cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8ph6b30
title: Data from: Diversity and its decomposition into variety, balance and disparity

description: Diversity is a central concept in many fields. Despite its importance,
 there is no unified methodological framework to measure diversity and its
 three components of variety, balance and disparity. Current approaches
 take into account disparity of the types by considering their pairwise
 similarities. Pairwise similarities between types may not adequately
 capture total disparity, since they do not take into account in which way
 pairs are similar. Hence, pairwise similarities do not discriminate
 between similarities of types in terms of the same feature and
 similarities in which all pairs share different features. This paper
 presents an alternative approach which is based on the overlap of features
 over the whole set of types. This results in a measure of diversity takes
 into account the aspects of variety, balance and disparity. Based on this
 measure, the 'ABC decomposition' is introduced, which provides
 separate measures for the variety, balance and disparity, allowing them to
 enter analysis separately. The method is illustrated by analyzing the
 industrial diversity from 1850 to present while taking into account the
 overlap in occupations they employ. Finally, the framework is extended to
 take into account disparity considering multiple features, providing a
 helpful tool in analysis of high-dimensional data.
description: IPUMS_national_diversities.csvcsv file containing national diversity values from 1850-2010IPUMS_ind_occ_statecsv file containing counts of people per year-state-industry-occupationdiv_decomp_RscriptThe R script is used to generate a .csv file from the data extracted from IPUMS-USA.div_decomp_makefigsThe makefigures jupyter notebook contains the code that generates the figures that are used in the paper.div_decomp_makedataThe makedata jupyter notebook 'cleans' the data that is the output of the R script by excluding miscallaneuous classes from the data.IPUMS_data_extract_details.cbkThe extraxt_details.txt file contains the details of the data extract from IPUMS-USA (Steven Ruggles, Sarah Flood, Ronald Goeken, Josiah Grover, Erin Meyer, Jose Pacas, and Matthew Sobek. IPUMS USA: Version 9.0 [dataset]. Minneapolis, MN: IPUMS, 2019. https://doi.org/10.18128/D010.V9.0)
DOI: 10.15468/dl.p6ak3g
title: Occurrence Download

description: A dataset containing 778074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-5.57721 39.6958,-4.34121 39.6958,-4.34121 40.51814,-5.57721 40.51814,-5.57721 39.6958))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 778074 records from 301 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001728-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jc06126
title: Data from: Ecophysiology and phylogeny of new terricolous and epiphytic chlorolichens in a fog oasis of the Atacama Desert

description: The Atacama Desert is one of the driest and probably oldest deserts on
 Earth where only a few extremophile organisms are able to survive. This
 study investigated two terricolous and two epiphytic lichens from the fog
 oasis “Las Lomitas” within the National Park Pan de Azúcar which
 represents a refugium for a few vascular desert plants and many lichens
 that can thrive on fog and dew alone. Ecophysiological measurements and
 climate records were combined with molecular data of the mycobiont, their
 green algal photobionts and lichenicolous fungi to gain information about
 the ecology of lichens within the fog oasis. Phylogenetic and
 morphological investigations led to the identification and description of
 the two new lichen species Ramalina reichenbergeri and Acarospora conafii
 as well as the lichenicolous fungi that accompanied them and revealed the
 trebouxioid character of all lichen photobionts. Their photosynthetic
 response during natural scenarios such as reactivation by high air
 humidity and in situ fog events were compared to elucidate the activation
 strategies of this lichen community. Epiphytic lichens showed
 photosynthetic activity that was rapidly induced by fog and additionally
 during high air humidity whereas terricolous lichens were only activated
 by fog.
description: concatenated_mycobiont_ITS_RPB1Data contain the alignment of four lichen mycobiont species (Acarospora conafii sp. nov., Placidium sp., Everniopsis trulla, Ramalina reichenbergeri sp. nov.). Data are fasta file that can be opened with the software Mega or Mega X. ITS bp position 1-959; RBP1 bp position 960-1538.lichenicolous_fungi_ITSThis data file is a fasta file that can be opened with the software Mega or Mega X. It contains aligned sequences from the ITS region of lichenicolous fungi from Polysporina sp., Neonectria sp. and Tremella sp.concatenated_photobiont_LR3-rbcL-Al1500afThis data file is a fasta format that can be opened with the software Mega or Mega X. It contains a concatenated alignment of lichen photobiont (trebouxioid) sequences of the LR3, rbcl and Al1500af regions. LR3 bp position 1-688; rbcL bp position 689-1619 ; 18S bp position 1620-2327.
DOI: 10.5061/dryad.43m733k
title: Data from: Disruption of the ascending arousal network in acute traumatic disorders of consciousness

description: Objective: To determine whether ascending arousal network (AAN)
 connectivity is reduced in patients presenting with traumatic coma.
 Methods: We performed high angular resolution diffusion imaging (HARDI) in
 16 patients with acute severe traumatic brain injury who were comatose on
 admission and in 16 matched controls. We used probabilistic tractography
 to measure the connectivity probability (CP) of AAN axonal pathways
 linking the brainstem tegmentum to the hypothalamus, thalamus and basal
 forebrain. To assess the spatial specificity of CP differences between
 patients and controls, we also measured CP within four subcortical
 pathways outside the AAN. Results: Compared to controls, patients showed a
 reduction in AAN pathways connecting the brainstem tegmentum to a region
 of interest encompassing the hypothalamus, thalamus, and basal forebrain.
 Examining each pathway individually, brainstem-hypothalamus and
 brainstem-thalamus CPs, but not brainstem-forebrain CP, were significantly
 reduced in patients. Only one subcortical pathway outside the AAN showed
 reduced CP in patients. Conclusions: We provide initial evidence for the
 reduced integrity of axonal pathways linking the brainstem tegmentum to
 the hypothalamus and thalamus in patients presenting with traumatic coma.
 Our findings support current conceptual models of coma as being caused by
 subcortical AAN injury. AAN connectivity mapping provides an opportunity
 to advance the study of human coma and consciousness.
description: Supplementary Video
 1Supplementary_Video_1_20181112.mp4Supplementary Video 2Supplementary_Video_2_20181112.mp4Supplementary Video 3Supplementary_Video_3_20181112.mp4Supplementary MaterialSupplementary_Material_Final_20190820.pdf
DOI: 10.5061/dryad.cq91j7v
title: Data from: Mitochondrial genotype influences the response to cold stress in the European green crab Carcinus maenas

description: Hybrid zones provide natural experiments in recombination within and
 between genomes that may have strong effects on organismal fitness. On the
 East Coast of North America, two distinct lineages of the European green
 crab (Carcinus maenas) have been introduced in the last two centuries.
 These two lineages with putatively different adaptive properties have
 hybridized along the coast of the eastern Gulf of Maine, producing new
 nuclear and mitochondrial combinations that show clinal variation
 correlated with water temperature. To test the hypothesis that
 mitochondrial or nuclear genes have effects on thermal tolerance, we first
 measured the response to cold stress in crabs collected throughout the
 hybrid zone, then sequenced the mitochondrial CO1 gene and two nuclear
 SNPs representative of nuclear genetic lineage. Mitochondrial haplotype
 had a strong association with the ability of crabs to right themselves at
 4.5 &[deg]C that was sex specific: haplotypes originally from
 northern Europe gave male crabs an advantage while there was no haplotype
 effect on righting in female crabs. By contrast, the two nuclear SNPs that
 were significant outliers in a comparison between northern and southern C.
 maenas populations had no effect on righting response at low temperature.
 These results add C. maenas to the short list of ectotherms in which
 mitochondrial variation has been shown to affect thermal tolerance, and
 suggests that natural selection is shaping the structure of the hybrid
 zone across the Gulf of Maine. Our limited genomic sampling does not
 eliminate the strong possibility that mitonuclear coadaptation may play a
 role in the differences in thermal phenotypes documented here. Linkage
 between mitochondrial genotype and thermal tolerance suggests a role for
 local adaptation in promoting the spread of invasive populations of C.
 maenas around the world.
description: Dryad_phenotype_genotype_dataSee readme fileNuclear SMC sequence reads in fasta formatSee readme fileNuclear_SMC.fastaNuclear UBE2H sequence reads in fasta formatNuclear_UBE2H.fasta
DOI: 10.5061/dryad.pb5374s
title: Data from: New net zooplankton geographical information system in the Far East seas and adjacent waters of the Pacific Ocean

description: Motivation: I describe the GIS that is based on a database of zooplankton
 collected by Juday net with 0.1 m^2 opening (0.168 mm mesh) Main types of
 variable contained The average density (mg/m3) of plankton and their
 different constituents in one-degree trapeziums Location: Chukchi, Bering,
 Okhotsk, Japan/East seas, Pacific Ocean Time period: 1984-2013 Taxa
 studied: All mesofauna – more than 214 species of holo- and meroplankton
 Methods: GIS creation, data analysis and literature review Software
 format: Any that is capable of working with shapefiles Results: Maps of
 the spatial-temporal distribution of plankton with various taxonomic
 groups and dimensions were compiled and analysed. Based on these maps and
 on the literature, a supposition was made regarding the negative
 correlation of the zooplankton size with temperature. It was also revealed
 that some fluctuations in the abundance of plankton in the Bering Sea and
 the ocean are in phase, while in the Sea of Okhotsk and the Sea of Japan,
 the fluctuations are fully out of phase. In particular, during the
 transition from the light to dark time of the day in the Sea of Okhotsk
 and Sea of Japan, the density of plankton almost everywhere throughout the
 epipelagic zone increases; however, in the Bering Sea and the ocean, over
 large parts of the water area, it decreases. This means that the common
 practice employed by trophologists of attempting to replace the day-time
 catch in plankton nets with the night-time catches to assess the food
 reserves for fish will give significantly different results in these
 waters. Main conclusion: This unique GIS could be useful for understanding
 patterns and drivers of plankton biomass variations at large scales.
 Unfortunately, due to lack of funding, it has not been brought to the
 levels of species and development stages that could be available in the
 final release
description: SupplementThe supplementary material contains zip-archived GIS layers with data on the average plankton concentrations in mg/m3 of the following: small (Sf), medium (Mf) and large (Lf) fractions, total zooplankton (Total), different groups (Protista, Jellyfish, Copepoda, Amphipoda, Euphausia, Chaetognat, Meroplankt, Cladocera, Pteropoda, Mysida, Cumacea, Isopoda, Ostracoda, and other), as well as total concentrations obtained in the day (D) and night (N) times, different seasons (Win, Spr, Sum, Aut), and long-term periods (Y1984_1990, Y1991_1995, Y1996_2005, Y2006_2013); this material is found as shapefiles and tab-delimited txt files. These data were used to construct Figures 2-8 of the paper.
DOI: 10.5061/dryad.876r5m5
title: Data from: Clinical Reasoning: Pes cavus and neuropathy: think beyond Charcot-Marie-Tooth disease

description: An 18-year-old woman was referred to a neuromuscular clinic for neuropathy
 and tremors. She had been born full-term and had mildly delayed walking at
 14 months. She was a toe-walker, clumsy, and when running, had difficulty
 keeping up with her peers. She was diagnosed with
 attention-deficit/hyperactivity disorder (ADHD) at age 7 and was found to
 have high arches and difficulty with heel-walking. EMG and nerve
 conduction studies (NCS) were performed, showing demyelinating neuropathy
 (table e-1, doi.org/10.5061/dryad.876r5m5). With her history and EMG/NCS
 findings, she was diagnosed with Charcot-Marie-Tooth (CMT) disease.
 Symptoms progressed over the next few years, characterized by tripping,
 occasional falls, and continued difficulty running. She could climb stairs
 without the use of a handrail, but was very cautious going down the
 stairs. She also developed tremors in the hands (left &gt; right),
 which would worsen when she approached objects. There was no loss of
 sensation, paresthesias, bladder or bowel problems, or hearing or visual
 symptoms. She graduated from high school and was accepted into college.
 Family history was negative for neurologic disorders. Neurologic
 examination showed normal mental status and cranial nerves. There were no
 abnormal eye movements or corticobulbar findings (no brisk jaw jerk, gag
 reflex, dysarthria, or pseudobulbar palsy). She had ankle contractures and
 pes cavus. She had mild lower limb spasticity without atrophy or
 fasciculations, and 5−/5 weakness of distal extremity muscles, including
 bilateral abductor digiti minimi, first dorsal interossei, tibialis
 anterior, and extensor hallucis longus. Tendon reflexes were 2+ in the
 upper extremities and brisk (3+) in the lower extremities; plantars were
 extensor. Sensation was intact to light touch, pain, temperature, and
 proprioception, but vibration was mildly reduced at the toes. She had
 cerebellar intention tremors (left &gt; right) and mild dysmetria on
 finger-to-nose testing without appreciable dysdiadochokinesia. Her gait
 was mildly wide-based and tandem gait was impaired.
description: Supplemental
 table
DOI: 10.5061/dryad.dp75314
title: Data from: Serum GFAP and neurofilament light as biomarkers of disease activity and disability in NMOSD

description: Objective: To test the hypothesis that serum levels of glial fibrillary
 acidic protein (GFAP) and neurofilament light chain (NfL), which are
 intermediate astrocyte and neuron filaments, respectively, are clinically
 useful biomarkers of disease activity and disability in neuromyelitis
 optica spectrum disorders (NMOSD). Methods: Levels of GFAP and NfL in
 serum (sGFAP and sNfL, respectively) and in CSF samples were measured in
 healthy controls (HCs) (n = 49; 49 serum samples), patients with NMOSD (n
 = 33; 42 CSF and 102 serum samples), and patients with multiple sclerosis
 (MS) (n = 49; 53 CSF and 91 serum samples) by ultrasensitive
 single-molecule array (Simoa) assays. Association of sGFAP and sNfL levels
 with clinical parameters was determined. Results: For both GFAP and NfL,
 CSF and serum levels were strongly correlated. Both were higher in the
 serum of patients with NMOSD than in HCs (both p &lt; 0.001).
 Moreover, sGFAP was higher in NMOSD than in MS (median: 207.7 vs. 121.1
 pg/ml, p &lt; 0.001). In NMOSD, sGFAP concentration increased after
 recent relapse (540.9 vs. 152.9 pg/ml, p &lt; 0.001). Multivariate
 analyses indicated that sGFAP and sNfL were associated with Expanded
 Disability Status Scale (EDSS) score in NMOSD (p = 0.026 and p &lt;
 0.001, respectively). Higher sGFAP/sNfL quotient at relapse differentiated
 NMOSD from MS with a sensitivity of 73.0% and a specificity of 75.8%.
 Conclusions: sGFAP and sNfL are likely to be good biomarkers of disease
 activity and disability, and the sGFAP/sNfL quotient at relapse is a
 potential diagnostic marker for NMOSD.
description: Supplementary
 dataTables e-1 to e-11 and
 figure e-1serumGFAPandNfLinNMOSD_Neurology_Supple_re-revised_final_plain.pdf
DOI: 10.5061/dryad.4q07cj1
title: Data from: Degree of serotonin reuptake inhibition of antidepressants and ischemic risk: a cohort study

description: Objective: To assess whether the use of antidepressants with strong
 inhibition of serotonin reuptake is associated with a decreased incidence
 of ischemic stroke and myocardial infarction (MI). Methods: We conducted a
 cohort study using the United Kingdom Clinical Practice Research Datalink
 and considering new users of selective serotonin reuptake inhibitors
 (SSRIs) or third-generation antidepressants aged ≥18 years between 1995
 and 2014. Using a nested case-control approach, each case of a first
 ischemic stroke or MI identified during follow-up was matched with up to
 30 controls on age, sex, calendar time, and duration of follow-up. We
 estimated incidence rate ratios (RRs) and 95% confidence intervals (CIs)
 of each outcome associated with current use of strong compared with weak
 inhibitors of serotonin reuptake using conditional logistic regression.
 Results: The cohort included 938,388 incident users of SSRIs (n = 868,755)
 or third-generation antidepressants (n = 69,633). Mean age at cohort entry
 was 46 years (64% women). During follow-up, 15,860 cases of ischemic
 stroke and 8626 cases of MI were identified and matched to 473,712 and
 258,022 controls, respectively. Compared with current use of weak
 inhibitors of serotonin reuptake, current use of strong inhibitors was
 associated with a decreased rate of ischemic stroke (RR, 0.88; 95% CI
 0.80-0.97), but the effect size was smaller in some sensitivity analyses.
 The rate of MI was similar between strong versus weak inhibitors (RR,
 1.00; 95% CI, 0.87-1.15). Conclusion: Our large population-based study
 suggests that antidepressants strongly inhibiting serotonin reuptake could
 modestly decrease the rate of ischemic stroke.
description: Douros_SSRI_CVD_R1_20190315_AppendixAppendix
DOI: 10.5061/dryad.bn0655b
title: Data from: Constitutive innate immunity of tropical House Wrens varies with season and reproductive activity

description: In lowland Neotropical regions, where air temperature and day length
 remain relatively constant year-round, seasonality is determined primarily
 by changes in rainfall. The wet season triggers the start of breeding for
 many Neotropical birds, but also alters the antigenic environment, likely
 increasing the risk of disease transmission. We explored two hypotheses
 about temporal variation in constitutive innate immunity of a Neotropical
 bird, the House Wren (Troglodytes aedon). One hypothesis proposes that
 Neotropical wrens up-regulate their immune function in the wet season
 either in anticipation of or in response to vectors that become more
 prevalent. A second hypotheses proposes that during periods of putative
 high resource demand, such as when parents are feeding young, immune
 function would be compromised and downregulated. Controlling for
 reproductive stage, we found that microbicidal capacity of blood against
 Escherichia coli was higher in the wet than the dry season, consistent
 with the antigen response hypothesis. Phagocytosis of E.coli and
 Staphylococcus aureus did not differ between wet and dry seasons.
 Microbicidal capacity and H/L-ration of tropical House Wrens did not vary
 among reproductive stages, and our data offered no support for the idea
 that immune function is compromised during the period when parents are
 feeding young.
description: Data_Tielemanetal_auk2019Data used for all analysis of Tieleman et al, Auk, 2019R_scriptsTielemanetal_auk_2019R-scripts for analyses in Tieleman et al., Auk, 2019
DOI: 10.5061/dryad.ps0qf4r
title: Data from: Graph splitting: a graph-based approach for superfamily-scale phylogenetic tree reconstruction

description: A protein superfamily contains distantly related proteins that have
 acquired diverse biological functions through a long evolutionary history.
 Phylogenetic analysis of the early evolution of protein superfamilies is a
 key challenge because existing phylogenetic methods show poor performance
 when protein sequences are too diverged to construct an informative
 multiple sequence alignment. Here, we propose the Graph Splitting (GS)
 method, which rapidly reconstructs a protein superfamily-scale
 phylogenetic tree using a graph-based approach. Evolutionary simulation
 showed that the GS method can accurately reconstruct phylogenetic trees
 and be robust to major problems in phylogenetic estimation, such as biased
 taxon sampling, heterogeneous evolutionary rates, and long-branch
 attraction when sequences are substantially diverged. Its application to
 an empirical dataset of the triosephosphate isomerase (TIM)-barrel
 superfamily suggests rapid evolution of protein-mediated pyrimidine
 biosynthesis, likely taking place after the RNA world. Furthermore, the GS
 method can also substantially improve performance of widely used multiple
 sequence alignment methods by providing accurate guide trees.
description: Supplementary
 MaterialSupplementary Material
 for Graph Splitting: A Graph-Based Approach for Superfamily-scale
 Phylogenetic Tree Reconstruction. Figures S1–S19, Table S1, Captions for
 Movies S1–S2, Text S1, and ReferencesMatsui_M_SupplementaryMaterials_190318.pdfSupplementary Movie S1Movie S1. Movie of a 3D structural alignment of a dihydroorotate (DHO) dehydrogenase (red, 4OQV), a dihydropyrimidine (DPY) dehydrogenase (blue, 1GTE), and a glutamate synthase (green, 1EA0).Supplementary_Movie_1.mp4Supplementary Movie S2Movie S2. Movie of a 3D structural alignment of a flavin oxidoreductase (group 1) (yellow, 1VHN), a DHO dehydrogenase (red, 4OQV), and a flavin oxidoreductase (group 2) (black, 1Z41).Supplementary_Movie_2.mp4
DOI: 10.5061/dryad.mn8v722
title: Data from: Tadpole body size and behavior alter the social acquisition of a defensive bacterial symbiont

description: Individual differences in host phenotypes can generate heterogeneity in
 the acquisition and transmission of microbes. Although this has become a
 prominent factor of disease epidemiology, host phenotypic variation might
 similarly underlie the transmission of microbial symbionts that defend
 against pathogen infection. Using green frog (Lithobates clamitans)
 tadpoles, we test whether body size and behavior influence the social
 acquisition of a skin bacterium, Janthinobacterium lividum, which in some
 hosts can confer protection against infection by Batrachochytrium
 dendrobatidis, the causative agent of the amphibian skin disease
 chytridiomycosis. We measured body size and boldness (time spent in an
 open field) of green frog tadpoles and haphazardly constructed groups of
 six individuals. In some groups we exposed one individual in each group to
 J. lividum and, in other groups, we inoculated a patch of aquarium pebbles
 to J. lividum. After 24hr, we swabbed each individual to estimate the
 presence of J. lividum on their skin. On average, tadpoles acquired nearly
 four times more bacteria when housed with an exposed individual compared
 to those housed with a patch of inoculated substrate. When tadpoles were
 housed with an exposed group-mate, larger and “bolder” individuals
 acquired more bacteria. These data suggest that phenotypically-biased
 acquisition of defensive symbionts might generate biased patterns of
 mortality from the pathogens against which they protect.
description: Data from Keiser et al -
 Tadpole bacterial acquisition