The block spectrum of RNA pseudoknot structures

Journal of Mathematical Biology - In this paper we analyze the length-spectrum of blocks in $$\gamma $$ -structures. $$\gamma $$ -structures are a class of RNA pseudoknot structures that play a key...     

Gamma-ray attenuation properties of some NLO materials: potential use in dosimetry

Mass attenuation coefficients ($$\mu _{\text {m}}$$) for some nonlinear optical materials such as potassium dihydrogen phosphate, ammonium dihydrogen phosphate, zinc tris-thiourea sulphate, and zinc thiourea chloride were measured using a $$2\times 2$$ NaI(Tl) scintillation detector at gamma energies of 122 keV, 356 keV, 511 keV, 662 keV, 840 keV, 1170 keV, 1270 keV, and 1330 keV. In addition, GEANT4 simulations were carried out to mimic the experiment at these energies. As a result, good agreement between the experimental and GEANT4 results was observed. The measured $$\mu _{\text {m}}$$ values were used to compute effective atomic numbers ($$Z_{\text {eff}}$$) for the selected materials. It was found that the $$Z_{\text {eff}}$$ values were in the range typical for dosimetric materials.     

Effects of common soil anions and pH on the uptake and accumulation of perchlorate in lettuce

A mechanistic understanding of perchlorate () entry into plants is important for establishing the human health risk associated with consumption of contaminated produce and for assessing the effectiveness of phytoremediation. To determine whether common soil anions affect uptake and accumulation in higher plants, a series of competition experiments using lettuce (Lactuca sativa L.) were conducted between (50 nM) and (4–12 mM), (1–10 mM), or Cl⁻ (5–15 mM) in hydroponic solution. The effects of (0–5 mM) and pH (5.5–7.5) on uptake were also examined. Increasing in solution significantly reduced the amount of taken up by green leaf, butter head, and crisphead lettuces. Sulfate and Cl⁻ had no significant effects on uptake in lettuce over the concentrations tested. Increasing pH significantly reduced the amount of taken up by crisphead and green leaf lettuces, whereas increasing significantly reduced uptake in butter head lettuce. The inhibition by across all lettuce genotypes suggests that may share an ion carrier with , and the decrease in uptake with increasing pH or provides macroscopic evidence for cotransport across the plasma membrane.     

Expansive Growth vs. pH Reflects a Poisson Point Process of Binding/Unbinding Events in Plant Cell Walls

Journal of Plant Growth Regulation - The paramount role of $$\mathrm{pH}$$ and temperature $$\left(T\right)$$ in the expansive growth of a plant coleoptile/hypocotyl non-meristematic zone or plant...     

Correlation between Langmuir Probe and Spectroscopic Temperatures in Inductively Coupled Neon–Argon Mixture Plasma

Plasma Physics Reports - In this study, many plasma parameters including excitation temperature $$({{T}_{{{\text{exc}}}}})$$ , electron temperature $$({{T}_{e}})$$ , skin depth $$({{\delta...     

Phy-X/ZeXTRa: a software for robust calculation of effective atomic numbers for photon,electron, proton,alpha particle,and carbon ion interactions

The purpose of the present work is robust calculation of effective atomic numbers ($${Z}_{\text{eff}}$$s) for photon, electron, proton, alpha particle and carbon ion interactions through the newly developed software, Phy-X/ZeXTRa (Zeff of materials for X-Type Radiation attenuation). A pool of total mass attenuation and energy absorption coefficients (for photons) and total mass stopping powers (for charged particles) for elements was constructed first. Then, a matrix of interaction cross sections for elements Z = 1–92 was constructed. Finally, effective atomic numbers were calculated for any material by interpolating adjacent cross sections through a linear logarithmic interpolation formula. The results for $${Z}_{\text{eff}}$$ for photon interaction were compared with those calculated through Mayneord’s formula, which suggests a single-valued $${Z}_{\text{eff}}$$ for any material for low-energy photons for which photoelectric absorption is the dominant interaction process. The single-valued $${Z}_{\text{eff}}$$ was found to agree well with that obtained by other methods, in the low-energy region. In addition, $${Z}_{\text{eff}}$$ values of various materials of biological interest were compared with those obtained experimentally at 59.54 keV. In general, the agreement between values calculated with Phy-X/ZeXTRa and Auto-Zeff and those measured were satisfactory. A comparison of $${Z}_{\text{eff}}$$ values for photon energy absorption calculated with Phy-X/ZeXTRa and literature values for a nucleotide base, adenine, was made, and the relative difference (RD) in $${Z}_{\text{eff}}$$ between Phy-X/ZeXTRa and literature values was found to be 2% < RD < 11%, at low photon energies (1–100 keV), while it was less than 1% at energies higher than 100 keV. Highest $${Z}_{\text{eff}}$$ values were observed at low photon energies, where photoelectric absorption dominates photon interaction. For electrons, corresponding RD(%) values in $${Z}_{\text{eff}}$$ were found to be in the range 0.4 ≤ RD(%) ≤ 1.7, while for heavy charged particle interactions it was 2.4 ≤ RD(%) ≤ 4.2 for total proton interaction and 0 ≤ RD(%) ≤ 8 for total alpha particle interaction. In view of the importance of $${Z}_{\text{eff}}$$ for identifying and differentiating tissues in diagnostic imaging as well as for estimating accurate dose in radiotherapy and particle-beam therapy, Phy-X/ZeXTRa could be used for fast and accurate calculation of $${Z}_{\text{eff}}$$ in a wide energy range for both photon and charged particle (electrons, protons, alpha particles and C ions) interactions.     

SIR epidemics and vaccination on random graphs with clustering

Journal of Mathematical Biology - In this paper we consider Susceptible $$\rightarrow $$ Infectious $$\rightarrow $$ Recovered (SIR) epidemics on random graphs with clustering. To incorporate group...     

Use of isotopic signatures to assess the food web in a tropical shallow marine ecosystem of Southeastern Brazil

A dual isotope approach was used to assess the relative importance of terrestrial vegetation detritus and other primary producers in the trophic web of Flamengo Sound (Ubatuba, SP), SE Brazil, surrounded by the Atlantic Rain Forest. Primary producers showed distinct C signatures and the observed values suggest that little terrestrial or bulk sediment organic matter enter the food web of the sound. Suspended particulate organic matter (POM, supports the bulk of the consumers, with some contribution by macroalgae . Consumers C values ranged from −17.4 to . At least three trophic levels were detectable in the food web. The N value of POM was , while that of sediment and detritus was . The N values of suspension feeding benthic invertebrates were 8.2–, deposit feeders 8.3–, and carnivores 10.7–. Values for fishes were for detritivore, 11.4– for benthic feeders, 12.4– for zooplanktivores, and for piscivores/benthic invertebrate feeders. Squid mean value was . There is a reasonable agreement between feeding habits information from the literature and N values from this study. In the sound, the first and second trophic steps seem to be about 1– higher than those of similar organisms studied in temperate waters and this may reflect an input of allochtonous anthropogenic nitrogen enriched in ¹⁵N from human activities.     

Regional Assessment of N Saturation using Foliar and Root \varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

Vitamin E Status of Healthy Swedish Cattle*

Using high pressure liquid chromatography the serum concentration of vitamin E was measured in dairy cows fed either hay or silage as their main roughage, in calves fed milk-replacer, and in young intensively fed bulls. The concentrates fed to the cows, calves and bulls were supplemented with 5–10, 25 and 5–10 mg DL-α-tocopheryl acetate per kg, respectively, and the milk-replacer for the calves was supplemented with 50 mg DL-α-tooopheryl acetate per kg powder. Cows fed silage as their main roughage had higher serum vitamin E concentrations ( $${\rm{\bar x}}$$ : 3.8–5.2 mg/l) than cows fed only hay ( $${\rm{\bar x}}$$ : 2.5–4.1 mg/1). Lactating cows had higher vitamin E concentrations than dry cows ( $${\rm{\bar x}}$$ : 4.1–5.2 and 2.5–3.8 mg/l, respectively) and calves and bulls had much lower vitamin E concentrations ( $${\rm{\bar x}}$$ : 1.4 and 1.2 mg/l, respectively) than cows. Thirty per cent of the calves and 41 % of the bulls had serum vitamin E concentrations less than 1.0 mg/l, suggesting that in these animals the conventional level of supplementation of feeds with DL-α-tocopheryl acetate in Sweden is probably inadequate for the prevention of nutritional muscular degeneration and other negative effects.     

Long-term changes in nutrient concentrations of the Changjiang River and principal tributaries

We present long-term nutrient data on the Changjiang River (Yangtze River) at six hydrological stations and eight principal tributaries during the period 1958–1985. Three patterns of temporal changes were observed in nitrate and nitrite : minimal variations in the upper catchment area, rapid increases in the middle watershed towards the end of the 1970s, and a gradual increase in the lower drainage basin. Prior to the 1970s, the level of throughout the Changjiang River system remained fairly constant. In the 1980s, however, this changed, with the lowest values in the upper Changjiang changing rapidly to the highest in the middle reaches and then declining slowly but steadily in the lower courses. Compared to and ammonium and soluble reactive phosphorus (SRP) showed smaller increases or no long-term variations, while dissolved silica (DSi) concentration generally decreased at most stations. These three patterns of and changes in the Changjiang River system were reflective of the difference in chemical fertilizer use and landscape features (e.g., slope, soil type and water body area) of the drainage basins of the primary tributaries. The decreases in DSi were most likely attributed to a reduction in suspended sediment loading due to dam constructions and increasing diatom consumption. The increase in and with a reduction in DSi concentrations in the Changjiang River could have significant effects on the stoichiometric balance of nutrients delivered to the East China Sea and the ecosystem in this dynamic region.     

Regional Assessment of N Saturation using Foliar and Root $\varvec {\delta}^{\bf 15}{\bf N}$\varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

The Impact of the Allee Effect in Dispersal and Patch-Occupancy Age on the Dynamics of Metapopulations

In this paper, we introduce a Levins-type metapopulation model with empty and occupied patches, and dispersing population. We structure the proportion of occupied patches according to the patch-occupancy age. We observe that patch-occupancy age may destabilize the metapopulation, leading to persistent oscillations. We also allow for the dispersal rate to vary with the proportion of empty patches in a monotone or unimodal way. The unimodal dependence leads to multiple non-trivial equilibria and bistability when the reproduction number of the metapopulation < 1 but greater than a lower critical value ^*. We show that the metapopulation will persist independently of its initial status if > 1.     

Inheritance of foliar stable carbon isotope discrimination and third-year height in Pinus taeda clones on contrasting sites in Florida and Georgia

Quantifying foliar stable carbon isotope discrimination (Δ) is a powerful approach for understanding genetic variation in gas exchange traits in large populations. The genetic architecture of Δ and third-year height is described for more than 1,000 clones of Pinus taeda tested on two contrasting sites. for Δ was 0.14 (±0.03), 0.20 (±0.07), and 0.09 (±0.04) at Florida, Georgia, and across sites, respectively. for stable carbon isotope discrimination ranged from 0.25 (±0.03) at the Florida site to 0.33 (±0.03) at the Georgia site, while the across-site estimate of was 0.19 (±0.02). For third-year height, ranged from 0.13 (±0.05) at the Georgia site to 0.20 (±0.06) at the Florida site with an across-site estimate of 0.09 (±0.05). Broad-sense heritability estimates for third-year height were 0.23 (±0.03), 0.28 (±0.03), and 0.13 (±0.02) at the Florida site, Georgia site, and across sites, respectively. Type B total genetic correlation for Δ was 0.70 ± 0.06, indicating that clonal rankings were relatively stable across sites, while for third-year height, rankings of clones were more unstable across the two trials . Third-year height and Δ were negatively correlated at the parental , full-sib family , and clonal levels, suggesting that genetic variation for Δ in P. taeda may be a result of differences in photosynthetic capacity. We conclude that Δ may be a useful selection trait to improve water-use efficiency and for guiding deployment decisions in P. taeda.     

Study of the Optical and Thermoplasmonics Properties of Gold Nanoparticle Embedded in Al2O3 Matrix

Plasmonics - In this paper, the optical and thermoplasmonics properties of nanocomposites consisting of spherical gold nanoparticles (AuNPs) integrated in $${Al}_{2}{O}_{3}$$ matrix are determined...     

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy

We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from the Boltzmann low-energy ensemble. This technique is simple and its implementation straight-forward, as it only requires a permutation in the order of some operations already performed in the stochastic traceback stage of these algorithms. It nevertheless greatly improves their worst-case complexity from to , for n the size of the original sequence. Moreover the average-case complexity of the generation is shown to be improved from to in an Boltzmann-weighted homopolymer model based on the Nussinov–Jacobson free-energy model. These results are extended to the more realistic Turner free-energy model through experiments performed on both structured (Drosophilia melanogaster mRNA 5S) and hybrid (Staphylococcus aureus RNAIII) RNA sequences, using a boustrophedon modified version of the popular software UnaFold. This improvement allows for the sampling of greater and more significant sets of structures in a given time.      

Comparative Analysis of Methods for Estimating the Rate of Population Aging

Biophysics - The essence of aging is a decline in total vitality with age, being basic personal characteristics of human potential. Viability ( $${v}$$ ) is defined as the probability of surviving...     

Altered expression of an ankyrin-repeat protein results in leaf abnormalities,necrotic lesions,and the elaboration of a systemic signal

Summary The PR-like proteins, class I -1,3-glucanase (GLU I) and chitinase (CHN I), are induced as part of a stereotypic response that can provide protection against viral, bacterial, and fungal pathogens. We have identified two Nicotiana plumbaginifolia ankyrin-repeat proteins, designated lucanohydrolase inding roteins (GBP) 1 and 2, that bind GLU I and CHN I both in vitro and when expressed in yeast cells. Sense as well as antisense transformants of tobacco carrying the GBP1 gene elaborated graft-transmissible acropetally moving signals that induced the downward curling of young leaves. This phenotype was associated with reduced starch, sucrose, and fructose accumulation; the formation of necrotic lesions; and, the induction of markers for the hypersensitive response. GBP1/2 are members of a conserved lant-specific yrin- repeat (PANK) family that includes proteins implicated in carbohydrate allocation, reactive oxygen metabolism, hypersensitive cell death, rapid elicitor responses, virus pathogenesis, and auxin signaling. The similarity in phenotype of PANK transformants and transformants altered in carbohydrate metabolism leads us to propose that PANK family members are multifunctional proteins involved in linking plant defense responses and carbohydrate metabolism.     

Topological research on diamagnetic susceptibilities of organic compounds

A novel molecular connectivity index, , based on the adjacency matrix of molecular graphs and novel atomic valence connectivities, , for predicting the molar diamagnetic susceptibilities of organic compounds is proposed. The is defined as: , where and E_i are the atomic valence connectivity and the valence orbital energy of atom i, respectively. A good QSPR model for molar diamagnetic susceptibilities can be constructed from and using multivariate linear regression (MLR). The correlation coefficient r, standard error, and average absolute deviation of the MLR model are 0.9918, 5.56 cgs, and 4.26 cgs, respectively, for the 721 organic compounds tested (training set). Cross-validation using the leave-one-out method demonstrates that the MLR model is highly reliable statistically. Using the MLR model, the average absolute deviations of the predicted values of molar diamagnetic susceptibility of another 360 organic compounds (test set) is 4.34 cgs. The results show that the current method is more effective than literature methods for estimating the molar diamagnetic susceptibility of an organic compound. The MLR method thus provides an acceptable model for the prediction of molar diamagnetic susceptibilities of organic compounds. Figure Plot of calculated vs experimental values of molar diamagnetic susceptibilities using the multivariate linear regression (MLR) model (Eq. 8)     

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Analysis of linkage disequilibrium (=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N _e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N _e based on for unlinked, diallelic gene loci are sharply biased downwards ( in some cases) if sample size (S) is less than true N _e. The bias is shown to arise from inaccuracies in published formula for when S and/or N _e are small. Empirically derived modifications to for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in % in most cases). The modified method also performs well in estimating N _e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect , but if N has recently increased from a bottleneck can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N _e in natural populations. However, a comprehensive assessment of performance of with highly polymorphic markers such as microsatellites is needed.The US Governmentȁ9s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.