cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.37pvmcvj9
title: Serial two-photon tomography (STPT) of the brain through bi-channel image registration and deep learning segmentation (BIRDS)

description: We have developed an open-source software called BIRDS (bi-channel image
 registration and deep learning segmentation) for the mapping and analysis
 of 3D microscopy data and applied this to the mouse brain. The BIRDS
 pipeline includes image pre-processing, bi-channel registration, automatic
 annotation, creation of a 3D digital frame, high-resolution visualization,
 and expandable quantitative analysis. This new bi-channel registration
 algorithm is adaptive to various types of whole-brain data from different
 microscopy platforms and shows dramatically improved registration
 accuracy. Additionally, as this platform combines registration with neural
 networks, its improved function relative to other platforms lies in the
 fact that the registration procedure can readily provide training data for
 network construction, while the trained neural network can efficiently
 segment incomplete/defective brain data that is otherwise difficult to
 register. Our software is thus optimized to enable either minute-timescale
 registration-based segmentation of cross-modality, whole-brain datasets or
 real-time inference-based image segmentation of various brain regions of
 interest. Jobs can be easily submitted and implemented via a Fiji plugin
 that can be adapted to most computing environments.
description: Acquisition of STPT image dataset<br> Brain 1 and 2 were
 obtained with STPT and each dataset encompassed ~180 Gigavoxels, e.g.,
 11980×7540×1075 in Dataset 1, with a voxel size of 1×1×10 μm3. The
 procedure of sample preparation and imaging acquisition were described in
 the paper. Briefly, the adult C57BL/6 mouse was anesthetized and
 craniotomy was performed on top of the right visual cortex. Individuals
 neuronal axons were labeled with pCAG-eGFP by two-photon microscopy guided
 single-cell electroporation and the brain was fixed by caridoperfusion of
 4% PFA 8 days later. Striatum-projecting neurons were labeled by
 stereotactically injecting PRV-cre into the right striatum of tdTomato
 reporter mice (Ai14, JAX) and the brain was fixed cardioperfusion 30 days
 later. The brains were embedded in 5% oxidized agarose and imaged with a
 commercial STPT (TissueVision, USA) excited at 940 nm. Coronally, the
 brain was optically scanned every 10 μm at 1 μm/pixel without averaging
 and physically sectioned every 50 μm. The power of excitation laser was
 adjusted to compensate the depth of optical sections.
  
description: There are two group of  1×1×10 μm high-resolution mouse brain
 datasets using serial two-photon tomography (STPT), and there are coronal
 sections.
DOI: 10.15468/dl.jp994u
title: Occurrence Download

description: A dataset containing 45351 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Typhlopidae"
 ]
}

 The dataset includes 45351 records from 318 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002689-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8prg
title: Microsatellite alleles of two species of Tetramorium ants in their native and invasive ranges

description: Microsatellite alleles at 16 loci, for 80 individuals of Tetramorium
 immigrans and 84 individuals of T. tsushimae from both their native and
 invasive ranges.
description: Abbreviations: imm_autoch: <em>Tetramorium
 immigrans</em>, native range (Europe) imm_invasive: <em>T.
 immigrans</em>, invasive range (North + South America)
 tsu_autoch: <em>T.
 tsushimae</em>, native range (East Asia) tsu_invasive: <em>T.
 tsushimae</em>, invasive range (North America)
 The dataset was
 created as part of the study "Effect of social structure and
 introduction history on genetic diversity and differentiation" by
 Flucher S.M., Krapf P., Arthofer W., Suarez A.V., Crozier R.H., Steiner
 F.M., Schlick-Steiner B.C. submitted in Molecular
 Ecology.
DOI: 10.5061/dryad.3bk3j9khv
title: Morphometric study and sexual dimorphism analyses in an Iranian population of Scorpio maurus (Arachnida: Scorpionidae)

description: Scorpio maurus (Scorpiones: Scorpionidae) which has a worldwide
 distribution, indicates levels of sexual dimorphism. Morphometry is used
 to determine the sexual dimorphism between the two sexes. In this study,
 53 morphological characters of 15 specimens of each sex of Scorpio maurus
 were studied, however dimorphism was only observed in 21 morphological
 characters, including chelicerae and carapace length, pedipalp characters,
 width of the second segment of metasoma, telson and pectin length, number
 of left pectin teeth, and some of the leg's segments.
DOI: 10.5061/dryad.zgmsbcc98
title: Niche partitioning among three snail-eating snakes revealed by dentition asymmetry and prey specialisation

description: 1. The level of dentition asymmetry in snail-eating snakes may reflect
 their prey choice and feeding efficiency on asymmetric land snails. The
 three species of Pareas snakes (Squamata: Pareidae) in Taiwan, which are
 partially sympatric distribution on the island, provide a potential case
 to test the hypothesis of niche partitioning and character displacement
 with regard to dentition asymmetry and specialisation in feeding
 behaviour. 2. In this study, behavioural experiments confirmed that P.
 formosensis feeds exclusively on slugs, whereas P. atayal and P. komaii
 consumed both. However, P. atayal more efficiently preys on land snails
 than P. komaii, exhibiting a shorter handling time and fewer mandibular
 retractions. 3. Micro-CT and ancestral character reconstruction
 demonstrated the lowest asymmetry in P. formosensis (the slug specialist),
 the highest dentition asymmetry in P. atayal (the land snail specialist),
 and flexibility in P. komaii (the niche switcher): increased dentition
 asymmetry when sympatrically distributed with the slug eater (character
 displacement), and decreased asymmetry when living alone (ecological niche
 release). 4. Ecological niche modelling showed that the distribution P.
 formosensis is associated with the presence of slugs, while that of P.
 atayal could be explained by the land snails. Combining the results from
 morphology, phylogeny, behavioural experiments and ecological niche
 modelling, we showed that competition in the sympatric region might have
 facilitated character displacement among congeners, while absence of
 competition in allopatric region has led to ecological niche release.
DOI: 10.5061/dryad.wpzgmsbkn
title: Reconstructing squamate biogeography in Afro-Arabia reveals the influence of a complex and dynamic geologic past

description: The geographic distribution of biodiversity is central to understanding
 evolutionary biology. Paleogeographic and paleoclimatic histories often
 help to explain how biogeographic patterns unfold through time. However,
 such patterns are also influenced by a variety of other factors, such as
 lineage diversification, that may affect the probability of certain types
 of biogeographic events. The complex and well-known geologic and climatic
 history of Afro-Arabia, together with the extensive research on reptile
 systematics in the region, makes Afro-Arabian squamate communities an
 ideal system to investigate biogeographic patterns and their drivers. Here
 we reconstruct the phylogenetic relationships and the ancestral geographic
 distributions of several Afro-Arabian reptile clades (totaling 430
 species) to estimate the number of dispersal, vicariance and range
 contraction events. We then compare the observed biogeographic history to
 a distribution of simulated biogeographic events based on the empirical
 phylogeny and the best-fit model. This allows us to identify periods in
 the past where the observed biogeographic history was likely shaped by
 forces beyond the ones included in the model. We find an increase in
 vicariance following the Oligocene, most likely caused by the
 fragmentation of the Afro-Arabian plate. In contrast, we did not find
 differences between observed and expected dispersal and range contraction
 levels. This is consistent with diversification enhanced by environmental
 processes and with the establishment of a dispersal corridor connecting
 Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show
 that our novel approach is useful to pinpoint events in the evolutionary
 history of lineages that might reflect external forces not predicted by
 the underlying biogeographic model.
description: Distribution data was collected manually from Reptile Database
 (https://reptile-database.reptarium.cz/), and the biogeographic analyses
 were entirely performed in the R framework. 
description: Information about directory structure can be found in the
 README.md file.
DOI: 10.5061/dryad.8w9ghx3kn
title: Data from: A Burgess Shale mandibulate arthropod with a pygidium – a case of convergent evolution

description: Cambrian ‘bivalved’ arthropods are a polyphyletic group of
 carapace-bearing arthropods which include stem euarthropods, stem
 mandibulates and crustaceans. Here, we describe Pakucaris apatis gen et.
 sp. nov. a new ‘bivalved’ mandibulate from the middle Cambrian (Wuliuan
 Stage) Burgess Shale (Marble Canyon, Kootenay National Park, British
 Columbia, Canada). Two morphotypes of this small arthropod (11.6–26.6 mm
 long) are recognized, differing mainly in their sizes and number of
 segments, possibly reflecting sexual dimorphism or different anamorphic
 stages. The carapace presents a dorsal crest extending anteriorly into a
 small recurved rostrum and two antero-lateral processes. Around 20% of the
 posteriormost body segments and limbs are covered by a large spine-bearing
 shield. The head bears a pair of eyes, a possible pair of unsegmented
 appendicular projections and two pairs of segmented appendages. The thorax
 is multisegmented, homonomous, with weakly sclerotized segments bearing
 biramous limbs, composed of a stenopodous endopod with c. 20 podomeres and
 a paddle-shaped exopod. Pakucaris is interpreted as a nektobenthic
 suspension feeder. A Bayesian phylogenetic analysis implies a position
 within Hymenocarina as stem mandibulates. The posterior shield is regarded
 as a pygidium, and represents a case of morpho-functional convergent
 evolution between a mandibulate, artiopodans and mollisoniids.
 Alternatively, the growing number of known pygidium-bearing arthropods may
 hint at a common developmental pattern across early arthropod evolution.
 This study not only increases our understanding of the early evolution of
 mandibulates but also illustrates a unique case of early evolutionary
 convergence during the Cambrian Explosion.
description: S1_AIL_JBC_2020_SupMaterial&SupFigures.pdf: contains
 Supplementary Figure 1 (phylogeny) as well as: List of specimens and
 figures, species and characters present in the phylogenetic analysis,
 phylogenetic constraints applied in the phylogenetic analysis and
 Synapomorphies of highlighted taxa. 
 S2_AIL_JBC_2020_Specimens&Measurements.xlsx: contains all
 specimens and measurements performed
 S3_AIL_JBC_2020_Phylomatrix_.xlsx: Phylogenetic matrix
 S4_AIL_JBC_2020_ Nexuscode.nex: Nexus code. Includes MrBayes
 parameters.
DOI: 10.5061/dryad.wstqjq2k4
title: Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean

description: The genetic diversity of a population is the foundation of its
 adaptability to environmental challenges. The South American fur seal is a
 widely distributed pinniped in the south cone of South America. However, a
 large gap in the Pacific coast separates two distinct evolutionary units
 for the species: the Peruvian and the Southern Pacific/Atlantic
 populations. Throughout the Pacific, one of the main breeding colonies is
 located in Guafo Island, in the southern Chilean Patagonia. As the closest
 reproductive population to the isolated Peruvian group, Guafo’s colony may
 potentially facilitate gene flow, contribute with new alleles and increase
 genetic variability to Peruvian populations’, connecting the entire
 Pacific’s distribution of the species. In this study, Guafo’s Island South
 American fur seal population was characterized by the identification and
 genotyping of species-specific microsatellite markers. As a result, we
 confirm that Guafo’s colony is a diverse group with mild evidence of
 genetic structure. Although a couple of family groups among seasons were
 observed, results indicate that half-siblings are rare and suggest that
 polygyny in this species is more relaxed than previously thought.
 Additionally, three full-sibling pairs were genetically identified within
 the 2017 season, which is the first genetic support that describes the
 presence of twins for the species. These attributes suggest that the
 colony at Guafo is a panmictic large group, and could serve as a potential
 genetic source for other isolated populations.
description: The fieldwork was conducted in Guafo Island. Animals were sampled
 weekly during the breeding seasons (December through March) from 2014 to
 2017. A 2 mm skin biopsy was collected from the distal portion of the
 third finger of the hind flipper and preserved in 95% ethanol.
 DNA was extracted from 128 animal samples using a commercial kit.
 Sixteen loci (NCBI accession number: MK934158-73) were amplified through
 conventional PCR using fluorescent-labeled primers. Genotyping was
 performed in an ABI 3500 genetic analyzer, and electropherograms were
 analyzed in Geneious Prime software (Kearse et al., 2012).
description: Missing values are coded as 0.
DOI: 10.5061/dryad.g1jwstqpw
title: Supplement to: Global impact of the COVID-19 pandemic on stroke care and intravenous thrombolysis

description: Objective:  The objectives of this study were to measure the
 global impact of the pandemic on the volumes for intravenous thrombolysis
 (IVT), IVT transfers, and stroke hospitalizations over 4 months at the
 height of the pandemic (March 1 to June 30, 2020) compared with two
 control 4-month periods.  Methods: We conducted a
 cross-sectional, observational, retrospective study across 6 continents,
 70 countries, and 457 stroke centers. Diagnoses were identified by their
 ICD-10 codes and/or classifications in stroke databases. 
 Results: There were 91,373 stroke admissions in the 4 months immediately
 before compared to 80,894 admissions during the pandemic months,
 representing an 11.5% (95%CI, -11.7 to - 11.3, p&lt;0.0001) decline.
 There were 13,334 IVT therapies in the 4 months preceding compared to
 11,570 procedures during the pandemic, representing a 13.2% (95%CI, -13.8
 to -12.7, p&lt;0.0001) drop. Interfacility IVT transfers decreased
 from 1,337 to 1,178, or an 11.9% decrease (95%CI, -13.7 to -10.3,
 p=0.001). Recovery of stroke hospitalization volume (9.5%, 95%CI 9.2-9.8,
 p&lt;0.0001) was noted over the two later (May, June) versus the two
 earlier (March, April) pandemic months. There was a 1.48% stroke rate
 across 119,967 COVID-19 hospitalizations. SARS-CoV-2 infection was noted
 in 3.3% (1,722/52,026) of all stroke admissions.  
 Conclusions:  The COVID-19 pandemic was associated with a global
 decline in the volume of stroke hospitalizations, IVT, and interfacility
 IVT transfers. Primary stroke centers and centers with higher COVID19
 inpatient volumes experienced steeper declines. Recovery of stroke
 hospitalization was noted in the later pandemic months.
description: We conducted a cross-sectional, observational, retrospective study across 6 continents, 70 countries, and 457 stroke centers. Diagnoses were identified by their ICD-10 codes and/or classifications in stroke databases.
DOI: 10.5061/dryad.zcrjdfn9d
title: Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape

description: Dispersal distances of 17 species of butterflies in tropical Singapore
 were significantly greater in forest than in urban habitat. Butterflies in
 urban plots frequently moved within suitable habitat (park/grassland)
 patches but rarely crossed non-habitat patches suggesting potential
 isolation and a need for urban corridors.
description: The dataset describes the number of marked and recaptured
 individuals by plots and habitat type in this study as well as the
 dispersal distance and the number of days after which the marked
 individuals were recaptured at the three forest and urban sites.
DOI: 10.5061/dryad.qnk98sff8
title: Macroinvertebrate and environmental data for Wudalianchi Lake

description: Macroinvertebrate and environmental data of Wudalianchi Lake contained
 macroinvertebrate composition and environmental variable data of
 three seasons. There were three groups of environmental data,
 i.e. lake morphology (i.e. surface area, maximum depth and
 perimeter) and human-induced environmental changes of lakes (land use
 types in the buffer zone of 100 m width around lakes and water quality).
 Water quality inclued dissolved oxygen, water temperature, secchi depth,
 water depth, total phosphorus, total nitrogen, and chlorophyll a
 concentration. Macroinvertebrate composition data was the abundance of
 each species at different sampling sites.
DOI: 10.15468/dl.dnc9bw
title: Occurrence Download

description: A dataset containing 1233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Crotalaria novae-hollandiae",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1233 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002691-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8gtht76nn
title: Adrenomedullin induces migraine-like attacks in patients with migraine without aura

description: Objective: To determine whether the intravenous infusion of
 adrenomedullin, a potent vasodilator belonging to calcitonin family of
 peptides, provokes attacks of migraine in patients. Methods: We have
 enlisted twenty migraine without aura patients to participate in a
 placebo-controlled and double-blinded clinical study. In a randomized and
 crossover design the patients received an intravenous infusion of human
 adrenomedullin (19.9 picomole/kg/min) or placebo (saline) administrated
 via an automated intravenous pump for period of (20 minutes). The patients
 participated in two study days with washout period of minimum of seven
 days. The main outcome of the study was predefined as a difference in
 migraine incidence (0–12 h). Results: Eleven migraine without aura
 patients (55%) fulfilled migraine attacks criteria after adrenomedullin
 infusion in comparison to only three patients reported attack (15%) after
 placebo (P= 0.039). We found that patients reported in a period of (0-12
 hours) stronger headache intensity after adrenomedullin in comparison to
 placebo infusion (P= 0.035). Conclusion: Our data implicate adrenomedullin
 in migraine pathogenesis. This suggests that adrenomedullin and/or its
 receptors are novel therapeutic targets for the treatment of migraine.
 However, we cannot discount for the possibility that adrenomedullin may be
 acting through the canonical CGRP receptor.
DOI: 10.5061/dryad.1g1jwstv0
title: Data from: Carbonate shelf development and early Paleozoic benthic diversity in Baltica: A hierarchical diversity partitioning approach using brachiopod data

description: The Ordovician–Silurian (~485–419 Ma) was a time of considerable
 evolutionary upheaval, encompassing both the largest evolutionary
 diversification and one of the first major mass extinctions. The
 Ordovician diversification coincided with global climatic cooling and
 paleocontinental collision, the ecological impacts of which were mediated
 by region-specific processes including substrate changes, biotic
 invasions, and tectonic movements. From the Sandbian–Katian (~453 Ma)
 onward, an extensive carbonate shelf developed in the eastern Baltic
 paleobasin in response to a tectonic shift to tropical latitudes and an
 increase in the abundance of calcareous macroorganisms. We quantify the
 contributions of environmental differentiation and temporal turnover to
 regional diversity through the Ordovician and Silurian, using brachiopod
 occurrences from the more shallow-water facies belts of the eastern Baltic
 paleobasin, an epicontinental sea on the Baltica paleocontinent. The
 results are consistent with carbonate shelf development as a driver of
 Ordovician regional diversification, both by enhancing broadscale
 differentiation between shallow- and deep-marine environments and by
 generating heterogeneous carbonate environments that allowed increasing
 numbers of brachiopod genera to coexist. However, temporal turnover also
 contributed significantly to apparent regional diversity, particularly in
 the Middle–Late Ordovician.
description: This upload contains the R scripts and data needed to replicate
 the analyses and data preparation in the manuscript. The data were
 originally downloaded from the Paleobiology Database (PBDB,
 https://paleobiodb.org) and the database of the Geoscience Collections of
 Estonia (SARV, https://geocollections.info).
description: To use this code and data,
 open the file baltic_calculations_neat_revised_26_02_21_neat.R, which
 explains what the different R scripts do and does most of the calculations
 and figure plotting in this manuscript. functions_baltic_cleaning.R,
 01_BS_lithologies.R, 02_BS_geokud.R, 03_BS_PBDB.R are for data downloads
 and cleaning 04_BS_diversity.R does
 capture-recapture diversity estimation 05_figs.R produces some of the
 figures. make_supp_tables.R converts some
 of the results tables into tables in the Supplementary Material.
 Results from the analyses are also included in this
 upload.
DOI: 10.5061/dryad.rv15dv473
title: Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests

description: The aim of the study was to investigate the influence of fertilizers on
 root-associated and soil residing fungi in beech forests. We report data
 from a fertilization experiment in three temperate beech forest with
 contrasting soil phosphorus concentrations. We used soil cores and the
 fractions of the organic layer and mineral topsoil separately of spring
 and fall 2018. We collected bulk soil and roots. We provide data on soil
 for pH, mineral elements, ammonium, nitrate, carbon, nitrogen. We provide
 data on root mineral nutrients, carbon and nitrogen. Illumina sequencing
 in soil and roots provides fungal amplicon sequence variant (ASV) and
 morphotyping of beech fine roots the active colonizing ectomycorrhizal
 fungi, including diversity parameters.
description: Plots were installed in beech (F. sylvatica L.) forests in three
 areas that differ in soil properties: Bad Brückenau (50°21'7.2"N
 9°55'44.5"E, 801 to 850m a.s.l.), a high-P (HP), Mitterfels
 (48°58'34.1"N 12°52'46.7"E), a medium-P (MP) and Luess
 (52°50'21.7"N 10°16'2.3"E, 115 m a.s.l.), a low-P (LP)
 site. For this study, twelve plots were installed in
 the forests in Fall 2016. Each plot had an area of 400 m². Four different
 fertilization treatments were used: control, N, P, P+N, with three
 replicates at each site. Phosphorus (P) was applied
 once in fall 2016 as KH2PO4 at the dosage of 50 kg P ha-1 to the P and N+P
 plots. Nitrogen (N) was applied as NH4NO3 five times (fall 2016, spring
 2017, summer 2017, fall 2017, spring 2018) corresponding to a dosage of 30
 kg N ha-1 per treatment on the N and N+P plots.<br> Samples were
 taken in spring and fall 2018.