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1,154 results for “Pooling”
Data from: Variability of Symbiodinium communities in waters, sediments, and corals of thermally distinct reef pools in American Samoa
Reef-building corals host assemblages of symbiotic algae (Symbiodinium spp.) whose diversity and abundance may fluctuate under different conditions, potentially facilitating acclimatization to environmental change. The composition of free-living Symbiodinium in reef waters and sediments may also be environmentally labile and may influence symbiotic assemblages by mediating supply and dispersal. The magnitude and spatial scales of environmental influence over Symbiodinium composition in different reef habitat compartments are, however, not well understood. We used pyrosequencing to compare Symbiodinium in sediments, water, and ten coral species between two backreef pools in American Samoa with contrasting thermal environments. We found distinct compartmental assemblages of clades A, C, D, F, and/or G Symbiodinium types, with strong differences between pools in water, sediments, and two coral species. In the pool with higher and more variable temperatures, abundance of various clade A and C types differed compared to the other pool, while abundance of D types was lower in sediments but higher in water and in Pavona venosa, revealing an altered habitat distribution and potential linkages among compartments. The lack of between-pool effects in other coral species was due to either low overall variability (in the case of Porites) or high within-pool variability. Symbiodinium communities in water and sediment also showed within-pool structure, indicating that environmental influences may operate over multiple, small spatial scales. This work suggests that Symbiodinium composition is highly labile in reef waters, sediments, and some corals, but the underlying drivers and functional consequences of this plasticity require further testing with high spatial resolution biological and environmental sampling.
Data from: Wisdom of the caregivers: pooling individual subjective reports to diagnose states of consciousness in brain injured patients, a monocentric prospective study
OBJECTIVES : The clinical distinction between vegetative state/unresponsive wakefulness syndrome (UWS) and minimally conscious state (MCS) is a key step to elaborate a prognosis and formulate an appropriate medical plan for any patient suffering from disorders of consciousness (DoC). However, this assessment is often challenging and may require specialized expertise. In this study, we hypothesized that pooling subjective reports of the level of consciousness of a given patient across several nursing staff members can be used to clinically detect MCS. SETTING AND PARTICIPANTS : Patients referred for consciousness assessment were prospectively screened. MCS (target condition) was defined according to the best Coma Recovery Scale-Revised score (CRS-R) obtained from expert physicians (reference standard). "DoC-feeling" score was defined as the median of individual subjective reports pooled from multiple staff members during a week of hospitalisation (index test). Individual ratings were collected at the end of each shift using a 100mm visual analog scale, blinded from the reference standard. Diagnostic accuracy was evaluated using area under the receiver operating characteristic curve (AUC), sensitivity and specificity metrics. RESULTS : 692 ratings performed by 83 nursing staff members were collected from 47 patients. Twenty patients were in a UWS and 27 in a MCS. DoC-feeling scores obtained by pooling all individual ratings obtained for a given patient were significantly greater in MCS than in UWS patients (59.2 mm [IQR: 27.3-77.3] vs. 7.2 mm [IQR: 2.4-11.4]; p<0.001) yielding an AUC of 0.92 (95%CI: 0.84-0.99). CONCLUSIONS: DoC-feeling capitalizes on the expertise of nursing staff to evaluate patients' consciousness. Together with the CRS-R as well as with brain imaging, DoC-feeling might improve diagnostic and prognostic accuracy of DoC patients.
Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic
California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species' geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.
Data from: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns
Although polyploidy is widespread, its significance to the generation of biodiversity remains unclear. Many polyploids have been derived recurrently. For a particular polyploid, gene-flow between the products of independent origin is typical where they come into contact. Here, we use AFLP DNA-fingerprinting and chloroplast DNA sequences to demonstrate parallel polyploid speciation within both of the ferns Asplenium cimmeriorum and A. gracillimum. Both of these taxa comprise at least two allopolyploids, recurrently derived from the same progenitor pair. Each of these allopolyploids remain genetically distinguishable even with extensive sympatry, and could therefore be considered distinct species. To our knowledge, parallel speciation on this scale amongst recurrent polyploids has not been previously reported. With their parallel origins, these 'evolutionary replicates' provide an unrivalled opportunity to investigate how the reproductive barriers and ecological differentiation necessary for speciation arise following polyploidy.
Data from: Long-term recovery of the functional community assembly and carbon pools in an African tropical forest succession
On the African continent, the population is expected to expand fourfold in the next century, which will increasingly impact the global carbon cycle and biodiversity conservation. Therefore, it is of vital importance to understand how carbon stocks and community assembly recover after slash-and-burn events in tropical second-growth forests. We inventoried a chronosequence of 15 1-hectare plots in lowland tropical forest of the central Congo Basin and evaluated changes in aboveground and soil organic carbon stocks and in tree species diversity, functional composition and community-weighted functional traits with succession. We aimed to track long-term recovery trajectories of species and carbon stocks in secondary forests, comparing 5 to 200+ year old secondary forest with reference primary forest. Along the successional gradient, the functional composition followed a trajectory from resource acquisition to resource conservation, except for nitrogen-related leaf traits. Despite a fast initial recovery of species diversity and functional composition, there were still important structural and carbon stock differences between old-growth secondary and pristine forest, which suggests that a full recovery of secondary forests might take much longer than currently shown. As such, the aboveground carbon stocks of 200+ year old forest were only 57% of those in the pristine reference forest, which suggests a slow recovery of aboveground carbon stocks, although more research is needed to confirm this observation. The results of this study highlight the need for more in-depth studies on forest recovery in Central Africa, to gain insight into the processes that control biodiversity and carbon stock recovery.
Data from: Taming the wild: resolving the gene pools of non-model Arabidopsis lineages
Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of the Arabidopsis supra-groups and hypothesized evolutionary lineages and none include sampling at a world-wide scale. Here we explore the gene pools of these various taxa using various molecular markers and cytological analyses. Results: Based on ITS, microsatellite, chloroplast and nuclear DNA content data we demonstrate the presence of three major evolutionary groups broadly characterized as A. lyrata group, A. halleri group and A. arenosa group. All are composed of further species and sub-species forming larger aggregates. Depending on the resolution of the marker, a few closely related taxa such as A. pedemontana, A. cebennensis and A. croatica are also clearly distinct evolutionary lineages. ITS sequences and a population-based screen based on microsatellites were highly concordant. The major gene pools identified by ITS sequences were also significantly differentiated by their homoploid nuclear DNA content estimated by flow cytometry. The chloroplast genome provided less resolution than the nuclear data, and it remains unclear whether the extensive haplotype sharing apparent between taxa results from gene flow or incomplete lineage sorting in this relatively young group of species with Pleistocene origins. Conclusions: Our study provides a comprehensive overview of the genetic variation within and among the various taxa of the genus Arabidopsis. The resolved gene pools and evolutionary lineages will set the framework for future comparative studies on genetic diversity. Extensive population-based phylogeographic studies will also be required, however, in particular for A. arenosa and their affiliated taxa and cytotypes.
FIGURE 12 in " Microturbellarian " flatworms (Platyhelminthes) from freshwater pools: New species and records from Israel
FIGURE 12: Castrada multispina sp. nov. A. Habitus. B. Male copulatory organ. C. Different kind of spines at the distal region of the blind sac.
FIGURE 13 in " Microturbellarian " flatworms (Platyhelminthes) from freshwater pools: New species and records from Israel
FIGURE 13: Castrada (Castradella) biacantha sp. nov. A. Habitus. B. Male copulatory organ. C. Detail of the spines.
FIGURE 4 in " Microturbellarian " flatworms (Platyhelminthes) from freshwater pools: New species and records from Israel
FIGURE 4: Gieysztoria cuspidata (Schmidt, 1861). A. Habitus. B. Habitus lightly squashed. C. Stylet.
FIGURE 5 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 5. Amphibolocypris arida sp.nov., all male. A. Hemipenis (OC.3167). B. Left, prehensile palp (OC.3167). C. Right T1, with prehensile palp (OC.3167). Scale: A-C = 78 μm.
FIGURE 6 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 6. Hemipenis outlines of four species of Amphibolocypris. Not to scale. A. A. arida sp.nov. (OC.3167). B. A. exigua Rome, 1965. C. A. sp. A. sp.nov. (KM.630). D. A. sp. B. sp.nov. (KM.657). B redrawn after Rome (1965).
FIGURE 4 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 4. Amphibolocypris arida sp.nov., male and female. A. Female, Mx1: palp and 3 endites, respiratory plates not shown (OC.3166). B. Female, T2 (OC.3166). C. Female, T3 (OC.3166). C'. female, T3, detail of distal pincer (OC.3171). D. Female, attachment of CR (OC.3166). E. Male, CR (OC.3167). F. Female, T1 (OC.3166). Scale: A-C,D = 78 μm, C '= 29 μm, E,F = 146 μm.
FIGURE 3 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 3. Amphibolocypris arida sp.nov., male and female. A. Male, A1 (OC.3167), B. Male, A2 (OC.3167). C. Female, A2 (OC.3166). D. Female, Md, detail of coxal plate (OC.3166). E. Female, Md-palp, chaetotaxy of terminal segment not shown (OC.3166). E'. Female, Md-palp, terminal segment (OC.3166). Scale: A = 100 μm, B-E' = 78 μm.
FIGURE 2 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 2. Amphibolocypris arida sp.nov., male and female. A. Male, LV, exterior view (OC.3167). B. Idem, RV, interior view. C. Female, LV, interior view (OC.3166). D. Idem, RV, exterior view. Specimen slightly damaged. E. Female, RV, exterior view, detail (OC.3168). F. Idem, higher magnification. Scale: A-D,G = 500 μm, E = 20 μm, F = 5 μm.
FIGURE 5. A in Scapheremaeus rodickae n. sp. (Acari: Oribatida: Cymbaeremaeidae) associated with temporary rock pools in Georgia, with key to Scapheremaeus species in eastern USA and Canada
FIGURE 5. A) type locality of Scapheremaeus rodickae n. sp., showing Grimmia laevigata moss alongside depressions in granite outcrop that accumulate water; B) Scapheremaeus rodickae n. sp. tritonymph, right gastronotic seta lp; C) same, dorsal aspect. Differential interference contrast illumination in B, C; layered from 4 and 10 sequentially focused images, respectively. Scale bars: B, 5 μm; C, 50 μm.
FIGURE 6 in Scapheremaeus rodickae n. sp. (Acari: Oribatida: Cymbaeremaeidae) associated with temporary rock pools in Georgia, with key to Scapheremaeus species in eastern USA and Canada
FIGURE 6. Scapheremaeus species from eastern USA and Canada, dorsal aspect: A) S. rodickae n. sp.; B) S. marginalis (Banks); C) S. palustris (Sellnick); D) S. parvulus (Banks). Differential interference contrast illumination, layered from 6–8 sequentially focused images. Scale bars 50 μm.
FIGURE 3. Scapheremaeus rodickae n in Scapheremaeus rodickae n. sp. (Acari: Oribatida: Cymbaeremaeidae) associated with temporary rock pools in Georgia, with key to Scapheremaeus species in eastern USA and Canada
FIGURE 3. Scapheremaeus rodickae n. sp.: A) right leg I, abaxial aspect (trochanter omitted); B) left leg IV, adaxial aspect (trochanter omitted). Scale bar = 25 µm.
FIGURE 2. Scapheremaeus rodickae n in Scapheremaeus rodickae n. sp. (Acari: Oribatida: Cymbaeremaeidae) associated with temporary rock pools in Georgia, with key to Scapheremaeus species in eastern USA and Canada
FIGURE 2. Scapheremaeus rodickae n. sp.: A) right bothridial region; B) right rostral region; C) right central region of prodorsum, showing costula terminating in tubercle bearing lamellar seta; D) left half of subcapitulum, ventral aspect; E) left palp, oblique adaxial aspect; F) right chelicera, adaxial aspect. Scale bar = 50 µm. Abbreviations: a, m, setae of gena; bo, bothridial seta (= sensillus); cha, chb, cheliceral setae; ex, exobothridial seta; h, hypostomal seta; le, lamellar seta; Tg, Trägårdh's organ.
FIGURE 1. Scapheremaeus rodickae n in Scapheremaeus rodickae n. sp. (Acari: Oribatida: Cymbaeremaeidae) associated with temporary rock pools in Georgia, with key to Scapheremaeus species in eastern USA and Canada
FIGURE 1. Scapheremaeus rodickae n. sp. (legs removed): A) dorsal aspect; B) ventral aspect; C) lateral aspect. Scale bar = 100 µm. See text for abbreviations
FIGURE 5. Hmoain pool, 7.5 in A new earthworm eel of the genus Chaudhuria from the Ayeyarwaddy River Drainage, Myanmar (Teleostei: Synbranchiformes: Chaudhuriidae)
FIGURE 5. Hmoain pool, 7.5 miles southwest of Einme, Ayeyarwaddy Division, Myanmar. Type locality of Chaudhuria ritvae.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.