Pareto genealogies arising from a Poisson branching evolution model with selection

We study a class of coalescents derived from a sampling procedure out of $N$ i.i.d. Pareto $\left( \alpha \right) $ random variables, normalized by their sum, including $\beta $ –size-biasing on total length effects ( $\beta <\alpha $ ). Depending on the range of $\alpha ,$ we derive the large $N$ limit coalescents structure, leading either to a discrete-time Poisson-Dirichlet $ \left(\alpha ,-\beta \right) \Xi -$ coalescent ( $\alpha \in \left[ 0,1\right) $ ), or to a family of continuous-time Beta $\left( 2-\alpha ,\alpha -\beta \right) \Lambda -$ coalescents ( $\alpha \in \left[ 1,2\right) $ ), or to the Kingman coalescent ( $\alpha \ge 2$ ). We indicate that this class of coalescent processes (and their scaling limits) may be viewed as the genealogical processes of some forward in time evolving branching population models including selection effects. In such constant-size population models, the reproduction step, which is based on a fitness-dependent Poisson Point Process with scaling power-law $\left( \alpha \right) $ intensity, is coupled to a selection step consisting of sorting out the $N$ fittest individuals issued from the reproduction step.     

Do calcium buffers always slow down the propagation of calcium waves?

Calcium buffers are large proteins that act as binding sites for free cytosolic calcium. Since a large fraction of cytosolic calcium is bound to calcium buffers, calcium waves are widely observed under the condition that free cytosolic calcium is heavily buffered. In addition, all physiological buffered excitable systems contain multiple buffers with different affinities. It is thus important to understand the properties of waves in excitable systems with the inclusion of buffers. There is an ongoing controversy about whether or not the addition of calcium buffers into the system always slows down the propagation of calcium waves. To solve this controversy, we incorporate the buffering effect into the generic excitable system, the FitzHugh–Nagumo model, to get the buffered FitzHugh–Nagumo model, and then to study the effect of the added buffer with large diffusivity on traveling waves of such a model in one spatial dimension. We can find a critical dissociation constant ( $K=K(a)$ ) characterized by system excitability parameter $a$ such that calcium buffers can be classified into two types: weak buffers ( $K\in (K(a),\infty )$ ) and strong buffers ( $K\in (0,K(a))$ ). We analytically show that the addition of weak buffers or strong buffers but with its total concentration $b_0^1$ below some critical total concentration $b_{0,c}^1$ into the system can generate a traveling wave of the resulting system which propagates faster than that of the origin system, provided that the diffusivity $D_1$ of the added buffers is sufficiently large. Further, the magnitude of the wave speed of traveling waves of the resulting system is proportional to $\sqrt{D_1}$ as $D_1\rightarrow \infty $ . In contrast, the addition of strong buffers with the total concentration $b_0^1>b_{0,c}^1$ into the system may not be able to support the formation of a biologically acceptable wave provided that the diffusivity $D_1$ of the added buffers is sufficiently large.     

A network with tunable clustering, degree correlation and degree distribution, and an epidemic thereon

A random network model which allows for tunable, quite general forms of clustering, degree correlation and degree distribution is defined. The model is an extension of the configuration model, in which stubs (half-edges) are paired to form a network. Clustering is obtained by forming small completely connected subgroups, and positive (negative) degree correlation is obtained by connecting a fraction of the stubs with stubs of similar (dissimilar) degree. An SIR (Susceptible $\rightarrow $ Infective $\rightarrow $ Recovered) epidemic model is defined on this network. Asymptotic properties of both the network and the epidemic, as the population size tends to infinity, are derived: the degree distribution, degree correlation and clustering coefficient, as well as a reproduction number $R_*$ , the probability of a major outbreak and the relative size of such an outbreak. The theory is illustrated by Monte Carlo simulations and numerical examples. The main findings are that (1) clustering tends to decrease the spread of disease, (2) the effect of degree correlation is appreciably greater when the disease is close to threshold than when it is well above threshold and (3) disease spread broadly increases with degree correlation $\rho $ when $R_*$ is just above its threshold value of one and decreases with $\rho $ when $R_*$ is well above one.     

Sensory uncertainty and stick balancing at the fingertip

The effects of sensory input uncertainty, $\varepsilon $ , on the stability of time-delayed human motor control are investigated by calculating the minimum stick length, $\ell _\mathrm{crit}$ , that can be stabilized in the inverted position for a given time delay, $\tau $ . Five control strategies often discussed in the context of human motor control are examined: three time-invariant controllers [proportional–derivative, proportional–derivative–acceleration (PDA), model predictive (MP) controllers] and two time-varying controllers [act-and-wait (AAW) and intermittent predictive controllers]. The uncertainties of the sensory input are modeled as a multiplicative term in the system output. Estimates based on the variability of neural spike trains and neural population responses suggest that $\varepsilon \approx 7$ –13 %. It is found that for this range of uncertainty, a tapped delay-line type of MP controller is the most robust controller. In particular, this controller can stabilize inverted sticks of the length balanced by expert stick balancers (0.25–0.5 m when $\tau \approx 0.08$  s). However, a PDA controller becomes more effective when $\varepsilon > 15\,\%$ . A comparison between $\ell _\mathrm{crit}$ for human stick balancing at the fingertip and balancing on the rubberized surface of a table tennis racket suggest that friction likely plays a role in balance control. Measurements of $\ell _\mathrm{crit},\,\tau $ , and a variability of the fluctuations in the vertical displacement angle, an estimate of $\varepsilon $ , may make it possible to study the changes in control strategy as motor skill develops.     

Topological classification and enumeration of RNA structures by genus

To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer–Zagier, we compute the generating function $\mathbf{D}_{g,\sigma }(z)=\sum _{n}\mathbf{d}_{g,\sigma }(n)z^n$ for the number $\mathbf{d}_{g,\sigma }(n)$ of those structures of fixed genus $g$ and minimum stack size $\sigma $ with $n$ nucleotides so that no two consecutive nucleotides are basepaired and show that $\mathbf{D}_{g,\sigma }(z)$ is algebraic. In particular, we prove that $\mathbf{d}_{g,2}(n)\sim k_g\,n^{3(g-\frac{1}{2})} \gamma _2^n$ , where $\gamma _2\approx 1.9685$ . Thus, for stack size at least two, the genus only enters through the sub-exponential factor, and the slow growth rate compared to the number of RNA molecules implies the existence of neutral networks of distinct molecules with the same structure of any genus. Certain RNA structures called shapes are shown to be in natural one-to-one correspondence with the cells in the Penner–Strebel decomposition of Riemann’s moduli space of a surface of genus $g$ with one boundary component, thus providing a link between RNA enumerative problems and the geometry of Riemann’s moduli space.     

Bone refilling in cortical basic multicellular units: insights into tetracycline double labelling from a computational model

Bone remodelling is carried out by ‘bone multicellular units’ ( $\text{ BMU }$ s) in which active osteoclasts and active osteoblasts are spatially and temporally coupled. The refilling of new bone by osteoblasts towards the back of the $\text{ BMU }$ occurs at a rate that depends both on the number of osteoblasts and on their secretory activity. In cortical bone, a linear phenomenological relationship between matrix apposition rate and $\text{ BMU }$ cavity radius is found experimentally. How this relationship emerges from the combination of complex, nonlinear regulations of osteoblast number and secretory activity is unknown. Here, we extend our previous mathematical model of cell development within a single cortical $\text{ BMU }$ to investigate how osteoblast number and osteoblast secretory activity vary along the $\text{ BMU }$ ’s closing cone. The mathematical model is based on biochemical coupling between osteoclasts and osteoblasts of various maturity and includes the differentiation of osteoblasts into osteocytes and bone lining cells, as well as the influence of $\text{ BMU }$ cavity shrinkage on osteoblast development and activity. Matrix apposition rates predicted by the model are compared with data from tetracycline double labelling experiments. We find that the linear phenomenological relationship observed in these experiments between matrix apposition rate and $\text{ BMU }$ cavity radius holds for most of the refilling phase simulated by our model, but not near the start and end of refilling. This suggests that at a particular bone site undergoing remodelling, bone formation starts and ends rapidly, supporting the hypothesis that osteoblasts behave synchronously. Our model also suggests that part of the observed cross-sectional variability in tetracycline data may be due to different bone sites being refilled by $\text{ BMU }$ s at different stages of their lifetime. The different stages of a $\text{ BMU }$ ’s lifetime (such as initiation stage, progression stage, and termination stage) depend on whether the cell populations within the $\text{ BMU }$ are still developing or have reached a quasi-steady state whilst travelling through bone. We find that due to their longer lifespan, active osteoblasts reach a quasi-steady distribution more slowly than active osteoclasts. We suggest that this fact may locally enlarge the Haversian canal diameter (due to a local lack of osteoblasts compared to osteoclasts) near the $\text{ BMU }$ ’s point of origin.     

Towards a conceptualization of ETL and physical storage of semantic data warehouses as a service

The data warehouse technology has become the incontestable tool for businesses and organizations to make strategic decisions to ensure their competitively. The construction of a data warehouse ( $\mathcal{D}\mathcal{W}$ ) passes by selecting relevant information sources, extracting relevant data and loading them into the $\mathcal{D}\mathcal{W}$ . These processes require a precise expertise from designers related to logical and physical implementations of information sources, which is not usually an easy task. The diversity and heterogeneity of information sources makes the construction process of the $\mathcal{D}\mathcal{W}$ complex and time consuming. Domain ontologies have been proposed to reduce heterogeneity between sources, platforms, services, etc. They resolve syntax and semantic conflicts. The phenomenon of adopting domain ontologies by organizations creates a new type of databases, called semantic databases ( $\mathcal{S}\mathcal{D}\mathcal{B}$ ). As a consequence, they become a candidate for building the semantic $\mathcal{D}\mathcal{W}$ ( $\mathcal{S}\mathcal{D}\mathcal{W}$ ). To handle the diversity of information sources and hide the implementations aspects of sources, proposing a generic framework for constructing $\mathcal{D}\mathcal{W}$ becomes a necessity. In this paper, we first proposed an ontology-based approach for designing $\mathcal{S}\mathcal {D}\mathcal{B}$ . Secondly, ETL phases are defined at ontological level to hide the implementation details. Thirdly, a storage service for ontologies and its associated data is given. Finally, our proposal is validated through a case study and a tool.     

Studies on mass attenuation coefficient, effective atomic number and electron density of some vitamins

Mass attenuation coefficient, $ \mu_{m} $ , atomic cross-section, $ \sigma_{i} $ , electronic cross-section, $ \sigma_{e} $ , effective atomic number, $ Z_{\text{eff}} $ and effective electron density, $ N_{\text{el}} $ , were determined experimentally and theoretically for some vitamins (retinol, beta-carotene, thiamine, riboflavin, niacinamide, pantothenic acid, pyridoxine, biotin, folic acid, cyanocobalamin, ascorbic acid, cholecalciferol, alpha-tocopherol, ketamine, hesperidin) at 30.82, 59.54, 80.99, 356.61, 661.66 and 1,408.01?keV photon energies using a NaI(Tl) scintillation detector. The theoretical mass attenuation coefficients were estimated using mixture rules. The calculated values were compared with the experimental values for all vitamins.     

Retention of Dissolved Inorganic Nitrogen by Foliage and Twigs of Four Temperate Tree Species

Nitrogen (N) retention by tree canopies is believed to be an important process for tree nutrient uptake, and its quantification is a key issue in determining the impact of atmospheric N deposition on forest ecosystems. Due to dry deposition and retention by other canopy elements, the actual uptake and assimilation by the tree canopy is often obscured in throughfall studies. In this study, ¹⁵N-labeled solutions ( $ ^{15} {\text{NH}}_{4}^{ + } $ and $ ^{15} {\text{NO}}_{3}^{ - } $ ) were used to assess dissolved inorganic N retention by leaves/needles and twigs of European beech, pedunculate oak, silver birch, and Scots pine saplings. The effects of N form, tree species, leaf phenology, and applied $ {\text{NO}}_{3}^{ - } $ to $ {\text{NH}}_{4}^{ + } $ ratio on the N retention were assessed. Retention patterns were mainly determined by foliar uptake, except for Scots pine. In twigs, a small but significant ¹⁵N enrichment was detected for $ {\text{NH}}_{4}^{ + } $ , which was found to be mainly due to physicochemical adsorption to the woody plant surface. The mean $ {{^{15} {\text{NH}}_{4}^{ + } } \mathord{\left/ {\vphantom {{^{15} {\text{NH}}_{4}^{ + } } {^{15} {\text{NO}}_{3}^{ - } }}} \right. \kern-0em} {^{15} {\text{NO}}_{3}^{ - } }} $ retention ratio varied considerably among species and phenological stadia, which indicates that the use of a fixed ratio in the canopy budget model could lead to an over- or underestimation of the total N retention. In addition, throughfall water under each branch was collected and analyzed for $ ^{15} {\text{NH}}_{4}^{ + } $ , $ ^{15} {\text{NO}}_{3}^{ - } $ , and all major ions. Net throughfall of $ ^{15} {\text{NH}}_{4}^{ + } $ was, on average, 20 times higher than the actual retention of $ ^{15} {\text{NH}}_{4}^{ + } $ by the plant material. This difference in $ ^{15} {\text{NH}}_{4}^{ + } $ retention could not be attributed to pools and fluxes measured in this study. The retention of $ ^{15} {\text{NH}}_{4}^{ + } $ was correlated with the net throughfall of K⁺, Mg²⁺, Ca²⁺, and weak acids during leaf development and the fully leafed period, while no significant relationships were found for $ ^{15} {\text{NO}}_{3}^{ - } $ retention. This suggests that the main driving factors for $ {\text{NH}}_{4}^{ + } $ retention might be ion exchange processes during the start and middle of the growing season and passive diffusion at leaf senescence. Actual assimilation or abiotic uptake of N through leaves and twigs was small in this study, for example, 1–5% of the applied dissolved ¹⁵N, indicating that the impact of canopy N retention from wet deposition on forest productivity and carbon sequestration is likely limited.     

Effects of collagen deposition on passive and active mechanical properties of large pulmonary arteries in hypoxic pulmonary hypertension

Proximal pulmonary artery (PA) stiffening is a strong predictor of mortality in pulmonary hypertension. Collagen accumulation is mainly responsible for PA stiffening in hypoxia-induced pulmonary hypertension (HPH) in mouse models. We hypothesized that collagen cross-linking and the type I isoform are the main determinants of large PA mechanical changes during HPH, which we tested by exposing mice that resist type I collagen degradation (Col1a1 $^\mathrm{R/R})$ and littermate controls (Col1a1 $^{+/+})$ to hypoxia for 10 days with or without $\beta $ -aminopropionitrile (BAPN) treatment to prevent cross-link formation. Static and dynamic mechanical tests were performed on isolated PAs with smooth muscle cells (SMC) in passive and active states. Percentages of type I and III collagen were quantified by histology; total collagen content and cross-linking were measured biochemically. In the SMC passive state, for both genotypes, hypoxia tended to increase PA stiffness and damping capacity, and BAPN treatment limited these increases. These changes were correlated with collagen cross-linking ( $p<0.05$ ). In the SMC active state, hypoxia increased PA dynamic stiffness and BAPN had no effect in Col1a1 $^{+/+}$ mice ( $p<0.05$ ). PA stiffness did not change in Col1a1 $^\mathrm{R/R}$ mice. Similarly, damping capacity did not change for either genotype. Type I collagen accumulated more in Col1a1 $^{+/+}$ mice, whereas type III collagen increased more in Col1a1 $^\mathrm{R/R}$ mice during HPH. In summary, PA passive mechanical properties (both static and dynamic) are related to collagen cross-linking. Type I collagen turnover is critical to large PA remodeling during HPH when collagen metabolism is not mutated and type III collagen may serve as a reserve.     

On the page number of RNA secondary structures with pseudoknots

Let ${\mathcal {S}}$ denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. ${\{i, j\} \in \mathcal {S}}$ if there is a hydrogen bond between the ith and jth nucleotide. The page number of ${\mathcal {S}}$ , denoted ${\pi(\mathcal {S})}$ , is the minimum number k such that ${\mathcal {S}}$ can be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NP-complete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary structures, for which the topological genus is known. We describe an approximation algorithm from which it follows that ${\omega(\mathcal {S}) \leq \pi(\mathcal {S}) \leq \omega(\mathcal {S}) \cdot \log n}$ , where the clique number of ${\mathcal {S}, \omega(\mathcal {S})}$ , denotes the maximum number of base pairs that pairwise cross each other.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

Analysis of {}^{13}{\text{C}}^{{{\upalpha}}} and {}^{13}{\text{C}}^{{{\upbeta}}} chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and $ {}^{13}{\text{C}}^{{{\upbeta}}} $ chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed $ {}^{13}{\text{C}}^{{{\upalpha}}} $ chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed $ {}^{13}{\text{C}}^{{{\upalpha}}} $ chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced ?SH $ {}^{13}{\text{C}}^{{{\upbeta}}} $ , but not for the $ {}^{13}{\text{C}}^{{{\upalpha}}} $ , chemical shifts, in good agreement with the observation of 375 $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and 337 $ {}^{13}{\text{C}}^{{{\upbeta}}} $ resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of $ {}^{13}{\text{C}}^{{{\upalpha}}} $ and $ {}^{13}{\text{C}}^{{{\upbeta}}} $ chemical shifts of cysteines in cystines.     

Edge removal in random contact networks and the basic reproduction number

Understanding the effect of edge removal on the basic reproduction number ${\mathcal{R}_0}$ for disease spread on contact networks is important for disease management. The formula for the basic reproduction number ${\mathcal{R}_0}$ in random network SIR models of configuration type suggests that for degree distributions with large variance, a reduction of the average degree may actually increase ${\mathcal{R}_0}$ . To understand this phenomenon, we develop a dynamical model for the evolution of the degree distribution under random edge removal, and show that truly random removal always reduces ${\mathcal{R}_0}$ . The discrepancy implies that any increase in ${\mathcal{R}_0}$ must result from edge removal changing the network type, invalidating the use of the basic reproduction number formula for a random contact network. We further develop an epidemic model incorporating a contact network consisting of two groups of nodes with random intra- and inter-group connections, and derive its basic reproduction number. We then prove that random edge removal within either group, and between groups, always decreases the appropriately defined ${\mathcal{R}_0}$ . Our models also allow an estimation of the number of edges that need to be removed in order to curtail an epidemic.     

Oxidative power and intracellular distribution of mitochondria control cell oxygen regime when arterial hypoxemia occurs

The regulatory impact of the mitochondria spatial distribution and enlargement in their oxidative power $q_{O_2 } $ on tissue oxygenation of skeletal muscle during hypoxia were studied. Investigations were performed by mathematical modeling of 3D O₂ diffusion-reaction in muscle fiber. The oxygen consumption rate $V_{O_2 } $ and tissue $p_{O_2 } $ were analyzed in response to a decrease in arterial blood oxygen concentration from 19.5 to 10 vol % at moderate load. Cells with evenly (case 1) and unevenly (case 2) distributed mitochondria were considered. According to calculations, owing to a rise in mitochondria oxidative power from 3.5 to 6.5 mL/min per 100 g of tissue it is possible to maintain muscle oxygen $V_{O_2 } $ at a constant level of 3.5 mL/min per 100 g despite a decrease in O₂ delivery. The minimum value of tissue $p_{O_2 } $ was about 0 and an area of hypoxia appeared inside the cell in case 1. Whereas hypoxia disappeared and minimum value of $p_{O_2 } $ increased from 0 to 4 mmHg if mitochondria were distributed unevenly (case 2). The possibilities of such regulation depended on the relationship “the degree of hypoxemia — the level of oxygen delivery.” It was assumed that an increase in mitochondrial enzyme activity and their migration to places of the greatest oxygen consumption rate can improve the oxygen regime in the cell as it adapts to hypoxia.     

Integrating qPLM and biomechanical test data with an anisotropic fiber distribution model and predictions of TGF-\upbeta 1 and IGF-1 regulation of articular cartilage fiber modulus

A continuum mixture model with distinct collagen (COL) and glycosaminoglycan elastic constituents was developed for the solid matrix of immature bovine articular cartilage. A continuous COL fiber volume fraction distribution function and a true COL fiber elastic modulus ( $E^\mathrm{f})$ were used. Quantitative polarized light microscopy (qPLM) methods were developed to account for the relatively high cell density of immature articular cartilage and used with a novel algorithm that constructs a 3D distribution function from 2D qPLM data. For specimens untreated and cultured in vitro, most model parameters were specified from qPLM analysis and biochemical assay results; consequently, $E^\mathrm{f}$ was predicted using an optimization to measured mechanical properties in uniaxial tension and unconfined compression. Analysis of qPLM data revealed a highly anisotropic fiber distribution, with principal fiber orientation parallel to the surface layer. For untreated samples, predicted $E^\mathrm{f}$ values were 175 and 422 MPa for superficial (S) and middle (M) zone layers, respectively. TGF- $\upbeta $ 1 treatment was predicted to increase and decrease $E^\mathrm{f}$ values for the S and M layers to 281 and 309 MPa, respectively. IGF-1 treatment was predicted to decrease $E^\mathrm{f}$ values for the S and M layers to 22 and 26 MPa, respectively. A novel finding was that distinct native depth-dependent fiber modulus properties were modulated to nearly homogeneous values by TGF- $\upbeta $ 1 and IGF-1 treatments, with modulated values strongly dependent on treatment.     

Increased Damping of Plasmon Resonances in Gold Nanoparticles Due to Broadening of the Band Structure

For the first time, systematic investigations of the damping parameter A of gold nanoparticles as a function of photon energy are presented. A is an essential parameter that quantifies the size-dependent optical properties of metal nanoparticles in the dielectric function. To determine the damping parameter, the dephasing time T ₂ of gold nanoparticles has been systematically determined under ultrahigh vacuum conditions as a function of photon energy. Dephasing times ranging from  $T_2 = 5$ fs to $T_2 = 17$ fs were measured, and subsequently, the damping parameter has been extracted. We found a strong resonance-like damping of the plasmon resonance in the vicinity of the onset of the interband transition. While the damping parameter scatters statistically around a value of  $A = 0.19$ nm/fs for photon energies below  $h\nu = 1.70$ eV, it increases rapidly to 0.32 nm/fs for  $h\nu = 1.85$ eV. For higher photon energies, A decreases steadily to $A = 0.24$ nm/fs at $h\nu = 2.15$ eV. A comparison to former measurements as well as to theoretical predictions reveals surface scattering and a discretizing and broadening of the band structure that influences the interband transition as the most dominant size-dependent damping mechanisms. The latter, i.e., a damping via increased interband transitions, assumes a coherent damping process of the oscillating electrons and, as a consequence, the plasmon is treated as a two-level system. Thus, the results deliver new physical insight to the fundamental understanding of surface plasmons.     

Theoretical study of the pH-dependent antioxidant properties of vitamin C

Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of utmost importance in the living cell. Vitamin C is known to be one of these molecules. In this study we have analyzed the reactivity of vitamin C toward the $ \cdot OH $ and $ \cdot OOH $ ROS species, in all acidic, neutral and basic media. In order to do so, density functional theory (DFT) have been used. More concretely, the meta-GGA functional MPW1B95 have been used. Two reaction types have been studied in each case: addition to the ring atoms, and hydrogen/proton abstraction. Our results show that $ \cdot OH $ is the most reactive species, while $ \cdot OOH $ displays low reactivity. In all three media, vitamin C reactions with two hydroxyl radicals show a wide variety of possible products.     

Provenance variation and genetic parameters of Eucalyptus viminalis in Argentina

Genetic parameters for growth, stem straightness, pilodyn penetration, relative bark thickness and survival were estimated in a base-population of five open-pollinated provenance/progeny trials of Eucalyptus viminalis. The trials, located in northern, central and southern Buenos Aires Province, Argentina, comprised 148 open-pollinated families from 13 Australian native provenances and eight local Argentinean seedlots. The Australian native provenances come from a limited range of the natural distribution. Overall survival, based on the latest assessment of each trial, was 62.4%. Single-site analyses showed that statistically significant provenances differences (p?<?0.05) for at least one of the studied traits in three out of the five trials analyzed. The local land race performed inconsistently in this study. The average narrow-sense individual-tree heritability estimate $ \left( {{{\hat{h}}^2}} \right) $ was 0.27 for diameter and 0.17 for total height. Values of $ {\hat{h}^2} $ also increased with age. Pilodyn penetration, assessed at only one site, was more heritable $ \left( {{{\hat{h}}^2} = 0.32} \right) $ than the average of growth traits. Estimated individual-tree heritabilities were moderate to low for stem straightness (average of 0.20) and relative bark thickness (0.16). The estimated additive genetic correlations $ \left( {{{{r}}_{{A}}}} \right) $ between diameter and height were consistently high and positive ( $ {{r}_{^A}} $ average of 0.90). High additive genetic correlations were observed between growth variables and pilodyn penetration ( $ {{r}_{^A}} $ average of 0.58). Relative bark thickness showed a negative correlation with diameter $ \left( {{{{r}}_{^A}} = - 0.39} \right) $ and height $ \left( {{{{r}}_{^A}} = - 0.51} \right) $ . The average estimated additive genetic correlation between sites was high for diameter (0.67). The implications of all these parameter estimates for genetic improvement of E. viminalis in Argentina are discussed.     

Quantifying the risk of mis-estimating correlation significance of climate–tree growth relationships

In dendroecology, sampling effort has a strong influence of both regional chronology properties and climate–tree growth relationships assessment. Recent studies evidenced that decreasing sample size leads to a weakening of the bootstrapped correlation coefficients ( ${\text{BCC}}$ BCC ). The present analysis focused on the risk of mis-estimating the significance of population ${\text{BCC}}\,\left( {{\text{BCC}}_{\text{POP}} } \right)$ BCC ( BCC POP ) from a sample of N trees, and then proposed an approach to detect and correct mis-estimations using the properties of the sample. The sample size effect and the limits of the correction were illustrated from 840 individual growth chronologies of Corsican pine (Pinus nigra Arnold ssp. laricio Poiret var. Corsicana) sampled in Western France. The 840 trees were used to assess the population characteristics, and the effect of sampling effort was investigated through a simulation approach based on a resampling procedure of N trees amongst 840 (N ? [5; 50]). Our results evidenced that the risk strongly varied amongst the climatic regressors. The highest risks were evidenced for significant ${\text{BCC}}_{\text{POP}}$ BCC POP , with a percentage of mis-estimation ranging from 25 to 80. On the contrary, small samples allowed providing an reliable estimation of the significance of non-significant ${\text{BCC}}_{\text{POP}}$ BCC POP . To a lesser extent, the risk slightly decreased with increasing N, according to a negative exponential trend. The detection and correction method was found relevant to detect mis-estimation only for significant ${\text{BCC}}_{\text{POP}}$ BCC POP ; otherwise, the ${\text{BCC}}_{\text{POP}}$ BCC POP significance was generally overestimated.