Long-term analysis of Hubbard Brook stable oxygen isotope ratios of streamwater and precipitation sulfate

In response to decreasing atmospheric emissions of sulfur (S) since the 1970s there has been a concomitant decrease in S deposition to watersheds in the Northeastern U.S. Previous study at the Hubbard Brook Experimental Forest, NH (USA) using chemical and isotopic analyzes ( $ \delta^{34} {\text{S}}_{{{\text{SO}}_{4} }} $ ) combined with modeling has suggested that there is an internal source of S within these watersheds that results in a net loss of S via sulfate in drainage waters. The current study expands these previous investigations by the utilization of δ¹⁸O analyzes of precipitation sulfate and streamwater sulfate. Archived stream and bulk precipitation samples at the Hubbard Brook Experimental Forest from 1968–2004 were analyzed for stable oxygen isotope ratios of sulfate ( $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ ). Overall decreasing temporal trends and seasonally low winter values of $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ in bulk precipitation are most likely attributed to similar trends in precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values. Regional climate trends and changes in temperature control precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values that are reflected in the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values of precipitation. The significant relationship between ambient temperature and the $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values of precipitation is shown from a nearby site in Ottawa, Ontario (Canada). Although streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values did not reveal temporal trends, a large difference between precipitation and streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values suggest the importance of internal cycling of S especially through the large organic S pool and the concomitant effect on the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values in drainage waters.     

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.     

Longitudinal distribution of nitrate δ15N and δ18O in two contrasting tropical rivers: implications for instream nitrogen cycling

The longitudinal variations in the nitrogen (δ¹⁵N) and oxygen (δ¹⁸O) isotopic compositions of nitrate (NO₃ ^?), the carbon isotopic composition (δ¹³C) of dissolved inorganic carbon (DIC) and the δ¹³C and δ¹⁵N of particulate organic matter were determined in two Southeast Asian rivers contrasting in the watershed geology and land use to understand internal nitrogen cycling processes. The $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ became higher longitudinally in the freshwater reach of both rivers. The $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ also increased longitudinally in the river with a relatively steeper longitudinal gradient and a less cultivated watershed, while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ gradually decreased in the other river. A simple model for the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ that accounts for simultaneous input and removal of NO₃ ^? suggested that the dynamics of NO₃ ^? in the former river were controlled by the internal production by nitrification and the removal by denitrification, whereas that in the latter river was significantly affected by the anthropogenic NO₃ ^? loading in addition to the denitrification and/or assimilation. In the freshwater-brackish transition zone, heterotrophic activities in the river water were apparently elevated as indicated by minimal dissolved oxygen, minimal δ¹³C_DIC and maximal pCO₂. The δ¹⁵N of suspended particulate nitrogen (PN) varied in parallel to the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ there, suggesting that the biochemical recycling processes (remineralization of PN coupled to nitrification, and assimilation of NO₃ ^?-N back to PN) played dominant roles in the instream nitrogen transformation. In the brackish zone of both rivers, the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ displayed a declining trend while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ increased sharply. The redox cycling of NO₃ ^?/NO₂ ^? and/or deposition of atmospheric nitrogen oxides may have been the major controlling factor for the estuarine $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ , however, the exact mechanism behind the observed trends is currently unresolved.     

The effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis)

To investigate the effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis), we measured the following: (1) the resting oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{rest}}}} } \right) $ , critical swimming speed (U _crit) and active oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} } \right) $ of fish at acclimation temperatures of 10, 15, 20, 25 and 30 °C and (2) the $ \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ , U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ of both exercise-trained (exhaustive chasing training for 14 days) and control fish at both low and high acclimation temperatures (15 and 25 °C). The relationship between U _crit and temperature (T) approximately followed a bell-shaped curve as temperature increased: U _crit = 8.21/{1 + [(T ? 27.2)/17.0]²} (R ² = 0.915, P < 0.001, N = 40). The optimal temperature for maximal U _crit (8.21 BL s^?1) in juvenile qingbo was 27.2 °C. Both the $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and the metabolic scope (MS, $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} - \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ ) of qingbo increased with temperature from 10 to 25 °C (P < 0.05), but there were no significant differences between fish acclimated to 25 and 30 °C. The relationships between $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ or MS and temperature were described as $ {\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} = 1,214.29/\left\{ {1 + \left[ {\left( {T - 28.8} \right)/10.6} \right]^{2} } \right\}\;\left( {R^{2} = 0.911,\;P < 0.001,\;N = 40} \right) $ and MS = 972.67/{1 + [(T ? 28.0)/9.34]²} (R ² = 0.878, P < 0.001, N = 40). The optimal temperatures for $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and MS in juvenile qingbo were 28.8 and 28.0 °C, respectively. Exercise training resulted in significant increases in both U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a low temperature (P < 0.05), but training exhibited no significant effect on either U _crit or $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a high temperature. These results suggest that exercise training had different effects on swimming performance at different temperatures. These differences may be related to changes in aerobic metabolic capability, arterial oxygen delivery, available dissolved oxygen, imbalances in ion fluxes and stimuli to remodel tissues with changes in temperature.     

Estimation of viscosity from passage time of liquids flowing through a microchannel array

Recently, a microchannel flow analyzer (MC-FAN) has been used to study the flow properties of blood. However, the correlation between blood passage time measured by use of the MC-FAN and hemorheology has not been clarified. In this study, a simple model is proposed for estimation of liquid viscosity from the passage time t _p of liquids. The t _p data for physiological saline were well represented by the model. According to the model, the viscosity of Newtonian fluids was estimated reasonably well from the t _p data. For blood samples, although the viscosity $ \eta_{\text{mc}} $ estimated from t _p was shown to be smaller than the viscosity $ \eta_{{450{\text{s}}^{ - 1} }} $ measured by use of a rotatory viscometer at a shear rate of 450 s^?1, $ \eta_{\text{mc}} $ was correlated with $ \eta_{{450{\text{s}}^{ - 1} }} $ . An empirical equation for estimation of $ \eta_{{450{\text{s}}^{ - 1} }} $ from $ \eta_{\text{mc}} $ of blood samples is proposed.     

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.     

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.     

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.     

The average local ionization energy as a tool for identifying reactive sites on defect-containing model graphene systems

In a continuing effort to further explore the use of the average local ionization energy $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ as a computational tool, we have investigated how well $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ computed on molecular surfaces serves as a predictive tool for identifying the sites of the more reactive electrons in several nonplanar defect-containing model graphene systems, each containing one or more pentagons. They include corannulene (C₂₀H₁₀), two inverse Stone-Thrower-Wales defect-containing structures C₂₆H₁₂ and C₄₂H₁₆, and a nanotube cap model C₂₂H₆, whose end is formed by three fused pentagons. Coronene (C₂₄H₁₂) has been included as a reference planar defect-free graphene model. We have optimized the structures of these systems as well as several monohydrogenated derivatives at the B3PW91/6-31G* level, and have computed their $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ on molecular surfaces corresponding to the 0.001 au, 0.003 au and 0.005 au contours of the electronic density. We find that (1) the convex sides of the interior carbons of the nonplanar models are more reactive than the concave sides, and (2) the magnitudes of the lowest $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ surface minima (the $ {{\overline{\mathrm{I}}}_{{\mathrm{S}\text{,}\min }}} $ ) correlate well with the interaction energies for hydrogenation at these sites. These $ {{\overline{\mathrm{I}}}_{{\mathrm{S}\text{,}\min }}} $ values decrease in magnitude as the nonplanarity of the site increases, consistent with earlier studies. A practical benefit of the use of $ \overline{\mathrm{I}}\left( \mathbf{r} \right) $ is that a single calculation suffices to characterize the numerous sites on a large molecular system, such as graphene and defect-containing graphene models.

Continuous cultivation of Lactobacillus brevis NCL912 for production of gamma-aminobutyric acid

A continuous cultivation method for Lactobacillus brevis NCL912 to synthesize gamma-aminobutyric acid was developed in this work. Different dilution rates were evaluated for obtaining steady state in continuous cultivation. The results showed that steady state could be achieved at dilution rates from 0.08 to 0.12 h^?1. The highest gamma-aminobutyric acid productivity (5.11 g L^?1?h^?1) was obtained at dilution rate of 0.09 h^?1. The kinetic models were established for continuous gamma-aminobutyric acid production by using the Monod equation for microbial growth, and the Luedeking–Piret equation for product formation. The microbial growth and product formation can be described by equations $ \mu = {{{0.1234{C_S}}} \left/ {{\left( {0.9338+{C_S}} \right)}} \right.} $ and $ {Q_P}=6.86\,\mathrm{g}\,{{\mathrm{g}}^{-1 }}\mathrm{cell}\,{{\mathrm{h}}^{-1 }} $ , respectively. The production of gamma-aminobutyric acid by L. brevis NCL912 was non-growth-associated.     

Obtain Quadruple Intense Plasmonic Resonances from Multilayered Gold Nanoshells by Silver Coating: Application in Multiplex Sensing

Four intense and separate localized surface plasmon resonance (LSPR) absorption peaks have been obtained in the gold-dielectric–gold–silver multilayer nanoshells. The silver coating on the gold shell results in a new LSPR peak at about 400 nm corresponding to the $ {{\left| {\omega_{+}^{-}} \right\rangle}_{Ag }} $ mode. The intense local electric field concentrated in the silver shell at the wavelength of 400 nm indicates that this new plasmonic band is coming from the symmetric coupling between the antibonding silver shell plasmon mode and the inner sphere plasmon. Increasing the silver shell thickness also leads to the intensity increasing of the $ {{\left| {\omega_{+}^{-}} \right\rangle}_{Au }} $ mode and blue shift of $ \left| {\omega_{-}^{+}} \right\rangle $ and $ \left| {\omega_{-}^{-}} \right\rangle $ modes. Therefore, quadruple intense plasmonic resonances in the visible region could be achieved in gold-dielectric–gold–silver multilayer nanoshells by tuning the geometrical parameters. And the quadruple intense plasmonic resonances in the visible region provide well potential for multiplex biosensing based on LSPR.     

Can the positive aromatic ring be as ��-electron donor in ��-halogen bond? A MP2 theoretical investigation on the unusual ��-halogen bond interaction between three-membered ring \left( {\hbox{BNN}} \right)_3^{+} and X1X2 (X1, X2?=?F, Cl, Br)

The unusual ??-halogen bond interactions are investigated between $ \left( {\hbox{BNN}} \right)_3^{+} $ and X1X2 (X1, X2?=?F, Cl, Br) employing MP2 at 6-311?+?G(2d) and aug-cc-pVDZ levels according to the ??CP (counterpoise) corrected potential energy surface (PES)?? method. The order of the ??-halogen bond interactions and stabilities of the complexes are obtained to be $ \left( {\hbox{BNN}} \right)_3^{+} \ldots {{\hbox{F}}_2} < \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{ClF < }}\left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{C}}{{\hbox{l}}_2} < \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{BrCl}}\quad { < }\quad \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{B}}{{\hbox{r}}_2}\quad { < }\quad \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{BrF}}{.} $ at MP2/aug-cc-pVDZ level. The analyses of the Mulliken charge transfer, natural bond orbital (NBO), atoms in molecules (AIM) theory and electron density shifts reveal that the nature of the ??-halogen bond interaction in the complexes of ClF, BrF and BrCl might partly be charge transfer from the delocalized ??-HOMO orbital of $ \left( {\hbox{BNN}} \right)_3^{+} $ to X1X2. This result suggests that the positive aromatic ring $ \left( {\hbox{BNN}} \right)_3^{+} $ might act as a ??-electron donor to form the ??-halogen bond.

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.     

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.     

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.     

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.     

Stress fermentation strategies for the production of hyperthermostable superoxide dismutase from Thermus thermophilus HB27: effects of ions

In this study, we explored how ammonium and metal ion stresses affected the production of recombinant hyperthermostable manganese superoxide dismutase (Mn-SOD). To improve Mn-SOD production, fed-batch culture in shake flasks and bioreactor fermentation were undertaken to examine the effects of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. Under the optimized feeding time and concentrations of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺, the maximal SOD activity obtained from bioreactor fermentation reached some 480 U/ml, over 4 times higher than that in batch cultivation (113 U/ml), indicating a major enhancement of the concentration of Mn-SOD in the scale-up of hyperthermostable Mn-SOD production. In contrast, when the fed-batch culture with appropriate $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding was carried out in the same 5-L stirred tank bioreactor, a maximal SOD concentration of some 450 U/ml was obtained, again indicating substantial increase in SOD activity as a result of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. The isoelectric point (pI) of the sample was found to be 6.2. It was highly stable at 90 °C and circular dichroism measurements indicated a high α-helical content of 70 % as well, consistent with known SOD properties. This study indicates that $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ play important roles in Mn-SOD expression. Stress fermentation strategies established in this study are useful for large-scale efficient production of hyperthermostable Mn-SOD and may also be valuable for the scale-up of other extremozymes.