cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pf1gt
title: Data from: Complete blood count reference intervals from a healthy adult urban population in Kenya

description: Background: There are racial, ethnic and geographical differences in
 complete blood count (CBC) reference intervals (RIs) and therefore it is
 necessary to establish RIs that are population specific. Several studies
 have been carried out in Africa to derive CBC RIs but many were not
 conducted with the rigor recommended for RI studies hence limiting the
 adoption and generalizability of the results. Method: By use of a Beckman
 Coulter ACT 5 DIFF CP analyser, we measured CBC parameters in samples
 collected from 528 healthy black African volunteers in a largely urban
 population. The latent abnormal values exclusion (LAVE) method was used
 for secondary exclusion of individuals who may have had sub-clinical
 diseases. The RIs were derived by both parametric and non-parametric
 methods with and without LAVE for comparative purposes. Results:
 Haemoglobin (Hb) levels were lower while platelet counts were higher in
 females across the 4 age stratifications. The lower limits for Hb and red
 blood cell parameters significantly increased after applying the LAVE
 method which eliminated individuals with latent anemia and inflammation.
 We adopted RIs by parametric method because 90% confidence intervals of
 the RI limits were invariably narrower than those by the non-parametric
 method. The male and female RIs for Hb after applying the LAVE method were
 14.5−18.7 g/dL and 12.0−16.5 g/dL respectively while the platelet count
 RIs were 133−356 and 152−443 x103 per µL respectively. Conclusion:
 Consistent with other studies from Sub-Saharan Africa, Hb and neutrophil
 counts were lower than Caucasian values. Our finding of higher Hb and
 lower eosinophil counts compared to other studies conducted in rural Kenya
 most likely reflects the strict recruitment criteria and healthier
 reference population after secondary exclusion of individuals with
 possible sub-clinical diseases.
description: CBC reference values
 obtained from a healthy adult black population in KenyaThis data file contains
 reference values for CBC parameters obtained from healthy adults living in
 selected urban towns in Kenya. The original study was carried out by the
 committee of reference intervals and decision limits under the
 International Federation of Clinical Chemistry. We collected additional
 data for CBC parameter so as to determine reference intervals for our
 Kenyan adult population using various statistical
 techniques.RRP data Kenya haematology_data
 repository.xlsx
DOI: 10.5061/dryad.c0751
title: Data from: Plant-mycorrhizal fungus co-occurrence network lacks substantial structure

description: The interactions between plants and arbuscular mycorrhizal fungi (AMF)
 maintain a crucial link between macroscopic organisms and the soil
 microbial world. These interactions are of extreme importance for the
 diversity of plant communities and ecosystem functioning. Despite this
 importance, only recently has the structure of plant–AMF interaction
 networks been studied. These recent studies, which used genetic data,
 suggest that these networks are highly structured, very similar to
 plant–animal mutualistic networks. However, the assembly process of
 plant–AMF communities is still largely unknown, and an important feature
 of plant–AMF interactions has not been incorporated: they occur at an
 extremely localized scale. Studying plant–AMF networks in a spatial
 context seems therefore a crucial step. This paper studies a plant–AMF
 spatial co-occurrence network using novel methodology based on information
 theory and a unique set of spatially explicit species-level data. We apply
 three null models of which only one accounts for spatial effects. We find
 that the data show substantial departures from null expectations for the
 two non-spatial null models. However, for the null model considering
 spatial effects, there are few significant co-occurrences compared with
 the other two null models. Thus, plant–AMF spatial co-occurrences seem to
 be mostly explained by stochasticity, with a small role for other factors
 related to plant–AMF specialization. Furthermore, we find that the network
 is not significantly nested or modular. We conclude that this plant–AMF
 spatial co-occurrence network lacks substantial structure and, therefore,
 plants and AMF species do not track each other over space. Thus, random
 encounters seem more important in the first step of the assembly of
 plant–AMF communities.
description: plant_spatial_presence_dataSpatial data of the plant species (presence(1)/absence(0)). The order of files (species names) follow the alphabetical order, as shown in Figure 1 of the manuscript.mycorrhiza_spatial_presence_dataAMF spatial data of the plant species (presence(1)/absence(0)). The order of files (species names) follow the alphabetical order, as shown in Figure 1 of the manuscript.null_models_plant_amf_co_occurrenceR script that includes three null models (fixed species presences, environmentally constrained and equiprobable null model). The script uses the data files of plants and AMF spatial data submitted here. It will calculate the different co-occurrence metrics (C-score, fij), asymmetry and nestedness of the different null matrices.abiotic_spatial_dataSpatial data of abiotic factors: pH and organic matter (OM).mutual_info_clusterR script that calculates mutual information on the null matrices and the significant species co-occurrences. Input files necessary are the null matrices ("Pnullmatrices.RData" and "anullmatrices.RData") produced on the null model R script "null_models_plant_am_co_occurrence.R".
DOI: 10.5061/dryad.bn46h
title: Data from: Density-dependent diel activity in stream-dwelling Arctic charr Salvelinus alpinus

description: Intraspecific competition plays a significant role in shaping how animals
 use and share habitats in space and time. However, the way individuals may
 modify their diel activity in response to increased competition has
 received limited attention. We used juvenile (age 1+) Arctic charr
 Salvelinus alpinus to test the prediction that individuals at high
 population density are more active and distribute their foraging activity
 over a greater portion of the 24-h cycle than individuals at low
 population density. Individually tagged fish were stocked in seminatural
 stream enclosures at low (2 fish/m2) and high (6 fish/m2) density. During
 each of two 2-week experimental rounds, activity of all fish within each
 enclosure was recorded every 3 h over seven 24-h cycles. At high density,
 fish were more active and distributed their activity over a greater
 portion of the 24-h cycle, with increased activity particularly at
 crepuscular times. Fluctuations in ecological conditions (e.g., water
 temperature and light intensity) also affected activity. Fish at high
 density grew as fast as fish at low density. This study demonstrates that
 individuals exhibit a degree of behavioral flexibility in their response
 to changes in ecological conditions and suggests that intraspecific
 competition can cause animals to modify temporal aspects of their activity
 to gain access to resources and maintain growth.
description: Invertebrate
 driftData collected in the
 field in 2013. Please see ReadMe file for a description of column
 headings.Drift_data.csvActivity of individual fishData collected in the field in 2013. Please see ReadMe file for a description of column headings.Fish_data.csvEnclosure scansData collected in the field in 2013. Please see ReadMe file for a description of column headings.Scan_data.csvSubstrate estimationsData collected in the field in 2013. Please see ReadMe file for a description of column headings.Substrate_data.csvWater current velocity measurementsData collected in the field in 2013. Please see ReadMe file for a description of column headings.Water_current_data.csvWater depth measurementsData collected in the field in 2013. Please see ReadMe file for a description of column headings.Water_depth_data.csv
DOI: 10.5061/dryad.5037s
title: Data from: Variable post-zygotic isolation in Drosophila melanogaster/D. simulans hybrids

description: The study of hybrid inviability reveals cryptic divergence between the
 genetic interactions that maintain stable phenotypes in the pure species.
 We characterized the effects of natural variation on the penetrance of
 hybrid inviability phenotypes in crosses between Drosophila melanogaster
 and two species of the D. simulans subcomplex, D. simulans and D.
 sechellia. Using a panel of wild-caught lines, we studied the levels of
 genetic variance present in D. simulans and D. sechellia affecting
 prezygotic and post-zygotic isolation in hybridizations with D.
 melanogaster females. We observed extensive variability in the viability
 of hybrid individuals, dependent on the genotype of the parents,
 suggesting that intraspecific natural variation manifests directly in
 hybrid phenotypes. Furthermore, we found that genetic background
 significantly affects the penetrance of a well-studied determinant of
 hybrid inviability: the interaction between Hmrmel–Lhrsim. Our results
 suggest that hybrid inviability – and reproductive isolation generally –
 can be modified by polymorphisms at multiple loci segregating within the
 parental species. Just as the penetrance of most mutant phenotypes can be
 modified by the genetic background within the pure species, the penetrance
 of hybrid inviability phenotypes is highly influenced by the parental
 genotypes.
description: Matute_etal_JEB_ReadMeDRM_JGS_GL_raw_data.zip
DOI: 10.5061/dryad.9c2j1
title: Data from: Effect of the early social environment on behavioural and genomic responses to a social challenge in a cooperatively breeding vertebrate

description: The early social environment can have substantial, lifelong effects on
 vertebrate social behaviour, which can be mediated by developmental
 plasticity of brain gene expression. Early life effects can influence
 immediate behavioural responses towards later-life social challenges and
 can activate different gene expression responses. However, while genomic
 responses to social challenges have been reported frequently, how
 developmental experience influences the shape of these genomic reaction
 norms remains largely unexplored. We tested how manipulating the early
 social environment of juvenile, cooperatively-breeding cichlids,
 Neolamprologus pulcher, affects their behavioural and brain genomic
 responses when competing over a resource. Juveniles were reared either
 with or without a breeder pair and a helper. Fish reared with family
 members behaved more appropriately in the competition than when reared
 without. We investigated whether the different social rearing environments
 also affected the genomic responses to the social challenge. A set of
 candidate genes, coding for hormones and receptors influencing social
 behaviour, were measured in the telencephalon and hypothalamus. Social
 environment and social challenge both influenced gene expression of egr-1
 (early growth response 1) and gr1 (glucocorticoid receptor 1) in the
 telencephalon and of bdnf (brain derived neurotrophic factor) in the
 hypothalamus. A global analysis of the 11 expression patterns in the two
 brain areas showed that neurogenomic states diverged more strongly between
 intruder fish and control fish when they had been reared in a natural
 social setting. Our results show that same molecular pathways may be used
 differently in response to a social challenge depending on early life
 experiences.
description: Nyman_etal_complete_datasetBehaviour and gene expression dataExplanatory_text_file_Nyman_etalAbbreviations of words used in the data file Nyman_etal_complete_dataset
DOI: 10.5061/dryad.pg0qd5c
title: Data from: Morphological novelty emerges from pre-existing phenotypic plasticity

description: Plasticity-first evolution (PFE) posits that novel features arise when
 selection refines pre-existing phenotypic plasticity into an adaptive
 phenotype. However, PFE is controversial because few tests have been
 conducted in natural populations. Here we present evidence that PFE
 fostered the origin of an evolutionary novelty that allowed certain
 amphibians to invade a new niche—a distinctive carnivore morph. We
 compared morphology, gene expression and growth of three species of
 spadefoot toad tadpoles when reared on alternative diets:
 Scaphiopus holbrookii, which (like most frogs) never produce carnivores;
 Spea multiplicata, which sometimes produce carnivores, but only through
 diet-induced plasticity; and Spea bombifrons, which often produce
 carnivores regardless of diet. Consistent with PFE, we found diet-induced
 plasticity—in morphology and gene expression—in Sc. holbrookii, adaptive
 refinement of this plasticity in Sp. multiplicata, and further refinement
 of the carnivore phenotype in Sp. bombifrons. Generally, phenotypic
 plasticity might play a significant, if underappreciated, role in
 evolutionary innovation.
description: Palate spike
 dataComparison of palate
 spike among lineagesSc. hol. gene expression
 dataSc. hol. morph
 dataSp. mult gene expression
 dataSp. multi. morph
 dataWild carnivore lineage
 morph data
DOI: 10.5061/dryad.mt3gr
title: Data from: Mammal decline, linked to invasive Burmese python, shifts host use of vector mosquito towards reservoir hosts of a zoonotic disease

description: Invasive apex predators have profound impacts on natural communities, yet
 the consequences of these impacts on the transmission of zoonotic
 pathogens are unexplored. Collapse of large- and medium-sized mammal
 populations in the Florida Everglades has been linked to the invasive
 Burmese python, Python bivittatus Kuhl. We used historic and current data
 to investigate potential impacts of these community effects on contact
 between the reservoir hosts (certain rodents) and vectors of Everglades
 virus, a zoonotic mosquito-borne pathogen that circulates in southern
 Florida. The percentage of blood meals taken from the primary reservoir
 host, the hispid cotton rat, Sigmodon hispidus Say and Ord, increased
 dramatically (422.2%) from 1979 (14.7%) to 2016 (76.8%), while blood meals
 from deer, raccoons and opossums decreased by 98.2%, reflecting
 precipitous declines in relative abundance of these larger mammals,
 attributed to python predation. Overall species diversity of hosts
 detected in Culex cedecei blood meals from the Everglades declined by
 40.2% over the same period (H(1979) = 1.68, H(2016) = 1.01). Predictions
 based upon the dilution effect theory suggest that increased relative
 feedings upon reservoir hosts translate into increased abundance of
 infectious vectors, and a corresponding upsurge of Everglades virus
 occurrence and risk of human exposure, although this was not tested in the
 current study. This work constitutes the first indication that an invasive
 predator can increase contact between vectors and reservoirs of a human
 pathogen and highlights unrecognized indirect impacts of invasive
 predators.
description: Culex cedecei host blood
 meals, Florida, USA 2016Sample modifiers and
 host species identification of blood-engorged females of Culex cedecei
 from Indian River County and Everglades National Park, Florida, USA,
 2016Hoyer_ESM.xlsx
DOI: 10.5061/dryad.31t0k
title: Data from: Testing the validity of functional response models using molecular gut content analysis for prey choice in soil predators

description: Analysis of predator - prey interactions is a core concept of animal
 ecology, explaining structure and dynamics of animal food webs. Measuring
 the functional response, i.e. the intake rate of a consumer as a function
 of prey density, is a powerful method to predict the strength of trophic
 links and assess motives of prey choice, particularly in arthropod
 communities. However, due to their reductionist set-up, functional
 responses, which are based on laboratory feeding experiments, may not
 display field conditions, possibly leading to skewed results. Here, we
 tested the validity of functional responses of centipede predators and
 their prey by comparing them with empirical gut content data from
 field-collected predators. Our predator - prey system included lithobiid
 and geophilomorph centipedes, abundant and widespread predators of forest
 soils and their soil-dwelling prey. First, we calculated the body
 size-dependent functional responses of centipedes using a published
 functional response model in which we included natural prey abundances and
 animal body masses. This allowed us to calculate relative proportions of
 specific prey taxa in the centipede diet. In a second step, we screened
 field-collected centipedes for DNA of eight abundant soil-living prey taxa
 and estimated their body size-dependent proportion of feeding events. We
 subsequently compared empirical data for each of the eight prey taxa, on
 proportional feeding events with functional response-derived data on prey
 proportions expected in the gut, showing that both approaches
 significantly correlate in five out of eight predator - prey links for
 lithobiid centipedes but only in one case for geophilomorph centipedes.
 Our findings suggest that purely allometric functional response models,
 which are based on predator-prey body size ratios are too simple to
 explain predator - prey interactions in a complex system such as soil. We
 therefore stress that specific prey traits, such as defence mechanisms,
 must be considered for accurate predictions.
description: Eitzinger et al_Testing
 validity Funct Respon_Raw dataMatrix of centipede
 predator individuals (collected from four forest sites in Thuringia,
 Germany on eight dates during 2009 and 2010) which were tested for
 consumption of 14 soil prey groups by molecular gut content analysis.
 Matrix contains taxonomic details of centipede predators as well as their
 sex, body size (mm), body mass (mg) and development stage. Consumption of
 prey (=positive detection of prey DNA) is denoted as '1',
 non-consumption as '0'. If predators were not tested cells
 contain 'NA'.
DOI: 10.5061/dryad.597ch
title: Data from: Comprehensive analysis of vitreous specimens for uveitis classification: a prospective multicentre observational study

description: Purpose: To determine the clinical relevance of vitreous biomarkers in
 uveitis patients. Design: Multicentre, prospective, observational study.
 Setting: Uveitis outpatient clinics of two academic medical centres in
 Japan. Patient Population: This study included 234 eyes of 191 patients
 with various uveitis aetiologies: definitive sarcoidosis (61 eyes of 46
 patients), suspected sarcoidosis (60 eyes of 45 patients), intraocular
 tumour (34 eyes of 27 patients), viral infection (20 eyes of 18 patients),
 non-sarcoidosis (16 eyes of 16 patients), and unknown aetiology (43 eyes
 of 39 patients). Observation Procedure: Vitreous samples (taken by pars
 planta vitrectomy) were analysed with flow cytometry, cytology, and
 multiplex PCR analysis. Main Outcome Measures: The primary outcome
 measures were the diagnostic values of various biomarkers (T-cells,
 B-cells and pathogen DNA) in vitreous samples. The secondary outcome was
 visual acuity after vitrectomy. Results: Sarcoidosis showed higher CD4/CD8
 or CD4+ measurements than other aetiologies (p&lt;0.01). In samples
 with viral infection, pathogen DNA was detected, and CD8+ counts were
 higher than the other aetiologies (p&lt;0.01). Eyes with tumour had
 higher CD19+ (p&lt;0.05). Non-sarcoidosis had lower CD4/CD8 than
 sarcoidosis, higher CD8+ than sarcoidosis, and lower CD19+ than tumour
 (p&lt;0.01). Unknown uveitis had lower CD4/CD8 than sarcoidosis
 (p&lt;0.01), and higher CD4/CD8 than non-sarcoidosis, viral infection,
 or tumour (p&lt;0.001). Visual acuity improved after vitrectomy
 (p&lt;0.001). Conclusions: Uveitis aetiologies had distinct vitreous
 biomarker profiles, especially of infiltrating lymphocytes., Analyses of
 CD4/CD8 ratio, T- and B-lymphocyte subset, and pathogen DNA in vitreous
 samples have good safety profiles and high diagnostic value for uveitis
 classification.
description: low data
 BMJ
DOI: 10.5061/dryad.j6567
title: Data from: Challenges in analysis and interpretation of microsatellite data for population genetic studies

description: Advancing technologies have facilitated the ever-widening application of
 genetic markers such as microsatellites into new systems and research
 questions in biology. In light of the data and experience accumulated from
 several years of using microsatellites, we present here a literature
 review that synthesizes the limitations of microsatellites in population
 genetic studies. With a focus on population structure, we review the
 widely used fixation (FST) statistics and Bayesian clustering algorithms
 and find that the former can be confusing and problematic for
 microsatellites and that the latter may be confounded by complex
 population models and lack power in certain cases. Clustering,
 multivariate analyses, and diversity-based statistics are increasingly
 being applied to infer population structure, but in some instances these
 methods lack formalization with microsatellites. Migration-specific
 methods perform well only under narrow constraints. We also examine the
 use of microsatellites for inferring effective population size, changes in
 population size, and deeper demographic history, and find that these
 methods are untested and/or highly context-dependent. Overall, each method
 possesses important weaknesses for use with microsatellites, and there are
 significant constraints on inferences commonly made using microsatellite
 markers in the areas of population structure, admixture, and effective
 population size. To ameliorate and better understand these constraints,
 researchers are encouraged to analyze simulated datasets both prior to and
 following data collection and analysis, the latter of which is formalized
 within the approximate Bayesian computation framework. We also examine
 trends in the literature and show that microsatellites continue to be
 widely used, especially in non-human subject areas. This review assists
 with study design and molecular marker selection, facilitates sound
 interpretation of microsatellite data while fostering respect for their
 practical limitations, and identifies lessons that could be applied toward
 emerging markers and high-throughput technologies in population genetics.
description: Search strings and
 scripts for analyzing literature trendsWeb of Science search
 strings, MySQL scripts, and other miscellaneous files used to analyze full
 article records for literature trends on use of genetic
 markers.Analysis-of-microsat-data_supplemental-files.zip