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Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
<p>Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher-order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher-order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. In contrast some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher-order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ~293 million years (Ma), the base of Teleostei at ~211 Ma and the radiation of percomorphs beginning at ~141 Ma (~350 Ma, ~250–283 Ma and ~120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.</p>
Single species acute lethal toxicity tests are not predictive of relative population, community and ecosystem effects of two salinity types
<p>Human mediated salinity increases are occurring in freshwaters globally, with consequent negative effects on freshwater biodiversity. Salinity comprises multiple anions and cations. While total concentrations are typically used to infer effects, individual ion concentrations and ion ratios are critical in determining effects. Moreover, estimates of toxicity from single species laboratory tests, may not accurately predict relative effects on populations, communities and ecosystems. Here we compare salinity increases from synthetic marine salts (SMS) and sodium bicarbonate (NaHCO3) in an outdoor mesocosm experiment in south-eastern Australia. We found different effects of salt types on stream macroinvertebrates at the population, community, and ecosystem function levels, where similar effects were predicted from single species laboratory tests. Our results caution against the use of single species laboratory derived toxicological data to predict both environmentally safe salinity levels and the relative effects of different salt sources on freshwater biodiversity.</p>
Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging
<p>We performed CODEX (co-detection by indexing) multiplexed imaging on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), and single cell segmentation. Output of this process was a dataframe of nearly 130,000 cells with fluorescence values quantified from each marker. We used this dataframe as input to 1 of the 5 normalization techniques of which we compared z, double-log(z), min/max, and arcsinh normalizations to the original unmodified dataset. We used these normalized dataframes as inputs for 4 unsupervised clustering algorithms: k-means, leiden, X-shift euclidian, and X-shift angular.</p> <p>From the clustering outputs, we then labeled the clusters that resulted for cells observed in the data producing 20 unique cell type labels. We also labeled cell types by hiearchical hand-gating data within cellengine (cellengine.com). We also created another gold standard for comparison by overclustering unormalized data with X-shift angular clustering. Finally, we created one last label as the major cell type call from each cell from all 21 cell type labels in the dataset. </p> <p>Consequently the dataset has individual cells segmented out in each row. Then there are columns for the X, Y position in pixels in the overall montage image of the dataset. There are also columns to indicate which region the data came from (4 total). The rest are labels generated by all the clustering and normalization techniques used in the manuscript and what were compared to each other. These also were the data that were used for neighborhood analysis for the last figure of the manuscript. These are provided at all four levels of cell type level granularity (from 7 cell types to 35 cell types). </p>
Data from: Plant-type dominates fine-root C:N:P stoichiometry across China: a meta-analysis
<p>Aim: Fine roots play an important role in biogeochemical cycling in terrestrial ecosystems. However, our understanding of large scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry is extremely limited.</p> <p>Location: China.</p> <p>Methods: We compiled data for fine-root carbon (C), nitrogen (N) and phosphorus (P) concentrations at 165 sites across China to explore large-scale biogeographic patterns and drivers of fine-root C:N:P stoichiometry.</p> <p>Results: The geometric means of fine-root C, N, and P concentrations were 448.81 mg g-1, 10.73 mg g-1, and 0.9 mg g-1, respectively, whereas C:N, C:P and N:P ratios were 41.84, 508.32 and 11.73, respectively. The fine-root elemental concentrations and their ratios varied widely among plant groups and biomes, and showed clear latitudinal and longitudinal trends, as a consequence of differences in climate, soil and plant-type. However, plant-type was the largest contributor to the total variance in fine-root C, N, and P and their ratios compared to climate factors or soil features.</p> <p>Main conclusions: The data reveal the existence of broad biogeographic patterns of fine-root C:N:P stoichiometry in China. These results advance our knowledge about the biogeochemical cycling of fine roots.</p>
Figure 15. Type locality for Trichonotuloides aphoderrans n in Trichonotuloides aphoderrans, n.sp. (Coleoptera: Scarabaeidae: Aphodiinae), a new genus and species for the United States
Figure 15. Type locality for Trichonotuloides aphoderrans n. sp.
FIG. 21. — Type d in Spécimens de Charles Plumier déposés à Paris dans les collections de ptéridophytes américains de Tournefort, Vaillant, Danty d'Isnard et Jussieu
FIG. 21. — Type d'Osmunda cicutaria Savigny ex Poir., planche 159 de Plumier (1705).
FIG. 3 in Type and new combination for Stellaria lanceolata and a new synonymy for S. rotundifolia (Caryophyllaceae)
FIG. 3. — Drymaria cordata (L.) Willd. ex Roem. & Schult. (S. rotundifolia Poir. type).
FIG. 2 in Type and new combination for Stellaria lanceolata and a new synonymy for S. rotundifolia (Caryophyllaceae)
FIG. 2. — Cerastium lanceolatum (Poir.) Volponi, comb. nov. (Stellaria lanceolata Poir. type).
Modern phenotypic typing technologies for monitoring and evaluating heterogeneity in bacterial populations
<p>Modern phenotypic typing technologies for monitoring and evaluating heterogeneity in bacterial populations</p> <p>Современные технологии фенотипического типирования для мониторинга и оценки гетерогенности бактериальных популяций</p>
How Did the COVID-19 Crisis Affect Different Types of Workers in the Developing World?
<p>Video presentation of paper submission 15 for the Data for Policy 2021 Conference with the main results of "HOW DID THE COVID-19 CRISIS AFFECT DIFFERENT TYPES OF WORKERS IN THE DEVELOPING WORLD?" research paper emanating from the JobsWatch World Bank project to monitor labor market outcomes across 40 developing countries in real time identifying women, youth, less educated and urban workers as bearing the brunt of the burden of the pandemic job and wage losses.</p>
FIG. 1. — Dominique Luizet vers l in Les Saxifraga L. de l'herbier Luizet: informatisation et numérisation des types et dissections
FIG. 1. — Dominique Luizet vers l'âge de 75 ans (Guétrot 1931).
Odontometric Data from of all Tooth Types from Skeletal Collections in South Africa
<p>Biological profiles are used to assist in the identification of an unknown person. Sex estimation is important in this process as other aspects of the biological profile such as age-at-death, population affinity and stature depend on accurate sex estimates. For this research, we estimated sex using the dentition of three socially identified South African groups, namely black, white and coloured South Africans. A total of 906 crania from dissection room cadavers from three medical schools, including the Pretoria Bone Collection (University of Pretoria), the Raymond A Dart Collection (University of Witwatersrand) and the Kristen Collection (Stellenbosch University) were used. Four measurements were taken from the left and right sides of incisors, canines, premolars and molars. Measurements were standard from Hillson 2005 and include four permanent tooth crown dimensions: maximum mesiodistal, maximum buccolingual and molar diagonal diameters (mesiobuccal - distolingual and mesiolingual - distobuccal).</p>
Figure 2 in The Nomenclature and Type Material of Crocodylus johnstoni (Krefft, 1873)
Figure 2. Dorsal view of holotype skin of Crocodilus johnsonii Krefft.
Figure 9. Image from Negative V342 in The Nomenclature and Type Material of Crocodylus johnstoni (Krefft, 1873)
Figure 9. Image from Negative V342 (Australian Museum Archives); dorsal
Figure 3 in The Nomenclature and Type Material of Crocodylus johnstoni (Krefft, 1873)
Figure 3. Left lateral view of holotype skin of Crocodilus johnsonii Krefft.
Figure 30 in Type Specimens of Non-fossil Mammals in the Australian Museum, Sydney
Figure 30. AM M.1350, syntype skin of Hapalotis boweri Ramsay, 1887b. (Photography by Sally Cowan).
Figure 1 in Type Specimens of Non-fossil Mammals in the Australian Museum, Sydney
Figure 1. AM PA.389, holotype skin of Echidna corealis Krefft, 1872a. (Photography by Sally Cowan).
Medicinal properties of Morus alba for the control of type 2 diabetes mellitus: a systematic review
<p><strong>Background:</strong> the objective of this review was to evaluate the medicinal potential of <em>Morus alba</em> leaves on the control of Type 2 Diabetes Mellitus (DM2). Research question: what is the medicinal potential of <em>Morus alba</em> leaves in the control of DM2? <strong>Methods:</strong> It was based on the PRISMA Declaration. The included studies were extracted from Scopus, Pubmed, ScienceDirect, Scielo, and Google Scholar; January 2015 to July 2021, Key search terms were MeSH and DeCS: <em>Morus alba</em>, mulberry, hypoglycemic agent. The inclusion criteria were: studies in rats administered <em>Morus alba</em> leaf extracts; studies that included the dimensions of lipidemia and glycemia; studies that included indicators such as fasting glucose, postprandial glucose, glycosylated hemoglobin, triglycerides, low-density lipoproteins, total cholesterol, and insulin resistance. Exclusion criteria: studies in which <em>Morus alba</em> leaves were administered with other plants; studies with other parts of the <em>Morus alba</em> plant; proteomic studies, cancer, duplicate studies, in vitro studies, and evaluation of included studies. All included investigations were evaluated for biases. <strong>Results:</strong> The extracts of <em>Morus alba</em> leaves at the phytochemical level improve glucose uptake. Chlorogenic acid, isoquercitrin, and quercitrin, present in the leaves of <em>Morus alba</em> have hypoglycemic properties and an ameliorating effect on diabetic nephropathy. This leaf has pharmacological effects such as glucose absorption, insulin secretion production, antioxidant and anti-inflammatory agent, antihyperglycemic and antihyperlipidemic activities, and obesity management. <strong>Conclusions:</strong> <em>Morus alba</em> leaves have pharmacological effects on DM2 that include glucose absorption, production of insulin secretion, antioxidant agent, antihyperglycemic and antihyperlipidemic activities, and obesity control. Beyond these results, there is a lack of studies on the potential and synergistic effects of the components of <em>Morus alba</em> leaves, which limit the possibility of a more effective therapy using the leaves of the plant.</p>
Figure 2 in Taxonomic overview of the greater fritillary genus Speyeria Scudder and the atlantis - hesperis species complexes, with species accounts, type images, and relevant literature (Lepidoptera: Nymphalidae)
Figure 2. Original description and colored illustrations for 'Idalia' reproduced from Drury 1773.
Fig. 2. Acanthocobitis pavonacea, NRM 40422, 96.6 in Type locality and synonymy of Paracanthocobitis marmorata and notes on Acanthocobitis (Teleostei: Nemacheilidae)
Fig. 2. Acanthocobitis pavonacea, NRM 40422, 96.6 mm; India: aquarium. (Photograph by M. Kottelat).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.