Final Abundance Research Articles

EVOLUTION AND NUCLEOSYNTHESIS OF ASYMPTOTIC GIANT BRANCH STELLAR MODELS OF LOW METALLICITY

We present stellar evolutionary tracks and nucleosynthetic predictions for a grid of stellar models of low- and intermediate-mass asymptotic giant branch (AGB) stars at $Z=0.001$ ([Fe/H]$=-1.2$). The models cover an initial mass range from 1 M$_{\odot}$ to 7 M$_{\odot}$. Final surface abundances and stellar yields are calculated for all elements from hydrogen to bismuth as well as isotopes up to the iron group. We present the first study of neutron-capture nucleosynthesis in intermediate-mass AGB models, including a super-AGB model, of [Fe/H] = $-1.2$. We examine in detail a low-mass AGB model of 2 M$_{\odot}$ where the $^{13}$C($\alpha$,$n$)$^{16}$O reaction is the main source of neutrons. We also examine an intermediate-mass AGB model of 5 M$_{\odot}$ where intershell temperatures are high enough to activate the $^{22}$Ne neutron source, which produces high neutron densities up to $\sim 10^{14}$ n cm$^{-3}$. Hot bottom burning is activated in models with $M \geq 3$ M$_{\odot}$. With the 3 M$_{\odot}$ model we investigate the effect of varying the extent in mass of the region where protons are mixed from the envelope into the intershell at the deepest extent of each third dredge-up. We compare the results of the low-mass models to three post-AGB stars with a metallicity of [Fe/H] $\simeq -1.2$. The composition is a good match to the predicted neutron-capture abundances except for Pb and we confirm that the observed Pb abundances are lower than what is calculated by AGB models.

Adaptive non-local Euclidean medians sparse unmixing for hyperspectral imagery

Sparse unmixing models based on sparse representation theory and a sparse regression model have been successfully applied to hyperspectral remote sensing image unmixing. To better utilize the abundant spatial information and improve the unmixing accuracy, spatial sparse unmixing methods such as the non-local sparse unmixing (NLSU) approach have been proposed. Although the NLSU method utilizes non-local spatial information as the spatial regularization term and obtains a satisfactory unmixing accuracy, the final abundances are affected by the non-local neighborhoods and drift away from the true abundance values when the observed hyperspectral images have high noise levels. Furthermore, NLSU contains two regularization parameters which need to be appropriately set in real applications, which is a difficult task and often has a high computational cost. To solve these problems, an adaptive non-local Euclidean medians sparse unmixing (ANLEMSU) method is proposed to improve NLSU by replacing the non-local means total variation spatial consideration with the non-local Euclidean medians filtering approach. In addition, ANLEMSU utilizes a joint maximum a posteriori (JMAP) strategy to acquire the relationships between the regularization parameters and the estimated abundances, and achieves the fractional abundances adaptively, without the need to set the two regularization parameters manually. The experimental results using both simulated data and real hyperspectral images indicate that ANLEMSU outperforms the previous sparse unmixing algorithms and, hence, provides an effective option for the unmixing of hyperspectral remote sensing imagery.

General limit on the relation between abundances of D andLi7in big bang nucleosynthesis with nucleon injections

The injections of energetic hadrons could have occurred in the early universe by decays of hypothetical long-lived exotic particles. The injections induce the showers of nonthermal hadrons via nuclear scattering. Neutrons generated at these events can react with $^7$Be nuclei and reduce $^7$Be abundance solving a problem of the primordial $^7$Li abundance. We suggest that thermal neutron injection is a way to derive a model independent conservative limit on the relation between abundances of D and $^7$Li in a hadronic energy injection model. We emphasize that an uncertainty in cross sections of inelastic $n+p$ scattering affects the total number of induced neutrons, which determines final abundances of D and $^7$Li. In addition, the annihilations of antinucleons with $^4$He result in higher D abundance and trigger nonthermal $^6$Li production. It is concluded that a reduction of $^7$Li abundance from a value in the standard big bang nucleosynthesis (BBN) model down to an observational two $\sigma$ upper limit is necessarily accompanied by an undesirable increase of D abundance up to at least an observational 12 $\sigma$ upper limit from observations of quasi-stellar object absorption line systems. The effects of antinucleons and secondary particles produced in the hadronic showers always lead to a severer constraint. The BBN models involving any injections of extra neutrons are thus unlikely to reproduce a small $^7$Li abundance consistent with observations.

A Data-Driven Stochastic Approach for Unmixing Hyperspectral Imagery

In this paper, we propose a two-step Bayesian approach to handle the ill-posed nature of the unmixing problem for accurately estimating the abundances. The abundances are dependent on the scene contents and they represent mixing proportions of the endmembers over an area. In this work, a linear mixing model (LMM) is used for the image formation process in order to derive the data term. In the first step, a Huber-Markov random field (HMRF)-based prior distribution is assumed to model the dependencies within the abundances across the spectral space of the data. The threshold used in the HMRF prior is derived from an initial estimate of abundances obtained using the matched filters. This makes the HMRF prior data-driven, i.e., dHMRF. Final abundance maps are obtained in the second step within a maximum a posteriori probability (MAP) framework, and the objective function is optimized using the particle swarm optimization (PSO). Theoretical analysis is carried out to show the effectiveness of the proposed method. The approach is evaluated using the synthetic and real AVIRIS Cuprite data. The proposed method has the following advantages. 1) The estimated abundances are resistant to noise since they are based on an initial estimate that has high signal-to-noise ratio (SNR). 2) The variance in the abundance maps is well preserved since the threshold in the dHMRF is derived from the data.

Constraining non-thermal and thermal properties of Dark Matter

We describe the evolution of Dark Matter (DM) abundance from the very onset of its creation from inflaton decay under the assumption of an instantaneous reheating. Based on the initial conditions such as the inflaton mass and its decay branching ratio to DM, reheating temperature, and the DM mass and interaction rate with the thermal bath, the DM particles can either thermalize (fully/partially) with the primordial bath or remain non-thermal throughout their evolution history. In the thermal case, the final abundance is set by the standard freeze-out mechanism for large annihilation rates, irrespective of the initial conditions. For smaller annihilation rates, it can be set by the freeze-in mechanism, also independent of the initial abundance, provided it is small to begin with. For even smaller interaction rates, the DM decouples while being non-thermal, and the relic abundance will be essentially set by the initial conditions. We put model-independent constraints on the DM mass and annihilation rate from over-abundance by exactly solving the relevant Boltzmann equations, and identify the thermal freeze-out, freeze-in and non-thermal regions of the allowed parameter space. We highlight a generic fact that inflaton decay to DM inevitably leads to an overclosure of the Universe for a large range of DM parameter space, and thus poses a stringent constraint that must be taken into account while constructing models of DM. For the thermal DM region, we also show the complementary constraints from indirect DM search experiments, Big Bang Nucleosynthesis, Cosmic Microwave Background, Planck measurements, and theoretical limits due to the unitarity of S-matrix. For the non-thermal DM scenario, we show the allowed parameter space in terms of the inflaton and DM masses for a given reheating temperature, and compute the comoving free-streaming length to identify the hot, warm and cold DM regimes.

Mass Spectrometry-based Workflow for Accurate Quantification of Escherichia coli Enzymes: How Proteomics Can Play a Key Role in Metabolic Engineering

Metabolic engineering aims to design high performance microbial strains producing compounds of interest. This requires systems-level understanding; genome-scale models have therefore been developed to predict metabolic fluxes. However, multi-omics data including genomics, transcriptomics, fluxomics, and proteomics may be required to model the metabolism of potential cell factories. Recent technological advances to quantitative proteomics have made mass spectrometry-based quantitative assays an interesting alternative to more traditional immuno-affinity based approaches. This has improved specificity and multiplexing capabilities. In this study, we developed a quantification workflow to analyze enzymes involved in central metabolism in Escherichia coli (E. coli). This workflow combined full-length isotopically labeled standards with selected reaction monitoring analysis. First, full-length (15)N labeled standards were produced and calibrated to ensure accurate measurements. Liquid chromatography conditions were then optimized for reproducibility and multiplexing capabilities over a single 30-min liquid chromatography-MS analysis. This workflow was used to accurately quantify 22 enzymes involved in E. coli central metabolism in a wild-type reference strain and two derived strains, optimized for higher NADPH production. In combination with measurements of metabolic fluxes, proteomics data can be used to assess different levels of regulation, in particular enzyme abundance and catalytic rate. This provides information that can be used to design specific strains used in biotechnology. In addition, accurate measurement of absolute enzyme concentrations is key to the development of predictive kinetic models in the context of metabolic engineering.

Quantification of γ-Aminobutyric Acid in Sri Lankan Tea by Means of Ultra Performance Tandem Mass Spectrometry

Gamma-Aminobutyric acid (GABA), an important bioactive component of tea, acts as a major inhibitory neurotransmitter and is considered to influence other physiological processes in human as well as in planta. In the hereby presented study, the content of this valuable metabolite was investigated in two novel types of Ceylon Tea, explicitly "Silver Tips" and "White Tea", originating from minimally processed buds of the unique cultivar, "TRI 2043". The samples were subjected to hot water infusion, equivalent to the traditional beverage preparation procedure, and analyzed by means of hydrophilic interaction ultra performance liquid chromatography coupled to tandem mass spectrometry (HILIC LC-MS/MS). The registered GABA levels were compared with those obtained for the classic "Black Tea" and "Green Tea" samples from Sri Lanka. A high variation of GABA content was observed among the different tea types, especially in the case of "Silver Tips" and "White Tea", indicating the crucial influence of the manufacturing procedure (processing extent) on the final abundance of the bioactive component of interest. Furthermore, "White Tea" samples boasted the highest GABA concentration reported for this type of tea so far, reaching up to 50% of that characteristic of the high-priced "GABA Tea". Therefore, "White Tea" and "Silver Tips" were proved to be high quality tea with amounts of gamma-aminobutyric acid comparable with those described for similar types before. To our knowledge, this is the first report on HILIC LC-MS/MS application for the quantification of GABA and for in-depth characterization of teas from Sri Lanka.

Sensitivity studies for the weak r process: neutron capture rates

Rapid neutron capture nucleosynthesis involves thousands of nuclear species far from stability, whose nuclear properties need to be understood in order to accurately predict nucleosynthetic outcomes. Recently sensitivity studies have provided a deeper understanding of how the r process proceeds and have identified pieces of nuclear data of interest for further experimental or theoretical study. A key result of these studies has been to point out the importance of individual neutron capture rates in setting the final r-process abundance pattern for a ‘main’ (A ∼ 130 peak and above) r process. Here we examine neutron capture in the context of a ‘weak’ r process that forms primarily the A ∼ 80 r-process abundance peak. We identify the astrophysical conditions required to produce this peak region through weak r-processing and point out the neutron capture rates that most strongly influence the final abundance pattern.

Sensitivity studies for the main r process: β-decay rates

The pattern of isotopic abundances produced in rapid neutron capture, or r-process, nucleosynthesis is sensitive to the nuclear physics properties of thousands of unstable neutron-rich nuclear species that participate in the process. It has long been recognized that the some of the most influential pieces of nuclear data for r-process simulations are β-decay lifetimes. In light of experimental advances that have pushed measurement capabilities closer to the classic r-process path, we revisit the role of individual β-decay rates in the r process. We perform β-decay rate sensitivity studies for a main (A > 120) r process in a range of potential astrophysical scenarios. We study the influence of individual rates during (n, γ)-(γ, n) equilibrium and during the post-equilibrium phase where material moves back toward stability. We confirm the widely accepted view that the most important lifetimes are those of nuclei along the r-process path for each astrophysical scenario considered. However, we find in addition that individual β-decay rates continue to shape the final abundance pattern through the post-equilibrium phase, for as long as neutron capture competes with β decay. Many of the lifetimes important for this phase of the r process are within current or near future experimental reach.

Variability in the relative quantity of human DNA resulted from metagenomic analysis of gut microbiota

We conducted the comparative study of seven different methods of total DNA extraction from human feces. All these methods are recommended in protocols for metagenomic analysis of human gut microbiota. We studied the relative quantity of human DNA calculated from shotgun sequencing on a SOLiD 4 genetic analyzer of metagenomic samples. It was shown that either initial amount of feces or a method applied for total DNA extraction do not affect on final relative human DNA abundance, which is less than 1% in healthy people. Invariance of this parameter allows to consider increased abundance of human DNA in metagenomic samples as a potential marker of inflammatory bowel diseases.

Gravitino dark matter production at finite temperature

The production and the final abundance of gravitino dark matter appear to depend crucially on the restoration of the global U(1) $R$-symmetry of GMSB sectors in a threefold way. An $R$-symmetric phase effectively suppresses the production of goldstinos from scatterings with the supersymmetric Standard Model particles and it generically initiates the goldstino production from the thermalized messenger particles. In addition, the GMSB spurion gets displaced from the zero temperature minimum and under certain conditions it dominates the energy density of the universe producing late entropy. We show that it is possible to have high enough reheating temperatures that thermal leptogenesis and thermal vacuum selection can be realized without gravitino overproduction. The gravitino dark matter can be produced either thermally or non-thermally. In the former case the messenger scale has to be less than about $10^6$ GeV with the gravitino relatively heavy, $m_{3/2}\geq {\cal O}(10)$ GeV. In the later case, the gravitino is generically produced by the decay of the GMSB spurion field a process that always takes place for large messenger scales. A connection of our results with current collider and observational data is performed.

Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion

To develop a targeted metagenomics approach for the analysis of novel multispecies microbial consortia involved in the bioconversion of lignocellulose and furanic compounds, we applied replicated sequential batch aerobic enrichment cultures with either pretreated or untreated wheat straw as the sources of carbon and energy. After each transfer, exponential growth of bacteria was detected using microscopic cell counts, indicating that the substrate was being utilized. In batch, the final bacterial abundances increased from an estimated 5 to 8.7-9.5 log 16S rRNA gene copy numbers/ml. The abundances of fungal propagules showed greater variation, i.e., between 5.4 and 8.0 log ITS1 copies/ml. Denaturing gradient gel electrophoresis analyses showed that the bacterial consortia in both treatments reached approximate structural stability after six transfers. Moreover, the structures of the fungal communities were strongly influenced by substrate treatment. A total of 124 bacterial strains were isolated from the two types of enrichment cultures. The most abundant strains were affiliated with the genera Raoultella/Klebsiella, Kluyvera, Citrobacter, Enterobacter, Pseudomonas, Acinetobacter, Flavobacterium and Arthrobacter. Totals of 43 and 11 strains obtained from the untreated and pretreated substrates, respectively, showed (hemi)cellulolytic activity (CMC-ase and xylanase), whereas 96 strains were capable of growth in 7.5 mM 5-hydroxymethylfurfural. About 50 % of the latter showed extracellular oxidoreductase activity as detected by a novel iodide oxidation method. Also, (hemi)cellulolytic fungal strains related to Coniochaeta, Plectosphaerella and Penicillium were isolated. One Trichosporon strain was isolated from pretreated wheat straw. The two novel bacterial-fungal consortia are starting points for lignocellulose degradation applications.

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

The effects of acoustic misclassification on cetacean species abundance estimation

To estimate the density or abundance of a cetacean species using acoustic detection data, it is necessary to correctly identify the species that are detected. Developing an automated species classifier with 100% correct classification rate for any species is likely to stay out of reach. It is therefore necessary to consider the effect of misidentified detections on the number of observed data and consequently on abundance or density estimation, and develop methods to cope with these misidentifications. If misclassification rates are known, it is possible to estimate the true numbers of detected calls without bias. However, misclassification and uncertainties in the level of misclassification increase the variance of the estimates. If the true numbers of calls from different species are similar, then a small amount of misclassification between species and a small amount of uncertainty around the classification probabilities does not have an overly detrimental effect on the overall variance. However, if there is a difference in the encounter rate between species calls and/or a large amount of uncertainty in misclassification rates, then the variance of the estimates becomes very large and this dramatically increases the variance of the final abundance estimate.

Timing of Favorable Conditions, Competition and Fertility Interact to Govern Recruitment of Invasive Chinese Tallow Tree in Stressful Environments

The rate of new exotic recruitment following removal of adult invaders (reinvasion pressure) influences restoration outcomes and costs but is highly variable and poorly understood. We hypothesize that broad variation in average reinvasion pressure of Triadica sebifera (Chinese tallow tree, a major invader) arises from differences among habitats in spatiotemporal availability of realized recruitment windows. These windows are periods of variable duration long enough to permit establishment given local environmental conditions. We tested this hypothesis via a greenhouse mesocosm experiment that quantified how the duration of favorable moisture conditions prior to flood or drought stress (window duration), competition and nutrient availability influenced Triadica success in high stress environments. Window duration influenced pre-stress seedling abundance and size, growth during stress and final abundance; it interacted with other factors to affect final biomass and germination during stress. Stress type and competition impacted final size and biomass, plus germination, mortality and changes in size during stress. Final abundance also depended on competition and the interaction of window duration, stress type and competition. Fertilization interacted with competition and stress to influence biomass and changes in height, respectively, but did not affect Triadica abundance. Overall, longer window durations promoted Triadica establishment, competition and drought (relative to flood) suppressed establishment, and fertilization had weak effects. Interactions among factors frequently produced different effects in specific contexts. Results support our ‘outgrow the stress’ hypothesis and show that temporal availability of abiotic windows and factors that influence growth rates govern Triadica recruitment in stressful environments. These findings suggest that native seed addition can effectively suppress superior competitors in stressful environments. We also describe environmental scenarios where specific management methods may be more or less effective. Our results enable better niche-based estimates of local reinvasion pressure, which can improve restoration efficacy and efficiency by informing site selection and optimal management.

Measurement of Radiative Proton Capture onF18and Implications for Oxygen-Neon Novae

The rate of the 18F(p,γ)19Ne reaction affects the final abundance of the γ-ray observable radioisotope 18F, produced in novae. However, no successful measurement of this reaction exists and the rate used is calculated from incomplete information on the contributing resonances. Of the two resonances thought to play a significant role, one has a radiative width estimated from the assumed analogue state in the mirror nucleus, 19F. The second does not have an analogue state assignment at all, resulting in an arbitrary radiative width being assumed. Here, we report the first successful direct measurement of the 18F(p,γ)^19Ne reaction. The strength of the 665 keV resonance (Ex=7.076 MeV) is found to be over an order of magnitude weaker than currently assumed in nova models. Reaction rate calculations show that this resonance therefore plays no significant role in the destruction of ^{18}F at any astrophysical energy.

Mirror matter can alleviate the cosmological lithium problem

The abundance of lithium-7 confronts cosmology with a long lasting problem between the predictions of standard big bang nucleosynthesis and the baryonic density determined from the cosmic microwave background observations. This article investigates the influence of the existence of a mirror world, focusing on models in which neutrons can oscillate into mirror neutrons. Such a mechanism allows for an effective late time neutron injection, which induces an increase of the destruction of beryllium-7, due to an increase of the neutron capture, and then a decrease of the final lithium-7 abundance. Big bang nucleosynthesis sets constraints on the oscillation time between the two types of neutrons and the possibility for such a mechanism to solve, or alleviate, the lithium problem is emphasized.

Non-thermal photons and H2 formation in the early Universe

The cosmological recombination of H and He at z \sim 1000 and the formation of H2 during the dark ages produce a non-thermal photon excess in the Wien tail of the cosmic microwave background (CMB) blackbody spectrum. Here we compute the effect of these photons on the H- photodetachment and H2+ photodissociation processes. We discuss the implications for the chemical evolution of the Universe in the post-recombination epoch, emphasizing how important a detailed account of the full vibrational manifold of H2 and H2+ in the chemical network is. We find that the final abundances of H2, H2+, H3+ and HD are significantly smaller than in previous calculations that neglected the effect of non-thermal photons. The suppression is mainly caused by extra hydrogen recombination photons and could affect the formation rate of first stars. We provide simple analytical approximations for the relevant rate coefficients and briefly discuss the additional effect of dark matter annihilation on the considered reaction rates.

IMPORTANCE OF Q-VALUES IN ASTROPHYSICAL RAPID PROTON CAPTURE PROCESS

The importance of measuring Q-values in rapid proton capture process has been investigated. The microscopic optical model, derived using a nucleon–nucleon interaction and densities from relativistic mean field (RMF) calculations, has been utilized to calculate the reaction rates. It has been observed that the Q-values involved in the reactions at waiting points at A = 60 and 64 are very important in determining the final abundance of the process. Some other Q-values also play a crucial role in the final abundance of nuclei near the end point of the process.

Insights into the Regular Patterns of Protein Abundance Regulation and Distribution

Protein is one of the fundamental building blocks of life, and its amount in one cell is closely related to biological function. Therefore, protein abundance is regulated strictly at multiple levels of gene expression. The determinants of protein abundance include its corresponding mRNA abundance, the rate of protein synthesis and degradation, so the final cellular protein abundance is determined by the balance of these three factors. Benefitting from the rapid advancement of quantitative proteomics and the outputting of large-scale protein abundance data, we can devote to uncovering the relationship between protein abundance and its intrinsic characteristics (such as evolutionary characteristics, structure characteristics and functional categories), which is of great significance for the deep understanding of the basic composition principle of life systems. Here we summarize the recent research advances of protein abundance regulation, and the regular patterns of the relationship between protein abundance and its intrinsic characteristics. In addition, we also discuss the biological significance underlying them.