cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.768dk4s
title: Data from: Site-specific structural order in Alzheimer’s Aβ42 fibrils

description: Deposition of amyloid fibrils is a pathological hallmark of Alzheimer’s
 disease. Aβ42 is the major protein whose aggregation leads to the
 formation of these fibrils. Understanding the detailed structure of Aβ42
 fibrils is of particular importance for delineating the mechanism of Aβ42
 aggregation and developing specific amyloid-targeting drugs. Here we use
 site-directed spin labeling and electron paramagnetic resonance
 spectroscopy to study the site-specific structural order at each and every
 residue position in Aβ42 fibrils. Strong interactions between spin labels
 indicate highly ordered protein backbone at the labeling site, while weak
 interactions suggest disordered local structure. Our results show that
 Aβ42 consists of 5 β-strands (residues 2-7, 10-13, 17-20, 31-36, 39-41), 3
 turns (residues 7-8, 14-16, 37-38), and 1 ordered loop (residues 21-30).
 Spin labels introduced at β-strand sites show strong spin-spin
 interactions, while spin labels at turn or loop sites show weak
 interactions. However, residues 24, 25, and 28 also show strong
 interactions between spin labels, suggesting that the loop 21-30 is partly
 ordered. In the context of recent structural work using solid-state NMR
 and cryoEM, the site-specific structural order revealed in this study
 provides a different perspective on backbone and side chain dynamics of
 Aβ42 fibrils.
description: All
 dataall_data.xls
DOI: 10.5281/zenodo.18389445
title: Data of control of photoassociation spectroscopy and dynamics beyond threshold law in an optical tweezer

description: Refer to the readme file
DOI: 10.5061/dryad.825kr16
title: Data from: Spatio-temporal and demographic variation in the diet of New Zealand lesser short-tailed bats (Mystacina tuberculata)

description: Variation in the diet of generalist insectivores can be affected by
 site-specific traits including weather, habitat, and season, as well as
 demographic traits like reproductive status and age. We used molecular
 methods to compare diets of three distinct New Zealand populations of
 lesser short-tailed bats, Mystacina tuberculata. Summer diets were
 compared between a southern cold-temperate (Eglinton) and a northern
 population (Puroera). Winter diets were compared between Pureora and a
 subtropical offshore island population (Hauturu). This also permitted
 seasonal diet comparisons within the Pureora population. Lepidoptera and
 Diptera accounted for &gt; 80% of amplicons identified from faecal
 matter at each site/season. The proportion of orders represented within
 prey and the Simpson diversity index, differed between sites and seasons
 within the Pureora population. For the Pureora population, the Simpson
 diversity index was higher in summer than winter and was higher in Pureora
 compared to Eglinton. Summer Eglinton samples revealed that juvenile diets
 appeared to be more diverse than other demographic groups. Lactating
 females had the lowest dietary diversity during summer in Pureora. In
 Hauturu, we found a significant negative relationship between mean ambient
 temperature and prey richness. Our data suggest that M. tuberculata
 incorporate a narrower diversity of terrestrial insects than previously
 reported. This provides novel insights into foraging behaviour and
 ecological interactions within different habitats. Our study is the first
 from the southern hemisphere to use molecular techniques to examine
 spatio-temporal variation in the diet of a generalist insectivore that
 inhabits a contiguous range with several habitat types and climates.
description: Files For
 AnalysisSample
 KeyReadMeFileA file which explains how to use the other files and data provided in this submission.
DOI: 10.5061/dryad.tt8n46q
title: Data from: Species divergence and maintenance of species cohesion of three closely related Primula species in the Qinghai-Tibet Plateau

description: Aim: Understanding the relative roles of geography and ecology in driving
 speciation, population divergence and maintenance of species cohesion is
 of great interest to molecular ecology. Closely related species that are
 parapatrically distributed in mountainous areas provide an ideal model to
 evaluate these key issues, especially when genomic data are analyzed
 within a spatially and ecologically explicit context. Here we used three
 closely related species of Primula that occur in the Himalayas, the
 Hengduan Mountains and Northeast Qinghai-Tibet Plateau (QTP) to examine
 spatial and ecological effects on interspecific divergence and maintenance
 of species cohesion. Location: Himalayas, the Hengduan Mountains and
 Northeast QTP Methods: We used genomic data for 770 samples of the three
 species using double-digest restriction site-associated DNA (ddRAD)
 sequencing and combined approximate Bayesian computation (ABC) modeling,
 generalized linear mixed modeling (GLMM) and niche-based species
 distribution modeling (SDM). Results: The three species are clearly
 delimited by the RADseq data. Further ABC modeling indicates that P.
 tibetica diverged first followed by a later divergence between P. nutans
 and P. fasciculata. The time frames of the divergences among the three
 species coincide with the uplifts of the Hengduan Mountains and the
 northern QTP during the late Miocene and Pliocene followed by a long
 period of founder events. SDMs indicate that the three species might have
 survived in different refugia during glaciations and came into secondary
 contact during the postglacial expansions but with no significant
 introgression. Finally, GLMM suggests that both the geographical and
 ecological factors play roles in population differentiation in P.
 fasciculata and P. tibetica, while for P. nutans, geography is the major
 driver of genomic variation. The different roles played by geographical
 and ecological factors in the three species may have affected the
 maintenance of species cohesion. Main conclusion: Our results provide
 insights of unprecedented details into the start and maintenance of
 interspecific divergence in the context of changing environments in
 mountains. Our findings highlight the significance of combining population
 genomics with environmental data when evaluating the effects of geography
 and ecology on interspecific divergence and maintenance of closely related
 species.
description: Final datasets used for
 outlier detection, population genetic analyses and ABC
 modelingD1-D3 were used for
 outlier detection; D4 was used for population genetic analyses; ten
 sub-datasets were used for ABC modeling.File1.zipInput data and scripts for GLMMInput data of the three species and scripts used for GLMM.File 2.zipSDM script for Primula fasciculata as an example.Scrip_JoB_2.R
DOI: 10.5061/dryad.89k5k30
title: Data from: Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

description: Premise of the Study: Targeted enrichment strategies for phylogenomic
 inference are a time‐ and cost‐efficient way to collect DNA sequence data
 for large numbers of individuals at multiple, independent loci. Automated
 and reproducible processing of these data is a crucial step for
 researchers conducting phylogenetic studies. Methods and Results: We
 present Fluidigm2PURC, an open source Python utility for processing
 paired‐end Illumina data from double‐barcoded PCR amplicons. In
 combination with the program PURC (Pipeline for Untangling Reticulate
 Complexes), our scripts process raw FASTQ files for analysis with PURC and
 use its output to infer haplotypes for diploids, polyploids, and samples
 with unknown ploidy. We demonstrate the use of the pipeline with an
 example data set from the genus Thalictrum (Ranunculaceae). Conclusions:
 Fluidigm2PURC is freely available for Unix‐like operating systems on
 GitHub (https://github.com/pblischak/fluidigm2purc) and for all operating
 systems through Docker (https://hub.docker.com/r/pblischak/fluidigm2purc).
description: Thalictrum
 DataPaired-end, Illumina
 MiSeq reads for 6 species of Thalictrum sequenced at two portions of the
 gene PISTILLATA (PIS_3 and PIS_4). The files present are
 Thalictrum_R1.fastq.gz and Thalictrum_R2.fastq.gz for paired-end reads 1
 and 2. The code to analyze these data using dbcAmplicons and Fluidigm2PURC
 are in the supplemental materials.Thalictrum-data.zip
DOI: 10.5061/dryad.9dr6j0c
title: Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences

description: • Incompleteness of reference sequence databases and unresolved taxonomic
 relationships complicates taxonomic placement of fungal sequences. We
 developed PROTAX-fungi, a general tool for taxonomic placement of fungal
 ITS sequences, and implemented it into the PlutoF platform of the UNITE
 database for molecular identification of fungi. • PROTAX-fungi
 outperformed the SINTAX and RDB classifiers in terms of increased accuracy
 and decreased calibration error when applied to data on mock communities
 representing species groups with poor sequence database coverage. • With
 empirical data on root- and wood-associated fungi, PROTAX-fungi identified
 reliably (with at least 90% identification probability) the majority of
 sequences to the order level but only ca. one fifth of them to the species
 level, reflecting the current limited coverage of the databases. • When
 applied to examine the internal consistencies of the Index Fungorum and
 UNITE databases, PROTAX-fungi revealed inconsistencies in the taxonomy
 database as well as mislabelling and sequence quality problems in the
 reference database. The according improvements were implemented in both
 databases. • PROTAX-fungi provides a robust tool for performing
 statistically reliable identifications of fungi in spite of the
 incompleteness of extant reference sequence databases and unresolved
 taxonomic relationships.
description: Root-associated fungi
 from GreenlandFungal ITS2 sequence
 data of root-associated fungi from Greenland in fasta format. DNA
 extracted from different plant species roots collected along the
 altitudinal gradient of Aucella mountain in the Zackenberg
 valley.root-associated fungi from
 Greenland.fas
DOI: 10.5281/zenodo.18348738
title: INRIM_Brand1_1F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 1F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18348737
title: INRIM_Brand1_1F_3_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 1F SC sample 3 INRIM   - EDLC Single - Brand1

Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.k4b688s
title: Data from: Evaluating active learning methods for annotating semantic predications

description: Objectives: This study evaluated and compared a variety of active learning
 strategies, including a novel strategy we proposed, as applied to the task
 of filtering incorrect SemRep semantic predications. Materials and
 Methods: We evaluated three types of active learning strategies –
 uncertainty, representative, and combined– on two datasets of semantic
 predications from SemMedDB covering the domains of substance interactions
 and clinical medicine, respectively. We also designed a novel combined
 strategy with dynamic β without hand-tuned hyperparameters. Each strategy
 was assessed by the Area under the Learning Curve (ALC) and the number of
 training examples required to achieve a target Area Under the ROC curve
 (AUC). We also visualized and compared the query patterns of the query
 strategies. Results: Combined strategies outperformed all other methods in
 terms of ALC, outperforming the baseline by over 0.05 ALC for both
 datasets and reducing 58% annotation efforts in the best case. While
 representative strategies performed well, their performance was matched or
 outperformed by the combined methods. All the uncertainty sampling methods
 beat the baseline but they were the worst performing methods overall. Our
 proposed AL method with dynamic β shows promising ability to achieve
 near-optimal performance across two datasets. Discussion: Our visual
 analysis of query patterns indicates that strategies which efficiently
 obtain a representative subsample perform better on this task. Conclusion:
 Active learning is shown to be effective at reducing annotation costs for
 filtering incorrect semantic predications from SemRep. Our proposed AL
 method demonstrated promising performance.
description: Annotated Semantic
 Predications from SemMedDBThis data was collected
 from the Semantic MEDLINE Database (SemMedDb) ver 30, December 2016
 release. It contains sentences, subject/object entity information, and
 predicate information as output by SemRep. It also contains annotations
 indicating whether each semantic predication is indeed expressed in the
 sentence.annotated_predications.csv
DOI: 10.5061/dryad.mp26fb1
title: Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy

description: PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN SUBSEQUENT PUBLICATIONS.
 PLEASE SEE http://dx.doi.org/10.1016/j.jclinepi.2017.05.007 FOR MORE
 INFORMATION. Objectives The objective of this study was to determine
 whether disagreements among multiple data sources affect systematic
 reviews of randomized clinical trials (RCTs). Study Design and Setting
 Eligible RCTs examined gabapentin for neuropathic pain and quetiapine for
 bipolar depression, reported in public (e.g., journal articles) and
 nonpublic sources (clinical study reports [CSRs] and individual
 participant data [IPD]). Results We found 21 gabapentin RCTs (74 reports,
 6 IPD) and 7 quetiapine RCTs (50 reports, 1 IPD); most were reported in
 journal articles (18/21 [86%] and 6/7 [86%], respectively). When
 available, CSRs contained the most trial design and risk of bias
 information. CSRs and IPD contained the most results. For the outcome
 domains “pain intensity” (gabapentin) and “depression” (quetiapine), we
 found single trials with 68 and 98 different meta-analyzable results,
 respectively; by purposefully selecting one meta-analyzable result for
 each RCT, we could change the overall result for pain intensity from
 effective (standardized mean difference [SMD] = −0.45; 95% confidence
 interval [CI]: −0.63 to −0.27) to ineffective (SMD = −0.06; 95% CI: −0.24
 to 0.12). We could change the effect for depression from a medium effect
 (SMD = −0.55; 95% CI: −0.85 to −0.25) to a small effect (SMD = −0.26; 95%
 CI: −0.41 to −0.1). Conclusions Disagreements across data sources affect
 the effect size, statistical significance, and interpretation of trials
 and meta-analyses.
description: MUDS
 ArchiveData and code from the
 Integrating Multiple Data Sources (MUDS) for Meta-Analysis project.
 (https://wwwcf.nlm.nih.gov/hsr_project/view_hsrproj_record.cfm?NLMUNIQUE_ID=20143578)
DOI: 10.5061/dryad.46g67n8
title: Data from: Robust estimates of a high Ne/N ratio in a top marine predator, southern bluefin tuna

description: Genetic studies of several marine species with high fecundity have
 produced “tiny” estimates (≤10−3) of the ratio of effective population
 size (Ne) to adult census size (N), suggesting that even very large
 populations might be at genetic risk. A recent study using close-kin
 mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for
 southern bluefin tuna (SBT), a highly fecund top predator that supports a
 lucrative (~$1 billion/year) fishery. We used the same genetic and life
 history data (almost 13,000 fish collected over 5 years) to generate
 genetic and demographic estimates of Ne per generation and Nb (effective
 number of breeders) per year and the Ne/N ratio. Demographic estimates,
 which accounted for age-specific vital rates, skip breeding, variation in
 fecundity at age, and persistent individual differences in reproductive
 success, suggest that Ne/N is &gt;0.1 and perhaps about 0.5. The
 genetic estimates supported this conclusion. Simulations using true Ne = 5
 × 105 (Ne/N = 0.25) produced results statistically consistent with the
 empirical genetic estimates, whereas simulations using Ne = 2 × 104 (Ne/N
 = 0.01) did not. Our results show that robust estimates of Ne and Ne/N can
 be obtained for large populations, provided sufficiently large numbers of
 individuals and genetic markers are used and temporal replication (here, 5
 years of adult and juvenile samples) is sufficient to provide a
 distribution of estimates. The high estimated Ne/N ratio in SBT is
 encouraging and suggests that the species will not be compromised by a
 lack of genetic diversity in responding to environmental change and
 harvest.
description: SBTadultsadult genotypes, genepop formatSBTjuvenilesgenotypes for juveniles, genepop format
DOI: 10.5061/dryad.8t0m6v7
title: Data from: Living on the edge: multiscale habitat selection by cheetahs in a human-wildlife landscape

description: Animals select habitats that will ultimately optimise their fitness
 through access to favourable resources, such as food, mates, and breeding
 sites. However, access to these resources may be limited by bottom-up
 effects, such as availability, and top-down effects such as risk avoidance
 and competition, including that with humans. Competition between wildlife
 and people over resources, specifically over space, has played a
 significant role in the worldwide decrease of large carnivores. The goal
 of this study was to determine the habitat selection of cheetahs (Acinonyx
 jubatus) in a human-wildlife landscape at multiple spatial scales.
 Cheetahs are a wide-ranging, large carnivore, whose significant decline is
 largely attributed to habitat loss and fragmentation. It is believed that
 77% of the global cheetah population ranges outside protected areas, yet
 little is known about cheetahs’ resource use in areas where they co-occur
 with people. The selection, or avoidance, of three anthropogenic variables
 (human footprint density, distance to main roads and wildlife areas) and
 five environmental variables (open habitat, semi-closed habitat, edge
 density, patch density and slope), at multiple spatial scales, was
 determined by analysing collar data from six cheetahs. Cheetahs selected
 variables at different scales; anthropogenic variables were selected at
 broader scales (720m - 1440m) than environmental variables (90m-180m),
 suggesting that anthropogenic pressures affect habitat selection at a
 home-range level, whilst environmental variables influence site-level
 habitat selection. Cheetah presence was best explained by human presence,
 wildlife areas, semi-closed habitat, edge density and slope. Cheetahs
 showed avoidance for humans and steep slopes and selected for wildlife
 areas and areas with high proportions of semi-closed habitat and edge
 density. Understanding a species’ resource requirements, and how these
 might be affected by humans, is crucial for conservation. Using a
 multiscale approach, we provide new insights into the habitat selection of
 a large carnivore living in a human-wildlife landscape.
description: Cheetah_habitat_data
DOI: 10.5061/dryad.1817
title: Data from: Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropod Orchesella cincta

description: Field-selected tolerance to heavy metals has been reported for Orchesella
 cincta (Arthropoda: Collembola) populations occurring at
 metal-contaminated mining sites. This tolerance is correlated with
 heritable increase of metal excretion efficiency; less pronounced cadmium
 (Cd) induced growth reduction and, over-expression of the metallothionein
 gene. We applied transcriptomics to determine differential gene expression
 caused by this abiotic stress in reference and Cd tolerant populations.
 Many cDNAs responded to Cd exposure in the reference population.
 Significantly fewer clones were Cd responsive in tolerant animals.
 Analysis of variance revealed transcripts that interact between Cd
 exposure and population. Hierarchical cluster analysis of these clones
 identified two major groups. The first one contained cDNAs that were up
 regulated by Cd in the reference culture, but non-responsive or down
 regulated in tolerant animals. This cluster was also characterized by
 elevated constitutive expression in the tolerant population. Gene ontology
 analysis revealed that these cDNAs were involved in structural integrity
 of the cuticle, anti-microbial defense, calcium-channel blocking, sulfur
 assimilation and chromatin remodeling. The second group consisted of cDNAs
 down regulated in reference animals but not responding or slightly up
 regulated in tolerant animals. Their functions involved carbohydrate
 metabolic processes, Ca2+ dependent stress signaling, redox state,
 proteolysis and digestion. The reference population showed a strong
 signature of stress-induced genome-wide perturbation of gene expression,
 whereas the tolerant animals maintained normal gene expression upon Cd
 exposure. We confirmed the micro-evolutionary processes occurring in soil
 arthropod populations and suggest a major contribution of gene regulation
 to the evolution of a stress-adapted phenotype.
description: MaanovainputCadOC.txtInput file for biostatistical analysis of the microarray data using R package Maanova. ID: DNA sequence identifier for each probe on the array. DNA sequences can be retrieved from www.collembase.org.
DOI: 10.5061/dryad.9387k41
title: Data from: Ecological stasis in Spinicaudata (Crustacea, Branchiopoda)? Early Cretaceous clam shrimp of the Yixian Formation of north‐east China occupied a broader realized ecological niche than extant members of the group

description: The palaeoecology of Spinicaudata, the dominant group of benthic
 invertebrates in many pre-Cenozoic freshwater environments, remains poorly
 understood. In analogy with extant taxa, it has been oversimplified and
 often reduced to shallow, temporary environments characterised by few
 trophic levels, implying ecological stasis from the Devonian to the
 Recent. We excavated 43 horizons of the Lower Cretaceous Yixian Formation
 (Anjiagou and Hengdaozi beds) to evaluate whether spinicaudatan ecology
 can be simplified to such an extent. Sedimentological evidence suggests
 general perennial conditions during the excavated lake interval. Based on
 33,226 specimen counts, we identified three arthropod-dominated
 macrobenthic associations and two assemblages. Response curves indicate
 that the spinicaudatan Eosestheria middendorfii was exceptionally tolerant
 to environmental gradients, followed, in decreasing order, by mayfly
 larvae, water boatmen and oligochaetes. Also, many spinicaudatan-yielding
 layers represent death after reproductive senescence rather than
 mass-mortality events. Spinicaudatan size varies significantly according
 to faunal association. A forward stepwise regression model suggests that
 growth responded to population density and diversity: lower densities and
 higher diversities triggered fast growth, and vice versa. The proposed
 strong density effect on carapace size has been corroborated by rearing
 experiments: As for E. middendorfii, natural log regression provided the
 best fit for the two extant species Eulimnadia texana and Eocyzicus
 argillaquus. Hence, Eosestheria middendorfii was a tolerant and
 morphologically variable species adapted to perennial waters and the
 frequent presence of higher trophic levels. Although there are rare
 records of extant taxa co-occurring with fish, the described Early
 Cretaceous environment is commonly not realized by extant Spinicaudata.
description: Supplementary
 1Supplementaries
 2-5Supplementary
 6Supplementary
 7Supplementary
 8Supplementary
 9
DOI: 10.15468/dl.qdb9ef
title: Occurrence Download

description: A dataset listing the 5 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neoseiulus barkeri"
 ]
}

 The dataset's 5 records were derived from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001521-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.