cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dz08kprsz
title: Data from: Convergent morphological responses to loss of flight in rails (Aves: Rallidae)

description: The physiological demands of flight exert strong selection pressure on
 avian morphology and so it is to be expected that the evolutionary loss of
 flight capacity would involve profound changes in traits. Here we
 investigate morphological consequences of flightlessness in a bird family
 where the condition has evolved repeatedly. The Rallidae include more than
 130 recognised species of which over 30 are flightless. Morphological and
 molecular phylogenetic data were used here to compare species with and
 without the ability to fly in order to determine major phenotypic effects
 of the transition from flighted to flightless. We find statistical support
 for similar morphological response among unrelated flightless lineages,
 characterised by a shift in energy allocation from the forelimbs to the
 hindlimbs. Indeed flightless birds exhibit smaller sterna and wings than
 flighted taxa in the same family along with wider pelves and more robust
 femora. Phylogenetic signal tests demonstrate that those differences are
 independent of phylogeny and instead demonstrate convergent morphological
 adaptation associated with a walking ecology. We found too that
 morphological variation was greater among flightless rails than flighted
 ones, suggesting that relaxation of physiological demands during the
 transition to flightlessness frees morphological traits to evolve in
 response to more varied ecological opportunities.
description: We assembled a matrix of morphological character data from
 measurements made by Livezey (2003). These data were supplemented by the
 standard body lengths of rails reported in the Handbook of the Birds of
 the World Alive Online (del Hoyo et al. 2015).
 Molecular data are available for 88 rail species and 7 outgroups
 species. Five genetic markers were used including 3 mitochondrial genes
 (COI, cyt-b, 16S) and 2 nuclear genes (FGB, RAG-1) from Garcia-R et. al
 (2014a).
description: Convergent morphological responses to loss of flight in rails
 (Aves: Rallidae)<br> Julien Gaspar*, Gillian C. Gibb1, Steve A.
 Trewick2 *,1,2Ecology Group, Institute of Agriculture
 and Environment, Massey University, Private Bag 11-222, Palmerston North,
 New Zealand<br> *j.gaspar@massey.ac.nz<br> *
 https://orcid.org/0000-0003-3985-4436<br> 1
 https://orcid.org/0000-0002-4283-9790<br> 2
 https://orcid.org/0000-0002-4680-8457 Alignment.phy :
 alignment used for phylogenetic analysis <br> RAxML_tree.nex :
 Phylogenetic tree from Appendix 1 Figure A1<br> Tree_52.nex :
 Phylogenetic tree used for Figure 4  Script.R : Script
 used to make the statistical analysis and create the graphs <br>
 Data_52_ratios: R input file <br> Data_52_S: R input file<br>
 Data_52_S_tips: R input file<br> Data_75_S: R input file<br>
 Data_90: R input file<br> Datasets_morphological_data.xlsx: Excel
 file including the matrix of morphological character
DOI: 10.5061/dryad.xgxd254bw
title: Urbanisation lowers great tit (Parus major) breeding success at multiple spatial scales

description: While numerous studies have reported negative effects of urbanisation on
 birds, few have examined the role of urban scale in influencing breeding
 success and many studies have relied on qualitative rather than
 quantitative assessments of urbanisation. This study sought to address
 these issues by testing the effects of urbanisation, measured at two
 spatial scales, on the breeding success of great tits Parus major. A
 nested study design, incorporating over 400 nestboxes, was used in study
 sites across northern Belgium with a priori quantified degrees of
 urbanisation at both local and regional scales. All measured breeding
 parameters were found to vary at one or both spatial scales of
 urbanisation; in more urbanised areas great tits displayed advanced laying
 dates but lower breeding success compared to rural areas, with smaller
 clutch sizes, lower nestling masses and fewer fledglings per egg.
 Importantly, urbanisation effects were not limited to big cities as birds
 breeding in gardens or parks in small towns also had comparatively low
 success. We found that both regional- and local-scale urbanisation had
 consistent significant effects on laying date, clutch size and nestling
 mass, while the number of fledglings per egg was negatively influenced by
 local-scale urbanisation only. Results of this study therefore highlight
 the importance of utilising multiple spatial scales in analysing
 urbanisation effects, as well as the potential negative impact of local
 urbanisation on breeding success. This calls for further investigation
 into mechanisms driving urbanisation effects and how these may vary at
 different scales.
DOI: 10.5061/dryad.zcrjdfn6j
title: Fluid-structure simulations outperform computational fluid dynamics in the differentiation of progressive dilation in Marfan syndrome patients

description: Introduction: Abnormal fluid dynamics at the ascending aorta may be at the
 origin of aortic aneurysms. This study was aimed at comparing the
 performance of computational fluid dynamics (CFD) and fluid-structure
 interaction (FSI) simulations against 4D-flow MRI data; and to assess the
 capacity of advanced fluid dynamics markers to stratify aneurysm
 progression risk. Methods: Eight Marfan syndrome patients, four with
 stable and four with dilating aneurysms of the proximal aorta, and four
 healthy controls were studied. FSI and CFD simulations were performed with
 MRI-derived geometry, inlet velocity field and Young’s modulus. Flow
 displacement, jet angle and maximum velocity evaluated from FSI and CFD
 simulations were compared to 4D-flow MRI data. A dimensionless parameter,
 the shear stress ratio, was evaluated from FSI and CFD simulations and
 assessed as potential correlate of aneurysm progression. Results: FSI
 simulations successfully matched MRI data regarding descending to
 ascending aorta flow rates (R2=0.92) and pulse wave velocity (R2=0.99).
 Compared to CFD, FSI simulations showed significantly lower percentage
 errors in ascending and descending aorta in flow displacement (-46%
 ascending, -41% descending), jet angle (-28% ascending, -50% descending)
 and maximum velocity (-37% ascending, -34% descending) with respect to
 4D-flow MRI. FSI- but not CFD-derived shear stress ratio differentiated
 between stable and dilating Marfan patients. Conclusions: Fluid dynamic
 simulations of the thoracic aorta require fluid-solid interaction to
 properly reproduce complex hemodynamics. FSI- but not CFD-derived shear
 stress ratio could help stratifying Marfan patients.
DOI: 10.15468/dl.mhcm4m
title: Occurrence Download

description: A dataset listing the 115 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is ZUEC-ARA - Coleção de Aracnideos do Museu de Zoologia da UNICAMP"
 ]
}

 The dataset's 115 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001985-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.34tmpg4fv
title: Efficacy and safety of semaglutide for type 2 diabetes by race and ethnicity: a post hoc analysis of the SUSTAIN trials

description: Context: Variations in the prevalence and aetiology of type 2 diabetes
 (T2D) across race and ethnicity may affect treatment responses.
 Semaglutide is a glucagon-like peptide-1 (GLP-1) analog approved for
 once–weekly, subcutaneous (s.c.) treatment of T2D. Objective: To compare
 semaglutide efficacy and safety in race and ethnicity subgroups across the
 SUSTAIN trials. Design: Post hoc analysis of data from phase 3 randomized
 SUSTAIN 1–5 and 7 (pooled) and SUSTAIN 6 trials. Participants: 3,074
 subjects (SUSTAIN 1–5 and 7); 1,648 subjects (SUSTAIN 6). Interventions:
 Semaglutide 0.5 or 1.0 mg, placebo or active comparator (sitagliptin
 100 mg, exenatide extended release 2.0 mg, insulin glargine
 100IU/ml and dulaglutide 0.75 or 1.5 mg). Main Outcome Measures:
 Change in HbA1c and body weight from baseline to week 30/40/104, other
 efficacy and safety endpoints. Results: HbA1c was reduced from baseline by
 1.0–1.5%-points and 1.3–2.0%-points, and body weight by 2.3–4.7 kg and
 3.6–6.1 kg with semaglutide 0.5 and 1.0 mg, respectively, across race and
 ethnicity subgroups. Minor changes in blood pressure and lipid profiles
 were observed. Adverse events (AEs) were reported in similar proportions
 of subjects across trials. More Asian vs other race subgroups discontinued
 treatment prematurely due to AEs. The most commonly reported AEs were
 gastrointestinal disorders. Conclusion(s): In this SUSTAIN trials post hoc
 analysis, semaglutide was associated with consistent and clinically
 relevant reductions in HbA1c and body weight in subjects with T2D, with
 minor variations in efficacy and safety outcomes associated with race or
 ethnicity.
DOI: 10.5061/dryad.gmsbcc2hr
title: Islands in a green ocean: spatially structured endemism in Amazonian white-sand vegetation

description: Here, we examine the influence of the spatial distribution of open
 White-Sand Campina (WSC) in the Amazon on the species richness and
 beta-diversity of their vascular plants. It is well known that
 beta-diversity tends to increase with geographical distance, but the
 influence of habitat insularity on floristic composition and endemism is
 still unclear. We surveyed WSC in Central and Southwestern Amazon,
 generating lists of species occurrences by rapid-inventory techniques to
 evaluate the influence of island area and connectivity on alpha and
 beta-diversity among five landscapes in the Amazon Basin. Effects of
 insularity were assessed by comparing alpha and beta-diversity within- and
 among-landscapes. A high proportion of species (~74%) and genera (~50%)
 were restricted to only one of the five landscapes and only three species
 and 28 genera were shared among all landscapes. At the regional scale,
 beta-diversity increased significantly with distance. Partitioning of
 beta-diversity showed that landscapes of higher connectivity have greater
 turnover and lower nestedness. We conclude that the flora of WSC is highly
 structured at regional scales, while at the local scale structure is
 evident only in low connectivity landscapes. Landscape metrics apparently
 play an important role in shaping patterns of diversity regionallyas a
 result of processes operating at larger geographical scales. This
 emphasizes that conservation policy should not be local in its geographic
 focus and should account for connectivity at larger scales. This study is
 the first to empirically and explicitly evaluate the pattern of endemism
 in lowland WSC in the Amazon.
DOI: 10.5061/dryad.hmgqnk9c0
title: Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

description: Conservation and management of marine biodiversity depends on
 biomonitoring of marine habitats, but current approaches are
 resource-intensive and require different approaches for different
 organisms. Environmental DNA (eDNA) extracted from water samples is an
 efficient and versatile approach to detecting aquatic animals. In the
 ocean, eDNA composition reflects local fauna at fine spatial scales, but
 little is known about the effectiveness of eDNA-based monitoring of marine
 communities at larger scales. We investigated the potential of eDNA to
 characterize and distinguish marine communities at large spatial scales by
 comparing vertebrate species composition among marine habitats in Qatar,
 the Arabian Gulf (also known as the Persian Gulf), based on eDNA
 metabarcoding of seawater samples. We conducted species accumulation
 analyses to estimate how much of the vertebrate diversity we detected. We
 obtained eDNA sequences from a diverse assemblage of marine vertebrates,
 spanning 191 taxa in 73 families. These included rare and endangered
 species and covered 36% of the bony fish genera previously recorded in the
 gulf. Sites of similar habitat type were also similar in eDNA composition.
 The species accumulation analyses showed that the number of sample
 replicates was insufficient for some sampling sites but suggested that a
 few hundred eDNA samples could potentially capture &gt;90% of the
 marine vertebrate diversity in the study area. Our results confirm that
 seawater samples contain habitat-characteristic molecular signatures and
 that eDNA monitoring can efficiently cover vertebrate diversity at scales
 relevant to national and regional conservation and management.
DOI: 10.5061/dryad.4b8gtht7t
title: How does timing of flowering affect competition for pollinators, flower visitation and seed set in an early spring grassland plant?

description: Knowledge on how the timing of flowering is related to plant fitness and
 species interactions is crucial to understand consequences of phenological
 shifts as they occur under climate change. Early flowering plants may face
 advantages of low competition for pollinators and disadvantages of low
 pollinator abundances and unfavourable weather conditions. However, it is
 unknown how this trade-off changes over the season and how the timing
 affects reproductive success. On eight grasslands we recorded
 intra-seasonal changes in pollinators, co-flowering plants, weather
 conditions, flower visitation rates, floral longevity and seed set of
 Pulsatilla vulgaris. Although bee abundances and the number of
 pollinator-suitable hours were low at the beginning of the season, early
 flowers of P. vulgaris received higher flower visitation rates and
 estimated total number of bee visits than later flowers, which was
 positively related to seed set. Flower visitation rates decreased over
 time and with increasing number of co-flowering plants, which competed
 with P. vulgaris for pollinators. Low interspecific competition for
 pollinators seems to be a major driver for early flowering dates. Thus,
 non-synchronous temporal shifts of co-flowering plants as they may occur
 under climate warming can be expected to strongly affect plant-pollinator
 interactions and the fitness of the involved plants.
DOI: 10.5061/dryad.000000006
title: Founder takes more: interspecific competition affects range expansion of North American mammals into deglaciated areas

description: Aim I assess the impact of interspecific competition on species
 post-glacial range expansions into previously glaciated areas. I
 hypothesize that expansion of one species (the founder) after the Last
 Glacial Maximum (LGM) into areas that were glaciated has hindered
 expansion of its competitor (the successor). If true, I predict that range
 and niche sizes of two congeners are more disproportionate within the
 previously glaciated areas (i.e., the areas of postglacial expansion) than
 within areas that were not glaciated. I also predict that niche
 partitioning is reduced within previously glaciated areas. If true, range
 and climatic niche overlap of two congeners is smaller in the previously
 glaciated areas than in non-glaciated areas.  Location North
 America Taxon Non-volant mammals Methods I calculate species range size
 for 87 congeneric species pairs and climatic niche hypervolume for 71
 pairs, separately for areas that were and were not glaciated during the
 LGM. I then compare (a) range and climatic niche size ratio and (b) range
 and climatic niche overlap for each species pair between areas that were
 and were not glaciated using a paired t-test. Results Congeneric species
 pairs exhibit more disproportionate range areas and climatic niche
 hypervolumes and smaller range and climatic niche overlap within
 previously glaciated areas in comparison with areas that were not
 glaciated during the LGM. Main conclusions Interspecific competition has
 likely hindered postglacial range expansion of some species into
 deglaciated areas. Similarly to the founder effect documented on the
 intraspecific level, the founder species may hinder the expansion of the
 successor species. Consequently, one species may expand over very large
 areas whereas its competitor may expand very little or not at all.
 Additionally, niche partitioning within the deglaciated areas may be
 reduced as the founder expands and fills biotopes that would otherwise be
 utilized by its competitor.
DOI: 10.5061/dryad.ghx3ffbjb
title: Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari

description: High-throughput DNA methods hold great promise for phylogenetic analysis
 of lineages that are difficult to study with conventional molecular and
 morphological approaches. The mites (Acari), and in particular the highly
 diverse soil-dwelling lineages, are among the least known branches of the
 metazoan Tree-of-Life. We extracted numerous minute mites from soils in an
 area of mixed forest and grassland in southern Iberia. Selected specimens
 representing the full morphological diversity were shotgun sequenced in
 bulk, followed by genome assembly of short reads from the mixture, which
 produced &gt;100 mitochondrial genomes representing diverse acarine
 lineages. Phylogenetic analyses in combination with taxonomically limited
 mitogenomes available publicly resulted in plausible trees defining basal
 relationships of the Acari. Several critical nodes were supported by
 ancestral-state reconstructions of mitochondrial gene rearrangements.
 Molecular calibration placed the minimum age for the common ancestor of
 the superorder Acariformes, which includes most soil-dwelling mites, to
 the Cambrian-Ordovician (likely within 455–552 Mya), while the origin of
 the superorder Parasitiformes was placed later in the
 Carboniferous-Permian. Most family-level taxa within the Acariformes were
 dated to the Jurassic and Triassic. The ancient origin of Acariformes and
 the early diversification of major extant lineages linked to the soil are
 consistent with a pioneering role for mites in building the earliest
 terrestrial ecosystems.
description: See Material & Methods.
description: This dataset includes: Illumina raw metagenomic data (4 files),
 nucleotide/aminoacid matrices (3 files) and phylogenetic trees (15
 files).
DOI: 10.5061/dryad.s7h44j12w
title: Is there an oxidative cost of acute stress? Characterization, implication of glucocorticoids, and modulation by prior stress experience

description: Acute rises in glucocorticoid hormones allow individuals to adaptively
 respond to environmental challenges but may also have negative
 consequences, including oxidative stress. While the effects of chronic
 glucocorticoid exposure on oxidative stress have been well characterized,
 those of acute stress or glucocorticoid exposure have mostly been
 overlooked. We examined the relationship between acute stress exposure,
 glucocorticoids, and oxidative stress in Japanese quail (Coturnix
 japonica). We (i) characterized the pattern of oxidative stress during an
 acute stressor in two phenotypically distinct breeds, (ii) determined
 whether corticosterone ingestion, in the absence of acute stress,
 increased oxidative stress, which we call Glucocorticoid-induced Oxidative
 Stress (GiOS), and (iii) explored how prior experience to stressful events
 affected GiOS. Both breeds exhibited an increase in oxidative stress in
 response to an acute stressor. Importantly, in the absence of acute
 stress, ingesting corticosterone caused an acute rise in plasma
 corticosterone and oxidative stress. Lastly, birds exposed to no previous
 acute stress or numerous stressful events had high levels of GiOS in
 response to acute stress, while birds with moderate prior exposure did
 not. Together, these findings suggest that an acute stress response
 results in GiOS, but prior experience to stressors may modulate that
 oxidative cost.
DOI: 10.5061/dryad.3r2280gbw
title: Development and uncertainty assessment of pedotransfer functions for predicting water contents at specific pressure heads

description: There has been much effort to improve the performance of pedotransfer
 functions (PTFs) using intelligent algorithms, but the issue of covariate
 shift, i.e. different probability distributions in training and testing
 datasets, and its impact on prediction uncertainty of PTFs has been rarely
 addressed. The common practice in PTF generation is to randomly separate
 the dataset in training and testing subsets, and outcomes of this random
 selection may be different if the process is subject to covariate shift.
 We evaluated the impact of covariate shift generated by data shuffling and
 detected by Kolmogorov-Smirnov test for prediction of water contents using
 soil databases from Denmark and Brazil. The soil water contents at
 different pressure heads were predicted by developing linear and stepwise
 regression besides machine learning based PTFs including Gaussian
 regression process and ensemble method. Regression based PTFs for the
 Brazilian dataset resulted in better predictions compared to machine
 learning methods that estimated high water contents in Danish soils more
 accurately. One hundred PTFs were developed for water content at specific
 pressure heads by data shuffling generating covariate shift. From these, a
 hundred sets of fitted van Genuchten parameters were obtained representing
 the generated uncertainty. Data shuffling led to covariate shift,
 resulting in uncertainty in water content prediction by the PTFs. Inherent
 variability of data may lead to increased prediction uncertainty. For
 correlated data, simple regression models performed as good as
 sophisticated machine learning methods. Using PTF-predicted water contents
 for van Genuchten retention parameter fitting may lead to a high
 uncertainty.
DOI: 10.21223/p3/kzwgt8
title: Dataset for: Parental value for tuber yield in potato clones with resistance to late blight and heat tolerance, under high temperatures conditions (SET 2)

description: The International Potato Center (CIP) has developed a population named LBHT, obtaining new clones that are more tolerant to high temperatures, resistant to late blight, virus and early maturity, and they are available for use by developing countries for the selection of varieties or as parents in their breeding programs. The potato is highly heterozygozus crop, the most important economical characters are governed by additive and non-aditive genes. Therefore, the parental value of a clone cannot be assessed from phenotypic value alone. It is very important to know its combining ability as an indicator of parental value. Combining ability analysis is a method very useful for choosing better parents, and in the formulation of a crossing plan for a plant breeding program. During 2012 and 2013, 6 advanced clones of LBHT population, were crossed using line x tester mating design, where the clones were used as female parents (lines), and as male parents (testers). The varieties, Katahdin (Solanum tuberosum spp tuberosum), Huagalina (Solanum tuberosum spp andigena) and clone CIP302533.31 were used in this experiment. Furthermore, during 2013 - 2014, 18 progenies were evaluated under field conditions in three locations in Peru: La Molina, San Ramon and Majes. All experiments were conducted using statistical design of randomized complete block with three replications of 40 plants per plot. At harvest, the number and weight of marketable and non- marketable tubers were recorded. Then, the average weight of tubers, weight of marketable and total tubers per hectare in tons were calculated. The analysis of variance for line by tester mating desing and determination of the effects of general combining ability (GCA) for these characters were performed using statistical software, SAS V. 9.4 (SAS Institute Inc., Cary, NC, USA).
DOI: 10.3886/e244688
title: Kurt ve 7 Küçük Keçi

description: Kurt ve 7 Küçük Keçi