cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8cz8w9gx7
title: Data from: Niche position accounts for the positive occupancy-abundance relationship of lake fishes

description: If the positive occupancy-abundance relationship prevails, locally
 abundant species are widely distributed. Although broadly supported,
 studies on lake fishes have thus far contributed little to this topic,
 especially at intermediate and small spatial scales. Here, the main
 objective was to investigate the relationship between occupancy and
 abundance of lake fish species within a large lake, as well as the
 relative importance of ecological niches, functional traits, and
 phylogenetic relatedness in forming the relationship. The study location
 was Poyang Lake, China. We calculated occupancy and mean abundance for 78
 fish species, and estimated niche position and niche breadth for each
 species based on a set of environmental variables. Additionally, we
 generated four functional trait vectors and one phylogenetic vector,
 describing trait similarity and phylogenetic relatedness, respectively.
 Linear models, hierarchical partitioning analyses, and boosted regression
 trees were used in combination to explore the relative role of niche
 position, niche breadth, trait vectors, and phylogenetic relatedness in
 determining fish occupancy, abundance, and their relationship. Occupancy
 and mean abundance of fish species in Poyang Lake showed a significantly
 positive and rather strong (R2﹦0.783) interspecific relationship.
 Interspecific variations in fish occupancy and abundance were well
 accounted for by niche position (individual importance using hierarchical
 partitioning: 0.644 and 0.494), followed by niche breadth (0.081 and
 0.040). Nonetheless, trait vectors (0.002 to 0.038 and -0.007 to 0.026)
 and phylogenetic relatedness (0.006 and -0.003) were of minor importance
 in affecting fish occupancy and abundance. Additionally, occupancy was
 better explained than abundance by the predictor variables used, which was
 shown by linear models (R2: 0.797 versus 0.547) and boosted regression
 trees (deviance: 0.889 versus 0.740). This study suggests that the
 positive correlation between occupancy and abundance also occurs in lake
 fish species. Furthermore, ecological niche features, especially niche
 position, were more important than functional traits and phylogenetic
 relatedness in accounting for occupancy and abundance of fish species in
 Poyang Lake.
description: # Niche position accounts for the positive occupancy-abundance
 relationship of lake fishes **File list:** *fish_model_data.csv*
 (explanatory and response variables for 78 fish species) **File
 description:** *fish_model_data.csv* Variables for each fish species:
 species, occupancy, total abundance, niche position, niche breadth,
 phylogenetic vector, trait vector 1, trait vector 2, trait vector 3, trait
 vector 4
DOI: 10.15468/dl.gpskwv
title: Occurrence Download

description: A dataset containing 2363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pteropus vampyrus"
 ]
}

 The dataset includes 2363 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003601-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8q6wn
title: Occurrence Download

description: A dataset containing 3801 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megisba malaya"
 ]
}

 The dataset includes 3801 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003604-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d51c5b08c
title: Paternal environment effects are driven by female reproductive fluid but not sperm age in an external fertiliser

description: Sperm ageing after ejaculation can generate paternal environmental effects
 that impact offspring fitness. In many species, female reproductive fluids
 (FRFs), i.e. ancillary fluids released by eggs or within the female
 reproductive tract, may protect sperm from ageing and can additionally
 interact with sperm to influence offspring viability. This raises the
 intriguing prospect that FRFs may alleviate paternal effects associated
 with sperm ageing. Here, we test this novel hypothesis using the broadcast
 spawning mussel, Mytilus galloprovincialis. We show that incubating sperm
 in FRF prior to fertilisation increases offspring viability and that these
 effects occur independently of sperm age. Our results provide novel
 evidence that FRFs allow females to selectively bias fertilisation toward
 higher quality sperm within an ejaculate, which in turn yields more viable
 offspring. We consider this FRF-mediated paternal effect in the context of
 female physiological control over fertilisation and the transgenerational
 effects of female-regulated haploid selection.
DOI: 10.5061/dryad.8w9ghx3sj
title: Molecular analysis of Ganoderma and Amauroderma species in the tropical rainforest of Sarawak, Borneo

description: This study aimed to record the genetic types of both Ganoderma australe
 sensu lato and Amauroderma subrugosum sensu lato with their morphological
 and ecological traits. Ganoderma australe sensu lato and Amauroderma
 subrugosum sensu lato were studied in three national parks in Sarawak:
 Santubong, Kubah (western area) and Lambir Hill (northeastern area). The
 decay stage and diameter of fallen logs from which fungal fruiting bodies
 appeared were recorded. The size of the pores and length of the tube of
 fruiting bodies were measured and recorded in the laboratory. Molecular
 phylogenetic trees were inferred from nucleotide sequence of the internal
 transcribed spacer (ITS) region of ribosomal RNA. In the phylogenetic tree
 analysis, Amauroderma subrugosum was grouped into a single genetic type
 while Ganoderma australe has been divided and classified into four genetic
 types: type 1, type 2, type 3, and type 5. All genetic types of Ganoderma
 australe fruiting bodies frequently appear in the intermediate stages of
 decayed wood (stage 3) from small and medium-sized (diameter) fallen trees
 or logs. In this study, no novel genetic types of Ganoderma australe were
 observed, and several genetic types were not observed in Amauroderma
 subrugosum. All genetic types of Ganoderma australe were found in the
 northeast (Lambir Hills) and west (Kubah, Santubong) areas of Sarawak.
 This suggests that these genetic types are widely distributed across
 Sarawak. Further study is needed to reveal the mechanisms that drive
 speciation and maintain genetic diversity in Ganoderma australe and the
 mechanisms that prevent speciation in Amauroderma subrugosum.
DOI: 10.5061/dryad.b2rbnzsn6
title: Data for: Early Eocene fossils elucidate the evolutionary history of the Charadriiformes (shorebirds and allies)

description: We report charadriiform and charadriiform-like birds from the early Eocene
 London Clay of Walton-on-the-Naze (Essex, UK). A partial skeleton of a
 small modern-type charadriiform is described as a new species,
 Charadriisimilis essexensis, gen. et sp. nov. and most closely resembles
 taxa of the Charadrii (plovers, stilts, oystercatchers, and other
 “wader-like” shorebirds). Affinities to this clade were also supported by
 phylogenetic analyses, which placed the fossil as the sister taxon of
 either the Burhinidae or all crown group Charadrii. In addition, we
 identify specimens of the charadriiform-like taxon Scandiavis, which was
 before only known from the early Eocene Fur Formation in Denmark.
 Associated limb elements of two individuals are classified as Scandiavis
 cf. mikkelseni, and remains of two further individuals are tentatively
 assigned to Scandiavis. The presence of a processus supracondylaris
 dorsalis on the previously unknown humerus corroborates charadriiform
 affinities of Scandiavis, whereas a plesiomorphic hypotarsus morphology
 indicates a position outside crown group Charadriiformes. Charadriisimilis
 essexensis is one of the earliest modern-type charadriiforms, and the
 holotype of the species is the most substantial early Paleogene fossil
 record of a charadriiform bird. Together with Scandiavis, as the
 best-represented taxon to be considered as a stem group charadriiform, it
 provides the basis for an improved understanding of the evolutionary
 history of charadriiform birds.
description: # Data for: Early Eocene fossils elucidate the evolutionary history of the
 Charadriiformes (shorebirds and allies) ---
 "Charadriisimilis.ss" is the nexus file used for the analysis\
 "Mayr and Kitchener Electronic Supplementary Material" contains
 the character descriptions and character matrix ## Description of the data
 and file structure "Charadriisimilis.ss" is the nexus file used
 for the analysis "Mayr and Kitchener Electronic Supplementary
 Material" contains the character descriptions and character matrix ##
 Sharing/Access information This is a section for linking to other ways to
 access the data, and for linking to sources the data is derived from, if
 any. Links to other publicly accessible locations of the data: N/A Data
 was derived from the following sources: N/A ## Code/Software N/A
DOI: 10.5061/dryad.m0cfxpp8t
title: Performance characteristics of an HIV risk screening tool in Uganda

description: Introduction: Improving HIV testing efficiency has been documented to save
 financial and material resources for health.  In October 2019,
 the Ministry of HealthH Uganda deployed an HIV risk screening tool for use
 in 24 health facilities targeting clients aged 15 years and above in both
 outpatient and Voluntary Counselling and Testing departments. Methods: We
 conducted a retrospective secondary data analysis of routinely collected
 HIV risk screening program data in Uganda, collected from October to
 November 2019, to determine the performance characteristics of the
 adolescent and adult HIV risk screening tool in public health facility
 settings. Statistical measures for the risk screening tool performance
 included sensitivity, specificity, positive and negative predictive
 values, and cost analysis.  Results: A total of 19,854 clients
 were screened for HIV testing eligibility; we excluded 150 records with
 incomplete testing information. The overall positivity rate
 (cluster-weighted prevalence of HIV) among those screened was 4.5% (95%
 CI: 4.1–4.8%) versus 3.71% (95% CI: 3.06–4.50) among those not screened.
 The sensitivity and specificity of the risk screening tool were found to
 be 90.7% (95% CI: 88.4%, 92.7%) and 75.8%, (75.2–76.4) respectively. With
 screening, the number needed to test to identify one PLHIV was reduced
 from 27 to 22. Although risk screening would have led to a 24.5%
 (4,825/19,704) reduction in testing volume, 9.3% (68/732) of PLHIV would
 have been missed as they were misclassified as not eligible for testing.
 The cost per PLHIV identified fell by 3% from $69 without screening to
 $66.9 with the implementation of the screening tool. 
 Conclusions: The use of an HIV risk screening tool in OPD settings in
 Uganda demonstrated improved HIV testing efficiency by reducing testing
 volumes but resulted in screening out of nine of every 100 people living
 with HIV. The team recommends the use of scientifically validated HIV risk
 screening tools, and a need to explore the use of HIV self-testing as a
 test for triage.
description: We conducted a secondary data analysis, of DHIS2 data from 24
 health facilities in Uganda, on clients who were screened for HIV testing
 eligibility using a risk screening tool, and tested for HIV. All clients
 that were screened were tested irrespective of their screening outcome.
 The data had been collected and de-identified before being reported in the
 DHIS2.  We received approval from Ministry of Health
 Uganda to access the DHIS2 data from district Biostatiscians, and we
 cleaned the dataset by removing entries with missing values, suing the
 excel sheet
description: Excel, Stata SPSS
 Epi info
DOI: 10.5061/dryad.63xsj3v7t
title: Data from: Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

description: Vicia sepium (bush vetch) is a perennial legume widely distributed
 throughout the Eurasian continent. However, its distribution in Japan is
 limited to Mt. Ibuki and small parts of central and southern Hokkaido.
 Therefore, each Japanese V. sepium lineage has been considered to have
 been introduced separately from Europe. Here, we examined whether the
 species was introduced or not on the basis of cpDNA sequences and
 genome-wide SNPs from Japanese and overseas samples. Both the cpDNA
 haplotype network and the nuclear DNA phylogenetic tree showed that
 Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA
 phylogenetic tree also showed that each lineage is clearly monophyletic,
 genetic admixture of the genetic cluster dominated in the Hokkaido lineage
 was also detected in the Mt. Ibuki lineage. Population divergence analysis
 showed that the two lineages diverged during the last glacial period. The
 Mt. Ibuki lineage showed a sudden population decline 300–400 years ago,
 indicating that some anthropogenic activity might be involved, while the
 Hokkaido lineage showed a gradual population decline from 5,000 years ago.
 Consequently, these two lineages show low current genetic diversity
 compared with overseas lineages. These results show that the Japanese V.
 sepium is not introduced but is native.
description: Six SNP data sets were generated for different data analyses
 shown in Table 2 in the main text.
description: All SNP data sets were stored in a VCF file, which is a simple
 text file and can be opened by a simple text editor. I also uploaded
 sample information as a simple CSV file.
DOI: 10.5061/dryad.ffbg79d12
title: Early detection and environmental drivers of sewage fungus outbreaks in rivers

description: Sewage effluent is a major ongoing threat to water quality and
 biodiversity in freshwater environments. It can cause outbreaks of sewage
 fungus (filamentous bacteria which form macroscopic masses) but, until
 now, these were only qualitatively recorded from visual inspection,
 ignoring microscopic forms. Here, we used an innovative method which
 combines machine learning, microscopy and flow cytometry, to rapidly and
 efficiently quantify the presence and abundance of sewage fungus in
 rivers. Our study involved 11 rivers with (n=6) and without (n=5) sewage
 input in the south-west of England over four sampling occasions. We were
 able to detect and enumerate the filaments before masses became visible to
 the naked eye and, as expected, we found a higher number of filaments
 downstream of sites where treated sewage was offloaded into the river.
 Therefore, our detection method could be used as a ‘canary in the coal
 mine’ for future outbreaks allowing early intervention. Combining our
 quantitative data on filaments with data on the physical and chemical
 parameters of the rivers, we found that high conductivity, sulphate,
 nitrates and TDS were associated with the presence and proliferation of
 sewage fungus. This information can be extremely useful for regulatory
 bodies and water companies to develop mitigating strategies and action to
 prevent future outbreaks.
description: We collected samples in UK rivers, upstream, downstream and in
 the final effluent. We collected physical and chemical
 data.<br>Physical parameters of the rivers were recorded for all
 sampling months, while the chemical parameters were tested in August,
 October, and November 2021. At each sampling site, we measured: water
 temperature, pH, total dissolved solids, total dissolved oxygen and
 electrical conductivity. We used a hand Combo pH and EC Hanna probe or a
 LT Lutron probe. Three replicates of 100mL of water
 were collected to analyse fluoride, chloride, bromide, nitrite, nitrate,
 phosphate, sulphate and total organic carbon. Water samples were done in
 the laboratory of the School of Geography and the Environment at the
 University of Oxford.
description: R studio was used to produce all the statistical analysis and the
 graphs.
DOI: 10.5061/dryad.931zcrjrq
title: Data for: Probing visual sensitivity and attention in mice using reverse correlation

description: Visual attention allows the brain to evoke behaviors based on the most
 important visual features. Mouse models offer immense potential to gain a
 circuit-level understanding of this phenomenon, yet, how mice distribute
 attention across features and locations is not well understood. Here, we
 describe a new approach to address this limitation, by training mice to
 detect weak vertical bars in a background of checkerboard noise while
 spatial cues manipulated their attention. By adapting a reverse
 correlation method from human studies, we linked behavioral decisions to
 stimulus features and locations. We show that mice voluntarily deploy
 attention to a small rostral region of the visual field. Within this
 region, mice attended to multiple features (orientation, spatial
 frequency, contrast) that indicated the presence of weak vertical bars.
 This attentional tuning grew with training, multiplicatively scaled
 behavioral sensitivity, approached that of an ideal observer, and
 resembled the effects of attention in humans. Taken together, we
 demonstrate that mice can simultaneously attend to multiple features and
 locations of a visual stimulus.
description: Sample dataset to run behavioral reverse correlation as described
 in Lehnert et al., 2023. Analysis code can be found at: https://github.com/Swamylab/Lehnert_et_al_Attention readme file contains a description of the code, variables and other details. Contact erik.cook@mcgill.ca for questions about the data format and analysis code.
DOI: 10.5061/dryad.3j9kd51qs
title: Investigating the effects of whole genome duplication on phenotypic plasticity: Implications for the invasion success of Giant Goldenrod (Solidago gigantea)

description: Polyploidy commonly occurs in invasive species and phenotypic plasticity
 (PP, the ability to alter one’s phenotype in different environments), is
 predicted to be enhanced in polyploids and contribute to their invasive
 success. However, empirical support that increased PP is frequent in
 polyploids and/or confers invasive success is limited. Here, we
 investigated if polyploids are more pre-adapted to become invasive than
 diploids via the scaling of trait values and PP with ploidy-level, and if
 post-introduction selection has led to a divergence in trait values and PP
 responses between native- and non-native cytotypes. We grew diploid,
 tetraploid (from both native North American and non-native European
 ranges), and hexaploid Solidago gigantea in pots outside with low, medium,
 and high soil nitrogen and phosphorus (NP) amendments, and measured traits
 related to growth, asexual reproduction, physiology, and insects/pathogen
 resistance. We found little evidence to suggest that polyploidy and
 post-selection shaped mean trait and PP responses. To examine invasion
 dynamics, we compared diploids to tetraploids (as their introduction into
 Europe was more likely), and found that tetraploids had greater pathogen
 resistance, photosynthetic capacities, and water-use efficiencies and
 generally performed better under NP enrichments. Furthermore, tetraploids
 invested more into roots than shoots in low NP and into shoots than roots
 in high NP and this resource strategy is beneficial under variable NP
 conditions. Lastly, native-tetraploids exhibited greater plasticity in
 biomass accumulation, clonal-ramet production and water-use efficiency.
 Cumulatively, tetraploid S. gigantea possesses traits that might have
 pre-disposed and enabled them to become successful invaders. Our findings
 highlight that trait expression and invasive species dynamics are nuance
 while also providing insight into the invasion success and cyto-geographic
 patterning of S. gigantea that can be broadly applied to other invasive
 species with polyploid complexes.
DOI: 10.13140/rg.2.2.16518.23361
title: Reconstruyendo el Fotón: Fase, Amplitud, Espín y la Geometría de la Luz
DOI: 10.5061/dryad.9p8cz8wns
title: Data and code for: Realized genetic gains via recurrent selection in a tropical maize haploid inducer population and optimizing simultaneous selection for the next cycles

description: Plant breeders widely use recurrent selection schemes to increase the
 frequency of favorable alleles for quantitative traits in a population.
 Although simultaneous selection is complex because it involves several
 traits combined with selection cycles, the use of selection indexes (SI)
 is applied to increase the chance of success of the breeding program. As
 many indices are available in the literature, simulations can help
 breeders to determine which selection index can be better adjusted
 considering the selection goals, the intensity, and the genetic
 correlation among traits over breeding cycles. In this context, we
 estimated the realized genetic gains in a tropical maize haploid inducer
 population after two cycles of recurrent selection, using external testers
 and optimizing the simultaneous selection for this breeding population in
 the long-term via stochastic simulations. Furthermore, we proposed a new
 approach to optimize the initial weights by applying the Smith-Hazel
 method to maximize the genetic gains for all traits in a balanced way.
 Overall, the estimated gains in real induction rate were about 63% per
 cycle, improving the population performance from 0.8 to 2.8%. Moreover,
 our results confirm that the traditional Smith-Hazel approach outperformed
 other methods for long-term response to selection. Finally, recurrent
 selection with external testers may be a suitable method to improve the
 haploid induction rate in tropical maize populations.
DOI: 10.5517/ccdc.csd.cc2mxfxx
title: CCDC 2440410: Experimental Crystal Structure Determination

description: Related Article: Andrea Orellana Ben Amor, Laure Vendier, Vincent César, Vincent Maurel, Julien Panetier, Nicolas Queyriaux|2025|ChemRxiv|||doi:10.26434/chemrxiv-2025-20l40
description: Related Article: Andrea Orellana Ben Amor, Laure Vendier, Vincent César, Vincent Maurel, Julien Panetier, Nicolas Queyriaux|2026|Chemical Science|17|2140|doi:10.1039/d5sc08152a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mxfyy
title: CCDC 2440411: Experimental Crystal Structure Determination

description: Related Article: Andrea Orellana Ben Amor, Laure Vendier, Vincent César, Vincent Maurel, Julien Panetier, Nicolas Queyriaux|2025|ChemRxiv|||doi:10.26434/chemrxiv-2025-20l40
description: Related Article: Andrea Orellana Ben Amor, Laure Vendier, Vincent César, Vincent Maurel, Julien Panetier, Nicolas Queyriaux|2026|Chemical Science|17|2140|doi:10.1039/d5sc08152a
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.