DNA damage by radiation as a function of electron energy and interaction at the atomic level with Monte Carlo simulation.

In radiotherapy, X-ray or heavy ion beams target tumors to cause damage to their cell DNA. This damage is mainly induced by secondary low energy electrons. In this paper, we report the DNA molecular breaks at the atomic level as a function of electron energy and types of electron interactions using of Monte Carlo simulation. The number of DNA single and double strand breaks are compared to those from experimental results based on electron energies. In recent years, DNA atomistic models were introduced but still the simulations consider energy deposition in volumes of DNA or water equivalent material. We simulated a model of atomistic B-DNA in vacuum, forming 1122 base pairs of 30 nm in length. Each atom has been represented by a sphere whose radius equals the radius of van der Waals. We repeatedly simulated 10 million electrons for each energy from 4 eV to 500 eV and counted each interaction type with its position x, y, z in the volume of DNA. Based on the number and types of interactions at the atomic level, the number of DNA single and double strand breaks were calculated. We found that the dissociative electron attachment has the dominant effect on DNA strand breaks at energies below 10 eV compared to excitation and ionization. In addition, it is straightforward with our simulation to discriminate the strand and base breaks as a function of radiation interaction type and energy. In conclusion, the knowledge of DNA damage at the atomic level helps design direct internal therapeutic agents of cancer treatment.

Ultrafast attosecond-magnetic-field generation of the charge migration process based on HeH2+ and H2 + electronically excited by circularly polarized laser pulses.

The ultrafast process by the electron in molecular ions from one site or region to another that has come to be known as charge migration (CM), which is of fundamental importance to photon induced chemical or physical reactions. In this work, we study the electron current and ultrafast magnetic-field generation based on CM process of oriented asymmetric (HeH2+) and symmetric (H2 +) molecular ions. Calculated results show that they are ascribed to quantum interference of electronic states for these molecular ions under intense circularly polarized (CP) laser pulses. The two scenarios of (i) resonance excitation and (ii) direct ionization are considered through appropriately utilizing designed laser pulses. By comparison, the magnetic field induced by the scenario (i) is stronger than that of scenario (ii) for molecular ions. However, the scheme (ii) is very sensitive to the helicity of CP field, which is opposite to the scenario (i). Moreover, the magnetic field generated by H2 + is stronger than that by HeH2+ through scenario (i). Our findings provide a guiding principle for producing ultrafast magnetic fields in molecular systems for future research in ultrafast magneto-optics.

The impact of total and partial inclusion or exclusion of active and inactive time invariant covariates in growth mixture models.

This article evaluates the impact of partial or total covariate inclusion or exclusion on the class enumeration performance of growth mixture models (GMMs). Study 1 examines the effect of including an inactive covariate when the population model is specified without covariates. Study 2 examines the case in which the population model is specified with 2 covariates influencing only the class membership. Study 3 examines a population model including 2 covariates influencing the class membership and the growth factors. In all studies, we contrast the accuracy of various indicators to correctly identify the number of latent classes as a function of different design conditions (sample size, mixing ratio, invariance or noninvariance of the variance-covariance matrix, class separation, and correlations between the covariates in Studies 2 and 3) and covariate specification (exclusion, partial or total inclusion as influencing class membership, partial or total inclusion as influencing class membership, and the growth factors in a class-invariant or class-varying manner). The accuracy of the indicators shows important variation across studies, indicators, design conditions, and specification of the covariates effects. However, the results suggest that the GMM class enumeration process should be conducted without covariates, and should rely mostly on the Bayesian information criterion (BIC) and consistent Akaike information criterion (CAIC) as the most reliable indicators under conditions of high class separation (as indicated by higher entropy), versus the sample size adjusted BIC or CAIC (SBIC, SCAIC) and bootstrapped likelihood ratio test (BLRT) under conditions of low class separation (indicated by lower entropy). (PsycINFO Database Record

Performance of growth mixture models in the presence of time-varying covariates.

Growth mixture modeling is often used to identify unobserved heterogeneity in populations. Despite the usefulness of growth mixture modeling in practice, little is known about the performance of this data analysis technique in the presence of time-varying covariates. In the present simulation study, we examined the impacts of five design factors: the proportion of the total variance of the outcome explained by the time-varying covariates, the number of time points, the error structure, the sample size, and the mixing ratio. More precisely, we examined the impact of these factors on the accuracy of parameter and standard error estimates, as well as on the class enumeration accuracy. Our results showed that the consistent Akaike information criterion (CAIC), the sample-size-adjusted CAIC (SCAIC), the Bayesian information criterion (BIC), and the integrated completed likelihood criterion (ICL-BIC) proved to be highly reliable indicators of the true number of latent classes in the data, across design conditions, and that the sample-size-adjusted BIC (SBIC) also proved quite accurate, especially in larger samples. In contrast, the Akaike information criterion (AIC), the entropy, the normalized entropy criterion (NEC), and the classification likelihood criterion (CLC) proved to be unreliable indicators of the true number of latent classes in the data. Our results also showed that substantial biases in the parameter and standard error estimates tended to be associated with growth mixture models that included only four time points.

Electron interference in molecular photoionization by attosecond laser pulses.

Molecular photoionization by intense attosecond linearly and circularly polarized X-ray laser pulses is investigated from numerical solutions of time-dependent Schrödinger equations for the one-electron systems H2(+) and H3(++). Both momentum stripes and rings in photoelectron angular distributions are observed. The first with momentum intervals Δp(s)=2 π/R, where R is the molecular internuclear distance, results from interference of the coherent continuum scattering electron wave packets, which is shown to be insensitive to the laser polarization and wavelength. Diffraction of the directly ionized electrons leads to the momentum rings defined by the angle theta(p(r)R=cos(-1)(2nπ)/p(r)R between the electron momentum p(r) and the molecular internuclear R axis. These patterns are well described by multi-center interference models. Such complex patterns allow us to probe intermolecular structures.

Molecular characterization of a thioredoxin h gene (HbTRX1) from Hevea brasiliensis showing differential expression in latex between self-rooting juvenile clones and donor clones.

The cDNA code of thioredoxin h, designated as HbTRX1, was isolated from Hevea brasiliensis by rapid amplification of cDNA ends. HbTRX1 contained a 542-bp open reading frame encoding 123 amino acids. The deduced HbTRX1 protein showing high identity to thioredoxin h of other plant species was predicted to possess the conserved catalytic site WCXPC. Semiquantitative reverse transcription-polymerase chain reaction analysis revealed that HbTRX1 was constitutively expressed in all tested tissues. HbTRX1 transcripts accumulated at relatively low levels in the flower, somatic embryo, and leaves, while HbTRX1 transcripts accumulated at relatively high levels in the callus and latex. The HbTRX1 transcript was expressed at different levels, with higher levels in self-rooting juvenile clones than in their donor clones. HbTRX1 was expressed in Escherichia coli, and its activity was demonstrated using the dithiothreitol-dependent insulin assay. This work provides a basis for studying the biological function of thioredoxin h in rubber tree.

Effect of nuclear motion on molecular high-order harmonics and on generation of attosecond pulses in intense laser pulses.

We calculate harmonic spectra and shapes of attosecond-pulse trains using numerical solutions of Non-Born-Oppenheimer time-dependent Shrödinger equation for 1D H2 molecules in an intense laser pulse. A very strong signature of nuclear motion is seen in the time profiles of high-order harmonics. In general the nuclear motion shortens the part of the attosecond-pulse train originating from the first electron contribution, but it may enhance the second electron contribution for longer pulses. The shape of time profiles of harmonics can thus be used for monitoring the nuclear motion.

Kazachstania aerobia sp. nov., an ascomycetous yeast species from aerobically deteriorating corn silage.

In an investigation of the yeast biota involved in silage deterioration, a considerable number of strains belonging to Saccharomyces and related genera were isolated from aerobically deteriorating corn silage in Tochigi, Japan. Analysis of sequences of the internal transcribed spacer and the large-subunit rRNA gene D1/D2 domain and electrophoretic karyotyping indicated that two of the strains, NS 14(T) and NS 26, represent a novel species with close phylogenetic relationships to Kazachstania servazzii and Kazachstania unispora. It is proposed that the novel species be named Kazachstania aerobia sp. nov., with NS 14(T) (=AS 2.2384(T)=CBS 9918(T)) as the type strain.

Bullera cylindrica sp. nov., Bullera hubeiensis sp. nov. and Bullera nakasei sp. nov., ballistoconidium-forming yeast species from plant leaves.

Among yeasts isolated from plant leaves collected in different regions of China that form whitish or yellowish colonies and symmetrical ballistoconidia, four strains were shown to represent three novel Bullera species by conventional and molecular taxonomic characterization. The novel species are described as Bullera cylindrica sp. nov. (type strain CB 169T = AS 2.2308T = CBS 9744T), Bullera hubeiensis sp. nov. (type strain HX 19.3T = AS 2.2466T = CBS 9747T) and Bullera nakasei sp. nov. (type strain HX 15.5T = AS 2.2435T = CBS 9746T). These three species, and another eight previously described Bullera species represented by Bullera mrakii, formed a strongly supported distinct clade among the hymenomycetous yeasts in each of the phylogenetic trees drawn from the 26S rDNA D1/D2 domain and the internal transcribed spacer region sequences.

Candida asparagi sp. nov., Candida diospyri sp. nov. and Candida qinlingensis sp. nov., novel anamorphic, ascomycetous yeast species.

Among ascomycetous yeasts that were isolated from several nature reserve areas in China, three anamorphic strains isolated from soil (QL 5-5T) and fruit (QL 21-2T and SN 15-1T) were revealed, by conventional characterization and molecular phylogenetic analysis based on internal transcribed spacer and large subunit (26S) rRNA gene D1/D2 region sequencing, to represent three novel species in the genus Candida. Candida qinlingensis sp. nov. (type strain, QL 5-5T=AS 2.2524T=CBS 9768T) was related closely to a teleomorphic species, Williopsis pratensis. The close relatives of Candida diospyri sp. nov. (type strain, QL 21-2T=AS 2.2525T=CBS 9769T) are Candida friedrichii and Candida membranifaciens. Candida asparagi sp. nov. (type strain, SN 15-1T=AS 2.2526T=CBS 9770T) forms a clade with Candida fructus.