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162 results for “truncating”
Dataset of "Thermal Truncation of Heptamethine Cyanine Dyes"
<p>Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. Unlike phototruncation, the thermal truncation (chain-shortening) reaction is a phenomenon that has rarely been described for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3′ and C4′ positions of the chain and different heterocyclic end groups, the presence of different bases, nucleophiles and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, demonstrating the need to model catalytic reactions by highly correlated wavefunction-based methods. We show that entropic effects control the course of this process. The study provides a critical insight into the reactivity of the polyene chains of cyanines and offers new approaches to the synthesis of meso-substituted symmetrical and unsymmetrical pentamethine cyanines from Cy7 derivatives.</p>
List of human genes and their probabilities of being intolerant to heterozygous protein truncating variants.
<p>Recalculation of the Supplementary Table 2 (doi:10.1371/journal.pcbi.1004647.s002) of the journal article "The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome" by Bartha and Rausell published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1004647). Probabilities in this dataset were computed using human variation data from the Exome Aggregation Consortium (http://exac.broadinstitute.org/).</p> <p>Methods described in that article is relevant for this dataset. All author and affiliation information in that article is relevant for this dataset.</p> <p>Credit for the original human variation data is for the Exome Aggregation Consortium (http://exac.broadinstitute.org/, doi:10.1038/nature19057).</p>
Data and code for 'Age truncation due to disease shrinks metapopulation viability for amphibians'
<p>This repository provides all data and R code from the analysis for the following paper:</p> <p>Heard, G.W., Scroggie, M.P., Hollanders, M., and Scheele, B.C. (in press). Age truncation due to disease shrinks metapopulation viability for amphibians. <em>Journal of Applied Ecology</em>. </p> <p>The data are provided as a series of .csv files. A GRD file is provided for the landscape rasters. R code is provided separately for each of the following components:</p> <p>1. A script to complete regression modelling of age structure data for populations of the focal species pre- and post-Bd, plus estimation of adult survival rates from the age structure data using the 'catch curve' approach ('Age_structure_analysis.R').</p> <p>2. A script to generate the sample landscapes used for simulations of metapopulation dynamics for the pre- and post-Bd time periods ('Derive_landscape_rasters.R').</p> <p>3. A script with functions for simulating metapopulation dynamics with the aid of the STEPS R package ('STEPS_model.R').</p> <p>4. A script to run the metapopulation simulations across all the demographic and connectivity scenarios, where connectivity scenarios are defined by the sample landscapes ('Run_STEPS_simulations.R'). </p> <p>5. A script to fit logistic regression models to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_GLM.R').</p> <p>6. A script to fit multivariate normal hypervolumes to the outcomes of the metapopulation simulations (extinction versus persistence) ('Metapop_sims_analysis_MVNH.R').</p> <p>7. A script to generate each of the figures in the manuscript, plus Table 2 which requires post-hoc data compilation ('Generate_figures.R'). </p> <p>In combination, the data files and scripts allow all analyses from the paper to be reproduced. </p>
Truncated Marginal Neural Ratio Estimation - Data
<p>The dataset accompanying <em>Truncated Marginal Neural Ratio Estimation</em>. The software repository can be found <a href="https://github.com/bkmi/tmnre">here</a>. The arxiv article can be found <a href="https://arxiv.org/abs/2107.01214">here</a>.</p>
Dataset for "Estimating truncation effects of quantum bosonic systems using sampling algorithms"
<p>Markov Chain Monte Carlo simulation data for the preprint.</p> <p>T010ad***S10000M*_1.txt: simulation history for a_{dig} = 0.3, 0.5, 0.7, m^2 = 1, -1, B_max = 5000, used for Table 1 and Figure 1.</p> <p>T010R100L401S10000M1_1.txt: simulation history for a_{dig} = 0.5, m^2 = 1, B_max = 1, used for Figure 2.</p> <p>Table2.zip: contains simulation history for Table 2 and Figure 3. File name "T1a0.2S1250M1L4s2101.txt" indicates that the temperature is 1, a_{dig} = 0.2, Delta = 1250, m^2 = 1, lattice size is 4 * 4, and the random seed is 2101. Lines contain the expectation values of the potential energy and the two correlation functions obtained for successive steps. The largest estimated auto-correlation length d_q, which is used for the analysis, is as follows:</p> <table align="center"> <tbody> <tr> <td><em>a</em><sub>dig</sub></td> <td><em>d</em><sub>(0,0)</sub></td> <td><em>d</em><sub>(π,π)</sub></td> </tr> <tr> <td>0.2</td> <td>37</td> <td>4</td> </tr> <tr> <td>0.25</td> <td>38</td> <td>4</td> </tr> <tr> <td>0.3</td> <td>37</td> <td>4</td> </tr> <tr> <td>0.4</td> <td>41</td> <td>4</td> </tr> <tr> <td>0.5</td> <td>59</td> <td>5</td> </tr> <tr> <td>0.6</td> <td>130</td> <td>7</td> </tr> <tr> <td>0.7</td> <td>369</td> <td>15</td> </tr> <tr> <td>0.8</td> <td>968</td> <td>55</td> </tr> <tr> <td>0.9</td> <td>2174</td> <td>148</td> </tr> <tr> <td>1.0</td> <td>4491</td> <td>319</td> </tr> </tbody> </table> <p>The initial 10 d_q steps are discarded as a burn-in period, regardless of whether we conducted a warm-up run prior to the steps contained in this dataset.</p>
Fig. 1. Seta shape terminologies. 1. Fine. 2–3. Stout and truncated. 4–5. Plank-like. 6–7. Acicular. 8. Narrowly elliptic. 9. Elliptic. 10. Linear. 11 in Further additions to the knowledge of Strumigenys (Formicidae: Myrmicinae) within South East Asia, with the descriptions of 20 new species
Fig. 1. Seta shape terminologies. 1. Fine. 2–3. Stout and truncated. 4–5. Plank-like. 6–7. Acicular. 8. Narrowly elliptic. 9. Elliptic. 10. Linear. 11. Short linear or short subspatulate. 12–13. Subspatulate. 14–15. Spatulate. 16–17. Oblanceolate. 18–19. Small obovate. 20. Large obovate. 21. Suborbicular / orbicular. 22. Orbicular. 23. Remiform. 24. Remiform / narrowly claviform (red arrow). 25–26. Claviform. 27. Shoehorn-shaped. 28. Spoon-shaped.
Forming Impressions from Self-Truncated Samples of Traits - Interplay of Thurstonian and Brunswikian Sampling Effects
<p>Data sets for both experiments of the article "Forming Impressions from Self-Truncated Samples of Traits - Interplay of Thurstonian and Brunswikian Sampling Effects" published in Journal of Personality and Social Psychology. Additionally norms for the trait adjectives used as stimulus materials in Experiment 2.</p>
Estimation of reinforced urn processes under left-truncation and right-censoring
<p>We propose a nonparametric estimator for bivariate left-truncated and right-censored (LTRC) observations that combines the Expectation-Maximization (EM) algorithm and the Reinforced Urn Process (RUP). The resulting Expectation-Reinforcement (ER) algorithm allows for the inclusion of experts' knowledge in the form of a prior distribution, thus belonging to the class of Bayesian models. This can be relevant in applications where the data is incomplete, due to biases in the sampling process, as in the case of left-truncation and right-censoring. With this new approach, the distribution of the truncation variables is also recovered, granting further insight into those biases, and playing an important role in applications like prevalent cohort studies. The estimators are tested numerically using artificial and empirical datasets and compared with other methodologies such as copula models and the Kaplan-Meier estimator.</p>
Fig. 46. Partial truncated map for Central and South America with species distributions for the M in Taxonomic notes on social wasps of the groups of Mischocyttarus wagneri (Buysson 1908) and M. barbatus Richards 1945 (Hymenoptera, Vespidae, Polistinae)
Fig. 46. Partial truncated map for Central and South America with species distributions for the M. barbatus group, and with the pooled distribution of the group of M. wagneri (see next figure for detailed representation of distributions of species of this group).
Fig. 5 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 5. Neophasis oculata metacercariae (A–F) and sexual adult (G). (A) General view of metacercaria (acetic carmine, DIC). (B–C) Histological sections, Mallory's trichrome stain, encysted metacercaria (B) and some of its inner structures (C). (D–F) SEM, ventral view (D) and magnified spines in the anterior (E) and posterior (F) regions. (G) Sexual adult (acetic carmine, DIC). Scale bars – 100 μm on A, B, D, G; 50 μm on C; 10 μm on E, F.Abbreviations: c – ceca; ci – cirrus; eg – eggs; ev – excretory vesicle; icy – inner cyst layer; ocy – outer cyst layer; os – oral sucker; ot – ootype; ov – ovary; pe – pigmented eyespots; ph – pharynx; sv – seminal vesicle; te – testes; ut – uterus; vi – vitelline follicles; vs – ventral sucker.
Fig. 2 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 2. Neophasis oculata intramolluscan stages: daughter redia (A), infective cercaria body structure (B) and general view (C).
Fig. 8 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 8. Phylogenetic position of Neophasis oculata and N. anarrhichae based on the concatenated 18S and 28S rDNA sequence data, inferred with Bayesian inference. Newly generated sequences are indicated in bold. Posterior probabilities are printed at nodes, followed by bootstrap values for the nodes that were also supported in the tree inferred with Maximum likelihood method. Scale bar shows the substitution rate. GenBank accession numbers for the 18S and 28S rDNA sequences are listed in the Supplementary Table S1.
Fig. 7 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 7. Neophasis anarrhichae successive life cycle stages. (A, B) whole mounts (toluidine blue, DIC) of the anterior end of daughter redia (A) and cercaria embryo (B). (C) Cercaria later embryo, CLSM, TRITC-phalloidin and phospho Y antibody staining. (D, E) whole mounts (toluidine blue, DIC) of cercaria (D) and metacercaria (E). (F) Anterior end of metacercaria with gland ducts, CLSM, acetylated α-tubulin and phospho Y antibody staining. (G) Sagittal section of metacercaria, Heidenhain's iron hematoxylin staining. (H) Sagittal section of metacercaria, Mallory's trichrome stain. (I) progenetic metacercaria (toluidine blue, DIC). (J) sexual adult (acetic carmine, DIC). Scale bars – 50 μm.Abbreviations: aс – anterior collecting duct; bp – birth pore canal; c – ceca; cd – caudal excretory duct; ci – cirrus; eg – eggs; ev – excretory vesicle; os – oral sucker; ot – ootype; ov – ovary; ovd – oviduct; pс – posterior collecting duct; pe – pigmented eyespots; pd – penetration gland ducts; ph – pharynx; sv – seminal vesicle; t – tail; te – testes; vi – vitelline follicles; vs – ventral sucker. Arrow indicate on site of main collecting duct division.. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 1. Consensus (99 threshold) neighbour-joining tree based on the concatenated ITS1 and ITS2 860- b.p. fragment, built with Tamura-Nei genetic distance method and 1000 bootstrap resamples; support values are printed at nodes. Repeat regions of the ITS1 were excluded from the alignment. Scale bar shows substitutions per site. The ingroup includes identified and putative life cycle stages of Neophasis oculata and N. anarrhichae, the numbers of isolates are as listed in Table 1. Brachycladium goliath serves as an outgroup.
Fig. 3 in Life cycle truncation in Digenea, a case study of Neophasis spp. (Acanthocolpidae)
Fig. 3. Neophasis oculata cercariae. (A) Infective cercaria, general structure and mucoid in the tegument (toluidine blue), differential interference contrast (DIC). (B) Ducts of the penetration glands in live cercaria. (C) Sagittal histological section of infective cercaria, Erlich's hematoxylin-eosin. (D–E) Mucoid in underdeveloped cercariae (toluidine blue, whole mount, DIC (D) and Azur II-eosin, histological section (E)). (F) SEM, ventral view. (G–I) CLSM, TRITC-phalloidin, acetylated α-tubulin and phospho Y antibody staining. (G) Infective cercaria, flame cells and nerves. (H–I) Underdeveloped cercariae, excretory ducts (H) and eyespots (I). Scale bars – 50 μm.Abbreviations: aс – anterior collecting duct; cd – caudal excretory duct; ev – excretory vesicle; fc – flame cells; ga – cerebral ganglion; mc – mucoid cytons; os – oral sucker; pс – posterior collecting duct; pe – pigmented eyespots; pg – penetration glands; pd – penetration gland ducts; ph – pharynx; t – tail; ue – unpigmented eyespot; vnc – ventral nerve chords; vs – ventral sucker. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular. in JHABAR MAL, RAJENDRA NAGAR & R. SWAMINATHAN (2014) Record of Natula matsuurai Sugimoto (Orthoptera: Gryllidae: Trigonidiinae) and other sword-tailed crickets from India. Zootaxa, 3760(3): 458-462.
PLATE IA. Natula Gorochov, 1987. (A–L), Natula matsuurai (Sugimoto, 2001): A, Male; B, Female; C, Face with a transverse dark strip near epistomal suture; D, Fifth joint of maxillary palpi hatchet shaped; E, Lateral field of tegmina deeper than lateral lobe of pronotum; F, Hind tibia with 3 pairs of dorsal spines on both sides but largest inner apical spurs as long as or half of basitarsus; G, Fore tibia with oval shaped outer and inner tympanum; H, Harp vein only one, Mirror area occupying half dorsal surface, not divided with a small concentric inner veinlet; I, Pronotum with roundly convex anterior margin; J, Female ovipositor strongly upcurved, half as long as hind femur, three fifth area from base widened and bumpy, with a dorsal groove, cerci as long as ovipositor; K, Male sub-genital plate longer than wide, hind margin narrowly truncated with a small projected median lobe, two styli present; L, Female sub-genital plate roundly triangular.
Text-fig. 3. Pazlia hilaris gen. et sp. nov. (a–e) from the Early Cretaceous Famalicão locality (sample 025), Portugal (holotype, S175096) and Pazliopsis reyi gen. et sp. nov. (f–i) from the Early Cretaceous Torres Vedras locality, Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings a–f, i) and scanning electron microscopy (SEM, g, h). a, b) Seed in lateral (a) and oblique apical (b) views showing the truncate hilar-micropylar region; note prominent hilar scar (hi) and micropyle (mi) at the seed apex and the raphe (ra) seen as slightly raised ridge; remains of mounting media (¤). c) Cut volume rendering (cut at yz0647) showing course of raphe (ra), hilar scar (hi) and micropyle (mi); note the strongly radially elongated cells below the hilar scar. d) Seed in antiraphal view. e) Seed surface showing the raised undulate anticlinal walls of the exotestal cells. f) Seed enclosed in remains of thin-walled fruit (fr) (S174632, Torres Vedras sample 298). g) Holotype, seed enclosed in remains of fruit (fr); raphal view showing the faintly ribbed surface of the seed (S171534, Torres Vedras sample 043). h) Apical view of seed fragment showing hilar scar (hi), position of raphe (ra) and the ribbed seed surface (S136683, Torres Vedras sample 044). i) Seed surface showing the raised undulate anticlinal walls of the exotestal cells (S171534; Torres Vedras sample 043). Scale bars = 250 µm (a–d, f–h); 125 µm (e, i). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 3. Pazlia hilaris gen. et sp. nov. (a–e) from the Early Cretaceous Famalicão locality (sample 025), Portugal (holotype, S175096) and Pazliopsis reyi gen. et sp. nov. (f–i) from the Early Cretaceous Torres Vedras locality, Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings a–f, i) and scanning electron microscopy (SEM, g, h). a, b) Seed in lateral (a) and oblique apical (b) views showing the truncate hilar-micropylar region; note prominent hilar scar (hi) and micropyle (mi) at the seed apex and the raphe (ra) seen as slightly raised ridge; remains of mounting media (¤). c) Cut volume rendering (cut at yz0647) showing course of raphe (ra), hilar scar (hi) and micropyle (mi); note the strongly radially elongated cells below the hilar scar. d) Seed in antiraphal view. e) Seed surface showing the raised undulate anticlinal walls of the exotestal cells. f) Seed enclosed in remains of thin-walled fruit (fr) (S174632, Torres Vedras sample 298). g) Holotype, seed enclosed in remains of fruit (fr); raphal view showing the faintly ribbed surface of the seed (S171534, Torres Vedras sample 043). h) Apical view of seed fragment showing hilar scar (hi), position of raphe (ra) and the ribbed seed surface (S136683, Torres Vedras sample 044). i) Seed surface showing the raised undulate anticlinal walls of the exotestal cells (S171534; Torres Vedras sample 043). Scale bars = 250 µm (a–d, f–h); 125 µm (e, i).
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f).
Truncated Cuboctahedra
<p>A set of tetrahedrally meshed truncated octahedron with a truncation factor of 0.7, where the truncation factor is the degree to which the base octahedron is truncated. The data set contains a top level directory containing subdirectories with names of the form NpNNNNNN, where N represents a digit (0-9) and p represents a decimal point, these represent truncated octahedra with varying degrees of oblateness (0 < aspect ratio < 1) and prolateness (1 < aspect ratio). Within each directory are files with a numerical file name that represents the size of the geometry in nanometer of equivalent spherical volume diameter. Files with the extension ".pat" represent patran neutral files, and files with extension ".e" are exodusII files (these are also hdf5 compatible). Additionally some directories contain files with ".stderr" and ".stdout" extensions - these are the standard error and standard output of the meshing program used (Coreform Cubit, https://coreform.com/); and "*.cubit" extensions these are the Coreform Cubit scripts used to generate the meshes.</p>
Estimation of reinforced urn processes under left-truncation and right-censoring
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