The applications entitled ERYA-Bulk and ERYA-Profiling (ERYA stands for Emitted Radiation Yield Analysis) are two programs which implement PIGE (Particle Induction Gamma-Ray Emission) analysis of ...samples which can be either homogeneous (handled by ERYA-Bulk) or heterogeneous (with multiple layers, which are simulated by ERYA-Profiling).
The homogeneous model uses an analytical method to evaluate the nuclear yield as function of the mass fraction of the element(s) of interest. A routine is available to fit the experimental yields in order to compute the correct sample atomic composition.
Otherwise, the heterogeneous model takes consideration of the physics with greater detail, including straggling in the energy lost by the projectiles, making a more realistic yield simulation, whose level of accuracy the user can control in exchange of computational time.
Here, we present the latest developments of these codes, which include new features, functionalities and direct handling of different source files. ERYA-Bulk and ERYA-Profiling are currently compiled and tested for Linux, Windows and Mac OS X operating systems.
Program Title: ERYA-Bulk, ERYA-Profiling
CPC Library link to program files:https://doi.org/10.17632/gnrvm4jt5v.1
Developer's repository link:https://github.com/Arucard1983/ERYA-Bulk (ERYA-Bulk), https://github.com/Arucard1983/ERYA-Profiling (ERYA-Profiling)
Licensing provisions: LGPL-v3
Programming language: C++
External routines: wxWidgets 1, wxMathPlot 2
Nature of problem: Compute the gamma-ray yield coming from a sample bombarded by a energetic (few MeV) beam of charged particles (namely protons). The yield corresponding to a given element depends on the mass fraction of this element and on the major composition of the sample which determines the rate of energy loss by the beam. It also depends on the detector efficiency, the collected beam charge (i.e., number of projectiles) and the cross-sections of the relevant gamma-producing nuclear reaction.
All data inputs can be loaded from a file or inserted by the user. The energy straggling along the beam interaction with the sample, irrelevant for bulk analysis, is determinant for depth profiling.
Solution method: The yield calculation is made by numerical integration of an analytical formula that depends on several quantities which can be analytical in nature or approximated by interpolation (the cross-section data interpolation is one example).
The straggling and energy dispersion also depends on energy distributions which have different numerical approximations. A modular approach using the object-oriented programming helps to implement different models to the main integration routine, and make the source code more readable and prone for future extensions.
A fitting feature was implemented on ERYA-Bulk to adjust the sample composition to the experimental yield results.
1wxWidgets webpage, https://www.wxwidgets.org.2wxMathPlot webpage, https://wxmathplot.sourceforge.io/.
The application entitled Emitted Radiation Yield Analysis (ERYA-Profiling) is a program for PIGE (Particle Induced Gamma-Ray Emission) analysis of in-depth heterogeneous samples.
Here, we present ...this code, which includes new features, functionalities, and direct handling of r33 and SRIM files, following the approach for a new version for ERYA-Bulk. Case studies are presented illustrating a good performance of the ERYA-Profiling program. ERYA-Profiling is currently compiled for Linux, Windows and Mac OS X operating systems and can be downloaded free from https://sites.fct.unl.pt/nuclear/software/erya-profiling.
The present article investigates the problems of zoological taxonomical categories in texts that range from the Warring States (ca. 453–221 BCE) to the Eastern Han periods (25–220 CE). It focuses its ...attention on the
(attested 3rd c. BCE), a work that had a pivotal role during the development of Chinese lexicography. This terse glossary is probably one of the first texts that deal with the problem of taxonomical classification in early China through the use of syntactical devices that I call “categorical markers”, i.e. normalised characters that introduce an ontologically independent category of entities. By dint of the analysis of selected case studies, it will be shown that along fairly well attested “categorical markers” that constitute dichotomous systems (such as
獸 “quadruped furred creatures” versus
鳥 “bipedal winged creatures”), early Chinese taxonomies reveal less explicit linguistic devices that are implied in zoological classification, e.g. the presence of “sub-categorical markers” as noun modifiers (
醜 “being physically similar” or
屬 “to belong to a category”) used in order to create embedded taxonomies within the standard “categorical markers”. This complexity reveals an organised taxonomical system that helps us to better define the early Chinese conception of the natural world.
PIGE has been widely used in the analysis of bulk samples, with quantification of data made usually through the use of reference samples. With a growing database of experimental cross sections ...becoming available, the use of first-principles data analysis methods is gaining ground. Only few codes capable of first principles analysis of PIGE data were available, but new codes have been recently developed. However, their accuracy has not been verified so far. In this work, the results of an inter-comparison of PIGE data analysis codes organised by the IAEA are presented. The inter-comparison was made through simulations for well-defined conditions, for bulk samples. Five analytical codes participated in the exercise: ERYA-Bulk, ERYA-Profiling, NDF, PiGreCo and SIMNRA. It is concluded that, although some differences are observed for some calculations, particularly in the presence of sharp resonances in the cross section, all four codes are appropriate for analysis of PIGE experimental data.
The diagenetic alteration of rhythmic successions remains one of the main challenges in paleoclimatology and cyclostratigraphy. To address this very important problem, thin sections and geochemical ...data of the limestone-marl alternations from Middle Permian carbonate successions in South China are examined to identify differential diagenetic effects in the petrography, organic and inorganic compositions, strontium concentrations and stable isotopic compositions of limestone beds and marl interlayers. In the Lengshuixi outcrop and the JY66-1 drill core, the most conspicuous features are that the limestone beds exhibit dense cementation, high strontium concentrations, negative oxygen isotopic values and positive carbon isotopic values. In contrast, the marl interlayers contain talc and exhibit strongly deformed and oriented bioclasts, low strontium concentrations, positive oxygen isotopic values and negative carbon isotopic values.
Although differential diagenesis has occurred, some paleoclimate proxies (e.g., computed gamma-ray values) still preserve their primary signals and thus are suitable for cyclostratigraphic research. Eccentricity rhythm and millennial-scale rhythm are obviously recorded in Middle Permian limestone-marl alternations in South China. The variations in the oxygen and carbon isotopic values of limestone-marl alternations from different basins represent responses to different processes of differential diagenesis. This knowledge assumes that differential diagenesis occurs in diagenetically closed systems under the deep sea-floor. However, this assumption may not be valid in diagenetically open systems, where exotic fluids may add unexpected disturbances. Hence, it is crucial to understand diagenetic systems by determining the variations in strontium concentrations, which are as important as variations in carbon and oxygen isotopic values.
•Although the differential diagenesis occurred, some primary signals are still preserved.•Dissolution-reprecipitation of CaCO3 occurred during the differential diagenesis.•The limestone-marl alternations result from millennial-scale rhythm.•Primary cycles of LMA differ significantly in diagenetic potential.•Organic matter decay and oxidation drive the aragonite dissolution in closed systems.
The ancient names huangniao, canggeng and several related terms, usually thought to represent the oriole, appear in Zhou and Han texts, for example in Shijing, Erya, Shanhaijing, and various ...commentaries. The present article comments on these names. It shows that there was an early stage in which a difference was made between canggeng and huangniao, while in later times, from the Han period onwards, these distinctions gradually disappeared. The article also suggests that, originally, canggeng probably stood for Oriolus chinensis, i.e., the black-naped oriole, while huangniao may have meant several other birds; later on, however, all terms were used for O. chinensis.
Brucellosis is a globally distributed zoonotic disease that causes animal and human diseases. However, the current Brucella abortus vaccines (S19 and RB51) are deficient; they can cause abortion in ...pregnant animals. Moreover, when the vaccine S19 is used, tests cannot differentiate natural from vaccinated infection. Therefore, a safer and more potent vaccine is needed. A Brucella abortus 2308 ery promoter mutant (Δery) was constructed to overcome these drawbacks. The growth of the Δery mutant was significantly attenuated in macrophages and mice and induced high protective immunity in mice. Moreover, Δery induced an anti-Brucella-specific IgG (immunoglobulin G) response and stimulated the expression of interferon-gamma (INF-γ) and interleukin-4 (IL-4). Furthermore, the expression of EryA antigen allowed for the serological differentiation between natural and vaccinated infection in mice. These results indicate that the Δery mutant is a potential attenuated live vaccine candidate against virulent Brucella abortus 2308 (S2308) infection.
A three-plasmid system for heterologous expression of 6-deoxy-erythronolide B synthase (DEBS) has been developed to facilitate combinatorial biosynthesis of polyketides made by type I modular ...polyketide synthases (PKSs). The eryA PKS genes encoding the three DEBS subunits were individually cloned into three compatible Streptomyces vectors carrying mutually selectable antibiotic resistance markers. A strain of Streptomyces lividans transformed with all three plasmids produced 6-deoxyerythronolide B at a level similar to that of a strain transformed with a single plasmid containing all three genes. The utility of this system in combinatorial biosynthesis was demonstrated through production of a library of modified polyketide macrolactones by using versions of each plasmid constructed to contain defined mutations. Combinations of these vector sets were introduced into S. lividans, resulting in strains producing a wide range of 6-deoxyerythronolide B analogs. This method can be extended to any modular PKS and has the potential to produce thousands of novel natural products, including ones derived from further modification of the PKS products by tailoring enzymes.
Bacterial modular polyketide synthase (PKS) genes are commonly associated with another gene that encodes a thioesterase II (TEII) believed to remove aberrantly loaded substrates from the PKS. ...Co-expression of the Saccharopolyspora erythraea ery-ORF5 TEII and eryA genes encoding 6-deoxyerythronolide B synthase (DEBS) in Streptomyces hosts eliminated or significantly lowered production of 8,8'-deoxyoleandolide 15-nor-6-deoxyerythronolide B (15-nor-6dEB), which arises from an acetate instead of a propionate starter unit. Disruption of the TEII gene in an industrial Sac. erythraea strain caused a notable amount of 15-norerythromycins to be produced by utilization of an acetate instead of a propionate starter unit and also resulted in moderately lowered production of erythromycin compared with the amount produced by the parental strain. A similar behaviour of the TEII gene was observed in Escherichia coli strains that produce 6dEB and 15-methyl-6dEB. Direct biochemical analysis showed that the ery-ORF5 TEII enzyme favours hydrolysis of acetyl groups bound to the loading acyl carrier protein domain (ACP(L)) of DEBS. These results point to a clear role of the TEII enzyme, i.e. removal of a specific type of acyl group from the ACP(L) domain of the DEBS1 loading module.
The biological activity of polyketide antibiotics is often strongly dependent on the presence and type of deoxysugar residues attached to the aglycone core. A system is described here, based on the ...erythromycin‐producing strain of Saccharopolyspora erythraea, for detection of hybrid glycoside formation, and this system has been used to demonstrate that an amino sugar characteristic of 14‐membered macrolides (d‐desosamine) can be efficiently attached to a 16‐membered aglycone substrate. First, the S. erythraea mutant strain DM was created by deletion of both eryBV and eryCIII genes encoding the respective ery glycosyltransferase genes. The glycosyltransferase OleG2 from Streptomyces antibioticus, which transfers l‐oleandrose, has recently been shown to transfer rhamnose to the oxygen at C‐3 of erythronolide B and 6‐deoxyerythronolide B. In full accordance with this finding, when oleG2 was expressed in S. erythraea DM, 3‐O‐rhamnosyl‐erythronolide B and 3‐O‐rhamnosyl‐6‐deoxyerythronolide B were produced. Having thus validated the expression system, endogenous aglycone production was prevented by deletion of the polyketide synthase (eryA) genes from S. erythraea DM, creating the triple mutant SGT2. To examine the ability of the mycaminosyltransferase TylM2 from Streptomyces fradiae to utilise a different amino sugar, tylM2 was integrated into S. erythraea SGT2, and the resulting strain was fed with the 16‐membered aglycone tylactone, the normal TylM2 substrate. A new hybrid glycoside was isolated in good yield and characterized as 5‐O‐desosaminyl‐tylactone, indicating that TylM2 may be a useful glycosyltransferase for combinatorial biosynthesis. 5‐O‐glucosyl‐tylactone was also obtained, showing that endogenous activated sugars and glycosyltransferases compete for aglycone in these cells.
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