changes in snow depth affect the turnover rate of the whole litter layer,
 and whether the responses vary between different steppes. Most current
 litter decomposition studies are site-based or short-term treated,
 limiting the exploration of the long-term response of litter layer
 turnover in regional pattern. 2. In this study, we selected six long-term
 (11-13 years) snow fence sites in Inner Mongolia, with three in the dry
 steppe and another three in the wet steppe, and investigated the responses
 of community-weighted litter residence time (LRT) to long-term increased
 snow treatment. 3. We found that LRT increased by 0.02 year for every 10
 cm increase in snow depth in the wet steppe, but was not affected in the
 dry steppe. The lack of effect of deepened snow on LRT in the dry steppe
 was attributed to the offset between the positive effect of the increased
 plant community-weighted height possibly via inhibiting photodegradation
 and the enhanced litter recalcitrance by producing higher proportion of
 stem litter, and the negative effect of the increased soil moisture via
 accelerating microbial decomposition. The significantly positive effect of
 the increased snow depth on LRT in the wet steppe was mainly due to the
 positive effect of the increased grass biomass via decreasing litter
 quality. 4. Overall, our findings indicated that deepened snow changed
 plant community, which altered environmental conditions and enhanced
 litter recalcitrance, thereby increasing LRT in temperate steppes.
 However, this effect was diminished by enhancing microbial decomposition
 in the dry but not wet steppe, resulting in different overall responses of
 LRT to deep-snow in the two steppes. The slow litter turnover rate in the
 wet steppe might result in greater litter accumulation under future
 increased snow depth, which could be unfavorable for seed germination and
 alter plant diversity.
DOI: 10.5061/dryad.qz612jm9p
title: What’s in a band? The function of the colour and banding pattern of the Banded Swallowtail

description: Butterflies have evolved a diversity of colour patterns, but the
 ecological functions for most of these patterns are still poorly
 understood. The Banded Swallowtail butterfly, Papilio demolion demolion,
 is a mostly black butterfly with a greenish-blue band that traverses the
 wings. The function of this wing pattern remains unknown. Here, we
 examined the morphology of black and green-blue coloured scales, and how
 the colour and banding pattern affects predation risk in the wild. The
 protective benefits of the transversal band and of its green-blue colour
 were tested via the use of paper model replicas of the Banded Swallowtail
 with variations in band shape and band colour in a full factorial design.
 A variant model where the continuous transversal green-blue band was
 shifted and made discontinuous tested the protective benefit of the
 transversal band, while greyscale variants of the wildtype and distorted
 band models assessed the protective benefit of the green-blue colour.
 Paper models of the variants and the wildtype were placed simultaneously
 in the field with live baits. Wildtype models were the least preyed upon
 compared to all other variants, while grey models with distorted bands
 suffered the greatest predation. The colour and the continuous band of the
 Banded Swallowtail hence confer antipredator qualities. We propose that
 the shape of the band hinders detection of the butterfly’s true shape
 through coincident disruptive coloration; while the green colour of the
 band prevents detection of the butterfly from its background via
 differential blending.  Differential blending is aided by the
 green-blue colour being due to pigments rather than via structural
 colouration. Both green and black scales have identical structures, and
 the scales follow the Bauplan of pigmented scales documented in
 other Papilio butterflies.
DOI: 10.5061/dryad.v15dv41sh
title: Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases

description: Glycosyltransferases (GTs) are prevalent across the tree of life and
 regulate nearly all aspects of cellular functions. The evolutionary basis
 for their complex and diverse modes of catalytic functions remain
 enigmatic. Here, based on deep mining of over half million GT-A fold
 sequences, we define a minimal core component shared among functionally
 diverse enzymes. We find that variations in the common core and emergence
 of hypervariable loops extending from the core contributed to GT-A
 diversity. We provide a phylogenetic framework relating diverse GT-A fold
 families for the first time and show that inverting and retaining
 mechanisms emerged multiple times independently during evolution. Using
 evolutionary information encoded in primary sequences, we trained a
 machine learning classifier to predict donor specificity with nearly 90%
 accuracy and deployed it for the annotation of understudied GTs. Our
 studies provide an evolutionary framework for investigating complex
 relationships connecting GT-A fold sequence, structure, function and
 regulation.
description: The GT-A sequences were collected by a similarity search strategy
 using multiply aligned manually curated GT-A fold profiles. The sequences
 were further aligned to the profiles to determine the GT-A domain bounds
 and insertions.
description: This dataset includes all putative GT-A fold sequences that
 belong to one of the 53 GT-A fold families. These were collected by
 searching the NCBI nr and the UniProt proteomes databases. The file
 hierarchy.tsv contains a table that lists the hierarchy of the families.
 For each level and family, there will be a corresponding _nr.fasta,
 _nr.tsv, _uniprot,fasta and _uniprot.tsv files that contain the sequences
 from the NCBInr and the Uniprot proteomes database in fasta and tsv
 formats respectively.
DOI: 10.5061/dryad.xksn02vbq
title: Calibration of probability predictions from machine-learning and statistical models

description: This data set describes the occurrence (yes/no) of a bird, the Southern
 Whiteface (Aphelocephala leucopsis) in Australia. A suite of environmental
 variables is provided, which are used in the paper to illustrate a
 statistical problem. The data are meant to allow reproduction of the
 analysis in this paper. They are not intended for actual ecological
 analysis. The data come as .Rdata-file, i.e. as an R-dataset (described
 technically here:
 https://www.loc.gov/preservation/digital/formats/fdd/fdd000470.shtml).
 Here is the paper's abstract: Aim: Predictions from statistical
 models may be uncalibrated, meaning that the predicted values do not have
 the nominal coverage probability. This is easiest seen with probability
 predictions in machine-learning classification, including the common
 species occurrence probabilities. Here, a predicted probability of, say,
 0.7 should indicate that out of 100 cases with these environmental
 conditions, and hence the same predicted probability, the species should
 be present in 70 and absent in 30. Innovation: A simple calibration plot
 shows that this is not necessarily the case, particularly not for
 over-fitted models or algorithms that use non-likelihood target functions.
 As a consequence, “raw” predictions from such model could easily be off by
 0.2, are unsuitable for averaging across model types, and resulting maps
 hence be substantially distorted. The solution, a flexible calibration
 regression, is simple and can be applied whenever deviations are observed.
 Conclusion: “Raw”, uncalibrated probability predictions should be
 calibrated before interpreting or averaging them in a probabilistic way.
description: The bird distribution data are from BirdLife International
 (http://datazone.birdlife.org/species/requestdis). The
 climate data are from WorldClim (https://www.worldclim.org/).
 The land cover data are from GLC 2000
 (https://forobs.jrc.ec.europa.eu/products/glc2000/glc2000.php).
 All data were reprojected to Lamberth Equal Area projection and
 gridded to 100 x 100 km.
description: This data set is a proof-of-principle data set, and its data are
 not fit meant for ecological analysis! Neither the
 climate nor the land cover data are selected to be the most sensible for
 this species. The species, Southern Whiteface, was a random decision and
 is not representative in any way. The purpose of this data set was to
 illustrate a statistical problem arising in a typical species distribution
 analysis. The sole purpose of providing this data set
 is to make the analysis reproducible.