cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18149223
title: Reconstruction of 8,994 metagenome-assembled genomes  from 2,378 global hot springs samples from 2003 to 2023

description: Hot springs, as a typical extreme aquatic environment, not only resemble the early Earth’s ecology but also provide abundant and unique microbiological resources. Here, we present a dataset of metagenome-assembled genomes (MAGs) and gene set derived from metagenome sequencing of 2,378 BioSamples from 1,873 BioProjects from 2003 to 2023. The raw sequencing data consist of 20.05 T bases, and a unified quality control and genome assembly and annotation bioinformatic workflow was conducted, generating 24,246 MAGs. Dereplication with a 95% average nucleotide identity (ANI) similarity threshold filtered 8,994 MAGs, among which 7,655 were bacteria and 1,335 were archaea. Notably, 90.25% of the MAGs could not be assigned to known species. A total of 37.7 million non-redundant protein-coding genes were annotated with their domain, Gene Ontology and pathway. This dataset provides a comprehensive resource of genomes and genes for hot springs biome.
DOI: 10.5061/dryad.55425
title: Data from: Pyrenean ptarmigan decline under climatic and human influences through the Holocene

description: In Europe, the Quaternary is characterized by climatic fluctuations known
 to have led to many cycles of contraction and expansion of species
 geographical ranges. In addition, during the Holocene, historical changes
 in human occupation such as colonization or abandonment of traditional
 land uses can also affect habitats. These climatically or anthropically
 induced geographic range changes are expected to produce considerable
 effective populations size change, measurable in terms of genetic
 diversity and organization. The rock ptarmigan (Lagopus muta) is a
 small-bodied grouse occurring throughout Northern hemispheric arctic and
 alpine tundra. This species is not considered threatened at a continental
 scale, but the populations in the Pyrenees are because of their small
 population size, geographical isolation, and low genetic diversity. Here,
 we used eleven microsatellites to investigate genetic variations and
 differentiations and infer the overall demographic history of Pyrenean
 rock ptarmigan populations. The low genetic variability found in these
 populations has been previously thought to be the result of a bottleneck
 that occurred following the last glacial maximum (i.e., 10,000 years ago)
 or more recently (i.e., during the last 200 years). Our results clearly
 indicate a major bottleneck affecting the populations in the last tenth of
 the Holocene. We discuss how this decline can be explained by a
 combination of unfavorable and successive events which all increased the
 degree of habitat fragmentation.
description: microsatellite raw
 dataFstat input file
 describing the microsatellite raw data. There is 11 microsatellite
 markers, 170 individuals and 7 populations distributed from Est to
 Westrock
 ptarmigan.txt
DOI: 10.5281/zenodo.18149222
title: Reconstruction of 8,994 metagenome-assembled genomes  from 2,378 global hot springs samples from 2003 to 2023

description: Hot springs, as a typical extreme aquatic environment, not only resemble the early Earth’s ecology but also provide abundant and unique microbiological resources. Here, we present a dataset of metagenome-assembled genomes (MAGs) and gene set derived from metagenome sequencing of 2,378 BioSamples from 1,873 BioProjects from 2003 to 2023. The raw sequencing data consist of 20.05 T bases, and a unified quality control and genome assembly and annotation bioinformatic workflow was conducted, generating 24,246 MAGs. Dereplication with a 95% average nucleotide identity (ANI) similarity threshold filtered 8,994 MAGs, among which 7,655 were bacteria and 1,335 were archaea. Notably, 90.25% of the MAGs could not be assigned to known species. A total of 37.7 million non-redundant protein-coding genes were annotated with their domain, Gene Ontology and pathway. This dataset provides a comprehensive resource of genomes and genes for hot springs biome.
DOI: 10.15468/dl.dga9h4
title: Occurrence Download

description: A dataset containing 7392 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Moneses uniflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 7392 records from 262 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001364-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j5n50
title: Data from: Altered development of synapse structure and function in striatum caused by Parkinson's disease-linked LRRK2-G2019S mutation

description: Mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) can
 cause Parkinson's disease (PD), and the most common
 disease-associated mutation, G2019S, increases kinase activity. Because
 LRRK2 expression levels rise during synaptogenesis and are highest in
 dorsal striatal spiny projection neurons (SPNs), we tested the hypothesis
 that the LRRK2–G2019S mutation would alter development of excitatory
 synaptic networks in dorsal striatum. To circumvent experimental confounds
 associated with LRRK2 overexpression, we used mice expressing LRRK2–G2019S
 or D2017A (kinase-dead) knockin mutations. In whole-cell recordings,
 G2019S SPNs exhibited a fourfold increase in sEPSC frequency compared with
 wild-type SPNs in postnatal day 21 mice. Such heightened neural activity
 was increased similarly in direct- and indirect-pathway SPNs, and action
 potential-dependent activity was particularly elevated. Excitatory
 synaptic activity in D2017A SPNs was similar to wild type, indicating a
 selective effect of G2019S. Acute exposure to LRRK2 kinase inhibitors
 normalized activity, supporting that excessive neural activity in G2019S
 SPNs is mediated directly and is kinase dependent. Although dendritic
 arborization and densities of excitatory presynaptic terminals and
 postsynaptic dendritic spines in G2019S SPNs were similar to wild type,
 G2019S SPNs displayed larger spines that were matched functionally by a
 shift toward larger postsynaptic response amplitudes. Acutely isolating
 striatum from overlying neocortex normalized sEPSC frequency in G2019S
 mutants, supporting that abnormal corticostriatal activity is involved.
 These findings indicate that the G2019S mutation imparts a
 gain-of-abnormal function to SPN activity and morphology during a stage of
 development when activity can permanently modify circuit structure and
 function.
description: Stats_Matikainen Ankney
 _Kezunovic et alSummary table of all
 statistics used. Means and n's are provided in the associated
 paper.STATS_for_Dryad_Matikainen.xlsx
DOI: 10.5061/dryad.nr353
title: Data from: Cross-ontology multi-level association rule mining in the Gene Ontology

description: The Gene Ontology (GO) has become the internationally accepted standard
 for representing function, process, and location aspects of gene products.
 The wealth of GO annotation data provides a valuable source of implicit
 knowledge of relationships among these aspects. We describe a new method
 for association rule mining to discover implicit co-occurrence
 relationships across the GO sub-ontologies at multiple levels of
 abstraction. Prior work on association rule mining in the GO has
 concentrated on mining knowledge at a single level of abstraction and/or
 between terms from the same sub-ontology. We have developed a bottom-up
 generalization procedure called Cross-ontology Data Mining-Level by Level
 (COLL) that takes into account the structure and semantics of the GO,
 generates generalized transactions from annotation data and mines
 interesting multi-level cross-ontology association rules. We applied our
 method on publicly available chicken and mouse GO annotation datasets and
 mined 5368 and 3959 multi-level cross ontology rules from the two datasets
 respectively. We show that our approach discovers more and higher quality
 association rules from the GO as evaluated by biologists in comparison to
 previously published methods. Biologically interesting rules discovered by
 our method reveal unknown and surprising knowledge about co-occurring GO
 terms.
description: Generalization-HostThis is the primary generalization and mining script.Remove_Duplicate_RulesREADMEThis readme file contains instructions of how to execute the other two scripts and other components necessary for the execution.
DOI: 10.5061/dryad.5c6bq
title: Data from: A novel nonparametric measure of explained variation for survival data with an easy graphical interpretation

description: Introduction: For survival data the coefficient of determination cannot be
 used to describe how good a model fits to the data. Therefore, several
 measures of explained variation for survival data have been proposed in
 recent years. Methods: We analyse an existing measure of explained
 variation with regard to minimisation aspects and demonstrate that these
 are not fulfilled for the measure. Results: In analogy to the least
 squares method from linear regression analysis we develop a novel measure
 for categorical covariates which is based only on the Kaplan-Meier
 estimator. Hence, the novel measure is a completely nonparametric measure
 with an easy graphical interpretation. For the novel measure different
 weighting possibilities are available and a statistical test of
 significance can be performed. Eventually, we apply the novel measure and
 further measures of explained variation to a dataset comprising persons
 with a histopathological papillary thyroid carcinoma. Conclusion: We
 propose a novel measure of explained variation with a comprehensible
 derivation as well as a graphical interpretation, which may be used in
 further analyses with survival data.
description: dataset
DOI: 10.5061/dryad.6jd59
title: Data from: Cross-modal individual recognition in wild African lions

description: Individual recognition is considered to have been fundamental in the
 evolution of complex social systems and is thought to be a widespread
 ability throughout the animal kingdom. Although robust evidence for
 individual recognition remains limited, recent experimental paradigms that
 examine cross-modal processing have demonstrated individual recognition in
 a range of captive non-human animals. It is now highly relevant to test
 whether cross-modal individual recognition exists within wild populations
 and thus examine how it is employed during natural social interactions. We
 address this question by testing audio–visual cross-modal individual
 recognition in wild African lions (Panthera leo) using an
 expectancy-violation paradigm. When presented with a scenario where the
 playback of a loud-call (roaring) broadcast from behind a visual block is
 incongruent with the conspecific previously seen there, subjects responded
 more strongly than during the congruent scenario where the call and
 individual matched. These findings suggest that lions are capable of
 audio–visual cross-modal individual recognition and provide a useful
 method for studying this ability in wild populations.
description: Gilfillan et al. Raw
 DataRaw data for the
 response of lions to the cross-modal playback
 experiments.
DOI: 10.5061/dryad.14955
title: Data from: Diagnosing depression in chronic pain patients: DSM-IV Major Depressive Disorder vs. Beck Depression Inventory (BDI)

description: Background: Diagnosing depression in chronic pain is challenging due to
 overlapping somatic symptoms. In questionnaires, such as the Beck
 Depression Inventory (BDI), responses may be influenced more by pain than
 by the severity of depression. In addition, previous studies have
 suggested that symptoms of negative self-image, a key element in
 depression, are uncommon in chronic pain-related depression. The object of
 this study is to assess the relationship of the somatic and
 cognitive-emotional items of BDI with the diagnosis of depression, pain
 intensity, and disability. Methods: One hundred consecutive chronic pain
 patients completed the Structured Clinical Interview for DSM Disorders
 (SCID) for the diagnosis of major depressive disorder (MDD) according to
 DSM-IV. Two subscales of BDI (negative view of self and somatic-physical
 function) were created according to the factor model presented by Morley.
 Results: In the regression analysis, the somatic-physical function factor
 associated with MDD, while the negative view of self factor did not.
 Patients with MDD had higher scores in several of the BDI items when
 analysed separately. Insomnia and weight loss were not dependent on the
 depression diagnosis. Limitations: The relatively small sample size and
 the selected patient sample limit the generalisability of the results.
 Conclusions: Somatic symptoms of depression are also common in chronic
 pain and should not be excluded when diagnosing depression in pain
 patients. Regardless of the assessment method, diagnosing depression in
 chronic pain remains a challenge and requires careful interpretation of
 symptoms.
description: Chronic pain and
 depressionDSM-IV majordepression
 diagnosis related to a two factor model of Beck depression inventory.
 Factors are Negative view of self and Physical function. Additional
 variables; Current pain intensity (Visual Analogue Scale) and Pain
 DisabilityPaindepression.xlsx
DOI: 10.5061/dryad.m6g5286d
title: Data from: Blocking the evolution of insecticide-resistant malaria vectors with a microsporidian

description: Finding a way to block the evolution insecticide-resistance would be a
 major breakthrough for the control of malaria. We suggest that this may be
 possible by introducing a stress into mosquito populations that restores
 the sensitivity of genetically resistant mosquitoes and that decreases
 their longevity when they are not exposed to insecticide. We use a
 mathematical model to show that, despite the intense selection pressure
 imposed by insecticides, moderate levels of stress might tip the
 evolutionary balance between costs and benefits of resistance towards
 maintaining sensitivity. Our experimental work with the microsporidian
 parasite Vavraia culicis infecting two lines of resistant mosquitoes and a
 sensitive line suggests that it may indeed be possible to stress the
 mosquitoes in the required way. The mortality of resistant mosquitoes 24h
 after exposure to the insecticide was up to 8.8 times higher in infected
 than in uninfected ones; if mosquitoes were not exposed to the
 insecticide, resistant mosquitoes infected by the microsporidian lived
 about half as long as uninfected ones and insecticide-sensitive mosquitoes
 (with or without the parasite). Our results suggest that biopesticides or
 other insecticides that interfere with the expression of resistance may
 help to manage insecticide-resistance in programs of malaria control.
description: restored sensitivity of
 RSP colonyText file, columns
 separated with commas. – Data from the experiment to measure restored
 sensitivity to permethrin of mildly permethrin-resistant mosquitoes (RSP
 colony). Some mosquitoes were exposed to the parasite Vavraia culicis.
 They were exposed to permethrin 0, 15 or 30 minutes. The data are
 organized according to testing tube, so the column 'Mosquitoes'
 gives the number of mosquitoes in the tube, the column 'Dead'
 gives the number of mosquitoes in the tube s that died within
 24h.
 restored.RSP.txtrestored sensitivity of
 ZANU colonyText file, columns
 separated with commas. – Data from the experiment to measure restored
 sensitivity to DDT of DDT-resistant mosquitoes (ZANU colony). Some
 mosquitoes were exposed to the parasite Vavraia culicis. They were exposed
 to permethrin 0, 45, 90 or 135 minutes. The experiment was run in blocks
 given by 'replicate'. The data are organized according to
 testing tube, so the column 'Mosquitoes' gives the number of
 mosquitoes in the tube, the column 'Dead' gives the number of
 mosquitoes in the tube s that died within 24h.
 restored.ZANU.txtincreased cost of
 resistanceText file, columns
 separated with commas. – Data from the experiment to measure how infection
 by Vavraia culicis increases the cost of insecticide-resistance. The
 mosquito lines are RSP (permethrin resistance), ZANU (DDT-resistant) and S
 (Kisumu, sensitive). Longevity is measured in days; if the mosquito lived
 more than 16 days, it was censored at 16.
 cost.txt
DOI: 10.5061/dryad.5s260
title: Data from: Understanding the recent colonization history of a plant pathogenic fungus using population genetic tools and Approximate Bayesian Computation

description: Understanding the processes by which new diseases are introduced in
 previously healthy areas is of major interest in elaborating prevention
 and management policies as well as in understanding the dynamics of
 pathogen diversity at large spatial scale. In this study, we aimed to
 decipher the dispersal processes that have led to the emergence of the
 plant pathogenic fungus Microcyclus ulei, which is responsible for the
 South American Leaf Blight (SALB) that has affected rubber trees across
 Latin America since the beginning of the twentieth century. As only
 imprecise historical information is available, the study of population
 evolutionary history based on population genetics appeared most
 appropriate. The distribution of genetic diversity in a continental
 sampling of four countries (Brazil, Ecuador, Guatemala and French Guiana)
 was studied using a set of 16 microsatellite markers developed
 specifically for this purpose. A very strong genetic structure was found
 (Fst = 0.70), demonstrating that there has been no regular gene flow
 between Latin American M. ulei populations. Strong bottlenecks probably
 occurred at the foundation of each population. The most likely scenario of
 colonization identified by the Approximate Bayesian Computation (ABC)
 method implemented in DIYABC suggested two independent sources from the
 Amazonian endemic area. The Brazilian, Ecuadorian and Guatemalan
 populations might stem from serial introductions through human-mediated
 movement of infected plant material from an unsampled source population,
 whereas the French Guiana population seems to have arisen from an
 independent colonization event through spore dispersal.
description: MU-Data_12-0612
DOI: 10.5061/dryad.2sp49
title: Data from: Biological soil crusts modulate nitrogen availability in semi-arid ecosystems: insights from a Mediterranean grassland

description: Biological soil crusts (BSCs) greatly influence the N cycle of semi-arid
 ecosystems, as some organisms forming them are able to fix atmospheric N.
 However, BSCs are not always taken into account when studying biotic
 controls on N cycling and transformations. Our main objective was to
 understand how BSCs modulate the availability of N in a semi-arid
 Mediterranean ecosystem dominated by the tussock grass Stipa tenacissima.
 We selected the six most frequent soil cover types in the study area: S.
 tenacissima tussocks (ST), Retama sphaerocarpa shrubs (RS), and open areas
 with very low (BS), low (LC) medium (MC) and high (HC) cover of well
 developed and lichen-dominated BSCs. The temporal dynamics of available N
 dynamics followed changes in soil moisture. Available NH4+-N did not
 differ between microsites, while available NO3--N was substantially higher
 in the RS than in any other microsite. No significant differences in the
 amount of available NO3--N were found between ST and BS microsites, but
 these microsites had more NO3--N than those dominated by BSCs (LC, MC and
 HC). Our results suggest that BSCs may be inhibiting nitrification, and
 highlight the importance of this biotic community as a modulator of the
 availability of N in semi-arid ecosystems.
description: Castillo_PlSO2010Soil NH4+-N and NO3--N measured seasonally in the field in different microsites (bare ground soil, two main plant species and three degrees of biological soil crust development) during 2007 and 2008.
DOI: 10.5061/dryad.70m919n6
title: Data from: Perspectives on chemotaxonomy: molecular data confirm the existence of two morphologically distinct species within a chemically defined Lepraria caesiella (Stereocaulaceae)

description: Lepraria caesiella as currently circumscribed includes two sets of
 populations with different thallus morphologies. The populations are
 chemically identical but differ ecologically and are rarely sympatric. A
 phylogeny was inferred from ITS1, 5.8S, and ITS2 sequence data generated
 from a geographically broad sampling of the populations with each thallus
 type. Two strongly-supported clades were recovered that correlate to the
 two different morphotypes present within the species. Thus, L. caesiella
 is restricted to populations with aggregate thalli. Populations with
 placodioid thalli are formally described as a new species, L. harrisiana.
 A detailed taxonomic treatment of both taxa is presented.
description: caesiella_alignmentsThis is a zipped folder containing: 1) the original alignment prior to analyses, 2) the input file for MP (Paup) analyses with recoded ambiguously aligned regions and step matrices, 3) the input file for ML (Paup) analyses, 4) the input file for ML (RAxML) with ambiguously aligned regions recorded, 5) the input file for BI (MrBayes) analyses.caesiella_datasets.zip
DOI: 10.5061/dryad.f6p6r
title: Data from: Fishing-down within populations harms seed dispersal mutualism

description: Large fish are often the most effective seed dispersers, but they are also
 the preferred target for fisheries. We recently started to comprehend the
 detrimental impacts of the extirpation of large frugivorous fish species
 on natural forest regeneration, but we lack a general understanding of how
 intraspecific size-selective harvest affects fish–fruit mutualism. Our
 literature review demonstrated that large individuals within populations
 positively affect diverse aspects of seed dispersal, from consuming a
 higher diversity of seeds to enhancing germination. Furthermore, we filled
 a research gap by studying how individual size variations within two small
 frugivorous fish species (&lt;16 cm) affect seed dispersal in flooded
 savannas. Even within small-bodied species, large individuals swallow a
 higher number of intact seeds, but not necessarily a higher proportion.
 Overall, our results demonstrate the disproportional role of large-bodied
 individuals as key seed dispersers in flooded habitats. Consequently,
 fishing-down within both large- and small-bodied species can negatively
 affect seed dispersal and natural regeneration in overfished wetlands.
description: Costa_Pereira_et_al.
 BiotropicaData on seed consumption
 by fish in the Pantanal wetlandCosta_Pereira_et_al.xlsx
DOI: 10.5061/dryad.q680n
title: Data from: The Electric Honeycomb; an investigation of the Rose window instability

description: The Rose-window instability is a little-explored electrohydrodynamic
 instability that manifests when a layer of low-conducting oil is placed in
 an electric field generated by corona discharge in a point-toplane
 configuration. Above a critical voltage, the instability starts as a
 single dimple in the oil layer right below the point electrode and
 subsequently evolves into a characteristic pattern of polygonal cells. In
 this study we experimentally explore governing parameters that guide the
 instability and document geometric attributes of the characteristic
 cellular pattern. The driving force for the instability has been
 attributed to the buildup of charged ions which in-turn apply an electric
 pressure on the oil surface. We confirm the charged surface distribution
 using thermal imaging and demonstrate that the instability can be locally
 inhibited by preventing charge buildup under an ion shadow.
description: DATAgraph data
 points