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Figure 4 in Lucinidae (Bivalvia) - the most diverse group of chemosymbiotic molluscs
Figure 4. General anatomy of Anodontia philippiana, Dampier, Western Australia, with left valve and mantle removed. Abbreviations: aa, anterior adductor muscle; exa, exhalant aperture; f, foot; fm, fused mantle; ld, left demibranch of ctenidia; me, mantle edge; mg, mantle gills on septum; p, periostracum; pa, posterior adductor muscle. Shell length = 40 mm
Figure 2 in Lucinidae (Bivalvia) - the most diverse group of chemosymbiotic molluscs
Figure 2. Molecular phylogeny of heterodont and palaeoheterodont bivalves produced by Bayesian analysis of partial sequences from the 18SrRNA gene. Branches with posterior probabilities <85% have been collapsed. Nodal support is posterior probability/bootstrap (Neighbour-joining using Maximum Likelihood distance, 10 000 reps). Details of taxa and methods in Taylor et al., 2005.
Figure 3 in Lucinidae (Bivalvia) - the most diverse group of chemosymbiotic molluscs
Figure 3. Molecular phylogeny of Lucinidae (from Williams et al., 2004) based on concatenated gene sequence data from 18S rRNA and 28S rRNA genes. Branches collapsed with posterior probabilities of> 90%. Nodal support is posterior probability/bootstrap (NJ using ML distance, 10 000 reps). *Bootstrap support is 96% for lucinid clade B excluding Phacoides pectinatus.
FIG. 8 in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 8. — Lingual view of m1/2 molar from two levels of Saint- Martin-de-Castillon: A, Eomys aff. E. antiquus (Aymard, 1853) from the level C (FSL 98156); B, Eomys aff. E. zitteli Schlosser, 1884 from the level J (FSL 98181). Scale bar: 0.5 mm.
FIG. 7 in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 7. — Measurements of Eomys Schlosser, 1884 teeth compared the neotype of E. zitteli Schlosser, 1884 are indicated by stars.
FIG. 6 in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 6. — Eomys minor Comte & Vianey-Liaud, 1987 teeth, La Blache: A, A', Lm1/2, FSL 98182; A, occlusal view; A', labial view; B, RM1/2, FSL 98183; C, LM3, FSL 98184; D, Rm1/2, FSL 98185; E, Rp4, FSL 98186. Scale bar: 0.5 mm.
FIG. 9. — A-D in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 9. — A-D, Eomys sp.teeth,MÖhren 20;A, LP4,BSP 1975 XXII 837; B, LM1/2, BSP 1975 XXII 846;C, Rm1/2, BSP 1975 XXII 845;D, Lm1/2, BSP 1975 XXII 742; E-G, Eomyidae gen. et sp.indet.teeth, MÖhren 20; E, LM1/2, BSP 1975 XXII 858; F, RP4? RM1/2?, BSP 1975 XXII 857; G, RM2, BSP 1975 XXII 853. Scale bar: 0.5 mm.
FIG. 5.— A-Q, Eomys aff. E in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 5.— A-Q, Eomys aff. E. antiquus (Aymard, 1853) teeth, Saint-Martin-de-Castillon C; A, RDP4, FSL 98150; B, RP4, FSL 98155; C, RP4, FSL 98157; D, LP4, FSL 98162; E, RM1/2, FSL 98164; F, LM1/2, FSL 98160; G, LM3, FSL 98153; H, LM3, FSL 98169; I, Rdp4, FSL 98167; J, Rp4, FSL 98166; K, Lp4, FSL 98159; L, Lp4, FSL 98154; M, Lp4, FSL 98158; N, Rm1/2, FSL 98151; O, Rm1/2, FSL 98156; P, Lm1/2, FSL 98163; Q, Lm3, FSL 98161; R-V, Eomys aff. E. zitteli Schlosser,1884 teeth, Saint-Martin-de-Castillon J; R, RDP4, FSL 98180; S, RM1/2, FSL 98178; T, RM1/2, FSL 98179; U, Rdp4, FSL 98176; V, Lm1/2, FSL 98177. Scale bar: 0.5 mm.
FIG. 1 in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 1. — Eomys antiquus (Aymard, 1853) upper teeth, MÖhren 13: A, RDP4, BSP 1972 XI 4263; B, RP4, BSP 1972 XI 3908; C, RP4, BSP 1972 XI 3920; D, LP4, BSP 1972 XI 3931; E, LP4, BSP 1972 XI 3926; F, LP4, BSP 1972 XI 3911; G, LP4, BSP 1972 XI 3945; H, LP4, BSP 1972 XI 3947; I, LP4, BSP 1972 XI 3909; J, RM1/2, BSP 1972 XI 4020; K, RM2, BSP 1972 XI 3949; L, RM1/2, BSP 1972 XI 3950; M, RM1/2, BSP 1972 XI 4023; N, LM2, BSP 1972 XI 3999; O, LM3, BSP 1972 XI 4041; P, LM3, BSP 1972 XI 4043; Q, LM3, BSP 1972 XI 4047; R, LM3, BSP 1972 XI 4052; S, LM3, BSP 1972 XI 4038. Scale bar: 0.5 mm.
FIG. 2 in New data about the diversity of Early Oligocene eomyids (Mammalia, Rodentia) in Western Europe
FIG. 2. — Eomys antiquus (Aymard, 1853) lower teeth, MÖhren 13: A, Rdp4, BSP 1972 XI 4261; B, Rdp4, BSP 1972 XI 4262; C, Rp4, BSP 1972 XI 4082; D, Rp4, BSP 1972 XI 4098; E, Lp4, BSP 1972 XI 4074; F, Lp4, BSP 1972 XI 4058; G, Lp4, BSP 1972 XI 4059; H, Lp4, BSP 1972 XI 4060; I, Lp4, BSP 1972 XI 4064; J, Rm1/2, BSP 1972 XI 4122;K, Rm1, BSP 1972 XI 4135; L, Rm1/2, BSP 1972 XI 4133;M, Rm1/2, BSP 1972 XI 4148; N, Lm2, BSP 1972 XI 4171; O, Lm2, BSP 1972 XI 4196; P, Lm1/2, BSP 1972 XI 4135; Q, Lm1, BSP 1972 XI 4118; R, Rm3, BSP 1972 XI 4210; S, Rm3, BSP 1972 XI 4245; T, Rm3, BSP 1972 XI 4251; U, Lm3, BSP 1972 XI 4232. Scale bar: 0.5 mm.
Data from: Species diversity promotes facilitation under stressful conditions.
<p>All the data can be used to reproduce the analysis found at: https://github.com/alaindanet/plant-interactions-stress-strategies</p><p>All the csv should be located in the `data-raw` folder to reproduce the analysis, expect `<a href="https://zenodo.org/api/records/10171339/draft/files/empty_file_for_traits-2.csv/content">empty_file_for_traits-2.csv</a>` that should be located under `data-raw/leaf/mars/` folder.</p>
FIG. 1 in Marine cyanobacteria diversity and biotechnological potential in Caribbean waters
FIG. 1. — Map showing Caribbean countries were studies on cyanobacteria have been reported (gray) and those that have no reports yet (white).
Diversity-aware Fairness Testing of Machine Learning Classifiers through Hashing-based Sampling
<p>The experimental results of the evaluation of VBT-X.</p> <h2>Abstract</h2> <div> <h3>Context:</h3> <p>There are growing concerns about algorithmic fairness, as some machine learning (ML)-based algorithms have been found to exhibit biases against protected attributes such as gender, race, age and so on. Individual fairness requires an ML classifier to produce similar outputs for similar individuals. Verification Based Testing (<span>Vbt</span>) is a state-of-the-art black-box testing algorithm for individual fairness that leverages constraint solving to generate test cases.</p> </div> <div> <h3>Objective:</h3> <p>Generating diverse test cases is expected to facilitate efficient detection of diverse discriminatory data instances (i. e., cases that violate individual fairness). Hashing-based sampling techniques draw a sample approximately uniformly at random from the set of solutions of given Boolean constraints. We propose <span>Vbt</span>-X, which improves <span>Vbt</span> with hashing-based sampling, aiming to improve its testing performance.</p> </div> <div> <h3>Method:</h3> <p>We realize hashing-based sampling for <span>Vbt</span>. The challenge is that the off-the-shelf hashing-based sampling techniques cannot be integrated in a straightforward manner because the constraints in <span>Vbt</span> are generally not Boolean. Moreover, we propose several enhancement techniques to make <span>Vbt</span>-X more efficient.</p> </div> <div> <h3>Results:</h3> <p>To evaluate our method, we conduct experiments, where <span>Vbt</span>-X is compared to <span>Vbt</span>, <span>Sg</span> and ExpGA (other well-known fairness testing algorithms) over a set of configurations consisting of several datasets, protected attributes, and ML classifiers. The results show that, with each configuration, <span>Vbt</span>-X detects more discriminatory data instances with higher diversity than <span>Vbt</span> and <span>Sg</span>. <span>Vbt</span>-X detects discriminatory data instances with higher diversity than ExpGA, though the number of discriminatory data instances detected by <span>Vbt</span>-X is lesser than ExpGA.</p> </div> <div> <h3>Conclusion:</h3> <p>Our proposed method performs better than other state-of-the-art black-box fairness testing algorithms, particularly in terms of diversity. Our method can serve to efficiently identify flaws in ML classifiers with respect to individual fairness for subsequent improvements of an ML classifier. On the other hand, although our method is specific to individual fairness, it could work for testing other aspects of a software system such as security and counterfactual explanations with some technical adaptations, which remains for future work.</p> </div> <p> </p> <div> <h2>Acknowledgments</h2> <p>This paper is partly based on results obtained from a project, JPNP20006, commissioned by the New Energy and Industrial Technology Development Organization (NEDO). This paper is supported by JST SPRING, Grant Number JPMJSP2131.</p> </div>
Multiple dimensions of phylogenetic diversity are needed to explain the complex aboveground-belowground diversity relationships
<p>The complex relationship between aboveground and belowground diversity and whether they act as surrogates for one another remains unresolved. Increasing evidence suggests that investigating phylogenetic diversity could provide valuable insights into the interplay between plants and soil microbes, but the proliferation of phylogenetic diversity metrics has hindered comparative studies and the identification of general patterns. To overcome this challenge, we implemented a multi-dimensional framework that classifies phylogenetic diversity metrics into three dimensions: richness, divergence, and regularity, each of which captures different ecological aspects of species differences. Then we applied this framework to investigate the relationship between above and belowground diversity in a subtropical forest in Eastern China. We found that phylogenetic diversity of plant and soil microbes, including bacteria and fungi, were more strongly correlated at the richness and regularity dimension compared with divergence dimension. Further analyses revealed that these observed correlation patterns can be attributed to the influence of soil total phosphorus content, which is the limiting factor of plant and microbial phylogenetic diversity at richness and regularity dimensions. Together, our study demonstrated the necessity of using a multi-dimensional approach to advance our understanding of the complex relationships between plant and soil microbial biodiversity.</p>
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies
<p>Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory and bioinformatics workflows to overcome many of these hurdles. The Pacific Biosciences single molecule real-time platform was used to sequence PCR amplicons derived from cDNA templates tagged with universal molecular identifiers (SMRT-UMI). Optimized laboratory protocols were developed through extensive testing of different sample preparation conditions to minimize between-template recombination during PCR and the use of UMI allowed accurate template quantitation as well as removal of point mutations introduced during PCR and sequencing to produce a highly accurate consensus sequence from each template. Handling of the large datasets produced from SMRT-UMI sequencing was facilitated by a novel bioinformatic pipeline, Probabilistic Offspring Resolver for Primer IDs (PORPIDpipeline), that automatically filters and parses reads by sample, identifies and discards reads with UMIs likely created from PCR and sequencing errors, generates consensus sequences, checks for contamination within the dataset, and removes any sequence with evidence of PCR recombination or early cycle PCR errors, resulting in highly accurate sequence datasets. The optimized SMRT-UMI sequencing method presented here represents a highly adaptable and established starting point for accurate sequencing of diverse pathogens. These methods are illustrated through characterization of human immunodeficiency virus (HIV) quasispecies.</p>
Data set of dorsal halfed shield outlines of specimens of Meiura, from the publication "Morphological diversity in true and false crabs reveals a common middle ground – the megalopa phase"
<p>Data set, containing all reconstructed shield shapes, all from representatives of Meiura, included in the analysis of the manuscript "Morphological diversity in true and false crabs reveals a common middle ground – the megalopa phase". The data sheet, detailing data origin can be found in the supplementarty material of the publication.</p>
Plant interaction networks reveal the limits of our understanding of diversity maintenance
<p>Species interactions are key drivers of biodiversity and ecosystem stability. Current theoretical frameworks for understanding the role of interactions make many assumptions which, unfortunately, do not always hold in natural, diverse communities. This mismatch extends to annual plants, a common model system for studying coexistence, where interactions are typically averaged across environmental conditions and transitive competitive hierarchies are assumed to dominate. We quantify interaction networks for a community of annual wildflowers in Western Australia across a natural shade gradient at local scales. Whilst competition dominated, intraspecific and interspecific facilitation were widespread in all shade categories. Interaction strengths and directions varied substantially despite close spatial proximity and similar levels of local species richness, with most species interacting in different ways under different environmental conditions. Contrary to expectations, all networks were predominantly intransitive. These findings encourage us to rethink how we conceive of and categorise the mechanisms driving biodiversity in plant systems.</p>
FIGURE 5 in Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria
FIGURE 5 Haplotype network of Moinidae lineages within species, based on the mitochondrial COI gene (478 bp). Each circle represents a unique haplotype and its size reflects the number of sequences. Segment sizes within circles indicate the distribution of haplotypes among different regions (color key to regions is on the left side of the figure). The lineage ID s are shown in columns relating to the species-delimitation methods, and those newly detected from Nigeria are indicated in colored squares. The number of marks on connecting lines shows the number of mutations separating haplotypes.
FIGURE 4 in Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria
FIGURE 4 Bayesian phylogenetic tree of the (a) ITS-1 region (677 bp) and (b) ITS-2 region (955 bp) of Moinidae lineages from Nigeria. Only posterior probabilities> 0.70 are shown. The lineage ID s are shown in columns relating to the species-delimitation methods, and those newly detected from Nigeria are indicated in colored squares. The mismatch assignments by COI and ITS-1 are in bold and highlighted with an asterisk. For abbreviations of country names refer to Fig. 3.
FIGURE 3 in Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria
FIGURE 3 Bayesian phylogenetic tree and species- delimitation of Moinidae from Southeast Nigeria, based on the mitochondrial COI gene (478 bp). A single representative of each haplotype (for reference sequences see Supplementary Table S1) is included in the tree. Codes of Moinidae haplotypes from Nigeria are provided in Table 1. Only posterior probabilities> 0.70 are shown. The numbers in the bands relating to the bPTP method indicate the statistical support (PP) for lineage membership. The lineage ID s are shown in columns relating to the species-delimitation methods, and the newly detected lineages from Nigeria are indicated in colored squares. Abbreviations of country names in which each haplotype was detected are, BO: Bolivia, CA: Canada, CN: China, CZ: Czech Republic, HU: Hungary, IN: India, JP: Japan, KZ: Kazakhstan, KR: Korea, MX: Mexico, MN: Mongolia, NG: Nigeria, RU: Russia, TH: Thailand, UA: Ukraine, US: U.S.A. Downloaded from Brill.com 12/12/2023 04:27:13PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
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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)
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DANDI Archive for NWB datasets
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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.