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26 results for “Derris”
Data for "Training data composition affects performance of protein structure analysis algorithms" by A. Derry, K. A. Carpenter, & R. B. Altman
<p><strong>Description</strong></p> <p>This repository contains all data used in "Training data composition affects performance of protein structure analysis algorithms", published in the Pacific Symposium on Biocomputing 2022 by A. Derry, K. A. Carpenter, & R. B. Altman. </p> <p>The data consists of the following files:</p> <ul> <li>ema_zenodo_data.tar.gz: train, validation, and test splits for Estimation of Model Accuracy task, in LMDB format</li> <li>design_zenodo_data.tar.gz: train, validation, and test splits for Protein Sequence Design task, in JSON format</li> <li>enz_cat_res_zenodo_data.tar.gz: train, validation, and test splits for Catalytic Residue and Enzyme Prediction task, in TF record format</li> </ul> <p>Details on dataset construction can be found in our paper and dataloaders can be found in our <a href="https://github.com/awfderry/ml-structure-bias">Github repo</a>.</p> <p><strong>Reference</strong></p> <p>A. Derry*, K. A. Carpenter*, & R. B. Altman, "Training data composition affects performance of protein structure analysis algorithms", 2021.</p> <p><strong>Dataset References</strong></p> <p>Datasets used were derived from the following works:</p> <p>Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2019). Critical assessment of methods of protein structure prediction (CASP)—Round XIII. In <em>Proteins: Structure, Function and Bioinformatics</em> (Vol. 87, Issue 12, pp. 1011–1020). https://doi.org/10.1002/prot.25823</p> <p>Ingraham, J., Garg, V. K., Barzilay, R., & Jaakkola, T. (2019). <em>Generative Models for Graph-Based Protein Design</em>. https://openreview.net/pdf?id=SJgxrLLKOE</p> <p>Furnham, N., Holliday, G. L., de Beer, T. A. P., Jacobsen, J. O. B., Pearson, W. R., & Thornton, J. M. (2014). The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. <em>Nucleic Acids Research</em>, <em>42 </em>(Database issue), D485–D489.</p>
FIGURE 3 in Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data
FIGURE 3. Derris taiwaniana (Hayata) Z.Q. Song. A. habit; B. stem with brown lenticels; C. leaflets, adaxial and abaxial view, scale bar = 2 cm; D. leaves; E. flowering branchlets; F. pseudoraceme, showing distinct brachyblasts; G. part of inflorescence; H. part of inflorescence with unopened flowers; I. flower and dissection of a flower, scale bar = 2 cm; J. part of ovary, showing 7 ovules; K. old pods covered with warts outside and reniform seeds, scale bar = 4 cm. Photographs by Zhu-Qiu Song (A–C, E–J), You-Sheng Chen (D), and Bo Pan (K).
FIGURE 5 in Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data
FIGURE 5. Distribution of Derris entadoides (Z. Wei) Z.Q. Song (red triangle) and Derris taiwaniana (Hayata) Z.Q. Song (blue dots, made by the software ArcGIS 10.2).
FIGURE 1 in Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data
FIGURE 1. Isotype of Derris entadoides (Z. Wei) Z.Q. Song (Chi-Wu Wang 72150, A00283892, https://kiki.huh.harvard.edu/databases/ specimen_search.php?barcode=A00283892). © Copyright of the Herbarium of the Arnold Arboretum of Harvard University.
FIGURE 4 in Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data
FIGURE 4. Consensus tree of maximum likelihood (ML) analysis of the combined dataset of all four markers (trnK-matK, trnL-F IGS, psbA-trnH IGS and ITS). Numbers near branches are SH-aLRT and ultrafast bootstrap (UFBoot) support values. Samples of Derris species were indicated with red fonts, and those of Millettia species were indicated with blue fonts. The Paraderris subclade (i.e. the DP subclade) within the clade D2 of the genus Derris is indicated in the shaded box.
FIGURE 2 in Transfer of Millettia pachycarpa and M. entadoides to Derris (Fabaceae), supported by morphological and molecular data
FIGURE 2. Derris entadoides (Z. Wei) Z.Q. Song. A. habit; B. stem with brown lenticels; C. cross section of stem, showing pithy inside; D. leaf, adaxial view; E. leaf, abaxial view, showing glaucous surface beneath; F. flowering branchlets; G. pseudoraceme, showing distinct brachyblasts; H. part of inflorescence with opened flowers; I. part of inflorescence with unopened flowers; J. brachyblast with one flower, and dissection of a flower, scale bar = 1 cm; K. part of ovary, showing 5 ovules; L. old pods, scale bar = 4 cm. Photographs by Zhu-Qiu Song
FIGURE 5. Derris tonkinensis Gagnep. A in Taxonomic notes on the genus Millettia (Fabaceae: Millettieae) in Vietnam
FIGURE 5. Derris tonkinensis Gagnep. A. lectotype of Millettia boniana Gagnep. (H. F. Bon 4871, P02141778, https://science.mnhn. fr/institution/mnhn/collection/p/item/p02141778); B. lectotype of D. tonkinensis Gagnep. (B. Balansa 1189, P00700373, https://science. mnhn.fr/institution/mnhn/collection/p/item/p00700373); C. flowering syntype of D. tonkinensis Gagnep. (H. F. Bon 3347, P02927191, https://science.mnhn.fr/institution/mnhn/collection/p/item/p02927191); D. fruiting specimen of D. tonkinensis Gagnep. (H. F. Bon 3381, P02927188, https://science.mnhn.fr/institution/mnhn/collection/p/item/p02927188). ©Copyright of Muséum national d'Histoire naturelle.
Fig. 3 in Derrisrobustones A-D, isoflavones from the twig extract of Derris robusta (DC.) Benth. and their α-glucosidase inhibitory activity
Fig. 3. ECD spectra of compounds 1–3. (A) Experimental and TDDFT calculated ECD spectra of (+)-(2′′S)-derrisrobustone A and ()-(2′′R)-derrisrobustone A at B3LYP/6311++G(d,p) level in MeOH (CPCM). (B) Experimental ECD spectra of (+)-(1′′R,2′′R)-derrisrobustone B and ()-(1′′S,2′′S)-derrisrobustone B at B3LYP/ 6311++G(d,p) level in MeOH (CPCM). (C) Experimental and TDDFT calculated ECD spectra of (+)-(1′′S,2′′R)-derrisrobustone C and ()-(1′′R,2′′S)-derrisrobustone C.
Supplementary material 2 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Maximum Parsimony (MP) analysis
Supplementary material 1 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Species, voucher specimen, and GenBank accession for sequence data reported in the study
Figure 7 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 7 Comparative anatomical characters of leaflet transverse sections A–L midrib M, O leaflet blade and N, P leaflet margin A, B, E, F, I, J, M, N the new Derris and C, D, G, H, K, L, O, PD. pubipetala. ar = adaxial ridge; cc = cortical cells; nt = non-glandular trichome; pf = perivascular fibers; pr = prism. Scale bars: 50 µm (M, N (below), O, P (above)); 100 µm (I–L); 200 µm (B, D, E–H, N (above), P (below)); 500 µm (A, C).
Figure 6 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 6 Comparative anatomical characters of the leaflet epidermis A–D adaxial leaflet epidermis E–H abaxial leaflet epidermis A, B, E, F, I, J the new Derris samples and C, D, G, H, K, LD. pubipetala. as = anomocytic stomata; bc = basal cell of trichome; nt = non-glandular trichome; ps = paracytic stomata. Scale bars: 50 µm (B, D, F, H–L); 100 µm (A, C, E, G).
Figure 3 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 3 D. rubricostaA inflorescence with leaf B close-up of inflorescence C flowers (top and side view) D outer surface and E inner surface of standard petal F outer surface and G inner surface of keel petals H outer surface and I inner surface of wing petals J staminal sheath K anthers L pistil M adaxial and N abaxial leaflet surfaces. Drawn by Punvarit Boonprajan from C. Leeratiwong 19-1666 (BKF). Scale bars: 5 mm (A, B); 1 mm (C–N).
Figure 9 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 9 Consensus tree from Bayesian Inference analysis (BI) of concatenated two plastid and one nuclear dataset. The posterior probabilities (PP) are shown above the branches. Bootstrap percentage support values of Maximum likelihood (MLBS) and Maximum parsimony (MPBS) are shown below the branches, respectively (- = MPBS and/or MLBS < 50%). Abbreviations and numbers after the scientific names indicate locality codes following Table 1: NN = Nopphitam district, Nakhon Si Thammarat province; RS = Rattaphum district, Songkhla province; SS = Sadao district, Songkhla province, Thailand. Red and blue lettering highlight the position of the three samples of the new Derris and D. pubipetala, respectively.
Figure 5 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 5 Scanning electron microscope (SEM) photographs showing leaflet micromorphology A–D) adaxial and I–L abaxial surfaces of leaflet lamina E–H adaxial and (M–P) abaxial surfaces of midrib Q–T non-glandular and glandular trichomes A, B, E, F, I, J, M, N, Q, R the new Derris samples and C, D, G, H, K, L, O, P, S, TD. pubipetala; bt = bicellular non-glandular trichome; ep = epidermal cell; gt = glandular trichome; mr = midrib; nt = non-glandular trichome; st = stoma. Scale bars: 5 µm (T); 10 µm (Q, S); 20 µm (J, L, R); 50 µm (B, D, N, P); 100 µm (F, I); 200 µm (E); 500 µm (A, C, H, K, M, O); 1000 µm (G).
Figure 8 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 8 High-performance liquid chromatography (HPLC) chromatograms of the new Derris samples and D. pubipetala roots (the lower, blueish lines) and stems (the upper, reddish lines) extracts A two standard compounds B The new Derris species samples CD. pubipetala; Each Arabic numeral represents the accession number of each sample presented in Table 1. Each Roman numeral represents each peak of HPLC chromatograms (chemical compound) with its retention time, i.e., (I) RT, 6.1 min; (II) DG, 6.7 min; (III) UK1, 13.3 min; (IV) UK2, 14.4 min; (V) UK3, 15.3 min; (VI) UK4, 24.0 min; (VII) UK5, 26.1 min; (VIII) UK6, 29.5 min; (IX) UK7, 32.2 min; RT = rotenone; DG = deguelin; UK = unknown.
Figure 4 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 4 Collection sites of the new Derris samples, represented by a yellow square (flowering specimen) and light-blue triangle (specimen without flowers) and D. pubipetala (orange circles) in Peninsular Thailand.
Figure 1 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 1 Derris rubricosta, sp. nov. A habit and habitat B leaves C stem D young reddish leaflets E reddish midribs of mature leaflets F, G close-up of midrib on adaxial and abaxial surface respectively H inflorescences and foliage I, J close-up of inflorescence, showing flower buds and brachyblasts K close-up of flower and buds. All photos were taken at Pha Dam Forest Ranger Unit in Songkhla province. Photos by Punvarit Boonprajan (A, B, D–G) and Charan Leeratiwong (C, H–K).
Figure 2 from: Boonprajan P, Leeratiwong C, Sirichamorn Y (2024) From morphology to molecules: A comprehensive study of a novel Derris species (Fabaceae) with a rare flowering habit and reddish leaflet midribs, discovered in Peninsular Thailand. PhytoKeys 237: 51-77. https://doi.org/10.3897/phytokeys.237.112860
Figure 2 Comparative macro- and micro-morphological characters of leaflets and flowers of Derris rubricosta (A, A1–A10) and D. pubipetala (B, B1–B10) A, B a branch with leaves and inflorescences A1, B1 outer surface and A2, B2 inner surface of standard petal A3, B3 outer surface and A4, B4 inner surface of keel petals A5, B5 outer surface and A6, B6 inner surface of wing petals A7.1, B7.1 stamens and A7.2, B7.2 close-up stamens A8.1, B8.1 pistil and A8.2, B8.2 close-up pistil apex A9, B9 adaxial and A10, B10 abaxial leaflet surfaces. Photos by Charan Leeratiwong (A, B) and Punvarit Boonprajan (A1–A10, B1–B10). Scale bars: 1 mm.
Fig. 2 in Derrisrobustones A-D, isoflavones from the twig extract of Derris robusta (DC.) Benth. and their α-glucosidase inhibitory activity
Fig. 2. COSY and selected HMBC (1H → 13C) correlations of compounds 1–3.
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