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Concatenated DNA matrix and BEAST tree used for phylogenetic, dating, biogeographic and diversification analyses of Caribbean Podocarpus
<p><b>Aim </b>The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been tested in the Caribbean due to its geological complexity. Here we use the conifer genus <i>Podocarpus</i> to explore this hypothesis. We infer the evolutionary history, biogeography, and diversification rates of this genus under a hypothesis testing framework.</p> <p><b>Location</b> The Caribbean archipelago (Antilles)</p> <p><b>Methods</b> We present the most comprehensive sampling for Caribbean <i>Podocarpus</i> to date in a Bayesian dated phylogenetic tree using a genotyping by sequencing DNA matrix of 67,589 bp. We inferred ancestral ranges and inter-island divergence patterns using several models available. We explored diversification rates associated with island colonization, and checked for diversification rate shifts in the phylogeny.</p> <p><b>Results</b> Caribbean <i>Podocarpus</i> is the result of colonization from the Andes during the Eocene to Oligocene (ca. 45-31 Ma). Lesser Antillean species originated during the Oligocene from the Andes or the Greater Antilles, depending on the model of choice. Vicariance can explain the divergence of Cuban and Hispaniolan species, with subsequent dispersals into Jamaica. Despite the availability of new habitat opportunities, which might promote cladogenesis, insular <i>Podocarpus</i> did not show higher diversification rates than continental taxa.</p> <p><b>Main</b> <b>conclusions </b>The conditions for progression rule were not met because colonization of younger islands (Lesser Antilles) occurred from the continent, or because suitable habitat in the partially emerged younger islands was likely present at the time older islands (Greater Antilles) were colonized. An improved paleogeographic knowledge of the Caribbean will allow testing this hypothesis in multiple lineages. Our finding that diversification rates did not increase with island colonization might be common in other Caribbean lineages. Genotyping by sequencing proved promising to reveal complex historical assembly processes of vicariance and dispersal at a fine phylogenetic scale.</p> <p> </p>
Results of matrix factorization decompositions for a set of 14 colon cancer transcriptomic datasets using different methods
<p>These are the results of application of several matrix factorization methods (ICA, StabilizedICA, NMF, PCA) for a set of 14 independent colon cancer transcriptomics datasets. The analysis was done to compare the methods in terms of their reproducibility (ability to generalize). </p> <p>The results of this analysis was published in </p> <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821374/pdf/btz225.pdf">Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinformatics. 2019 Nov 1;35(21):4307-4313. doi: 10.1093/bioinformatics/btz225. </a></p> <p> </p>
Figure 4 from: Rojanarata T, Maithongdee K, Yuwansri N, Kaewprasert S, Thanayutsiri T, Phadungcharoen N, Chinsriwongkul A (2022) Investigating matrix interference in the pharmacopeial limit test for aluminum in citric acid: a re-examination, for revision of the method. Pharmacia 69(1): 9-13. https://doi.org/10.3897/pharmacia.69.e78631
Figure 4 Concentration of aluminum in the aqueous phase in the extraction of 0.04 mg/ml aluminum solution prepared in water and in the solution containing 0.2 g/ml citric acid. Phase.
Figure 2 from: Rojanarata T, Maithongdee K, Yuwansri N, Kaewprasert S, Thanayutsiri T, Phadungcharoen N, Chinsriwongkul A (2022) Investigating matrix interference in the pharmacopeial limit test for aluminum in citric acid: a re-examination, for revision of the method. Pharmacia 69(1): 9-13. https://doi.org/10.3897/pharmacia.69.e78631
Figure 2 Effect of the concentration of citric acid co-existing in 0.04 mg/ml aluminum solution on the fluorescence intensity of the extract as measured using RF-6000 spectrofluorometer (Shimadzu).
Figure 1 from: Rojanarata T, Maithongdee K, Yuwansri N, Kaewprasert S, Thanayutsiri T, Phadungcharoen N, Chinsriwongkul A (2022) Investigating matrix interference in the pharmacopeial limit test for aluminum in citric acid: a re-examination, for revision of the method. Pharmacia 69(1): 9-13. https://doi.org/10.3897/pharmacia.69.e78631
Figure 1 Standard curves of aluminum in water and in citric acid solutions, prepared using chemicals and instruments of different manufacturers; (a) citric acid of Merck/8-hydroxyquinoline of Sigma-aldrich/ spectrofluorometer RF-1501, (b) citric acid of BDH Chem/8-hydroxyquinoline of Sigma-aldrich/spectrofluorometer RF-1501, (c) citric acid of Merck/8-hydroxyquinoline of Fluka/spectrofluorometer RF-1501, (d) citric acid of Merck/8-hydroxyquinoline of Sigma-aldrich/spectrofluorometer RF-6000.
Figure 3 from: Rojanarata T, Maithongdee K, Yuwansri N, Kaewprasert S, Thanayutsiri T, Phadungcharoen N, Chinsriwongkul A (2022) Investigating matrix interference in the pharmacopeial limit test for aluminum in citric acid: a re-examination, for revision of the method. Pharmacia 69(1): 9-13. https://doi.org/10.3897/pharmacia.69.e78631
Figure 3 Effect of pH of 0.04 mg/ml aluminum solution prepared in 0.2 g/ml citric acid solution, on the fluorescence intensity of the extract, compared with that of a solution prepared in water. The measurements were done using RF-6000 spectrofluorometer (Shimadzu).
NicheNet 2.0. Ligand-Target matrix and Networks
<p>NicheNet 2.0. ligand-target matrix and networks for both mouse and human</p>
Cladistic matrix targeted at resolving relationships between fossil birds from the Changma locality of the Lower Cretaceous Xiagou Formation
<p>We describe six specimens consisting of cranial remains and associated partial presacral axial series belonging to ornithuromorph birds from the Changma locality of the Lower Cretaceous Xiagou Formation of northwestern Gansu Province, China. Comparison among specimens is limited by the paucity of overlapping elements, their differing exposed views, and, in some specimens, poor preservation. Despite this, three separate taxa are represented, evidenced by differences in their dentary dentitions: one specimen is edentulous, another has sharp, closely spaced, relatively high-crowned and peg-like teeth, and a third preserves blunt, relatively low-crowned teeth placed in a communal groove, a morphology previously reported among adult birds only in Hesperornithiformes. We propose that the high-crowned specimen may be referred to Gansus yumenensis based on shared similarities with the closely related Iteravis huchzermeyeri, including a very similar dentition and an edentulous premaxilla with elongate, unfused frontal processes and no palatal processes. The two other specimens are considered new taxa, for which we erect the names Meemannavis ductrix gen. et sp. nov. and Brevidentavis zhangi gen. et sp. nov. These new specimens confirm that the Changma locality is dominated by ornithuromorph birds and contribute to a better understanding of this important avifauna. The observed variation in dental morphology hints at trophic diversity like that observed in ornithuromorphs from the penecontemporaneous Jehol Group of northeastern China.</p>
Supplementary material 1 from: Cirino DW, Lupinetti-Cunha A, Freitas CH, de Freitas SR (2022) Do the roadkills of different mammal species respond the same way to habitat and matrix? In: Santos S, Grilo C, Shilling F, Bhardwaj M, Papp CR (Eds) Linear Infrastructure Networks with Ecological Solutions. Nature Conservation 47: 65-85. https://doi.org/10.3897/natureconservation.47.73010
Correlation plot and R script for building and selecting best models
Sampling plot × species matrix from: Climate-driven elevational variation in range sizes of vascular plants in the central Himalayas: a supporting case for Rapoport's rule
<p>A fundamental yet controversial topic in biogeography is how and why species range sizes vary along spatial gradients. To advance our understanding of these questions and to provide insights into biological conservation, we assessed elevational variations in the range sizes of vascular plants with different life forms and biogeographical affinities and explored the main drivers underlying these variations in the longest valley in China's Himalayas, the Gyirong Valley. Elevational range sizes of vascular plants were documented in 96 sampling plots along an elevational gradient ranging from 1,800 to 5,400 m above sea level. We assessed the elevational variations in range size by averaging the range sizes of all recorded species within each sampling plot. We then related the range size to climate, disturbance, and the mid-domain effect, and explored the relative importance of these factors in explaining the range size variations using the Random Forest model. A total of 545 vascular plants were recorded in the sampling plots along the elevational gradient. Of these, 158, 387, 337, and 112 were woody, herbaceous, temperate, and tropical species, respectively. The range size of each group of vascular plants exhibited uniform increasing trends along the elevational gradient, which was consistent with the prediction of Rapoport's rule. Climate was the main driver of the increasing trends of vascular plant range sizes in the Gyirong Valley. The climate variability hypothesis and mean climate condition hypothesis could both explain the elevation-range size relationships. Our results reinforce the previous notion that Rapoport's rule applies to regions where the influence of climate is the most pronounced, and call for close attention to the impact of climate change to prevent species range contraction and even extinction due to global warming. </p>
Data from: Extracellular matrix-associated gene expression in adult sensory neurons cultured on laminin substrates
Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.
A 2018 Social Accounting Matrix for Germany depicting waste and recycling accounts for a circular economy
<p>The 2018 SAM for Germany comprises of 160 accounts including 63 activities, 85 commodities, margins, labor, capital, household, government, social contributions, taxes on products, activity tax, direct tax, stock change, savings and investment and the rest of the world. It is entirely based on data from the Federal Statistical Office of Germany (Destatis), which guarantees the highest possible degree of data-consistency. Because the initial version of the SAM (Proto-SAM) has imbalances in the government, savings and investment and the rest of the world accounts, a balanced SAM is estimated using the cross-entropy method. To ensure the consistency of the data through the estimation process, macro totals are enforced as controls for total imports, total value-added, total private consumption, total government consumption and total exports.</p>
Similarity matrix between the core genome sequences
<p>Data table.</p>
The Pearson correlation coefficient matrix for all study items (N = 507)
<p>The Pearson correlation coefficient matrix for all study items (N = 507)</p>
Raw allelic matrix and supplementary materials: Origin and dispersion pathways of guava in the Galapagos Islands inferred through genetics and historical records
<p>Guava (<i>Psidium guajava</i>) is an aggressive invasive plant in the Galapagos Islands. Determining its provenance and genetic diversity could explain its adaptability and spread, and how this relates to past human activities. With this purpose, we analyzed 11 SSR markers in guava individuals from Isabela, Santa Cruz, San Cristobal and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. We consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. Through Approximate Bayesian Computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, then it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed in the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven by either a single event or a series of introduction events in rapid succession. We thus show that genetic analyses supported by historical sources can be used to track the arrival and spread of invasive species in novel habitats and the potential role of human activities in such processes.</p>
FIGURES 21, 22 in Larval description of Setodes acutus Navás 1936, (Trichoptera: Leptoceridae) from Algeria, including a discriminatory matrix to the known Setodes larvae from the Maghreb region
FIGURES 21, 22. Collection site of S. acutus; Bouilef stream, NE Algeria.
I. ANSOFF'S MATRIX AND ITS ADVANTAGES WHEN APPLYING MARKETING STRATEGIES IN INTERNATIONAL MARKETS.
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COMPSs RandomSVD CFD Matrix
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Matrix table (The Mutual Influence between Entrepreneurial Marketing and Causal and Effectual Entrepreneurship: An Empirical Study in an Emerging and Developing Economy)
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Table-Matrix, containing all the codes generated from the inductive analysis process of the 78 articles that made up the final sample. (Not only Opportunity, but also Uncertainty: A systematic review of how entrepreneurship literature appropriates both constructs.)
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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
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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.