cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3s3
title: Exploring intraspecific variation in migratory destinations to investigate the drivers of migration

description: Various benefits (e.g. tracking of resources and of climate niche) and
 costs (e.g. distance travelled) are hypothesized to drive seasonal animal
 migrations. Until now, these potential factors have been investigated
 together at the species level, but migratory movements are made at the
 individual level, leading to intraspecific variability. Here, we use
 ringing/recovery data from 1308 individuals belonging to thirteen North
 American bird species to analyse patterns in intraspecific variability of
 migratory destinations in order to investigate which factors underpin bird
 migration and how individuals trade-off among multiple factors. Our
 results suggest that migratory destinations have been shaped by access to
 resources (most important during the breeding season) and climatic niche
 tracking (during winter, mostly). However, the benefits of resource
 surpluses and climate niche tracking appear to be traded off against the
 cost of migratory distance, which seems to strongly constrain where
 individuals migrate. Data and codes used in this analysis are presented
 here.
description: This data was obtained from a dataset of bird ringing/recovery
 (USGS Bird Banding Lab), selecting individuals as described in the
 manuscript (only alive birds, at least one location in the winter and one
 location in the summer, etc.). From location data, environmental
 conditions were extracted, and distance between the breeding and the
 wintering locations was calculated for each individual.
DOI: 10.25934/pr00012475.0
title: Available datapackage for study 'Optimization of a New Adaptive Intervention to Increase COVID-19 Testing Among People at High Risk in an Urban Community'

description: This study tests an adaptation of the HIV Continuum of Prevention, Care, and Treatment Framework (CoPCT) for use in tracking COVID-19 testing and follow-up in a medically and socially vulnerable population. This study uses an integrated research collaborative framework that facilitates dialogue among researchers, community members, and service providers as a tool for optimizing the adaptive intervention and will take place at the North Jersey Community Research Initiative (NJCRI)
DOI: 10.15468/dl.t4en4j
title: Occurrence Download

description: A dataset containing 1778 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Mabea speciosa, Mabea speciosa speciosa, Mabea caudata)"
 ]
}

 The dataset includes 1778 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002272-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.34tmpg4gj
title: Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

description: Background Native Swedish sheep breeds are part of the North European
 short-tailed sheep group; characterized in part by their genetic
 uniqueness. Our objective was to study the population structure of native
 Swedish sheep. Five breeds were genotyped using the 600 K SNP array.
 Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute
 sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from
 northern Sweden. We studied population structure by: principal component
 analysis (PCA), cluster-based analysis of admixture, and an estimated
 population tree. Results The analyses of the five Swedish breeds revealed
 that these breeds are five distinct breeds, while Gute and Gotland are
 more closely related to each other as seen in all analyses. All breeds had
 long branch lengths in the population tree indicating they’ve been
 subjected to drift. We repeated our analyses using 39 K SNP and including
 50 K SNP genotypes from other European and southwestern Asian breeds from
 the Sheep HapMap project and 600 K SNP genotypes from a dataset of French
 sheep. Results arranged breeds into five groups: south-west Asia,
 south-west Europe, central Europe, north Europe and north European
 short-tailed sheep. Within this last group, Norwegian and Icelandic
 breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland
 sheep were more closely related while the remaining Swedish breeds and
 Ouessant sheep were distinct from all breeds and had longer branches in
 the population tree. Conclusions We showed population structure of five
 Swedish breeds and their structure within European and southwestern Asian
 breeds. Swedish breeds are unique, distinct breeds that have been
 subjected to drift but group with other north European short-tailed sheep.
description: From the methods of Rochus et al. 2020 (for full details please
 see: http://dx.doi.org/10.1186/s12863-020-0827-8):
 "Blood samples were collected from native Swedish sheep.
 Ethical permission was obtained prior to the collection of blood samples.
 Genomic DNA used in this study was extracted from fresh blood samples
 using a QIAsymphony® DSP DNA extraction robot and DSP DNA Midi Kit
 (QIAGEN). For this study 21 Dalapäls, 10 Fjällnäs, 19 Gotland, 22 Gute and
 21 Klövsjö sheep were genotyped for 653,305 autosomal SNPs (Ovine
 Infinium® HD SNP BeadChip) at Labogena, INRA, Paris, France. 
 Quality control and filtering of SNPs included removing SNPs with
 a minor allele frequency of zero, removing SNPs with a missing rate
 greater than 0.01 and removing sheep with a missing genotype rate greater
 than 0.15 using PLINK 1.9 [18, 19]. All of the 93 sheep, and a total of 502,144 SNPs passed quality control and filtering steps."
DOI: 10.5061/dryad.m37pvmczg
title: Modelling the distribution of Amazonian tree species in response to long-term climate change during the mid-late Holocene

description: Aim: To (a) assess the environmental suitability for rainforest
 tree species of Moraceae and Urticaceae across Amazonia during the
 Mid-Late Holocene and (b) determine the extent to which their
 distributions increased in response to long-term climate change over this
 period. Location: Amazonia. Methods: We used MaxEnt and
 inverse distance weighting interpolation to produce environmental
 suitability and relative abundance models at 0.5-degree resolution for
 tree species of Moraceae and Urticaceae, based on natural history
 collections and a large plot dataset. To test the response of the Amazon
 rainforest to long-term climate change, we quantified the increase in
 environmental suitability and modelled species richness for both families
 since the Mid-Holocene (past 6,000 years). To test the correlation between
 the relative abundance of these species in modern vegetation versus modern
 pollen assemblages, we analysed the surface pollen spectra from 46
 previously published paleoecological sites. Results: We found
 that the mean environmental suitability in Amazonia for species of
 Moraceae and Urticaceae showed a slight increase (6.5%) over the past
 6,000 years, although southern ecotonal Amazonia and the Guiana Shield
 showed much higher in- creases (up to 68%). The accompanied modelled mean
 species richness increased by as much as 120% throughout Amazonia. The
 mean relative abundance of Moraceae and Urticaceae correlated
 significantly with the modern pollen assemblages for these families. Main
 Conclusions: Increasing precipitation between the Mid- and Late
 Holocene ex- panded suitable environmental conditions for Amazonian humid
 rainforest tree spe- cies of Moraceae and Urticaceae, leading to
 rainforest expansion in ecotonal areas of Amazonia, consistent with
 previously published fossil pollen data.
description: The occurrence dataset of Moraceae and Urticaceae species was
 downloaded from the Global Biodiversity Information Facility (GBIF,
 http://www.gbif.org/, January 2018), using the function ‘gbif’ from the R
 package ‘dismo’ (Hijmans, Phillips, Leathwick, & Elith, 2017),
 based on the most recent list of Amazonian tree species (ter Steege et
 al., 2019). We assigned all individuals to species level. All species
 occurrence were checked for inconsistencies using a cleaning pipeline
 (Gomes et al., 2018), removing all records with: imprecise georeferences,
 duplicates at 0.5-degree spatial resolution, records assigned to capital
 cities or centroids of provinces, latitude equal to longitude or equal to
 exactly zero. We used occurrence data from the entire Neotropics to
 prevent SMD deficiencies that are associated with models based on a
 species' partial geographical range (Raes, 2012). Species with a
 small number of records (&lt;6) were not used as they may develop
 inaccurate predictions (van Proosdij, Sosef, Wieringa, & Raes,
 2016).
DOI: 10.7272/q6sx6bd9
title: Data from: Evaluation of a person-centered quality improvement intervention for maternal health and family planning in Kenya

description: This data is from a 5 year project on person-centered quality for
 delivery, family planning, and abortion in both India and Kenya. We
 conducted a quality improvement collaborative to improve person-centered
 quality for maternal health and family planning services in Nairobi and
 Kiambu County, Kenya. Data was collected pre and post intervention. The
 aim was to evaluate if quality improvement cycles were effective at
 improving women's experiences while seeking care
DOI: 10.5061/dryad.gf1vhhmkh
title: Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs

description: Colonization of extreme habitats requires extensive adaptation to novel
 environmental challenges. Deep-water environments (&gt;50 m) have high
 hydrostatic pressure, low temperature, and low light, requiring
 physiological and visual system adaptation, but genomic mechanisms
 underlying evolution in these environments are rarely known. Post-glacial
 colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr
 (Salvelinus alpinus) provides the opportunity to study the genomic basis
 of adaptation to extreme deep-water environments. Here, we compare genomic
 and morphometric divergence between a phenotypically divergent deep-water,
 demersal morph adapted to depths of up to 288m and a larger, piscivorous
 morph occupying shallower depths. Using a SNP array and resequencing of
 nuclear and mitochondrial genomes, we find moderate genetic divergence
 (FST = 0.15 - 0.11) between morphs, consistent with divergence in body
 shape and size, despite absence of mitochondrial genome divergence.
 Outlier analyses identified three key genes with very high divergence
 against a genome-wide distribution of diverged genomic islands containing
 genes with functions related to deep-water adaptation such as sensory
 processes, ligand binding and regulation of transcription. Quantification
 of SNP array signal intensity variation associated with complex
 polymorphisms (e.g. copy number variants), similarly uncovered genetic
 separation of morphs and coincided with several islands of genomic
 divergence, but also revealed additional genomic regions and molecular
 mechanisms associated with depth adaptation. Together, these results show
 that adaptation to an extreme deep-water environment has been facilitated
 by multiple polymorphism types with roles in cellular and physiological
 processes, providing insight into the genomic basis of adaptation in
 extreme environments.
DOI: 10.5061/dryad.z34tmpg95
title: Extracellular matrix protein signature of recurrent spontaneous cervical artery dissection

description: Objective To assess whether connective tissue disorder is evident in
 patients with spontaneous cervical artery dissection and therefore
 identify patients at risk of recurrence using a cutting-edge quantitative
 proteomics approach. Methods In the ReSect-study all patients with
 spontaneous cervical artery dissection treated at the Innsbruck University
 Hospital since 1996 were invited to attend a standardized clinical
 follow-up examination. Protein abundance in skin punch biopsies (n=50) was
 evaluated by a cutting-edge quantitative proteomics approach (liquid
 chromatography-mass spectrometry) which has hitherto not been applied to
 such patients. Results Patients with one-time single-vessel (n=19) or
 –multiple-vessel (n=13) dissections did not differ between each other or
 compared to healthy controls (n=12) in protein composition. Patients with
 recurrent spontaneous cervical artery dissection (n=6) however, showed
 significantly different expression of 25 proteins compared to the other
 groups combined. Literature review and gene ontology term annotation check
 revealed that 13 of the differently expressed proteins play a major role
 in the structural integrity of connective tissue or are linked to
 connective tissue disorders. These proteins showed clustering to a
 collagen/elastin cluster and one consisting of desmosome related proteins.
 Conclusion This study unravels an extracellular matrix protein signature
 of recurrent spontaneous cervical artery dissection. On a long run and
 dependent on large-scale validation, our findings may well assist in
 identifying patients at risk of recurrent spontaneous cervical artery
 dissection and thus guide therapy.
DOI: 10.6078/d1gx19
title: Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility

description: Thermodynamic models of gene regulation can predict transcriptional
 regulation in bacteria, but in eukaryotes chromatin accessibility and
 energy expenditure may call for a different framework. Here we
 systematically tested the predictive power of models of DNA accessibility
 based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits
 that chromatin fluctuates between accessible and inaccessible states. We
 dissected the regulatory dynamics of hunchback by the activator Bicoid and
 the pioneer-like transcription factor Zelda in living Drosophila embryos
 and showed that no thermodynamic or non-equilibrium MWC model can
 recapitulate hunchback transcription. Therefore, we explored a model where
 DNA accessibility is not the result of thermal fluctuations but is
 catalyzed by Bicoid and Zelda, possibly through histone acetylation, and
 found that this model can predict hunchback dynamics. Thus, our
 theory-experiment dialogue uncovered potential molecular mechanisms of
 transcriptional regulatory dynamics, a key step toward reaching a
 predictive understanding of developmental decision-making.
description: Data were collected using fluorescent confocal microscopy as
 described in the Methods and Materials section of the main text, and
 processed using the image processing techniques described therein. The
 file 'v1_TrapezoidalFits.mat' represents the post-processed
 analyzed transcription data using the fitting schemes described in the
 main text.
description: Data files are in MATLAB .mat file structures.
DOI: 10.6071/m3rq38
title: Multiplex networks reveal geographic constraints on illicit wildlife trafficking

description: Illicit wildlife trafficking poses a threat to the conservation of species
 and ecosystems, and represents a fundamental source of biodiversity loss,
 alongside climate change and large-scale land degradation. Despite the
 seriousness of this issue, little is known about various socio-cultural
 demand sources underlying trafficking networks, for example the forthright
 consumption of endangered species on different cultural contexts. Our
 study illustrates how wildlife trafficking represents a wicked problem at
 the intersection of criminal enforcement, cultural heritage and
 environmental systems management. As with similar network-based crimes,
 institutions are frequently ineffective at curbing wildlife trafficking,
 partly due to the lack of information detailing activities within illicit
 trading networks. To address this shortcoming, we leverage official
 government records documenting the illegal trade of reptiles in Colombia.
 As such, our study contributes to the understanding of how and why
 wildlife trafficking persists across robust trafficking networks, which
 are conduits for a broader range of black-market goods. Leveraging
 geo-spatial data, we construct a multiplex representation of wildlife
 trafficking networks, which facilitates identifying network properties
 that are signatures of strategic trafficker behavior. In particular, our
 results indicate that traffickers’ actions are constrained by spatial and
 market customs, a result which is apparent only within an integrated
 multiplex representation. Characteristic levels of sub-network coupling
 further indicate that traffickers strategically leverage knowledge of the
 entire system. We argue that this multiplex representation is essential
 for prioritizing crime enforcement strategies aimed at disrupting robust
 trade networks, thereby enhancing the effectiveness and resources
 allocation of institutions charged with curbing illicit trafficking. We
 develop a generalizable model of multiplex criminal trade networks
 suitable for communicating with policy makers and practitioners, thereby
 facilitating rapid translation into public policy and environmental
 conservation efforts.
DOI: 10.25338/b8hs5z
title: Phylogenies of fungi isolated from the seagrass, Zostera marina

description: Fungi in the marine environment are often neglected, despite that they
 having critical roles on land as decomposers, pathogens or beneficial
 endophytes. We used culture-dependent methods to survey the fungi
 associated with the seagrass, Zostera marina, and then placed these
 sequences in the fungal tree of life. Four different sequence alignments
 were generated, (1) an alignment to investigate seagrass isolates in the
 Basidiomycota and Zygomycota phyla, (2) an alignment to investigate
 seagrass isolates in the Eurotiomycetes class in the Ascomycota phylum,
 (3) an alignment to investigate seagrass isolates in the Sordariomycetes
 class in the Ascomycota phylum, and (4) an alignment to investigate
 seagrass isolates in the Dothideomycetes class in the Ascomycota
 phylum. 
description: Each of the four sequence alignments was generated using MAFFT
 (v. 7.402) (Katoh et al., 2002) with default parameters on the CIPRES
 Science Gateway web server and trimmed using trimAl (v.1.2) with the
 -gappyout method (Capella-Gutierrez et al., 2009). Sequence alignments
 were then further trimmed to the D1/D2 regions of the 28S rRNA gene with
 trimAl using the select option (e.g. Basidiomycota / Zygomycota alignment
 { 614-2899 }, Eurotiomycetes alignment { 0-569 }, Sordariomycetes
 alignment { 501-1224 }, and Dothideomycetes alignment { 0-429, 993-1755
 }). Spurious sequences (e.g. sequences which contained few or no
 nucleotides after trimming) were then removed with trimAl using
 -resoverlap .75 -seqoverlap 50. The resulting alignments contained: 80
 sequences with 614 positions (Basidiomycota / Zygomycota), 91 sequences
 with 509 positions (Eurotiomycetes), 96 sequences with 501 positions
 (Sordariomycetes), and 107 sequences with 563 positions
 (Dothideomycetes). JModelTest2 (v. 2.1.10) was run and
 the best-fit model for all alignments was the GTR + I + G evolutionary
 model. Bayesian phylogenetic inference for each alignment was performed
 using MrBayes (v. 3.2.2) with four incrementally heated simultaneous Monte
 Carlo Markov Chains (MCMC) run over 10,000,000 generations. The analysis
 stopped early if the optimal number of generations to reach a stop value
 of 0.01 or less for the convergence diagnostic was achieved (Huelsenbeck
 & Ronquist, 2001). This occurred for the Eurotiomycetes,
 Sordariomycetes and Dothideomycetes alignments at 2,150,000 generations,
 1,375,000 generations and 2,140,000 generations, respectively. The
 Basidiomycota / Zygomycota alignment ran for the full 10,000,000
 generations, only achieving an average standard deviation of split
 frequencies of 0.049. The first 25% of trees generated for each alignment
 were discarded as burn-in and for the remaining trees, a majority rule
 consensus tree was generated and used to calculate the Bayesian Posterior
 Probabilities.
description: Here we provide the trimmed alignment files used to generate all
 four phylogenetic trees and the four phylogenies themselves.
DOI: 10.5061/dryad.9kd51c5d9
title: Genetic variants beyond amyloid and tau associated cognitive decline: a cohort study

description: Objective: To identify single nucleotide polymorphisms (SNPs) associated
 with cognitive decline independent of amyloid &[beta]
 (A&[beta]) and tau pathology in Alzheimer’s disease (AD). Methods:
 Discovery and replication datasets consisting of 414 subjects (94
 cognitively normal control [CN), 185 with mild cognitive impairment [MCI],
 and 135 AD) and 72 subjects (22 CN, 39 MCI, and 11 AD), respectively, were
 obtained from the Alzheimer’s Disease Neuroimaging Initiative database.
 Genome-wide association analysis was conducted to identify SNPs associated
 with individual cognitive function (measured using the MMSE and ADAS-cog)
 while controlling for the level of A&[beta] and tau (measured as
 CSF p-tau/A&[beta]1-42). Gene ontology analysis was performed on
 SNP associated genes. Results: We identified one significant (rs55906536,
 &[beta]=-1.91,standard error 0.34, P =4.07×10-8) and four
 suggestive variants on chromosome 6, which were associated with poorer
 cognitive function. Congruent results were found in the replication data.
 A structural equation model showed that the identified SNP deteriorated
 cognitive function partially through cortical thinning of the brain in a
 region-specific manner. Furthermore, a bioinformatics analysis showed that
 the identified SNPs were associated with genes related to glutathione
 metabolism. Conclusions: In this study, we identified SNPs related to
 cognitive decline, in a manner which could not be explained by
 A&[beta] and tau levels. Our findings provide insight into the
 complexity of AD pathogenesis and support the growing literature on the
 role of glutathione in AD. This study suggests anti-oxidative agents may
 serve therapeutic for AD subjects with the identified SNPs.
description: The dataset which supports the conclusions from our genome-wide
 association analysis is available in the ADNI public database
 (http://adni.loni.usc.edu/data-samples/access-data/). Anonymized patient
 identification numbers, imaging, genetic, and biospecimen data are
 available from the ADNI database at the request of qualified
 researchers.