3,172 research outputs found
ropensci/drake: First release under rOpenSci
No full text<p>TL;DR: this is the first release in which <code>drake</code> is part of rOpenSci. Relative to 4.4.0, this release has major changes to cache internals, user-level function names, and documentation.</p>
<ul>
<li>Transfer <code>drake</code> to rOpenSci: <a href="https://github.com/ropensci/drake">https://github.com/ropensci/drake</a></li>
<li>Several functions now require an explicit <code>config</code> argument, which you can get from
<code>drake_config()</code> or <code>make()</code>. Examples:<ul>
<li>outdated()</li>
<li>missed()</li>
<li>rate_limiting_times()</li>
<li>predict_runtime()</li>
<li>vis_drake_graph()</li>
<li>dataframes_graph()</li>
</ul>
</li>
<li>Always process all the imports before building any targets. This is part of the solution to #168: if imports and targets are processed together, the full power of parallelism is taken away from the targets. Also, the way parallelism happens is now consistent for all parallel backends.</li>
<li>Major speed improvement: dispense with internal inventories and rely on <code>cache$exists()</code> instead.</li>
<li>Let the user define a trigger for each target to customize when <code>make()</code> decides to build targets.</li>
<li>Document triggers and other debugging/testing tools in the new <a href="https://github.com/ropensci/drake/blob/master/vignettes/debug.Rmd">debug vignette</a>.</li>
<li>Restructure the internals of the <code>storr</code> cache in a way that is not back-compatible with projects from versions 4.4.0 and earlier. The main change is to make more intelligent use of <code>storr</code> namespaces, improving efficiency (both time and storage) and opening up possibilities for new features. If you attempt to run drake >= 5.0.0 on a project from drake <= 4.0.0, drake will stop you before any damage to the cache is done, and you will be instructed how to migrate your project to the new drake.</li>
<li>Use <code>formatR::tidy_source()</code> instead of <code>parse()</code> in <code>tidy_command()</code> (originally <code>tidy()</code> in <code>R/dependencies.R</code>). Previously, <code>drake</code> was having problems with an edge case: as a command, the literal string <code>"A"</code> was interpreted as the symbol <code>A</code> after tidying. With <code>tidy_source()</code>, literal quoted strings stay literal quoted strings in commands. This may put some targets out of date in old projects, yet another loss of back compatibility in version 5.0.0.</li>
<li>Speed up clean() by refactoring the cache inventory and using light parallelism.</li>
<li>Implement <code>rescue_cache()</code>, exposed to the user and used in <code>clean()</code>. This function removes dangling orphaned files in the cache so that a broken cache can be cleaned and used in the usual ways once more.</li>
<li>Change the default <code>cpu</code> and <code>elapsed</code> arguments of <code>make()</code> to <code>NULL</code>. This solves an elusive bug in how drake imposes timeouts.</li>
<li>Allow users to set target-level timeouts (overall, cpu, and elapsed) with columns in the workflow plan data frame.</li>
<li>Document timeouts and retries in the new <a href="https://github.com/ropensci/drake/blob/master/vignettes/debug.Rmd">debug vignette</a>.</li>
<li>Add a new <code>graph</code> argument to functions <code>make()</code>, <code>outdated()</code>, and <code>missed()</code>.</li>
<li>Export a new <code>prune_graph()</code> function for igraph objects.</li>
<li>Delete long-deprecated functions <code>prune()</code> and <code>status()</code>.</li>
<li>Deprecate and rename functions:<ul>
<li><code>analyses()</code> => <code>plan_analyses()</code></li>
<li><code>as_file()</code> => <code>as_drake_filename()</code></li>
<li><code>backend()</code> => <code>future::plan()</code></li>
<li><code>build_graph()</code> => <code>build_drake_graph()</code></li>
<li><code>check()</code> => <code>check_plan()</code></li>
<li><code>config()</code> => <code>drake_config()</code></li>
<li><code>evaluate()</code> => <code>evaluate_plan()</code></li>
<li><code>example_drake()</code> => <code>drake_example()</code></li>
<li><code>examples_drake()</code> => <code>drake_examples()</code></li>
<li><code>expand()</code> => <code>expand_plan()</code></li>
<li><code>gather()</code> => <code>gather_plan()</code></li>
<li><code>plan()</code>, <code>workflow()</code>, <code>workplan()</code> => <code>drake_plan()</code></li>
<li><code>plot_graph()</code> => <code>vis_drake_graph()</code></li>
<li><code>read_config()</code> => <code>read_drake_config()</code></li>
<li><code>read_graph()</code> => <code>read_drake_graph()</code></li>
<li><code>read_plan()</code> => <code>read_drake_plan()</code></li>
<li><code>render_graph()</code> => <code>render_drake_graph()</code></li>
<li><code>session()</code> => <code>drake_session()</code></li>
<li><code>summaries()</code> => <code>plan_summaries()</code></li>
</ul>
</li>
<li>Disallow <code>output</code> and <code>code</code> as names in the workflow plan data frame. Use <code>target</code> and <code>command</code> instead. This naming switch has been formally deprecated for several months prior.</li>
<li>Deprecate the ..analysis.. and ..dataset.. wildcards in favor of analysis<strong> and dataset</strong>, respectively. The new wildcards are stylistically better an pass linting checks.</li>
<li>Add new functions <code>drake_quotes()</code>, <code>drake_unquote()</code>, and <code>drake_strings()</code> to remove the silly dependence on the <code>eply</code> package.</li>
<li>Add a <code>skip_safety_checks</code> flag to <code>make()</code> and <code>drake_config()</code>. Increases speed.</li>
<li>In <code>sanitize_plan()</code>, remove rows with blank targets "".</li>
<li>Add a <code>purge</code> argument to <code>clean()</code> to optionally remove all target-level information.</li>
<li>Add a <code>namespace</code> argument to <code>cached()</code> so users can inspect individual <code>storr</code> namespaces.</li>
<li>Change <code>verbose</code> to numeric: 0 = print nothing, 1 = print progress on imports only, 2 = print everything.</li>
<li>Add a new <code>next_stage()</code> function to report the targets to be made in the next parallelizable stage.</li>
<li>Add a new <code>session_info</code> argument to <code>make()</code>. Apparently, <code>sessionInfo()</code> is a bottleneck for small <code>make()</code>s, so there is now an option to suppress it. This is mostly for the sake of speeding up unit tests.</li>
<li>Add a new <code>log_progress</code> argument to <code>make()</code> to suppress progress logging. This increases storage efficiency and speeds some projects up a tiny bit.</li>
<li>Add an optional <code>namespace</code> argument to <code>loadd()</code> and <code>readd()</code>. You can now load and read from non-default <code>storr</code> namespaces.</li>
<li>Add <code>drake_cache_log()</code>, <code>drake_cache_log_file()</code>, and <code>make(..., cache_log_file = TRUE)</code> as options to track changes to targets/imports in the drake cache.</li>
<li>Detect knitr code chunk dependencies in response to commands with <code>rmarkdown::render()</code>, not just <code>knit()</code>.</li>
<li>Add a new general best practices vignette to clear up misconceptions about how to use <code>drake</code> properly.</li>
</ul>
Tangle-bearing neurons survive despite disruption of membrane integrity in a mouse model of tauopathy
Get PDFNeurofibrillary tangles (NFTs) are associated with neuronal loss and correlate with cognitive impairment in Alzheimer disease, but how NFTs relate to neuronal death is not clear. We studied cell death in Tg4510 mice that reversibly express P301L mutant human tau and accumulate NFTs using in vivo multiphoton imaging of neurofibrillary pathology, propidium iodide (PI) incorporation into cells, caspase activation, and DNA labeling. We first observed that in live mice, a minority of neurons were labeled with the caspase probe or with PI fluorescence. These markers of cell stress were localized in the same cells and appeared specifically within NFT-bearing neurons. Contrary to expectations, the PI-stained neurons did not die during a day of observation; the presence of Hoechst-positive nuclei in them on the subsequent day indicated that the NFT-associated membrane disruption, as suggested by PI staining, and caspase activation do not lead to immediate death of neurons in this tauopathy model. This unique combination of in vivo multiphoton imaging with markers of cell death and pathological alteration is a powerful tool for investigating neuronal damage associated with neurofibrillary pathology
The charge transfer and ion formation in liquid Li-Tl alloys
Get PDFThe 7Li NMR Knight shift, K, and the spin-lattice relaxation time, T1, were measured for liquid Li–Tl alloys. The K decreases rapidly with the addition of Tl up to 20 at.% Tl. In the concentration from 20 to 50 at.% Tl, the K decreases only slightly and the K of 50 at.% Tl is 60% of K for the pure liquid Li. Such a decrease of K is considered as an indication for the strong charge transfer from Li to Tl. These tendencies are similar to those from previous studies for liquid Li–Ga and Li–In alloys. However, beyond 50 at.% Tl, the K increases and reaches to an almost constant value (70% of K for the pure liquid Li). Such a back donation of charge is absent for liquid Li–Ga and Li–In alloys. It is considered that the tendency of the formation of ionic structural unit for liquid Li–Tl alloys is slightly weaker compared with the cases of liquid Li–Ga and Li–In alloys. The T1 is also discussed with the relation to the Knight shift and the electronic properties
THE VISIBLE EMISSION SPECTRA OF Zn , Cd , Zn Tl, AND Cd Tl MOLECULES
No full textAuthor Institution: Department of Physics, Indian Institute of Technology; Department of Physics, State University of New York at BuffaloNew Spectra have been obtained for Zn-Tl and Cd-Tl mixtures excited by a high frequency oscillator and studied under a dispersion of 5\AA/mm. Both the mixtures show one system in the red, one in the blue and continuous bands attached to the Tl lines 3775 and 5350 \AA. The red system of Zn-Tl mixture exhibits an isotope effect, which shows Zn as the emitter. The emitter for the red system of Cd-Tl mixture is Cd . The blue systems and continuous bands are due to diatomic ZnTl and CdTl molecules. A vibrational analysis of all these systems, wherever possible has been carried out and the constants determined
TL and OSL properties of beta irradiated Y2O3 nanocrystal
No full textNanocrystalline yttrium oxide (Y2O3) is synthesized by low temperature sol-gel technique and synthesized material is annealed at 900°C. The annealed β-rayed Y2O3 two TL glows with prominent peak at 407 K and weak glow peak at 643 K were observed in all irradiated samples. It is found that TL glow peaks intensity linearly increases with increase in β-dose from 0.813 - 40.625 Gy. The TL kinetic parameters are calculated using glow curve deconvoluted (GCD) method. The TL glows exhibits general order kinetics. Intense optical stimulated luminescence (OSL) is observed in the Y2O3 sample. These material exhibits linearity and reproducibility and hence, it suggests that this material may be used as dosimetric applications. © 2017 Author(s)
Preparation of (R)-2-chloro-1-(m-chlorophenyl)ethanol by Lipozyme TL IM-catalyzed second resolution
No full text(R)-2-Chloro-1-(m-chlorophenyl)ethanol, a precursor of (R)-3-chlorostyrene oxide which is the key chiral intermediate for the preparation of several beta 3-adrenergic receptor agonists was prepared in 40% yield and 99% ee by the Lipozyme TL IM-catalyzed second resolution of the corresponding racemate in the presence of vinyl acetate. (C) 2012 Shi Wen Xia. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved
Millettia pachyloba Drake 1891
No full text7. Millettia pachyloba Drake (1891: 188) ≡ Callerya pachyloba (Drake) H. Sun (2006: 409). Type: — VIETNAM. Tonkin, Tu-Phap, dans les bois, 12 May 1887, B. Balansa 2306 (first-step lectotype designated by Dunn 1912: 185, second-step lectotype designated here: P02141840 image!; isolectotypes: A!, K000848750!, L0019106 image!, P02141839 image!, P02141841 image!). = Millettia spireana Gagnepain (1913: 364) ≡ Millettia pachyloba var. spireana (Gagnep.) P.K. Lôc in Lôc & Vidal (2001: 150). Type: — THAILAND. foret des Peunongs, de Bang-muc a La-khon, Nonkay, 1866–1868, C. Thorel 2442 (lectotype designated here: K000848784!; isolectotype: P 02141844 image!). = Millettia obovata Gagnepain (1913: 361). Type: — CHINA. Hainan, Lav-tai-shee, 4 May 1893, Chinese Collector 371A (lectotype designated here: P02141842 image!; isolectotypes: IBSC0154409!, P02141843 image!). = Millettia lasiopetala (Hayata) Merrill (1924: 16) ≡ Millettia pachyloba var. lasiopetala (Hayata) P.K. Lôc in Lôc & Vidal (2001: 152) ≡ Derris lasiopetala Hayata (1913: 78). Type: — CHINA. Hainan, June 1909, N. Konishi s.n. (lectotype designated here: K000848707!). Millettia pachyloba was first described by Drake (1891) with citation of four gatherings collected by B. Balansa (2305– 2308) in Tonkin, Vietnam, of which Balansa 2306 was indicated by Dunn (1912) as its type [first-step lectotype] without specifying a herbarium. Lôc & Vidal (2001) designated the specimen in P as type, but this typification was not effective according to Art. 7.11 (Turland et al. 2018). We designate the specimen (P 02141840) as the second-step lectotype of the name. Four collections were cited by Gagnepain (1913) in the protologue of M. spireana, namely, C. Thorel 2442, C. J. Spire 47 (actually 447), 349 and F. J. Harmand s.n., of which Thorel 2442 (lecto, cf. Craib 1928, P!) was indicated by Lôc & Vidal (2001) as its type. But we found that Craib (1928) did not clearly indicate the type of the name, and the lectotypification by Lôc & Vidal (2001) is not effective according to the Art. 7.11 (Turland et al. 2018). We designate the specimen of Thorel 2442 (K000848784) with a much better conserved status as the lectotype of M. spireana. In the protologue of M. obovata, a single collection (Herb. Hong-kong 371A) was provided by Gagnepain (1913). S. Coll. 371A (holo-, HK) was indicated by Lôc & Vidal (2001) as type, but this typification was not effective according to Art. 7.11 (also see Art. 40.2 Ex. 3, Turland et al. 2018). We did not find the specimen in HK, but traced three specimens of this gathering in P. We designate the specimen (P 02141842) with two dissected flowers as the lectotype of M. obovata. For the name Derris lasiopetala, the protologue provided a detailed description and its vouchers (“Hab. Hainan, leg. N. Konishi, 1909, Juli”, Hayata 1913). Lôc & Vidal (2001) gave the type information of D. lasiopetala [“Type: Konishi s.n. (juill. 1909), Chine. Hainan (lecto-, cf. Hayata 1913, non vu)”]. According to Taxonomic Literature II (https://www.sil.si.edu/DigitalCollections/tl-2/), the types used by Hayata are mainly kept in the herbarium TI, and further material are kept in A, C, K, and P. We examined the Konishi specimen in K (K000848707), which match the protologue of D. lasiopetala, and thus it is designated here as the lectotype of the name.Published as part of Song, Zhu-Qiu, Li, Shi-Jin, Vu, Quang Nam & Khang, Nguyen Sinh, 2022, Taxonomic notes on the genus Millettia (Fabaceae: Millettieae) in Vietnam, pp. 169-185 in Phytotaxa 571 (2) on page 175, DOI: 10.11646/phytotaxa.571.2.4, http://zenodo.org/record/728433
Crystal Dynamics and Anharmonic Properties of Bi-Pb-Tl Alloys
Get PDFTitle: Crystal Dynamics and Anharmonic Properties of Bi-Pb-Tl Alloys, Author: Aditya P. Roy, Location: ThodeThe crystal dynamics and anharmonic properties have
been investigated in disordered alloys of Bi-Pb-Tl using slow
neutron spectrometry. Damping of phonons caused by phonon-phonon
interaction and the effect of the force constant
disorder on the lifetime of the phonons have been studied in
the alloys. Measurements of the coefficients of thermal
expansion are reported. An experimental method of determining
the lattice frequency spectra by coherent inelastic scattering
of neutrons from polycrystalline materials is described.ThesisDoctor of Philosophy (PhD
Synthesis optimization and charge carrier transfer mechanism in LiLuSiO<sub>4</sub>:Ce, Tm storage phosphor
No full textLiLuSiO4:Ce and LiLuSiO4:Ce, Tm show very efficient charge carrier storage properties upon beta irradiation after samples have received treatment in vacuum. They outperform the commercial storage phosphor BaFBr(I):Eu2+ in many aspects. The influence of the synthesis conditions, Ce and Tm concentration, nonstoichiometry and codoping with Ca, Hf, Al and Ge are reported. Based on the results of the synthesis optimization, thermoluminescence (TL) emission and TL excitation spectra a mechanism of charge carrier transfer, storage, and recombination during irradiation and thermal or optical readout is proposed.Accepted Author ManuscriptRST/Fundamental Aspects of Materials and EnergyRST/Luminescence Material
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