cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kq23s
title: Data from: Prognosis of chronic kidney disease with normal-range proteinuria: The CKD-ROUTE study

description: Background: Although lower estimated glomerular filtration rate (eGFR) and
 higher proteinuria are high risks for mortality and kidney outcomes, the
 prognosis of chronic kidney disease (CKD) in patients with normal-range
 proteinuria remains unclear. Methods: In this prospective cohort study,
 1138 newly visiting stage G2-G5 CKD patients were stratified into
 normal-range and abnormal-range proteinuria groups. Study endpoints were
 CKD progression (&gt;50% eGFR loss or initiation of dialysis),
 cardiovascular events, and all-cause death. Results: In total, 927
 patients who were followed for &gt;6 months were included in the
 analysis. The mean age was 67 years, and 70.2% were male. During a median
 follow-up of 35 months, CKD progression, cardiovascular events, and
 mortality were observed in 223, 110, and 55 patients, respectively.
 Patients with normal-range proteinuria had a significantly lower risk for
 CKD progression (hazard ratio, 0.20; 95% confidence interval, 0.10-0.38)
 than those with abnormal-proteinuria by multivariate Cox proportional
 hazard analysis. We also analyzed patients with normal-range proteinuria
 (n=351). Nephrosclerosis was the most frequent cause of CKD among all
 patients with normal-range proteinuria (59.7%). During a median follow-up
 of 36 months, CKD progression, cardiovascular events, and mortality were
 observed in 10, 28, and 18 patients, respectively. The Kaplan-Meyer
 analysis demonstrated that the risks of CKD progression and cardiovascular
 events were not significantly different among CKD stages, whereas the risk
 of death was significantly higher in patients with advanced-stage CKD.
 Multivariate Cox proportional hazard analysis showed that the risk of
 three endpoints did not significantly differ among CKD stages. Conclusion:
 Newly visiting CKD patients with normal-range proteinuria, who tend to be
 overlooked during health checkups did not exhibit a decrease in kidney
 function even in advanced CKD stages under specialized nephrology care.
description: ROUTE_proteinuria
DOI: 10.5061/dryad.383q4
title: Data from: Density-dependent movement and the consequences of the Allee effect in the model organism Tetrahymena

description: 1. Movement and dispersal are critical processes for almost all organisms
 in natural populations. Understanding their causes and consequences is
 therefore of high interest. While both theoretical and empirical work
 suggests that dispersal, more exactly emigration, is plastic and may be a
 function of local population density, the functional relationship between
 the underlying movement strategies and population density has received
 less attention. 2. We here present evidence for the shape of this reaction
 norm and are able to differentiate between three possible cues: the
 relative number of individuals, the presence of metabolites (chemical
 cues) and resource availability. 3. We performed microcosm experiments
 with the ciliate model organism Tet-rahymena in order to understand the
 plasticity of movement strategies with respect to local density while
 controlling for possible confounding effects mediated by the availability
 of different cues. In addition, we investigated how an Allee effect can
 influence movement and dispersal plasticity. 4. Our findings suggest that
 movement strategies in Tetrahymena are plastic and density-dependent. The
 observed movement reaction norm was ushaped. This may be due to an Allee
 effect which led to negative densitydependence at low population densities
 and generally positive density-dependence at high population densities due
 to local competition. This possibly adaptive density-dependent movement
 strategy was likely mediated by chemical cues. 5. Our experimental work in
 highly controlled conditions indicates that both environmental cues as
 well as inherent population dynamics must be considered to understand
 movement and dispersal.
description: Fronhofer_et_al_JAE
DOI: 10.5061/dryad.bq7q0
title: Data from: Do the historical biogeography and evolutionary history of the digenean Margotrema spp. across central Mexico mirror those of their freshwater fish hosts (Goodeinae)?

description: Host-parasite systems provide an ideal platform to study evolution at
 different levels, including codivergence in a historical biogeography
 context. In this study we aim to describe biogeographic and codivergent
 patterns and associated processes of the Goodeinae freshwater fish and
 their digenean parasite (Margotrema spp.) over the last 6.5 Ma (million
 years), identifying the main factors (host and/or hydrogeomorphology) that
 influenced the evolution of Margotrema. We obtained a species tree for
 Margotrema spp. using DNA sequence data from mitochondrial and nuclear
 molecular markers (COI and ITS1, respectively) and performed molecular
 dating to discern divergence events within the genus. The
 dispersal-extinction-cladogenesis (DEC) model was used to describe the
 historical biogeography of digeneans and applied to cophylogenetic
 analyses of Margotrema and their goodeine hosts. Our results showed that
 the evolutionary history of Margotrema has been shaped in close
 association with its geographic context, especially with the geological
 history of central Mexico during the Pleistocene. Host-specificity has
 been established at three levels of historical association: a)
 Species-Species, represented by Xenotaenia resolanae-M. resolanae
 exclusively found in the Cuzalapa River Basin; b) Species-Lineage,
 represented by Characodon audax-M. bravoae Lineage II, exclusive to the
 Upper and Middle Mezquital River Basin, and c) Tribe-Lineage, including
 two instances of historical associations among parasites and hosts at the
 taxonomical level of tribe, one represented by Ilyodontini-M. bravoae
 Lineage I (distributed across the Ayuquila and Balsas River Basins), and
 another comprised of Girardinichthyini/Chapalichthyini-M. bravoae Lineage
 III, found only in the Lerma River Basin. We show that the evolutionary
 history of the parasites is, on several occasions, in agreement with the
 phylogenetic and biogeographic history of their hosts. A series of
 biogeographic and host-parasite events explain the codivergence patterns
 observed, in which cospeciation and colonisation via host-switching and
 vicariant plus dispersal events are appreciated, at different times during
 the diversification history of both associates, particularly during the
 Pleistocene.
description: DRYAD_1_MartinezAquino_et_al_PLOS1_COI_ITS_alignmentDRYAD_2_Martinez_Aquino_et_al_PLOS_starBEAST_YP_n_uDRYAD_3_MartinezAquino_et_al_PLOS1_lagrange_Margo_loc.lagrangeDRYAD_4_MartinezAquino_et_al_PLOS1_lagrange_Margo_loc_2.lagrangeDRYAD_5_MartinezAquino_et_al_PLOS1_lagrange_Margo_loc_3.lagrangeDRYAD_6_MartinezAquino_et_al_PLOS1_lagrange_Margo_host.lagrangeDRYAD_7_MartinezAquino_et_al_PLOS1_lagrange_Margo_host2.lagrangeDRYAD_8_MartinezAquino_et_al_PLOS1_TreeMap.tgl
DOI: 10.5061/dryad.5vr09
title: Data from: Incorporating intraspecific trait variation into functional diversity: impacts of selective logging on birds in Borneo

description: As conservation increasingly recognizes the importance of species’
 functional roles in ecosystem processes, studies are shifting away from
 measuring species richness towards measures that account for the
 functional differences between species in a community. These functional
 diversity (FD) indices have received much recent attention and refinement,
 but their greatest limitation remains their inability to incorporate
 information about intraspecific trait variation (ITV). We use an
 individual-based model to account for ITV when calculating the functional
 diversity of two avian communities in Borneo; one in primary (unlogged)
 forest and one in selectively logged forest. We deal with the scarcity of
 trait data for individual species by developing a simulation approach,
 taking data from the literature where necessary. Using a bootstrapping
 procedure, we produce a range of ecologically feasible FD values taking
 account of ITV for five commonly used FD indices, and we quantify the
 confidence that can be placed in these values, using a newly developed
 bootstrapping method: btFD. We find that incorporating ITV significantly
 alters the FD values of all indices used in our models. The rank order of
 FD for the two communities, indicating whether diversity was higher in
 primary or selectively logged forest, is largely unchanged by the
 inclusion of ITV. However, by accounting for ITV, we are able to reveal
 previously unrecognized impacts of selective logging on avian functional
 diversity through a narrower dispersion of individuals in functional trait
 space in logged forest. Our results highlight the importance of
 incorporating ITV into measures of functional diversity, whilst our
 simulation approach addresses the frequently encountered difficulty of
 working with sparse trait data and quantifies the confidence that should
 be placed in such findings.
description: Avian Community
 Composition of primary and logged forest, Sabah Borneo -
 PDFData originally
 collected in the field (see Edwards et al. 2013; doi: 10.1111/cobi.12059)
 and published previously in Edwards et al. (2013) supplementary
 information. Data represent species identity and abundance for all bird
 species originally recorded in Edwards et al. (2013). (PDF
 format)Ross
 et al. MEE - Dryad.pdfAvian Community
 Composition of primary and logged forest, Sabah Borneo -
 CSVData originally
 collected in the field (see Edwards et al. 2013; doi: 10.1111/cobi.12059)
 and published previously in Edwards et al. (2013) supplementary
 information. Data represent species identity and abundance for all bird
 species originally recorded in Edwards et al. (2013). (CSV
 format)Ross
 et al. MEE - Dryad.csv
DOI: 10.5061/dryad.ng473mj
title: Data from: A theory for polymicrogyria and brain arteriovenous malformations in HHT

description: Hereditary hemorrhagic telangiectasia (HHT) is generally considered a
 disorder of endothelial dysfunction, characterized by the development of
 multiple systemic arteriovenous malformations (AVMs), including within the
 brain. However, there have recently been a number of reports correlating
 HHT with malformations of cortical development, of which polymicrogyria is
 the most common type. Here we present seven new cases demonstrating
 polymicrogyria in HHT, six of which demonstrate a brain AVM (bAVM) in
 close spatial proximity, with the aim of providing a common origin for the
 association. Upon reviewing patient genetics and imaging data and
 comparing with previously reported findings, we form two new conclusions:
 i) polymicrogyria in HHT appears exclusively associated with a subset of
 mutations in the transmembrane protein endoglin that is involved with
 blood flow related mechanotransduction signaling during angiogenesis, and
 ii) the polymicrogyria is characteristically unilateral, typically focal,
 and correlates with vascular regions experiencing low fluid shear stress
 during corticogenesis in utero. Integrating these with findings in the
 literature from genetics and molecular biology experiments, we propose a
 theory suggesting dominant-negative endoglin mutations may predispose
 focal, aberrant hypersprouting angiogenesis during corticogenesis that
 leads to the production of polymicrogyria. This hypoxic insult may further
 serve as the revealing trigger for later development of a spatially
 coincident bAVM. This hypothesis suggests an essential role for
 endoglin-mediated hemodynamic mechanotransduction in normal
 corticogenesis.
description: Supplemental Materials -
 A Theory for Polymicrogyria and Brain Arteriovenous Malformations in
 HHTMethods, Table e-1, and
 Figures e-1, e-2, and e-3 for manuscript
DOI: 10.5061/dryad.13bp2
title: Data from: Changing patterns of cataract services in North-West Nigeria: 2005–2016

description: Purpose This study was conducted to assess the impact of the eye care
 programme on cataract blindness and cataract surgical services in Sokoto,
 Nigeria over a 12 year period 2005-2016. Methods Data from the 2005
 population based cross-sectional study of blindness in Sokoto state was
 re-analysed to obtain baseline estimates of the prevalence of cataract
 blindness and cataract surgical coverage for persons 50 years and over in
 Wurno health zone. A population based survey of a representative sample of
 persons 50 years and over in Wurno health zone was conducted in July 2016.
 Data on eye health workforce, infrastructure and cataract surgical
 services between 2005 and 2016 were analysed from relevant documents.
 Results In 2005 the unadjusted prevalence of bilateral cataract blindness
 (&lt;3/60) in people 50 years and over in Wurno health zone was 5.6%
 (95% CI: 3.1, 10.1). By 2016 this had fallen to 2.1% (95% CI 1.5%, 2.7%),
 with the age-sex adjusted prevalence being 1.9% (95% CI 1.3%, 2.5%). The
 CSC for persons with visual acuity &lt;3/60, &lt;6/60,
 &lt;6/18 for Wurno health zone was 9.1%, 7.1% and 5.5% respectively in
 2005 and this had increased to 67.3%, 62.1% and 34.7% respectively in
 2016. The CSR in Sokoto state increased from 272 (1005 operations) in
 2006, to 596 (2799 operations) in 2014. In the 2005 survey, couching (a
 procedure used by traditional practitioners to dislocate the lens into the
 vitreous cavity) accounted for 87.5% of all cataract interventions,
 compared to 45.8% in the 2016 survey participants. In 2016 18% of eyes
 having a cataract operation with IOL implantation had a presenting visual
 acuity of &lt;6/60 (poor outcome) with the main causes being
 postoperative complications (53%) and uncorrected refractive error (29%).
 Conclusion Between 2005 and 2016 there was a doubling in cataract surgical
 rate, a 7 times increase in cataract surgical coverage (&lt;3/60), and
 a decrease in cataract blindness and the proportion of eyes being couched.
 However, there remains a high prevalence of un-operated cataract in 2016
 indicating a need to further improve access to affordable and good quality
 cataract surgical services.
description: Wurno zone Sokoto
 Nigeria_2005This data was part of an
 all-age blindness prevalence survey conducted in Sokoto state Nigeria in
 2005. The data is for persons aged 50 years and over who were examined in
 Wurno health of Sokoto state. The sample were selected using a stratified
 sampling strategy. The operational definitions were based on WHO/PBL
 coding instructions for eye examination record.
DOI: 10.5061/dryad.975kk
title: Data from: Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence

description: BACKGROUND: Heroin dependence is a debilitating psychiatric disorder with
 complex inheritance. Since the dopaminergic system has a key role in
 rewarding mechanism of the brain, which is directly or indirectly targeted
 by most drugs of abuse, we focus on the effects and interactions among
 dopaminergic gene variants. OBJECTIVE: To study the potential association
 between allelic variants of dopamine D2 receptor (DRD2), ANKK1 (ankyrin
 repeat and kinase domain containing 1), dopamine D4 receptor (DRD4),
 Catechol-O-methyl transferase (COMT) and dopamine transporter (SLC6A3)
 genes and heroin dependence in Hungarian patients. METHODS: 303 heroin
 dependent subjects and 555 healthy controls were genotyped for 7 single
 nucleotide polymorphisms (SNPs): rs4680 of the COMT gene; rs1079597 and
 rs1800498 of the DRD2 gene; rs1800497 of the ANKK1 gene; rs1800955,
 rs936462 and rs747302 of the DRD4 gene. Four variable number of tandem
 repeats (VNTRs) were also genotyped: 120 bp duplication and 48 bp VNTR in
 exon 3 of DRD4 and 40 bp VNTR and intron 8 VNTR of SLC6A3. We also provide
 a multivariate model for the associations among them implying Bayesian
 networks in Bayesian multilevel analysis. FINDINGS AND CONCLUSIONS: In
 single marker analysis the TaqIA (rs1800497) and TaqIB (rs1079597)
 variants were associated with heroin dependence. Moreover, -521 C/T SNP
 (rs1800955) of the DRD4 gene showed nominal association with a possible
 protective effect of the C allele. After applying the Bonferroni
 correction TaqIB was still significant suggesting that the minor (A)
 allele of the TaqIB SNP is a risk component in the genetic background of
 heroin dependence. The findings of the additional multiple marker analysis
 are consistent with the results of the single marker analysis, but this
 method was able to reveal an indirect effect of a promoter polymorphism
 (rs936462) of the DRD4 gene and this effect is mediated through the -521
 C/T (rs1800955) polymorphism in the promoter.
description: Vereczkei et al -
 Hungarian heroin303_control555Spreadsheet containing
 all genotype-phenotype data on 303 Hungarian heroin dependent patients and
 555 healthy controls including DRD2, DRD4, SLC6A3 (DAT1) and COMT gene
 variants.
DOI: 10.5061/dryad.dn048
title: Data from: Is there a temperate bias in our understanding of how climate change will alter plant-herbivore interactions? A meta-analysis of experimental studies

description: Climate change can drive major shifts in community composition and
 interactions between resident species. However, the magnitude of these
 changes depends on the type of interactions and the biome in which they
 take place. We review the existing conceptual framework for how climate
 change will influence tropical plant-herbivore interactions and formalize
 a similar framework for the temperate zone. We then conduct the first
 biome-specific tests of how plant-herbivore interactions change in
 response to climate-driven changes in temperature, precipitation, ambient
 CO2, and ozone. We used quantitative meta-analysis to compare predicted
 and observed changes in experimental studies. Empirical studies were
 heavily biased toward temperate systems, so testing predicted changes in
 tropical plant-herbivore interactions was virtually impossible.
 Furthermore, most studies investigated the effects of CO2 with limited
 plant and herbivore species. Irrespective of location, most studies
 manipulated only one climate change factor despite the fact that different
 factors can act in synergy to alter responses of plants and herbivores.
 Finally, studies of belowground plant-herbivore interactions were also
 rare; those conducted suggest that climate change could have major effects
 on belowground subsystems. Our results suggest that there is a
 disconnection between the growing literature proposing how climate change
 will influence plant-herbivore interactions and the studies testing these
 predictions. General conclusions will also be hampered without better
 integration of above- and belowground systems, assessing the effects of
 multiple climate change factors simultaneously, and using greater
 diversity of species in experiments.
description: Mundim and
 Bruna_AMNAT_metadataMetadata describing the
 information used in the file "Mundim_Bruna AMNAT
 2016_data".Mundim_Bruna AMNAT
 2016_dataTable with the data
 collected from all the publications between 1993-2013 used in the
 meta-analysis.Mundim_Bruna AMNAT
 2016_referencesReferences of the
 studies used to extract data for the meta-analysis.
DOI: 10.5061/dryad.qp313np
title: Data from: TAK-071, a muscarinic M1 receptor positive allosteric modulator, attenuates scopolamine-induced quantitative electroencephalogram power spectral changes in cynomolgus monkeys

description: Activation of the muscarinic M1 receptor is a promising approach to
 improve cognitive deficits associated with cholinergic dysfunction in
 Alzheimer’s disease, dementia with Lewy bodies, and schizophrenia. TAK-071
 is an M1-selective positive allosteric modulator that improves cognitive
 deficits induced by scopolamine, a non-selective muscarinic receptor
 antagonist, with reduced side effects on gastrointestinal function in
 rats. In this study, we explored changes in quantitative
 electroencephalography (qEEG) power bands, with or without scopolamine
 challenge, as a non-invasive translational biomarker for the effect of
 TAK-071 in cynomolgus monkeys. Scopolamine has been reported to increase
 theta and delta power bands and decrease alpha power band in healthy
 volunteers. In line with the clinical observations, scopolamine (25‒100
 μg/kg, subcutaneous administration [s.c.]) increased theta and delta power
 bands in cynomolgus monkeys in a dose-dependent manner, whereas it had the
 opposite effect on alpha power band. The effects of TAK-071 on scopolamine
 (25 μg/kg, s.c.)-induced qEEG spectral changes were examined using an
 acetylcholinesterase inhibitor donepezil and a muscarinic M1/M4 receptor
 agonist xanomeline as comparative cholinomimetics. TAK-071 (0.3‒3 mg/kg,
 oral administration [p.o.]), donepezil (3 mg/kg, p.o.), and xanomeline (1
 mg/kg, s.c.) suppressed the scopolamine-induced increases in alpha, theta,
 and delta power bands. These results suggest that changes in specific qEEG
 power bands, in particular theta and delta power bands in the context of
 scopolamine challenge, could be used as translational biomarkers for the
 evaluation of TAK-071 in clinical studies.
description: Monkey EEG data for
 DryadMonkey
 EEG data.xlsx
DOI: 10.5061/dryad.qj864
title: Data from: Home loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

description: Genetic introgression from a resident species into an invading close
 relative can result from repeated hybridisation along the invasion front
 and/or allele surfing on the expansion wave. Cases where the phenomenon is
 massive and systematic, such as for hares (genus Lepus) in Iberia, would
 be best explained by recurrent hybridisation but this is difficult to
 prove since the donor populations are generally extinct. In the Pyrenean
 foothills, Lepus europaeus presumably replaced Lepus granatensis recently
 and the present species border is parallel to the direction of invasion,
 so that populations of L. granatensis in the contact zone represent
 proxies of existing variation before the invasion. Among three pairs of
 populations sampled across this border, we find less differentiation of
 mtDNA across than along it, as predicted under recurrent hybridisation at
 the invasion front. Using autosomal microsatellite loci and X and Y-linked
 diagnostic loci, we show that admixture across the border is quasi-absent,
 making it unlikely that lack of interspecific mtDNA differentiation result
 from ongoing gene flow. Furthermore, we find that the local species ranges
 are climatically contrasted, making it also unlikely that ongoing
 ecology-driven movement of the contact account for mtDNA introgression.
 The lack of mtDNA differentiation across the boundary is mostly due to
 sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus
 timidus) whose mitochondria have thus remained in place since the last
 deglaciation despite successive invasions by two other species. Home
 loving mitochondria thus witness past species distribution rather than
 ongoing exchanges across stabilised contact zones.
description: Melo-Ferreira_et_al_GenotypesGenotypes of 6 microsatellite loci (Sat2, Sat8, Sat12, INRACCDDv358, Lsa2, Sol30Le) from a total of 342 specimens from three species: Lepus granatensis, Lepus europaeus and Lepus timidus. Population code and number are indicated in the second and third column respectively.Melo-Ferreira_et_al_Data_Microsatellites.xlsxMelo_Ferreira_et_al_PHKA2_completeFinal alignment of PHKA2 sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b.Melo_Ferreira_et_al_SMCX_completeFinal alignment of SMCX sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b.Melo_Ferreira_et_al_MSN_completeFinal alignment of MSN sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b.Melo_Ferreira_et_al_HPRT1_completeFinal alignment of HPRT1 sequences used in this work. Data is phased - alternative alleles in females are indicated by a and b. A polymorphic poly-T of undetermined length was removed.