Rhenium-Oxygen Interactions at High Temperatures

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.; Myers, Dwight L.; Zhu, Dongming; Humphrey, Donald

2000-01-01

The reaction of pure rhenium metal with dilute oxygen/argon mixtures was studied from 600 to 1400 C. Temperature, oxygen pressure, and flow rates were systematically varied to determine the rate-controlling steps. At lower temperatures the oxygen/rhenium chemical reaction is rate limiting; at higher temperatures gas-phase diffusion of oxygen through the static boundary layer is rate limiting. At all temperatures post-reaction microstructures indicate preferential attack along certain crystallographic planes and defects.

Roles of conformational stability and colloidal stability in the aggregation of recombinant human granulocyte colony-stimulating factor

PubMed Central

Chi, Eva Y.; Krishnan, Sampathkumar; Kendrick, Brent S.; Chang, Byeong S.; Carpenter, John F.; Randolph, Theodore W.

2003-01-01

We studied the non-native aggregation of recombinant human granulocyte stimulating factor (rhGCSF) in solution conditions where native rhGCSF is both conformationally stable compared to its unfolded state and at concentrations well below its solubility limit. Aggregation of rhGCSF first involves the perturbation of its native structure to form a structurally expanded transition state, followed by assembly process to form an irreversible aggregate. The energy barriers of the two steps are reflected in the experimentally measured values of free energy of unfolding (ΔGunf) and osmotic second virial coefficient (B22), respectively. Under solution conditions where rhGCSF conformational stability dominates (i.e., large ΔGunf and negative B22), the first step is rate-limiting, and increasing ΔGunf (e.g., by the addition of sucrose) decreases aggregation. In solutions where colloidal stability is high (i.e., large and positive B22 values) the second step is rate-limiting, and solution conditions (e.g., low pH and low ionic strength) that increase repulsive interactions between protein molecules are effective at reducing aggregation. rhGCSF aggregation is thus controlled by both conformational stability and colloidal stability, and depending on the solution conditions, either could be rate-limiting. PMID:12717013

Lignocellulose hydrolysis by multienzyme complexes

USDA-ARS?s Scientific Manuscript database

Lignocellulosic biomass is the most abundant renewable resource on the planet. Converting this material into a usable fuel is a multi-step process, the rate-limiting step being enzymatic hydrolysis of organic polymers into monomeric sugars. While the substrate can be complex and require a multitud...

Kinetic aspects of chain growth in Fischer-Tropsch synthesis.

PubMed

Filot, Ivo A W; Zijlstra, Bart; Broos, Robin J P; Chen, Wei; Pestman, Robert; Hensen, Emiel J M

2017-04-28

Microkinetics simulations are used to investigate the elementary reaction steps that control chain growth in the Fischer-Tropsch reaction. Chain growth in the FT reaction on stepped Ru surfaces proceeds via coupling of CH and CR surface intermediates. Essential to the growth mechanism are C-H dehydrogenation and C hydrogenation steps, whose kinetic consequences have been examined by formulating two novel kinetic concepts, the degree of chain-growth probability control and the thermodynamic degree of chain-growth probability control. For Ru the CO conversion rate is controlled by the removal of O atoms from the catalytic surface. The temperature of maximum CO conversion rate is higher than the temperature to obtain maximum chain-growth probability. Both maxima are determined by Sabatier behavior, but the steps that control chain-growth probability are different from those that control the overall rate. Below the optimum for obtaining long hydrocarbon chains, the reaction is limited by the high total surface coverage: in the absence of sufficient vacancies the CHCHR → CCHR + H reaction is slowed down. Beyond the optimum in chain-growth probability, CHCR + H → CHCHR and OH + H → H 2 O limit the chain-growth process. The thermodynamic degree of chain-growth probability control emphasizes the critical role of the H and free-site coverage and shows that at high temperature, chain depolymerization contributes to the decreased chain-growth probability. That is to say, during the FT reaction chain growth is much faster than chain depolymerization, which ensures high chain-growth probability. The chain-growth rate is also fast compared to chain-growth termination and the steps that control the overall CO conversion rate, which are O removal steps for Ru.

Kinetic characterization of thermophilic and mesophilic anaerobic digestion for coffee grounds and waste activated sludge.

PubMed

Li, Qian; Qiao, Wei; Wang, Xiaochang; Takayanagi, Kazuyuki; Shofie, Mohammad; Li, Yu-You

2015-02-01

This study was conducted to characterize the kinetics of an anaerobic process (hydrolysis, acetogenesis, acidogenesis and methanogenesis) under thermophilic (55 °C) and mesophilic (35 °C) conditions with coffee grounds and waste activated sludge (WAS) as the substrates. Special focus was given to the kinetics of propionic acid degradation to elucidate the accumulation of VFAs. Under the thermophilic condition, the methane production rate of all substrates (WAS, ground coffee and raw coffee) was about 1.5 times higher than that under the mesophilic condition. However, the effects on methane production of each substrate under the thermophilic condition differed: WAS increased by 35.8-48.2%, raw coffee decreased by 76.3-64.5% and ground coffee decreased by 74.0-57.9%. Based on the maximum reaction rate (Rmax) of each anaerobic stage obtained from the modified Gompertz model, acetogenesis was found to be the rate-limiting step for coffee grounds and WAS. This can be explained by the kinetics of propionate degradation under thermophilic condition in which a long lag-phase (more than 18 days) was observed, although the propionate concentration was only 500 mg/L. Under the mesophilic condition, acidogenesis and hydrolysis were found to be the rate-limiting step for coffee grounds and WAS, respectively. Even though reducing the particle size accelerated the methane production rate of coffee grounds, but did not change the rate-limiting step: acetogenesis in thermophilic and acidogenesis in mesophilic. Copyright © 2014 Elsevier Ltd. All rights reserved.

Transient state kinetics of transcription elongation by T7 RNA polymerase.

PubMed

Anand, Vasanti Subramanian; Patel, Smita S

2006-11-24

The single subunit DNA-dependent RNA polymerase (RNAP) from bacteriophage T7 catalyzes both promoter-dependent transcription initiation and promoter-independent elongation. Using a promoter-free substrate, we have dissected the kinetic pathway of single nucleotide incorporation during elongation. We show that T7 RNAP undergoes a slow conformational change (0.01-0.03 s(-1)) to form an elongation competent complex with the promoter-free substrate (dissociation constant (Kd) of 96 nM). The complex binds to a correct NTP (Kd of 80 microM) and incorporates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C). An overall free energy change (-5.5 kcal/mol) and internal free energy change (-3.7 kcal/mol) of single NMP incorporation was calculated from the measured equilibrium constants. In the presence of inorganic pyrophosphate (PPi), the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 s(-1) with PPi Kd of 1.2 mM. Several experiments were designed to investigate the rate-limiting step in the pathway of single nucleotide addition. Acid-quench and pulse-chase kinetics indicated that an isomerization step before chemistry is rate-limiting. The very similar rate constants of sequential incorporation of two nucleotides indicated that the steps after chemistry are fast. Based on available data, we propose that the preinsertion to insertion isomerization of NTP observed in the crystallographic studies of T7 RNAP is a likely candidate for the rate-limiting step. The studies here provide a kinetic framework to investigate structure-function and fidelity of RNA synthesis and to further explore the role of the conformational change in nucleotide selection during RNA synthesis.

Validation of a single-stage fixed-rate step test for the prediction of maximal oxygen uptake in healthy adults.

PubMed

Hansen, Dominique; Jacobs, Nele; Thijs, Herbert; Dendale, Paul; Claes, Neree

2016-09-01

Healthcare professionals with limited access to ergospirometry remain in need of valid and simple submaximal exercise tests to predict maximal oxygen uptake (VO2max ). Despite previous validation studies concerning fixed-rate step tests, accurate equations for the estimation of VO2max remain to be formulated from a large sample of healthy adults between age 18-75 years (n > 100). The aim of this study was to develop a valid equation to estimate VO2max from a fixed-rate step test in a larger sample of healthy adults. A maximal ergospirometry test, with assessment of cardiopulmonary parameters and VO2max , and a 5-min fixed-rate single-stage step test were executed in 112 healthy adults (age 18-75 years). During the step test and subsequent recovery, heart rate was monitored continuously. By linear regression analysis, an equation to predict VO2max from the step test was formulated. This equation was assessed for level of agreement by displaying Bland-Altman plots and calculation of intraclass correlations with measured VO2max . Validity further was assessed by employing a Jackknife procedure. The linear regression analysis generated the following equation to predict VO2max (l min(-1) ) from the step test: 0·054(BMI)+0·612(gender)+3·359(body height in m)+0·019(fitness index)-0·012(HRmax)-0·011(age)-3·475. This equation explained 78% of the variance in measured VO2max (F = 66·15, P<0·001). The level of agreement and intraclass correlation was high (ICC = 0·94, P<0·001) between measured and predicted VO2max . From this study, a valid fixed-rate single-stage step test equation has been developed to estimate VO2max in healthy adults. This tool could be employed by healthcare professionals with limited access to ergospirometry. © 2015 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

Altering lipase activity and enantioselectivity in organic media using organo-soluble bases: Implication for rate-limiting proton transfer in acylation step.

PubMed

Chen, Chun-Chi; Chen, Teh-Liang; Tsai, Shau-Wei

2006-06-05

With the hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl esters via a partially purified papaya lipase (PCPL) in water-saturated isooctane as the model system, the enzyme activity, and enantioselectivty is altered by adding a variety of organo-soluble bases that act as either enzyme activators (i.e., TEA, MP, TOA, DPA, PY, and DMA) or enzyme inhibitors (i.e., PDP, DMAP, and PP). Triethylamine (TEA) is selected as the best enzyme activator as 2.24-fold increase of the initial rate for the (S)-ester is obtained when adding 120 mM of the base. By using an expanded Michaelis-Menten mechanism for the acylation step, the kinetic analysis indicates that the proton transfer for the breakdown of tetrahedral intermediates to acyl-enzyme intermediates is the rate-limiting step, or more sensitive than that for the formation of tetrahedral intermediates when the enzyme activators of different pKa are added. However, no correlation for the proton transfers in the acylation step is found when adding the bases acting as enzyme deactivators. Copyright 2006 Wiley Periodicals, Inc.

11S Storage globulin from pumpkin seeds: regularities of proteolysis by papain.

PubMed

Rudakova, A S; Rudakov, S V; Kakhovskaya, I A; Shutov, A D

2014-08-01

Limited proteolysis of the α- and β-chains and deep cleavage of the αβ-subunits by the cooperative (one-by-one) mechanism was observed in the course of papain hydrolysis of cucurbitin, an 11S storage globulin from seeds of the pumpkin Cucurbita maxima. An independent analysis of the kinetics of the limited and cooperative proteolyses revealed that the reaction occurs in two successive steps. In the first step, limited proteolysis consisting of detachments of short terminal peptides from the α- and β-chains was observed. The cooperative proteolysis, which occurs as a pseudo-first order reaction, started at the second step. Therefore, the limited proteolysis at the first step plays a regulatory role, impacting the rate of deep degradation of cucurbitin molecules by the cooperative mechanism. Structural alterations of cucurbitin induced by limited proteolysis are suggested to generate its susceptibility to cooperative proteolysis. These alterations are tentatively discussed on the basis of the tertiary structure of the cucurbitin subunit pdb|2EVX in comparison with previously obtained data on features of degradation of soybean 11S globulin hydrolyzed by papain.

Uncovering the Atomistic Mechanism for Calcite Step Growth

DOE PAGES

De La Pierre, Marco; Raiteri, Paolo; Stack, Andrew G.; ...

2017-04-13

Determining a complete atomic-level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO 3) in water, computer simulations have been used in this paper to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca 2+ only adsorbs after CO 3 2-. In contrast to the conventional picture, ion pairs prefer to bind at themore » upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Finally, migration of the first carbonate ion to a growth site is found to be rate-limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.« less

Retinoic acid biosynthesis catalyzed by retinal dehydrogenases relies on a rate-limiting conformational transition associated with substrate recognition

PubMed Central

Bchini, Raphaël; Vasiliou, Vasilis; Branlant, Guy; Talfournier, François; Rahuel-Clermont, Sophie

2012-01-01

Retinoic acid (RA), a metabolite of vitamin A, exerts pleiotropic effects throughout life in vertebrate organisms. Thus, RA action must be tightly regulated through the coordinated action of biosynthetic and degradating enzymes. The last step of retinoic acid biosynthesis is irreversibly catalyzed by the NAD-dependent retinal dehydrogenases (RALDH), which are members of the aldehyde dehydrogenase (ALDH) superfamily. Low intracellular retinal concentrations imply efficient substrate molecular recognition to ensure high affinity and specificity of RALDHs for retinal. This study addresses the molecular basis of retinal recognition in human ALDH1A1 (or RALDH1) and rat ALDH1A2 (or RALDH2), through the comparison of the catalytic behavior of retinal analogs and use of the fluorescence properties of retinol. We show that, in contrast to long chain unsaturated substrates, the rate-limiting step of retinal oxidation by RALDHs is associated with acylation. Use of the fluorescence resonance energy transfer upon retinol interaction with RALDHs provides evidence that retinal recognition occurs in two steps: binding into the substrate access channel, and a slower structural reorganization with a rate constant of the same magnitude as the kcat for retinal oxidation: 0.18 vs. 0.07 s−1 and 0.25 vs. 0.1 s−1 for ALDH1A1 and ALDH1A2, respectively. This suggests that the conformational transition of the RALDH-retinal complex significantly contributes to the rate-limiting step that controls the kinetics of retinal oxidation, as a prerequisite for the formation of a catalytically competent Michaelis complex. This conclusion is consistent with the general notion that structural flexibility within the active site of ALDH enzymes has been shown to be an integral component of catalysis. PMID:23220587

Breastfeeding Practices and Barriers to Implementing the Ten Steps to Successful Breastfeeding in Mississippi Hospitals.

PubMed

Alakaam, Amir; Lemacks, Jennifer; Yadrick, Kathleen; Connell, Carol; Choi, Hwanseok Winston; Newman, Ray G

2018-05-01

Mississippi has the lowest rates of breastfeeding in the United States at 6 and 12 months. There is growing evidence that the rates and duration of infant breastfeeding improve after hospitals implement the Ten Steps to Successful Breastfeeding; moreover, the Ten Steps approach is considered the standard model for evaluation of breastfeeding practices in birthplaces. Research aim: This study aimed to examine the implementation level of the Ten Steps and identify barriers to implementing the Ten Steps in Mississippi hospitals. A cross-sectional self-report survey was used to answer the research aim. Nurse managers of the birthing and maternity units of all 43 Mississippi hospitals that provided birthing and maternity care were recruited. A response rate of 72% ( N = 31) was obtained. Implementation of the Ten Steps in these hospitals was categorized as low, partial, moderate, or high. The researcher classified implementation in 29% of hospitals as moderate and in 71% as partial. The hospital level of implementation was significantly positively associated with the hospital delivery rate along with the hospital cesarean section rate per year. The main barriers for the implementation process of the Ten Steps reported were resistance to new policies, limited financial and human resources, and lack of support from national and state governments. Breastfeeding practices in Mississippi hospitals need to be improved. New policies need to be established in Mississippi to encourage hospitals to adopt the Ten Steps policies and practice in the maternity and birthing units.

Force generation and temperature-jump and length-jump tension transients in muscle fibers.

PubMed Central

Davis, J S; Rodgers, M E

1995-01-01

Muscle tension rises with increasing temperature. The kinetics that govern the tension rise of maximally Ca(2+)-activated, skinned rabbit psoas fibers over a temperature range of 0-30 degrees C was characterized in laser temperature-jump experiments. The kinetic response is simple and can be readily interpreted in terms of a basic three-step mechanism of contraction, which includes a temperature-sensitive rapid preequilibrium(a) linked to a temperature-insensitive rate-limiting step and followed by a temperature-sensitive tension-generating step. These data and mechanism are compared and contrasted with the more complex length-jump Huxley-Simmons phases in which all states that generate tension or bear tension are perturbed. The rate of the Huxley-Simmons phase 4 is temperature sensitive at low temperatures but plateaus at high temperatures, indicating a change in rate-limiting step from a temperature-sensitive (phase 4a) to a temperature-insensitive reaction (phase 4b); the latter appears to correlate with the slow, temperature-insensitive temperature-jump relaxation. Phase 3 is absent in the temperature-jump, which excludes it from tension generation. We confirm that de novo tension generation occurs as an order-disorder transition during phase 2slow and the equivalent, temperature-sensitive temperature-jump relaxation. PMID:7612845

Differences in the catalytic mechanisms of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures.

PubMed

Zaccardi, Margot J; Mannweiler, Olga; Boehr, David D

2012-02-10

Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An alternative hypothesis, however, is that complementary thermophilic-mesophilic enzyme pairs simply operate through different evolutionary-optimized catalytic mechanisms. In this communication, we present evidence that while the steps of the catalytic mechanisms for mesophilic and thermophilic indole-3-glycerol phosphate synthase (IGPS) enzymes are fundamentally similar, the identity of the rate-determining step changes as a function of temperature. Our findings indicate that while product release is rate-determining at 25°C for thermophilic IGPS, near its adaptive temperature (75°C), a proton transfer event, involving a general acid, becomes rate-determining. The rate-determining steps for thermophilic and mesophilic IGPS enzymes are also different at their respective, adaptive temperatures with the mesophilic IGPS-catalyzed reaction being rate-limited before irreversible CO2 release, and the thermophilic IGPS-catalyzed reaction being rate limited afterwards. Copyright © 2012 Elsevier Inc. All rights reserved.

Niche filling slows the diversification of Himalayan songbirds.

PubMed

Price, Trevor D; Hooper, Daniel M; Buchanan, Caitlyn D; Johansson, Ulf S; Tietze, D Thomas; Alström, Per; Olsson, Urban; Ghosh-Harihar, Mousumi; Ishtiaq, Farah; Gupta, Sandeep K; Martens, Jochen; Harr, Bettina; Singh, Pratap; Mohan, Dhananjai

2014-05-08

Speciation generally involves a three-step process--range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.

Physiological Response of Plants Grown on Porous Ceramic Tubes

NASA Technical Reports Server (NTRS)

Tsao, David; Okos, Martin

1997-01-01

This research involves the manipulation of the root-zone water potential for the purposes of discriminating the rate limiting step in the inorganic nutrient uptake mechanism utilized by higher plants. This reaction sequence includes the pathways controlled by the root-zone conditions such as water tension and gradient concentrations. Furthermore, plant based control mechanisms dictated by various protein productions are differentiated as well. For the nutrients limited by the environmental availability, the kinetics were modeled using convection and diffusion equations. Alternatively, for the nutrients dependent upon enzyme manipulations, the uptakes are modeled using Michaelis-Menten kinetics. In order to differentiate between these various mechanistic steps, an experimental apparatus known as the Porous Ceramic Tube - Nutrient Delivery System (PCT-NDS) was used. Manipulation of the applied suction pressure circulating a nutrient solution through this system imposes a change in the matric component of the water potential. This compensates for the different osmotic components of water potential dictated by nutrient concentration. By maintaining this control over the root-zone conditions, the rate limiting steps in the uptake of the essential nutrients into tomato plants (Lycopersicon esculentum cv. Cherry Elite) were differentiated. Results showed that the uptake of some nutrients were mass transfer limited while others were limited by the enzyme kinetics. Each of these were adequately modeled with calculations and discussions of the parameter estimations provided.

Implementation of Time-Resolved Step-Scan Fourier Transform Infrared (FT-IR) Spectroscopy Using a kHz Repetition Rate Pump Laser

PubMed Central

MAGANA, DONNY; PARUL, DZMITRY; DYER, R. BRIAN; SHREVE, ANDREW P.

2011-01-01

Time-resolved step-scan Fourier transform infrared (FT-IR) spectroscopy has been shown to be invaluable for studying excited-state structures and dynamics in both biological and inorganic systems. Despite the established utility of this method, technical challenges continue to limit the data quality and more wide ranging applications. A critical problem has been the low laser repetition rate and interferometer stepping rate (both are typically 10 Hz) used for data acquisition. Here we demonstrate significant improvement in the quality of time-resolved spectra through the use of a kHz repetition rate laser to achieve kHz excitation and data collection rates while stepping the spectrometer at 200 Hz. We have studied the metal-to-ligand charge transfer excited state of Ru(bipyridine)3Cl2 in deuterated acetonitrile to test and optimize high repetition rate data collection. Comparison of different interferometer stepping rates reveals an optimum rate of 200 Hz due to minimization of long-term baseline drift. With the improved collection efficiency and signal-to-noise ratio, better assignments of the MLCT excited-state bands can be made. Using optimized parameters, carbonmonoxy myoglobin in deuterated buffer is also studied by observing the infrared signatures of carbon monoxide photolysis upon excitation of the heme. We conclude from these studies that a substantial increase in performance of ss-FT-IR instrumentation is achieved by coupling commercial infrared benches with kHz repetition rate lasers. PMID:21513597

Probing the mechanism of proton coupled electron transfer to dioxygen: the oxidative half-reaction of bovine serum amine oxidase.

PubMed

Su, Q; Klinman, J P

1998-09-08

Bovine serum amine oxidase (BSAO) catalyzes the oxidative deamination of primary amines, concomitant with the reduction of molecular oxygen to hydrogen peroxide via a ping-pong mechanism. A protocol has been developed for an analysis of chemical and kinetic mechanisms in the conversion of dioxygen to hydrogen peroxide. Steady-state kinetics show that two groups need to be deprotonated to facilitate the oxidative half-reaction. The pH dependence of Vmax/Km(O2) reveals pKa's of 6.2 +/- 0.3 and 7.0 +/- 0.2, respectively. A pKa of 7.2 +/- 0.1 has been obtained from a titration of anaerobically reduced BSAO using UV-vis spectrophotometry. The near identity of the pKa obtained from the reduced enzyme titration with the second pKa from steady-state kinetics suggests that this second pKa arises from the reduced cofactor. The assignment of pKa is supported by the observed pH dependence for formation of the cofactor semiquinone signal, detected by EPR spectroscopy under anaerobic conditions. To address the nature of rate-limiting steps in the oxidative half-reaction, the solvent isotope effect, viscosity effect, and O-18 isotope effect on Vmax/Km(O2) have been determined. The solvent isotope effect is indistinguishable from unity, ruling out a proton transfer as a rate-determining step. Use of glucose as a solvent viscosogen shows no viscosity effect, indicating that binding of oxygen is not in the rate-determining step. The O-18 kinetic isotope effect is independent of pH with an average value of 18(V/K) = 1.0097 +/- 0. 0010. This has been compared to calculated equilibrium O-18 isotope effects for various dioxygen intermediate species [Tian and Klinman (1993) J. Am. Chem. Soc. 115, 8891], leading to the conclusion that either the first electron transfer to dioxygen or the desorption of product peroxide from a Cu(II)-OOH complex could be the rate-limiting step. The distribution of steady-state enzyme species was, therefore, analyzed through a combination of stopped-flow experiments and analysis of DV and D(V/K) for benzylamine oxidation. We conclude that the major species accumulating in the steady state are the oxidized cofactor-substrate Schiff base complex and the reduced, aminoquinol form of cofactor. These data rule out a slow release of product hydroperoxide from the aminoquinone form of enzyme, leading to the conclusion that the first electron transfer from substrate-reduced cofactor to dioxygen is the rate-determining step in the oxidative half-reaction. This step is also estimated to be 40% rate-limiting in kcat. An important mechanistic conclusion from this study is that dioxygen binding is a separate step from the rate-limiting electron-transfer step to form superoxide. On the basis of a recently determined X-ray structure for the active form of a yeast amine oxidase from Hansenula polymorpha [Li et al. (1998) Structure 6, 293], a hydrophobic space has been identified near the O-2 position of reduced cofactor as the putative dioxygen binding site. Movement of superoxide from this site onto the Cu(II) at the active site may occur prior to further electron transfer from cofactor to superoxide.

Exploring the energy landscape for Q(A)(-) to Q(B) electron transfer in bacterial photosynthetic reaction centers: effect of substrate position and tail length on the conformational gating step.

PubMed

Xu, Qiang; Baciou, Laura; Sebban, Pierre; Gunner, M R

2002-08-06

The ability to initiate reactions with a flash of light and to monitor reactions over a wide temperature range allows detailed analysis of reaction mechanisms in photosynthetic reaction centers (RCs) of purple bacteria. In this protein, the electron transfer from the reduced primary quinone (Q(A)(-)) to the secondary quinone (Q(B)) is rate-limited by conformational changes rather than electron tunneling. Q(B) movement from a distal to a proximal site has been proposed to be the rate-limiting change. The importance of quinone motion was examined by shortening the Q(B) tail from 50 to 5 carbons. No change in rate was found from 100 to 300 K. The temperature dependence of the rate was also measured in three L209 proline mutants. Under conditions where Q(B) is in the distal site in wild-type RCs, it is trapped in the proximal site in the Tyr L209 mutant [Kuglstatter, A., et al. (2001) Biochemistry 40, 4253-4260]. The electron transfer slows at low temperature for all three mutants as it does in wild-type protein, indicating that conformational changes still limit the reaction rate. Thus, Q(B) movement is unlikely to be the sole, rate-limiting conformational gating step. The temperature dependence of the reaction in the L209 mutants differs somewhat from wild-type RCs. Entropy-enthalpy compensation reduces the difference in rates and free energy changes at room temperature.

Examining attrition rates at one specialty addiction treatment provider in the United States: a case study using a retrospective chart review.

PubMed

Loveland, David; Driscoll, Hilary

2014-09-25

Engaging individuals who have a substance use disorder (SUD) in treatment continues to be a challenge for the specialty addiction treatment field. Research has consistently revealed high rates of missed appointments at each step of the enrollment process: 1. between calling for services and assessment, 2. between assessment and enrollment, and 3. between enrollment and completion of treatment. Extensive research has examined each step of the process; however, there is limited research examining the overall attrition rate across all steps. A single case study of a specialty addiction treatment agency was used to examine the attrition rates across the first three steps of the enrollment process. Attrition rates were tracked between August 1, 2011 and July 31, 2012. The cohort included 1822 unique individuals who made an initial request for addiction treatment services. Monthly retrospective reviews of medical records, phone logs, and billing data were used to calculate attrition rates. Attrition rates reported in the literature were collected and compared to the rates found at the target agency. Median time between request for treatment and assessment was 6 days (mean 7.5) and between assessment and treatment enrollment was 8 days (mean 12.5). An overall attrition rate of 80% was observed, including 45% between call and assessment, 32% between assessment and treatment enrollment (another 17% could not be determined), and 37% left or were removed from treatment before 30 days. Women were less likely to complete 30 days of treatment compared to men. No other demographics were related to attrition rates. One out of every five people who requested treatment completed a minimum of 30 days of a treatment. The attrition rate was high, yet similar to rates noted in the literature. Limitations of the single case study are noted. Attrition rates in the U.S. are high with approximately 75% to 80% of treatment seekers disengaging at one of the multiple stages of the enrollment and treatment process. Significant changes in the system are needed to improve engagement rates.

Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

Treesearch

J.S. Norman; J.E. Barrett

2014-01-01

Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

Influence of redox mediators and salinity level on the (bio)transformation of Direct Blue 71: kinetics aspects.

PubMed

Alvarez, Luis H; Meza-Escalante, Edna R; Gortáres-Moroyoqui, Pablo; Morales, Luz; Rosas, Krystal; García-Reyes, Bernardo; García-González, Alicone

2016-12-01

The rate-limiting step of azo dye decolorization was elucidated by exploring the microbial reduction of a model quinone and the chemical decolorization by previously reduced quinone at different salinity conditions (2-8%). Microbial experiments were performed in batch with a marine consortium. The decolorization of Direct Blue 71 (DB71) by the marine consortium at 2% salinity, mediated with anthraquinone-2,6-disulfonate (AQDS), showed the highest rate of decolorization as compared with those obtained with riboflavin, and two samples of humic acids. Moreover, the incubations at different salinity conditions (0-8%) performed with AQDS showed that the highest rate of decolorization of DB71 by the marine consortium occurred at 2% and 4% salinity. In addition, the highest microbial reduction rate of AQDS occurred in incubations at 0%, 2%, and 4% of salinity. The chemical reduction of DB71 by reduced AQDS occurred in two stages and proceeded faster at 4% and 6% salinity. The results indicate that the rate-limiting step during azo decolorization was the microbial reduction of AQDS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving the Accuracy of the Chebyshev Rational Approximation Method Using Substeps

DOE PAGES

Isotalo, Aarno; Pusa, Maria

2016-05-01

The Chebyshev Rational Approximation Method (CRAM) for solving the decay and depletion of nuclides is shown to have a remarkable decrease in error when advancing the system with the same time step and microscopic reaction rates as the previous step. This property is exploited here to achieve high accuracy in any end-of-step solution by dividing a step into equidistant sub-steps. The computational cost of identical substeps can be reduced significantly below that of an equal number of regular steps, as the LU decompositions for the linear solves required in CRAM only need to be formed on the first substep. Themore » improved accuracy provided by substeps is most relevant in decay calculations, where there have previously been concerns about the accuracy and generality of CRAM. Lastly, with substeps, CRAM can solve any decay or depletion problem with constant microscopic reaction rates to an extremely high accuracy for all nuclides with concentrations above an arbitrary limit.« less

Bed crisis and elective surgery late cancellations: An approach using the theory of constraints.

PubMed

Sahraoui, Abderrazak; Elarref, Mohamed

2014-01-01

Late cancellations of scheduled elective surgery limit the ability of the surgical care service to achieve its goals. Attributes of these cancellations differ between hospitals and regions. The rate of late cancellations of elective surgery conducted in Hamad General Hospital, Doha, Qatar was found to be 13.14% which is similar to rates reported in hospitals elsewhere in the world; although elective surgery is performed six days a week from 7:00 am to 10:00 pm in our hospital. Simple and systematic analysis of these attributes typically provides limited solutions to the cancellation problem. Alternatively, the application of the theory of constraints with its five focusing steps, which analyze the system in its totality, is more likely to provide a better solution to the cancellation problem. To find the constraint, as a first focusing step, we carried out a retrospective and descriptive study using a quantitative approach combined with the Pareto Principle to find the main causes of cancellations, followed by a qualitative approach to find the main and ultimate underlying cause which pointed to the bed crisis. The remaining four focusing steps provided workable and effective solutions to reduce the cancellation rate of elective surgery.

Bed crisis and elective surgery late cancellations: An approach using the theory of constraints

PubMed Central

Sahraoui, Abderrazak; Elarref, Mohamed

2014-01-01

Late cancellations of scheduled elective surgery limit the ability of the surgical care service to achieve its goals. Attributes of these cancellations differ between hospitals and regions. The rate of late cancellations of elective surgery conducted in Hamad General Hospital, Doha, Qatar was found to be 13.14% which is similar to rates reported in hospitals elsewhere in the world; although elective surgery is performed six days a week from 7:00 am to 10:00 pm in our hospital. Simple and systematic analysis of these attributes typically provides limited solutions to the cancellation problem. Alternatively, the application of the theory of constraints with its five focusing steps, which analyze the system in its totality, is more likely to provide a better solution to the cancellation problem. To find the constraint, as a first focusing step, we carried out a retrospective and descriptive study using a quantitative approach combined with the Pareto Principle to find the main causes of cancellations, followed by a qualitative approach to find the main and ultimate underlying cause which pointed to the bed crisis. The remaining four focusing steps provided workable and effective solutions to reduce the cancellation rate of elective surgery. PMID:25320686

Organizational Factors and the Cancer Screening Process

PubMed Central

Zapka, Jane; Edwards, Heather; Taplin, Stephen H.

2010-01-01

Cancer screening is a process of care consisting of several steps and interfaces. This article reviews what is known about the association between organizational factors and cancer screening rates and examines how organizational strategies can address the steps and interfaces of cancer screening in the context of both intraorganizational and interorganizational processes. We reviewed 79 studies assessing the relationship between organizational factors and cancer screening. Screening rates are largely driven by strategies to 1) limit the number of interfaces across organizational boundaries; 2) recruit patients, promote referrals, and facilitate appointment scheduling; and 3) promote continuous patient care. Optimal screening rates can be achieved when health-care organizations tailor strategies to the steps and interfaces in the cancer screening process that are most critical for their organizations, the providers who work within them, and the patients they serve. PMID:20386053

Organizational factors and the cancer screening process.

PubMed

Anhang Price, Rebecca; Zapka, Jane; Edwards, Heather; Taplin, Stephen H

2010-01-01

Cancer screening is a process of care consisting of several steps and interfaces. This article reviews what is known about the association between organizational factors and cancer screening rates and examines how organizational strategies can address the steps and interfaces of cancer screening in the context of both intraorganizational and interorganizational processes. We reviewed 79 studies assessing the relationship between organizational factors and cancer screening. Screening rates are largely driven by strategies to 1) limit the number of interfaces across organizational boundaries; 2) recruit patients, promote referrals, and facilitate appointment scheduling; and 3) promote continuous patient care. Optimal screening rates can be achieved when health-care organizations tailor strategies to the steps and interfaces in the cancer screening process that are most critical for their organizations, the providers who work within them, and the patients they serve.

Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions

NASA Astrophysics Data System (ADS)

Karaman, Rafik; Ghareeb, Hiba; Dajani, Khuloud Kamal; Scrano, Laura; Hallak, Hussein; Abu-Lafi, Saleh; Mecca, Gennaro; Bufo, Sabino A.

2013-07-01

Based on density functional theory (DFT) calculations for the acid-catalyzed hydrolysis of several maleamic acid amide derivatives four tranexamic acid prodrugs were designed. The DFT results on the acid catalyzed hydrolysis revealed that the reaction rate-limiting step is determined on the nature of the amine leaving group. When the amine leaving group was a primary amine or tranexamic acid moiety, the tetrahedral intermediate collapse was the rate-limiting step, whereas in the cases by which the amine leaving group was aciclovir or cefuroxime the rate-limiting step was the tetrahedral intermediate formation. The linear correlation between the calculated DFT and experimental rates for N-methylmaleamic acids 1- 7 provided a credible basis for designing tranexamic acid prodrugs that have the potential to release the parent drug in a sustained release fashion. For example, based on the calculated B3LYP/6-31G(d,p) rates the predicted t1/2 (a time needed for 50 % of the prodrug to be converted into drug) values for tranexamic acid prodrugs ProD 1- ProD 4 at pH 2 were 556 h [50.5 h as calculated by B3LYP/311+G(d,p)] and 6.2 h as calculated by GGA: MPW1K), 253 h, 70 s and 1.7 h, respectively. Kinetic study on the interconversion of the newly synthesized tranexamic acid prodrug ProD 1 revealed that the t1/2 for its conversion to the parent drug was largely affected by the pH of the medium. The experimental t1/2 values in 1 N HCl, buffer pH 2 and buffer pH 5 were 54 min, 23.9 and 270 h, respectively.

Kinetic coupling of phosphate release, force generation and rate-limiting steps in the cross-bridge cycle.

PubMed

Stehle, Robert; Tesi, Chiara

2017-08-01

A basic goal in muscle research is to understand how the cyclic ATPase activity of cross-bridges is converted into mechanical force. A direct approach to study the chemo-mechanical coupling between P i release and the force-generating step is provided by the kinetics of force response induced by a rapid change in [P i ]. Classical studies on fibres using caged-P i discovered that rapid increases in [P i ] induce fast force decays dependent on final [P i ] whose kinetics were interpreted to probe a fast force-generating step prior to P i release. However, this hypothesis was called into question by studies on skeletal and cardiac myofibrils subjected to P i jumps in both directions (increases and decreases in [P i ]) which revealed that rapid decreases in [P i ] trigger force rises with slow kinetics, similar to those of calcium-induced force development and mechanically-induced force redevelopment at the same [P i ]. A possible explanation for this discrepancy came from imaging of individual sarcomeres in cardiac myofibrils, showing that the fast force decay upon increase in [P i ] results from so-called sarcomere 'give'. The slow force rise upon decrease in [P i ] was found to better reflect overall sarcomeres cross-bridge kinetics and its [P i ] dependence, suggesting that the force generation coupled to P i release cannot be separated from the rate-limiting transition. The reasons for the different conclusions achieved in fibre and myofibril studies are re-examined as the recent findings on cardiac myofibrils have fundamental consequences for the coupling between P i release, rate-limiting steps and force generation. The implications from P i -induced force kinetics of myofibrils are discussed in combination with historical and recent models of the cross-bridge cycle.

Can quantum transition state theory be defined as an exact t = 0+ limit?

NASA Astrophysics Data System (ADS)

Jang, Seogjoo; Voth, Gregory A.

2016-02-01

The definition of the classical transition state theory (TST) as a t → 0+ limit of the flux-side time correlation function relies on the assumption that simultaneous measurement of population and flux is a well defined physical process. However, the noncommutativity of the two measurements in quantum mechanics makes the extension of such a concept to the quantum regime impossible. For this reason, quantum TST (QTST) has been generally accepted as any kind of quantum rate theory reproducing the TST in the classical limit, and there has been a broad consensus that no unique QTST retaining all the properties of TST can be defined. Contrary to this widely held view, Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)] recently suggested that a true QTST can be defined as the exact t → 0+ limit of a certain kind of quantum flux-side time correlation function and that it is equivalent to the ring polymer molecular dynamics (RPMD) TST. This work seeks to question and clarify certain assumptions underlying these suggestions and their implications. First, the time correlation function used by HA as a starting expression is not related to the kinetic rate constant by virtue of linear response theory, which is the first important step in relating a t = 0+ limit to a physically measurable rate. Second, a theoretical analysis calls into question a key step in HA's proof which appears not to rely on an exact quantum mechanical identity. The correction of this makes the true t = 0+ limit of HA's QTST different from the RPMD-TST rate expression, but rather equal to the well-known path integral quantum transition state theory rate expression for the case of centroid dividing surface. An alternative quantum rate expression is then formulated starting from the linear response theory and by applying a recently developed formalism of real time dynamics of imaginary time path integrals [S. Jang, A. V. Sinitskiy, and G. A. Voth, J. Chem. Phys. 140, 154103 (2014)]. It is shown that the t → 0+ limit of the new rate expression vanishes in the exact quantum limit.

Rate-limiting steps of stereochemistry retaining ß-D-xylosidase from Geobacillus stearothermophilus acting as substrates

USDA-ARS?s Scientific Manuscript database

Kinetic experiments of GSXynB2, a ß-xylosidase, acting on 2-nitrophenyl-ß-D-xylopyranoside (2NPX), 4-nitrophenyl-ß-D-xylopyranoside (4NPX), 4-methylumbelliferyl-ß-D-xylopyanoside (MuX) and xylobiose (X2) were conducted at pH 7.0 and 25 °C. Catalysis proceeds in two steps: E + substrate TO E-xylose ...

Step-by-step design of a single phase 3.3 kV/200 a resistive type superconducting fault current limiter (R-SFCL) and cryostat

NASA Astrophysics Data System (ADS)

Kar, Soumen; Rao, V. V.

2018-07-01

In our first attempt to design a single phase R-SFCL in India, we have chosen the typical rating of a medium voltage level (3.3 kVrms, 200 Arms, 1Φ) R-SFCL. The step-by-step design procedure for the R-SFCL involves conductor selection, time dependent electro-thermal simulations and recovery time optimization after fault removal. In the numerical analysis, effective fault limitation for a fault current of 5 kA for the medium voltage level R-SFCL are simulated. Maximum normal state resistance and maximum temperature rise in the SFCL coil during current limitation are estimated using one-dimensional energy balance equation. Further, a cryogenic system is conceptually designed for aforesaid MV level R-SFCL by considering inner and outer vessel materials, wall-thickness and thermal insulation which can be used for R-SFCL system. Finally, the total thermal load is calculated for the designed R-SFCL cryostat to select a suitable cryo-refrigerator for LN2 re-condensation.

Nonaqueous electrocatalytic water oxidation by a surface-bound Ru(bda)(L)₂ complex.

PubMed

Sheridan, Matthew V; Sherman, Benjamin D; Wee, Kyung-Ryang; Marquard, Seth L; Gold, Alexander S; Meyer, Thomas J

2016-04-21

The rate of electrocatalytic water oxidation by the heterogeneous water oxidation catalyst [Ru(bda)(4-O(CH2)3P(O3H2)2-pyr)2], , (pyr = pyridine; bda = 2,2'-bipyridine-6,6'-dicarboxylate) on metal oxide surfaces is greatly enhanced relative to water as the solvent. In these experiments with propylene carbonate (PC) as the nonaqueous solvent, water is the limiting reagent. Mechanistic studies point to atom proton transfer (APT) as the rate limiting step in water oxidation catalysis.

Extravascular transport in normal and tumor tissues.

PubMed

Jain, R K; Gerlowski, L E

1986-01-01

The transport characteristics of the normal and tumor tissue extravascular space provide the basis for the determination of the optimal dosage and schedule regimes of various pharmacological agents in detection and treatment of cancer. In order for the drug to reach the cellular space where most therapeutic action takes place, several transport steps must first occur: (1) tissue perfusion; (2) permeation across the capillary wall; (3) transport through interstitial space; and (4) transport across the cell membrane. Any of these steps including intracellular events such as metabolism can be the rate-limiting step to uptake of the drug, and these rate-limiting steps may be different in normal and tumor tissues. This review examines these transport limitations, first from an experimental point of view and then from a modeling point of view. Various types of experimental tumor models which have been used in animals to represent human tumors are discussed. Then, mathematical models of extravascular transport are discussed from the prespective of two approaches: compartmental and distributed. Compartmental models lump one or more sections of a tissue or body into a "compartment" to describe the time course of disposition of a substance. These models contain "effective" parameters which represent the entire compartment. Distributed models consider the structural and morphological aspects of the tissue to determine the transport properties of that tissue. These distributed models describe both the temporal and spatial distribution of a substance in tissues. Each of these modeling techniques is described in detail with applications for cancer detection and treatment in mind.

The Determination of Rate-Limiting Steps during Soot Formation

DTIC Science & Technology

1990-06-08

and a CH3N precursor of acetonitrile such as 2H-aziridine although other intermediates of lower energy such as ketenimine have been identified on the...precursor of acetonitrile such as 2H-aziridine or ketenimine . Experimentally it was found that the overall rate of disappearance of pyrrole is first order

Some considerations in the combustion of AP/composite propellants

NASA Technical Reports Server (NTRS)

Kumar, R. N.

1972-01-01

Theoretical studies are presented on the time-independent and oscillatory combustion of nonmetallized AP/composite propellants. Three hypotheses are introduced: (1) The extent of propellant degradation at the vaporization step has to be specified through a scientific criterion. (2) The condensed phase degradation reaction of ammonium perchlorate to a vaporizable state is the overall rate-limiting step. (3) Gas phase combustion rate is controlled by the mixing rate of fuel and oxidizer vapors. In the treatment of oscillatory combustion, the assumption of quasi-steady fluctuations in the gas phase is used to supplement these hypotheses. In comparison with experimental data, this study predicts several of the observations including a few that remain inconsistent with theoretical results.

Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution.

PubMed

Piana, Stefano; Gale, Julian D

2005-02-16

Both the dissolution and growth of a molecular crystalline material, urea, has been studied using dynamical atomistic simulation. The kinetic steps of dissolution and growth are clearly identified, and the activation energies for each possible step are calculated. Our molecular dynamics simulations indicate that crystal growth on the [001] face is characterized by a nucleation and growth mechanism. Nucleation on the [001] urea crystal face is predicted to occur at a very high rate, followed by rapid propagation of the steps. The rate-limiting step for crystallization is actually found to be the removal of surface defects, rather than the initial formation of the next surface layer. Through kinetic Monte Carlo modeling of the surface growth, it is found that this crystal face evolves via a rough surface topography, rather than a clean layer-by-layer mechanism.

HVS-based quantization steps for validation of digital cinema extended bitrates

NASA Astrophysics Data System (ADS)

Larabi, M.-C.; Pellegrin, P.; Anciaux, G.; Devaux, F.-O.; Tulet, O.; Macq, B.; Fernandez, C.

2009-02-01

In Digital Cinema, the video compression must be as transparent as possible to provide the best image quality to the audience. The goal of compression is to simplify transport, storing, distribution and projection of films. For all those tasks, equipments need to be developed. It is thus mandatory to reduce the complexity of the equipments by imposing limitations in the specifications. In this sense, the DCI has fixed the maximum bitrate for a compressed stream to 250 Mbps independently from the input format (4K/24fps, 2K/48fps or 2K/24fps). The work described in this paper This parameter is discussed in this paper because it is not consistent to double/quadruple the input rate without increasing the output rate. The work presented in this paper is intended to define quantization steps ensuring the visually lossless compression. Two steps are followed first to evaluate the effect of each subband separately and then to fin the scaling ratio. The obtained results show that it is necessary to increase the bitrate limit for cinema material in order to achieve the visually lossless.

In Situ Graphene Growth Dynamics on Polycrystalline Catalyst Foils

PubMed Central

2016-01-01

The dynamics of graphene growth on polycrystalline Pt foils during chemical vapor deposition (CVD) are investigated using in situ scanning electron microscopy and complementary structural characterization of the catalyst with electron backscatter diffraction. A general growth model is outlined that considers precursor dissociation, mass transport, and attachment to the edge of a growing domain. We thereby analyze graphene growth dynamics at different length scales and reveal that the rate-limiting step varies throughout the process and across different regions of the catalyst surface, including different facets of an individual graphene domain. The facets that define the domain shapes lie normal to slow growth directions, which are determined by the interfacial mobility when attachment to domain edges is rate-limiting, as well as anisotropy in surface diffusion as diffusion becomes rate-limiting. Our observations and analysis thus reveal that the structure of CVD graphene films is intimately linked to that of the underlying polycrystalline catalyst, with both interfacial mobility and diffusional anisotropy depending on the presence of step edges and grain boundaries. The growth model developed serves as a general framework for understanding and optimizing the growth of 2D materials on polycrystalline catalysts. PMID:27576749

Oxidation-driven surface dynamics on NiAl(100)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Hailang; Chen, Xidong; Li, Liang

Atomic steps, a defect common to all crystal surfaces, can play an important role in many physical and chemical processes. However, attempts to predict surface dynamics under nonequilibrium conditions are usually frustrated by poor knowledge of the atomic processes of surface motion arising from mass transport from/to surface steps. Using low-energy electron microscopy that spatially and temporally resolves oxide film growth during the oxidation of NiAl(100) we demonstrate that surface steps are impermeable to oxide film growth. The advancement of the oxide occurs exclusively on the same terrace and requires the coordinated migration of surface steps. The resulting piling upmore » of surface steps ahead of the oxide growth front progressively impedes the oxide growth. This process is reversed during oxide decomposition. The migration of the substrate steps is found to be a surface-step version of the well-known Hele-Shaw problem, governed by detachment (attachment) of Al atoms at step edges induced by the oxide growth (decomposition). As a result, by comparing with the oxidation of NiAl(110) that exhibits unimpeded oxide film growth over substrate steps, we suggest that whenever steps are the source of atoms used for oxide growth they limit the oxidation process; when atoms are supplied from the bulk, the oxidation rate is not limited by the motion of surface steps.« less

Oxidation-driven surface dynamics on NiAl(100)

DOE PAGES

Qin, Hailang; Chen, Xidong; Li, Liang; ...

2014-12-29

Atomic steps, a defect common to all crystal surfaces, can play an important role in many physical and chemical processes. However, attempts to predict surface dynamics under nonequilibrium conditions are usually frustrated by poor knowledge of the atomic processes of surface motion arising from mass transport from/to surface steps. Using low-energy electron microscopy that spatially and temporally resolves oxide film growth during the oxidation of NiAl(100) we demonstrate that surface steps are impermeable to oxide film growth. The advancement of the oxide occurs exclusively on the same terrace and requires the coordinated migration of surface steps. The resulting piling upmore » of surface steps ahead of the oxide growth front progressively impedes the oxide growth. This process is reversed during oxide decomposition. The migration of the substrate steps is found to be a surface-step version of the well-known Hele-Shaw problem, governed by detachment (attachment) of Al atoms at step edges induced by the oxide growth (decomposition). As a result, by comparing with the oxidation of NiAl(110) that exhibits unimpeded oxide film growth over substrate steps, we suggest that whenever steps are the source of atoms used for oxide growth they limit the oxidation process; when atoms are supplied from the bulk, the oxidation rate is not limited by the motion of surface steps.« less

Chemical reactions at aqueous interfaces

NASA Astrophysics Data System (ADS)

Vecitis, Chad David

2009-12-01

Interfaces or phase boundaries are a unique chemical environment relative to individual gas, liquid, or solid phases. Interfacial reaction mechanisms and kinetics are often at variance with homogeneous chemistry due to mass transfer, molecular orientation, and catalytic effects. Aqueous interfaces are a common subject of environmental science and engineering research, and three environmentally relevant aqueous interfaces are investigated in this thesis: 1) fluorochemical sonochemistry (bubble-water), 2) aqueous aerosol ozonation (gas-water droplet), and 3) electrolytic hydrogen production and simultaneous organic oxidation (water-metal/semiconductor). Direct interfacial analysis under environmentally relevant conditions is difficult, since most surface-specific techniques require relatively `extreme' conditions. Thus, the experimental investigations here focus on the development of chemical reactors and analytical techniques for the completion of time/concentration-dependent measurements of reactants and their products. Kinetic modeling, estimations, and/or correlations were used to extract information on interfacially relevant processes. We found that interfacial chemistry was determined to be the rate-limiting step to a subsequent series of relatively fast homogeneous reactions, for example: 1) Pyrolytic cleavage of the ionic headgroup of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) adsorbed to cavitating bubble-water interfaces during sonolysis was the rate-determining step in transformation to their inorganic constituents carbon monoxide, carbon dioxide, and fluoride; 2) ozone oxidation of aqueous iodide to hypoiodous acid at the aerosol-gas interface is the rate-determining step in the oxidation of bromide and chloride to dihalogens; 3) Electrolytic oxidation of anodic titanol surface groups is rate-limiting for the overall oxidation of organics by the dichloride radical. We also found chemistry unique to the interface, for example: 1) Adsorption of dilute PFOS(aq) and PFOA(aq) to acoustically cavitating bubble interfaces was greater than equilibrium expectations due to high-velocity bubble radial oscillations; 2) Relative ozone oxidation kinetics of aqueous iodide, sulfite, and thiosulfate were at variance with previously reported bulk aqueous kinetics; 3) Organics that directly chelated with the anode surface were oxidized by direct electron transfer, resulting in immediate carbon dioxide production but slower overall oxidation kinetics. Chemical reactions at aqueous interfaces can be the rate-limiting step of a reaction network and often display novel mechanisms and kinetics as compared to homogeneous chemistry.

One Step Quantum Key Distribution Based on EPR Entanglement.

PubMed

Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

2016-06-30

A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper's attack would introduce at least an error rate of 46.875%. Compared with the "Ping-pong" protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step.

Bifurcation and extinction limit of stretched premixed flames with chain-branching intermediate kinetics and radiative loss

NASA Astrophysics Data System (ADS)

Zhang, Huangwei; Chen, Zheng

2018-05-01

Premixed counterflow flames with thermally sensitive intermediate kinetics and radiation heat loss are analysed within the framework of large activation energy. Unlike previous studies considering one-step global reaction, two-step chemistry consisting of a chain branching reaction and a recombination reaction is considered here. The correlation between the flame front location and stretch rate is derived. Based on this correlation, the extinction limit and bifurcation characteristics of the strained premixed flame are studied, and the effects of fuel and radical Lewis numbers as well as radiation heat loss are examined. Different flame regimes and their extinction characteristics can be predicted by the present theory. It is found that fuel Lewis number affects the flame bifurcation qualitatively and quantitatively, whereas radical Lewis number only has a quantitative influence. Stretch rates at the stretch and radiation extinction limits respectively decrease and increase with fuel Lewis number before the flammability limit is reached, while the radical Lewis number shows the opposite tendency. In addition, the relation between the standard flammability limit and the limit derived from the strained near stagnation flame is affected by the fuel Lewis number, but not by the radical Lewis number. Meanwhile, the flammability limit increases with decreased fuel Lewis number, but with increased radical Lewis number. Radical behaviours at flame front corresponding to flame bifurcation and extinction are also analysed in this work. It is shown that radical concentration at the flame front, under extinction stretch rate condition, increases with radical Lewis number but decreases with fuel Lewis number. It decreases with increased radiation loss.

EDEM2 initiates mammalian glycoprotein ERAD by catalyzing the first mannose trimming step

PubMed Central

Ninagawa, Satoshi; Okada, Tetsuya; Sumitomo, Yoshiki; Kamiya, Yukiko; Kato, Koichi; Horimoto, Satoshi; Ishikawa, Tokiro; Takeda, Shunichi; Sakuma, Tetsushi; Yamamoto, Takashi

2014-01-01

Glycoproteins misfolded in the endoplasmic reticulum (ER) are subjected to ER-associated glycoprotein degradation (gpERAD) in which Htm1-mediated mannose trimming from the oligosaccharide Man8GlcNAc2 to Man7GlcNAc2 is the rate-limiting step in yeast. In contrast, the roles of the three Htm1 homologues (EDEM1/2/3) in mammalian gpERAD have remained elusive, with a key controversy being whether EDEMs function as mannosidases or as lectins. We therefore conducted transcription activator-like effector nuclease–mediated gene knockout analysis in human cell line and found that all endogenous EDEMs possess mannosidase activity. Mannose trimming from Man8GlcNAc2 to Man7GlcNAc2 is performed mainly by EDEM3 and to a lesser extent by EDEM1. Most surprisingly, the upstream mannose trimming from Man9GlcNAc2 to Man8GlcNAc2 is conducted mainly by EDEM2, which was previously considered to lack enzymatic activity. Based on the presence of two rate-limiting steps in mammalian gpERAD, we propose that mammalian cells double check gpERAD substrates before destruction by evolving EDEM2, a novel-type Htm1 homologue that catalyzes the first mannose trimming step from Man9GlcNAc2. PMID:25092655

Competing growth processes induced by next-nearest-neighbor interactions: Effects on meandering wavelength and stiffness

NASA Astrophysics Data System (ADS)

Blel, Sonia; Hamouda, Ajmi BH.; Mahjoub, B.; Einstein, T. L.

2017-02-01

In this paper we explore the meandering instability of vicinal steps with a kinetic Monte Carlo simulations (kMC) model including the attractive next-nearest-neighbor (NNN) interactions. kMC simulations show that increase of the NNN interaction strength leads to considerable reduction of the meandering wavelength and to weaker dependence of the wavelength on the deposition rate F. The dependences of the meandering wavelength on the temperature and the deposition rate obtained with simulations are in good quantitative agreement with the experimental result on the meandering instability of Cu(0 2 24) [T. Maroutian et al., Phys. Rev. B 64, 165401 (2001), 10.1103/PhysRevB.64.165401]. The effective step stiffness is found to depend not only on the strength of NNN interactions and the Ehrlich-Schwoebel barrier, but also on F. We argue that attractive NNN interactions intensify the incorporation of adatoms at step edges and enhance step roughening. Competition between NNN and nearest-neighbor interactions results in an alternative form of meandering instability which we call "roughening-limited" growth, rather than attachment-detachment-limited growth that governs the Bales-Zangwill instability. The computed effective wavelength and the effective stiffness behave as λeff˜F-q and β˜eff˜F-p , respectively, with q ≈p /2 .

Reliability of wireless monitoring using a wearable patch sensor in high-risk surgical patients at a step-down unit in the Netherlands: a clinical validation study.

PubMed

Breteler, Martine J M; Huizinga, Erik; van Loon, Kim; Leenen, Luke P H; Dohmen, Daan A J; Kalkman, Cor J; Blokhuis, Taco J

2018-02-27

Intermittent vital signs measurements are the current standard on hospital wards, typically recorded once every 8 hours. Early signs of deterioration may therefore be missed. Recent innovations have resulted in 'wearable' sensors, which may capture patient deterioration at an earlier stage. The objective of this study was to determine whether a wireless 'patch' sensor is able to reliably measure respiratory and heart rate continuously in high-risk surgical patients. The secondary objective was to explore the potential of the wireless sensor to serve as a safety monitor. In an observational methods comparisons study, patients were measured with both the wireless sensor and bedside routine standard for at least 24 hours. University teaching hospital, single centre. Twenty-five postoperative surgical patients admitted to a step-down unit. Primary outcome measures were limits of agreement and bias of heart rate and respiratory rate. Secondary outcome measures were sensor reliability, defined as time until first occurrence of data loss. 1568 hours of vital signs data were analysed. Bias and 95% limits of agreement for heart rate were -1.1 (-8.8 to 6.5) beats per minute. For respiration rate, bias was -2.3 breaths per minute with wide limits of agreement (-15.8 to 11.2 breaths per minute). Median filtering over a 15 min period improved limits of agreement of both respiration and heart rate. 63% of the measurements were performed without data loss greater than 2 min. Overall data loss was limited (6% of time). The wireless sensor is capable of accurately measuring heart rate, but accuracy for respiratory rate was outside acceptable limits. Remote monitoring has the potential to contribute to early recognition of physiological decline in high-risk patients. Future studies should focus on the ability to detect patient deterioration on low care environments and at home after discharge. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remec, Igor; Ronningen, Reginald Martin

The research studied one-step and two-step Isotope Separation on Line (ISOL) targets for future radioactive beam facilities with high driver-beam power through advanced computer simulations. As a target material uranium carbide in the form of foils was used because of increasing demand for actinide targets in rare-isotope beam facilities and because such material was under development in ISAC at TRIUMF when this project started. Simulations of effusion were performed for one-step and two step targets and the effects of target dimensions and foil matrix were studied. Diffusion simulations were limited by availability of diffusion parameters for UC x material atmore » reduced density; however, the viability of the combined diffusion?effusion simulation methodology was demonstrated and could be used to extract physical parameters such as diffusion coefficients and effusion delay times from experimental isotope release curves. Dissipation of the heat from the isotope-producing targets is the limiting factor for high-power beam operation both for the direct and two-step targets. Detailed target models were used to simulate proton beam interactions with the targets to obtain the fission rates and power deposition distributions, which were then applied in the heat transfer calculations to study the performance of the targets. Results indicate that a direct target, with specification matching ISAC TRIUMF target, could operate in 500-MeV proton beam at beam powers up to ~40 kW, producing ~8 10 13 fission/s with maximum temperature in UCx below 2200 C. Targets with larger radius allow higher beam powers and fission rates. For the target radius in the range 9-mm to 30-mm the achievable fission rate increases almost linearly with target radius, however, the effusion delay time also increases linearly with target radius.« less

Mechanism of two-step vapour-crystal nucleation in a pore

NASA Astrophysics Data System (ADS)

van Meel, J. A.; Liu, Y.; Frenkel, D.

2015-09-01

We present a numerical study of the effect of hemispherical pores on the nucleation of Lennard-Jones crystals from the vapour phase. As predicted by Page and Sear, there is a narrow range of pore radii, where vapour-liquid nucleation can become a two-step process. A similar observation was made for different pore geometries by Giacomello et al. We find that the maximum nucleation rate depends on both the size and the adsorption strength of the pore. Moreover, a poe can be more effective than a planar wall with the same strength of attraction. Pore-induced vapour-liquid nucleation turns out to be the rate-limiting step for crystal nucleation. This implies that crystal nucleation can be enhanced by a judicious choice of the wetting properties of a microporous nucleating agent.

Simultaneous multielement atomic absorption spectrometry with graphite furnace atomization

NASA Astrophysics Data System (ADS)

Harnly, James M.; Miller-Ihli, Nancy J.; O'Haver, Thomas C.

The extended analytical range capability of a simultaneous multielement atomic absorption continuum source spectrometer (SIMAAC) was tested for furnace atomization with respect to the signal measurement mode (peak height and area), the atomization mode (from the wall or from a platform), and the temperature program mode (stepped or ramped atomization). These parameters were evaluated with respect to the shapes of the analytical curves, the detection limits, carry-over contamination and accuracy. Peak area measurements gave more linear calibration curves. Methods for slowing the atomization step heating rate, the use of a ramped temperature program or a platform, produced similar calibration curves and longer linear ranges than atomization with a stepped temperature program. Peak height detection limits were best using stepped atomization from the wall. Peak area detection limits for all atomization modes were similar. Carry-over contamination was worse for peak area than peak height, worse for ramped atomization than stepped atomization, and worse for atomization from a platform than from the wall. Accurate determinations (100 ± 12% for Ca, Cu, Fe, Mn, and Zn in National Bureau of Standards' Standard Reference Materials Bovine Liver 1577 and Rice Flour 1568 were obtained using peak area measurements with ramped atomization from the wall and stepped atomization from a platform. Only stepped atomization from a platform gave accurate recoveries for K. Accurate recoveries, 100 ± 10%, with precisions ranging from 1 to 36 % (standard deviation), were obtained for the determination of Al, Co, Cr, Fe, Mn, Mo, Ni. Pb, V and Zn in Acidified Waters (NBS SRM 1643 and 1643a) using stepped atomization from a platform.

Effects of Engineered Wettability on the Efficiency of Dew Collection.

PubMed

Gerasopoulos, Konstantinos; Luedeman, William L; Ölçeroglu, Emre; McCarthy, Matthew; Benkoski, Jason J

2018-01-31

Surface wettability plays an important role in dew collection. Nucleation is faster on hydrophilic surfaces, while droplets slide more readily on hydrophobic surfaces. Plants and animals in coastal desert environments appear to overcome this trade-off through biphilic surfaces with patterned wettability. In this study, we investigate the effects of millimeter-scale wettability patterns, mimicking those of the Stenocara beetle, on the rate of water collection from humid air. The rate of water collection per unit area is measured as a function of subcooling (ΔT = 1, 7, and 27 °C) and angle of inclination (from 10° to 90°). It is then compared for superbiphilic, hydrophilic, hydrophobic, and surperhydrophobic surfaces. For large subcooling, neither wettability nor tilt angle has a significant effect because the rate of condensation is so great. For 1 °C subcooling and large angles, hydrophilic surfaces perform best because condensation is the rate-limiting step. For low angles of inclination, superhydrophobic samples are best because droplet sliding is the rate-limiting step. Superbiphilic surfaces, in contrast to their superior fog collecting capabilities, generally collected dew at the slowest rate due to their inherent contact angle hysteresis. Theoretical considerations suggest that this finding may apply more generally to surfaces with patterned wettability.

Coupling a Reactive Transport Code with a Global Land Surface Model for Mechanistic Biogeochemistry Representation: 1. Addressing the Challenge of Nonnegativity

DOE PAGES

Tang, Guoping; Yuan, Fengming; Bisht, Gautam; ...

2016-01-01

Reactive transport codes (e.g., PFLOTRAN) are increasingly used to improve the representation of biogeochemical processes in terrestrial ecosystem models (e.g., the Community Land Model, CLM). As CLM and PFLOTRAN use explicit and implicit time stepping, implementation of CLM biogeochemical reactions in PFLOTRAN can result in negative concentration, which is not physical and can cause numerical instability and errors. The objective of this work is to address the nonnegativity challenge to obtain accurate, efficient, and robust solutions. We illustrate the implementation of a reaction network with the CLM-CN decomposition, nitrification, denitrification, and plant nitrogen uptake reactions and test the implementation atmore » arctic, temperate, and tropical sites. We examine use of scaling back the update during each iteration (SU), log transformation (LT), and downregulating the reaction rate to account for reactant availability limitation to enforce nonnegativity. Both SU and LT guarantee nonnegativity but with implications. When a very small scaling factor occurs due to either consumption or numerical overshoot, and the iterations are deemed converged because of too small an update, SU can introduce excessive numerical error. LT involves multiplication of the Jacobian matrix by the concentration vector, which increases the condition number, decreases the time step size, and increases the computational cost. Neither SU nor SE prevents zero concentration. When the concentration is close to machine precision or 0, a small positive update stops all reactions for SU, and LT can fail due to a singular Jacobian matrix. The consumption rate has to be downregulated such that the solution to the mathematical representation is positive. A first-order rate downregulates consumption and is nonnegative, and adding a residual concentration makes it positive. For zero-order rate or when the reaction rate is not a function of a reactant, representing the availability limitation of each reactant with a Monod substrate limiting function provides a smooth transition between a zero-order rate when the reactant is abundant and first-order rate when the reactant becomes limiting. When the half saturation is small, marching through the transition may require small time step sizes to resolve the sharp change within a small range of concentration values. Our results from simple tests and CLM-PFLOTRAN simulations caution against use of SU and indicate that accurate, stable, and relatively efficient solutions can be achieved with LT and downregulation with Monod substrate limiting function and residual concentration.« less

Warming rate drives microbial limitation and enzyme expression during peat decomposition

NASA Astrophysics Data System (ADS)

Inglett, P.; Sihi, D.; Inglett, K. S.

2015-12-01

Recent developments of enzyme-based decomposition models highlight the importance of enzyme kinetics with warming, but most modeling exercises are based on studies with a step-wise warming. This approach may mask the effect of temperature in controlling in-situ activities as in most ecosystems soil temperature change more gradually than air temperature. We conducted an experiment to test the effects of contrasting warming rates on the kinetics of C, N, and P degradation enzymes in subtropical peat soils. We also wanted to evaluate if the stoichiometry of enzyme kinetics shifts under contrasting warming rates and if so, how does it relate to the stoichiometry in microbial biomass. Contrasting warming rates altered microbial biomass stoichiometry leading to differing patterns of enzyme expression and microbial nutrient limitation. Activity (higher Vmax) and efficiency (lower Km) of C acquisition enzymes were greater in the step treatment; however, expressions of nutrient (N and P) acquiring enzymes were enhanced in the ramp treatment at the end of the experiment. In the step treatment, there was a typical pattern of an initial peak in the Vmax and drop in the Km for all enzyme groups followed by later adjustments. On the other hand, a consistent increase in Vmax and decline in Km of all enzyme groups were observed in the slow warming treatment. These changes were sufficient to alter microbial identity (as indicated by enzyme Km and biomass stoichiometry) with two apparently stable endpoints under contrasting warming rates. This observation resembles the concept of alternate stable states and highlights a need for improved representation of warming in models.

DFT investigations of phosphotriesters hydrolysis in aqueous solution: a model for DNA single strand scission induced by N-nitrosoureas.

PubMed

Liu, Tingting; Zhao, Lijiao; Zhong, Rugang

2013-02-01

DNA phosphotriester adducts are common alkylation products of DNA phosphodiester moiety induced by N-nitrosoureas. The 2-hydroxyethyl phosphotriester was reported to hydrolyze more rapidly than other alkyl phosphotriesters both in neutral and in alkaline conditions, which can cause DNA single strand scission. In this work, DFT calculations have been employed to map out the four lowest activation free-energy profiles for neutral and alkaline hydrolysis of triethyl phosphate (TEP) and diethyl 2-hydroxyethyl phosphate (DEHEP). All the hydrolysis pathways were illuminated to be stepwise involving an acyclic or cyclic phosphorane intermediate for TEP or DEHEP, respectively. The rate-limiting step for all the hydrolysis reactions was found to be the formation of phosphorane intermediate, with the exception of DEHEP hydrolysis in alkaline conditions that the decomposition process turned out to be the rate-limiting step, owing to the extraordinary low formation barrier of cyclic phosphorane intermediate catalyzed by hydroxide. The rate-limiting barriers obtained for the four reactions are all consistent with the available experimental information concerning the corresponding hydrolysis reactions of phosphotriesters. Our calculations performed on the phosphate triesters hydrolysis predict that the lower formation barriers of cyclic phosphorane intermediates compared to its acyclic counter-part should be the dominant factor governing the hydrolysis rate enhancement of DEHEP relative to TEP both in neutral and in alkaline conditions.

Step training improves reaction time, gait and balance and reduces falls in older people: a systematic review and meta-analysis.

PubMed

Okubo, Yoshiro; Schoene, Daniel; Lord, Stephen R

2017-04-01

To examine the effects of stepping interventions on fall risk factors and fall incidence in older people. Electronic databases (PubMed, EMBASE, CINAHL, Cochrane, CENTRAL) and reference lists of included articles from inception to March 2015. Randomised (RCT) or clinical controlled trials (CCT) of volitional and reactive stepping interventions that included older (minimum age 60) people providing data on falls or fall risk factors. Meta-analyses of seven RCTs (n=660) showed that the stepping interventions significantly reduced the rate of falls (rate ratio=0.48, 95% CI 0.36 to 0.65, p<0.0001, I 2 =0%) and the proportion of fallers (risk ratio=0.51, 95% CI 0.38 to 0.68, p<0.0001, I 2 =0%). Subgroup analyses stratified by reactive and volitional stepping interventions revealed a similar efficacy for rate of falls and proportion of fallers. A meta-analysis of two RCTs (n=62) showed that stepping interventions significantly reduced laboratory-induced falls, and meta-analysis findings of up to five RCTs and CCTs (n=36-416) revealed that stepping interventions significantly improved simple and choice stepping reaction time, single leg stance, timed up and go performance (p<0.05), but not measures of strength. The findings indicate that both reactive and volitional stepping interventions reduce falls among older adults by approximately 50%. This clinically significant reduction may be due to improvements in reaction time, gait, balance and balance recovery but not in strength. Further high-quality studies aimed at maximising the effectiveness and feasibility of stepping interventions are required. CRD42015017357. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Pre-Steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase: Analysis and Implications†

PubMed Central

Robertson, Brooklyn A.; Schroeder, Gottfried K.; Jin, Zhinan; Johnson, Kenneth A.; Whitman, Christian P.

2009-01-01

Isomer-specific 3-chloroacrylic acid dehalogenases catalyze the hydrolytic dehalogenation of the cis- and trans-isomers of 3-chloroacrylate to yield malonate semialdehyde. These reactions represent key steps in the degradation of the nematocide, 1,3-dichloropropene. The kinetic mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) has now been examined using stopped-flow and chemical-quench techniques. Stopped-flow analysis of the reaction, following the fluorescence of an active site tryptophan, is consistent with a minimal three-step model involving substrate binding, chemistry, and product release. Chemical quench experiments show burst kinetics, indicating that product release is at least partially rate limiting. Global fitting of all of the kinetic results by simulation is best accommodated by a four-step mechanism. In the final kinetic model, the enzyme binds substrate and isomerizes to an alternate fluorescent form, chemistry occurs, and is followed by the ordered release of two products, with the release of the first product as the rate-limiting step. Bromide ion is a competitive inhibitor of the reaction indicating that it binds to the free enzyme rather than to the enzyme with one product still bound. This observation suggests that malonate semialdehyde is the first product released by the enzyme (rate limiting), followed by halide. A comparison of the unliganded cis-CaaD crystal structure with that of an inactivated cis-CaaD where the prolyl nitrogen of Pro-1 is covalently attached to (R)-2-hydroxypropanoate provides a possible explanation for the isomerization step. The structure of the covalently modified enzyme shows that a 7-residue loop comprised of residues 32-38 is closed down on the active site cavity where the backbone amides of two residues (Phe-37 and Leu-38) interact with the carboxylate group of the adduct. In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop to close down on the active site and sequester the reaction from the external environment. PMID:19856961

One Step Quantum Key Distribution Based on EPR Entanglement

PubMed Central

Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

2016-01-01

A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper’s attack would introduce at least an error rate of 46.875%. Compared with the “Ping-pong” protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step. PMID:27357865

The Relaxation of Vicinal (001) with ZigZag [110] Steps

NASA Astrophysics Data System (ADS)

Hawkins, Micah; Hamouda, Ajmi Bh; González-Cabrera, Diego Luis; Einstein, Theodore L.

2012-02-01

This talk presents a kinetic Monte Carlo study of the relaxation dynamics of [110] steps on a vicinal (001) simple cubic surface. This system is interesting because [110] steps have different elementary excitation energetics and favor step diffusion more than close-packed [100] steps. In this talk we show how this leads to relaxation dynamics showing greater fluctuations on a shorter time scale for [110] steps as well as 2-bond breaking processes being rate determining in contrast to 3-bond breaking processes for [100] steps. The existence of a steady state is shown via the convergence of terrace width distributions at times much longer than the relaxation time. In this time regime excellent fits to the modified generalized Wigner distribution (as well as to the Berry-Robnik model when steps can overlap) were obtained. Also, step-position correlation function data show diffusion-limited increase for small distances along the step as well as greater average step displacement for zigzag steps compared to straight steps for somewhat longer distances along the step. Work supported by NSF-MRSEC Grant DMR 05-20471 as well as a DOE-CMCSN Grant.

Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient

Treesearch

S. Pierre; I. Hewson; J. P. Sparks; C. M. Litton; C. Giardina; P. M. Groffman; T. J. Fahey

2017-01-01

Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lobo, R.; Revah, S.; Viveros-Garcia, T.

An analysis of the local processes occurring in a trickle-bed bioreactor (TBB) with a first-order bioreaction shows that the identification of the TBB operating regime requires knowledge of the substrate concentration in the liquid phase. If the substrate liquid concentration is close to 0, the rate-controlling step is mass transfer at the gas-liquid interface; when it is close to the value in equilibrium with the gas phase, the controlling step is the phenomena occurring in the biofilm, CS{sub 2} removal rate data obtained in a TBB with a Thiobacilii consortia biofilm are analyzed to obtain the mass transfer and kineticmore » parameters, and to show that the bioreactor operates in a regime mainly controlled by mass transfer. A TBB model with two experimentally determined parameters is developed and used to show how the bioreactor size depends on the rate-limiting step, the absorption factor, the substrate fractional conversion, and on the gas and liquid contact pattern. Under certain conditions, the TBB size is independent of the flowing phases` contact pattern. The model effectively describes substrate gas and liquid concentration data for mass transfer and biodegradation rate controlled processes.« less

Elucidation of Kinetic Mechanisms of Human Translesion DNA Polymerase κ Using Tryptophan Mutants

PubMed Central

Zhao, Linlin; Pence, Matthew G.; Eoff, Robert L.; Yuan, Shuai; Fercu, Catinca A.; Guengerich, F. Peter

2014-01-01

In order to investigate the conformational dynamics of human DNA polymerase κ (hpol κ), we generated two mutants, Y50W (N-clasp region) and Y408W (linker between the thumb and little finger domains), using a Trp-null mutant (W214Y/W392H) of the hpol κ catalytic core enzyme. These mutants retained catalytic activity and similar patterns of selectivity for bypassing the DNA adduct 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-oxoG), as judged by the results of steady-state and pre-steady-state kinetic experiments. Stopped-flow kinetic assays with hpol κ Y50W and T408W revealed a decrease in Trp fluorescence with the template G:dCTP pair but not for any mispairs. This decrease in fluorescence was not rate-limiting and is considered to be related to a conformational change necessary for correct nucleotidyl transfer. When a free 3′-hydroxyl was present on the primer, the Trp fluorescence returned to the baseline level at a rate similar to the observed kcat, suggesting that this change occurs during or after nucleotidyl transfer. However, polymerization rates (kpol) of extended-product formation were fast, indicating that the slow fluorescence step follows phosphodiester bond formation and is rate-limiting. Pyrophosphate formation and release were fast and are likely to precede the slower relaxation step. The available kinetic data were used to fit a simplified minimal model. The extracted rate constants confirmed that the conformational change after phosphodiester formation was rate-limiting for hpol κ catalysis with the template G:dCTP pair. PMID:25065501

From Sequences to Insights in Microbial Ecology

PubMed Central

Knight, R.

2010-01-01

s4-3 Rapid declines in the cost of sequencing have made large volumes of DNA sequence data available to individual investigators. Now, data analysis is the rate-limiting step: providing a user with sequences alone typically leads to bewilderment, frustration, and skepticism about the technology. In this talk, I focus on how to extract insights from 16S rRNA data, including key lab steps (barcoding and normalization) and on which tools are available to perform routine but essential processing steps such as denoising, chimera detection, taxonomy assignment, and diversity analyses (including detection of biological clusters and gradients in the samples). Providing users with advice on these points and with a standard pipeline they can exploit (but modify if circumstances require) can greatly accelerate the rate of understanding, publication, and acquisition of funding for further studies.

The Parkinson Disease-linked LRRK2 Protein Mutation I2020T Stabilizes an Active State Conformation Leading to Increased Kinase Activity*

PubMed Central

Ray, Soumya; Bender, Samantha; Kang, Stephanie; Lin, Regina; Glicksman, Marcie A.; Liu, Min

2014-01-01

The effect of leucine-rich repeat kinase 2 (LRRK2) mutation I2020T on its kinase activity has been controversial, with both increased and decreased effects being reported. We conducted steady-state and pre-steady-state kinetic studies on LRRKtide and its analog LRRKtideS. Their phosphorylation differs by the rate-limiting steps: product release is rate-limiting for LRRKtide and phosphoryl transfer is rate-limiting for LRRKtideS. As a result, we observed that the I2020T mutant is more active than wild type (WT) LRRK2 for LRRKtideS phosphorylation, whereas it is less active than WT for LRRKtide phosphorylation. Our pre-steady-state kinetic data suggest that (i) the I2020T mutant accelerates the rates of phosphoryl transfer of both reactions by 3–7-fold; (ii) this increase is masked by a rate-limiting product release step for LRRKtide phosphorylation; and (iii) the observed lower activity of the mutant for LRRKtide phosphorylation is a consequence of its instability: the concentration of the active form of the mutant is 3-fold lower than WT. The I2020T mutant has a dramatically low KATP and therefore leads to resistance to ATP competitive inhibitors. Two well known DFG-out or type II inhibitors are also weaker toward the mutant because they inhibit the mutant in an unexpected ATP competitive mechanism. The I2020 residue lies next to the DYG motif of the activation loop of the LRRK2 kinase domain. Our modeling and metadynamic simulations suggest that the I2020T mutant stabilizes the DYG-in active conformation and creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP competitive fashion. PMID:24695735

Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.

PubMed

Robin, Adeline Y; Giustini, Cécile; Graindorge, Matthieu; Matringe, Michel; Dumas, Renaud

2016-09-01

Growing pharmaceutical interest in benzylisoquinoline alkaloids (BIA) coupled with their chemical complexity make metabolic engineering of microbes to create alternative platforms of production an increasingly attractive proposition. However, precise knowledge of rate-limiting enzymes and negative feedback inhibition by end-products of BIA metabolism is of paramount importance for this emerging field of synthetic biology. In this work we report the structural characterization of (S)-norcoclaurine-6-O-methyltransferase (6OMT), a key rate-limiting step enzyme involved in the synthesis of reticuline, the final intermediate to be shared between the different end-products of BIA metabolism, such as morphine, papaverine, berberine and sanguinarine. Four different crystal structures of the enzyme from Thalictrum flavum (Tf 6OMT) were solved: the apoenzyme, the complex with S-adenosyl-l-homocysteine (SAH), the complexe with SAH and the substrate and the complex with SAH and a feedback inhibitor, sanguinarine. The Tf 6OMT structural study provides a molecular understanding of its substrate specificity, active site structure and reaction mechanism. This study also clarifies the inhibition of Tf 6OMT by previously suggested feedback inhibitors. It reveals its high and time-dependent sensitivity toward sanguinarine. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Manipulating the Rate-Limiting Step in Water Oxidation Catalysis by Ruthenium Bipyridine–Dicarboxylate Complexes

DOE PAGES

Shaffer, David W.; Xie, Yan; Szalda, David J.; ...

2016-11-01

In order to gain a deeper mechanistic understanding of water oxidation by [(bda)Ru(L) 2] catalysts (bdaH 2 = [2,2'-bipyridine]-6,6'-dicarboxylic acid; L = pyridine-type ligand), a series of modified catalysts with one and two trifluoromethyl groups in the 4 position of the bda 2– ligand was synthesized and studied using stopped-flow kinetics. The additional $-$CF 3 groups increased the oxidation potentials for the catalysts and enhanced the rate of electrocatalytic water oxidation at low pH. Stopped-flow measurements of cerium(IV)-driven water oxidation at pH 1 revealed two distinct kinetic regimes depending on catalyst concentration. At relatively high catalyst concentration (ca. ≥10 –4more » M), the rate-determining step (RDS) was a proton-coupled oxidation of the catalyst by cerium(IV) with direct kinetic isotope effects (KIE > 1). At low catalyst concentration (ca. ≤10 –6 M), the RDS was a bimolecular step with k H/k D ≈ 0.8. The results support a catalytic mechanism involving coupling of two catalyst molecules. The rate constants for both RDSs were determined for all six catalysts studied. The presence of $-$CF 3 groups had inverse effects on the two steps, with the oxidation step being fastest for the unsubstituted complexes and the bimolecular step being faster for the most electron-deficient complexes. Finally, though the axial ligands studied here did not significantly affect the oxidation potentials of the catalysts, the nature of the ligand was found to be important not only in the bimolecular step but also in facilitating electron transfer from the metal center to the sacrificial oxidant.« less

Ligand-accelerated activation of strong C-H bonds of alkanes by a (salen)ruthenium(VI)-nitrido complex.

PubMed

Man, Wai-Lun; Lam, William W Y; Kwong, Hoi-Ki; Yiu, Shek-Man; Lau, Tai-Chu

2012-09-03

Kinetic and mechanistic studies on the intermolecular activation of strong C-H bonds of alkanes by a (salen)ruthenium(VI) nitride were performed. The initial, rate-limiting step, the hydrogen atom transfer (HAT) from the alkane to Ru(VI)≡N, generates Ru(V)=NH and RC·HCH(2)R. The following steps involve N-rebound and desaturation. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study.

PubMed

Ma, Yingying; Sun, Qiao; Smith, Sean C

2017-05-24

Oxidation is viewed as the second and rate-limiting step in the chromophore maturation process of the wild-type green fluorescent protein (GFP) under aerobic conditions. Molecular oxygen is the necessary oxidant for GFP chromophore biosynthesis. In this study, density functional theory (DFT) calculations were employed to study the mechanism of oxidation. Our results indicate that the deprotonation of the Tyr66 α-carbon is probably the rate-limiting step in the oxidation step. Electron transfer from the enolate form of the five-membered heterocycle (EFMH) to molecular oxygen, generating the triplet radical complex [EFMH˙O 2 - ˙] T , is an important step. This complex undergoes intersystem crossing to form an open-shell singlet diradical complex before it forms the closed-shell singlet hydroperoxy adduct. The formation of the hydroperoxy adduct is a proton-coupled electron transfer process. The energy barrier of H 2 O 2 elimination is 16.5 kcal mol -1 . The oxidation product IFMHH 2 O 2 that we discovered is a hydroxylated cyclic imine structure, which is consistent with the crystal structure trapped in the colorless Y66L variant. The relative energy of the oxidation product is -48.7 kcal mol -1 , which is in accordance with the experimental observation that the thermodynamically unfavourable cyclized product is trapped by oxidation. The results herein support the cyclization-oxidation-dehydration mechanism for the chromophore maturation of GFP.

Simplified Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two time step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting rates of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx are obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

Structure-function analysis of diacylglycerol acyltransferase sequences from 70 organisms

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferases (DGATs) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. Understanding the roles of DGATs will help to create transgenic plants with value-added properties and provide clues for therapeutic intervention for obes...

Expression and purification of membrane protein diacylglycerol acyltransferase

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferases (DGATs) catalyze the last and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. Plants and animals deficient in DGATs accumulate less TAG. Over-expression of DGATs increases TAG in seeds and other tissues. DGAT knockout mice are resista...

Bioengineering recombinant diacylglycerol acyltransferases

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferases (DGATs) catalyze the last and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. At least 115 DGAT sequences are identified from 69 organisms in the GenBank databases. Only a few papers have been published in the last 28 years on the exp...

Analyzing the dependence of oxygen incorporation current density on overpotential and oxygen partial pressure in mixed conducting oxide electrodes.

PubMed

Guan, Zixuan; Chen, Di; Chueh, William C

2017-08-30

The oxygen incorporation reaction, which involves the transformation of an oxygen gas molecule to two lattice oxygen ions in a mixed ionic and electronic conducting solid, is a ubiquitous and fundamental reaction in solid-state electrochemistry. To understand the reaction pathway and to identify the rate-determining step, near-equilibrium measurements have been employed to quantify the exchange coefficients as a function of oxygen partial pressure and temperature. However, because the exchange coefficient contains contributions from both forward and reverse reaction rate constants and depends on both oxygen partial pressure and oxygen fugacity in the solid, unique and definitive mechanistic assessment has been challenging. In this work, we derive a current density equation as a function of both oxygen partial pressure and overpotential, and consider both near and far from equilibrium limits. Rather than considering specific reaction pathways, we generalize the multi-step oxygen incorporation reaction into the rate-determining step, preceding and following quasi-equilibrium steps, and consider the number of oxygen ions and electrons involved in each. By evaluating the dependence of current density on oxygen partial pressure and overpotential separately, one obtains the reaction orders for oxygen gas molecules and for solid-state species in the electrode. We simulated the oxygen incorporation current density-overpotential curves for praseodymium-doped ceria for various candidate rate-determining steps. This work highlights a promising method for studying the exchange kinetics far away from equilibrium.

Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle.

PubMed

Alves, Tiago C; Pongratz, Rebecca L; Zhao, Xiaojian; Yarborough, Orlando; Sereda, Sam; Shirihai, Orian; Cline, Gary W; Mason, Graeme; Kibbey, Richard G

2015-11-03

Mass isotopomer multi-ordinate spectral analysis (MIMOSA) is a step-wise flux analysis platform to measure discrete glycolytic and mitochondrial metabolic rates. Importantly, direct citrate synthesis rates were obtained by deconvolving the mass spectra generated from [U-(13)C6]-D-glucose labeling for position-specific enrichments of mitochondrial acetyl-CoA, oxaloacetate, and citrate. Comprehensive steady-state and dynamic analyses of key metabolic rates (pyruvate dehydrogenase, β-oxidation, pyruvate carboxylase, isocitrate dehydrogenase, and PEP/pyruvate cycling) were calculated from the position-specific transfer of (13)C from sequential precursors to their products. Important limitations of previous techniques were identified. In INS-1 cells, citrate synthase rates correlated with both insulin secretion and oxygen consumption. Pyruvate carboxylase rates were substantially lower than previously reported but showed the highest fold change in response to glucose stimulation. In conclusion, MIMOSA measures key metabolic rates from the precursor/product position-specific transfer of (13)C-label between metabolites and has broad applicability to any glucose-oxidizing cell. Copyright © 2015 Elsevier Inc. All rights reserved.

On the interpretation of quantitative structure–function activity relationship data for lactate oxidase

PubMed Central

Yorita, Kazuko; Misaki, Hideo; Palfey, Bruce A.; Massey, Vincent

2000-01-01

The native flavin, FMN, has been removed from the l-lactate oxidase of Aerococcus viridans, and the apoprotein reconstituted with 12 FMN derivatives with various substituents at the flavin 6- and 8-positions. Impressive linear relationships are exhibited between the sum of the Hammett σpara and σortho parameters and the redox potentials of the free flavins, and between the redox potentials of the free and enzyme-bound flavins. Rapid reaction kinetics studies of the reconstituted enzymes with the substrates l-lactate and l-mandelate show an increase in the reduction rate constant with increasing redox potential, except that, with lactate, a limiting rate constant of ≈700 s−1 is obtained with flavins of high potential. Similar breakpoints are found in plots of the rate constants for flavin N5-sulfite adduct formation and for the reaction of the reduced enzymes with molecular oxygen. These results are interpreted in terms of a two-step equilibrium preceding the chemical reaction step, in which the second equilibrium step provides an upper limit to the rate with which the particular substrate or ligand is positioned with the flavin in the correct fashion for the observed chemical reaction to occur. The relationship of rate constants for flavin reduction and N5-sulfite adduct formation with flavin redox potential below the observed breakpoint indicate development of significant negative charge in the transition states of the reactions. In the case of reduction by substrate, the results are consistent either with a hydride transfer mechanism or with the so called “carbanion” mechanism, in which the substrate α-proton is abstracted by an enzyme base protected from exchange with solvent. These conclusions are supported by substrate α-deuterium isotope effects and by solvent viscosity effects on sulfite binding. PMID:10706608

Contribution of Glucose Transport to the Control of the Glycolytic Flux in Trypanosoma brucei

NASA Astrophysics Data System (ADS)

Bakker, Barbara M.; Walsh, Michael C.; Ter Kuile, Benno H.; Mensonides, Femke I. C.; Michels, Paul A. M.; Opperdoes, Fred R.; Westerhoff, Hans V.

1999-08-01

The rate of glucose transport across the plasma membrane of the bloodstream form of Trypanosoma brucei was modulated by titration of the hexose transporter with the inhibitor phloretin, and the effect on the glycolytic flux was measured. A rapid glucose uptake assay was developed to measure the transport activity independently of the glycolytic flux. Phloretin proved a competitive inhibitor. When the effect of the intracellular glucose concentration on the inhibition was taken into account, the flux control coefficient of the glucose transporter was between 0.3 and 0.5 at 5 mM glucose. Because the flux control coefficients of all steps in a metabolic pathway sum to 1, this result proves that glucose transport is not the rate-limiting step of trypanosome glycolysis. Under physiological conditions, transport shares the control with other steps. At glucose concentrations much lower than physiological, the glucose carrier assumed all control, in close agreement with model predictions.

Real-Space Formation and Dissipation Dynamics of Hexagonal Reconstruction on Au(100) in Aqueous Media as Explored by Potentiodynamic Scanning Tunneling Microscopy

DTIC Science & Technology

1993-04-01

the clusters appear to form monoatomic layers on the (i x 1) substrate. This assertion, derived from the apparent z-corrugation in the STH images, is...top-layer lattice and thereby displacing one of the nearest-neighbor atoms. A related , although more concerted, atomic motion can also provide a viable...microscopic rate-limiting step(s) for this process are not necessarily related straightforwardly to the free- energy difference for the overall macroscopic

Design principles and optimal performance for molecular motors under realistic constraints

NASA Astrophysics Data System (ADS)

Tu, Yuhai; Cao, Yuansheng

2018-02-01

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forward stepping in a narrow window in configuration space is needed for generating high power at physiologically relevant loads. By deriving general thermodynamics laws for nonequilibrium motors, we find that the maximum torque (force) at stall is less than its theoretical limit for any realistic motor-track interactions due to speed fluctuations. Our study reveals a tradeoff for the motor-track interaction: while a strong interaction generates a high power output for forward steps, it also leads to a higher probability of wasteful spontaneous back steps. Our analysis and simulations show that this tradeoff sets a fundamental limit to the maximum motor efficiency in the presence of spontaneous back steps, i.e., loose-coupling. Balancing this tradeoff leads to an optimal design of the motor-track interaction for achieving a maximum efficiency close to 1 for realistic motors that are not perfectly coupled with the energy source. Comparison with existing data and suggestions for future experiments are discussed.

Photopigment quenching is Ca2+ dependent and controls response duration in salamander L-cone photoreceptors

PubMed Central

2010-01-01

The time scale of the photoresponse in photoreceptor cells is set by the slowest of the steps that quench the light-induced activity of the phototransduction cascade. In vertebrate photoreceptor cells, this rate-limiting reaction is thought to be either shutoff of catalytic activity in the photopigment or shutoff of the pigment's effector, the transducin-GTP–phosphodiesterase complex. In suction pipette recordings from isolated salamander L-cones, we found that preventing changes in internal [Ca2+] delayed the recovery of the light response and prolonged the dominant time constant for recovery. Evidence that the Ca2+-sensitive step involved the pigment itself was provided by the observation that removal of Cl− from the pigment's anion-binding site accelerated the dominant time constant for response recovery. Collectively, these observations indicate that in L-cones, unlike amphibian rods where the dominant time constant is insensitive to [Ca2+], pigment quenching rate limits recovery and provides an additional mechanism for modulating the cone response during light adaptation. PMID:20231373

Robust numerical solution of the reservoir routing equation

NASA Astrophysics Data System (ADS)

Fiorentini, Marcello; Orlandini, Stefano

2013-09-01

The robustness of numerical methods for the solution of the reservoir routing equation is evaluated. The methods considered in this study are: (1) the Laurenson-Pilgrim method, (2) the fourth-order Runge-Kutta method, and (3) the fixed order Cash-Karp method. Method (1) is unable to handle nonmonotonic outflow rating curves. Method (2) is found to fail under critical conditions occurring, especially at the end of inflow recession limbs, when large time steps (greater than 12 min in this application) are used. Method (3) is computationally intensive and it does not solve the limitations of method (2). The limitations of method (2) can be efficiently overcome by reducing the time step in the critical phases of the simulation so as to ensure that water level remains inside the domains of the storage function and the outflow rating curve. The incorporation of a simple backstepping procedure implementing this control into the method (2) yields a robust and accurate reservoir routing method that can be safely used in distributed time-continuous catchment models.

Defining the Status of RNA Polymerase at Promoters

PubMed Central

Core, Leighton J.; Waterfall, Joshua J.; Gilchrist, Daniel A.; Fargo, David C.; Kwak, Hojoong; Adelman, Karen; Lis, John T.

2012-01-01

Summary Recent genome-wide studies in metazoans have shown that RNA Polymerase II (Pol II) accumulates to high densities on many promoters at a rate-limited step in transcription. However, the status of this Pol II remains an area of debate. Here, we compare quantitative outputs of GRO-seq and ChIP-seq assays and demonstrate the majority of the Pol II on Drosophila promoters is transcriptionally-engaged - very little exists in a preinitiation or arrested complex. These promoter-proximal polymerases are inhibited from further elongation by detergent sensitive factors, and knockdown of negative elongation factor, NELF, reduces their levels. These results not only solidify that pausing occurs at most promoters, but demonstrate that it is the major rate-limiting step in early transcription at these promoters. Finally, the divergent elongation complexes seen at mammalian promoters are far less prevalent in Drosophila, and this specificity in orientation correlates with directional core promoter elements, which are abundant in Drosophila. PMID:23062713

Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.

PubMed

Ryu, Kyoung-Seok; Tugarinov, Vitali; Clore, G Marius

2014-10-15

The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by (15)Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5-1 s) is many orders of magnitude larger than the calculated transfer time (1-100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.

General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding.

PubMed

Lucius, Aaron L; Maluf, Nasib K; Fischer, Christopher J; Lohman, Timothy M

2003-10-01

Helicase-catalyzed DNA unwinding is often studied using "all or none" assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using "n-step" sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the "kinetic step size", m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using "n-step" sequential mechanisms has previously been limited by an inability to float the number of "unwinding steps", n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, f(ss)(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain f(ss)(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation.

Phosphoryl transfer is not rate-limiting for the ROCK I-catalyzed kinase reaction.

PubMed

Futer, Olga; Saadat, Ahmad R; Doran, John D; Raybuck, Scott A; Pazhanisamy, S

2006-06-27

Rho-associated coiled-coil kinase, ROCK, is implicated in Rho-mediated cell adhesion and smooth muscle contraction. Animal models suggest that the inhibition of ROCK can ameliorate conditions, such as vasospasm, hypertension, and inflammation. As part of our effort to design novel inhibitors of ROCK, we investigated the kinetic mechanism of ROCK I. Steady-state bisubstrate kinetics, inhibition kinetics, isotope partition analysis, viscosity effects, and presteady-state kinetics were used to explore the kinetic mechanism. Plots of reciprocals of initial rates obtained in the presence of nonhydrolyzable ATP analogues and the small molecule inhibitor of ROCK, Y-27632, against the reciprocals of the peptide concentrations yielded parallel lines (uncompetitive pattern). This pattern is indicative of an ordered binding mechanism, with the peptide adding first. The staurosporine analogue K252a, however, gave a noncompetitive pattern. When a pulse of (33)P-gamma-ATP mixed with ROCK was chased with excess unlabeled ATP and peptide, 0.66 enzyme equivalent of (33)P-phosphate was incorporated into the product in the first turnover. The presence of ATPase activity coupled with the isotope partition data is a clear evidence for the existence of a viable [E-ATP] complex in the kinase reaction and implicates a random binding mechanism. The k(cat)/K(m) parameters were fully sensitive to viscosity (viscosity effects of 1.4 +/- 0.2 and 0.9 +/- 0.3 for ATP and peptide 5, respectively), and therefore, the barriers to dissociation of either substrate are higher than the barrier for the phosphoryl transfer step. As a consequence, not all the binding steps are at fast equilibrium. The observation of a burst in presteady-state kinetics (k(b) = 10.2 +/- 2.1 s(-)(1)) and the viscosity effect on k(cat) of 1.3 +/- 0.2 characterize the phosphoryl transfer step to be fast and the release of product and/or the enzyme isomerization step accompanying it as rate-limiting at V(max) conditions. From the multiple kinetic studies, most of the rate constants for the individual steps were either evaluated or estimated.

Exploring transduction mechanisms of protein transduction domains (PTDs) in living cells utilizing single-quantum dot tracking (SQT) technology.

PubMed

Suzuki, Yasuhiro

2012-01-01

Specific protein domains known as protein transduction domains (PTDs) can permeate cell membranes and deliver proteins or bioactive materials into living cells. Various approaches have been applied for improving their transduction efficacy. It is, therefore, crucial to clarify the entry mechanisms and to identify the rate-limiting steps. Because of technical limitations for imaging PTD behavior on cells with conventional fluorescent-dyes, how PTDs enter the cells has been a topic of much debate. Utilizing quantum dots (QDs), we recently tracked the behavior of PTD that was derived from HIV-1 Tat (TatP) in living cells at the single-molecule level with 7-nm special precision. In this review article, we initially summarize the controversy on TatP entry mechanisms; thereafter, we will focus on our recent findings on single-TatP-QD tracking (SQT), to identify the major sequential steps of intracellular delivery in living cells and to discuss how SQT can easily provide direct information on TatP entry mechanisms. As a primer for SQT study, we also discuss the latest findings on single particle tracking of various molecules on the plasma membrane. Finally, we discuss the problems of QDs and the challenges for the future in utilizing currently available QD probes for SQT. In conclusion, direct identification of the rate-limiting steps of PTD entry with SQT should dramatically improve the methods for enhancing transduction efficiency.

Kinetics of dissolution of UO2 in nitric acid solutions: A multiparametric study of the non-catalysed reaction

NASA Astrophysics Data System (ADS)

Cordara, T.; Szenknect, S.; Claparede, L.; Podor, R.; Mesbah, A.; Lavalette, C.; Dacheux, N.

2017-12-01

UO2 pellets were prepared by densification of oxides obtained from the conversion of the oxalate precursor. Then characterized in order to perform a multiparametric study of the dissolution in nitric acid medium. In this frame, for each sample, the densification rate, the grain size and the specific surface area of the prepared pellets were determined prior to the final dissolution experiments. By varying the concentration of the nitric acid solution and temperature, three different and successive steps were identified during the dissolution. Under the less aggressive conditions considered, a first transient step corresponding to the dissolution of the most reactive phases was observed at the solid/solution interface. Then, for all the tested conditions, a steady state step was established during which the normalised dissolution rate was found to be constant. It was followed by a third step characterized by a strong and continuous increase of the normalised dissolution rate. The duration of the steady state, also called "induction period", was found to vary drastically as a function of the HNO3 concentration and temperature. However, independently of the conditions, this steady state step stopped at almost similar dissolved material weight loss and dissolved uranium concentration. During the induction period, no important evolution of the topology of the solid/liquid interface was evidenced authorizing the use of the starting reactive specific surface area to evaluate the normalised dissolution rates thus the chemical durability of the sintered pellets. From the multiparametric study of UO2 dissolution proposed, oxidation of U(IV) to U(VI) by nitrate ions at the solid/liquid interface constitutes the limiting step in the overall dissolution mechanism associated to this induction period.

Selective nickel-catalyzed conversion of model and lignin-derived phenolic compounds to cyclohexanone-based polymer building blocks.

PubMed

Schutyser, Wouter; Van den Bosch, Sander; Dijkmans, Jan; Turner, Stuart; Meledina, Maria; Van Tendeloo, Gustaaf; Debecker, Damien P; Sels, Bert F

2015-05-22

Valorization of lignin is essential for the economics of future lignocellulosic biorefineries. Lignin is converted into novel polymer building blocks through four steps: catalytic hydroprocessing of softwood to form 4-alkylguaiacols, their conversion into 4-alkylcyclohexanols, followed by dehydrogenation to form cyclohexanones, and Baeyer-Villiger oxidation to give caprolactones. The formation of alkylated cyclohexanols is one of the most difficult steps in the series. A liquid-phase process in the presence of nickel on CeO2 or ZrO2 catalysts is demonstrated herein to give the highest cyclohexanol yields. The catalytic reaction with 4-alkylguaiacols follows two parallel pathways with comparable rates: 1) ring hydrogenation with the formation of the corresponding alkylated 2-methoxycyclohexanol, and 2) demethoxylation to form 4-alkylphenol. Although subsequent phenol to cyclohexanol conversion is fast, the rate is limited for the removal of the methoxy group from 2-methoxycyclohexanol. Overall, this last reaction is the rate-limiting step and requires a sufficient temperature (>250 °C) to overcome the energy barrier. Substrate reactivity (with respect to the type of alkyl chain) and details of the catalyst properties (nickel loading and nickel particle size) on the reaction rates are reported in detail for the Ni/CeO2 catalyst. The best Ni/CeO2 catalyst reaches 4-alkylcyclohexanol yields over 80 %, is even able to convert real softwood-derived guaiacol mixtures and can be reused in subsequent experiments. A proof of principle of the projected cascade conversion of lignocellulose feedstock entirely into caprolactone is demonstrated by using Cu/ZrO2 for the dehydrogenation step to produce the resultant cyclohexanones (≈80 %) and tin-containing beta zeolite to form 4-alkyl-ε-caprolactones in high yields, according to a Baeyer-Villiger-type oxidation with H2 O2 . © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism of Copper(I)/TEMPO-Catalyzed Aerobic Alcohol Oxidation

PubMed Central

Hoover, Jessica M.; Ryland, Bradford L.; Stahl, Shannon S.

2013-01-01

Homogeneous Cu/TEMPO catalyst systems (TEMPO = 2,2,6,6-tetramethylpiperidine-N-oxyl) have emerged as some of the most versatile and practical catalysts for aerobic alcohol oxidation. Recently, we disclosed a (bpy)CuI/TEMPO/NMI catalyst system (NMI = N-methylimidazole) that exhibits fast rates and high selectivities, even with unactivated aliphatic alcohols. Here, we present a mechanistic investigation of this catalyst system, in which we compare the reactivity of benzylic and aliphatic alcohols. This work includes analysis of catalytic rates by gas-uptake and in situ IR kinetic methods and characterization of the catalyst speciation during the reaction by EPR and UV–visible spectroscopic methods. The data support a two-stage catalytic mechanism consisting of (1) “catalyst oxidation” in which CuI and TEMPO–H are oxidized by O2 via a binuclear Cu2O2 intermediate and (2) “substrate oxidation” mediated by CuII and the nitroxyl radical of TEMPO via a CuII-alkoxide intermediate. Catalytic rate laws, kinetic isotope effects, and spectroscopic data show that reactions of benzylic and aliphatic alcohols have different turnover-limiting steps. Catalyst oxidation by O2 is turnover limiting with benzylic alcohols, while numerous steps contribute to the turnover rate in the oxidation of aliphatic alcohols. PMID:23317450

Structure-function analysis of diacylglycerol acyltransferase sequences for metabolic engineering and drug discovery

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferase families (DGATs) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGAT knockout mice are resistant to diet-induced obesity and lack milk secretion. Over-expression of DGATs increases TAG in plants. Therefore, unde...

Yeast metabolic engineering for hemicellulosic ethanol production

Treesearch

Jennifer Van Vleet; Thomas W. Jeffries

2009-01-01

Efficient fermentation of hemicellulosic sugars is critical for the bioconversion of lignocellulosics to ethanol. Efficient sugar uptake through the heterologous expression of yeast and fungal xylose/glucose transporters can improve fermentation if other metabolic steps are not rate limiting. Rectification of cofactor imbalances through heterologous expression of...

The natural weathering of staurolite: crystal-surface textures, relative stability, and the rate-determining step

Treesearch

Michael A. Velbel; Charles L. Basso; Michael J. Zieg

1996-01-01

Mineral surface-textures on naturally weathered crystals of staurolite [monoclinic, pseudo-orthorhombic; Fe4Al18Si8O46(OH)2] indicate that staurolite weathering is generally interface-limited. Etch pits on naturally weathered staurolites are disk-shaped,...

The Impact of Data Fragmentation on High-Throughput Clinical Phenotyping

ERIC Educational Resources Information Center

Wei, Weiqi

2012-01-01

Subject selection is essential and has become the rate-limiting step for harvesting knowledge to advance healthcare through clinical research. Present manual approaches inhibit researchers from conducting deep and broad studies and drawing confident conclusions. High-throughput clinical phenotyping (HTCP), a recently proposed approach, leverages…

Kinetics of piroxicam release from low-methylated pectin/zein hydrogel microspheres

USDA-ARS?s Scientific Manuscript database

The kinetics of a model drug (piroxicam) release from pectin/zein hydrogel microspheres was studied under conditions simulating the gastrointestinal tract. It is established that the rate-limiting step in the release mechanism is drug diffusion out of the microspheres rather than its dissolution. ...

Event-Triggered Distributed Average Consensus Over Directed Digital Networks With Limited Communication Bandwidth.

PubMed

Li, Huaqing; Chen, Guo; Huang, Tingwen; Dong, Zhaoyang; Zhu, Wei; Gao, Lan

2016-12-01

In this paper, we consider the event-triggered distributed average-consensus of discrete-time first-order multiagent systems with limited communication data rate and general directed network topology. In the framework of digital communication network, each agent has a real-valued state but can only exchange finite-bit binary symbolic data sequence with its neighborhood agents at each time step due to the digital communication channels with energy constraints. Novel event-triggered dynamic encoder and decoder for each agent are designed, based on which a distributed control algorithm is proposed. A scheme that selects the number of channel quantization level (number of bits) at each time step is developed, under which all the quantizers in the network are never saturated. The convergence rate of consensus is explicitly characterized, which is related to the scale of network, the maximum degree of nodes, the network structure, the scaling function, the quantization interval, the initial states of agents, the control gain and the event gain. It is also found that under the designed event-triggered protocol, by selecting suitable parameters, for any directed digital network containing a spanning tree, the distributed average consensus can be always achieved with an exponential convergence rate based on merely one bit information exchange between each pair of adjacent agents at each time step. Two simulation examples are provided to illustrate the feasibility of presented protocol and the correctness of the theoretical results.

Relationship of Catalysis and Active Site Loop Dynamics in the (βα)8-Barrel Enzyme Indole-3-glycerol Phosphate Synthase.

PubMed

Schlee, Sandra; Klein, Thomas; Schumacher, Magdalena; Nazet, Julian; Merkl, Rainer; Steinhoff, Heinz-Jürgen; Sterner, Reinhard

2018-03-08

It is important to understand how the catalytic activity of enzymes is related to their conformational flexibility. We have studied this activity-flexibility correlation using the example of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (ssIGPS), which catalyzes the fifth step in the biosynthesis of tryptophan. ssIGPS is a thermostable representative of enzymes with the frequently encountered and catalytically versatile (βα) 8 -barrel fold. Four variants of ssIGPS with increased catalytic turnover numbers were analyzed by transient kinetics at 25 °C, and wild-type ssIGPS was likewise analyzed both at 25 °C and at 60 °C. Global fitting with a minimal three-step model provided the individual rate constants for substrate binding, chemical transformation, and product release. The results showed that in both cases, namely, the application of activating mutations and temperature increase, the net increase in the catalytic turnover number is afforded by acceleration of the product release rate relative to the chemical transformation steps. Measurements of the solvent viscosity effect at 25 °C versus 60 °C confirmed this change in the rate-determining step with temperature, which is in accordance with a kink in the Arrhenius diagram of ssIGPS at ∼40 °C. When rotational diffusion rates of electron paramagnetic spin-labels attached to active site loop β1α1 are plotted in the form of an Arrhenius diagram, kinks are observed at the same temperature. These findings, together with molecular dynamics simulations, demonstrate that a different degree of loop mobility correlates with different rate-limiting steps in the catalytic mechanism of ssIGPS.

Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics.

PubMed

Urakawa, Atsushi; Iannuzzi, Marcella; Hutter, Jürg; Baiker, Alfons

2007-01-01

Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.

Mechanisms of deep benzene oxidation on the Pt(1 1 1) surface using temperature-programmed reaction methods

NASA Astrophysics Data System (ADS)

Marsh, Anderson L.; Gland, John L.

2003-06-01

The catalytic oxidation of benzene on the Pt(1 1 1) surface has been characterized using temperature-programmed reaction spectroscopy (TPRS) over a wide range of benzene and oxygen coverages. Coadsorbed atomic oxygen and benzene are the primary reactants on the surface during the initial oxidation step. Benzene is oxidized over the 300-500 K range to produce carbon dioxide and water. Carbon-hydrogen and carbon-carbon bond activation are clearly rate-limiting steps for these reactions. Preferential oxidation causes depletion of bridge-bonded benzene, suggesting enhanced reactivity in this bonding configuration. When oxygen is in excess on the surface, all of the surface carbon and hydrogen is oxidized. When benzene is in excess on the surface, hydrogen produced by dehydrogenation is desorbed after all of the surface oxygen has been consumed. Repulsive interactions between benzene and molecular oxygen dominate at low temperatures. Preadsorption of oxygen inhibits adsorption of less reactive benzene in threefold hollow sites. The desorption temperature of this non-reactive chemisorbed benzene decreases and overlaps with the multilayer desorption peak with increasing oxygen exposure. The results presented here provide a clear picture of rate-limiting steps during deep oxidation of benzene on the Pt(1 1 1) surface.

Conformational Changes Represent the Rate-Limiting Step in the Transport Cycle of Maize SUCROSE TRANSPORTER1[C][W

PubMed Central

Derrer, Carmen; Wittek, Anke; Bamberg, Ernst; Carpaneto, Armando; Dreyer, Ingo; Geiger, Dietmar

2013-01-01

Proton-driven Suc transporters allow phloem cells of higher plants to accumulate Suc to more than 1 M, which is up to ∼1000-fold higher than in the surrounding extracellular space. The carrier protein can accomplish this task only because proton and Suc transport are tightly coupled. This study provides insights into this coupling by resolving the first step in the transport cycle of the Suc transporter SUT1 from maize (Zea mays). Voltage clamp fluorometry measurements combining electrophysiological techniques with fluorescence-based methods enable the visualization of conformational changes of SUT1 expressed in Xenopus laevis oocytes. Using the Suc derivate sucralose, binding of which hinders conformational changes of SUT1, the association of protons to the carrier could be dissected from transport-associated movements of the protein. These combined approaches enabled us to resolve the binding of protons to the carrier and its interrelationship with the alternating movement of the protein. The data indicate that the rate-limiting step of the reaction cycle is determined by the accessibility of the proton binding site. This, in turn, is determined by the conformational change of the SUT1 protein, alternately exposing the binding pockets to the inward and to the outward face of the membrane. PMID:23964025

In Situ Observation of Calcium Aluminate Inclusions Dissolution into Steelmaking Slag

NASA Astrophysics Data System (ADS)

Miao, Keyan; Haas, Alyssa; Sharma, Mukesh; Mu, Wangzhong; Dogan, Neslihan

2018-06-01

The dissolution rate of calcium aluminate inclusions in CaO-SiO2-Al2O3 slags has been studied using confocal scanning laser microscopy (CSLM) at elevated temperatures: 1773 K, 1823 K, and 1873 K (1500 °C, 1550 °C, and 1600 °C). The inclusion particles used in this experimental work were produced in our laboratory and their production technique is explained in detail. Even though the particles had irregular shapes, there was no rotation observed. Further, the total dissolution time decreased with increasing temperature and decreasing SiO2 content in the slag. The rate limiting steps are discussed in terms of shrinking core models and diffusion into a stagnant fluid model. It is shown that the rate limiting step for dissolution is mass transfer in the slag at 1823 K and 1873 K (1550 °C and 1600 °C). Further investigations are required to determine the dissolution mechanism at 1773 K (1500 °C). The calculated diffusion coefficients were inversely proportional to the slag viscosity and the obtained values for the systems studied ranged between 5.64 × 10-12 and 5.8 × 10-10 m2/s.

The Kinetics of Myosin Light Chain Kinase Activation of Smooth Muscle Myosin in an In Vitro Model System

PubMed Central

Hong, Feng; Facemyer, Kevin C.; Carter, Michael S.; Jackson, Del R.; Haldeman, Brian D.; Ruana, Nick; Sutherland, Cindy; Walsh, Michael P.; Cremo, Christine R.; Baker, Josh E.

2013-01-01

During activation of smooth muscle contraction, one myosin light chain kinase (MLCK) molecule rapidly phosphorylates many smooth muscle myosin (SMM) molecules, suggesting that muscle activation rates are influenced by the kinetics of MLCK-SMM interactions. To determine the rate-limiting step underlying activation of SMM by MLCK, we measured the kinetics of calcium-calmodulin (Ca2+-CaM)-MLCK-mediated SMM phosphorylation and the corresponding initiation of SMM-based F-actin motility in an in vitro system with SMM attached to a coverslip surface. Fitting the time course of SMM phosphorylation to a kinetic model gave an initial phosphorylation rate, kpo, of ~1.17 heads s−1·MLCK−1. Also we measured the dwell time of single QD-labeled MLCK molecules interacting with surface-attached SMM and phosphorylated SMM using total internal reflection fluorescence microscopy. From these data, the dissociation rate constant from phosphorylated SMM was 0.80 s−1, which was similar to kpo mentioned above and with rates measured in solution. This dissociation rate was essentially independent of the phosphorylation state of SMM. From calculations using our measured dissociation rates and Kds, and estimates of [SMM] and [MLCK] in muscle, we predict that the dissociation of MLCK from phosphorylated SMM is rate-limiting and that the rate of the phosphorylation step is faster than this dissociation rate. Also, association to SMM (11-46 s−1) would be much faster than to pSMM (<0.1-0.2 s−1). This suggests that the probability of MLCK interacting with unphosphorylated versus pSMM is 55-460 times greater. This would avoid sequestering MLCK to unproductive interactions with previously phosphorylated SMM, potentially leading to faster rates of phosphorylation in muscle. PMID:24144337

Predator-prey-subsidy population dynamics on stepping-stone domains.

PubMed

Shen, Lulan; Van Gorder, Robert A

2017-05-07

Predator-prey-subsidy dynamics on stepping-stone domains are examined using a variety of network configurations. Our problem is motivated by the interactions between arctic foxes (predator) and lemmings (prey) in the presence of seal carrion (subsidy) provided by polar bears. We use the n-Patch Model, which considers space explicitly as a "Stepping Stone" system. We consider the role that the carrying capacity, predator migration rate, input subsidy rate, predator mortality rate, and proportion of predators surviving migration play in the predator-prey-subsidy population dynamics. We find that for certain types of networks, added mobility will help predator populations, allowing them to survive or coexist when they would otherwise go extinct if confined to one location, while in other situations (such as when sparsely distributed nodes in the network have few resources available) the added mobility will hurt the predator population. We also find that a combination of favourable conditions for the prey and subsidy can lead to the formation of limit cycles (boom and bust dynamic) from stable equilibrium states. These modifications to the dynamics vary depending on the specific network structure employed, highlighting the fact that network structure can strongly influence the predator-prey-subsidy dynamics in stepping-stone domains. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient Green's Function Reaction Dynamics (GFRD) simulations for diffusion-limited, reversible reactions

NASA Astrophysics Data System (ADS)

Bashardanesh, Zahedeh; Lötstedt, Per

2018-03-01

In diffusion controlled reversible bimolecular reactions in three dimensions, a dissociation step is typically followed by multiple, rapid re-association steps slowing down the simulations of such systems. In order to improve the efficiency, we first derive an exact Green's function describing the rate at which an isolated pair of particles undergoing reversible bimolecular reactions and unimolecular decay separates beyond an arbitrarily chosen distance. Then the Green's function is used in an algorithm for particle-based stochastic reaction-diffusion simulations for prediction of the dynamics of biochemical networks. The accuracy and efficiency of the algorithm are evaluated using a reversible reaction and a push-pull chemical network. The computational work is independent of the rates of the re-associations.

Amylolysis of raw corn by Aspergillus niger for simultaneous ethanol fermentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, I.Y.; Steinberg, M.P.

The novelty of this approach was hydrolysis of the raw starch in ground corn to fermentable sugars that are simultaneously fermented to ethanol by yeast in a nonsterile environment. Thus, the conventional cooking step can be eliminated for energy conservation. A koji of Aspergillus niger grown on whole corn for 3 days was the crude enzyme source. A ratio of 0.2 g dry koji/g total solids was found sufficient. Optimum pH was 4.2. Ethanol concentration was 7.7% (w/w) in the aqueous phase with 92% raw starch conversion. Agitation increased rate. Sacharification was the rate-limiting step. The initial ethanol concentration preventingmore » fermentation was estimated to be 8.3% by weight. (Refs. 96).« less

Structure-function analysis of diacylglycerol acyltransferase sequences from tung tree and 82 other Organisms

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferase family (DGATs) catalyzes the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGATs esterify sn-1,2-diacylglycerol with a long-chain fatty acyl-CoA. Understanding the roles of DGATs will help to create transgenic plants with v...

A versatile phenotyping system and analytics platform reveals diverse temporal responses to water availability in Setaria

USDA-ARS?s Scientific Manuscript database

With rapid advances in DNA sequencing, phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping platform for controlled-environment plant growth and automated, multimodal phenotyping is described. T...

Variant amino acid residues alter the enzyme activity of peanut type 2 Diacylglycerol Acyltransferases

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferase (DGAT) catalyzes the final, rate-limiting step in triacylglycerol (TAG) biosynthesis via the acyl-CoA-dependent acylation of diacylglycerol. In this study, type-2 DGAT2 genes were cloned from eleven peanut cultivars. Sequence analysis revealed at least eight peanut D...

Developmental regulation of diacylglycerol acyltransferase family gene expression in tung tree tissues

USDA-ARS?s Scientific Manuscript database

Diacylglycerol acyltransferases (DGAT) are responsible for the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGAT genes have been identified in numerous organisms. Multiple isoforms of DGAT are present in eukaryotes, including DGAT1 and DGAT2 of tung tre...

Isolation of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase from Leaves

USDA-ARS?s Scientific Manuscript database

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a multi-functional enzyme that catalyzes the fixation of CO2 and O2 in photosynthesis and photorespiration, respectively. As the rate-limiting step in photosynthesis, improving the catalytic properties of Rubisco has long been viewed as a...

NONEQUILIBRIUM SORPTION DURING DISPLACEMENT OF HYRDOPHOBIC ORGANIC CHEMICALS AND 45CA THROUGH SOIL COLUMNS WITH AQUEOUS AND MIXED SOLVENTS

EPA Science Inventory

A series of miscible displacement experiments was conducted to investigate the significance of intraorganic matter diffusion (IOMD) as the rate-limiting step in sorption of organic and inorganic solutes during steady water flow in soil columns. Displacement studies were performed...

Watch Your Step: The Impacts of Personal Consumption on the Environment.

ERIC Educational Resources Information Center

Camill, Philip

2002-01-01

Presents a case study on sustainability using the concept "Ecological Footprint" to focus on the Biosphere II experiment. Discusses the increasing rate of population growth and Earth's capability of sustaining humans with its limited natural resources, material consumption, and pollution and how to measure sustainability. Includes…

Kinetics of Reduction of CaO-FeO x -MgO-PbO-SiO2 Slags by CO-CO2 Gas Mixtures

NASA Astrophysics Data System (ADS)

Jahanshahi, Sharif; Wright, Steven

2017-08-01

Kinetics of the reaction of lead slags (PbO-CaO-SiO2-FeO x -MgO) with CO-CO2 gas mixtures was studied by monitoring the changes in the slag composition when a stream of CO-CO2 gas mixture was blown on the surface of thin layers of slags (3 to 10 mm) at temperatures in the range of 1453 K to 1593 K (1180 °C to 1320 °C). These measurements were carried out under conditions where mass transfer in the gas phase was not the rate-limiting step and the reduction rates were insensitive to factors affecting mass transfer in the slag phase. The results show simultaneous reduction of PbO and Fe2O3 in the slag. The measured specific rate of oxygen removal from the melts varied from about 1 × 10-6 to 4 × 10-5 mol O cm-2 s-1 and was strongly dependent on the slag chemistry and its oxidation state, partial pressure of CO in the reaction gas mixture, and temperature. The deduced apparent first-order rate constant increased with increasing iron oxide content, oxidation state of the slag, and temperature. The results indicate that under the employed experimental conditions, the rate of formation of CO2 at the gas-slag interface is likely to be the rate-limiting step.

Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us.

PubMed

Penning, Trevor M

2016-07-01

Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily. Copyright © 2015 Elsevier Ltd. All rights reserved.

A kinetic model for the synthesis of high-molecular-weight alcohols over a sulfided Co-K-Mo/C catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunturu, A.K.; Kugler, E.L.; Cropley, J.B.

A statistically designed set of experiments was run in a recycle reactor to evaluate the kinetics of the formation of higher-molecular-weight alcohols (higher alcohols) and total hydrocarbon byproducts from synthesis gas (hydrogen and carbon monoxide) in a range of experimental conditions that mirrors the limits of commercial production. The alkali-promoted, C-supported Co-Mo sulfide catalyst that was employed in this study is well known for its sulfur resistance. The reaction was carried out in a gradientless Berty-type recycle reactor. A two-level fractional-factorial set consisting of 16 experiments was performed. Five independent variables were selected for this study, namely, temperature, partial pressuremore » of carbon monoxide, partial pressure of hydrogen, partial pressure of inerts, and methanol concentration in the feed. The major oxygenated products were linear alcohols up to n-butanol, but alcohols of higher carbon number were also detected, and analysis of the liquid product revealed the presence of trace amounts of ethers also. Yields of hydrocarbons were non-negligible. The alcohol product followed an Anderson-Schultz-Flory distribution. From the results of the factorial experiments, a preliminary power-law model was developed, and the statistically significant variables in the rate expression for the production of each alcohol were found. Based on the results of the power-law models, rate expressions of the Langmuir-Hinshelwood type were fitted. The observed kinetics are consistent with the rate-limiting step for the production of each higher alcohol being a surface reaction of the alcohol of next-lower carbon number. All other steps, including CO-insertion, H{sub 2}-cleavage, and hydrogenation steps, do not appear to affect the rate correlations.« less

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

PubMed

Pan, Jing; Cha, Tae-Gon; Li, Feiran; Chen, Haorong; Bragg, Nina A; Choi, Jong Hyun

2017-01-01

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s -1 ) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers

PubMed Central

Pan, Jing; Cha, Tae-Gon; Li, Feiran; Chen, Haorong; Bragg, Nina A.; Choi, Jong Hyun

2017-01-01

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers’ small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s−1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps. PMID:28116353

Ultra High Strain Rate Nanoindentation Testing.

PubMed

Sudharshan Phani, Pardhasaradhi; Oliver, Warren Carl

2017-06-17

Strain rate dependence of indentation hardness has been widely used to study time-dependent plasticity. However, the currently available techniques limit the range of strain rates that can be achieved during indentation testing. Recent advances in electronics have enabled nanomechanical measurements with very low noise levels (sub nanometer) at fast time constants (20 µs) and high data acquisition rates (100 KHz). These capabilities open the doors for a wide range of ultra-fast nanomechanical testing, for instance, indentation testing at very high strain rates. With an accurate dynamic model and an instrument with fast time constants, step load tests can be performed which enable access to indentation strain rates approaching ballistic levels (i.e., 4000 1/s). A novel indentation based testing technique involving a combination of step load and constant load and hold tests that enables measurement of strain rate dependence of hardness spanning over seven orders of magnitude in strain rate is presented. A simple analysis is used to calculate the equivalent uniaxial response from indentation data and compared to the conventional uniaxial data for commercial purity aluminum. Excellent agreement is found between the indentation and uniaxial data over several orders of magnitude of strain rate.

Physical Activity and Falls in Older Men: The Critical Role of Mobility Limitations

PubMed Central

JEFFERIS, BARBARA J.; MEROM, DAFNA; SARTINI, CLAUDIO; WANNAMETHEE, S. GOYA; ASH, SARAH; LENNON, LUCY T.; ILIFFE, STEVE; KENDRICK, DENISE; WHINCUP, PETER H.

2015-01-01

ABSTRACT Background Physical activity (PA) has many health benefits but may increase falls risk among older adults. We study how objectively measured habitual daily PA is related to falls by exploring the modifying effect of mobility limitations and the mediating roles of fitness and lower-limb strength. Methods One thousand six hundred fifty-five (53%) of 3137 surviving participants (men age 71–91 yr) in an ongoing UK-population-based cohort study wore an ActiGraph GT3x accelerometer over the hip for 1 wk in 2010–2012 to measure PA (exposure) and reported demographic and health status, including mobility limitations. One year later, 825 men reported falls history (outcome). Results Seven hundred of 825 men had ≥600 min·d−1 of accelerometer wear for ≥3 d. Nineteen percent (n = 128) reported falls 1 yr later. Associations between PA and falls differed by presence of mobility limitations. Among 66% (n = 471) of men without mobility limitations, number of falls increased incrementally (for every 30 min of moderate to vigorous PA [MVPA]: incidence rate ratio [IRR], 1.50; 95% confidence interval [CI], 1.10–2.03, adjusted for falls risk factors). Step count was not related to number of falls below 9000 steps per day but was related to number of falls ≥9000 steps per day (for every additional 1000 steps per day: IRR, 1.59; 95% CI, 1.16–2.18). Among 33% (n = 229) of men with mobility limitations, falls risk declined with increasing activity (for every 1000 steps per day: IRR, 0.80; 95% CI, 0.70–0.91; for every 30 min of MVPA: IRR, 0.61; 95% CI, 0.42–0.89; for every additional 30 min of sedentary behavior ≥600 min·d−1: IRR, 1.22; 95% CI, 1.07–1.40). Conclusions Interventions to promote MVPA in older men should incorporate falls prevention strategies. Among adults with mobility limitations, trials should investigate whether increasing MVPA levels can reduce falls risk. PMID:25668406

Modeling of Hall Thruster Lifetime and Erosion Mechanisms (Preprint)

DTIC Science & Technology

2007-09-01

Hall thruster plasma discharge has been upgraded to simulate the erosion of the thruster acceleration channel, the degradation of which is the main life-limiting factor of the propulsion system. Evolution of the thruster geometry as a result of material removal due to sputtering is modeled by calculating wall erosion rates, stepping the grid boundary by a chosen time step and altering the computational mesh between simulation runs. The code is first tuned to predict the nose cone erosion of a 200 W Busek Hall thruster , the BHT-200. Simulated erosion

Computational Studies on the Pt(II)-Catalyzed Cycloisomerization of 1,6-dienes into Bicyclopropanes: A Mechanistic Quandary Evaluated by DFT

PubMed Central

Bell, Franziska; Holland, Jason; Green, Jennifer C.; Gagné, Michel R.

2009-01-01

The mechanism of the (bis(phosphanylethyl)phosphane)Pt2+ catalyzed cyclo-isomerization reaction of 7-methyl-octa-1,6-diene to form 1-isopropylbicyclo[3.1.0]hexane was studied using computational methods. The cyclopropanation step was found to be the turnover-limiting step. The overall reaction proceeds via both a 5-exo and a 6-endo route. W conformations were shown to facilitate cyclopropanation, but do not have any influence on the rate of the 1,2-hydride shifts. PMID:20161262

Dynamic tuning of optical absorbers for accelerated solar-thermal energy storage.

PubMed

Wang, Zhongyong; Tong, Zhen; Ye, Qinxian; Hu, Hang; Nie, Xiao; Yan, Chen; Shang, Wen; Song, Chengyi; Wu, Jianbo; Wang, Jun; Bao, Hua; Tao, Peng; Deng, Tao

2017-11-14

Currently, solar-thermal energy storage within phase-change materials relies on adding high thermal-conductivity fillers to improve the thermal-diffusion-based charging rate, which often leads to limited enhancement of charging speed and sacrificed energy storage capacity. Here we report the exploration of a magnetically enhanced photon-transport-based charging approach, which enables the dynamic tuning of the distribution of optical absorbers dispersed within phase-change materials, to simultaneously achieve fast charging rates, large phase-change enthalpy, and high solar-thermal energy conversion efficiency. Compared with conventional thermal charging, the optical charging strategy improves the charging rate by more than 270% and triples the amount of overall stored thermal energy. This superior performance results from the distinct step-by-step photon-transport charging mechanism and the increased latent heat storage through magnetic manipulation of the dynamic distribution of optical absorbers.

Aeration control of thermophilic aerobic digestion using fluorescence monitoring.

PubMed

Kim, Young-Kee; Oh, Byung-Keun

2009-01-01

The thermophilic aerobic digestion (TAD) process is recognized as an effective method for rapid waste activated sludge (WAS) degradation and the deactivation of pathogenic microorganisms. Yet, high energy costs due to heating and aeration have limited the commercialization of economical TAD processes. Previous research on autothermal thermophilic aerobic digestion (ATAD) has already reduced the heating cost. However, only a few studies have focused on reducing the aeration cost. Therefore, this study applied a two-step aeration control strategy to a fill-and-draw mode semicontinuous TAD process. The NADH-dependent fluorescence was monitored throughout the TAD experiment, and the aeration rate shifted according to the fluorescence intensity. As a result, the simple two-step aeration control operation achieved a 20.3% reduction in the total aeration, while maintaining an effective and stable operation. It is also expected that more savings can be achieved with a further reduction of the lower aeration rate or multisegmentation of the aeration rate.

Simplified Two-Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydorgen/Oxygen

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two-time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (> 1 x 10(exp -20) moles/cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T4). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/air fuel and for the H2/O2. A similar correlation is also developed using data from NASA s Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T4) as a function of overall fuel/air ratio, pressure and initial temperature (T3). High values of the regression coefficient R2 are obtained.

Summary of Simplified Two Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydrogen/Oxygen

NASA Technical Reports Server (NTRS)

Marek, C. John; Molnar, Melissa

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (greater than l x 10(exp -20)) moles per cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T(sub 4)). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/Air fuel and for H2/O2. A similar correlation is also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T(sub 4)) as a function of overall fuel/air ratio, pressure and initial temperature (T(sub 3)). High values of the regression coefficient R squared are obtained.

A theory of growing crystalline nanorods - Mode I

NASA Astrophysics Data System (ADS)

Du, Feng; Huang, Hanchen

2018-08-01

Nanorods grow in two possible modes during physical vapor deposition (PVD). In mode I, monolayer surface steps dictate the diameter of nanorods. In mode II, multiple-layer surface steps dictate the diameter, which is the smallest possible under physical vapor deposition [5,10]. This paper reports closed-form theories of terrace lengths and nanorod diameter during the growth in mode I, as a function of deposition conditions. The accompanying lattice kinetic Monte Carlo simulations verify these theories. This study reveals that (1) quasi-steady growth exists for each set of nanorod growth conditions, and (2) the characteristic length scales, including terrace lengths and nanorod diameter at the quasi-steady state, depend on the deposition conditions - deposition rate F, substrate temperature T, and incidence angle θ - only as a function of l2D/tan θ, with l2 D = 2(v2 D/Fcosθ) 1/3 as a diffusion-limited length scale and v2D as the atomic diffusion jump rate over monolayer surface steps.

Toxin-Induced Activation of Rat Hepatocyte Prostaglandin Synthesis and Phospholipid Metabolism

DTIC Science & Technology

1989-12-22

rate-limiting step in prostaglandin synthesis, which is controlled by balancing deacylating and reacylating activities (4,5). Several natural toxins...1980) Nature 288, 597- 600. 4. Ferber, E. and Ecker, B. (1984) Agents and Actions 15, 27-28. 5. Flesch, I., Ecker, B. and Ferber, E. (1984) Eur. J

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melchior, Jan-Patrick; Frick, Bernhard

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE PAGES

Melchior, Jan-Patrick; Frick, Bernhard

2017-09-22

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics

ERIC Educational Resources Information Center

Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel

2010-01-01

When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficients…

Maturation of hepatic lipase. Formation of functional enzyme in the endoplasmic reticulum is the rate-limiting step in its secretion.

PubMed

Ben-Zeev, Osnat; Doolittle, Mark H

2004-02-13

Among three lipases in the lipase gene family, hepatic lipase (HL), lipoprotein lipase, and pancreatic lipase, HL exhibits the lowest intracellular specific activity (i.e. minimal amounts of catalytic activity accompanied by massive amounts of inactive lipase mass in the endoplasmic reticulum (ER)). In addition, HL has a distinctive sedimentation profile, where the inactive mass overlaps the region containing active dimeric HL and trails into progressively larger molecular forms. Eventually, at least half of the HL inactive mass in the ER reaches an active, dimeric conformation (t(1/2) = 2 h) and is rapidly secreted. The remaining inactive mass is degraded. HL maturation occurs in the ER and is strongly dependent on binding to calnexin in the early co-/post-translational stages. Later stages of HL maturation occur without calnexin assistance, although inactive HL at all stages appears to be associated in distinct complexes with other ER proteins. Thus, unlike other lipases in the gene family, HL maturation is the rate-limiting step in its secretion as a functional enzyme.

Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

PubMed Central

Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

2014-01-01

The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

Myofilament properties comprise the rate-limiting step for cardiac relaxation at body temperature in the rat.

PubMed

Janssen, Paul M L; Stull, Linda B; Marbán, Eduardo

2002-02-01

The majority of studies aimed at characterizing basic contractile mechanisms have been conducted at room temperature. To elucidate the mechanism of cardiac relaxation under more physiological conditions, we investigated contractile function and calcium handling in ultrathin rat cardiac trabeculae. Active developed tension was unaltered between 22.5 and 30.0 degrees C (from 89 +/- 10 to 86 +/- 11 mN/mm(2), P = not significant) but steeply declined at 37.5 degrees C (30 +/- 5 mN/mm(2)). Meanwhile, the speed of relaxation (time from peak force to 50% relaxation) declined from 22.5 to 30.0 degrees C (from 360 +/- 40 to 157 +/- 17 ms) and further declined at 37.5 degrees C to 76 +/- 13 ms. Phase-plane analysis of calcium versus force revealed that, with increasing temperature, the relaxation phase is shifted rightward, indicating that the rate-limiting step of relaxation tends to depend more on calcium kinetics as temperature rises. The force-frequency relationship, which was slightly negative at 22.5 degrees C (0.1 vs. 1 Hz: 77 +/- 12 vs. 66 +/- 7 mN/mm(2)), became clearly positive at 37.5 degrees C (1 vs. 10 Hz: 30 +/- 5 vs. 69 +/- 9 mN/mm(2)). Phase-plane analyses indicated that, with increasing frequency, the relaxation phase is shifted leftward. We conclude that temperature independently affects contraction and relaxation, and cross-bridge cycling kinetics become rate limiting for cardiac relaxation under experimental conditions closest to those in vivo.

From minerals to hillslopes: Towards an integrated framework for interpreting chemical and physical erosion

NASA Astrophysics Data System (ADS)

Hahm, W.; Riebe, C. S.; Ferrier, K.; Kirchner, J. W.

2011-12-01

Traditional frameworks for conceptualizing hillslope denudation distinguish between the movement of mass in solution (chemical erosion) and mass moved via mechanical processes (physical erosion). At the hillslope scale, physical and chemical erosion rates can be quantified by combining measurements of regolith chemistry with cosmogenic nuclide concentrations in bedrock and sediment, while basin-scale rates are often inferred from riverine solute and sediment loads. These techniques integrate the effects of numerous weathering and erosion mechanisms and do not provide prima facie information about the precise nature and scale of those mechanisms. For insight into erosional process, physical erosion has been considered in terms of two limiting regimes. When physical erosion outpaces weathering front advance, regolith is mobilized downslope as soon as it is sufficiently loosened by weathering, and physical erosion rates are limited by rates of mobile regolith production. This is commonly termed weathering-limited erosion. Conversely, when weathering front advance outpaces erosion, the mobile regolith layer grows thicker over time, and physical erosion rates are limited by the efficiency of downslope transport processes. This is termed transport-limited erosion. This terminology brings the description of hillslope evolution closer to the realm of essential realism, to the extent that measurable quantities from the field can be cast in a process-based framework. An analogous process-limitation framework describes chemical erosion. In supply-limited chemical erosion, chemical weathering depletes regolith of its reactive phases during residence on a hillslope, and chemical erosion rates are limited by the supply of fresh minerals to the weathering zone. Alternatively, hillslopes may exhibit kinetic-limited chemical erosion, where physical erosion transports regolith downslope before weatherable phases are completely removed by chemical erosion. We show how supply- and kinetic-limited chemical erosion can be distinguished from one another using data from a global compilation of physical and chemical erosion rates. As a step towards understanding these rates at the level of essential realism, we explore how the hillslope-scale regimes of supply- and kinetic-limited chemical erosion relate to existing conceptual frameworks that interpret weathering rates in terms of transport- and kinetic-limitation at the mineral scale.

Chained Kullback-Leibler Divergences

PubMed Central

Pavlichin, Dmitri S.; Weissman, Tsachy

2017-01-01

We define and characterize the “chained” Kullback-Leibler divergence minw D(p‖w) + D(w‖q) minimized over all intermediate distributions w and the analogous k-fold chained K-L divergence min D(p‖wk−1) + … + D(w2‖w1) + D(w1‖q) minimized over the entire path (w1,…,wk−1). This quantity arises in a large deviations analysis of a Markov chain on the set of types – the Wright-Fisher model of neutral genetic drift: a population with allele distribution q produces offspring with allele distribution w, which then produce offspring with allele distribution p, and so on. The chained divergences enjoy some of the same properties as the K-L divergence (like joint convexity in the arguments) and appear in k-step versions of some of the same settings as the K-L divergence (like information projections and a conditional limit theorem). We further characterize the optimal k-step “path” of distributions appearing in the definition and apply our findings in a large deviations analysis of the Wright-Fisher process. We make a connection to information geometry via the previously studied continuum limit, where the number of steps tends to infinity, and the limiting path is a geodesic in the Fisher information metric. Finally, we offer a thermodynamic interpretation of the chained divergence (as the rate of operation of an appropriately defined Maxwell’s demon) and we state some natural extensions and applications (a k-step mutual information and k-step maximum likelihood inference). We release code for computing the objects we study. PMID:29130024

Kinetics of Schottky defect formation and annihilation in single crystal TlBr.

PubMed

Bishop, Sean R; Tuller, Harry L; Kuhn, Melanie; Ciampi, Guido; Higgins, William; Shah, Kanai S

2013-07-28

The kinetics for Schottky defect (Tl and Br vacancy pair) formation and annihilation in ionically conducting TlBr are characterized through a temperature induced conductivity relaxation technique. Near room temperature, defect generation-annihilation was found to take on the order of hours before equilibrium was reached after a step change in temperature, and that mechanical damage imparted on the sample rapidly increases this rate. The rate limiting step to Schottky defect formation-annihilation is identified as being the migration of lower mobility Tl (versus Br), with an estimate for source-sink density derived from calculated diffusion lengths. This study represents one of the first investigations of Schottky defect generation-annihilation kinetics and demonstrates its utility in quantifying detrimental mechanical damage in radiation detector materials.

A sandpile model of grain blocking and consequences for sediment dynamics in step-pool streams

NASA Astrophysics Data System (ADS)

Molnar, P.

2012-04-01

Coarse grains (cobbles to boulders) are set in motion in steep mountain streams by floods with sufficient energy to erode the particles locally and transport them downstream. During transport, grains are often blocked and form width-spannings structures called steps, separated by pools. The step-pool system is a transient, self-organizing and self-sustaining structure. The temporary storage of sediment in steps and the release of that sediment in avalanche-like pulses when steps collapse, leads to a complex nonlinear threshold-driven dynamics in sediment transport which has been observed in laboratory experiments (e.g., Zimmermann et al., 2010) and in the field (e.g., Turowski et al., 2011). The basic question in this paper is if the emergent statistical properties of sediment transport in step-pool systems may be linked to the transient state of the bed, i.e. sediment storage and morphology, and to the dynamics in sediment input. The hypothesis is that this state, in which sediment transporting events due to the collapse and rebuilding of steps of all sizes occur, is analogous to a critical state in self-organized open dissipative dynamical systems (Bak et al., 1988). To exlore the process of self-organization, a cellular automaton sandpile model is used to simulate the processes of grain blocking and hydraulically-driven step collapse in a 1-d channel. Particles are injected at the top of the channel and are allowed to travel downstream based on various local threshold rules, with the travel distance drawn from a chosen probability distribution. In sandpile modelling this is a simple 1-d limited non-local model, however it has been shown to have nontrivial dynamical behaviour (Kadanoff et al., 1989), and it captures the essence of stochastic sediment transport in step-pool systems. The numerical simulations are used to illustrate the differences between input and output sediment transport rates, mainly focussing on the magnification of intermittency and variability in the system response by the processes of grain blocking and step collapse. The temporal correlation in input and output rates and the number of grains stored in the system at any given time are quantified by spectral analysis and statistics of long-range dependence. Although the model is only conceptually conceived to represent the real processes of step formation and collapse, connections will be made between the modelling results and some field and laboratory data on step-pool systems. The main focus in the discussion will be to demonstrate how even in such a simple model the processes of grain blocking and step collapse may impact the sediment transport rates to the point that certain changes in input are not visible anymore, along the lines of "shredding the signals" proposed by Jerolmack and Paola (2010). The consequences are that the notions of stability and equilibrium, the attribution of cause and effect, and the timescales of process and form in step-pool systems, and perhaps in many other fluvial systems, may have very limited applicability.

The role of the chemical burns caused by hydroxide ion in the toxicity of dermal exposure to tetramethylammonium ion in a rat model.

PubMed

Wu, Chen-Long; Su, Shih-Bin; Lien, Hsiao-Yin; Guo, How-Ran

2012-11-01

To evaluate the role of the chemical burns caused by hydroxide ion in the fatal effects of tetramethylammonium ion (TMA) in dermal exposure to tetramethylammonium hydroxide (TMAH), we conducted a rat study consisting of two-step treatments with dermal exposure to NaOH and tetramethylammonium chloride (TMACl). In the first step, NaOH or saline was administered in the gauze on the shaved skin for 5 min, and in the second step, TMAH, TMACl, or saline was administered in the same way. The mean blood pressure (MBP), heart rate (HR), and survival in rats were compared among seven groups. Dermal exposure to saline and then 2.75 M TMACl introduced limited and temporary non-fatal effects. Exposure to 2.75 M NaOH and then saline had almost no effects and caused no deaths. Treatments with more concentrated NaOH or TMACl resulted in suppressions of MBP and HR, and deaths were observed after the dosing of TMACl. The toxicity of dermal exposure to TMA alone is limited, but fatal effects can be introduced by pre-treatment with hydroxide ion. Therefore, the chemical burn caused by hydroxide ion plays an essential role in the toxicity, implicating that effective neutralizing may help decreasing the fatality rate. Copyright © 2012 Elsevier Ltd and ISBI. All rights reserved.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects.

PubMed

Świderek, Katarzyna; Nödling, Alexander R; Tsai, Yu-Hsuan; Luk, Louis Y P; Moliner, Vicent

2018-01-11

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1-C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C-C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects

PubMed Central

2017-01-01

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1–C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C–C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent. PMID:29256614

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

PubMed Central

Min, Irene M.; Waterfall, Joshua J.; Core, Leighton J.; Munroe, Robert J.; Schimenti, John; Lis, John T.

2011-01-01

Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome's primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally engaged RNA polymerases in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ∼40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II's entry into elongation. Furthermore, “bivalent” ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb group complexes PRC1 (Polycomb-repressive complex 1) and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5′ proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation. PMID:21460038

New Reduced Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2004-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes that are being developed at Glenn. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx were obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

The Oxidation of AlN in Dry and Wet Oxygen

NASA Technical Reports Server (NTRS)

Opila, Elizabeth; Humphrey, Donald; Jacobson, Nathan; Yoshio, Tetsuo; Oda, Kohei

1998-01-01

The oxidation kinetics of AlN containing 3.5 wt% Y2O3 were studied by thermogravimetric analysis in dry oxygen and 10% H2O/balance oxygen at temperatures between 1000 and 1200 C for times between 48 and 100 h. The oxidation kinetics for AlN in dry oxygen were parabolic and of approximately the same magnitude and temperature dependence as other alumina forming materials. In this case, diffusion of oxygen and/or aluminum through the alumina scale is the rate limiting mechanism. The oxidation kinetics for AlN in wet oxygen were nearly linear and much more rapid than rates observed in dry oxygen. Numerous micropores were observed in the alumina formed on AIN in wet oxygen. These pores provide a fast path for oxygen transport. The linear kinetics observed in this case suggest that the interface reaction rate of AlN with wet oxygen is the oxidation rate limiting step.

Kinetic Analysis of DNA Strand Joining by Chlorella Virus DNA Ligase and the Role of Nucleotidyltransferase Motif VI in Ligase Adenylylation*

PubMed Central

Samai, Poulami; Shuman, Stewart

2012-01-01

Chlorella virus DNA ligase (ChVLig) is an instructive model for mechanistic studies of the ATP-dependent DNA ligase family. ChVLig seals 3′-OH and 5′-PO4 termini via three chemical steps: 1) ligase attacks the ATP α phosphorus to release PPi and form a covalent ligase-adenylate intermediate; 2) AMP is transferred to the nick 5′-phosphate to form DNA-adenylate; 3) the 3′-OH of the nick attacks DNA-adenylate to join the polynucleotides and release AMP. Each chemical step requires Mg2+. Kinetic analysis of nick sealing by ChVLig-AMP revealed that the rate constant for phosphodiester synthesis (kstep3 = 25 s−1) exceeds that for DNA adenylylation (kstep2 = 2.4 s−1) and that Mg2+ binds with similar affinity during step 2 (Kd = 0.77 mm) and step 3 (Kd = 0.87 mm). The rates of DNA adenylylation and phosphodiester synthesis respond differently to pH, such that step 3 becomes rate-limiting at pH ≤ 6.5. The pH profiles suggest involvement of one and two protonation-sensitive functional groups in catalysis of steps 2 and 3, respectively. We suggest that the 5′-phosphate of the nick is the relevant protonation-sensitive moiety and that a dianionic 5′-phosphate is necessary for productive step 2 catalysis. Motif VI, located at the C terminus of the OB-fold domain of ChVLig, is a conserved feature of ATP-dependent DNA ligases and GTP-dependent mRNA capping enzymes. Presteady state and burst kinetic analysis of the effects of deletion and missense mutations highlight the catalytic contributions of ChVLig motif VI, especially the Asp-297 carboxylate, exclusively during the ligase adenylylation step. PMID:22745124

Real-time traffic sign detection and recognition

NASA Astrophysics Data System (ADS)

Herbschleb, Ernst; de With, Peter H. N.

2009-01-01

The continuous growth of imaging databases increasingly requires analysis tools for extraction of features. In this paper, a new architecture for the detection of traffic signs is proposed. The architecture is designed to process a large database with tens of millions of images with a resolution up to 4,800x2,400 pixels. Because of the size of the database, a high reliability as well as a high throughput is required. The novel architecture consists of a three-stage algorithm with multiple steps per stage, combining both color and specific spatial information. The first stage contains an area-limitation step which is performance critical in both the detection rate as the overall processing time. The second stage locates suggestions for traffic signs using recently published feature processing. The third stage contains a validation step to enhance reliability of the algorithm. During this stage, the traffic signs are recognized. Experiments show a convincing detection rate of 99%. With respect to computational speed, the throughput for line-of-sight images of 800×600 pixels is 35 Hz and for panorama images it is 4 Hz. Our novel architecture outperforms existing algorithms, with respect to both detection rate and throughput

Square Wave Voltammetry of TNT at Gold Electrodes Modified with Self-Assembled Monolayers Containing Aromatic Structures

PubMed Central

Trammell, Scott A.; Zabetakis, Dan; Moore, Martin; Verbarg, Jasenka; Stenger, David A.

2014-01-01

Square wave voltammetry for the reduction of 2,4,6-trinitrotoluene (TNT) was measured in 100 mM potassium phosphate buffer (pH 8) at gold electrodes modified with self-assembled monolayers (SAMs) containing either an alkane thiol or aromatic ring thiol structures. At 15 Hz, the electrochemical sensitivity (µA/ppm) was similar for all SAMs tested. However, at 60 Hz, the SAMs containing aromatic structures had a greater sensitivity than the alkane thiol SAM. In fact, the alkane thiol SAM had a decrease in sensitivity at the higher frequency. When comparing the electrochemical response between simulations and experimental data, a general trend was observed in which most of the SAMs had similar heterogeneous rate constants within experimental error for the reduction of TNT. This most likely describes a rate limiting step for the reduction of TNT. However, in the case of the alkane SAM at higher frequency, the decrease in sensitivity suggests that the rate limiting step in this case may be electron tunneling through the SAM. Our results show that SAMs containing aromatic rings increased the sensitivity for the reduction of TNT when higher frequencies were employed and at the same time suppressed the electrochemical reduction of dissolved oxygen. PMID:25549081

Improving a natural enzyme activity through incorporation of unnatural amino acids.

PubMed

Ugwumba, Isaac N; Ozawa, Kiyoshi; Xu, Zhi-Qiang; Ely, Fernanda; Foo, Jee-Loon; Herlt, Anthony J; Coppin, Chris; Brown, Sue; Taylor, Matthew C; Ollis, David L; Mander, Lewis N; Schenk, Gerhard; Dixon, Nicholas E; Otting, Gottfried; Oakeshott, John G; Jackson, Colin J

2011-01-19

The bacterial phosphotriesterases catalyze hydrolysis of the pesticide paraoxon with very fast turnover rates and are thought to be near to their evolutionary limit for this activity. To test whether the naturally evolved turnover rate could be improved through the incorporation of unnatural amino acids and to probe the role of peripheral active site residues in nonchemical steps of the catalytic cycle (substrate binding and product release), we replaced the naturally occurring tyrosine amino acid at position 309 with unnatural L-(7-hydroxycoumarin-4-yl)ethylglycine (Hco) and L-(7-methylcoumarin-4-yl)ethylglycine amino acids, as well as leucine, phenylalanine, and tryptophan. Kinetic analysis suggests that the 7-hydroxyl group of Hco, particularly in its deprotonated state, contributes to an increase in the rate-limiting product release step of substrate turnover as a result of its electrostatic repulsion of the negatively charged 4-nitrophenolate product of paraoxon hydrolysis. The 8-11-fold improvement of this already highly efficient catalyst through a single rationally designed mutation using an unnatural amino acid stands in contrast to the difficulty in improving this native activity through screening hundreds of thousands of mutants with natural amino acids. These results demonstrate that designer amino acids provide easy access to new and valuable sequence and functional space for the engineering and evolution of existing enzyme functions.

Biochemical Kinetics Model of DSB Repair and GammaH2AX FOCI by Non-homologous End Joining

NASA Technical Reports Server (NTRS)

Cucinotta, Francis, A.; Pluth, Janice M.; Anderson, Jennifer A.; Harper, Jane V.; O'Neill, Peter

2007-01-01

We developed a biochemical kinetics approach to describe the repair of double strand breaks (DSB) produced by low LET radiation by modeling molecular events associated with the mechanisms of non-homologous end-joining (NHEJ). A system of coupled non-linear ordinary differential equations describes the induction of DSB and activation pathways for major NHEJ components including Ku(sub 70/80), DNA-PK(sub cs), and the Ligase IV-XRCC4 hetero-dimer. The autophosphorylation of DNA-PK(sub cs and subsequent induction of gamma-H2AX foci observed after ionizing radiation exposure were modeled. A two-step model of DNA-PK(sub cs) regulation of repair was developed with the initial step allowing access of other NHEJ components to breaks, and a second step limiting access to Ligase IV-XRCC4. Our model assumes that the transition from the first to second-step depends on DSB complexity, with a much slower-rate for complex DSB. The model faithfully reproduced several experimental data sets, including DSB rejoining as measured by pulsed-field electrophoresis (PFGE), quantification of the induction of gamma-H2AX foci, and live cell imaging of the induction of Ku(sub 70/80). Predictions are made for the behaviors of NHEJ components at low doses and dose-rates, where a steady-state is found at dose-rates of 0.1 Gy/hr or lower.

Catalysis by Orotidine 5′-Monophosphate Decarboxylase: Effect of 5-Fluoro and 4′-Substituents on the Decarboxylation of Two-Part Substrates†

PubMed Central

Goryanova, Bogdana; Spong, Krisztina; Amyes, Tina L.; Richard, John P.

2013-01-01

The syntheses of two novel truncated analogs of the natural substrate orotidine 5′-monophosphate (OMP) for orotidine 5′-monophosphate decarboxylase (OMPDC) with enhanced reactivity towards decarboxylation are reported: 1-(β-D-erythrofuranosyl)-5-fluoroorotic acid (FEO) and 5′-deoxy-5-fluoroorotidine (5′-dFO). A comparison of the second-order rate constants for the OMPDC-catalyzed decarboxylations of FEO (10 M−1 s−1) and 1-(β-D-erythrofuranosyl)orotic acid (EO, 0.026 M−1 s−1) shows that the vinyl carbanion-like transition state is stabilized by 3.5 kcal/mol by interactions with the 5-F substituent of FEO. The OMPDC-catalyzed decarboxylations of FEO and EO are both activated by exogenous phosphite dianion (HPO32−), but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction of FEO. This provides strong evidence that the phosphite-activated OMPDC-catalyzed reaction of FEO is not limited by the chemical step of decarboxylation of the enzyme-bound substrate. Evidence is presented that there is a change in rate-limiting step from the chemical step of decarboxylation for the phosphite-activated reaction of EO, to closure of the phosphate gripper loop and an enzyme conformational change at the ternary E·FEO·HPO32− complex for the reaction of FEO. The 4′-CH3 and 4′-CH2OH groups of 5′-dFO and orotidine, respectively, result in identical destabilizations of the transition state for the unactivated decarboxylation of 2.9 kcal/mol. By contrast, the 4′-CH3 group of 5′-dFO and the 4′-CH2OH group of orotidine result in very different 4.7 and 8.3 kcal/mol destabilizations of the transition state for the phosphite-activated decarboxylation. Here, the destabilizing effect of the 4′-CH3 substituent at 5′-dFO is masked by the rate-limiting conformational change that depresses the third-order rate constant for the phosphite-activated reaction of the parent substrate FEO. PMID:23276261

Catalysis by orotidine 5'-monophosphate decarboxylase: effect of 5-fluoro and 4'-substituents on the decarboxylation of two-part substrates.

PubMed

Goryanova, Bogdana; Spong, Krisztina; Amyes, Tina L; Richard, John P

2013-01-22

The syntheses of two novel truncated analogs of the natural substrate orotidine 5'-monophosphate (OMP) for orotidine 5'-monophosphate decarboxylase (OMPDC) with enhanced reactivity toward decarboxylation are reported: 1-(β-d-erythrofuranosyl)-5-fluoroorotic acid (FEO) and 5'-deoxy-5-fluoroorotidine (5'-dFO). A comparison of the second-order rate constants for the OMPDC-catalyzed decarboxylations of FEO (10 M⁻¹ s⁻¹) and 1-(β-d-erythrofuranosyl)orotic acid (EO, 0.026 M⁻¹ s⁻¹) shows that the vinyl carbanion-like transition state is stabilized by 3.5 kcal/mol by interactions with the 5-F substituent of FEO. The OMPDC-catalyzed decarboxylations of FEO and EO are both activated by exogenous phosphite dianion (HPO₃²⁻), but the 5-F substituent results in only a 0.8 kcal stabilization of the transition state for the phosphite-activated reaction of FEO. This provides strong evidence that the phosphite-activated OMPDC-catalyzed reaction of FEO is not limited by the chemical step of decarboxylation of the enzyme-bound substrate. Evidence is presented that there is a change in the rate-limiting step from the chemical step of decarboxylation for the phosphite-activated reaction of EO, to closure of the phosphate gripper loop and an enzyme conformational change at the ternary E•FEO•HPO₃²⁻ complex for the reaction of FEO. The 4'-CH₃ and 4'-CH₂OH groups of 5'-dFO and orotidine, respectively, result in identical destabilizations of the transition state for the unactivated decarboxylation of 2.9 kcal/mol. By contrast, the 4'-CH₃ group of 5'-dFO and the 4'-CH₂OH group of orotidine result in very different 4.7 and 8.3 kcal/mol destabilizations of the transition state for the phosphite-activated decarboxylation. Here, the destabilizing effect of the 4'-CH₃ substituent at 5'-dFO is masked by the rate-limiting conformational change that depresses the third-order rate constant for the phosphite-activated reaction of the parent substrate FEO.

Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review.

PubMed

Jeoh, Tina; Cardona, Maria J; Karuna, Nardrapee; Mudinoor, Akshata R; Nill, Jennifer

2017-07-01

Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

On Electron-Positron Pair Production by a Spatially Inhomogeneous Electric Field

NASA Astrophysics Data System (ADS)

Chervyakov, A.; Kleinert, H.

2018-05-01

A detailed analysis of electron-positron pair creation induced by a spatially non-uniform and static electric field from vacuum is presented. A typical example is provided by the Sauter potential. For this potential, we derive the analytic expressions for vacuum decay and pair production rate accounted for the entire range of spatial variations. In the limit of a sharp step, we recover the divergent result due to the singular electric field at the origin. The limit of a constant field reproduces the classical result of Euler, Heisenberg and Schwinger, if the latter is properly averaged over the width of a spatial variation. The pair production by the Sauter potential is described for different regimes from weak to strong fields. For all these regimes, the locally constant-field rate is shown to be the upper limit.

Increasing preferred step rate during running reduces plantar pressures.

PubMed

Gerrard, James M; Bonanno, Daniel R

2018-01-01

Increasing preferred step rate during running is a commonly used strategy in the management of running-related injuries. This study investigated the effect of different step rates on plantar pressures during running. Thirty-two healthy runners ran at a comfortable speed on a treadmill at five step rates (preferred, ±5%, and ±10%). For each step rate, plantar pressure data were collected using the pedar-X in-shoe system. Compared to running with a preferred step rate, a 10% increase in step rate significantly reduced peak pressure (144.5±46.5 vs 129.3±51 kPa; P=.033) and maximum force (382.3±157.6 vs 334.0±159.8 N; P=.021) at the rearfoot, and reduced maximum force (426.4±130.4 vs 400.0±116.6 N; P=.001) at the midfoot. In contrast, a 10% decrease in step rate significantly increased peak pressure (144.5±46.5 vs 161.5±49.3 kPa; P=.011) and maximum force (382.3±157.6 vs 425.4±155.3 N; P=.032) at the rearfoot. Changing step rate by 5% provided no effect on plantar pressures, and no differences in plantar pressures were observed at the medial forefoot, lateral forefoot or hallux between the step rates. This study's findings indicate that increasing preferred step rate by 10% during running will reduce plantar pressures at the rearfoot and midfoot, while decreasing step rate by 10% will increase plantar pressures at the rearfoot. However, changing preferred step rate by 5% will provide no effect on plantar pressures, and forefoot pressures are unaffected by changes in step rate. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Steps that count: physical activity recommendations, brisk walking, and steps per minute--how do they relate?

PubMed

Pillay, Julian D; Kolbe-Alexander, Tracy L; Proper, Karin I; van Mechelen, Willem; Lambert, Estelle V

2014-03-01

Brisk walking is recommended as a form of health-enhancing physical activity. This study determines the steps/minute rate corresponding to self-paced brisk walking (SPBW); a predicted steps/minute rate for moderate physical activity (MPA) and a comparison of the 2 findings. A convenience sample (N = 58: 34 men, 24 women, 31.7 ± 7.7 yrs), wearing pedometers and a heart rate (HR) monitor, performed SPBW for 10 minutes and 5 indoor sessions, regulated by a metronome (ranging from 60-120 steps/minute). Using steps/minute and HR data of the trials, a steps/minute rate for MPA was predicted. Adjustments were subsequently made for aerobic fitness (using maximal oxygen uptake (VO2max) estimates), age, and sex as possible contributors to stepping rate differences. Average steps/minute rate for SPBW was 118 ± 9 (116 ± 9; 121 ± 8 for men/women, respectively; P = .022); predicted steps/minute rate for MPA was 122 ± 37 (127 ± 36; 116 ± 39 for men/women, respectively; P < .99) and was similar to steps/minute rate of SPBW (P = .452), even after adjusting for age, sex, and aerobic fitness. Steps/minute rates of SPBW correlates closely with targeted HR for MPA, independent of aerobic fitness; predicted steps/minute rate for MPA relates closely to steps/minute rates of SPBW. Findings support current PA messages that use the term brisk walking as a reference for MPA.

Criteria for software modularization

NASA Technical Reports Server (NTRS)

Card, David N.; Page, Gerald T.; Mcgarry, Frank E.

1985-01-01

A central issue in programming practice involves determining the appropriate size and information content of a software module. This study attempted to determine the effectiveness of two widely used criteria for software modularization, strength and size, in reducing fault rate and development cost. Data from 453 FORTRAN modules developed by professional programmers were analyzed. The results indicated that module strength is a good criterion with respect to fault rate, whereas arbitrary module size limitations inhibit programmer productivity. This analysis is a first step toward defining empirically based standards for software modularization.

Individual Differences in Beat Perception Affect Gait Responses to Low- and High-Groove Music

PubMed Central

Leow, Li-Ann; Parrott, Taylor; Grahn, Jessica A.

2014-01-01

Slowed gait in patients with Parkinson’s disease (PD) can be improved when patients synchronize footsteps to isochronous metronome cues, but limited retention of such improvements suggest that permanent cueing regimes are needed for long-term improvements. If so, music might make permanent cueing regimes more pleasant, improving adherence; however, music cueing requires patients to synchronize movements to the “beat,” which might be difficult for patients with PD who tend to show weak beat perception. One solution may be to use high-groove music, which has high beat salience that may facilitate synchronization, and affective properties, which may improve motivation to move. As a first step to understanding how beat perception affects gait in complex neurological disorders, we examined how beat perception ability affected gait in neurotypical adults. Synchronization performance and gait parameters were assessed as healthy young adults with strong or weak beat perception synchronized to low-groove music, high-groove music, and metronome cues. High-groove music was predicted to elicit better synchronization than low-groove music, due to its higher beat salience. Two musical tempi, or rates, were used: (1) preferred tempo: beat rate matched to preferred step rate and (2) faster tempo: beat rate adjusted to 22.5% faster than preferred step rate. For both strong and weak beat-perceivers, synchronization performance was best with metronome cues, followed by high-groove music, and worst with low-groove music. In addition, high-groove music elicited longer and faster steps than low-groove music, both at preferred tempo and at faster tempo. Low-groove music was particularly detrimental to gait in weak beat-perceivers, who showed slower and shorter steps compared to uncued walking. The findings show that individual differences in beat perception affect gait when synchronizing footsteps to music, and have implications for using music in gait rehabilitation. PMID:25374521

Two-step rating-based 'double-faced applicability' test for sensory analysis of spread products as an alternative to descriptive analysis with trained panel.

PubMed

Kim, In-Ah; den-Hollander, Elyn; Lee, Hye-Seong

2018-03-01

Descriptive analysis with a trained sensory panel has thus far been the most well defined methodology to characterize various products. However, in practical terms, intensive training in descriptive analysis has been recognized as a serious defect. To overcome this limitation, various novel rapid sensory profiling methodologies have been suggested in the literature. Among these, attribute-based methodologies such as check-all-that-apply (CATA) questions showed results comparable to those of conventional sensory descriptive analysis. Kim, Hopkinson, van Hout, and Lee (2017a, 2017b) have proposed a novel attribute-based methodology termed the two-step rating-based 'double-faced applicability' test with a novel output measure of applicability magnitude (d' A ) for measuring consumers' product usage experience throughout various product usage stages. In this paper, the potential of the two-step rating-based 'double-faced applicability' test with d' A was investigated as an alternative to conventional sensory descriptive analysis in terms of sensory characterization and product discrimination. Twelve commercial spread products were evaluated using both conventional sensory descriptive analysis with a trained sensory panel and two-step rating-based 'double-faced applicability' test with an untrained sensory panel. The results demonstrated that the 'double-faced applicability' test can be used to provide a direct measure of the applicability magnitude of sensory attributes of the samples tested in terms of d' A for sensory characterization of individual samples and multiple sample comparisons. This suggests that when the appropriate list of attributes to be used in the questionnaire is already available, the two-step rating-based 'double-faced applicability' test with d' A can be used as a more efficient alternative to conventional descriptive analysis, without requiring any intensive training process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Single Turnover Kinetics of Tryptophan Hydroxylase: Evidence for a New Intermediate in the Reaction of the Aromatic Amino Acid Hydroxylases

PubMed Central

Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T.; Fitzpatrick, Paul F.

2010-01-01

Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH·Fe(II), TrpH·Fe(II)·tryptophan, TrpH·Fe(II)·6MePH4·tryptophan, and TrpH·Fe(II)·6MePH4·phenylalanine complexes with O2 were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH·Fe(II) has a value of 104 M−1s−1 irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH·Fe(II)·6MePH4·tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s−1 of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s−1, matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s−1, and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s−1. All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release. PMID:20687613

Regulation of Epithelial Sodium Transport via Epithelial Na+ Channel

PubMed Central

Marunaka, Yoshinori; Niisato, Naomi; Taruno, Akiyuki; Ohta, Mariko; Miyazaki, Hiroaki; Hosogi, Shigekuni; Nakajima, Ken-ichi; Kusuzaki, Katsuyuki; Ashihara, Eishi; Nishio, Kyosuke; Iwasaki, Yoshinobu; Nakahari, Takashi; Kubota, Takahiro

2011-01-01

Renal epithelial Na+ transport plays an important role in homeostasis of our body fluid content and blood pressure. Further, the Na+ transport in alveolar epithelial cells essentially controls the amount of alveolar fluid that should be kept at an appropriate level for normal gas exchange. The epithelial Na+ transport is generally mediated through two steps: (1) the entry step of Na+ via epithelial Na+ channel (ENaC) at the apical membrane and (2) the extrusion step of Na+ via the Na+, K+-ATPase at the basolateral membrane. In general, the Na+ entry via ENaC is the rate-limiting step. Therefore, the regulation of ENaC plays an essential role in control of blood pressure and normal gas exchange. In this paper, we discuss two major factors in ENaC regulation: (1) activity of individual ENaC and (2) number of ENaC located at the apical membrane. PMID:22028593

Experimental and Analytical Evaluation of Stressing-Rate State Evolution in Rate-State Friction Laws

NASA Astrophysics Data System (ADS)

Bhattacharya, P.; Rubin, A. M.; Bayart, E.; Savage, H. M.; Marone, C.; Beeler, N. M.

2013-12-01

Standard rate and state friction laws fail to explain the full range of observations from laboratory friction experiments. A new state evolution law has been proposed by Nagata et al. (2012) that adds a linear stressing-rate-dependent term to the Dieterich (aging) law, which may provide a remedy. They introduce a parameter c that controls the contribution of the stressing rate to state evolution. We show through analytical approximations that the new law can transition between the responses of the traditional Dieterich (aging) and Ruina (slip) laws in velocity step up/down experiments when the value of c is tuned properly. In particular, for c = 0 the response is pure aging while for finite, non-zero c one observes slip law like behavior for small velocity jumps but aging law like response for larger jumps. The magnitude of the velocity jump required to see this transition between aging and slip behaviour increases as c increases. In the limit of c >> 1 the response to velocity steps becomes purely slip law like. In this limit, numerical simulations show that this law loses its appealing time dependent healing property. An approach using Markov Chain Monte Carlo parameter search on data for large magnitude velocity step tests reveals that it is only possible to determine a lower bound on c using datasets that are well explained by the slip law. For a dataset with velocity steps of two orders of magnitude on simulated fault gouge we find this lower bound to be c ≈ 10.0. This is significantly larger than c ≈ 2.0 used by Nagata et al. (2012) to fit their data (mainly bare rock experiments with smaller excursions from steady state than our dataset). Similar parameter estimation exercises on slide hold slide data reveal that none of the state evolution laws considered - Dieterich, Ruina, Kato-Tullis and Nagata - match the relevant features of the data. In particular, even the aging law predicts only the correct rate of healing for long hold times but not the correct amount of healing. For c = 10.0, the Nagata law shows significant slip dependence in healing rate for long hold times which is at odds with the lab data and similar to the slip law response. If one accepts frictional healing observed in the laboratory as a ';proper' analog for fault strengthening over the interseismic period, we conclude that none of the investigated state evolution laws provides a comprehensive and correct constitutive relation.

An investigation of the kinetics of hydrogen chemisorption on iron metal surfaces

NASA Technical Reports Server (NTRS)

Shanabarger, M. R.

1982-01-01

The isothermal kinetics of H2, H2S, and O2 chemisorption onto epitaxially grown (III) oriented Fe films were studied. The measurements were made using the techniques of chemisorption induced resistance change and Auger electron spectroscopy (for adsorbed sulfur and oxygen). Also the origin of the chemisorption induced resistance change for these systems and its applicability to kinetic measurements were established. The chemisorption kinetics were interpreted as dissociative chemisorption via an adsorbed molecular species. The applicable rate constants were established. In none of the studies were the rate constants observed to be coverage dependent. By comparing the temperature dependence of the rate constants with absolute rate theory, the binding energies and activation energies of all the kinetic processes were obtained for the H2/Fe system. The initial sticking coefficient was pressure dependent for both the H2/Fe and H2S/Fe systems. This results from the step between the adsorbed molecular state and the dissociated chemisorbed state being the rate limiting step for absorption at certain pressures and temperatures. Estimates were obtained for the temperature dependence of the rate constants for the O2/Fe system.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

PubMed

Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

2018-03-09

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

Fast production of methane by anaerobic digestion. Annual progress report, May 24, 1976--May 23, 1977

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finney, C.D.; Evans II, R.S.; Finney, K.A.

1977-06-01

Since the productional cost of methane generated by anaerobic digestion of cellulose is on the economic borderline and the cost could be reduced by increasing the rate of the digestion process, a research program was undertaken to delineate the most promising areas of development. The concept that the step involving transfer of products from solution is rate-limiting and inhibiting in anaerobic digestion was supported by all evidence available. The most significant design implication of this concept is that faster gas production can be achieved in a two-stage digestion system in which unreactive solids are eliminated after the hydrolysis step somore » that the effluent to the gas-producing stage possesses a low viscosity. The advantages and disadvantages of three hydrolysis methods (enzymatic, anaerobic, and acid) are reviewed.« less

Turnover of cyclic 2,3-diphosphoglycerate in Methanobacterium thermoautotrophicum. Phosphate flux in P1- and H2-limited chemostat cultures.

PubMed

Krueger, R D; Campbell, J W; Fahrney, D E

1986-09-15

The archaebacterium Methanobacterium thermoautotrophicum was grown at 65 degrees C in H2- and Pi-limited chemostat cultures at dilution rates corresponding to 3- and 4-h doubling times, respectively. Under these conditions the steady state concentration of cyclic 2,3-diphosphoglycerate was 44 mM in the H2-limited cells and 13 mM in the cells grown under Pi limitation. Flux of Pi into the cyclic pyrophosphate pool was estimated by two 32P-labeling procedures: approach to isotopic equilibrium and replacement of prelabeled cyclic diphosphoglycerate with unlabeled compound. The results unequivocally demonstrate turnover of the phosphoryl groups; either both phosphoryl groups of the cyclic pyrophosphate leave together or the second leaves at a faster rate. The half-life of the rate-determining step for loss of the phosphoryl groups was approximately equal to the culture doubling time. The Pi flowing into the cyclic diphosphoglycerate pool accounted for 19% of the total Pi flux into Pi-limited cells and 43% of the total for H2-limited cells. The high phosphate flux through the large cyclic diphosphoglycerate pool suggests that this molecule plays an important role in the phosphorus metabolism of this methanogen.

Alternative mechanistic explanation for ligand-dependent selectivities in copper-catalyzed N- and O-arylation reactions.

PubMed

Yu, Hai-Zhu; Jiang, Yuan-Ye; Fu, Yao; Liu, Lei

2010-12-29

The ligand-dependent selectivities in Ullmann-type reactions of amino alcohols with iodobenzene by β-diketone- and 1,10-phenanthroline-ligated Cu(I) complexes were recently explained by the single-electron transfer and iodine atom transfer mechanisms (Jones, G. O., Liu, P., Houk, K. N., and Buchwald, S. L. J. Am. Chem. Soc. 2010, 132, 6205.). The present study shows that an alternative, oxidative addition/reductive elimination mechanism may also explain the selectivities. Calculations indicate that a Cu(I) complex with a negatively charged β-diketone ligand is electronically neutral, so that oxidative addition of ArI to a β-diketone-ligated Cu(I) prefers to occur (and occur readily) in the absence of the amino alcohol. Thus, coordination of the amino alcohol in its neutral form can only occur at the Cu(III) stage where N-coordination is favored over O-coordination. The coordination step is the rate-limiting step and the outcome is that N-arylation is favored with the β-diketone ligand. On the other hand, a Cu(I) complex with a neutral 1,10-phenanthroline ligand is positively charged, so that oxidative addition of ArI to a 1,10-phenanthroline-ligated Cu(I) has to get assistance from a deprotonated amino alcohol substrate. This causes oxidative addition to become the rate-limiting step in the 1,10-phenanthroline-mediated reaction. The immediate product of the oxidative addition step is found to undergo facile reductive elimination to provide the arylation product. Because O-coordination of a deprotonated amino alcohol is favored over N-coordination in the oxidative addition transition state, O-arylation is favored with the 1,10-phenanthroline ligand.

Notes on the ExactPack Implementation of the DSD Rate Stick Solver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaul, Ann

It has been shown above that the discretization scheme implemented in the ExactPack solver for the DSD Rate Stick equation is consistent with the Rate Stick PDE. In addition, a stability analysis has provided a CFL condition for a stable time step. Together, consistency and stability imply convergence of the scheme, which is expected to be close to first-order in time and second-order in space. It is understood that the nonlinearity of the underlying PDE will affect this rate somewhat. In the solver I implemented in ExactPack, I used the one-sided boundary condition described above at the outer boundary. Inmore » addition, I used 80% of the time step calculated in the stability analysis above. By making these two changes, I was able to implement a solver that calculates the solution without any arbitrary limits placed on the values of the curvature at the boundary. Thus, the calculation is driven directly by the conditions at the boundary as formulated in the DSD theory. The chosen scheme is completely coherent and defensible from a mathematical standpoint.« less

Explanation by the double-metal-ion mechanism of catalysis for the differential metal ion effects on the cleavage rates of 5′-oxy and 5′-thio substrates by a hammerhead ribozyme

PubMed Central

Zhou, De-Min; Zhang, Li-He; Taira, Kazunari

1997-01-01

In a previous examination using natural all-RNA substrates that contained either a 5′-oxy or 5′-thio leaving group at the cleavage site, we demonstrated that (i) the attack by the 2′-oxygen at C17 on the phosphorus atom is the rate-limiting step only for the substrate that contains a 5′-thio group (R11S) and (ii) the departure of the 5′ leaving group is the rate-limiting step for the natural all-RNA substrate (R11O) in both nonenzymatic and hammerhead ribozyme-catalyzed reactions; the energy diagrams for these reactions were provided in our previous publication. In this report we found that the rate of cleavage of R11O by a hammerhead ribozyme was enhanced 14-fold when Mg2+ ions were replaced by Mn2+ ions, whereas the rate of cleavage of R11S was enhanced only 2.2-fold when Mg2+ ions were replaced by Mn2+ ions. This result appears to be exactly the opposite of that predicted from the direct coordination of the metal ion with the leaving 5′-oxygen, because a switch in metal ion specificity was not observed with the 5′-thio substrate. However, our quantitative analyses based on the previously provided energy diagram indicate that this result is in accord with the double-metal-ion mechanism of catalysis. PMID:9405614

Determination of the diffusion coefficient and phase-transfer rate parameter in LaNi{sub 5} and MmNi{sub 3.6}Co{sub 0.8}Mn{sub 0.4}Al{sub 0.3} using microelectrodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundqvist, A.; Lindbergh, G.

1998-11-01

A potential-step method for determining the diffusion coefficient and phase-transfer parameter in metal hydrides by using microelectrodes was investigated. It was shown that a large potential step is not enough to ensure a completely diffusion-limited mass transfer if a surface-phase transfer reaction takes place at a finite rate. It was shown, using a kinetic expression for the surface phase-transfer reaction, that the slope of the logarithm of the current vs. time curve will be constant both in the case of the mass-transfer limited by diffusion or by diffusion and a surface-phase transfer. The diffusion coefficient and phase-transfer rate parameter weremore » accurately determined for MmNi{sub 3.6}Co{sub 0.8}Mn{sub 0.4}Al{sub 0.3} using a fit to the whole transient. The diffusion coefficient was found to be (1.3 {+-} 0.3) {times} 10{sup {minus}13} m{sup 2}/s. The fit was good and showed that a pure diffusion model was not enough to explain the observed transient. The diffusion coefficient and phase-transfer rate parameter were also estimated for pure LaNi{sub 5}. A fit of the whole curve showed that neither a pure diffusion model nor a model including phase transfer could explain the whole transient.« less

Dynamic subcellular partitioning of the nucleolar transcription factor TIF-IA under ribotoxic stress.

PubMed

Szymański, Jedrzej; Mayer, Christine; Hoffmann-Rohrer, Urs; Kalla, Claudia; Grummt, Ingrid; Weiss, Matthias

2009-07-01

TIF-IA is a basal transcription factor of RNA polymerase I (Pol I) that is a major target of the JNK2 signaling pathway in response to ribotoxic stress. Using advanced fluorescence microscopy and kinetic modeling we elucidated the subcellular localization of TIF-IA and its exchange dynamics between the nucleolus, nucleoplasm and cytoplasm upon ribotoxic stress. In steady state, the majority of (GFP-tagged) TIF-IA was in the cytoplasm and the nucleus, a minor portion (7%) localizing to the nucleoli. We observed a rapid shuttling of GFP-TIF-IA between the different cellular compartments with a mean residence time of approximately 130 s in the nucleus and only approximately 30 s in the nucleoli. The import rate from the cytoplasm to the nucleus was approximately 3-fold larger than the export rate, suggesting an importin/exportin-mediated transport rather than a passive diffusion. Upon ribotoxic stress, GFP-TIF-IA was released from the nucleoli with a half-time of approximately 24 min. Oxidative stress and inhibition of protein synthesis led to a relocation of GFP-TIF-IA with slower kinetics while osmotic stress had no effect. The observed relocation was much slower than the nucleo-cytoplasmic and nucleus-nucleolus exchange rates of GFP-TIF-IA, indicating a time-limiting step upstream of the JNK2 pathway. In support of this, time-course experiments on the activity of JNK2 revealed the activation of the JNK kinase as the rate-limiting step.

Large-scale production of kappa-carrageenan droplets for gel-bead production: theoretical and practical limitations of size and production rate.

PubMed

Hunik, J H; Tramper, J

1993-01-01

Immobilization of biocatalysts in kappa-carrageenan gel beads is a widely used technique nowadays. Several methods are used to produce the gel beads. The gel-bead production rate is usually sufficient to make the relatively small quantities needed for bench-scale experiments. The droplet diameter can, within limits, be adjusted to the desired size, but it is difficult to predict because of the non-Newtonian fluid behavior of the kappa-carrageenan solution. Here we present the further scale-up of the extrusion technique with the theory to predict the droplet diameters for non-Newtonian fluids. The emphasis is on the droplet formation, which is the rate-limiting step in this extrusion technique. Uniform droplets were formed by breaking up a capillary jet with a sinusoidal signal of a vibration exciter. At the maximum production rate of 27.6 dm3/h, uniform droplets with a diameter of (2.1 +/- 0.12) x 10(-3) m were obtained. This maximum flow rate was limited by the power transfer of the vibration exciter to the liquid flow. It was possible to get a good prediction of the droplet diameter by estimating the local viscosity from shear-rate calculations and an experimental relation between the shear rate and viscosity. In this way the theory of Newtonian fluids could be used for the non-Newtonian kappa-carrageenan solution. The calculated optimal break-up frequencies and droplet sizes were in good agreement with those found in the experiments.

Robust estimation-free prescribed performance back-stepping control of air-breathing hypersonic vehicles without affine models

NASA Astrophysics Data System (ADS)

Bu, Xiangwei; Wu, Xiaoyan; Huang, Jiaqi; Wei, Daozhi

2016-11-01

This paper investigates the design of a novel estimation-free prescribed performance non-affine control strategy for the longitudinal dynamics of an air-breathing hypersonic vehicle (AHV) via back-stepping. The proposed control scheme is capable of guaranteeing tracking errors of velocity, altitude, flight-path angle, pitch angle and pitch rate with prescribed performance. By prescribed performance, we mean that the tracking error is limited to a predefined arbitrarily small residual set, with convergence rate no less than a certain constant, exhibiting maximum overshoot less than a given value. Unlike traditional back-stepping designs, there is no need of an affine model in this paper. Moreover, both the tedious analytic and numerical computations of time derivatives of virtual control laws are completely avoided. In contrast to estimation-based strategies, the presented estimation-free controller possesses much lower computational costs, while successfully eliminating the potential problem of parameter drifting. Owing to its independence on an accurate AHV model, the studied methodology exhibits excellent robustness against system uncertainties. Finally, simulation results from a fully nonlinear model clarify and verify the design.

Method of detecting system function by measuring frequency response

DOEpatents

Morrison, John L.; Morrison, William H.; Christophersen, Jon P.; Motloch, Chester G.

2013-01-08

Methods of rapidly measuring an impedance spectrum of an energy storage device in-situ over a limited number of logarithmically distributed frequencies are described. An energy storage device is excited with a known input signal, and a response is measured to ascertain the impedance spectrum. An excitation signal is a limited time duration sum-of-sines consisting of a select number of frequencies. In one embodiment, magnitude and phase of each frequency of interest within the sum-of-sines is identified when the selected frequencies and sample rate are logarithmic integer steps greater than two. This technique requires a measurement with a duration of one period of the lowest frequency. In another embodiment, where selected frequencies are distributed in octave steps, the impedance spectrum can be determined using a captured time record that is reduced to a half-period of the lowest frequency.

The Determination of Rate-Limiting Steps during Soot Formation

DTIC Science & Technology

1989-04-27

acceleration in chemistry due to the presence of oxygen . Quantitative prediction of soot production , should it become a reality, will require knowledge of...PAH ..... ... ..................... 7 Fig. 4 1.25% Benzene/1% Oxygen - Light Products ........ .................... 8 Fig. 5 1.25% Benzene/0.3% Oxygen ...Benzene/0.3% Oxygen - PAH Production ....... .................. 11 Fig. 8 Evolution of Closed Ring Aromatics (t(source) = oo) .................... .15 Fig

Discovery of a new mechanism for regulation of plant triacylglycerol metabolism: The peanut diacylglycerol acyltransferase-1 gene family transcriptome is highly enriched in alternative splicing variants

USDA-ARS?s Scientific Manuscript database

Triacylglycerols (TAGs) are the most important energy storage form in oilseed crops. Diacylglycerol acyltransferase (DGAT) catalyzes the rate-limiting step of the Kennedy pathway of TAG biosynthesis. To date, little is known about the regulation of DGAT activity in peanut (Arachis hypogaea), an agr...

Porcine NAMPT gene: search for polymorphism, mapping and association studies

USDA-ARS?s Scientific Manuscript database

NAMPT encodes for an enzyme catalysing the rate-limiting step in NAD biosynthesis. The extracellular form of the enzyme is known as adipokine visfatin. We detected SNP AM999341:g.669T>C in intron 9 and SNP FN392209:g.358A>G in the promoter of the gene. RH mapping linked the gene to microsatellite SW...

A bill to amend the Servicemembers Civil Relief Act to extend the interest rate limitation on debt entered into during military service to debt incurred during military service to consolidate or refinance student loans incurred before military service.

THOMAS, 113th Congress

Sen. Durbin, Richard J. [D-IL

2013-07-30

Senate - 10/30/2013 Committee on Veterans' Affairs. Hearings held. Hearings printed: S.Hrg. 113-280. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Metabolic and gene expression analysis of apple (Malus × domestica) carotenogenesis

PubMed Central

Allan, Andrew C.

2012-01-01

Carotenoid accumulation confers distinct colouration to plant tissues, with effects on plant response to light and as well as health benefits for consumers of plant products. The carotenoid pathway is controlled by flux of metabolites, rate-limiting enzyme steps, feed-back inhibition, and the strength of sink organelles, the plastids, in the cell. In apple (Malus × domestica Borkh), fruit carotenoid concentrations are low in comparison with those in other fruit species. The apple fruit flesh, in particular, begins development with high amounts of chlorophylls and carotenoids, but in all commercial cultivars a large proportion of this is lost by fruit maturity. To understand the control of carotenoid concentrations in apple fruit, metabolic and gene expression analysis of the carotenoid pathway were measured in genotypes with varying flesh and skin colour. Considerable variation in both carotenoid concentrations and compound profile was observed between tissues and genotypes, with carotenes and xanthophylls being found only in fruit accumulating high carotenoid concentrations. The study identified potential rate-limiting steps in carotenogenesis, which suggested that the expression of ZISO, CRTISO,and LCY-ε, in particular, were significant in predicting final carotenoid accumulation in mature apple fruit. PMID:22717407

Metabolic and gene expression analysis of apple (Malus x domestica) carotenogenesis.

PubMed

Ampomah-Dwamena, Charles; Dejnoprat, Supinya; Lewis, David; Sutherland, Paul; Volz, Richard K; Allan, Andrew C

2012-07-01

Carotenoid accumulation confers distinct colouration to plant tissues, with effects on plant response to light and as well as health benefits for consumers of plant products. The carotenoid pathway is controlled by flux of metabolites, rate-limiting enzyme steps, feed-back inhibition, and the strength of sink organelles, the plastids, in the cell. In apple (Malus × domestica Borkh), fruit carotenoid concentrations are low in comparison with those in other fruit species. The apple fruit flesh, in particular, begins development with high amounts of chlorophylls and carotenoids, but in all commercial cultivars a large proportion of this is lost by fruit maturity. To understand the control of carotenoid concentrations in apple fruit, metabolic and gene expression analysis of the carotenoid pathway were measured in genotypes with varying flesh and skin colour. Considerable variation in both carotenoid concentrations and compound profile was observed between tissues and genotypes, with carotenes and xanthophylls being found only in fruit accumulating high carotenoid concentrations. The study identified potential rate-limiting steps in carotenogenesis, which suggested that the expression of ZISO, CRTISO, and LCY-ε, in particular, were significant in predicting final carotenoid accumulation in mature apple fruit.

The Steroidogenic Acute Regulatory Protein (StAR) Is Regulated by the H19/let-7 Axis.

PubMed

Men, Yi; Fan, Yanhong; Shen, Yuanyuan; Lu, Lingeng; Kallen, Amanda N

2017-02-01

The steroidogenic acute regulatory protein (StAR) governs the rate-limiting step in steroidogenesis, and its expression varies depending on the needs of the specific tissue. Tight control of steroid production is essential for multiple processes involved in reproduction, including follicular development, ovulation, and endometrial synchronization. Recently, there has been a growing interest in the role of noncoding RNAs in the regulation of reproduction. Here we demonstrate that StAR is a novel target of the microRNA let-7, which itself is regulated by the long noncoding RNA (lncRNA) H19. Using human and murine cell lines, we show that overexpression of H19 stimulates StAR expression by antagonizing let-7, which inhibits StAR at the post-transcriptional level. Our results uncover a novel mechanism underlying the regulation of StAR expression and represent the first example of lncRNA-mediated control of the rate-limiting step of steroidogenesis. This work thus adds to the body of literature describing the multiple roles in oncogenesis, cellular growth, glucose metabolism, and now regulation of steroidogenesis, of this complex lncRNA. Copyright © 2017 by the Endocrine Society.

Kinetic and spectroscopic studies of the [palladium(Ar-bian)]-catalyzed semi-hydrogenation of 4-octyne.

PubMed

Kluwer, Alexander M; Koblenz, Tehila S; Jonischkeit, Thorsten; Woelk, Klaus; Elsevier, Cornelis J

2005-11-09

The kinetics of the stereoselective semi-hydrogenation of 4-octyne in THF by the highly active catalyst [Pd{(m,m'-(CF(3))(2)C(6)H(3))-bian}(ma)] (2) (bian = bis(imino)acenaphthene; ma = maleic anhydride) has been investigated. The rate law under hydrogen-rich conditions is described by r = k[4-octyne](0.65)[Pd][H(2)], showing first order in palladium and dihydrogen and a broken order in substrate. Parahydrogen studies have shown that a pairwise transfer of hydrogen atoms occurs in the rate-limiting step. In agreement with recent theoretical results, the proposed mechanism consists of the consecutive steps: alkyne coordination, heterolytic dihydrogen activation (hydrogenolysis of one Pd-N bond), subsequent hydro-palladation of the alkyne, followed by addition of N-H to palladium, reductive coupling of vinyl and hydride and, finally, substitution of the product alkene by the alkyne substrate. Under hydrogen-limiting conditions, side reactions occur, that is, formation of catalytically inactive palladacycles by oxidative alkyne coupling. Furthermore, it has been shown that (Z)-oct-4-ene is the primary reaction product, from which the minor product (E)-oct-4-ene is formed by an H(2)-assisted, palladium-catalyzed isomerization reaction.

Production of oxygen from lunar ilmenite

NASA Technical Reports Server (NTRS)

Zhao, Y.; Shadman, F.

1990-01-01

The following subjects are addressed: (1) the mechanism and kinetics of carbothermal reduction of simulated lunar ilmenite using carbon and, particularly, CO as reducing agents; (2) the determination of the rate-limiting steps; (3) the investigation of the effect of impurities, particularly magnesium; (4) the search for catalysts suitable for enhancement of the rate-limiting step; (5) the comparison of the kinetics of carbothermal reduction with those of hydrogen reduction; (6) the study of the combined use of CO and hydrogen as products of gasification of carbonaceous solids; (7) the development of reduction methods based on the use of waste carbonaceous compounds for the process; (8) the development of a carbothermal reaction path that utilizes gasification of carbonaceous solids to reducing gaseous species (hydrocarbons and carbon monoxide) to facilitate the reduction reaction kinetics and make the process more flexible in using various forms of carbonaceous feeds; (9) the development of advanced gas separation techniques, including the use of high-temperature ceramic membranes; (10) the development of an optimum process flow sheet for carbothermal reduction, and comparison of this process with the hydrogen reduction scheme, as well as a general comparison with other leading oxygen production schemes; and (11) the use of new and advanced material processing and separation techniques.

New insights into aldol reactions of methyl isocyanoacetate catalyzed by heterogenized homogeneous catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Rong; Zhao, Jie; Yuan, Bing

The Hayashi–Ito aldol reaction of methyl isocyanoacetate (MI) and benzaldehydes, a classic homogeneous Au(I)-catalyzed reaction, was studied with heterogenized homogeneous catalysts. Among dendrimer encapsulated nanoparticles (NPs) of Au, Pd, Rh, or Pt loaded in mesoporous supports and the homogeneous analogues, the Au NPs led to the highest yield and highest diastereoselectivity of products in toluene at room temperature. The Au catalyst was stable and was recycled for at least six runs without substantial deactivation. Moreover, larger pore sizes of the support and the use of a hydrophobic solvent led to a high selectivity for the trans diastereomer of the product.more » The activation energy is sensitive to neither the size of Au NPs nor the support. A linear Hammett plot was obtained with a positive slope, suggesting an increased electron density on the carbonyl carbon atom in the rate-limiting step. As a result, IR studies revealed a strong interaction between MI and the gold catalyst, supporting the proposed mechanism, in which rate-limiting step involves an electrophilic attack of the aldehyde on the enolate formed from the deprotonated MI.« less

New insights into aldol reactions of methyl isocyanoacetate catalyzed by heterogenized homogeneous catalysts

DOE PAGES

Ye, Rong; Zhao, Jie; Yuan, Bing; ...

2016-12-14

The Hayashi–Ito aldol reaction of methyl isocyanoacetate (MI) and benzaldehydes, a classic homogeneous Au(I)-catalyzed reaction, was studied with heterogenized homogeneous catalysts. Among dendrimer encapsulated nanoparticles (NPs) of Au, Pd, Rh, or Pt loaded in mesoporous supports and the homogeneous analogues, the Au NPs led to the highest yield and highest diastereoselectivity of products in toluene at room temperature. The Au catalyst was stable and was recycled for at least six runs without substantial deactivation. Moreover, larger pore sizes of the support and the use of a hydrophobic solvent led to a high selectivity for the trans diastereomer of the product.more » The activation energy is sensitive to neither the size of Au NPs nor the support. A linear Hammett plot was obtained with a positive slope, suggesting an increased electron density on the carbonyl carbon atom in the rate-limiting step. As a result, IR studies revealed a strong interaction between MI and the gold catalyst, supporting the proposed mechanism, in which rate-limiting step involves an electrophilic attack of the aldehyde on the enolate formed from the deprotonated MI.« less

An approximate stationary solution for multi-allele neutral diffusion with low mutation rates.

PubMed

Burden, Conrad J; Tang, Yurong

2016-12-01

We address the problem of determining the stationary distribution of the multi-allelic, neutral-evolution Wright-Fisher model in the diffusion limit. A full solution to this problem for an arbitrary K×K mutation rate matrix involves solving for the stationary solution of a forward Kolmogorov equation over a (K-1)-dimensional simplex, and remains intractable. In most practical situations mutations rates are slow on the scale of the diffusion limit and the solution is heavily concentrated on the corners and edges of the simplex. In this paper we present a practical approximate solution for slow mutation rates in the form of a set of line densities along the edges of the simplex. The method of solution relies on parameterising the general non-reversible rate matrix as the sum of a reversible part and a set of (K-1)(K-2)/2 independent terms corresponding to fluxes of probability along closed paths around faces of the simplex. The solution is potentially a first step in estimating non-reversible evolutionary rate matrices from observed allele frequency spectra. Copyright © 2016 Elsevier Inc. All rights reserved.

Rate-dependent carbon and nitrogen kinetic isotope fractionation in hydrolysis of isoproturon.

PubMed

Penning, Holger; Cramer, Christopher J; Elsner, Martin

2008-11-01

Stable isotope fractionation permits quantifying contaminant degradation in the field when the transformation reaction is associated with a consistent isotope enrichment factor epsilon. When interpreted in conjunction with dual isotope plots, isotope fractionation is also particularly useful for elucidating reaction mechanisms. To assess the consistency of epsilon and dual isotope slopes in a two-step reaction, we investigated the abiotic hydrolysis of the herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) using a fragmentation method that allows measuring isotope ratios in different parts of the molecule. Carbon and nitrogen position-specific isotope fractionation, as well as slopes in dual isotope plots, varied linearly with rate constants k(obs) depending on the presence of buffers that mediate the initial zwitterion formation. The correlation can be explained by two consecutive reaction steps (zwitterion formation followed by dimethylamine elimination) each of which has a different kinetic isotope effect and may be rate-limiting. Intrinsic isotope effects for both steps, extracted from our kinetic data using a novel theoretical treatment, agree well with values computed from density functional calculations. Our study therefore demonstrates that more variable isotope fractionation may be observed in simple chemical reactions than commonly thought, but that consistent epsilon or dual isotope slopes may nonetheless be encountered in certain molecular fragments.

Porting the synthetic D-glucaric acid pathway from Escherichia coli to Saccharomyces cerevisiae.

PubMed

Gupta, Amita; Hicks, Michael A; Manchester, Shawn P; Prather, Kristala L J

2016-09-01

D-Glucaric acid can be produced as a value-added chemical from biomass through a de novo pathway in Escherichia coli. However, previous studies have identified pH-mediated toxicity at product concentrations of 5 g/L and have also found the eukaryotic myo-inositol oxygenase (MIOX) enzyme to be rate-limiting. We ported this pathway to Saccaromyces cerevisiae, which is naturally acid-tolerant and evaluate a codon-optimized MIOX homologue. We constructed two engineered yeast strains that were distinguished solely by their MIOX gene - either the previous version from Mus musculus or a homologue from Arabidopsis thaliana codon-optimized for expression in S. cerevisiae - in order to identify the rate-limiting steps for D-glucaric acid production both from a fermentative and non-fermentative carbon source. myo-Inositol availability was found to be rate-limiting from glucose in both strains and demonstrated to be dependent on growth rate, whereas the previously used M. musculus MIOX activity was found to be rate-limiting from glycerol. Maximum titers were 0.56 g/L from glucose in batch mode, 0.98 g/L from glucose in fed-batch mode, and 1.6 g/L from glucose supplemented with myo-inositol. Future work focusing on the MIOX enzyme, the interplay between growth and production modes, and promoting aerobic respiration should further improve this pathway. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5'-Monophosphate Decarboxylase.

PubMed

Goryanova, Bogdana; Goldman, Lawrence M; Ming, Shonoi; Amyes, Tina L; Gerlt, John A; Richard, John P

2015-07-28

The caged complex between orotidine 5'-monophosphate decarboxylase (ScOMPDC) and 5-fluoroorotidine 5'-monophosphate (FOMP) undergoes decarboxylation ∼300 times faster than the caged complex between ScOMPDC and the physiological substrate, orotidine 5'-monophosphate (OMP). Consequently, the enzyme conformational changes required to lock FOMP at a protein cage and release product 5-fluorouridine 5'-monophosphate (FUMP) are kinetically significant steps. The caged form of ScOMPDC is stabilized by interactions between the side chains from Gln215, Tyr217, and Arg235 and the substrate phosphodianion. The control of these interactions over the barrier to the binding of FOMP and the release of FUMP was probed by determining the effect of all combinations of single, double, and triple Q215A, Y217F, and R235A mutations on kcat/Km and kcat for turnover of FOMP by wild-type ScOMPDC; its values are limited by the rates of substrate binding and product release, respectively. The Q215A and Y217F mutations each result in an increase in kcat and a decrease in kcat/Km, due to a weakening of the protein-phosphodianion interactions that favor fast product release and slow substrate binding. The Q215A/R235A mutation causes a large decrease in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of OMP, which are limited by the rate of the decarboxylation step, but much smaller decreases in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of FOMP, which are limited by the rate of enzyme conformational changes. By contrast, the Y217A mutation results in large decreases in kcat/Km for ScOMPDC-catalyzed decarboxylation of both OMP and FOMP, because of the comparable effects of this mutation on rate-determining decarboxylation of enzyme-bound OMP and on the rate-determining enzyme conformational change for decarboxylation of FOMP. We propose that kcat = 8.2 s(-1) for decarboxylation of FOMP by the Y217A mutant is equal to the rate constant for cage formation from the complex between FOMP and the open enzyme, that the tyrosyl phenol group stabilizes the closed form of ScOMPDC by hydrogen bonding to the substrate phosphodianion, and that the phenyl group of Y217 and F217 facilitates formation of the transition state for the rate-limiting conformational change. An analysis of kinetic data for mutant enzyme-catalyzed decarboxylation of OMP and FOMP provides estimates for the rate and equilibrium constants for the conformational change that traps FOMP at the enzyme active site.

Kinetics of inactivation and dilution effects on the mass balance of fungal phytopathogens in anaerobic digesters.

PubMed

Plöchl, Matthias; Heiermann, Monika; Rodemann, Bernd; Bandte, Martina; Büttner, Carmen

2014-01-15

Knowledge of fate and behavior of plant pathogens in the biogas production chain is limited and hampers the estimation and evaluation of the potential phytosanitary risk if digestate is spread on arable land as a fertilizer. Therefore, simulation is an appropriate tool to demonstrate the effects which influence the steady state of pathogen infected plant material in both digesters and digestate. Simple approaches of kinetics of inactivation and mass balances of infected material were carried out considering single-step as well as two-step digestion. The simulation revealed a very fast to fast reduction of infected material after a singular feeding, reaching a cutback to less than 1% of input within 4 days even for D90-values of 68 h. Steady state mass balances below input rate could be calculated with D90-values of less than 2 h at a continuous hourly feeding. At higher D90-values steady state mass balances exceed the input rate but are still clearly below the sum of input mass. Dilution further decreases mass balances to values 10(-5) to 10(-6) Mg m(-3) for first-step digestion and 10(-8) to 10(-9) for second-step. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ultrasonic disintegration of biosolids for improved biodegradation.

PubMed

Nickel, Klaus; Neis, Uwe

2007-04-01

Biological cell lysis is known to be the rate-limiting step of anaerobic biosolids degradation. Shear forces generated by low frequency ultrasound can be used to disintegrate bacterial cells in sewage sludge. Thus, the quantity of dissolved organic substrate is increased. Consequently, the degradation rate and the biodegradability of organic biosolids mass are improved. Fundamental pilot-studies showed a significantly accelerated biosolids degradation with less digested sludge being produced and increased biogas production being attained. A full-scale ultrasound reactor system was developed for continuous operation under real life conditions on sewage treatment plants (STP).

Increasing Running Step Rate Reduces Patellofemoral Joint Forces

PubMed Central

Lenhart, Rachel L.; Thelen, Darryl G.; Wille, Christa M.; Chumanov, Elizabeth S.; Heiderscheit, Bryan C.

2013-01-01

Purpose Increasing step rate has been shown to elicit changes in joint kinematics and kinetics during running, and has been suggested as a possible rehabilitation strategy for runners with patellofemoral pain. The purpose of this study was to determine how altering step rate affects internal muscle forces and patellofemoral joint loads, and then to determine what kinematic and kinetic factors best predict changes in joint loading. Methods We recorded whole body kinematics of 30 healthy adults running on an instrumented treadmill at three step rate conditions (90%, 100%, and 110% of preferred step rate). We then used a 3D lower extremity musculoskeletal model to estimate muscle, patellar tendon, and patellofemoral joint forces throughout the running gait cycles. Additionally, linear regression analysis allowed us to ascertain the relative influence of limb posture and external loads on patellofemoral joint force. Results Increasing step rate to 110% of preferred reduced peak patellofemoral joint force by 14%. Peak muscle forces were also altered as a result of the increased step rate with hip, knee and ankle extensor forces, and hip abductor forces all reduced in mid-stance. Compared to the 90% step rate condition, there was a concomitant increase in peak rectus femoris and hamstring loads during early and late swing, respectively, at higher step rates. Peak stance phase knee flexion decreased with increasing step rate, and was found to be the most important predictor of the reduction in patellofemoral joint loading. Conclusion Increasing step rate is an effective strategy to reduce patellofemoral joint forces and could be effective in modulating biomechanical factors that can contribute to patellofemoral pain. PMID:23917470

External and Intraparticle Diffusion of Coumarin 102 with Surfactant in the ODS-silica Gel/water System by Single Microparticle Injection and Confocal Fluorescence Microspectroscopy.

PubMed

Nakatani, Kiyoharu; Matsuta, Emi

2015-01-01

The release mechanism of coumarin 102 from a single ODS-silica gel microparticle into the water phase in the presence of Triton X-100 was investigated by confocal fluorescence microspectroscopy combined with the single microparticle injection technique. The release rate significantly depended on the Triton X-100 concentration in the water phase and was not limited by diffusion in the pores of the microparticle. The release rate constant was inversely proportional to the microparticle radius squared, indicating that the rate-determining step is the external diffusion between the microparticle and the water phase.

Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system

PubMed Central

Abin-Fuentes, Andres; Leung, James C.; Mohamed, Magdy El-Said; Wang, Daniel IC; Prather, Kristala LJ

2014-01-01

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m3 and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates. PMID:24284557

The Associations Between Clerkship Objective Structured Clinical Examination (OSCE) Grades and Subsequent Performance.

PubMed

Dong, Ting; Zahn, Christopher; Saguil, Aaron; Swygert, Kimberly A; Yoon, Michelle; Servey, Jessica; Durning, Steven

2017-01-01

Construct: We investigated the extent of the associations between medical students' clinical competency measured by performance in Objective Structured Clinical Examinations (OSCE) during Obstetrics/Gynecology and Family Medicine clerkships and later performance in both undergraduate and graduate medical education. There is a relative dearth of studies on the correlations between undergraduate OSCE scores and future exam performance within either undergraduate or graduate medical education and almost none on linking these simulated encounters to eventual patient care. Of the research studies that do correlate clerkship OSCE scores with future performance, these often have a small sample size and/or include only 1 clerkship. Students in USU graduating classes of 2007 through 2011 participated in the study. We investigated correlations between clerkship OSCE grades with United States Medical Licensing Examination Step 2 Clinical Knowledge, Clinical Skills, and Step 3 Exams scores as well as Postgraduate Year 1 program director's evaluation scores on Medical Expertise and Professionalism. We also conducted contingency table analysis to examine the associations between poor performance on clerkship OSCEs with failing Step 3 and receiving poor program director ratings. The correlation coefficients were weak between the clerkship OSCE grades and the outcomes. The strongest correlations existed between the clerkship OSCE grades and the Step 2 CS Integrated Clinical Encounter component score, Step 2 Clinical Skills, and Step 3 scores. Contingency table associations between poor performances on both clerkships OSCEs and poor Postgraduate Year 1 Program Director ratings were significant. The results of this study provide additional but limited validity evidence for the use of OSCEs during clinical clerkships given their associations with subsequent performance measures.

Determination of the mass transfer limiting step of dye adsorption onto commercial adsorbent by using mathematical models.

PubMed

Marin, Pricila; Borba, Carlos Eduardo; Módenes, Aparecido Nivaldo; Espinoza-Quiñones, Fernando R; de Oliveira, Silvia Priscila Dias; Kroumov, Alexander Dimitrov

2014-01-01

Reactive blue 5G dye removal in a fixed-bed column packed with Dowex Optipore SD-2 adsorbent was modelled. Three mathematical models were tested in order to determine the limiting step of the mass transfer of the dye adsorption process onto the adsorbent. The mass transfer resistance was considered to be a criterion for the determination of the difference between models. The models contained information about the external, internal, or surface adsorption limiting step. In the model development procedure, two hypotheses were applied to describe the internal mass transfer resistance. First, the mass transfer coefficient constant was considered. Second, the mass transfer coefficient was considered as a function of the dye concentration in the adsorbent. The experimental breakthrough curves were obtained for different particle diameters of the adsorbent, flow rates, and feed dye concentrations in order to evaluate the predictive power of the models. The values of the mass transfer parameters of the mathematical models were estimated by using the downhill simplex optimization method. The results showed that the model that considered internal resistance with a variable mass transfer coefficient was more flexible than the other ones and this model described the dynamics of the adsorption process of the dye in the fixed-bed column better. Hence, this model can be used for optimization and column design purposes for the investigated systems and similar ones.

A conjugate heat transfer procedure for gas turbine blades.

PubMed

Croce, G

2001-05-01

A conjugate heat transfer procedure, allowing for the use of different solvers on the solid and fluid domain(s), is presented. Information exchange between solid and fluid solution is limited to boundary condition values, and this exchange is carried out at any pseudo-time step. Global convergence rate of the procedure is, thus, of the same order of magnitude of stand-alone computations.

Development of a high efficiency thin silicon solar cell

NASA Technical Reports Server (NTRS)

Lindmayer, J.; Wrigley, C. Y.

1977-01-01

A key to the success of this program was the breakthrough development of a technology for producing ultra-thin silicon slices which are very flexible, resilient, and tolerant of moderate handling abuse. Experimental topics investigated were thinning technology, gaseous junction diffusion, aluminum back alloying, internal reflectance, tantalum oxide anti-reflective coating optimization, slice flexibility, handling techniques, production rate limiting steps, low temperature behavior, and radiation tolerance.

Interaction of rate- and size-effect using a dislocation density based strain gradient viscoplasticity model

NASA Astrophysics Data System (ADS)

Nguyen, Trung N.; Siegmund, Thomas; Tomar, Vikas; Kruzic, Jamie J.

2017-12-01

Size effects occur in non-uniform plastically deformed metals confined in a volume on the scale of micrometer or sub-micrometer. Such problems have been well studied using strain gradient rate-independent plasticity theories. Yet, plasticity theories describing the time-dependent behavior of metals in the presence of size effects are presently limited, and there is no consensus about how the size effects vary with strain rates or whether there is an interaction between them. This paper introduces a constitutive model which enables the analysis of complex load scenarios, including loading rate sensitivity, creep, relaxation and interactions thereof under the consideration of plastic strain gradient effects. A strain gradient viscoplasticity constitutive model based on the Kocks-Mecking theory of dislocation evolution, namely the strain gradient Kocks-Mecking (SG-KM) model, is established and allows one to capture both rate and size effects, and their interaction. A formulation of the model in the finite element analysis framework is derived. Numerical examples are presented. In a special virtual creep test with the presence of plastic strain gradients, creep rates are found to diminish with the specimen size, and are also found to depend on the loading rate in an initial ramp loading step. Stress relaxation in a solid medium containing cylindrical microvoids is predicted to increase with decreasing void radius and strain rate in a prior ramp loading step.

Two-Step Amyloid Aggregation: Sequential Lag Phase Intermediates

NASA Astrophysics Data System (ADS)

Castello, Fabio; Paredes, Jose M.; Ruedas-Rama, Maria J.; Martin, Miguel; Roldan, Mar; Casares, Salvador; Orte, Angel

2017-01-01

The self-assembly of proteins into fibrillar structures called amyloid fibrils underlies the onset and symptoms of neurodegenerative diseases, such as Alzheimer’s and Parkinson’s. However, the molecular basis and mechanism of amyloid aggregation are not completely understood. For many amyloidogenic proteins, certain oligomeric intermediates that form in the early aggregation phase appear to be the principal cause of cellular toxicity. Recent computational studies have suggested the importance of nonspecific interactions for the initiation of the oligomerization process prior to the structural conversion steps and template seeding, particularly at low protein concentrations. Here, using advanced single-molecule fluorescence spectroscopy and imaging of a model SH3 domain, we obtained direct evidence that nonspecific aggregates are required in a two-step nucleation mechanism of amyloid aggregation. We identified three different oligomeric types according to their sizes and compactness and performed a full mechanistic study that revealed a mandatory rate-limiting conformational conversion step. We also identified the most cytotoxic species, which may be possible targets for inhibiting and preventing amyloid aggregation.

Investigating rate-limiting barriers to nanoscale nonviral gene transfer with nanobiophotonics

NASA Astrophysics Data System (ADS)

Chen, Hunter H.

Nucleic acids are a novel class of therapeutics poised to address many unmet clinical needs. Safe and efficient delivery remains a significant challenge that has delayed the realization of the full therapeutic potential of nucleic acids. Nanoscale nonviral vectors offer an attractive alternative to viral vectors as natural and synthetic polymers or polypeptides may be rationally designed to meet the unique demands of individual applications. A mechanistic understanding of cellular barriers is necessary to develop guidelines for designing custom gene carriers which are expected to greatly impact this delivery challenge. The work herein focused on the relationships among nanocomplex stability, intracellular trafficking and unpacking kinetics, and DNA degradation. Ultrasensitive nanosensors based on QD-FRET were developed to characterize the biophysical properties of nanocomplexes and study these rate-limiting steps. Quantitative image analysis enabled the distributions of the subpopulation of condensed or released DNA to be determined within the major cellular compartments encountered during gene transfer. The steady state stability and unpacking kinetics within these compartments were found to impact transgene expression, elucidating multiple design strategies to achieve efficient gene transfer. To address enzymatic barriers, a novel two-step QD-FRET nanosensor was developed to analyze unpacking and DNA degradation simultaneously, which has not been accomplished previously. Bioresponsive strategies such as disulfide crosslinking and thermosensitivity were evaluated by QD-FRET and quantitative compartmental analysis as case studies to determine appropriate design specifications for thiolated polymers and thermoresponsive polypeptides. Relevant nanobiophotonic tools were developed as a platform to study major rate-limiting barriers to nanomedicine and demonstrated the feasibility of using mechanistic information gained from these tools to guide the rational design of gene carriers and achieve the desired properties that enable efficient gene transfer.

X-ray crystallography and QM/MM investigation on the oligosaccharide synthesis mechanism of rice BGlu1 glycosynthases.

PubMed

Wang, Jinhu; Pengthaisong, Salila; Cairns, James R Ketudat; Liu, Yongjun

2013-02-01

Nucleophile mutants of retaining β-glycosidase can act as glycosynthases to efficiently catalyze the synthesis of oligosaccharides. Previous studies proved that rice BGlu1 mutants E386G, E386S and E386A catalyze the oligosaccharide synthesis with different rates. The E386G mutant gave the fastest transglucosylation rate, which was approximately 3- and 19-fold faster than those of E386S and E386A. To account for the differences of their activities, in this paper, the X-ray crystal structures of BGlu1 mutants E386S and E386A were solved and compared with that of E386G mutant. However, they show quite similar active sites, which implies that their activities cannot be elucidated from the crystal structures alone. Therefore, a combined quantum mechanical/molecular mechanical (QM/MM) calculations were further performed. Our calculations reveal that the catalytic reaction follows a single-step mechanism, i.e., the extraction of proton by the acid/base, E176, and the formation of glycosidic bond are concerted. The energy barriers are calculated to be 19.9, 21.5 and 21.9kcal/mol for the mutants of E386G, E386S and E386A, respectively, which is consistent with the order of their experimental relative activities. But based on the calculated activation energies, 1.1kcal/mol energy difference may translate to nearly 100 fold rate difference. Although the rate limiting step in these mutants has not been established, considering the size of the product and the nature of the active site, it is likely that the product release, rather than chemistry, is rate limiting in these oligosaccharides synthesis catalyzed by BGlu1 mutants. Copyright © 2012 Elsevier B.V. All rights reserved.

A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.

PubMed

Bahira, Meriem; McCauley, Micah J; Almaqwashi, Ali A; Lincoln, Per; Westerlund, Fredrik; Rouzina, Ioulia; Williams, Mark C

2015-10-15

Several multi-component DNA intercalating small molecules have been designed around ruthenium-based intercalating monomers to optimize DNA binding properties for therapeutic use. Here we probe the DNA binding ligand [μ-C4(cpdppz)2(phen)4Ru2](4+), which consists of two Ru(phen)2dppz(2+) moieties joined by a flexible linker. To quantify ligand binding, double-stranded DNA is stretched with optical tweezers and exposed to ligand under constant applied force. In contrast to other bis-intercalators, we find that ligand association is described by a two-step process, which consists of fast bimolecular intercalation of the first dppz moiety followed by ∼10-fold slower intercalation of the second dppz moiety. The second step is rate-limited by the requirement for a DNA-ligand conformational change that allows the flexible linker to pass through the DNA duplex. Based on our measured force-dependent binding rates and ligand-induced DNA elongation measurements, we are able to map out the energy landscape and structural dynamics for both ligand binding steps. In addition, we find that at zero force the overall binding process involves fast association (∼10 s), slow dissociation (∼300 s), and very high affinity (Kd ∼10 nM). The methodology developed in this work will be useful for studying the mechanism of DNA binding by other multi-step intercalating ligands and proteins. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Modeling the effect of adsorption on the degradation rate of propiconazole in profiles of Polish Luvisols.

PubMed

Paszko, Tadeusz; Jankowska, Monika

2018-06-18

Laboratory adsorption and degradation studies were carried out to determine the effect of time-dependent adsorption on propiconazole degradation rates in samples from three Polish Luvisols. Strong propiconazole adsorption (organic carbon normalized adsorption coefficients K oc in the range of 1217-7777 mL/g) was observed in batch experiments, with a typical biphasic mechanism with a fast initial step followed by the time-dependent step, which finished within 48 h in the majority of soils. The time-dependent step observed in incubation experiments was longer (duration from 5 to 23 d), and its contribution to total adsorption was from 20% to 34%. The half-lives obtained at 25 °C and 40% maximum water holding capacity of soil, were in the range of 34.7-112.9 d in the Ap horizon and in the range of 42.3-448.8 d for subsoils. The very strong correlations, between degradation rates in pore water and soil organic carbon and soil microbial activity, indicated that microbial degradation of propiconazole was most likely the only significant process responsible for the decay of this compound under aerobic conditions for the whole of the examined soil profiles. Modeling of the processes showed that only models coupling adsorption and degradation were able to correctly describe the experimental data. The analysis of the bioavailability factor values showed that degradation was not limited by the rate of propiconazole desorption from soil, but sorption affected the degradation rate by decreasing its availability for microorganisms. Copyright © 2018. Published by Elsevier Inc.

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

PubMed

Biedermannová, Lada; Prokop, Zbyněk; Gora, Artur; Chovancová, Eva; Kovács, Mihály; Damborsky, Jiří; Wade, Rebecca C

2012-08-17

Many enzymes have buried active sites. The properties of the tunnels connecting the active site with bulk solvent affect ligand binding and unbinding and also the catalytic properties. Here, we investigate ligand passage in the haloalkane dehalogenase enzyme LinB and the effect of replacing leucine by a bulky tryptophan at a tunnel-lining position. Transient kinetic experiments show that the mutation significantly slows down the rate of product release. Moreover, the mechanism of bromide ion release is changed from a one-step process in the wild type enzyme to a two-step process in the mutant. The rate constant of bromide ion release corresponds to the overall steady-state turnover rate constant, suggesting that product release became the rate-limiting step of catalysis in the mutant. We explain the experimental findings by investigating the molecular details of the process computationally. Analysis of trajectories from molecular dynamics simulations with a tunnel detection software reveals differences in the tunnels available for ligand egress. Corresponding differences are seen in simulations of product egress using a specialized enhanced sampling technique. The differences in the free energy barriers for egress of a bromide ion obtained using potential of mean force calculations are in good agreement with the differences in rates obtained from the transient kinetic experiments. Interactions of the bromide ion with the introduced tryptophan are shown to affect the free energy barrier for its passage. The study demonstrates how the mechanism of an enzymatic catalytic cycle and reaction kinetics can be engineered by modification of protein tunnels.

Synthesis, characterization, and controlled release anticorrosion behavior of benzoate intercalated Zn-Al layered double hydroxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi; Zhang, Dun, E-mail: zhangdun@qdio.ac.cn

2011-11-15

Graphical abstract: The benzoate anion released from Zn-Al LDHs provides a more effective long-term protection against corrosion of Q235 carbon steel in 3.5% NaCl solution. Highlights: {yields} A benzoate anion corrosion inhibitor intercalated Zn-Al layered double hydroxides (LDHs) has been assembled by coprecipitation method. {yields} The kinetic simulation indicates that the ion-exchange one is responsible for the release process and the diffusion through particle is the rate limiting step. {yields} A significant reduction of the corrosion rate is observed when the LDH nanohybrid is present in the corrosive media. -- Abstract: Corrosion inhibitor-inorganic clay composite including benzoate anion intercalated Zn-Almore » layered double hydroxides (LDHs) are assembled by coprecipitation. Powder X-ray diffraction (XRD) and Fourier transform infrared (FT-IR) spectrum analyses indicate that the benzoate anion is successfully intercalated into the LDH interlayer and the benzene planes are vertically bilayer-positioned as a quasi-guest ion-pair form in the gallery space. Kinetic simulation for the release data, XRD and FT-IR analyses of samples recovered from the release medium indicate that ion-exchange is responsible for the release process and diffusion through the particle is also indicated to be the rate-limiting step. The anticorrosion capabilities of LDHs loaded with corrosion inhibitor toward Q235 carbon steel are analyzed by polarization curve and electrochemical impedance spectroscopy methods. Significant reduction of corrosion rate is observed when the LDH nanohybrid is present in the corrosive medium. This hybrid material may potentially be applied as a nanocontainer in self-healing coatings.« less

The Predominant Molecular State of Bound Enzyme Determines the Strength and Type of Product Inhibition in the Hydrolysis of Recalcitrant Polysaccharides by Processive Enzymes*

PubMed Central

Kuusk, Silja; Sørlie, Morten; Väljamäe, Priit

2015-01-01

Processive enzymes are major components of the efficient enzyme systems that are responsible for the degradation of the recalcitrant polysaccharides cellulose and chitin. Despite intensive research, there is no consensus on which step is rate-limiting for these enzymes. Here, we performed a comparative study of two well characterized enzymes, the cellobiohydrolase Cel7A from Hypocrea jecorina and the chitinase ChiA from Serratia marcescens. Both enzymes were inhibited by their disaccharide product, namely chitobiose for ChiA and cellobiose for Cel7A. The products behaved as noncompetitive inhibitors according to studies using the 14C-labeled crystalline polymeric substrates 14C chitin nanowhiskers and 14C-labeled bacterial microcrystalline cellulose for ChiA and Cel7A, respectively. The resulting observed Ki(obs) values were 0.45 ± 0.08 mm for ChiA and 0.17 ± 0.02 mm for Cel7A. However, in contrast to ChiA, the Ki(obs) of Cel7A was an order of magnitude higher than the true Ki value governed by the thermodynamic stability of the enzyme-inhibitor complex. Theoretical analysis of product inhibition suggested that the inhibition strength and pattern can be accounted for by assuming different rate-limiting steps for ChiA and Cel7A. Measuring the population of enzymes whose active site was occupied by a polymer chain revealed that Cel7A was bound predominantly via its active site. Conversely, the active-site-mediated binding of ChiA was slow, and most ChiA exhibited a free active site, even when the substrate concentration was saturating for the activity. Collectively, our data suggest that complexation with the polymer chain is rate-limiting for ChiA, whereas Cel7A is limited by dissociation. PMID:25767120

The predominant molecular state of bound enzyme determines the strength and type of product inhibition in the hydrolysis of recalcitrant polysaccharides by processive enzymes.

PubMed

Kuusk, Silja; Sørlie, Morten; Väljamäe, Priit

2015-05-01

Processive enzymes are major components of the efficient enzyme systems that are responsible for the degradation of the recalcitrant polysaccharides cellulose and chitin. Despite intensive research, there is no consensus on which step is rate-limiting for these enzymes. Here, we performed a comparative study of two well characterized enzymes, the cellobiohydrolase Cel7A from Hypocrea jecorina and the chitinase ChiA from Serratia marcescens. Both enzymes were inhibited by their disaccharide product, namely chitobiose for ChiA and cellobiose for Cel7A. The products behaved as noncompetitive inhibitors according to studies using the (14)C-labeled crystalline polymeric substrates (14)C chitin nanowhiskers and (14)C-labeled bacterial microcrystalline cellulose for ChiA and Cel7A, respectively. The resulting observed Ki (obs) values were 0.45 ± 0.08 mm for ChiA and 0.17 ± 0.02 mm for Cel7A. However, in contrast to ChiA, the Ki (obs) of Cel7A was an order of magnitude higher than the true Ki value governed by the thermodynamic stability of the enzyme-inhibitor complex. Theoretical analysis of product inhibition suggested that the inhibition strength and pattern can be accounted for by assuming different rate-limiting steps for ChiA and Cel7A. Measuring the population of enzymes whose active site was occupied by a polymer chain revealed that Cel7A was bound predominantly via its active site. Conversely, the active-site-mediated binding of ChiA was slow, and most ChiA exhibited a free active site, even when the substrate concentration was saturating for the activity. Collectively, our data suggest that complexation with the polymer chain is rate-limiting for ChiA, whereas Cel7A is limited by dissociation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Near-thermal reactions of Au(+)(1S,3D) with CH3X (X = F,Cl).

PubMed

Taylor, William S; Matthews, Cullen C; Hicks, Ashley J; Fancher, Kendall G; Chen, Li Chen

2012-01-26

Reactions of Au(+)((1)S) and Au(+)((3)D) with CH(3)F and CH(3)Cl have been carried out in a drift cell in He at a pressure of 3.5 Torr at both room temperature and reduced temperatures in order to explore the influence of the electronic state of the metal on reaction outcomes. State-specific product channels and overall two-body rate constants were identified using electronic state chromatography. These results indicate that Au(+)((1)S) reacts to yield an association product in addition to AuCH(2)(+) in parallel steps with both neutrals. Product distributions for association vs HX elimination were determined to be 79% association/21% HX elimination for X = F and 50% association/50% HX elimination when X = Cl. Reaction of Au(+)((3)D) with CH(3)F also results in HF elimination, which in this case is thought to produce (3)AuCH(2)(+). With CH(3)Cl, Au(+)((3)D) reacts to form AuCH(3)(+) and CH(3)Cl(+) in parallel steps. An additional product channel initiated by Au(+)((3)D) is also observed with both methyl halides, which yields CH(2)X(+) as a higher-order product. Kinetic measurements indicate that the reaction efficiency for both Au(+) states is significantly greater with CH(3)Cl than with CH(3)F. The observed two-body rate constant for depletion of Au(+)((1)S) by CH(3)F represents less than 5% of the limiting rate constant predicted by the average dipole orientation model (ADO) at room temperature and 226 K, whereas CH(3)Cl reacts with Au(+)((1)S) at the ADO limit at both room temperature and 218 K. Rate constants for depletion of Au(+)((3)D) by CH(3)F and CH(3)Cl were measured at 226 and 218 K respectively, and indicate that Au(+)((3)D) is consumed at approximately 2% of the ADO limit by CH(3)F and 69% of the ADO limit by CH(3)Cl. Product formation and overall efficiency for all four reactions are consistent with previous experimental results and available theoretical models.

The effect of processing parameters and solid concentration on the mechanical and microstructural properties of freeze-casted macroporous hydroxyapatite scaffolds.

PubMed

Farhangdoust, S; Zamanian, A; Yasaei, M; Khorami, M

2013-01-01

The design and fabrication of macroporous hydroxyapatite scaffolds, which could overcome current bone tissue engineering limitations, have been considered in recent years. In the current study, controlled unidirectional freeze-casting at different cooling rates was investigated. In the first step, different slurries with initial hydroxyapatite concentrations of 7-37.5 vol.% were prepared. In the next step, different cooling rates from 2 to 14 °C/min were applied to synthesize the porous scaffold. Additionally, a sintering temperature of 1350 °C was chosen as an optimum temperature. Finally, the phase composition (by XRD), microstructure (by SEM), mechanical characteristics, and the porosity of sintered samples were assessed. The porosity of the sintered samples was in a range of 45-87% and the compressive strengths varied from 0.4 MPa to 60 MPa. The mechanical strength of the scaffolds increased as a function of initial concentration, cooling rate, and sintering temperature. With regards to mechanical strength and pore size, the samples with the initial concentration and the cooling rate of 15 vol.% and 5 °C/min, respectively, showed better results. Copyright © 2012 Elsevier B.V. All rights reserved.

General solutions for the oxidation kinetics of polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillen, K.T.; Clough, R.L.; Wise, J.

1996-08-01

The simplest general kinetic schemes applicable to the oxidation of polymers are presented, discussed and analyzed in terms of the underlying kinetic assumptions. For the classic basic autoxidation scheme (BAS), which involves three bimolecular termination steps and is applicable mainly to unstabilized polymers, typical assumptions used singly or in groups include (1) long kinetic chain length, (2) a specific ratio of the termination rate constants and (3) insensitivity to the oxygen concentration (e.g., domination by a single termination step). Steady-state solutions for the rate of oxidation are given in terms of one, two, three, or four parameters, corresponding respectively tomore » three, two, one, or zero kinetic assumptions. The recently derived four-parameter solution predicts conditions yielding unusual dependencies of the oxidation rate on oxygen concentration and on initiation rate, as well as conditions leading to some unusual diffusion-limited oxidation profile shapes. For stabilized polymers, unimolecular termination schemes are typically more appropriate than bimolecular. Kinetics incorporating unimolecular termination reactions are shown to result in very simple oxidation expressions which have been experimentally verified for both radiation-initiated oxidation of an EPDM and thermoxidative degradation of nitrile and chloroprene elastomers.« less

Effects of step rate manipulation on joint mechanics during running.

PubMed

Heiderscheit, Bryan C; Chumanov, Elizabeth S; Michalski, Max P; Wille, Christa M; Ryan, Michael B

2011-02-01

the objective of this study was to characterize the biomechanical effects of step rate modification during running on the hip, knee, and ankle joints so as to evaluate a potential strategy to reduce lower extremity loading and risk for injury. three-dimensional kinematics and kinetics were recorded from 45 healthy recreational runners during treadmill running at constant speed under various step rate conditions (preferred, ± 5%, and ± 10%). We tested our primary hypothesis that a reduction in energy absorption by the lower extremity joints during the loading response would occur, primarily at the knee, when step rate was increased. less mechanical energy was absorbed at the knee (P < 0.01) during the +5% and +10% step rate conditions, whereas the hip (P < 0.01) absorbed less energy during the +10% condition only. All joints displayed substantially (P < 0.01) more energy absorption when preferred step rate was reduced by 10%. Step length (P < 0.01), center of mass vertical excursion (P < 0.01), braking impulse (P < 0.01), and peak knee flexion angle (P < 0.01) were observed to decrease with increasing step rate. When step rate was increased 10% above preferred, peak hip adduction angle (P < 0.01) and peak hip adduction (P < 0.01) and internal rotation (P < 0.01) moments were found to decrease. we conclude that subtle increases in step rate can substantially reduce the loading to the hip and knee joints during running and may prove beneficial in the prevention and treatment of common running-related injuries.

Characterization of Folding Mechanisms of Trp-cage and WW-domain by Network Analysis of Simulations with a Hybrid-resolution Model

PubMed Central

Han, Wei; Schulten, Klaus

2013-01-01

In this study, we apply a hybrid-resolution model, namely PACE, to characterize the free energy surfaces (FESs) of trp-cage and a WW domain variant along with the respective folding mechanisms. Unbiased, independent simulations with PACE are found to achieve together multiple folding and unfolding events for both proteins, allowing us to perform network analysis of the FESs to identify folding pathways. PACE reproduces for both proteins expected complexity hidden in the folding FESs, in particular, meta-stable non-native intermediates. Pathway analysis shows that some of these intermediates are, actually, on-pathway folding intermediates and that intermediates kinetically closest to the native states can be either critical on-pathway or off-pathway intermediates, depending on the protein. Apart from general insights into folding, specific folding mechanisms of the proteins are resolved. We find that trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step of folding, which, however, may not be the rate-limiting step. For the WW domain variant studied we observe two main folding pathways with opposite orders of formation of the two hairpins involved in the structure; for either pathway, formation of hairpin 1 is more likely to be the rate-limiting step. Altogether, our results suggest that PACE combined with network analysis is a computationally efficient and valuable tool for the study of protein folding. PMID:23915394

Hydrothermal atomic force microscopy observations of barite step growth rates as a function of the aqueous barium-to-sulfate ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bracco, Jacquelyn N.; Gooijer, Yiscka; Higgins, Steven R.

The rate of growth of ionic minerals from solutions with varying aqueous cation:anion ratios may result in significant errors in mineralization rates predicted by commonly-used affinity-based rate equations. To assess the potential influence of solute stoichiometry on barite growth, step velocities on the barite (001) surface have been measured at 108 °C using hydrothermal atomic force microscopy (HAFM) at moderate supersaturation and as a function of the aqueous barium:sulfate ratio (r). Barite growth hillocks at r ~ 1 were bounded bymore » $$\\langle$$120$$\\rangle$$ steps, however at r < 1, kink site densities increased, steps followed a direction vicinal to $$\\langle$$120$$\\rangle$$, and the [010] steps developed. At r > 1, steps roughened and rounded as the kink site density increased. Step velocities peaked at r = 1 and decreased roughly symmetrically as a function of r, indicating the attachment rates of barium and sulfate ions are similar under these conditions. We hypothesize that the differences in our observations at high and low r arise from differences in the attachment rate constants for the obtuse and acute $$\\langle$$120$$\\rangle$$ steps. Based on results at low r, the data suggests the attachment rate constant for barium ions is similar for obtuse and acute steps. Based on results at high r, the data suggests the attachment rate constant for sulfate is greater for obtuse steps than acute steps. In conclusion, utilizing a step growth model developed by Stack and Grantham (2010) the experimental step velocities as a function of r were readily fit while attempts to fit the data using a model developed by Zhang and Nancollas (1998) were less successful.« less

Hydrothermal atomic force microscopy observations of barite step growth rates as a function of the aqueous barium-to-sulfate ratio

DOE PAGES

Bracco, Jacquelyn N.; Gooijer, Yiscka; Higgins, Steven R.

2016-03-19

The rate of growth of ionic minerals from solutions with varying aqueous cation:anion ratios may result in significant errors in mineralization rates predicted by commonly-used affinity-based rate equations. To assess the potential influence of solute stoichiometry on barite growth, step velocities on the barite (001) surface have been measured at 108 °C using hydrothermal atomic force microscopy (HAFM) at moderate supersaturation and as a function of the aqueous barium:sulfate ratio (r). Barite growth hillocks at r ~ 1 were bounded bymore » $$\\langle$$120$$\\rangle$$ steps, however at r < 1, kink site densities increased, steps followed a direction vicinal to $$\\langle$$120$$\\rangle$$, and the [010] steps developed. At r > 1, steps roughened and rounded as the kink site density increased. Step velocities peaked at r = 1 and decreased roughly symmetrically as a function of r, indicating the attachment rates of barium and sulfate ions are similar under these conditions. We hypothesize that the differences in our observations at high and low r arise from differences in the attachment rate constants for the obtuse and acute $$\\langle$$120$$\\rangle$$ steps. Based on results at low r, the data suggests the attachment rate constant for barium ions is similar for obtuse and acute steps. Based on results at high r, the data suggests the attachment rate constant for sulfate is greater for obtuse steps than acute steps. In conclusion, utilizing a step growth model developed by Stack and Grantham (2010) the experimental step velocities as a function of r were readily fit while attempts to fit the data using a model developed by Zhang and Nancollas (1998) were less successful.« less

A variable-step-size robust delta modulator.

NASA Technical Reports Server (NTRS)

Song, C. L.; Garodnick, J.; Schilling, D. L.

1971-01-01

Description of an analytically obtained optimum adaptive delta modulator-demodulator configuration. The device utilizes two past samples to obtain a step size which minimizes the mean square error for a Markov-Gaussian source. The optimum system is compared, using computer simulations, with a linear delta modulator and an enhanced Abate delta modulator. In addition, the performance is compared to the rate distortion bound for a Markov source. It is shown that the optimum delta modulator is neither quantization nor slope-overload limited. The highly nonlinear equations obtained for the optimum transmitter and receiver are approximated by piecewise-linear equations in order to obtain system equations which can be transformed into hardware. The derivation of the experimental system is presented.

Role of Reversible Histidine Coordination in Hydroxylamine Reduction by Plant Hemoglobins (Phytoglobins).

PubMed

Athwal, Navjot Singh; Alagurajan, Jagannathan; Andreotti, Amy H; Hargrove, Mark S

2016-10-18

Reduction of hydroxylamine to ammonium by phytoglobin, a plant hexacoordinate hemoglobin, is much faster than that of other hexacoordinate hemoglobins or pentacoordinate hemoglobins such as myoglobin, leghemoglobin, and red blood cell hemoglobin. The reason for differences in reactivity is not known but could be intermolecular electron transfer between protein molecules in support of the required two-electron reduction, hydroxylamine binding, or active site architecture favoring the reaction. Experiments were conducted with phytoglobins from rice, tomato, and soybean along with human neuroglobin and soybean leghemoglobin that reveal hydroxylamine binding as the rate-limiting step. For hexacoordinate hemoglobins, binding is limited by the dissociation rate constant for the distal histidine, while leghemoglobin is limited by an intrinsically low affinity for hydroxylamine. When the distal histidine is removed from rice phytoglobin, a hydroxylamine-bound intermediate is formed and the reaction rate is diminished, indicating that the distal histidine imidazole side chain is critical for the reaction, albeit not for electron transfer but rather for direct interaction with the substrate. Together, these results demonstrate that phytoglobins are superior at hydroxylamine reduction because they have distal histidine coordination affinity constants near 1, and facile rate constants for binding and dissociation of the histidine side chain. Hexacoordinate hemoglobins such as neuroglobin are limited by tighter histidine coordination that blocks hydroxylamine binding, and pentacoordinate hemoglobins have intrinsically lower hydroxylamine affinities.

Is the catalytic activity of triosephosphate isomerase fully optimized? An investigation based on maximization of entropy production.

PubMed

Bonačić Lošić, Željana; Donđivić, Tomislav; Juretić, Davor

2017-03-01

Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states. The maximal entropy production (MaxEP) requirement for any of the first three transitions between TIM functional states leads to decreased total entropy production. Only the MaxEP requirement for the product (R-glyceraldehyde-3-phosphate) release step led to a 30% increase in enzyme activity, specificity constant k cat /K M , and overall entropy production. The product release step, due to the TIM molecular machine working in the physiological direction of glycolysis, has not been identified before as the rate-limiting step by using irreversible thermodynamics. Together with structural studies, our results open the possibility for finding amino acid substitutions leading to an increased frequency of loop six opening and product release.

Theoretical evidence of the observed kinetic order dependence on temperature during the N(2)O decomposition over Fe-ZSM-5.

PubMed

Guesmi, Hazar; Berthomieu, Dorothee; Bromley, Bryan; Coq, Bernard; Kiwi-Minsker, Lioubov

2010-03-28

The characterization of Fe/ZSM5 zeolite materials, the nature of Fe-sites active in N(2)O direct decomposition, as well as the rate limiting step are still a matter of debate. The mechanism of N(2)O decomposition on the binuclear oxo-hydroxo bridged extraframework iron core site [Fe(II)(mu-O)(mu-OH)Fe(II)](+) inside the ZSM-5 zeolite has been studied by combining theoretical and experimental approaches. The overall calculated path of N(2)O decomposition involves the oxidation of binuclear Fe(II) core sites by N(2)O (atomic alpha-oxygen formation) and the recombination of two surface alpha-oxygen atoms leading to the formation of molecular oxygen. Rate parameters computed using standard statistical mechanics and transition state theory reveal that elementary catalytic steps involved into N(2)O decomposition are strongly dependent on the temperature. This theoretical result was compared to the experimentally observed steady state kinetics of the N(2)O decomposition and temperature-programmed desorption (TPD) experiments. A switch of the reaction order with respect to N(2)O pressure from zero to one occurs at around 800 K suggesting a change of the rate determining step from the alpha-oxygen recombination to alpha-oxygen formation. The TPD results on the molecular oxygen desorption confirmed the mechanism proposed.

A Multi-stage Carcinogenesis Model to Investigate Caloric Restriction as a Potential Tool for Post-irradiation Mitigation of Cancer Risk

PubMed Central

Tani, Shusuke; Blyth, Benjamin John; Shang, Yi; Morioka, Takamitsu; Kakinuma, Shizuko; Shimada, Yoshiya

2016-01-01

The risk of radiation-induced cancer adds to anxiety in low-dose exposed populations. Safe and effective lifestyle changes which can help mitigate excess cancer risk might provide exposed individuals the opportunity to pro-actively reduce their cancer risk, and improve mental health and well-being. Here, we applied a mathematical multi-stage carcinogenesis model to the mouse lifespan data using adult-onset caloric restriction following irradiation in early life. We re-evaluated autopsy records with a veterinary pathologist to determine which tumors were the probable causes of death in order to calculate age-specific mortality. The model revealed that in both irradiated and unirradiated mice, caloric restriction reduced the age-specific mortality of all solid tumors and hepatocellular carcinomas across most of the lifespan, with the mortality rate dependent more on age owing to an increase in the number of predicted rate-limiting steps. Conversely, irradiation did not significantly alter the number of steps, but did increase the overall transition rate between the steps. We show that the extent of the protective effect of caloric restriction is independent of the induction of cancer from radiation exposure, and discuss future avenues of research to explore the utility of caloric restriction as an example of a potential post-irradiation mitigation strategy. PMID:27390741

Combined 34S, 33S and 18O isotope fractionations record different intracellular steps of microbial sulfate reduction

NASA Astrophysics Data System (ADS)

Antler, Gilad; Turchyn, Alexandra V.; Ono, Shuhei; Sivan, Orit; Bosak, Tanja

2017-04-01

Several enzymatic steps in microbial sulfate reduction (MSR) fractionate the isotope ratios of 33S/32S, 34S/32S and 18O/16O in extracellular sulfate, but the effects of different intracellular processes on the isotopic composition of residual sulfate are still not well quantified. We measured combined multiple sulfur (33S/32S, 34S/32S) and oxygen (18O/16O) isotope ratios of sulfate in pure cultures of a marine sulfate reducing bacterium Desulfovibrio sp. DMSS-1 grown on different organic substrates. These measurements are consistent with the previously reported correlations of oxygen and sulfur isotope fractionations with the cell-specific rate of MSR: faster reduction rates produced smaller isotopic fractionations for all isotopes. Combined isotope fractionation of oxygen and multiple sulfur isotopes are also consistent with the relationship between the rate limiting step during microbial sulfate reduction and the availability of the DsrC subunit. These experiments help reconstruct and interpret processes that operate in natural pore waters characterized by high 18O/16O and moderate 34S/32S ratios and suggest that some multiple isotope signals in the environment cannot be explained by microbial sulfate reduction alone. Instead, these signals support the presence of active, but slow sulfate reduction as well as the reoxidation of sulfide.

Accelerating the Rate-Limiting Step in Novel Enzymatic Carbohydrate-to-Hydrogen Technology by Enzyme Engineering

DTIC Science & Technology

2011-10-30

stable phosphoglucose isomerase through immobilization of cellulose-binding module-tagged thermophilic enzyme on low- cost high-capacity celiulosic...NOVEL ENZYMATIC CARBOHYDRATE-TO-HYDROGEN TECHNOLOGY BY ENZYME ENGINEERING Grant/Contract Number: FA9550-08-1-0145 Program Manager: Dr. Walt...bbtransformation (SyPaB) is the implementation of complicated biochemical reactions by in vitro assembly of enzyme and coenzymes. Different from in vivo

Synthesis, characterization, and controlled release antibacterial behavior of antibiotic intercalated Mg–Al layered double hydroxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yi; Zhang, Dun, E-mail: zhangdun@qdio.ac.cn

Graphical abstract: The antibiotic anion released from Mg–Al LDHs provides a controlled release antibacterial activity against the growth of Micrococcus lysodeikticus in 3.5% NaCl solution. Highlights: ► Antibiotic anion intercalated LDHs were synthesized and characterized. ► The ion-exchange one is responsible for the release process. ► The diffusion through particle is the release rate limiting step. ► LDHs loaded with antibiotic anion have high antibacterial capabilities. -- Abstract: Antibiotic–inorganic clay composites including four antibiotic anions, namely, benzoate (BZ), succinate (SU), benzylpenicillin (BP), and ticarcillin (TC) anions, intercalated Mg–Al layered double hydroxides (LDHs) were synthesized via ion-exchange. Powder X-ray diffraction andmore » Fourier transform infrared spectrum analyses showed the successful intercalation of antibiotic anion into the LDH interlayer. BZ and BP anions were accommodated in the interlayer region as a bilayer, whereas SU and TC anions were intercalated in a monolayer arrangement. Kinetic simulation of the release data indicated that ion-exchange was responsible for the release process, and the diffusion through the particles was the rate-limiting step. The antibacterial capabilities of LDHs loaded with antibiotic anion toward Micrococcus lysodeikticus growth were analyzed using a turbidimetric method. Significant high inhibition rate was observed when LDH nanohybrid was introduced in 3.5% NaCl solution. Therefore, this hybrid material may be applied as nanocontainer in active antifouling coating for marine equipment.« less

Review of Manganese Processing for Production of TRIP/TWIP Steels, Part 2: Reduction Studies

NASA Astrophysics Data System (ADS)

Elliott, R.; Coley, K.; Mostaghel, S.; Barati, M.

2018-02-01

Production of ultrahigh-manganese steels is expected to result in significant increase in demand for low-carbon (LC) ferromanganese (FeMn) and silicomanganese (SiMn). Current manganese processing techniques are energy intensive and typically yield a high-carbon product. The present work therefore reviews available literature regarding carbothermic reduction of Mn oxides and ores, with the objective of identifying opportunities for future process development to mitigate the cost of LC FeMn and SiMn. In general, there is consensus that carbothermic reduction of Mn oxides and ores is limited by gasification of carbon. Conditions which enhance or bypass this step (e.g., by application of CH4) show higher rates of reduction at lower temperatures. This phenomenon has potential application in solid-state reduction of Mn ore. Other avenues for process development include optimization of the prereduction step in conventional FeMn production and metallothermic reduction as a secondary reduction step.

When procedures discourage insight: epistemological consequences of prompting novice physics students to construct force diagrams

NASA Astrophysics Data System (ADS)

Kuo, Eric; Hallinen, Nicole R.; Conlin, Luke D.

2017-05-01

One aim of school science instruction is to help students become adaptive problem solvers. Though successful at structuring novice problem solving, step-by-step problem-solving frameworks may also constrain students' thinking. This study utilises a paradigm established by Heckler [(2010). Some consequences of prompting novice physics students to construct force diagrams. International Journal of Science Education, 32(14), 1829-1851] to test how cuing the first step in a standard framework affects undergraduate students' approaches and evaluation of solutions in physics problem solving. Specifically, prompting the construction of a standard diagram before problem solving increases the use of standard procedures, decreasing the use of a conceptual shortcut. Providing a diagram prompt also lowers students' ratings of informal approaches to similar problems. These results suggest that reminding students to follow typical problem-solving frameworks limits their views of what counts as good problem solving.

Development of Quality Metrics in Ambulatory Pediatric Cardiology.

PubMed

Chowdhury, Devyani; Gurvitz, Michelle; Marelli, Ariane; Anderson, Jeffrey; Baker-Smith, Carissa; Diab, Karim A; Edwards, Thomas C; Hougen, Tom; Jedeikin, Roy; Johnson, Jonathan N; Karpawich, Peter; Lai, Wyman; Lu, Jimmy C; Mitchell, Stephanie; Newburger, Jane W; Penny, Daniel J; Portman, Michael A; Satou, Gary; Teitel, David; Villafane, Juan; Williams, Roberta; Jenkins, Kathy

2017-02-07

The American College of Cardiology Adult Congenital and Pediatric Cardiology (ACPC) Section had attempted to create quality metrics (QM) for ambulatory pediatric practice, but limited evidence made the process difficult. The ACPC sought to develop QMs for ambulatory pediatric cardiology practice. Five areas of interest were identified, and QMs were developed in a 2-step review process. In the first step, an expert panel, using the modified RAND-UCLA methodology, rated each QM for feasibility and validity. The second step sought input from ACPC Section members; final approval was by a vote of the ACPC Council. Work groups proposed a total of 44 QMs. Thirty-one metrics passed the RAND process and, after the open comment period, the ACPC council approved 18 metrics. The project resulted in successful development of QMs in ambulatory pediatric cardiology for a range of ambulatory domains. Copyright © 2017 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Stepped care in the treatment of trichotillomania.

PubMed

Rogers, Kate; Banis, Maria; Falkenstein, Martha J; Malloy, Elizabeth J; McDonough, Lauren; Nelson, Samuel O; Rusch, Natalie; Haaga, David A F

2014-04-01

There are effective treatments of trichotillomania (TTM), but access to expert providers is limited. This study tested a stepped care model aimed at improving access. Participants were 60 (95% women, 75% Caucasian, 2% Hispanic) adults (M = 33.18 years) with TTM. They were randomly assigned to immediate versus waitlist (WL) conditions for Step 1 (10 weeks of web-based self-help via StopPulling.com). After Step 1, participants chose whether to engage in Step 2 (8 sessions of in-person habit reversal training [HRT]). In Step 1, the immediate condition had a small (d = .21) but significant advantage, relative to WL, in reducing TTM symptom ratings by interviewers (masked to experimental condition but not to assessment point); there were no differences in self-reported TTM symptoms, alopecia, functional impairment, or quality of life. Step 1 was more effective for those who used the site more often. Stepped care was highly acceptable: Motivation did not decrease during Step 1; treatment satisfaction was high, and 76% enrolled in Step 2. More symptomatic patients self-selected into HRT, and on average they improved significantly. Over one third (36%) made clinically significant improvement in self-reported TTM symptoms. Considering the entire stepped care program, participants significantly reduced symptoms, alopecia, and impairment, and increased quality of life. For quality of life and symptom severity, there was some relapse by 3-month follow-up. Stepped care is acceptable, and HRT was associated with improvement. Further work is needed to determine which patients with TTM can benefit from self-help and how to reduce relapse.

Plasma polymerization of ethylene in an atmospheric pressure-pulsed discharge

NASA Technical Reports Server (NTRS)

Donohoe, K.; Wydeven, T.

1979-01-01

The polymerization of ethylene in an atmospheric pressure-pulsed discharge has been studied. Partial pressures of ethylene up to 4 kN/sq m were used with helium as a diluent. Deposition rates (on glass slides) were the same throughout the discharge volume over a wide range of operating conditions. These rates were in the 1-2 A/sec range. The films were clear, soft, and showed good adhesion to the glass substrates. Oligomers large enough to visibly scatter 637.8-nm light were observed in the gas phase under all conditions in which film deposition occurred. The experimental results suggest that Brownian diffusion of these oligomers was the rate-limiting step in the film deposition process.

Continuous-variable quantum key distribution with 1 Mbps secure key rate.

PubMed

Huang, Duan; Lin, Dakai; Wang, Chao; Liu, Weiqi; Fang, Shuanghong; Peng, Jinye; Huang, Peng; Zeng, Guihua

2015-06-29

We report the first continuous-variable quantum key distribution (CVQKD) experiment to enable the creation of 1 Mbps secure key rate over 25 km standard telecom fiber in a coarse wavelength division multiplexers (CWDM) environment. The result is achieved with two major technological advances: the use of a 1 GHz shot-noise-limited homodyne detector and the implementation of a 50 MHz clock system. The excess noise due to noise photons from local oscillator and classical data channels in CWDM is controlled effectively. We note that the experimental verification of high-bit-rate CVQKD in the multiplexing environment is a significant step closer toward large-scale deployment in fiber networks.

Effects of Step Rate Manipulation on Joint Mechanics during Running

PubMed Central

Heiderscheit, Bryan C.; Chumanov, Elizabeth S.; Michalski, Max P.; Wille, Christa M.; Ryan, Michael B.

2010-01-01

Purpose The objective of this study was to characterize the biomechanical effects of step rate modification during running on the hip, knee and ankle joints, so as to evaluate a potential strategy to reduce lower extremity loading and risk for injury. Methods Three-dimensional kinematics and kinetics were recorded from 45 healthy recreational runners during treadmill running at constant speed under various step rate conditions (preferred, ± 5% and ± 10%). We tested our primary hypothesis that a reduction in energy absorption by the lower extremity joints during the loading response would occur, primarily at the knee, when step rate was increased. Results Less mechanical energy was absorbed at the knee (p<0.01) during the +5% and +10% step rate conditions, while the hip (p<0.01) absorbed less energy during the +10% condition only. All joints displayed substantially (p<0.01) more energy absorption when preferred step rate was reduced by 10. Step length (p<0.01), center of mass vertical excursion (p<0.01), breaking impulse (p<0.01) and peak knee flexion angle (p<0.01) were observed to decrease with increasing step rate. When step rate was increased 10% above preferred, peak hip adduction angle (p<0.01), as well as peak hip adduction (p<0.01) and internal rotation (p<0.01) moments, were found to decrease. Conclusion We conclude that subtle increases in step rate can substantially reduce the loading to the hip and knee joints during running and may prove beneficial in the prevention and treatment of common running-related injuries. PMID:20581720

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

THE EFFECT OF STEP RATE MANIPULATION ON FOOT STRIKE PATTERN OF LONG DISTANCE RUNNERS.

PubMed

Allen, Darrell J; Heisler, Hollie; Mooney, Jennifer; Kring, Richard

2016-02-01

Running gait retraining to change foot strike pattern in runners from a heel strike pattern to a non heel- strike pattern has been shown to reduce impact forces and may help to reduce running related injuries. Step rate manipulation above preferred is known to help decrease step length, foot inclination angle, and vertical mass excursion, but has not yet been evaluated as a method to change foot strike pattern. The purpose of this study was to investigate the effect of step rate manipulation on foot strike pattern in shod recreational runners who run with a heel strike pattern. A secondary purpose was to describe the effect of step rate manipulation at specific percentages above preferred on foot inclination angle at initial contact. Forty volunteer runners, who were self-reported heel strikers and had a weekly running mileage of at least 10 miles, were recruited. Runners were confirmed to be heel strikers during the warm up period on the treadmill. The subject's step rate was determined at their preferred running pace. A metronome was used to increase step rate above the preferred step rate by 5%, 10% and 15%. 2D video motion analysis was utilized to determine foot strike pattern and to measure foot inclination angle at initial contact for each step rate condition. There was a statistically significant change in foot strike pattern from a heel strike pattern to a mid-foot or forefoot strike pattern at both 10% and 15% step rates above preferred. Seven of the 40 subjects (17.5%) changed from a heel- strike pattern to a non- heel strike pattern at +10% and 12 of the 40 subjects (30%) changed to a non-heel strike pattern at +15%. Mean foot inclination angle at initial contact showed a statistically significant change (reduction) as step rate increased. Step rate manipulation of 10% or greater may be enough to change foot strike pattern from a heel strike to a mid-foot or forefoot strike pattern in a small percentage of recreational runners who run in traditional running shoes. If changing the foot strike pattern is the main goal, other gait re-training methods may be needed to make a change from a heel strike to a non-heel strike pattern. Step rate manipulation shows a progressive reduction of foot inclination angle at 5%, 10%, and 15% above preferred step rate which reduces the severity of the heel strike at initial contact. Step rate manipulation of at least +10% above preferred may be an effective running gait retraining method for clinicians to decrease the severity of heel strike and possibly assist a runner to change to a non-heel strike pattern. 3.

Calorimetric Studies of Precipitation and Dissolution Kinetics in Aluminum Alloys 2219 and 7075

NASA Astrophysics Data System (ADS)

Papazian, John M.

1982-05-01

Differential scanning calorimetry (DSC) was used to study the kinetics of precipitation and dissolution of metastable and stable phases in aluminum alloys 2219 and 7075. A comparison of DSC scans obtained at heating rates of 1, 5, 10, and 20 K per minute showed that, during a DSC scan, the rates of precipitation of θ' and θ in 2219 and η' and η in 7075 were limited by their reaction kinetics. Likewise, the rates of dissolution of GP zones, θ' and η', were found to be dominated by kinetics. In contrast, the dissolution of θ and η was dominated by the thermodynamic equilibrium between these phases and the matrix. Analysis of the kinetically dominated reaction peaks and their dependence on heating rate and particle size showed that the GP zone dissolution reaction could best be described by a three-dimensional volume diffusion limited rate expression with an activation energy equal to that for diffusion. The rate of formation of θ' was best described by an Avrami expression with n = 1.1, indicating that nucleation was not the rate controlling step. A pronounced dependence of the θ' formation rate on prior plastic deformation was observed and ascribed to the influence of the matrix dislocation density on diffusivity.

Step-rate cut-points for physical activity intensity in patients with multiple sclerosis: The effect of disability status.

PubMed

Agiovlasitis, Stamatis; Sandroff, Brian M; Motl, Robert W

2016-02-15

Evaluating the relationship between step-rate and rate of oxygen uptake (VO2) may allow for practical physical activity assessment in patients with multiple sclerosis (MS) of differing disability levels. To examine whether the VO2 to step-rate relationship during over-ground walking differs across varying disability levels among patients with MS and to develop step-rate thresholds for moderate- and vigorous-intensity physical activity. Adults with MS (N=58; age: 51 ± 9 years; 48 women) completed one over-ground walking trial at comfortable speed, one at 0.22 m · s(-1) slower, and one at 0.22 m · s(-1) faster. Each trial lasted 6 min. VO2 was measured with portable spirometry and steps with hand-tally. Disability status was classified as mild, moderate, or severe based on Expanded Disability Status Scale scores. Multi-level regression indicated that step-rate, disability status, and height significantly predicted VO2 (p<0.05). Based on this model, we developed step-rate thresholds for activity intensity that vary by disability status and height. A separate regression without height allowed for development of step-rate thresholds that vary only by disability status. The VO2 during over-ground walking differs among ambulatory patients with MS based on disability level and height, yielding different step-rate thresholds for physical activity intensity. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluation of the biophysical limitations on photosynthesis of four varietals of Brassica rapa

NASA Astrophysics Data System (ADS)

Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B.; Weinig, C.

2014-12-01

Evaluating performance of agricultural varietals can support the identification of genotypes that will increase yield and can inform management practices. The biophysical limitations of photosynthesis are amongst the key factors that necessitate evaluation. This study evaluated how four biophysical limitations on photosynthesis, stomatal response to vapor pressure deficit, maximum carboxylation rate by Rubisco (Ac), rate of photosynthetic electron transport (Aj) and triose phosphate use (At) vary between four Brassica rapa genotypes. Leaf gas exchange data was used in an ecophysiological process model to conduct this evaluation. The Terrestrial Regional Ecosystem Exchange Simulator (TREES) integrates the carbon uptake and utilization rate limiting factors for plant growth. A Bayesian framework integrated in TREES here used net A as the target to estimate the four limiting factors for each genotype. As a first step the Bayesian framework was used for outlier detection, with data points outside the 95% confidence interval of model estimation eliminated. Next parameter estimation facilitated the evaluation of how the limiting factors on A different between genotypes. Parameters evaluated included maximum carboxylation rate (Vcmax), quantum yield (ϕJ), the ratio between Vc-max and electron transport rate (J), and trios phosphate utilization (TPU). Finally, as trios phosphate utilization has been shown to not play major role in the limiting A in many plants, the inclusion of At in models was evaluated using deviance information criteria (DIC). The outlier detection resulted in a narrowing in the estimated parameter distributions allowing for greater differentiation of genotypes. Results show genotypes vary in the how limitations shape assimilation. The range in Vc-max , a key parameter in Ac, was 203.2 - 223.9 umol m-2 s-1 while the range in ϕJ, a key parameter in AJ, was 0.463 - 0.497 umol m-2 s-1. The added complexity of the TPU limitation did not improve model performance in the genotypes assessed based on DIC. By identifying how varietals differ in their biophysical limitations on photosynthesis genotype selection can be informed for agricultural goals. Further work aims at applying this approach to a fifth limiting factor on photosynthesis, mesophyll conductance.

Modelling river bank retreat by combining fluvial erosion, seepage and mass failure

NASA Astrophysics Data System (ADS)

Dapporto, S.; Rinaldi, M.

2003-04-01

Streambank erosion processes contribute significantly to the sediment yielded from a river system and represent an important issue in the contexts of soil degradation and river management. Bank retreat is controlled by a complex interaction of hydrologic, geotechnical, and hydraulic processes. The capability of modelling these different components allows for a full reconstruction and comprehension of the causes and rates of bank erosion. River bank retreat during a single flow event has been modelled by combining simulation of fluvial erosion, seepage, and mass failures. The study site, along the Sieve River (Central Italy), has been subject to extensive researches, including monitoring of pore water pressures for a period of 4 years. The simulation reconstructs fairly faithfully the observed changes, and is used to: a) test the potentiality and discuss advantages and limitations of such type of methodology for modelling bank retreat; c) quantify the contribution and mutual role of the different processes determining bank retreat. The hydrograph of the event is divided in a series of time steps. Modelling of the riverbank retreat includes for each step the following components: a) fluvial erosion and consequent changes in bank geometry; b) finite element seepage analysis; c) stability analysis by limit equilibrium method. Direct fluvial shear erosion is computed using empirically derived relationships expressing lateral erosion rate as a function of the excess of shear stress to the critical entrainment value for the different materials along the bank profile. Lateral erosion rate has been calibrated on the basis of the total bank retreat measured by digital terrestrial photogrammetry. Finite element seepage analysis is then conducted to reconstruct the saturated and unsaturated flow within the bank and the pore water pressure distribution for each time step. The safety factor for mass failures is then computed, using the pore water pressure distribution obtained by the seepage analysis, and the geometry of the upper bank is modified in case of failure.

Overcoming the rate-distance limit of quantum key distribution without quantum repeaters.

PubMed

Lucamarini, M; Yuan, Z L; Dynes, J F; Shields, A J

2018-05-01

Quantum key distribution (QKD) 1,2 allows two distant parties to share encryption keys with security based on physical laws. Experimentally, QKD has been implemented via optical means, achieving key rates of 1.26 megabits per second over 50 kilometres of standard optical fibre 3 and of 1.16 bits per hour over 404 kilometres of ultralow-loss fibre in a measurement-device-independent configuration 4 . Increasing the bit rate and range of QKD is a formidable, but important, challenge. A related target, which is currently considered to be unfeasible without quantum repeaters 5-7 , is overcoming the fundamental rate-distance limit of QKD 8 . This limit defines the maximum possible secret key rate that two parties can distil at a given distance using QKD and is quantified by the secret-key capacity of the quantum channel 9 that connects the parties. Here we introduce an alternative scheme for QKD whereby pairs of phase-randomized optical fields are first generated at two distant locations and then combined at a central measuring station. Fields imparted with the same random phase are 'twins' and can be used to distil a quantum key. The key rate of this twin-field QKD exhibits the same dependence on distance as does a quantum repeater, scaling with the square-root of the channel transmittance, irrespective of who (malicious or otherwise) is in control of the measuring station. However, unlike schemes that involve quantum repeaters, ours is feasible with current technology and presents manageable levels of noise even on 550 kilometres of standard optical fibre. This scheme is a promising step towards overcoming the rate-distance limit of QKD and greatly extending the range of secure quantum communications.

Sanov and central limit theorems for output statistics of quantum Markov chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horssen, Merlijn van, E-mail: merlijn.vanhorssen@nottingham.ac.uk; Guţă, Mădălin, E-mail: madalin.guta@nottingham.ac.uk

2015-02-15

In this paper, we consider the statistics of repeated measurements on the output of a quantum Markov chain. We establish a large deviations result analogous to Sanov’s theorem for the multi-site empirical measure associated to finite sequences of consecutive outcomes of a classical stochastic process. Our result relies on the construction of an extended quantum transition operator (which keeps track of previous outcomes) in terms of which we compute moment generating functions, and whose spectral radius is related to the large deviations rate function. As a corollary to this, we obtain a central limit theorem for the empirical measure. Suchmore » higher level statistics may be used to uncover critical behaviour such as dynamical phase transitions, which are not captured by lower level statistics such as the sample mean. As a step in this direction, we give an example of a finite system whose level-1 (empirical mean) rate function is independent of a model parameter while the level-2 (empirical measure) rate is not.« less

REVIEW ARTICLE: How do biomolecular systems speed up and regulate rates?

NASA Astrophysics Data System (ADS)

Zhou, Huan-Xiang

2005-09-01

The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.

Amination with Pd-NHC complexes: rate and computational studies involving substituted aniline substrates.

PubMed

Hoi, Ka Hou; Çalimsiz, Selçuk; Froese, Robert D J; Hopkinson, Alan C; Organ, Michael G

2012-01-02

The amination of aryl chlorides with various aniline derivatives using the N-heterocyclic carbene-based Pd complexes Pd-PEPPSI-IPr and Pd-PEPPSI-IPent (PEPPSI=pyridine, enhanced precatalyst, preparation, stabilization, and initiation; IPr=diisopropylphenylimidazolium derivative; IPent= diisopentylphenylimidazolium derivative) has been studied. Rate studies have shown a reliance on the aryl chloride to be electron poor, although oxidative addition is not rate limiting. Anilines couple best when they are electron rich, which would seem to discount deprotonation of the intermediate metal ammonium complex as being rate limiting in favour of reductive elimination. In previous studies with secondary amines using PEPPSI complexes, deprotonation was proposed to be the slow step in the cycle. These experimental findings relating to mechanism were corroborated by computation. Pd-PEPPSI-IPr and the more hindered Pd-PEPPSI-IPent catalysts were used to couple deactivated aryl chlorides with electron poor anilines; while the IPr catalysis was sluggish, the IPent catalyst performed extremely well, again showing the high reactivity of this broadly useful catalyst. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gas hydrate formation rates from dissolved-phase methane in porous laboratory specimens

USGS Publications Warehouse

Waite, William F.; Spangenberg, E.K.

2013-01-01

Marine sands highly saturated with gas hydrates are potential energy resources, likely forming from methane dissolved in pore water. Laboratory fabrication of gas hydrate-bearing sands formed from dissolved-phase methane usually requires 1–2 months to attain the high hydrate saturations characteristic of naturally occurring energy resource targets. A series of gas hydrate formation tests, in which methane-supersaturated water circulates through 100, 240, and 200,000 cm3 vessels containing glass beads or unconsolidated sand, show that the rate-limiting step is dissolving gaseous-phase methane into the circulating water to form methane-supersaturated fluid. This implies that laboratory and natural hydrate formation rates are primarily limited by methane availability. Developing effective techniques for dissolving gaseous methane into water will increase formation rates above our observed (1 ± 0.5) × 10−7 mol of methane consumed for hydrate formation per minute per cubic centimeter of pore space, which corresponds to a hydrate saturation increase of 2 ± 1% per day, regardless of specimen size.

Simultaneous pharmacodynamic analysis of the lag and bactericidal phases exhibited by beta-lactams against Escherichia coli.

PubMed Central

Li, R C

1996-01-01

Antibiotic-bacterium interactions are complex in nature. In many cases, bacterial killing does not commence immediately after the addition of an antibiotic, and a lag period is observed. Antibiotic permeation and/or the intermediate steps that exist between antibiotic-receptor binding and expression of cell death are two major possible causes for such lag period. This study was primarily designed to determine the relationship, if any, between antibiotic concentrations and the lag periods by a modeling approach. Short-term time-kill studies were conducted for amoxicillin, ampicillin, penicillin-G, oxacillin, and dicloxacillin against Escherichia coli. In conjunction with the use of a saturable rate model to describe the concentration-dependent killing process, a first-order induction (initiation) rate constant was used to characterize the delay in bacterial killing during the lag period. For all of the beta-lactams tested, parameters describing the bactericidal effect suggest that amoxicillin and ampicillin were much more potent than oxacillin and dicloxacillin. The induction rate constant estimates for both ampicillin and amoxicillin were found to relate linearly to concentrations. Nevertheless, these induction rate constant estimates were lower for penicillin-G, oxacillin, and dicloxacillin and increased nonlinearly with concentrations until an apparent plateau was observed. These findings support the hypothesis that the permeation process is potentially a rate-limiting step for the rapid bactericidal beta-lactams such as ampicillin and amoxicillin. However, as suggested by previous observations of the various morphological changes induced by beta-lactams, the contribution of the steps following antibiotic-receptor complex formation to the lag period might be significant for the less bactericidal antibiotics such as oxacillin and dicloxacillin. Findings from the present modeling approach can potentially be used to guide future bench experimentation. PMID:8891135

Photosynthesis and Ribulose 1,5-Bisphosphate Concentrations in Intact Leaves of Xanthium strumarium L. 1

PubMed Central

Mott, Keith A.; Jensen, Richard G.; O'Leary, James W.; Berry, Joseph A.

1984-01-01

The interacting effects of the rate of ribulose 1,5-bisphosphate (RuBP) regeneration and the rate of RuBP utilization as influenced by the amount and activation of RuBP carboxylase on photosynthesis and RuBP concentrations were resolved in experiments which examined the kinetics of the response of photosynthesis and RuBP concentrations after step changes from a rate-saturating to a rate-limiting light intensity in Xanthium strumarium. Because RuBP carboxylase requires several minutes to deactivate in vivo, it was possible to observe the effect of reducing the rate of RuBP regeneration on the RuBP concentration at constant enzyme activation state by sampling very soon after reducing the light intensity. Samples taken over longer time periods showed the effect of changes in enzyme activation at constant RuBP regeneration rate on RuBP concentration and photosynthetic rate. Within 15 s of lowering the light intensity from 1500 to 600 microEinsteins per square meter per second the RuBP concentration in the leaves dropped below the enzyme active site concentration, indicating that RuBP regeneration rate was limiting for photosynthesis. After longer intervals of time, the RuBP concentration in the leaf increased as the RuBP carboxylase assumed a new steady state activation level. No change in the rate of photosynthesis was observed during the interval that RuBP concentration increased. It is concluded that the rate of photosynthesis at the lower light intensity was limited by the rate of RuBP regeneration and that parallel changes in the activation of RuBP carboxylase occurred such that concentrations of RuBP at steady state were not altered by changes in light intensity. PMID:16663982

Photosynthesis and Ribulose 1,5-Bisphosphate Concentrations in Intact Leaves of Xanthium strumarium L.

PubMed

Mott, K A; Jensen, R G; O'leary, J W; Berry, J A

1984-12-01

The interacting effects of the rate of ribulose 1,5-bisphosphate (RuBP) regeneration and the rate of RuBP utilization as influenced by the amount and activation of RuBP carboxylase on photosynthesis and RuBP concentrations were resolved in experiments which examined the kinetics of the response of photosynthesis and RuBP concentrations after step changes from a rate-saturating to a rate-limiting light intensity in Xanthium strumarium. Because RuBP carboxylase requires several minutes to deactivate in vivo, it was possible to observe the effect of reducing the rate of RuBP regeneration on the RuBP concentration at constant enzyme activation state by sampling very soon after reducing the light intensity. Samples taken over longer time periods showed the effect of changes in enzyme activation at constant RuBP regeneration rate on RuBP concentration and photosynthetic rate. Within 15 s of lowering the light intensity from 1500 to 600 microEinsteins per square meter per second the RuBP concentration in the leaves dropped below the enzyme active site concentration, indicating that RuBP regeneration rate was limiting for photosynthesis. After longer intervals of time, the RuBP concentration in the leaf increased as the RuBP carboxylase assumed a new steady state activation level. No change in the rate of photosynthesis was observed during the interval that RuBP concentration increased. It is concluded that the rate of photosynthesis at the lower light intensity was limited by the rate of RuBP regeneration and that parallel changes in the activation of RuBP carboxylase occurred such that concentrations of RuBP at steady state were not altered by changes in light intensity.

Formation of aqueous-phase sulfate during the haze period in China: Kinetics and atmospheric implications

NASA Astrophysics Data System (ADS)

Zhang, Haijie; Chen, Shilu; Zhong, Jie; Zhang, Shaowen; Zhang, Yunhong; Zhang, Xiuhui; Li, Zesheng; Zeng, Xiao Cheng

2018-03-01

Sulfate is one of the most important components in the aerosol due to its key role in air pollution and global climate change. Recent work has suggested that reactive nitrogen chemistry in aqueous water can explain the missing source of sulfate in the aqueous water. Herein, we have mapped out the energy profile of the oxidization process of SO2 leading from NO2 and two feasible three-step mechanisms have been proposed. For the oxidation of HOSO2- and HSO3- by the dissolved NO2 in weakly acidic and neutral aerosol (pH ≤ 7), the main contribution to the missing sulfate production comes from the oxidation of HOSO2-. The whole process is a self-sustaining process. For the oxidation of SO32- in alkaline aerosol (pH > 7), the third step - decomposition step of H2O or hydrolysis of SO3 step which are two parallel processes are the rate-limiting steps. The present results are of avail to better understand the missing source of sulfate in the aerosol and hence may lead to better science-based solutions for resolving the severe haze problems in China.

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes.

PubMed

Hernandez-Perez, Ruth; García-Cordero, José L; Escobar, Juan V

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes

NASA Astrophysics Data System (ADS)

Hernandez-Perez, Ruth; García-Cordero, José L.; Escobar, Juan V.

2017-12-01

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depending on whether evaporation is limited by the diffusion of vapor molecules or by the transfer rate across the liquid-vapor interface. For the diffusion-limited regime, we find that a mass-loss rate equal to 3/7 of that of a free-standing evaporating droplet brings a good balance between simplicity and physical correctness. We also find a scaling law for the evaporation of multicomponent solutions. The scaling laws found are validated against experiments of the evaporation of droplets of (1) water, (2) blood plasma, and (3) a mixture of water and polyethylene glycol, pinned on acrylic pillars of different diameters. These results shed light on the macroscopic dynamics of evaporation on pillars as a first step towards the understanding of other complex phenomena that may be taking place during the evaporation process, such as particle transport and chemical reactions.

The reductive half-reaction of xanthine dehydrogenase from Rhodobacter capsulatus: the role of Glu232 in catalysis.

PubMed

Hall, James; Reschke, Stefan; Cao, Hongnan; Leimkühler, Silke; Hille, Russ

2014-11-14

The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that kred, the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both kred and kred/Kd from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pKa of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Irreversible Denaturation of Maltodextrin Glucosidase Studied by Differential Scanning Calorimetry, Circular Dichroism, and Turbidity Measurements

PubMed Central

Goyal, Megha; Chaudhuri, Tapan K.; Kuwajima, Kunihiro

2014-01-01

Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5–1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was kinetically controlled. The absence of a protein-concentration effect on the thermal transition indicated that the denaturation was rate-limited by a mono-molecular process. From the analysis of the calorimetric thermograms, a one-step irreversible model well represented the thermal denaturation of the protein. The calorimetrically observed thermal transitions showed excellent coincidence with the turbidity transitions monitored by UV-absorption as well as with the unfolding transitions monitored by circular dichroism. The thermal denaturation of the protein was thus rate-limited by conformational unfolding, which was followed by a rapid irreversible formation of aggregates that produced the solution turbidity. It is thus important to note that the absence of the protein-concentration effect on the irreversible thermal denaturation does not necessarily means the absence of protein aggregation itself. The turbidity measurements together with differential scanning calorimetry in the irreversible thermal denaturation of the protein provided a very effective approach for understanding the mechanisms of the irreversible denaturation. The Arrhenius-equation parameters obtained from analysis of the thermal denaturation were compared with those of other proteins that have been reported to show the one-step irreversible thermal denaturation. Maltodextrin glucosidase had sufficiently high kinetic stability with a half-life of 68 days at a physiological temperature (37°C). PMID:25548918

Irreversible denaturation of maltodextrin glucosidase studied by differential scanning calorimetry, circular dichroism, and turbidity measurements.

PubMed

Goyal, Megha; Chaudhuri, Tapan K; Kuwajima, Kunihiro

2014-01-01

Thermal denaturation of Escherichia coli maltodextrin glucosidase was studied by differential scanning calorimetry, circular dichroism (230 nm), and UV-absorption measurements (340 nm), which were respectively used to monitor heat absorption, conformational unfolding, and the production of solution turbidity. The denaturation was irreversible, and the thermal transition recorded at scan rates of 0.5-1.5 K/min was significantly scan-rate dependent, indicating that the thermal denaturation was kinetically controlled. The absence of a protein-concentration effect on the thermal transition indicated that the denaturation was rate-limited by a mono-molecular process. From the analysis of the calorimetric thermograms, a one-step irreversible model well represented the thermal denaturation of the protein. The calorimetrically observed thermal transitions showed excellent coincidence with the turbidity transitions monitored by UV-absorption as well as with the unfolding transitions monitored by circular dichroism. The thermal denaturation of the protein was thus rate-limited by conformational unfolding, which was followed by a rapid irreversible formation of aggregates that produced the solution turbidity. It is thus important to note that the absence of the protein-concentration effect on the irreversible thermal denaturation does not necessarily means the absence of protein aggregation itself. The turbidity measurements together with differential scanning calorimetry in the irreversible thermal denaturation of the protein provided a very effective approach for understanding the mechanisms of the irreversible denaturation. The Arrhenius-equation parameters obtained from analysis of the thermal denaturation were compared with those of other proteins that have been reported to show the one-step irreversible thermal denaturation. Maltodextrin glucosidase had sufficiently high kinetic stability with a half-life of 68 days at a physiological temperature (37°C).

Selenium Potentiates Chemotherapeutic Selectivity: Improving Efficacy and Reducing Toxicity

DTIC Science & Technology

2007-04-01

regulates the rate-limiting step in global genomic repair through transcriptional control of the DNA damage recognition proteins xeroderma pigmentosum ...31). Xeroderma pigmentosum XPA cells defective in DNA repair served as a negative control for some experiments, as previously described (28). Cell...simian virus 40-transformed human cells. Mol Carcinog 2000;29:17–24. 14. Hwang BJ, Ford JM, Hanawalt PC, Chu G. Expression of the p48 xeroderma pigmentosum

Chloroform Hydrodechlorination over Palladium–Gold Catalysts: A First-Principles DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Lang; Yao, Xiaoqian; Khan, Ahmad

2016-04-20

Hydrodechlorination is a promising method for treating toxic chlorocarbon compounds. Pd is among the most effective catalysts for chloroform hydrodechlorination, and experiments have shown that the Pd–Au alloy catalyst yields superior catalytic performance over pure Pd. In this paper, we examine the chloroform hydrodechlorination mechanism over Pd(1 1 1) and Pd ML/Au(1 1 1) surfaces using periodic, self-consistent density functional theory calculations (DFT, GGA–PW91) and maximum rate analysis. We suggest that the reaction occurs on both surfaces through complete dechlorination of chloroform followed by hydrogenation of CH* to methane, and that the initial dechlorination step is likely the rate-limiting step.more » Finally, on Pd(1 1 1), the chloroform dechlorination barrier is 0.24 eV higher than the desorption barrier, whereas on Pd ML/Au(1 1 1), the chloroform dechlorination barrier is 0.07 eV lower than the desorption barrier, which can explain the higher hydrodechlorination activity of the Pd–Au alloy catalyst.« less

Multiresponse kinetic modelling of Maillard reaction and caramelisation in a heated glucose/wheat flour system.

PubMed

Kocadağlı, Tolgahan; Gökmen, Vural

2016-11-15

The study describes the kinetics of the formation and degradation of α-dicarbonyl compounds in glucose/wheat flour system heated under low moisture conditions. Changes in the concentrations of glucose, fructose, individual free amino acids, lysine and arginine residues, glucosone, 1-deoxyglucosone, 3-deoxyglucosone, 3,4-dideoxyglucosone, 5-hydroxymethyl-2-furfural, glyoxal, methylglyoxal and diacetyl concentrations were determined to form a multiresponse kinetic model for isomerisation and degradation reactions of glucose. Degradation of Amadori product mainly produced 1-deoxyglucosone. Formation of 3-deoxyglucosone proceeded directly from glucose and also Amadori product degradation. Glyoxal formation was predominant from glucosone while methylglyoxal and diacetyl originated from 1-deoxyglucosone. Formation of 5-hydroxymethyl-2-furfural from fructose was found to be a key step. Multi-response kinetic modelling of Maillard reaction and caramelisation simultaneously indicated quantitatively predominant parallel and consecutive pathways and rate limiting steps by estimating the reaction rate constants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Platinum and rhenium extraction from a spent refinery catalyst using Bacillus megaterium as a cyanogenic bacterium: statistical modeling and process optimization.

PubMed

Motaghed, M; Mousavi, S M; Rastegar, S O; Shojaosadati, S A

2014-11-01

The present study evaluated the potential of Bacillus megaterium as a cyanogenic bacterium to produce cyanide for solubilization of platinum and rhenium from a spent refinery catalyst. Response surface methodology was applied to study the effects and interaction between two main effective parameters including initial glycine concentration and pulp density. Maximum Pt and Re recovery was obtained 15.7% and 98%, respectively, under optimum conditions of 12.8 g/l initial glycine concentration and 4% (w/v) pulp density after 7 days. Increasing the free cyanide concentration to 3.6 mg/l, varying the pH from 6.7 to 9, and increasing the dissolved oxygen from 2 to 5mg/l demonstrated the growth characteristics of B. megaterium during bioleaching process. The modified shrinking core model was used to determine the rate limiting step of the process. It was found that diffusion through the product layer is the rate controlling step. Copyright © 2014 Elsevier Ltd. All rights reserved.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics.

PubMed

Chapman, Brian

2017-06-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

PubMed Central

2017-01-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687

Pretraining and posttraining assessment of residents' performance in the fourth accreditation council for graduate medical education competency: patient communication skills.

PubMed

Chandawarkar, Rajiv Y; Ruscher, Kimberly A; Krajewski, Aleksandra; Garg, Manish; Pfeiffer, Carol; Singh, Rekha; Longo, Walter E; Kozol, Robert A; Lesnikoski, Beth; Nadkarni, Prakash

2011-08-01

Structured communication curricula will improve surgical residents' ability to communicate effectively with patients. A prospective study approved by the institutional review board involved 44 University of Connecticut general surgery residents. Residents initially completed a written baseline survey to assess general communication skills awareness. In step 1 of the study, residents were randomized to 1 of 2 simulations using standardized patient instructors to mimic patients receiving a diagnosis of either breast or rectal cancer. The standardized patient instructors scored residents' communication skills using a case-specific content checklist and Master Interview Rating Scale. In step 2 of the study, residents attended a 3-part interactive program that comprised (1) principles of patient communication; (2) experiences of a surgeon (role as physician, patient, and patient's spouse); and (3) role-playing (3-resident groups played patient, physician, and observer roles and rated their own performance). In step 3, residents were retested as in step 1, using a crossover case design. Scores were analyzed using Wilcoxon signed rank test with a Bonferroni correction. Case-specific performance improved significantly, from a pretest content checklist median score of 8.5 (65%) to a posttest median of 11.0 (84%) (P = .005 by Wilcoxon signed rank test for paired ordinal data)(n = 44). Median Master Interview Rating Scale scores changed from 58.0 before testing (P = .10) to 61.5 after testing (P = .94). Difference between overall rectal cancer scores and breast cancer scores also were not significant. Patient communication skills need to be taught as part of residency training. With limited training, case-specific skills (herein, involving patients with cancer) are likely to improve more than general communication skills.

Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease

NASA Astrophysics Data System (ADS)

Martínez-González, José Ángel; Rodríguez, Alex; Puyuelo, María Pilar; González, Miguel; Martínez, Rodrigo

2015-01-01

The main reactions of the hepatitis C virus NS3/NS4A serine protease are studied using the second-order Møller-Plesset ab initio method and rather large basis sets to correct the previously reported AM1/CHARMM22 potential energy surfaces. The reaction efficiencies measured for the different substrates are explained in terms of the tetrahedral intermediate formation step (the rate-limiting process). The energies of the barrier and the corresponding intermediate are so close that the possibility of a concerted mechanism is open (especially for the NS5A/5B substrate). This is in contrast to the suggested general reaction mechanism of serine proteases, where a two-step mechanism is postulated.

FAD C(4a)-hydroxide stabilized in a naturally fused styrene monooxygenase

PubMed Central

Schlömann, Michael; van Berkel, Willem J.H.; Gassner, George T.

2013-01-01

StyA2B represents a new class of styrene monooxygenases that integrates flavin-reductase and styrene-epoxidase activities into a single polypeptide. This naturally-occurring fusion protein offers new avenues for studying and engineering biotechnologically relevant enantioselective biochemical epoxidation reactions. Stopped-flow kinetic studies of StyA2B reported here identify reaction intermediates similar to those reported for the separate reductase and epoxidase components of related two-component systems. Our studies identify substrate epoxidation and elimination of water from the FAD C(4a)-hydroxide as rate-limiting steps in the styrene epoxidation reaction. Efforts directed at accelerating these reaction steps are expected to greatly increase catalytic efficiency and the value of StyA2B as biocatalyst. PMID:24157359

Free energy landscape of electrocatalytic CO2 reduction to CO on aqueous FeN4 center embedded graphene studied by ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sheng, Tian; Sun, Shi-Gang

2017-11-01

Experiments have found that the porphyrin-like FeN4 site in Fe-N-C materials is highly efficient for the electrochemical reduction of CO2 into CO. In this work, we investigated the reduction mechanisms on FeN4 embedded graphene layer catalyst with some explicit water molecules by combining the constrained ab initio molecular dynamics simulations and thermodynamic integrations. The reaction free energy and electron transfer in each elementary step were identified. The initial CO2 activation was identified to go through the first electron transfer to form adsorbed CO2- anion and the CO desorption was the rate limiting step in the overall catalytic cycle.

Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

PubMed

Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

2015-08-25

Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

Low levels of glutathione are sufficient for survival of keratinocytes after UV irradiation and for healing of mouse skin wounds.

PubMed

Telorack, Michèle; Abplanalp, Jeannette; Werner, Sabine

2016-08-01

Reduced levels of the cellular antioxidant glutathione are associated with premature skin aging, cancer and impaired wound healing, but the in vivo functions of glutathione in the skin remain largely unknown. Therefore, we analyzed mice lacking the modifier subunit of the glutamate cysteine ligase (Gclm), the enzyme that catalyzes the rate-limiting step of glutathione biosynthesis. Glutathione levels in the skin of these mice were reduced by 70 %. However, neither skin development and homeostasis, nor UVA- or UVB-induced apoptosis in the epidermis were affected. Histomorphometric analysis of excisional wounds did not reveal wound healing abnormalities in young Gclm-deficient mice, while the area of hyperproliferative epithelium as well as keratinocyte proliferation were affected in aged mice. These findings suggest that low levels of glutathione are sufficient for wound repair in young mice, but become rate-limiting upon aging.

Experimental Proof of the Bifunctional Mechanism for the Hydrogen Oxidation in Alkaline Media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jingkun; Ghoshal, Shraboni; Bates, Michael K.

Realization of the hydrogen economy relies on effective hydrogen production, storage, and utilization. The slow kinetics of hydrogen evolution and oxidation reaction (HER/HOR) in alkaline media limits many practical applications involving hydrogen generation and utilization, and how to overcome this fundamental limitation remains debatable. Here we present a kinetic study of the HOR on representative catalytic systems in alkaline media. Electrochemical measurements show that the HOR rate of Pt-Ru/C and Ru/C systems is decoupled to their hydrogen binding energy (HBE), challenging the current prevailing HBE mechanism. The alternative bifunctional mechanism is verified by combined electrochemical and in situ spectroscopic data,more » which provide convincing evidence for the presence of hydroxy groups on surface Ru sites in the HOR potential region and its key role in promoting the rate-determining Volmer step. The conclusion presents important references for design and selection of HOR catalysts.« less

Experimental Proof of the Bifunctional Mechanism for the Hydrogen Oxidation in Alkaline Media

DOE PAGES

Li, Jingkun; Ghoshal, Shraboni; Bates, Michael K.; ...

2017-10-16

Realization of the hydrogen economy relies on effective hydrogen production, storage, and utilization. The slow kinetics of hydrogen evolution and oxidation reaction (HER/HOR) in alkaline media limits many practical applications involving hydrogen generation and utilization, and how to overcome this fundamental limitation remains debatable. Here we present a kinetic study of the HOR on representative catalytic systems in alkaline media. Electrochemical measurements show that the HOR rate of Pt-Ru/C and Ru/C systems is decoupled to their hydrogen binding energy (HBE), challenging the current prevailing HBE mechanism. The alternative bifunctional mechanism is verified by combined electrochemical and in situ spectroscopic data,more » which provide convincing evidence for the presence of hydroxy groups on surface Ru sites in the HOR potential region and its key role in promoting the rate-determining Volmer step. The conclusion presents important references for design and selection of HOR catalysts.« less

Possible Mechanism for Modulating Cardiovascular System During Running in Humans

DTIC Science & Technology

2001-10-25

odulated by rhythmic muscle contractions during running. It cillates when step rate and heart rate are not synchronised but abilises when they are... synchronised . A maximum cardiac output n be achieved by synchronising step rate with heart rate at an timal phase delay. eywords – Cardiovascular model...trained athletes. Researches from [3][4][5] suggest at synchronization between the heart rate and the step rate uring running may favor an athlete with

Stabilization of miscible viscous fingering by a step-growth polymerization reaction

NASA Astrophysics Data System (ADS)

Bunton, Patrick; Stewart, Simone; Marin, Daniela; Tullier, Michael; Meiburg, Eckart; Pojman, John

2017-11-01

Viscous fingering is a hydrodynamic instability that occurs when a more mobile fluid displaces a fluid of lower mobility. Viscous fingering is often undesirable in industrial processes such as secondary petroleum recovery where it limits resource recovery. Linear stability analysis by Hejazi et al. (2010) has predicted that a non-monotonic viscosity profile at an otherwise unstable interface can in some instances stabilize the flow. We use step-growth polymerization at the interface between two miscible monomers as a model system. A dithiol monomer displacing a diacrylate react to form a linear polymer that behaves as a Newtonian fluid. Viscous fingering was imaged in a horizontal Hele-Shaw cell via Schlieren, which is sensitive to polymer conversion. By varying reaction rate via initiator concentration along with flow rate, we demonstrated increasing stabilization of the flow with increasing Damkohler number (ratio of the reaction rate to the flow rate). Results were compared with regions of predicted stability from the results of Hejazi et al. (2010). When the advection outran the reaction, viscous fingering occurred as usual. However, when the reaction was able to keep pace with the advection, the increased viscosity at the interface stabilized the flow. We acknowledge support from NSF CBET-1335739 and NSF CBET 1511653.

Kinematic and behavioral analyses of protective stepping strategies and risk for falls among community living older adults.

PubMed

Bair, Woei-Nan; Prettyman, Michelle G; Beamer, Brock A; Rogers, Mark W

2016-07-01

Protective stepping evoked by externally applied lateral perturbations reveals balance deficits underlying falls. However, a lack of comprehensive information about the control of different stepping strategies in relation to the magnitude of perturbation limits understanding of balance control in relation to age and fall status. The aim of this study was to investigate different protective stepping strategies and their kinematic and behavioral control characteristics in response to different magnitudes of lateral waist-pulls between older fallers and non-fallers. Fifty-two community-dwelling older adults (16 fallers) reacted naturally to maintain balance in response to five magnitudes of lateral waist-pulls. The balance tolerance limit (BTL, waist-pull magnitude where protective steps transitioned from single to multiple steps), first step control characteristics (stepping frequency and counts, spatial-temporal kinematic, and trunk position at landing) of four naturally selected protective step types were compared between fallers and non-fallers at- and above-BTL. Fallers took medial-steps most frequently while non-fallers most often took crossover-back-steps. Only non-fallers varied their step count and first step control parameters by step type at the instants of step initiation (onset time) and termination (trunk position), while both groups modulated step execution parameters (single stance duration and step length) by step type. Group differences were generally better demonstrated above-BTL. Fallers primarily used a biomechanically less effective medial-stepping strategy that may be partially explained by reduced somato-sensation. Fallers did not modulate their step parameters by step type at first step initiation and termination, instances particularly vulnerable to instability, reflecting their limitations in balance control during protective stepping. Copyright © 2016. Published by Elsevier Ltd.

Mechanical work for step-to-step transitions is a major determinant of the metabolic cost of human walking.

PubMed

Donelan, J Maxwell; Kram, Rodger; Kuo, Arthur D

2002-12-01

In the single stance phase of walking, center of mass motion resembles that of an inverted pendulum. Theoretically, mechanical work is not necessary for producing the pendular motion, but work is needed to redirect the center of mass velocity from one pendular arc to the next during the transition between steps. A collision model predicts a rate of negative work proportional to the fourth power of step length. Positive work is required to restore the energy lost, potentially exacting a proportional metabolic cost. We tested these predictions with humans (N=9) walking over a range of step lengths (0.4-1.1 m) while keeping step frequency fixed at 1.8 Hz. We measured individual limb external mechanical work using force plates, and metabolic rate using indirect calorimetry. As predicted, average negative and positive external mechanical work rates increased with the fourth power of step length (from 1 W to 38 W; r(2)=0.96). Metabolic rate also increased with the fourth power of step length (from 7 W to 379 W; r(2)=0.95), and linearly with mechanical work rate. Mechanical work for step-to-step transitions, rather than pendular motion itself, appears to be a major determinant of the metabolic cost of walking.

5 CFR 531.405 - Waiting periods for within-grade increase.

Code of Federal Regulations, 2011 CFR

2011-01-01

... step 4-260 days of creditable service in a pay status over a period of not less than 52 calendar weeks... step 4-52 calendar weeks of creditable service; (ii) Rate of basic pay equal to or greater than the rate of basic pay at step 4 and less than the rate of basic pay at step 7-104 calendar weeks of...

The mechanism of GTP hydrolysis by dynamin II: a transient kinetic study.

PubMed

Binns, D D; Helms, M K; Barylko, B; Davis, C T; Jameson, D M; Albanesi, J P; Eccleston, J F

2000-06-20

Dynamin II is a 98 kDa protein (870 amino acids) required for the late stages of clathrin-mediated endocytosis. The GTPase activity of dynamin is required for its function in the budding stages of receptor-mediated endocytosis and synaptic vesicle recycling. This activity is stimulated when dynamin self-associates on multivalent binding surfaces, such as microtubules and anionic liposomes. We first investigated the oligomeric state of dynamin II by analytical ultracentrifuge sedimentation equilibrium measurements at high ionic strength and found that it was best described by a monomer-tetramer equilibrium. We then studied the intrinsic dynamin GTPase mechanism by using a combination of fluorescence stopped-flow and HPLC methods using the fluorescent analogue of GTP, mantdGTP (2'-deoxy-3'-O-(N-methylanthraniloyl) guanosine-5'-triphosphate), under the same ionic strength conditions. The results are interpreted as showing that mantdGTP binds to dynamin in a two-step mechanism. The dissociation constant of mantdGTP binding to dynamin, calculated from the ratio of the off-rate to the on-rate (k(off)/k(on)), was 0.5 microM. Cleavage of mantdGTP then occurs to mantdGDP and P(i) followed by the rapid release of mantdGDP and P(i). No evidence of reversibility of hydrolysis was observed. The cleavage step itself is the rate-limiting step in the mechanism. This mechanism more closely resembles that of the Ras family of proteins involved in cell signaling than the myosin ATPase involved in cellular motility.

Analysis of the track- and dose-averaged LET and LET spectra in proton therapy using the geant4 Monte Carlo code

PubMed Central

Guan, Fada; Peeler, Christopher; Bronk, Lawrence; Geng, Changran; Taleei, Reza; Randeniya, Sharmalee; Ge, Shuaiping; Mirkovic, Dragan; Grosshans, David; Mohan, Radhe; Titt, Uwe

2015-01-01

Purpose: The motivation of this study was to find and eliminate the cause of errors in dose-averaged linear energy transfer (LET) calculations from therapeutic protons in small targets, such as biological cell layers, calculated using the geant 4 Monte Carlo code. Furthermore, the purpose was also to provide a recommendation to select an appropriate LET quantity from geant 4 simulations to correlate with biological effectiveness of therapeutic protons. Methods: The authors developed a particle tracking step based strategy to calculate the average LET quantities (track-averaged LET, LETt and dose-averaged LET, LETd) using geant 4 for different tracking step size limits. A step size limit refers to the maximally allowable tracking step length. The authors investigated how the tracking step size limit influenced the calculated LETt and LETd of protons with six different step limits ranging from 1 to 500 μm in a water phantom irradiated by a 79.7-MeV clinical proton beam. In addition, the authors analyzed the detailed stochastic energy deposition information including fluence spectra and dose spectra of the energy-deposition-per-step of protons. As a reference, the authors also calculated the averaged LET and analyzed the LET spectra combining the Monte Carlo method and the deterministic method. Relative biological effectiveness (RBE) calculations were performed to illustrate the impact of different LET calculation methods on the RBE-weighted dose. Results: Simulation results showed that the step limit effect was small for LETt but significant for LETd. This resulted from differences in the energy-deposition-per-step between the fluence spectra and dose spectra at different depths in the phantom. Using the Monte Carlo particle tracking method in geant 4 can result in incorrect LETd calculation results in the dose plateau region for small step limits. The erroneous LETd results can be attributed to the algorithm to determine fluctuations in energy deposition along the tracking step in geant 4. The incorrect LETd values lead to substantial differences in the calculated RBE. Conclusions: When the geant 4 particle tracking method is used to calculate the average LET values within targets with a small step limit, such as smaller than 500 μm, the authors recommend the use of LETt in the dose plateau region and LETd around the Bragg peak. For a large step limit, i.e., 500 μm, LETd is recommended along the whole Bragg curve. The transition point depends on beam parameters and can be found by determining the location where the gradient of the ratio of LETd and LETt becomes positive. PMID:26520716

Proton Mediated Chemistry and Catalysis in a Self-Assembled Supramolecular Host

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pluth, Michael; Bergman, Robert; Raymond, Kenneth

2009-04-10

Synthetic supramolecular host assemblies can impart unique reactivity to encapsulated guest molecules. Synthetic host molecules have been developed to carry out complex reactions within their cavities, despite the fact that they lack the type of specifically tailored functional groups normally located in the analogous active sites of enzymes. Over the past decade, the Raymond group has developed a series of self-assembled supramolecules and the Bergman group has developed and studied a number of catalytic transformations. In this Account, we detail recent collaborative work between these two groups, focusing on chemical catalysis stemming from the encapsulation of protonated guests and expandingmore » to acid catalysis in basic solution. We initially investigated the ability of a water-soluble, self-assembled supramolecular host molecule to encapsulate protonated guests in its hydrophobic core. Our study of encapsulated protonated amines revealed rich host-guest chemistry. We established that self-exchange (that is, in-out guest movement) rates of protonated amines were dependent on the steric bulk of the amine rather than its basicity. The host molecule has purely rotational tetrahedral (T) symmetry, so guests with geminal N-methyl groups (and their attendant mirror plane) were effectively desymmetrized; this allowed for the observation and quantification of the barriers for nitrogen inversion followed by bond rotation. Furthermore, small nitrogen heterocycles, such as N-alkylaziridines, N-alkylazetidines, and N-alkylpyrrolidines, were found to be encapsulated as proton-bound homodimers or homotrimers. We further investigated the thermodynamic stabilization of protonated amines, showing that encapsulation makes the amines more basic in the cavity. Encapsulation raises the effective basicity of protonated amines by up to 4.5 pK{sub a} units, a difference almost as large as that between the moderate and strong bases carbonate and hydroxide. The thermodynamic stabilization of protonated guests was translated into chemical catalysis by taking advantage of the potential for accelerating reactions that take place via positively charged transition states, which could be potentially stabilized by encapsulation. Orthoformates, generally stable in neutral or basic solution, were found to be suitable substrates for catalytic hydrolysis by the assembly. Orthoformates small enough to undergo encapsulation were readily hydrolyzed by the assembly in basic solution, with rate acceleration factors up to 3900 compared with those of the corresponding uncatalyzed reactions. Furthering the analogy to enzymes that obey Michaelis-Menten kinetics, we observed competitive inhibition with the inhibitor NPr{sub 4}{sup +}, thereby confirming that the interior cavity of the assembly was the active site for catalysis. Mechanistic studies revealed that the assembly is required for catalysis and that the rate-limiting step of the reaction involves proton transfer from hydronium to the encapsulated substrate. Encapsulation in the assembly changes the orthoformate hydrolysis from an A-1 mechanism (in which decomposition of the protonated substrate is the rate-limiting step) to an A-S{sub E}2 mechanism (in which proton transfer is the rate-limiting step). The study of hydrolysis in the assembly was next extended to acetals, which were also catalytically hydrolyzed by the assembly in basic solution. Acetal hydrolysis changed from the A-1 mechanism in solution to an A-2 mechanism inside the assembly, where attack of water on the protonated substrate is rate limiting. This work provides rare examples of assembly-catalyzed reactions that proceed with substantial rate accelerations despite the absence of functional groups in the cavity and with mechanisms fully elucidated by quantitative kinetic studies.« less

Associations Between Rate of Force Development Metrics and Throwing Velocity in Elite Team Handball Players: a Short Research Report

PubMed Central

Marques, Mário C.; Saavedra, Francisco J.; Abrantes, Catarina; Aidar, Felipe J.

2011-01-01

Performance assessment has become an invaluable component of monitoring participant’s development in distinct sports, yet limited and contradictory data are available in trained subjects. The purpose of this study was to examine the relationship between ball throwing velocity during a 3-step running throw in elite team handball players and selected measures of rate of force development like force, power, velocity, and bar displacement during a concentric only bench press exercise in elite male handball players. Fitteen elite senior male team handball players volunteered to participate. Each volunteer had power and bar velocity measured during a concentric only bench press test with 25, 35, and 45 kg as well as having one-repetition maximum strength determined. Ball throwing velocity was evaluated with a standard 3-step running throw using a radar gun. The results of this study indicated significant associations between ball velocity and time at maximum rate of force development (0, 66; p<0.05) and rate of force development at peak force (0,56; p<0.05) only with 25kg load. The current research indicated that ball velocity was only median associated with maximum rate of force development with light loads. A training regimen designed to improve ball-throwing velocity in elite male team handball players should emphasize bench press movement using light loads. PMID:23487363

Associations between rate of force development metrics and throwing velocity in elite team handball players: a short research report.

PubMed

Marques, Mário C; Saavedra, Francisco J; Abrantes, Catarina; Aidar, Felipe J

2011-09-01

Performance assessment has become an invaluable component of monitoring participant's development in distinct sports, yet limited and contradictory data are available in trained subjects. The purpose of this study was to examine the relationship between ball throwing velocity during a 3-step running throw in elite team handball players and selected measures of rate of force development like force, power, velocity, and bar displacement during a concentric only bench press exercise in elite male handball players. Fitteen elite senior male team handball players volunteered to participate. Each volunteer had power and bar velocity measured during a concentric only bench press test with 25, 35, and 45 kg as well as having one-repetition maximum strength determined. Ball throwing velocity was evaluated with a standard 3-step running throw using a radar gun. The results of this study indicated significant associations between ball velocity and time at maximum rate of force development (0, 66; p<0.05) and rate of force development at peak force (0,56; p<0.05) only with 25kg load. The current research indicated that ball velocity was only median associated with maximum rate of force development with light loads. A training regimen designed to improve ball-throwing velocity in elite male team handball players should emphasize bench press movement using light loads.

Ecosystem and physiological controls over methane production in northern wetlands

NASA Technical Reports Server (NTRS)

Valentine, David W.; Holland, Elisabeth A.; Schimel, David S.

1994-01-01

Peat chemistry appears to exert primary control over methane production rates in the Canadian Northern Wetlands Study (NOWES) area. We determined laboratory methane production rate potentials in anaerobic slurries of samples collected from a transect of sites through the NOWES study area. We related methane production rates to indicators of resistance to microbial decay (peat C: N and lignin: N ratios) and experimentally manipulated substrate availability for methanogenesis using ethanol (EtOH) and plant litter. We also determined responses of methane production to pH and temperature. Methane production potentials declined along the gradient of sites from high rates in the coastal fens to low rates in the interior bogs and were generally highest in surface layers. Strong relationships between CH4 production potentials and peat chemistry suggested that methanogenesis was limited by fermentation rates. Methane production at ambient pH responded strongly to substrate additions in the circumneutral fens with narrow lignin: N and C: N ratios (delta CH4/delta EtOH = 0.9-2.3 mg/g) and weakly in the acidic bogs with wide C: N and lignin: N ratios (delta CH4/delta EtOH = -0.04-0.02 mg/g). Observed Q(sub 10) values ranged from 1.7 to 4.7 and generally increased with increasing substrate availability, suggesting that fermentation rates were limiting. Titration experiments generally demonstrated inhibition of methanogenesis by low pH. Our results suggest that the low rates of methane emission observed in interior bogs during NOWES likely resulted from pH and substrate quality limitation of the fermentation step in methane production and thus reflect intrinsically low methane production potentials. Low methane emission rates observed during NOWES will likely be observed in other northern wetland regions with similar vegetation chemistry.

Step-by-step guideline for disease-specific costing studies in low- and middle-income countries: a mixed methodology

PubMed Central

Hendriks, Marleen E.; Kundu, Piyali; Boers, Alexander C.; Bolarinwa, Oladimeji A.; te Pas, Mark J.; Akande, Tanimola M.; Agbede, Kayode; Gomez, Gabriella B.; Redekop, William K.; Schultsz, Constance; Tan, Siok Swan

2014-01-01

Background Disease-specific costing studies can be used as input into cost-effectiveness analyses and provide important information for efficient resource allocation. However, limited data availability and limited expertise constrain such studies in low- and middle-income countries (LMICs). Objective To describe a step-by-step guideline for conducting disease-specific costing studies in LMICs where data availability is limited and to illustrate how the guideline was applied in a costing study of cardiovascular disease prevention care in rural Nigeria. Design The step-by-step guideline provides practical recommendations on methods and data requirements for six sequential steps: 1) definition of the study perspective, 2) characterization of the unit of analysis, 3) identification of cost items, 4) measurement of cost items, 5) valuation of cost items, and 6) uncertainty analyses. Results We discuss the necessary tradeoffs between the accuracy of estimates and data availability constraints at each step and illustrate how a mixed methodology of accurate bottom-up micro-costing and more feasible approaches can be used to make optimal use of all available data. An illustrative example from Nigeria is provided. Conclusions An innovative, user-friendly guideline for disease-specific costing in LMICs is presented, using a mixed methodology to account for limited data availability. The illustrative example showed that the step-by-step guideline can be used by healthcare professionals in LMICs to conduct feasible and accurate disease-specific cost analyses. PMID:24685170

A Semi-Empirical Two Step Carbon Corrosion Reaction Model in PEM Fuel Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Alan; Colbow, Vesna; Harvey, David

2013-01-01

The cathode CL of a polymer electrolyte membrane fuel cell (PEMFC) was exposed to high potentials, 1.0 to 1.4 V versus a reversible hydrogen electrode (RHE), that are typically encountered during start up/shut down operation. While both platinum dissolution and carbon corrosion occurred, the carbon corrosion effects were isolated and modeled. The presented model separates the carbon corrosion process into two reaction steps; (1) oxidation of the carbon surface to carbon-oxygen groups, and (2) further corrosion of the oxidized surface to carbon dioxide/monoxide. To oxidize and corrode the cathode catalyst carbon support, the CL was subjected to an accelerated stressmore » test cycled the potential from 0.6 VRHE to an upper potential limit (UPL) ranging from 0.9 to 1.4 VRHE at varying dwell times. The reaction rate constants and specific capacitances of carbon and platinum were fitted by evaluating the double layer capacitance (Cdl) trends. Carbon surface oxidation increased the Cdl due to increased specific capacitance for carbon surfaces with carbon-oxygen groups, while the second corrosion reaction decreased the Cdl due to loss of the overall carbon surface area. The first oxidation step differed between carbon types, while both reaction rate constants were found to have a dependency on UPL, temperature, and gas relative humidity.« less

Isotopic Exchange in Porous and Dense Magnesium Borohydride.

PubMed

Zavorotynska, Olena; Deledda, Stefano; Li, Guanqiao; Matsuo, Motoaki; Orimo, Shin-ichi; Hauback, Bjørn C

2015-09-01

Magnesium borohydride (Mg(BH4)2) is one of the most promising complex hydrides presently studied for energy-related applications. Many of its properties depend on the stability of the BH4(-) anion. The BH4(-) stability was investigated with respect to H→D exchange. In situ Raman measurements on high-surface-area porous Mg(BH4 )2 in 0.3 MPa D2 have shown that the isotopic exchange at appreciable rates occurs already at 373 K. This is the lowest exchange temperature observed in stable borohydrides. Gas-solid isotopic exchange follows the BH4(-) +D˙ →BH3D(-) +H˙ mechanism at least at the initial reaction steps. Ex situ deuteration of porous Mg(BH4)2 and its dense-phase polymorph indicates that the intrinsic porosity of the hydride is the key behind the high isotopic exchange rates. It implies that the solid-state H(D) diffusion is considerably slower than the gas-solid H→D exchange reaction at the surface and it is a rate-limiting steps for hydrogen desorption and absorption in Mg(BH4)2. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic investigation of DNA bending and wrapping by type II topoisomerases

NASA Astrophysics Data System (ADS)

Shao, Qing; Finzi, Laura; Dunlap, David

2009-11-01

Type II topoisomerases catalyze DNA decatenation and unwinding which is crucial for cell division, and therefore type II topoisomerases are some of the main targets of anti-cancer drugs. A recent crystal structure shows that, during the catalytic cycle, a yeast type II topoimerase can bend a 10 base pair DNA segment by up to 150 degrees. Bacterial gyrase, another type II topoisomerase, can wrap DNA into a tight 180 degree turn. Bending a stiff polymer like DNA requires considerable energy and could represent the rate limiting step in the catalytic (topological) cycle. Using modified deoxyribonucleotides in PCR reactions, stiffer DNA fragments have been produced and used as substrates for topoisomerase II-mediated relaxation of plectonemes introduced in single molecules using magnetic tweezers. The wrapping ability of gyrase decreases for diamino-purine-substituted DNA in which every base pair has three hydrogen-bonds. The overall rate of relaxation of plectonemes by recombinant human topoisomerase II alpha also decreases. These results reveal the dynamic properties of DNA bending and wrapping by type II topisomerases and suggest that A:T base pair melting is a rate determining step for bending and wrapping.

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

PubMed Central

Prentiss, Michael C.; Wales, David J.; Wolynes, Peter G.

2010-01-01

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N terminus knotted and the C terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N and C termini into the knot occurs late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly. PMID:20617197

Malonyl-CoA Decarboxylase (MCD) as a Potential Therapeutic Target for Breast Cancer

DTIC Science & Technology

2010-05-01

Kreb cycle and electron transport activity. Clinical and biochemical studies of MCD deficiency, a rare inborn error of metabolism, provide another... mitochondria and is the rate limiting enzymatic step of mitochondrial fatty acid oxidation (Figure 1) (McGarry and Brown, 1997). Indeed, the 10-fold...1 activity and fatty acid oxidation, thereby preventing a futile cycle of fatty acid synthesis and oxidation. As FAS could consume malonyl-CoA, it was

Intramolecular Hydroamination of Unbiased and Functionalized Primary Aminoalkenes Catalyzed by a Rhodium Aminophosphine Complex

PubMed Central

Julian, Lisa D.; Hartwig, John F.

2010-01-01

We report a rhodium catalyst that exhibits high reactivity for the hydroamination of primary aminoalkenes that are unbiased toward cyclization and that possess functional groups that would not be tolerated in hydroaminations catalyzed by more electrophilic systems. This catalyst contains an unusual diaminophosphine ligand that binds to rhodium in a κ3-P,O,P mode. The reactions catalyzed by this complex typically proceed at mild temperatures (room temperature to 70 °C), occur with primary aminoalkenes lacking substituents on the alkyl chain that bias the system toward cyclization, occur with primary aminoalkenes containing chloride, ester, ether, enolizable ketone, nitrile, and unprotected alcohol functionality, and occur with primary aminoalkenes containing internal olefins. Mechanistic data imply that these reactions occur with a turnover-limiting step that is different from that of reactions catalyzed by late transition metal complexes of Pd, Pt, and Ir. This change in the turnover-limiting step and resulting high activity of the catalyst stem from favorable relative rates for protonolysis of the M-C bond to release the hydroamination product vs reversion of the aminoalkyl intermediate to regenerate the acyclic precursor. Probes for the origin of the reactivity of the rhodium complex of L1 imply that the aminophosphine groups lead to these favorable rates by effects beyond steric demands and simple electron donation to the metal center. PMID:20839807

An on-line pre-concentration system for determination of cadmium in drinking water using FAAS.

PubMed

dos Santos, Walter N L; Costa, Jorge L O; Araujo, Rennan G O; de Jesus, Djane S; Costa, Antônio C S

2006-10-11

In the present paper, a minicolumn of polyurethane foam loaded with 4-(2-pyridylazo)-resorcinol (PAR) is proposed as pre-concentration system for cadmium determination in drinking water samples by flame atomic absorption spectrometry. The optimization step was performed using two-level full factorial design and Doehlert matrix, involving the variables: sampling flow rate, elution concentration, buffer concentration and pH. Using the established experimental conditions in the optimization step of: pH 8.2, sampling flow rate 8.5 mL min(-1), buffer concentration 0.05 mol L(-1) and elution concentration of 1.0 mol L(-1), this system allows the determination of cadmium with detection limit (LD) (3sigma/S) of 20.0 ng L(-1) and quantification limit (LQ) (10sigma/S) of 64 ng L(-1), precision expressed as relative standard deviation (R.S.D.) of 5.0 and 4.7% for cadmium concentration of 5.0 and 40.0 microg L(-1), respectively, and a pre-concentration factor of 158 for a sample volume of 20.0 mL. The accuracy was confirmed by cadmium determination in the standard reference material, NIST SRM 1643d trace elements in natural water. This procedure was applied for cadmium determination in drinking water samples collected from Salvador City, Bahia, Brazil. For five samples analyzed, the achieved concentrations varied from 0.31 to 0.86 microg L(-1).

A first principles study of the oxidation energetics and kinetics of realgar

NASA Astrophysics Data System (ADS)

Renock, Devon; Becker, Udo

2010-08-01

Quantum-mechanical calculations allow resolving and quantifying in detail important aspects of reaction mechanisms such as spin transitions and oxygen dissociation that can be the major rate-limiting steps in redox processes on sulfide and oxide surfaces. In addition, this knowledge can help experimentalists in setting up the framework of rate equations that can be used to describe the kinetics of, e.g., oxidation processes. The unique molecular crystal structure of realgar, As 4S 4 clusters held together by van der Waals bonds, allows for a convenient quantum-mechanical (q.m.) cluster approach to investigate the thermodynamics and kinetic pathways of oxidation. The interaction of As 4S 4 clusters with oxygen and co-adsorbed ions provides a model system for understanding the molecular-scale processes that underpin empirically-derived rate expressions, and provides clues to the oxidation mechanisms of other sulfides and oxides. Two activated processes are shown to dominate the kinetics of oxidation by molecular oxygen: (i) a paramagnetic 3O to diamagnetic 1O spin transition and (ii) oxygen dissociation on the surface, in that order. The activation energies for the spin transition and O 2 dissociation step were determined to be 1.1 eV (106 kJ/mol) and 0.9 eV (87 kJ/mol), respectively, if molecular oxygen is the only reactant on the surface. In the case of As 4S 4, q.m. calculations reveal that 3O transfers its spin to the cluster and forms a low-spin, peroxo intermediate on the surface before dissociating. The adsorption of a hydroxide ion on the surface proximate to the 3O adsorption site changes the adsorption mechanism by lowering the activation energy barriers for both the spin transition (0.30 eV/29 kJ/mol) and the O 2 dissociation step (0.72 eV/69 kJ/mol). Thus, while spin transition is rate limiting for oxidation with O 2 alone, dissociation becomes the rate-limiting step for oxidation with co-adsorption of OH -. First-principles, periodic calculations of the realgar (1¯20) surface show that the energetics and structural changes that accompany oxidation of As 4S 4 clusters on the surface are similar to those involving individual As 4S 4 clusters. Thus, assuming that an As 4S 4 cluster with an adsorbed hydroxyl group is a reasonable approximation of the surface of As 4S 4 at high pH, the theoretically calculated oxidation rate (˜1 × 10 -10 mol m -2 s -1) is of the same order as empirically-derived rates from experiments at T = 298 K, pH = 8, and similar dissolved oxygen concentrations. In addition, the co-adsorption of other anions found in alkaline waters (i.e. carbonate, bicarbonate, sulfate, and sulfite) were shown to energetically promote the oxidation of As 4S 4 (on the order of 5-40 kJ/mol depending on the co-adsorbed anion, OH -, CO32-, HCO3-, SO42-, or SO32-, and accounting for changes in the hydration of products and reactants). The effect of the co-adsorbate on the kinetics and thermodynamics of oxidation is due to each adsorbate modifying the electronic and structural environment of the other adsorption site. Activation-energy barriers due to spin transitions are rarely discussed in the literature as key factors for controlling oxidation rates of mineral surfaces, even though the magnitude of these barriers is enough to alter the kinetics significantly. The attenuation of the activation energy by co-adsorbed anions suggests the possibility of pH- or p(co-adsorbate)-dependent activation energies that can be used to refine oxidation rate laws for sulfide minerals and other, especially semiconducting minerals, such as oxides.

Chlorophyllase is a rate-limiting enzyme in chlorophyll catabolism and is posttranslationally regulated.

PubMed

Harpaz-Saad, Smadar; Azoulay, Tamar; Arazi, Tzahi; Ben-Yaakov, Eran; Mett, Anahit; Shiboleth, Yoel M; Hörtensteiner, Stefan; Gidoni, David; Gal-On, Amit; Goldschmidt, Eliezer E; Eyal, Yoram

2007-03-01

Chlorophyll is a central player in harvesting light energy for photosynthesis, yet the rate-limiting steps of chlorophyll catabolism and the regulation of the catabolic enzymes remain unresolved. To study the role and regulation of chlorophyllase (Chlase), the first enzyme of the chlorophyll catabolic pathway, we expressed precursor and mature versions of citrus (Citrus sinensis) Chlase in two heterologous plant systems: (1) squash (Cucurbita pepo) plants using a viral vector expression system; and (2) transiently transformed tobacco (Nicotiana tabacum) protoplasts. Expression of full-length citrus Chlase resulted in limited chlorophyll breakdown in protoplasts and no visible leaf phenotype in whole plants, whereas expression of a Chlase version lacking the N-terminal 21 amino acids (ChlaseDeltaN), which corresponds to the mature protein, led to extensive chlorophyll breakdown in both tobacco protoplasts and squash leaves. ChlaseDeltaN-expressing squash leaves displayed a dramatic chlorotic phenotype in plants grown under low-intensity light, whereas under natural light a lesion-mimic phenotype occurred, which was demonstrated to follow the accumulation of chlorophyllide, a photodynamic chlorophyll breakdown product. Full-length and mature citrus Chlase versions were localized to the chloroplast membrane fraction in expressing tobacco protoplasts, where processing of the N-terminal 21 amino acids appears to occur. Results obtained in both plant systems suggest that Chlase functions as a rate-limiting enzyme in chlorophyll catabolism controlled via posttranslational regulation.

A thermal NO(x) prediction model - Scalar computation module for CFD codes with fluid and kinetic effects

NASA Technical Reports Server (NTRS)

Mcbeath, Giorgio; Ghorashi, Bahman; Chun, Kue

1993-01-01

A thermal NO(x) prediction model is developed to interface with a CFD, k-epsilon based code. A converged solution from the CFD code is the input to the postprocessing model for prediction of thermal NO(x). The model uses a decoupled analysis to estimate the equilibrium level of (NO(x))e which is the constant rate limit. This value is used to estimate the flame (NO(x)) and in turn predict the rate of formation at each node using a two-step Zeldovich mechanism. The rate is fixed on the NO(x) production rate plot by estimating the time to reach equilibrium by a differential analysis based on the reaction: O + N2 = NO + N. The rate is integrated in the nonequilibrium time space based on the residence time at each node in the computational domain. The sum of all nodal predictions yields the total NO(x) level.

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stack, Andrew G; Raiten, Paolo; Gale, Julian D.

2012-01-01

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentallymore » during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.« less

[Comparison of potential yield and resource utilization efficiency of main food crops in three provinces of Northeast China under climate change].

PubMed

Wang, Xiao-yu; Yang, Xiao-guang; Sun, Shuang; Xie, Wen-juan

2015-10-01

Based on the daily data of 65 meteorological stations from 1961 to 2010 and the crop phenology data in the potential cultivation zones of thermophilic and chimonophilous crops in Northeast China, the crop potential yields were calculated through step-by-step correction method. The spatio-temporal distribution of the crop potential yields at different levels was analyzed. And then we quantified the limitations of temperature and precipitation on the crop potential yields and compared the differences in the climatic resource utilization efficiency. The results showed that the thermal potential yields of six crops (including maize, rice, spring wheat, sorghum, millet and soybean) during the period 1961-2010 deceased from west to east. The climatic potential yields of the five crops (spring wheat not included) were higher in the south than in the north. The potential yield loss rate due to temperature limitations of the six crops presented a spatial distribution pattern and was higher in the east than in the west. Among the six main crops, the yield potential loss rate due to temperature limitation of the soybean was the highest (51%), and those of the other crops fluctuated within the range of 33%-41%. The potential yield loss rate due to water limitation had an obvious regional difference, and was high in Songnen Plain and Changbai Mountains. The potential yield loss rate of spring wheat was the highest (50%), and those of the other four rainfed crops fluctuated within the range of 8%-10%. The solar energy utilization efficiency of the six main crops ranged from 0.9% to 2.7%, in the order of maize> sorghum>rice>millet>spring wheat>soybean. The precipitation utilization efficiency of the maize, sorghum, spring wheat, millet and soybean under rainfed conditions ranged from 8 to 35 kg . hm-2 . mm-1, in the order of maize>sorghum>spring wheat>millet>soybean. In those areas with lower efficiency of solar energy utilization and precipitation utilization, such as Changbai Mountains and the south of Lesser Khingan Mountains, measures could be taken to increase the efficiency of resource utilization such as rational close-planting, selection of droughtresistant varieties, proper and timely fertilization, farming for soil water storage, optimization of crop layout and so on.

Mechanism and kinetics for ammonium dinitramide (ADN) sublimation: a first-principles study.

PubMed

Zhu, R S; Chen, Hui-Lung; Lin, M C

2012-11-08

The mechanism for sublimation of NH(4)N(NO(2))(2) (ADN) has been investigated quantum-mechanically with generalized gradient approximation plane-wave density functional theory calculations; the solid surface is represented by a slab model and the periodic boundary conditions are applied. The calculated lattice constants for the bulk ADN, which were found to consist of NH(4)(+)[ON(O)NNO(2)](-) units, instead of NH(4)(+)[N(NO(2))(2)](-), agree quite well with experimental values. Results show that three steps are involved in the sublimation/decomposition of ADN. The first step is the relaxation of the surface layer with 1.6 kcal/mol energy per NH(4)ON(O)NNO(2) unit; the second step is the sublimation of the surface layer to form a molecular [NH(3)]-[HON(O)NNO(2)] complex with a 29.4 kcal/mol sublimation energy, consistent with the experimental observation of Korobeinichev et al. (10) The last step is the dissociation of the [H(3)N]-[HON(O)NNO(2)] complex to give NH(3) and HON(O)NNO(2) with the dissociation energy of 13.9 kcal/mol. Direct formation of NO(2) (g) from solid ADN costs a much higher energy, 58.3 kcal/mol. Our calculated total sublimation enthalpy for ADN(s) → NH(3)(g) + HON(O)NNO(2)) (g), 44.9 kcal/mol via three steps, is in good agreement with the value, 42.1 kcal/mol predicted for the one-step sublimation process in this work and the value 44.0 kcal/mol computed by Politzer et al. (11) using experimental thermochemical data. The sublimation rate constant for the rate-controlling step 2 can be represented as k(sub) = 2.18 × 10(12) exp (-30.5 kcal/mol/RT) s(-1), which agrees well with available experimental data within the temperature range studied. The high pressure limit decomposition rate constant for the molecular complex H(3)N···HON(O)NNO(2) can be expressed by k(dec) = 3.18 × 10(13) exp (-15.09 kcal/mol/RT) s(-1). In addition, water molecules were found to increase the sublimation enthalpy of ADN, contrary to that found in the ammonium perchlorate system, in which water molecules were shown to reduce pronouncedly the enthalpy of sublimation.

Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting

PubMed Central

Lamb, John R.; Zhang, Chunsheng; Xie, Tao; Wang, Kai; Zhang, Bin; Hao, Ke; Chudin, Eugene; Fraser, Hunter B.; Millstein, Joshua; Ferguson, Mark; Suver, Christine; Ivanovska, Irena; Scott, Martin; Philippar, Ulrike; Bansal, Dimple; Zhang, Zhan; Burchard, Julja; Smith, Ryan; Greenawalt, Danielle; Cleary, Michele; Derry, Jonathan; Loboda, Andrey; Watters, James; Poon, Ronnie T. P.; Fan, Sheung T.; Yeung, Chun; Lee, Nikki P. Y.; Guinney, Justin; Molony, Cliona; Emilsson, Valur; Buser-Doepner, Carolyn; Zhu, Jun; Friend, Stephen; Mao, Mao; Shaw, Peter M.; Dai, Hongyue; Luk, John M.; Schadt, Eric E.

2011-01-01

Background In hepatocellular carcinoma (HCC) genes predictive of survival have been found in both adjacent normal (AN) and tumor (TU) tissues. The relationships between these two sets of predictive genes and the general process of tumorigenesis and disease progression remains unclear. Methodology/Principal Findings Here we have investigated HCC tumorigenesis by comparing gene expression, DNA copy number variation and survival using ∼250 AN and TU samples representing, respectively, the pre-cancer state, and the result of tumorigenesis. Genes that participate in tumorigenesis were defined using a gene-gene correlation meta-analysis procedure that compared AN versus TU tissues. Genes predictive of survival in AN (AN-survival genes) were found to be enriched in the differential gene-gene correlation gene set indicating that they directly participate in the process of tumorigenesis. Additionally the AN-survival genes were mostly not predictive after tumorigenesis in TU tissue and this transition was associated with and could largely be explained by the effect of somatic DNA copy number variation (sCNV) in cis and in trans. The data was consistent with the variance of AN-survival genes being rate-limiting steps in tumorigenesis and this was confirmed using a treatment that promotes HCC tumorigenesis that selectively altered AN-survival genes and genes differentially correlated between AN and TU. Conclusions/Significance This suggests that the process of tumor evolution involves rate-limiting steps related to the background from which the tumor evolved where these were frequently predictive of clinical outcome. Additionally treatments that alter the likelihood of tumorigenesis occurring may act by altering AN-survival genes, suggesting that the process can be manipulated. Further sCNV explains a substantial fraction of tumor specific expression and may therefore be a causal driver of tumor evolution in HCC and perhaps many solid tumor types. PMID:21750698

Evaluation of the role of three candidate human kinases in the conversion of the hepatitis C virus inhibitor 2'-C-methyl-cytidine to its 5'-monophosphate metabolite.

PubMed

Golitsina, Nina L; Danehy, Francis T; Fellows, Ross; Cretton-Scott, Erika; Standring, David N

2010-03-01

Nucleoside analogs are effective inhibitors of the hepatitis C virus (HCV) in the clinical setting. One such molecule, 2'-C-methyl-cytidine (2'-MeC), entered clinical development as NM283, a valine ester prodrug form of 2'-MeC possessing improved oral bioavailability. To be active against HCV, 2'-MeC must be converted to 2'-MeC triphosphate which inhibits NS5B, the HCV RNA-dependent RNA polymerase. Conversion of 2'-MeC to 2'-MeC monophosphate is the first step in 2'-MeC triphosphate production and is thought to be the rate-limiting step. Here we investigate which of three possible enzymes, deoxycytidine kinase (dCK), uridine-cytidine kinase 1 (UCK1), or uridine-cytidine kinase 2 (UCK2), mediate this first phosphorylation step. Purified recombinant enzymes UCK2 and dCK, but not UCK1, could phosphorylate 2'-MeC in vitro. However, siRNA knockdown experiments in three human cell lines (HeLa, Huh7 and HepG2) defined UCK2 and not dCK as the key kinase for the formation of 2'-MeC monophosphate in cultured human cells. These results underscore the importance of confirming enzymatic kinase data with appropriate cell-based assays. Finally, we present data suggesting that inefficient phosphorylation by UCK2 likely limits the antiviral activity of 2'-MeC against HCV. This paves the way for the use of a nucleotide prodrug approach to overcome this limitation.

Miscoding-induced stalling of substrate translocation on the bacterial ribosome.

PubMed

Alejo, Jose L; Blanchard, Scott C

2017-10-10

Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.

Miscoding-induced stalling of substrate translocation on the bacterial ribosome

PubMed Central

Alejo, Jose L.; Blanchard, Scott C.

2017-01-01

Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G–catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors. PMID:28973849

Step width alters iliotibial band strain during running.

PubMed

Meardon, Stacey A; Campbell, Samuel; Derrick, Timothy R

2012-11-01

This study assessed the effect of step width during running on factors related to iliotibial band (ITB) syndrome. Three-dimensional (3D) kinematics and kinetics were recorded from 15 healthy recreational runners during overground running under various step width conditions (preferred and at least +/- 5% of their leg length). Strain and strain rate were estimated from a musculoskeletal model of the lower extremity. Greater ITB strain and strain rate were found in the narrower step width condition (p < 0.001, p = 0.040). ITB strain was significantly (p < 0.001) greater in the narrow condition than the preferred and wide conditions and it was greater in the preferred condition than the wide condition. ITB strain rate was significantly greater in the narrow condition than the wide condition (p = 0.020). Polynomial contrasts revealed a linear increase in both ITB strain and strain rate with decreasing step width. We conclude that relatively small decreases in step width can substantially increase ITB strain as well as strain rates. Increasing step width during running, especially in persons whose running style is characterized by a narrow step width, may be beneficial in the treatment and prevention of running-related ITB syndrome.

A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism

PubMed Central

Arnò, Barbara; Coletta, Andrea; Tesauro, Cinzia; Zuccaro, Laura; Fiorani, Paola; Lentini, Sara; Galloni, Pierluca; Conte, Valeria; Floris, Barbara; Desideri, Alessandro

2013-01-01

The different steps of the human Top1 (topoisomerase I) catalytic cycle have been analysed in the presence of a pentacyclic-diquinoid synthetic compound. The experiments indicate that it efficiently inhibits the cleavage step of the enzyme reaction, fitting well into the catalytic site. Surprisingly the compound, when incubated with the binary topoisomerase–DNA cleaved complex, helps the enzyme to remove itself from the cleaved DNA and close the DNA gap, increasing the religation rate. The compound also induces the religation of the stalled enzyme–CPT (camptothecin)–DNA ternary complex. Analysis of the molecule docked over the binary complex, together with its chemical properties, suggests that the religation enhancement is due to the presence on the compound of two oxygen atoms that act as hydrogen acceptors. This property facilitates the deprotonation of the 5′ DNA end, suggesting that this is the limiting step in the topoisomerase religation mechanism. PMID:23368812

Evaluating within-population variability in behavior and demography for the adaptive potential of a dispersal-limited species to climate change

USGS Publications Warehouse

Muñoz, David J.; Miller Hesed, Kyle; Grant, Evan H. Campbell; Miller, David A.W.

2016-01-01

Multiple pathways exist for species to respond to changing climates. However, responses of dispersal-limited species will be more strongly tied to ability to adapt within existing populations as rates of environmental change will likely exceed movement rates. Here, we assess adaptive capacity in Plethodon cinereus, a dispersal-limited woodland salamander. We quantify plasticity in behavior and variation in demography to observed variation in environmental variables over a 5-year period. We found strong evidence that temperature and rainfall influence P. cinereus surface presence, indicating changes in climate are likely to affect seasonal activity patterns. We also found that warmer summer temperatures reduced individual growth rates into the autumn, which is likely to have negative demographic consequences. Reduced growth rates may delay reproductive maturity and lead to reductions in size-specific fecundity, potentially reducing population-level persistence. To better understand within-population variability in responses, we examined differences between two common color morphs. Previous evidence suggests that the color polymorphism may be linked to physiological differences in heat and moisture tolerance. We found only moderate support for morph-specific differences for the relationship between individual growth and temperature. Measuring environmental sensitivity to climatic variability is the first step in predicting species' responses to climate change. Our results suggest phenological shifts and changes in growth rates are likely responses under scenarios where further warming occurs, and we discuss possible adaptive strategies for resulting selective pressures.

Comparison of rate constants for (PO3-) transfer by the Mg(II), Cd(II), and Li(I) forms of phosphoglucomutase.

PubMed

Ray, W J; Post, C B; Puvathingal, J M

1989-01-24

Net rate constants that define the steady-state rate through a sequence of steps and the corresponding effective energy barriers for two (PO3-)-transfer steps in the phosphoglucomutase reaction were compared as a function of metal ion, M, where M = Mg2+ and Cd2+. These steps involve the reaction of either the 1-phosphate or the 6-phosphate of glucose 1,6-bisphosphate (Glc-P2) bound to the dephosphoenzyme (ED) to produce the phosphoenzyme (EP) and the free monophosphates, glucose 1-phosphate (Glc-1-P) or glucose 6-phosphate (Glc-6-P): EP.M + Glc-1-P----ED.M.Glc-P2----EP.M.Glc-6-P6. Before this comparison was made, net rate constants for the Cd2+ enzyme, obtained at high enzyme concentration via 31P NMR saturation-transfer studies [Post, C. B., Ray, W. J., Jr., & Gorenstein, D. G. (1989) Biochemistry (preceding paper in this issue)], were appropriately scaled by using the observed constants to calculate both the expected isotope-transfer rate at equilibrium and the steady-state rate under initial velocity conditions and comparing the calculated values with those measured in dilute solution. For the Mg2+ enzyme, narrow limits on possible values of the corresponding net rate constants were imposed on the basis of initial velocity rate constants for the forward and reverse directions plus values for the equilibrium distribution of central complexes, since direct measurement is not feasible. The effective energy barriers for both the Mg2+ and Cd2+ enzymes, calculated from the respective net rate constants, together with previously values for the equilibrium distribution of complexes in both enzymic systems [Ray, W. J., Jr., & Long, J. W. (1976) Biochemistry 15, 4018-4025], show that the 100-fold decrease in the kappa cat for the Cd2+ relative to the Mg2+ enzyme is caused by two factors: the increased stability of the intermediate bisphosphate complex and the decreased ability to cope with the phosphate ester involving the 1-hydroxyl group of the glucose ring. In fact, it is unlikely that the efficiency of (PO3-) transfer to the 6-hydroxyl group of bound Glc-1-P (thermodynamically favorable direction) is reduced by more than an order of magnitude in the Cd2+ enzyme. By contrast, the efficiency of the Li+ enzyme in the same (PO3-)-transfer step is less than 4 x 10(-8) that of the Mg2+ enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)

An item response theory evaluation of the young mania rating scale and the montgomery-asberg depression rating scale in the systematic treatment enhancement program for bipolar disorder (STEP-BD).

PubMed

Prisciandaro, James J; Tolliver, Bryan K

2016-11-15

The Young Mania Rating Scale (YMRS) and Montgomery-Asberg Depression Rating Scale (MADRS) are among the most widely used outcome measures for clinical trials of medications for Bipolar Disorder (BD). Nonetheless, very few studies have examined the measurement characteristics of the YMRS and MADRS in individuals with BD using modern psychometric methods. The present study evaluated the YMRS and MADRS in the Systematic Treatment Enhancement Program for BD (STEP-BD) study using Item Response Theory (IRT). Baseline data from 3716 STEP-BD participants were available for the present analysis. The Graded Response Model (GRM) was fit separately to YMRS and MADRS item responses. Differential item functioning (DIF) was examined by regressing a variety of clinically relevant covariates (e.g., sex, substance dependence) on all test items and on the latent symptom severity dimension, within each scale. Both scales: 1) contained several items that provided little or no psychometric information, 2) were inefficient, in that the majority of item response categories did not provide incremental psychometric information, 3) poorly measured participants outside of a narrow band of severity, 4) evidenced DIF for nearly all items, suggesting that item responses were, in part, determined by factors other than symptom severity. Limited to outpatients; DIF analysis only sensitive to certain forms of DIF. The present study provides evidence for significant measurement problems involving the YMRS and MADRS. More work is needed to refine these measures and/or develop suitable alternative measures of BD symptomatology for clinical trials research. Copyright © 2016 Elsevier B.V. All rights reserved.

Estimation for general birth-death processes

PubMed Central

Crawford, Forrest W.; Minin, Vladimir N.; Suchard, Marc A.

2013-01-01

Birth-death processes (BDPs) are continuous-time Markov chains that track the number of “particles” in a system over time. While widely used in population biology, genetics and ecology, statistical inference of the instantaneous particle birth and death rates remains largely limited to restrictive linear BDPs in which per-particle birth and death rates are constant. Researchers often observe the number of particles at discrete times, necessitating data augmentation procedures such as expectation-maximization (EM) to find maximum likelihood estimates. For BDPs on finite state-spaces, there are powerful matrix methods for computing the conditional expectations needed for the E-step of the EM algorithm. For BDPs on infinite state-spaces, closed-form solutions for the E-step are available for some linear models, but most previous work has resorted to time-consuming simulation. Remarkably, we show that the E-step conditional expectations can be expressed as convolutions of computable transition probabilities for any general BDP with arbitrary rates. This important observation, along with a convenient continued fraction representation of the Laplace transforms of the transition probabilities, allows for novel and efficient computation of the conditional expectations for all BDPs, eliminating the need for truncation of the state-space or costly simulation. We use this insight to derive EM algorithms that yield maximum likelihood estimation for general BDPs characterized by various rate models, including generalized linear models. We show that our Laplace convolution technique outperforms competing methods when they are available and demonstrate a technique to accelerate EM algorithm convergence. We validate our approach using synthetic data and then apply our methods to cancer cell growth and estimation of mutation parameters in microsatellite evolution. PMID:25328261

Estimation for general birth-death processes.

PubMed

Crawford, Forrest W; Minin, Vladimir N; Suchard, Marc A

2014-04-01

Birth-death processes (BDPs) are continuous-time Markov chains that track the number of "particles" in a system over time. While widely used in population biology, genetics and ecology, statistical inference of the instantaneous particle birth and death rates remains largely limited to restrictive linear BDPs in which per-particle birth and death rates are constant. Researchers often observe the number of particles at discrete times, necessitating data augmentation procedures such as expectation-maximization (EM) to find maximum likelihood estimates. For BDPs on finite state-spaces, there are powerful matrix methods for computing the conditional expectations needed for the E-step of the EM algorithm. For BDPs on infinite state-spaces, closed-form solutions for the E-step are available for some linear models, but most previous work has resorted to time-consuming simulation. Remarkably, we show that the E-step conditional expectations can be expressed as convolutions of computable transition probabilities for any general BDP with arbitrary rates. This important observation, along with a convenient continued fraction representation of the Laplace transforms of the transition probabilities, allows for novel and efficient computation of the conditional expectations for all BDPs, eliminating the need for truncation of the state-space or costly simulation. We use this insight to derive EM algorithms that yield maximum likelihood estimation for general BDPs characterized by various rate models, including generalized linear models. We show that our Laplace convolution technique outperforms competing methods when they are available and demonstrate a technique to accelerate EM algorithm convergence. We validate our approach using synthetic data and then apply our methods to cancer cell growth and estimation of mutation parameters in microsatellite evolution.

Determination of the apparent transfer coefficient for CO oxidation on Pt(poly), Pt(111), Pt(665) and Pt(332) using a potential modulation technique.

PubMed

Wang, Han-Chun; Ernst, Siegfried; Baltruschat, Helmut

2010-03-07

The apparent transfer coefficient, which gives the magnitude of the potential dependence of the electrochemical reaction rates, is the key quantity for the elucidation of electrochemical reaction mechanisms. We introduce the application of an ac method to determine the apparent transfer coefficient alpha' for the oxidation of pre-adsorbed CO at polycrystalline and single-crystalline Pt electrodes in sulfuric acid. The method allows to record alpha' quasi continuously as a function of potential (and time) in cyclic voltammetry or at a fixed potential, with the reaction rate varying with time. At all surfaces (Pt(poly), Pt(111), Pt(665), and Pt(332)) we clearly observed a transition of the apparent transfer coefficient from values around 1.5 at low potentials to values around 0.5 at higher potentials. Changes of the apparent transfer coefficients for the CO oxidation with potential were observed previously, but only from around 0.7 to values as low as 0.2. In contrast, our experimental findings completely agree with the simulation by Koper et al., J. Chem. Phys., 1998, 109, 6051-6062. They can be understood in the framework of a Langmuir-Hinshelwood mechanism. The transition occurs when the sum of the rate constants for the forward reaction (first step: potential dependent OH adsorption, second step: potential dependent oxidation of CO(ad) with OH(ad)) exceeds the rate constant for the back-reaction of the first step. We expect that the ac method for the determination of the apparent transfer coefficient, which we used here, will be of great help also in many other cases, especially under steady conditions, where the major limitations of the method are avoided.

The effect of cation:anion ratio in solution on the mechanism of barite growth at constant supersaturation: Role of the desolvation process on the growth kinetics

NASA Astrophysics Data System (ADS)

Kowacz, M.; Putnis, C. V.; Putnis, A.

2007-11-01

The mechanism of barite growth has been investigated in a fluid cell of an Atomic Force Microscope by passing solutions of constant supersaturation ( Ω) but variable ion activity ratio ( r=a/a) over a barite substrate.The observed dependence of step-spreading velocity on solution stoichiometry can be explained by considering non-equivalent attachment frequency factors for the cation and anion. We show that the potential for two-dimensional nucleation changes under a constant thermodynamic driving force due to the kinetics of barium integration into the surface, and that the growth mode changes from preexisting step advancement to island spreading as the cation/anion activity ratio increases. Scanning electron microscopy studies of crystals grown in bulk solutions support our findings that matching the ion ratio in the fluid to that of the crystal lattice does not result in maximum growth and nucleation rates. Significantly more rapid rates correspond to solution stoichiometries where [Ba 2+] is in excess with respect to [ SO42-]. Experiments performed in dilute aqueous solutions of methanol show that even 0.02 molar fraction of organic cosolvent in the growth solution significantly accelerates step growth velocity and nucleation rates (while keeping Ω the same as in the reference solution in water). Our observations suggest that the effect of methanol on barite growth results first of all from reduction of the barrier that prevents the Ba 2+ from reaching the surface and corroborate the hypothesis that desolvation of the cation and of the surface is the rate limiting kinetic process for two-dimensional nucleation and for crystal growth.

Density functional theory and RRKM calculations of decompositions of the metastable E-2,4-pentadienal molecular ions.

PubMed

Solano Espinoza, Eduardo A; Vallejo Narváez, Wilmer E

2010-07-01

The potential energy profiles for the fragmentations that lead to [C(5)H(5)O](+) and [C(4)H(6)](+*) ions from the molecular ions [C(5)H(6)O](+*) of E-2,4-pentadienal were obtained from calculations at the UB3LYP/6-311G + + (3df,3pd)//UB3LYP/6-31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice-Ramsperger-Kassel-Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre-equilibrium and rate-controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C-H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E-2,4-pentadienal ions. The direct dissociation, however, can only become important in the high-energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2-hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion-neutral complex which, in turn, decomposes rapidly to the s-trans-1,3-butadiene ion [C(4)H(6)](+*). The predominating metastable channel is the second one, that is, a multi-step ring closure which starts with a rate-limiting cis-trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C(5)H(5)O](+). These results can be used to rationalize the CID mass spectrum of E-2,4-pentadienal in a low-energy regime. 2010 John Wiley & Sons, Ltd.

Mechanisms and rates of proton transfer to coordinated carboxydithioates: studies on [Ni(S2CR){PhP(CH2CH2PPh2)2}](+) (R = Me, Et, Bu(n) or Ph).

PubMed

Alwaaly, Ahmed; Clegg, William; Henderson, Richard A; Probert, Michael R; Waddell, Paul G

2015-02-21

The complexes [Ni(S2CR)(triphos)]BPh4 (R = Me, Et, Bu(n) or Ph; triphos = PhP{CH2CH2PPh2}2) have been prepared and characterised. X-ray crystallography (for R = Et, Ph, C6H4Me-4, C6H4OMe-4 and C6H4Cl-4) shows that the geometry of the five-coordinate nickel in the cation is best described as distorted trigonal bipyramidal, containing a bidentate carboxydithioate ligand with the two sulfur atoms spanning axial and equatorial sites, the other axial site being occupied by the central phosphorus of triphos. The reactions of [Ni(S2CR)(triphos)](+) with mixtures of HCl and Cl(-) in MeCN to form equilibrium solutions containing [Ni(SH(S)CR)(triphos)](2+) have been studied using stopped-flow spectrophotometry. The kinetics show that proton transfer is slower than the diffusion-controlled limit and involves at least two coupled equilibria. The first step involves the rapid association between [Ni(S2CR)(triphos)](+) and HCl to form the hydrogen-bonded precursor, {[Ni(S2CR)(triphos)](+)HCl} (K) and this is followed by the intramolecular proton transfer (k) to produce [Ni(SH(S)CR)(triphos)](2+). In the reaction of [Ni(S2CMe)(triphos)](+) the rate law is consistent with the carboxydithioate ligand undergoing chelate ring-opening after protonation. It seems likely that chelate ring-opening occurs for all [Ni(S2CR)(triphos)](+), but only with [Ni(S2CMe)(triphos)](+) is the protonation step sufficiently fast that chelate ring-opening is rate-limiting. With all other systems, proton transfer is rate-limiting. DFT calculations indicate that protonation can occur at either sulfur atom, but only protonation at the equatorial sulfur results in chelate ring-opening. The ways in which protonation of either sulfur atom complicates the analyses and interpretation of the kinetics are discussed.

A Conjugate Gradient Algorithm with Function Value Information and N-Step Quadratic Convergence for Unconstrained Optimization.

PubMed

Li, Xiangrong; Zhao, Xupei; Duan, Xiabin; Wang, Xiaoliang

2015-01-01

It is generally acknowledged that the conjugate gradient (CG) method achieves global convergence--with at most a linear convergence rate--because CG formulas are generated by linear approximations of the objective functions. The quadratically convergent results are very limited. We introduce a new PRP method in which the restart strategy is also used. Moreover, the method we developed includes not only n-step quadratic convergence but also both the function value information and gradient value information. In this paper, we will show that the new PRP method (with either the Armijo line search or the Wolfe line search) is both linearly and quadratically convergent. The numerical experiments demonstrate that the new PRP algorithm is competitive with the normal CG method.

Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.

PubMed

Hirozane-Kishikawa, Tomoko; Shiraki, Toshiyuki; Waki, Kazunori; Nakamura, Mari; Arakawa, Takahiro; Kawai, Jun; Fagiolini, Michela; Hensch, Takao K; Hayashizaki, Yoshihide; Carninci, Piero

2003-09-01

The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.

Discovering New Diseases to Accelerate Precision Medicine.

PubMed

Macrae, Calum A

2017-01-01

A rate-limiting step in multiple areas of medicine is the limited number of discrete disorders that current technologies are able to identify. Most clinical disease entities are aggregates of large numbers of discrete biological processes that simply happen to share one or two common features. We have begun to translate a wide range of new technologies to the clinic in an effort to improve the resolution and the efficiency of bedside diagnostics with a view to improving drug trials, genetic studies, and the effectiveness of the clinician in a digital environment. The general trajectory for change that new technologies will bring is outlined with some specific examples of areas where such change has already begun to occur.

Towards a Passive Low-Cost In-Home Gait Assessment System for Older Adults

PubMed Central

Wang, Fang; Stone, Erik; Skubic, Marjorie; Keller, James M.; Abbott, Carmen; Rantz, Marilyn

2013-01-01

In this paper, we propose a webcam-based system for in-home gait assessment of older adults. A methodology has been developed to extract gait parameters including walking speed, step time and step length from a three-dimensional voxel reconstruction, which is built from two calibrated webcam views. The gait parameters are validated with a GAITRite mat and a Vicon motion capture system in the lab with 13 participants and 44 tests, and again with GAITRite for 8 older adults in senior housing. An excellent agreement with intra-class correlation coefficients of 0.99 and repeatability coefficients between 0.7% and 6.6% was found for walking speed, step time and step length given the limitation of frame rate and voxel resolution. The system was further tested with 10 seniors in a scripted scenario representing everyday activities in an unstructured environment. The system results demonstrate the capability of being used as a daily gait assessment tool for fall risk assessment and other medical applications. Furthermore, we found that residents displayed different gait patterns during their clinical GAITRite tests compared to the realistic scenario, namely a mean increase of 21% in walking speed, a mean decrease of 12% in step time, and a mean increase of 6% in step length. These findings provide support for continuous gait assessment in the home for capturing habitual gait. PMID:24235111

Elucidation of the mechanism of N-demethylation catalyzed by cytochrome P450 monooxygenase is facilitated by exploiting nitrogen-15 heavy isotope effects.

PubMed

Kwiecień, Renata A; Molinié, Roland; Paneth, Piotr; Silvestre, Virginie; Lebreton, Jacques; Robins, Richard J

2011-06-01

(15)N heavy isotope effects are especially useful when detail is sought pertaining to the reaction mechanism for the cleavage of a C-N bond. Their potential in assisting to describe the mechanism of N-demethylation of tertiary amines by the action of cytochrome P450 monooxygenase has been investigated. As a working model for the first step, oxidation of the N-methyl group to N-methoxyl, tropine and a cytochrome P450 monooxygenase reaction centre composed of a truncated heme with sulfhydryl as the axial ligand were used. It is apparent that this first step of the reaction proceeds via a hydrogen atom transfer mechanism. Transition states for this step are described for both the high spin ((4)TS(H)) and low spin ((2)TS(H)) pathways in both gas and solvation states. Hence, overall normal secondary (15)N KIE could be calculated for the reaction path modeled in the low spin state, and inverse for the reaction modeled in the high spin state. This partial reaction has been identified as the probable rate limiting step. The model for the second step, fission of the C-N bond, consisted of N-methoxylnortropine and two molecules of water. A transition state described for this step, TS(CN), gives a strongly inverse overall theoretical (15)N KIE. Copyright © 2011 Elsevier Inc. All rights reserved.

The STEP database through the end-users eyes--USABILITY STUDY.

PubMed

Salunke, Smita; Tuleu, Catherine

2015-08-15

The user-designed database of Safety and Toxicity of Excipients for Paediatrics ("STEP") is created to address the shared need of drug development community to access the relevant information of excipients effortlessly. Usability testing was performed to validate if the database satisfies the need of the end-users. Evaluation framework was developed to assess the usability. The participants performed scenario based tasks and provided feedback and post-session usability ratings. Failure Mode Effect Analysis (FMEA) was performed to prioritize the problems and improvements to the STEP database design and functionalities. The study revealed several design vulnerabilities. Tasks such as limiting the results, running complex queries, location of data and registering to access the database were challenging. The three critical attributes identified to have impact on the usability of the STEP database included (1) content and presentation (2) the navigation and search features (3) potential end-users. Evaluation framework proved to be an effective method for evaluating database effectiveness and user satisfaction. This study provides strong initial support for the usability of the STEP database. Recommendations would be incorporated into the refinement of the database to improve its usability and increase user participation towards the advancement of the database. Copyright © 2015 Elsevier B.V. All rights reserved.

Reflectance-difference spectroscopy of GaAs crystal growth by OMCVD

NASA Astrophysics Data System (ADS)

Colas, Etienne G.; Aspnes, David E.; Bhat, Rajaram J.; Studna, A. A.; Koza, M. A.; Keramidas, Vassilis G.

1990-02-01

This paper summarizes results of our investigations of growth on (001) and (110) GaAs by atmospheric-pressure organometallic chemical vapor deposition (OMCVD). We follow evolutions of surface species to a sensitivity of 0.01 monolayer (ML) on a time scale of 0.1 s under alternating flows of trimethylgallium (TMG) and arsine (AsH3) as functions of partial pressure, sample temperature, and surface orienta-tion. The reaction of TMG with an AsH3-saturated (001) surface is rate-limited by com-petition between desorption and decomposition of TMG molecules chemisorbed to surface lattice sites via an excluded-volume mechanism, while the reaction of AsH3 with the TMG-saturated (001) surface is essentially instantaneous. In contrast, TMG reacts essentially instantaneously with the AsH3 -saturated (110) surface while the AsH3 reaction with the TMG-saturated (110) surface is the rate-limiting step. However, the latter rate is not intrinsic to the AsH3-surface reaction but appears to be determined by desorption of adsorbed species that block active sites.

Dynamic Modeling of the Main Blow in Basic Oxygen Steelmaking Using Measured Step Responses

NASA Astrophysics Data System (ADS)

Kattenbelt, Carolien; Roffel, B.

2008-10-01

In the control and optimization of basic oxygen steelmaking, it is important to have an understanding of the influence of control variables on the process. However, important process variables such as the composition of the steel and slag cannot be measured continuously. The decarburization rate and the accumulation rate of oxygen, which can be derived from the generally measured waste gas flow and composition, are an indication of changes in steel and slag composition. The influence of the control variables on the decarburization rate and the accumulation rate of oxygen can best be determined in the main blow period. In this article, the measured step responses of the decarburization rate and the accumulation rate of oxygen to step changes in the oxygen blowing rate, lance height, and the addition rate of iron ore during the main blow are presented. These measured step responses are subsequently used to develop a dynamic model for the main blow. The model consists of an iron oxide and a carbon balance and an additional equation describing the influence of the lance height and the oxygen blowing rate on the decarburization rate. With this simple dynamic model, the measured step responses can be explained satisfactorily.

Regioselective Formation of α-Vinylpyrroles from the Ruthenium-Catalyzed Coupling Reaction of Pyrroles and Terminal Alkynes Involving C–H Bond Activation

PubMed Central

Gao, Ruili; Yi, Chae S.

2010-01-01

The cationic ruthenium catalyst, Ru3(CO)12/NH4PF6, was found to be highly effective for the intermolecular coupling reaction of pyrroles and terminal alkynes to give gem-selective α-vinylpyrroles. The carbon isotope effect on the α-pyrrole carbon and the Hammett correlation from a series of para-substituted N-arylpyrroles (ρ = −0.90) indicate a rate-limiting C–C bond formation step of the coupling reaction. PMID:20384382

Army Science Conference Proceedings Held in Orlando, Florida on June 22 - 25, 1992. Volume 3, Principal Authors N Through Z.

DTIC Science & Technology

1992-06-25

SD. The CFA/ll microsphere vaccine (Lot 74F2) percent water content was found using the Karl Fischer titrimeter method to be 2.154% using triplicate...cooling of the reaction is necessary. Under prior synthetic methods the removal of heat has been the rate limiting step, thus necessitating several...Janine I 471 Bhattacharya, P.K. See Tober, Richard L. III 221 Billingsley, Daniel See Watkins, Wendell R. III 275 Binder, Michael Method for Increasing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell Feder and Mahmoud Z. Yousef

Neutronics analysis to find nuclear heating rates and personnel dose rates were conducted in support of the integration of diagnostics in to the ITER Upper Port Plugs. Simplified shielding models of the Visible-Infrared diagnostic and of the ECH heating system were incorporated in to the ITER global CAD model. Results for these systems are representative of typical designs with maximum shielding and a small aperture (Vis-IR) and minimal shielding with a large aperture (ECH). The neutronics discrete-ordinates code ATTILA® and SEVERIAN® (the ATTILA parallel processing version) was used. Material properties and the 500 MW D-T volume source were taken frommore » the ITER “Brand Model” MCNP benchmark model. A biased quadrature set equivelant to Sn=32 and a scattering degree of Pn=3 were used along with a 46-neutron and 21-gamma FENDL energy subgrouping. Total nuclear heating (neutron plug gamma heating) in the upper port plugs ranged between 380 and 350 kW for the Vis-IR and ECH cases. The ECH or Large Aperture model exhibited lower total heating but much higher peak volumetric heating on the upper port plug structure. Personnel dose rates are calculated in a three step process involving a neutron-only transport calculation, the generation of activation volume sources at pre-defined time steps and finally gamma transport analyses are run for selected time steps. ANSI-ANS 6.1.1 1977 Flux-to-Dose conversion factors were used. Dose rates were evaluated for 1 full year of 500 MW DT operation which is comprised of 3000 1800-second pulses. After one year the machine is shut down for maintenance and personnel are permitted to access the diagnostic interspace after 2-weeks if dose rates are below 100 μSv/hr. Dose rates in the Visible-IR diagnostic model after one day of shutdown were 130 μSv/hr but fell below the limit to 90 μSv/hr 2-weeks later. The Large Aperture or ECH style shielding model exhibited higher and more persistent dose rates. After 1-day the dose rate was 230 μSv/hr but was still at 120 μSv/hr 4-weeks later. __________________________________________________« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell E. Feder and Mahmoud Z. Youssef

Neutronics analysis to find nuclear heating rates and personnel dose rates were conducted in support of the integration of diagnostics in to the ITER Upper Port Plugs. Simplified shielding models of the Visible-Infrared diagnostic and of a large aperture diagnostic were incorporated in to the ITER global CAD model. Results for these systems are representative of typical designs with maximum shielding and a small aperture (Vis-IR) and minimal shielding with a large aperture. The neutronics discrete-ordinates code ATTILA® and SEVERIAN® (the ATTILA parallel processing version) was used. Material properties and the 500 MW D-T volume source were taken from themore » ITER “Brand Model” MCNP benchmark model. A biased quadrature set equivelant to Sn=32 and a scattering degree of Pn=3 were used along with a 46-neutron and 21-gamma FENDL energy subgrouping. Total nuclear heating (neutron plug gamma heating) in the upper port plugs ranged between 380 and 350 kW for the Vis-IR and Large Aperture cases. The Large Aperture model exhibited lower total heating but much higher peak volumetric heating on the upper port plug structure. Personnel dose rates are calculated in a three step process involving a neutron-only transport calculation, the generation of activation volume sources at pre-defined time steps and finally gamma transport analyses are run for selected time steps. ANSI-ANS 6.1.1 1977 Flux-to-Dose conversion factors were used. Dose rates were evaluated for 1 full year of 500 MW DT operation which is comprised of 3000 1800-second pulses. After one year the machine is shut down for maintenance and personnel are permitted to access the diagnostic interspace after 2-weeks if dose rates are below 100 μSv/hr. Dose rates in the Visible-IR diagnostic model after one day of shutdown were 130 μSv/hr but fell below the limit to 90 μSv/hr 2-weeks later. The Large Aperture style shielding model exhibited higher and more persistent dose rates. After 1-day the dose rate was 230 μSv/hr but was still at 120 μSv/hr 4-weeks later.« less

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE PAGES

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

2017-07-17

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Simultaneous biodegradation of phenol and carbon tetrachloride mediated by humic acids.

PubMed

Martínez, Claudia M; Alvarez, Luis H; Cervantes, Francisco J

2012-09-01

The capacity of an anaerobic sediment to achieve the simultaneous biodegradation of phenol and carbon tetrachloride (CT) was evaluated, using humic acids (HA) as redox mediator. The presence of HA in sediment incubations increased the rate of biodegradation of phenol and the rate of dehalogenation (2.5-fold) of CT compared to controls lacking HA. Further experiments revealed that the electron-accepting capacity of HA derived from different organic-rich environments was not associated with their reducing capacity to achieve CT dechlorination. The collected kinetic data suggest that the reduction of CT by reduced HA was the rate-limiting step during the simultaneous biodegradation of phenol and CT. To our knowledge, the present study constitutes the first demonstration of the simultaneous biodegradation of two priority pollutants mediated by HA.

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

PubMed Central

Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

2003-01-01

Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

Reaction mechanism for the aqueous-phase mineral carbonation of heat-activated serpentine at low temperatures and pressures in flue gas conditions.

PubMed

Pasquier, Louis-César; Mercier, Guy; Blais, Jean-François; Cecchi, Emmanuelle; Kentish, Sandra

2014-05-06

Mineral carbonation is known as one of the safest ways to sequester CO2. Nevertheless, the slow kinetics and low carbonation rates constitute a major barrier for any possible industrial application. To date, no studies have focused on reacting serpentinite with a relatively low partial pressure of CO2 (pCO2) close to flue gas conditions. In this work, finely ground and heat-treated serpentinite [Mg3Si2O5(OH)4] extracted from mining residues was reacted with a 18.2 vol % CO2 gas stream at moderate global pressures to investigate the effect on CO2 solubility and Mg leaching. Serpentinite dissolution rates were also measured to define the rate-limiting step. Successive batches of gas were contacted with the same serpentinite to identify surface-limiting factors using scanning electron microscopy (SEM) analysis. Investigation of the serpentinite carbonation reaction mechanisms under conditions close to a direct flue gas treatment showed that increased dissolution rates could be achieved relative to prior work, with an average Mg dissolution rate of 3.55 × 10(-11) mol cm(-2) s(-1). This study provides another perspective of the feasibility of applying a mineral carbonation process to reduce industrial greenhouse gas (GHG) emissions from large emission sources.

Planning energy-efficient bipedal locomotion on patterned terrain

NASA Astrophysics Data System (ADS)

Zamani, Ali; Bhounsule, Pranav A.; Taha, Ahmad

2016-05-01

Energy-efficient bipedal walking is essential in realizing practical bipedal systems. However, current energy-efficient bipedal robots (e.g., passive-dynamics-inspired robots) are limited to walking at a single speed and step length. The objective of this work is to address this gap by developing a method of synthesizing energy-efficient bipedal locomotion on patterned terrain consisting of stepping stones using energy-efficient primitives. A model of Cornell Ranger (a passive-dynamics inspired robot) is utilized to illustrate our technique. First, an energy-optimal trajectory control problem for a single step is formulated and solved. The solution minimizes the Total Cost Of Transport (TCOT is defined as the energy used per unit weight per unit distance travelled) subject to various constraints such as actuator limits, foot scuffing, joint kinematic limits, ground reaction forces. The outcome of the optimization scheme is a table of TCOT values as a function of step length and step velocity. Next, we parameterize the terrain to identify the location of the stepping stones. Finally, the TCOT table is used in conjunction with the parameterized terrain to plan an energy-efficient stepping strategy.

Marrying Step Feed with Secondary Clarifier Improvements to Significantly Increase Peak Wet Weather Treatment Capacity: An Integrated Methodology.

PubMed

Daigger, Glen T; Siczka, John S; Smith, Thomas F; Frank, David A; McCorquodale, J A

2017-08-01

  The need to increase the peak wet weather secondary treatment capacity of the City of Akron, Ohio, Water Reclamation Facility (WRF) provided the opportunity to test an integrated methodology for maximizing the peak wet weather secondary treatment capacity of activated sludge systems. An initial investigation, consisting of process modeling of the secondary treatment system and computational fluid dynamics (CFD) analysis of the existing relatively shallow secondary clarifiers (3.3 and 3.7 m sidewater depth in 30.5 m diameter units), indicated that a significant increase in capacity from 416 000 to 684 000 m3/d or more was possible by adding step feed capabilities to the existing bioreactors and upgrading the existing secondary clarifiers. One of the six treatment units at the WRF was modified, and an extensive 2-year testing program was conducted to determine the total peak wet weather secondary treatment capacity achievable. The results demonstrated that a peak wet weather secondary treatment capacity approaching 974 000 m3/d is possible as long as secondary clarifier solids and hydraulic loadings could be separately controlled using the step feed capability provided. Excellent sludge settling characteristics are routinely experienced at the City of Akron WRF, raising concerns that the identified peak wet weather secondary treatment capacity could not be maintained should sludge settling characteristics deteriorate for some reason. Computational fluid dynamics analysis indicated that the impact of the deterioration of sludge settling characteristics could be mitigated and the identified peak wet weather secondary treatment capacity maintained by further use of the step feed capability provided to further reduce secondary clarifier solids loading rates at the identified high surface overflow rates. The results also demonstrated that effluent limits not only for total suspended solids (TSS) and five-day carbonaceous biochemical oxygen demand (cBOD5) could be maintained, but also for ammonia-nitrogen and total phosphorous (TP). Although hydraulic limitations in other parts of the WRP prevent this full capacity to be realized, the City is proceeding to implement the modifications identified using this integrated methodology.

Direct carbon-carbon coupling of furanics with acetic acid over Brønsted zeolites

PubMed Central

Gumidyala, Abhishek; Wang, Bin; Crossley, Steven

2016-01-01

Effective carbon-carbon coupling of acetic acid to form larger products while minimizing CO2 emissions is critical to achieving a step change in efficiency for the production of transportation fuels from sustainable biomass. We report the direct acylation of methylfuran with acetic acid in the presence of water, all of which can be readily produced from biomass. This direct coupling limits unwanted polymerization of furanics while producing acetyl methylfuran. Reaction kinetics and density functional theory calculations illustrate that the calculated apparent barrier for the dehydration of the acid to form surface acyl species is similar to the experimentally measured barrier, implying that this step plays a significant role in determining the net reaction rate. Water inhibits the overall rate, but selectivity to acylated products is not affected. We show that furanic species effectively stabilize the charge of the transition state, therefore lowering the overall activation barrier. These results demonstrate a promising new route to C–C bond–forming reactions for the production of higher-value products from biomass. PMID:27652345

Direct carbon-carbon coupling of furanics with acetic acid over Bronsted zeolites

DOE PAGES

Gumidyala, Abhishek; Wang, Bin; Crossley, Steven

2016-09-16

Effective carbon-carbon coupling of acetic acid to form larger products while minimizing CO 2 emissions is critical to achieving a step change in efficiency for the production of transportation fuels from sustainable biomass. Here, we report the direct acylation of methylfuran with acetic acid in the presence ofwater, all ofwhich can be readily produced from biomass. This direct coupling limits unwanted polymerization of furanics while producing acetyl methylfuran. Reaction kinetics and density functional theory calculations illustrate that the calculated apparent barrier for the dehydration of the acid to form surface acyl species is similar to the experimentally measured barrier, implyingmore » that this step plays a significant role in determining the net reaction rate. Water inhibits the overall rate, but selectivity to acylated products is not affected.We show that furanic species effectively stabilize the charge of the transition state, therefore lowering the overall activation barrier. These results demonstrate a promising new route to C–C bond–forming reactions for the production of higher-value products from biomass.« less

Relative binding affinities of monolignols to horseradish peroxidase

DOE PAGES

Sangha, Amandeep K.; Petridis, Loukas; Cheng, Xiaolin; ...

2016-07-22

Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that p-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. p-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic –OH group andmore » a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic –OH group instead interacting with Pro139. Furthermore, since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate.« less

Enrichment of a mixed microbial culture for polyhydroxyalkanoates production: Effect of pH and N and P concentrations.

PubMed

Montiel-Jarillo, Gabriela; Carrera, Julián; Suárez-Ojeda, María Eugenia

2017-04-01

Polyhydroxyalkanoates (PHA) are biopolymers that can be an alternative against conventional plastics. The study reported herein evaluated the enrichment of a mixed microbial culture (MMC) operated under feast/famine regime and different pHs in a sequencing batch reactor (SBR) using acetate as sole carbon source to produce polyhydroxyalkanoates (PHAs). The enrichment step was evaluated at controlled pH of 7.5 and also without pH control (averaged value of 9.0). The acetate uptake rate (-q S ) of both enrichments at the end of the experimental period exhibited similar behaviour being about 0.18CmolAcCmolX -1 h -1 and 0.19CmolAcCmolX -1 h -1 for SBR-A and SBR-B, respectively. However, the PHA-storing capacity of the biomass enriched without pH control was better, exhibiting a maximum PHA content of 36% (gPHAg -1 VSS) with a PHA production rate (q PHA ) of 0.16CmolPHACmolX -1 h -1 . Batch experiments were performed to evaluate PHA-storing capacity of the enriched culture at different pHs and nutrients concentrations. In the pH experiments (without nutrient limitation), it was found that in the absence of controlled pH, the enriched biomass exhibited a PHA content of 44% gPHAg -1 VSS with -q S and PHA to substrate yield (Y PHA/Ac ) of 0.57CmolAcCmolX -1 h -1 and 0.33CmolPHACmolAc -1 , respectively. Regarding the experiments at variable nutrients concentration (pH ranging 8.8 to 9.2), the results indicate that the PHA content in the enriched biomass is significantly higher being around 51% gPHAg -1 VSS under nitrogen limitation. This work demonstrated the feasibility of the enrichment of a MMC with PHA storage ability without pH control. Results also suggest that better PHAs contents and substrate uptake rates are obtained without controlling the pH in the accumulation step. Finally, this work also highlights the importance of understanding the role of nutrients concentration during the accumulation step. Copyright © 2017 Elsevier B.V. All rights reserved.

Health Facility Staff Training for Improving Breastfeeding Outcome: A Systematic Review for Step 2 of the Baby-Friendly Hospital Initiative.

PubMed

Balogun, Olukunmi O; Dagvadorj, Amarjargal; Yourkavitch, Jennifer; da Silva Lopes, Katharina; Suto, Maiko; Takemoto, Yo; Mori, Rintaro; Rayco-Solon, Pura; Ota, Erika

2017-11-01

The Baby-Friendly Hospital Initiative (BFHI) implemented through the "Ten Steps to Successful Breastfeeding" has been widely promoted as an intervention that improves breastfeeding rates. Step 2 requires the training of all healthcare staff in skills that are necessary to implement the policy. This systematic review provides evidence about the effect of training healthcare staff in hospitals and birth centers on breastfeeding outcomes. Randomized controlled trials (RCT), quasi-RCT, and controlled before and after (CBA) studies comparing training of healthcare staff on breastfeeding and supportive feeding practices with no training were included in this review. We searched CENTRAL PubMed, EMBASE, CINAHL, Web of Science, and the British Nursing Index for studies. Studies were screened against predetermined criteria, and risk of bias of included studies was assessed using the Risk of Bias Assessment tool for Non-Randomized Studies for non-RCT studies and the Cochrane Handbook for Systematic Reviews of Interventions for RCT studies. Of the six studies included in this review, three were RCT whereas three were CBA studies. The studies were conducted in 5 countries and involved 390 healthcare staff. Provision of educational interventions aimed at increasing knowledge and practice of BFHI and support was found to improve health worker's knowledge, attitude, and compliance with the BFHI practices. In one study, the rate of exclusive breastfeeding increased at the intervention site but no differences were found for breastfeeding initiation rates. All included studies had methodological limitations, and study designs and methodologies lacked comparability.

Visual Recognition of the Elderly Concerning Risks of Falling or Stumbling Indoors in the Home

PubMed Central

Katsura, Toshiki; Miura, Norio; Hoshino, Akiko; Usui, Kanae; Takahashi, Yasuro; Hisamoto, Seiichi

2011-01-01

Objective: The objective of this study was to verify the recognition of dangers and obstacles within a house in the elderly when walking based on analyses of gaze point fixation. Materials and Methods: The rate of recognizing indoor dangers was compared among 30 elderly, 14 middle-aged and 11 young individuals using the Eye Mark Recorder. Results: 1) All of the elderly, middle-aged and young individuals showed a high recognition rate of 100% or near 100% when ascending outdoor steps but a low rate of recognizing obstacles placed on the steps. They showed a recognition rate of about 60% when descending steps from residential premises to the street. The rate of recognizing middle steps in the elderly was significantly lower than that in younger and middle-aged individuals. Regarding recognition indoors, when ascending stairs, all of the elderly, middle-aged and young individuals showed a high recognition rate of nearly 100%. When descending stairs, they showed a recognition rate of 70-90%. However, although the recognition rate in the elderly was lower than in younger and middle-aged individuals, no significant difference was observed. 2) When moving indoors, all of the elderly, middle-aged and young individuals showed a recognition rate of 70%-80%. The recognition rate was high regarding obstacles such as floors, televisions and chests of drawers but low for obstacles in the bathroom and steps on the path. The rate of recognizing steps of doorsills forming the division between a Japanese-style room and corridor as well as obstacles in a Japanese-style room was low, and the rate in the elderly was low, being 40% or less. Conclusion: The rate of recognizing steps of doorsills as well as obstacles in a Japanese-style room was lower in the elderly in comparison with middle-aged or young individuals. PMID:25648876

Two-Step Oxidation of Refractory Gold Concentrates with Different Microbial Communities.

PubMed

Wang, Guo-Hua; Xie, Jian-Ping; Li, Shou-Peng; Guo, Yu-Jie; Pan, Ying; Wu, Haiyan; Liu, Xin-Xing

2016-11-28

Bio-oxidation is an effective technology for treatment of refractory gold concentrates. However, the unsatisfactory oxidation rate and long residence time, which cause a lower cyanide leaching rate and gold recovery, are key factors that restrict the application of traditional bio-oxidation technology. In this study, the oxidation rate of refractory gold concentrates and the adaption of microorganisms were analyzed to evaluate a newly developed two-step pretreatment process, which includes a high temperature chemical oxidation step and a subsequent bio-oxidation step. The oxidation rate and recovery rate of gold were improved significantly after the two-step process. The results showed that the highest oxidation rate of sulfide sulfur could reach to 99.01 % with an extreme thermophile microbial community when the pulp density was 5%. Accordingly, the recovery rate of gold was elevated to 92.51%. Meanwhile, the results revealed that moderate thermophiles performed better than acidophilic mesophiles and extreme thermophiles, whose oxidation rates declined drastically when the pulp density was increased to 10% and 15%. The oxidation rates of sulfide sulfur with moderate thermophiles were 93.94% and 65.73% when the pulp density was increased to 10% and 15%, respectively. All these results indicated that the two-step pretreatment increased the oxidation rate of refractory gold concentrates and is a potential technology to pretreat the refractory sample. Meanwhile, owing to the sensitivity of the microbial community under different pulp density levels, the optimization of microbial community in bio-oxidation is necessary in industry.

Analysis of the track- and dose-averaged LET and LET spectra in proton therapy using the GEANT4 Monte Carlo code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Fada; Peeler, Christopher; Taleei, Reza

Purpose: The motivation of this study was to find and eliminate the cause of errors in dose-averaged linear energy transfer (LET) calculations from therapeutic protons in small targets, such as biological cell layers, calculated using the GEANT 4 Monte Carlo code. Furthermore, the purpose was also to provide a recommendation to select an appropriate LET quantity from GEANT 4 simulations to correlate with biological effectiveness of therapeutic protons. Methods: The authors developed a particle tracking step based strategy to calculate the average LET quantities (track-averaged LET, LET{sub t} and dose-averaged LET, LET{sub d}) using GEANT 4 for different tracking stepmore » size limits. A step size limit refers to the maximally allowable tracking step length. The authors investigated how the tracking step size limit influenced the calculated LET{sub t} and LET{sub d} of protons with six different step limits ranging from 1 to 500 μm in a water phantom irradiated by a 79.7-MeV clinical proton beam. In addition, the authors analyzed the detailed stochastic energy deposition information including fluence spectra and dose spectra of the energy-deposition-per-step of protons. As a reference, the authors also calculated the averaged LET and analyzed the LET spectra combining the Monte Carlo method and the deterministic method. Relative biological effectiveness (RBE) calculations were performed to illustrate the impact of different LET calculation methods on the RBE-weighted dose. Results: Simulation results showed that the step limit effect was small for LET{sub t} but significant for LET{sub d}. This resulted from differences in the energy-deposition-per-step between the fluence spectra and dose spectra at different depths in the phantom. Using the Monte Carlo particle tracking method in GEANT 4 can result in incorrect LET{sub d} calculation results in the dose plateau region for small step limits. The erroneous LET{sub d} results can be attributed to the algorithm to determine fluctuations in energy deposition along the tracking step in GEANT 4. The incorrect LET{sub d} values lead to substantial differences in the calculated RBE. Conclusions: When the GEANT 4 particle tracking method is used to calculate the average LET values within targets with a small step limit, such as smaller than 500 μm, the authors recommend the use of LET{sub t} in the dose plateau region and LET{sub d} around the Bragg peak. For a large step limit, i.e., 500 μm, LET{sub d} is recommended along the whole Bragg curve. The transition point depends on beam parameters and can be found by determining the location where the gradient of the ratio of LET{sub d} and LET{sub t} becomes positive.« less

Endoclip Magnetic Resonance Imaging Screening: A Local Practice Review.

PubMed

Accorsi, Fabio; Lalonde, Alain; Leswick, David A

2018-05-01

Not all endoscopically placed clips (endoclips) are magnetic resonance imaging (MRI) compatible. At many institutions, endoclip screening is part of the pre-MRI screening process. Our objective is to determine the contribution of each step of this endoclip screening protocol in determining a patient's endoclip status at our institution. A retrospective review of patients' endoscopic histories on general MRI screening forms for patients scanned during a 40-day period was performed to assess the percentage of patients that require endoclip screening at our institution. Following this, a prospective evaluation of 614 patients' endoclip screening determined the percentage of these patients ultimately exposed to each step in the protocol (exposure), and the percentage of patients whose endoclip status was determined with reasonable certainty by each step (determination). Exposure and determination values for each step were calculated as follows (exposure, determination): verbal interview (100%, 86%), review of past available imaging (14%, 36%), review of endoscopy report (9%, 57%), and new abdominal radiograph (4%, 96%), or CT (0.2%, 100%) for evaluation of potential endoclips. Only 1 patient did not receive MRI because of screening (in situ gastrointestinal endoclip identified). Verbal interview is invaluable to endoclip screening, clearing 86% of patients with minimal monetary and time investment. Conversely, the limited availability of endoscopy reports and relevant past imaging somewhat restricts the determination rates of these. New imaging (radiograph or computed tomography) is required <5% of the time, and although costly and associated with patient irradiation, has excellent determination rates (above 96%) when needed. Copyright © 2017 Canadian Association of Radiologists. Published by Elsevier Inc. All rights reserved.

Global research priorities for interpersonal violence prevention: a modified Delphi study.

PubMed

Mikton, Christopher R; Tanaka, Masako; Tomlinson, Mark; Streiner, David L; Tonmyr, Lil; Lee, Bandy X; Fisher, Jane; Hegadoren, Kathy; Pim, Joam Evans; Wang, Shr-Jie Sharlenna; MacMillan, Harriet L

2017-01-01

To establish global research priorities for interpersonal violence prevention using a systematic approach. Research priorities were identified in a three-round process involving two surveys. In round 1, 95 global experts in violence prevention proposed research questions to be ranked in round 2. Questions were collated and organized according to the four-step public health approach to violence prevention. In round 2, 280 international experts ranked the importance of research in the four steps, and the various substeps, of the public health approach. In round 3, 131 international experts ranked the importance of detailed research questions on the public health step awarded the highest priority in round 2. In round 2, "developing, implementing and evaluating interventions" was the step of the public health approach awarded the highest priority for four of the six types of violence considered (i.e. child maltreatment, intimate partner violence, armed violence and sexual violence) but not for youth violence or elder abuse. In contrast, "scaling up interventions and evaluating their cost-effectiveness" was ranked lowest for all types of violence. In round 3, research into "developing, implementing and evaluating interventions" that addressed parenting or laws to regulate the use of firearms was awarded the highest priority. The key limitations of the study were response and attrition rates among survey respondents. However, these rates were in line with similar priority-setting exercises. These findings suggest it is premature to scale up violence prevention interventions. Developing and evaluating smaller-scale interventions should be the funding priority.

Global research priorities for interpersonal violence prevention: a modified Delphi study

PubMed Central

Tanaka, Masako; Tomlinson, Mark; Streiner, David L; Tonmyr, Lil; Lee, Bandy X; Fisher, Jane; Hegadoren, Kathy; Pim, Joam Evans; Wang, Shr-Jie Sharlenna; MacMillan, Harriet L

2017-01-01

Abstract Objective To establish global research priorities for interpersonal violence prevention using a systematic approach. Methods Research priorities were identified in a three-round process involving two surveys. In round 1, 95 global experts in violence prevention proposed research questions to be ranked in round 2. Questions were collated and organized according to the four-step public health approach to violence prevention. In round 2, 280 international experts ranked the importance of research in the four steps, and the various substeps, of the public health approach. In round 3, 131 international experts ranked the importance of detailed research questions on the public health step awarded the highest priority in round 2. Findings In round 2, “developing, implementing and evaluating interventions” was the step of the public health approach awarded the highest priority for four of the six types of violence considered (i.e. child maltreatment, intimate partner violence, armed violence and sexual violence) but not for youth violence or elder abuse. In contrast, “scaling up interventions and evaluating their cost–effectiveness” was ranked lowest for all types of violence. In round 3, research into “developing, implementing and evaluating interventions” that addressed parenting or laws to regulate the use of firearms was awarded the highest priority. The key limitations of the study were response and attrition rates among survey respondents. However, these rates were in line with similar priority-setting exercises. Conclusion These findings suggest it is premature to scale up violence prevention interventions. Developing and evaluating smaller-scale interventions should be the funding priority. PMID:28053363

An Automated Method of Scanning Probe Microscopy (SPM) Data Analysis and Reactive Site Tracking for Mineral-Water Interface Reactions Observed at the Nanometer Scale

NASA Astrophysics Data System (ADS)

Campbell, B. D.; Higgins, S. R.

2008-12-01

Developing a method for bridging the gap between macroscopic and microscopic measurements of reaction kinetics at the mineral-water interface has important implications in geological and chemical fields. Investigating these reactions on the nanometer scale with SPM is often limited by image analysis and data extraction due to the large quantity of data usually obtained in SPM experiments. Here we present a computer algorithm for automated analysis of mineral-water interface reactions. This algorithm automates the analysis of sequential SPM images by identifying the kinetically active surface sites (i.e., step edges), and by tracking the displacement of these sites from image to image. The step edge positions in each image are readily identified and tracked through time by a standard edge detection algorithm followed by statistical analysis on the Hough Transform of the edge-mapped image. By quantifying this displacement as a function of time, the rate of step edge displacement is determined. Furthermore, the total edge length, also determined from analysis of the Hough Transform, combined with the computed step speed, yields the surface area normalized rate of the reaction. The algorithm was applied to a study of the spiral growth of the calcite(104) surface from supersaturated solutions, yielding results almost 20 times faster than performing this analysis by hand, with results being statistically similar for both analysis methods. This advance in analysis of kinetic data from SPM images will facilitate the building of experimental databases on the microscopic kinetics of mineral-water interface reactions.

Characterization of pulsed flow attenuation on a regulated montane river

NASA Astrophysics Data System (ADS)

Fong, C. S.; Yarnell, S. M.; Fleenor, W. E.; Viers, J. H.

2013-12-01

A major benefit of hydropower is its ability to respond quickly to fluctuating electrical loads. However, the sharp changes in discharge caused by this practice have detrimental environmental effects downstream. This study investigated the effects of hydrograph shape on attenuation of regulated pulsed flow events by first categorizing, then modeling the downstream movement of representative pulses on the upper Tuolumne River below Holm Powerhouse in the Sierra Nevada mountains of California. This system was managed by a public utility and produced flow pulses primarily for hydroelectricity generation and/or whitewater recreation. Operations were highly influenced by a system-wide "Water First" policy, which prioritized drinking water supply and quality over other beneficial uses. Pulses were therefore associated with a spectrum of time scales, from predetermined schedules decided far in advance to hydropeaking operations responding to real-time demands. We extracted underlying hydrograph shape patterns using principal component analysis on individual pulsed flow events released from 1988-2012 (n=4439). From principal component loadings, six shape categories were determined: rectangular, front-step, back-step, goalpost, centered tower, and other. The rectangular and stepped shapes were the most frequent, composing 62% and 24% of total events, respectively. The rectangular shape was often produced by 'standard' hydropeaking or recreational releases, while the stepped shapes were often used for water conservation or were recreational flows bordered by periods of electricity generation. The stepped shape increased in occurrence after the "Water First" policy took effect in 1993 and dominated two drier years (2007 and 2009). After categorization by shape, magnitude and durational indices were used to fabricate representative pulsed flow events. Attenuation of these representative pulses was then modeled using a 1D hydraulic model of 42 river km prepared in HEC-RAS. As no operational measures or physical structures existed within the system to counter the adverse effects of pulsed flow events, natural attenuation was the only potential major mitigation agent. However, model results demonstrated a clear durational threshold for representative pulses (~ 3-5 hrs) over which the degree of attenuation of ramping rates and peak discharge approached a limit. These thresholds were unique to the study reach and were dependent upon river morphology, bed characteristics, and flow rates. Increasing baseflows did not necessarily increase attenuation of pulses, most likely due to minimal increases in bed friction forces in this fairly steep and confined channel. Simulations of front and back-step representative pulses showed trade-offs between attenuation of peak magnitudes and steepness of ramping rates. Finally, a range of rising ramping rates were shown to steepen downstream above initial rates due to the study reach's channel morphology. Reshaping pulses to be more ecologically benign at all points downstream was infeasible if the system was required to maintain current electricity production and recreational service levels.

Transient shear viscosity of weakly aggregating polystyrene latex dispersions

NASA Astrophysics Data System (ADS)

de Rooij, R.; Potanin, A. A.; van den Ende, D.; Mellema, J.

1994-04-01

The transient behavior of the viscosity (stress growth) of a weakly aggregating polystyrene latex dispersion after a step from a high shear rate to a lower shear rate has been measured and modeled. Single particles cluster together into spherical fractal aggregates. The steady state size of these aggregates is determined by the shear stresses exerted on the latter by the flow field. The restructuring process taking place when going from a starting situation with monodisperse spherical aggregates to larger monodisperse spherical aggregates is described by the capture of primary fractal aggregates by growing aggregates until a new steady state is reached. It is assumed that the aggregation mechanism is diffusion limited. The model is valid if the radii of primary aggregates Rprim are much smaller than the radii of the growing aggregates. Fitting the model to experimental data at two volume fractions and a number of step sizes in shear rate yielded physically reasonable values of Rprim at fractal dimensions 2.1≤df≤2.2. The latter range is in good agreement with the range 2.0≤df≤2.3 obtained from steady shear results. The experimental data have also been fitted to a numerical solution of the diffusion equation for primary aggregates for a cell model with moving boundary, also yielding 2.1≤df≤2.2. The range for df found from both approaches agrees well with the range df≊2.1-2.2 determined from computer simulations on diffusion-limited aggregation including restructuring or thermal breakup after formation of bonds. Thus a simple model has been put forward which may capture the basic features of the aggregating model dispersion on a microstructural level and leads to physically acceptable parameter values.

The accuracy of matrix population model projections for coniferous trees in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, P.J.; Stephenson, N.L.

2005-01-01

1 We assess the use of simple, size-based matrix population models for projecting population trends for six coniferous tree species in the Sierra Nevada, California. We used demographic data from 16 673 trees in 15 permanent plots to create 17 separate time-invariant, density-independent population projection models, and determined differences between trends projected from initial surveys with a 5-year interval and observed data during two subsequent 5-year time steps. 2 We detected departures from the assumptions of the matrix modelling approach in terms of strong growth autocorrelations. We also found evidence of observation errors for measurements of tree growth and, to a more limited degree, recruitment. Loglinear analysis provided evidence of significant temporal variation in demographic rates for only two of the 17 populations. 3 Total population sizes were strongly predicted by model projections, although population dynamics were dominated by carryover from the previous 5-year time step (i.e. there were few cases of recruitment or death). Fractional changes to overall population sizes were less well predicted. Compared with a null model and a simple demographic model lacking size structure, matrix model projections were better able to predict total population sizes, although the differences were not statistically significant. Matrix model projections were also able to predict short-term rates of survival, growth and recruitment. Mortality frequencies were not well predicted. 4 Our results suggest that simple size-structured models can accurately project future short-term changes for some tree populations. However, not all populations were well predicted and these simple models would probably become more inaccurate over longer projection intervals. The predictive ability of these models would also be limited by disturbance or other events that destabilize demographic rates. ?? 2005 British Ecological Society.

Kinetics during the redox biotransformation of pollutants mediated by immobilized and soluble humic acids.

PubMed

Cervantes, Francisco J; Martínez, Claudia M; Gonzalez-Estrella, Jorge; Márquez, Arturo; Arriaga, Sonia

2013-03-01

The aim of this study was to elucidate the kinetic constraints during the redox biotransformation of the azo dye, Reactive Red 2 (RR2), and carbon tetrachloride (CT) mediated by soluble humic acids (HAs) and immobilized humic acids (HAi), as well as by the quinoid model compounds, anthraquinone-2,6-disulfonate (AQDS) and 1,2-naphthoquinone-4-sulfonate (NQS). The microbial reduction of both HAs and HAi by anaerobic granular sludge (AGS) was the rate-limiting step during decolorization of RR2 since the reduction of RR2 by reduced HAi proceeded at more than three orders of magnitute faster than the electron-transferring rate observed during the microbial reduction of HAi by AGS. Similarly, the reduction of RR2 by reduced AQDS proceeded 1.6- and 1.9-fold faster than the microbial reduction of AQDS by AGS when this redox mediator (RM) was supplied in soluble and immobilized form, respectively. In contrast, the reduction of NQS by AGS occurred 1.6- and 19.2-fold faster than the chemical reduction of RR2 by reduced NQS when this RM was supplied in soluble and immobilized form, respectively. The microbial reduction of HAs and HAi by a humus-reducing consortium proceeded 1,400- and 790-fold faster than the transfer of electrons from reduced HAs and HAi, respectively, to achieve the reductive dechlorination of CT to chloroform. Overall, the present study provides elucidation on the rate-limiting steps involved in the redox biotransformation of priority pollutants mediated by both HAs and HAi and offers technical suggestions to overcome the kinetic restrictions identified in the redox reactions evaluated.

Role of protons in the pump cycle of KdpFABC investigated by time-resolved kinetic experiments.

PubMed

Damnjanovic, Bojana; Apell, Hans-Jürgen

2014-05-20

The time-resolved kinetics of the KdpFABC complex solubilized in Aminoxide WS-35 was investigated by ATP concentration jump experiments. ATP was photoreleased from its inactive precursor, caged ATP, and charge movements in the membrane domain of the KdpFABC were detected by the electrochromic dye RH421. At low ATP concentrations, the ATP binding step became rate-limiting with an apparent, pH-independent ATP binding affinity of ~70 μM. At saturating ATP concentrations, the rate-limiting step is the conformational transition (E1-P → P-E2) with a rate constant of ~1.7 s(-1) at 20 °C that was independent of K(+) concentration. This observation together with the detected fluorescence decrease indicates that K(+) (or another positive ion) is bound in the membrane domain after enzyme phosphorylation and the conformational transition to the P-E2 state. pH dependence experiments revealed different roles of H(+) in the transport mechanism. Two different functions of protons for the ion pump must be distinguished. On one hand, there are electrogenically bound "functional" protons, which are not transported but prerequisite for the performance of the ATP-driven half-cycle. On the other hand, protons bind to the transport sites, acting as weak congeners of K(+). There possibly are noncompetitively bound protons, affecting the enzyme activity and/or coupling between KdpA and KdpB subunits. Finally, the recently proposed Post-Albers model for the KdpFABC complex was supplemented with stoichiometry factors of 2 for K(+) and 3 for H(+), and additional inhibitory side reactions controlled by H(+) were introduced, which are relevant at pH <6.5 and/or in the absence of K(+).

Fundamental rate-loss tradeoff for optical quantum key distribution.

PubMed

Takeoka, Masahiro; Guha, Saikat; Wilde, Mark M

2014-10-24

Since 1984, various optical quantum key distribution (QKD) protocols have been proposed and examined. In all of them, the rate of secret key generation decays exponentially with distance. A natural and fundamental question is then whether there are yet-to-be discovered optical QKD protocols (without quantum repeaters) that could circumvent this rate-distance tradeoff. This paper provides a major step towards answering this question. Here we show that the secret key agreement capacity of a lossy and noisy optical channel assisted by unlimited two-way public classical communication is limited by an upper bound that is solely a function of the channel loss, regardless of how much optical power the protocol may use. Our result has major implications for understanding the secret key agreement capacity of optical channels-a long-standing open problem in optical quantum information theory-and strongly suggests a real need for quantum repeaters to perform QKD at high rates over long distances.

77 FR 56895 - Self-Regulatory Organizations; New York Stock Exchange LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-14

... Transaction Fees To Eliminate the Step-Up Rate for Non-Floor Broker Transactions September 10, 2012. Pursuant... its Price List to eliminate the step-up rate for non-Floor broker transactions. The text of the... its Price List to eliminate the step-up rate for non-Floor broker transactions. The Exchange proposes...

The influence of the region of interest width on two-dimensional speckle tracking-based measurements of strain and strain rate.

PubMed

Spriestersbach, Hendrik; Oh-Icí, Darach; Schmitt, Boris; Berger, Felix; Schmitz, Lothar

2015-01-01

There are significant variations in the published normal values of two-dimensional speckle tracking-derived strain and strain rate. These occur even when authors use the same software. To measure strain, the operator creates a region of interest (ROI) to define the myocardium to be analyzed. The purpose of this study was to test the hypothesis that measurements vary significantly with the chosen ROI width. In 20 healthy subjects (11 males, mean age 17.6 ± 6.18 years) an apical four-chamber view (4CH) and parasternal short-axis view (SAX) were analyzed. Initially ROI width was set automatically by the software. Two subsequent measurements were obtained from each cine loop by choosing the ROI width one step narrower and one step wider than the automatic ROI width. The mean differences between the measurements of narrower and automatic ROI and between automatic and wider ROI were -1.8 ± 0.7% and -0.9 ± 0.5% for global longitudinal strain (SL), -2.2 ± 0.6% and -1.7 ± 0.7% for global circumferential strain (SC), -0.10 ± 0.06/sec and -0.07 ± 0.06/sec for global longitudinal strain rate (SrL), and -0.15 ± 0.09/sec and -0.12 ± 0.07/sec for global circumferential strain rate (SrC) (all P < 0.000). This corresponds to a relative difference to the mean of both measurements of -4.4 to -11.0%. Layer-specific myocardial deformation and curvature dependency lead to an inverse correlation between the chosen ROI width and strain and strain rate measurements. Just one step of ROI-width change leads to a significant bias. Precise ROI-width definition is essential but technical factors limit its feasibility. © 2014, Wiley Periodicals, Inc.

Development of Ultra-Fine Multigroup Cross Section Library of the AMPX/SCALE Code Packages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeon, Byoung Kyu; Sik Yang, Won; Kim, Kang Seog

The Consortium for Advanced Simulation of Light Water Reactors Virtual Environment for Reactor Applications (VERA) neutronic simulator MPACT is being developed by Oak Ridge National Laboratory and the University of Michigan for various reactor applications. The MPACT and simplified MPACT 51- and 252-group cross section libraries have been developed for the MPACT neutron transport calculations by using the AMPX and Standardized Computer Analyses for Licensing Evaluations (SCALE) code packages developed at Oak Ridge National Laboratory. It has been noted that the conventional AMPX/SCALE procedure has limited applications for fast-spectrum systems such as boiling water reactor (BWR) fuels with very highmore » void fractions and fast reactor fuels because of its poor accuracy in unresolved and fast energy regions. This lack of accuracy can introduce additional error sources to MPACT calculations, which is already limited by the Bondarenko approach for resolved resonance self-shielding calculation. To enhance the prediction accuracy of MPACT for fast-spectrum reactor analyses, the accuracy of the AMPX/SCALE code packages should be improved first. The purpose of this study is to identify the major problems of the AMPX/SCALE procedure in generating fast-spectrum cross sections and to devise ways to improve the accuracy. For this, various benchmark problems including a typical pressurized water reactor fuel, BWR fuels with various void fractions, and several fast reactor fuels were analyzed using the AMPX 252-group libraries. Isotopic reaction rates were determined by SCALE multigroup (MG) calculations and compared with continuous energy (CE) Monte Carlo calculation results. This reaction rate analysis revealed three main contributors to the observed differences in reactivity and reaction rates: (1) the limitation of the Bondarenko approach in coarse energy group structure, (2) the normalization issue of probability tables, and (3) neglect of the self-shielding effect of resonance-like cross sections at high energy range such as (n,p) cross section of Cl35. The first error source can be eliminated by an ultra-fine group (UFG) structure in which the broad scattering resonances of intermediate-weight nuclides can be represented accurately by a piecewise constant function. A UFG AMPX library was generated with modified probability tables and tested against various benchmark problems. The reactivity and reaction rates determined with the new UFG AMPX library agreed very well with respect to Monte Carlo Neutral Particle (MCNP) results. To enhance the lattice calculation accuracy without significantly increasing the computational time, performing the UFG lattice calculation in two steps was proposed. In the first step, a UFG slowing-down calculation is performed for the corresponding homogenized composition, and UFG cross sections are collapsed into an intermediate group structure. In the second step, the lattice calculation is performed for the intermediate group level using the condensed group cross sections. A preliminary test showed that the condensed library reproduces the results obtained with the UFG cross section library. This result suggests that the proposed two-step lattice calculation approach is a promising option to enhance the applicability of the AMPX/SCALE system to fast system analysis.« less

Disilane chemisorption on Si(x)Ge(1-x)(100)-(2 x 1): molecular mechanisms and implications for film growth rates.

PubMed

Ng, Rachel Qiao-Ming; Tok, E S; Kang, H Chuan

2009-07-28

At low temperatures, hydrogen desorption is known to be the rate-limiting process in silicon germanium film growth via chemical vapor deposition. Since surface germanium lowers the hydrogen desorption barrier, Si(x)Ge((1-x)) film growth rate increases with the surface germanium fraction. At high temperatures, however, the molecular mechanisms determining the epitaxial growth rate are not well established despite much experimental work. We investigate these mechanisms in the context of disilane adsorption because disilane is an important precursor used in film growth. In particular, we want to understand the molecular steps that lead, in the high temperature regime, to a decrease in growth rate as the surface germanium increases. In addition, there is a need to consider the issue of whether disilane adsorbs via silicon-silicon bond dissociation or via silicon-hydrogen bond dissociation. It is usually assumed that disilane adsorption occurs via silicon-silicon bond dissociation, but in recent work we provided theoretical evidence that silicon-hydrogen bond dissociation is more important. In order to address these issues, we calculate the chemisorption barriers for disilane on silicon germanium using first-principles density functional theory methods. We use the calculated barriers to estimate film growth rates that are then critically compared to the experimental data. This enables us to establish a connection between the dependence of the film growth rate on the surface germanium content and the kinetics of the initial adsorption step. We show that the generally accepted mechanism where disilane chemisorbs via silicon-silicon bond dissociation is not consistent with the data for film growth kinetics. Silicon-hydrogen bond dissociation paths have to be included in order to give good agreement with the experimental data for high temperature film growth rate.

A novel integrated step-feed biofilm process for the treatment of decentralized domestic wastewater in rural areas of China.

PubMed

Liang, Hanwen; Gao, Min; Liu, Junxin; Wei, Yuansong; Guo, Xuesong

2010-01-01

For wastewater treatment in rural areas, a novel three-stage step-feed wastewater treatment system, combined with a drop-aeration biofilm process, was tested in the laboratory to investigate its performance in removing suspended solids (SS), chemical oxygen demand (COD), NH4(+)-N, total nitrogen (TN), and total phosphorus (TP). The removal rates of SS, COD and NH4(+)-N were 90%, 80%, and 90% in effluent concentrations less than 10 mg/L, 50 mg/L and 8 mg/L, respectively. The TP removal rate was less satisfactory. The C/N ratio in the raw wastewater was often less than 3.5, and the removal efficiency of TN was therefore limited. A carbon-release batch experiment was carried out to measure the feasibility of enhancing denitrification at low influent C/N ratios. The result showed that the C/N could be over 9.0 in the supernatant. Polymerase chain reaction denaturing gradient gel electrophoresis technology was used to reveal the changes in the bacterial community during different stages of the integrated step-feed biofilm process. The results showed that banding patterns and the distribution of dominant bands for the same experimental period in different aerobic zones were similar. Phylogenetic analysis indicated that lanes 10, 11 and 12, which presented three aerobic zones at the same operation period, had the closest phylogenetic relationship among the lanes.

Controlled loading of cryoprotectants (CPAs) to oocyte with linear and complex CPA profiles on a microfluidic platform.

PubMed

Heo, Yun Seok; Lee, Ho-Joon; Hassell, Bryan A; Irimia, Daniel; Toth, Thomas L; Elmoazzen, Heidi; Toner, Mehmet

2011-10-21

Oocyte cryopreservation has become an essential tool in the treatment of infertility by preserving oocytes for women undergoing chemotherapy. However, despite recent advances, pregnancy rates from all cryopreserved oocytes remain low. The inevitable use of the cryoprotectants (CPAs) during preservation affects the viability of the preserved oocytes and pregnancy rates either through CPA toxicity or osmotic injury. Current protocols attempt to reduce CPA toxicity by minimizing CPA concentrations, or by minimizing the volume changes via the step-wise addition of CPAs to the cells. Although the step-wise addition decreases osmotic shock to oocytes, it unfortunately increases toxic injuries due to the long exposure times to CPAs. To address limitations of current protocols and to rationally design protocols that minimize the exposure to CPAs, we developed a microfluidic device for the quantitative measurements of oocyte volume during various CPA loading protocols. We spatially secured a single oocyte on the microfluidic device, created precisely controlled continuous CPA profiles (step-wise, linear and complex) for the addition of CPAs to the oocyte and measured the oocyte volumetric response to each profile. With both linear and complex profiles, we were able to load 1.5 M propanediol to oocytes in less than 15 min and with a volumetric change of less than 10%. Thus, we believe this single oocyte analysis technology will eventually help future advances in assisted reproductive technologies and fertility preservation.

Preparation of epoxy-based macroporous monolithic columns for the fast and efficient immunofiltration of Staphylococcus aureus.

PubMed

Ott, Sonja; Niessner, Reinhard; Seidel, Michael

2011-08-01

Macroporous epoxy-based monolithic columns were used for immunofiltration of bacteria. The prepared monolithic polymer support is hydrophilic and has large pore sizes of 21 μm without mesopores. A surface chemistry usually applied for immobilization of antibodies on glass slides is successfully transferred to monolithic columns. Step-by-step, the surface of the epoxy-based monolith is hydrolyzed, silanized, coated with poly(ethylene glycol diamine) and activated with the homobifunctional crosslinker di(N-succinimidyl)carbonate for immobilization of antibodies on the monolithic columns. The functionalization steps are characterized to ensure the coating of each monolayer. The prepared antibody-immobilized monolithic column is optimized for immunofiltration to enrich Staphylococcus aureus as an important food contaminant. Different kinds of geometries of monolithic columns, flow rates and elution buffers are tested with the goal to get high recoveries in the shortest enrichment time as possible. An effective capture of S. aureus was achieved at a flow rate of 7.0 mL/min with low backpressures of 20.1±5.4 mbar enabling a volumetric enrichment of 1000 within 145 min. The bacteria were quantified by flow cytometry using a double-labeling approach. After immunofiltration the sensitivity was significantly increased and a detection limit of the total system of 42 S. aureus/mL was reached. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zeolite catalysis in the synthesis of isobutylene from hydrous ethanol

NASA Astrophysics Data System (ADS)

Phillips, Cory Bernard

1999-11-01

This work deals with the synthesis of isobutylene from a hydrous ethanol feedstock over zeolites. The synthesis is accomplished in three steps: (1) low-temperature direct ethanol conversion to ethylene on H-ZSM-5 zeolite, (2) ethylene conversion to butene products over metal-exchanged zeolites, and (3) butene skeletal rearrangement to isobutylene over FER zeolites. The key to understanding and optimizing each synthesis step lies in the ability to control and regulate the zeolite acidity (Bronsted and Lewis)---both strength and number. Therefore, the continuous temperature programmed amine desorption (CTPAD) technique was further developed to simultaneously count the Bronsted acid sites and quantitatively characterize their strength. The adsorption of ethanol, reaction products, amines, coke and ethanol-derived residue (EDR) were monitored gravimetrically using the highly sensitive, novel Tapered Element Oscillating Microreactor (TEOM) apparatus. The TEOM was also used also in conjunction with CTPAD to characterize Bronsted acidity which is a new application for the instrument. For the first synthesis step, a parallel reaction exists which simultaneously produces diethyl ether and ethylene directly over H-ZSM-5. The reaction rates for each pathway were measured directly using a differential reactor operating at low temperatures (<473 K). Water in the ethanol feed enhances the rate of ethylene formation. A mechanism and kinetic expression are proposed for this reaction over H-ZSM-5, with diethyl-ether desorption and ethylene formation as the rate limiting steps. Heat of adsorption values measured from the independent microcalorimetry work reported in the literature are incorporated into the kinetic analysis which reduces the number of regressed parameters. For the remaining synthesis steps, several zeolite structures (ZSM-5, Y, FER) partially exchanged with Pd, Ti, Ni and Au were prepared and tested. It was determined from this screening study that the zeolites containing Pd are the most efficient catalysts for the dimerization reaction. Characterization results from x-ray diffraction (XRD), electron paramagnetic resonance (EPR) spectroscopy, and CTPAD suggest a stable, Pd species with a low oxidation state as part of the active site in Pd-exchanged zeolites. Isobutylene was present in the C4 fraction at reasonable quantities for most of the catalyst candidates, especially those containing an alkali metal co-cation.

l-Tartaric acid synthesis from vitamin C in higher plants

PubMed Central

DeBolt, Seth; Cook, Douglas R.; Ford, Christopher M.

2006-01-01

The biosynthetic pathway of l-tartaric acid, the form most commonly encountered in nature, and its catabolic ties to vitamin C, remain a challenge to plant scientists. Vitamin C and l-tartaric acid are plant-derived metabolites with intrinsic human value. In contrast to most fruits during development, grapes accumulate l-tartaric acid, which remains within the berry throughout ripening. Berry taste and the organoleptic properties and aging potential of wines are intimately linked to levels of l-tartaric acid present in the fruit, and those added during vinification. Elucidation of the reactions relating l-tartaric acid to vitamin C catabolism in the Vitaceae showed that they proceed via the oxidation of l-idonic acid, the proposed rate-limiting step in the pathway. Here we report the use of transcript and metabolite profiling to identify candidate cDNAs from genes expressed at developmental times and in tissues appropriate for l-tartaric acid biosynthesis in grape berries. Enzymological analyses of one candidate confirmed its activity in the proposed rate-limiting step of the direct pathway from vitamin C to tartaric acid in higher plants. Surveying organic acid content in Vitis and related genera, we have identified a non-tartrate-forming species in which this gene is deleted. This species accumulates in excess of three times the levels of vitamin C than comparably ripe berries of tartrate-accumulating species, suggesting that modulation of tartaric acid biosynthesis may provide a rational basis for the production of grapes rich in vitamin C. PMID:16567629

Mutation in cyclophilin B that causes hyperelastosis cutis in American Quarter Horse does not affect peptidylprolyl cis-trans isomerase activity but shows altered cyclophilin B-protein interactions and affects collagen folding.

PubMed

Ishikawa, Yoshihiro; Vranka, Janice A; Boudko, Sergei P; Pokidysheva, Elena; Mizuno, Kazunori; Zientek, Keith; Keene, Douglas R; Rashmir-Raven, Ann M; Nagata, Kazuhiro; Winand, Nena J; Bächinger, Hans Peter

2012-06-22

The rate-limiting step of folding of the collagen triple helix is catalyzed by cyclophilin B (CypB). The G6R mutation in cyclophilin B found in the American Quarter Horse leads to autosomal recessive hyperelastosis cutis, also known as hereditary equine regional dermal asthenia. The mutant protein shows small structural changes in the region of the mutation at the side opposite the catalytic domain of CypB. The peptidylprolyl cis-trans isomerase activity of the mutant CypB is normal when analyzed in vitro. However, the biosynthesis of type I collagen in affected horse fibroblasts shows a delay in folding and secretion and a decrease in hydroxylysine and glucosyl-galactosyl hydroxylysine. This leads to changes in the structure of collagen fibrils in tendon, similar to those observed in P3H1 null mice. In contrast to cyclophilin B null mice, where little 3-hydroxylation was found in type I collagen, 3-hydroxylation of type I collagen in affected horses is normal. The mutation disrupts the interaction of cyclophilin B with the P-domain of calreticulin, with lysyl hydroxylase 1, and probably other proteins, such as the formation of the P3H1·CypB·cartilage-associated protein complex, resulting in less effective catalysis of the rate-limiting step in collagen folding in the rough endoplasmic reticulum.

Studies of Cu adatom island ripening on Cu(100) by LEEM

NASA Astrophysics Data System (ADS)

Bussmann, Ezra; Kellogg, Gary L.

2007-03-01

Simple metal surfaces are model systems for characterizing kinetic processes governing the growth and stability of nanoscale structures. It is generally presumed that diffusive transport of adatoms across terraces determines the rate of these processes. However, STM studies in the temperature range T˜330-420 K reveal that transport between step edges on the Cu(100) surface is limited by detachment barriers at the step edges, rather than by the adatom diffusion barrier.^1 This is because on the Cu(100) surface, mass transport is mediated primarily by vacancies, instead of adatoms. We have used low energy electron microscopy (LEEM) movies to characterize coarsening of Cu islands on the Cu(100) surface in the range T˜460-560 K. By measuring the temperature dependence of the island decay rate we find an activation barrier of 0.9±0.1 eV. This value is comparable to the 0.80±0.03 eV barrier found in STM studies.^1 However, we are not able to conclude that transport is entirely detachment limited at these elevated temperatures. This work serves as background to establish whether or not Pd alloying in the Cu(100) surface will slow Cu surface transport. ^2 1. C. Kl"unker, et al., PRB 58, R7556 (1998). 2. M. L. Grant, et al., PRL 86, 4588 (2001). Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. DOE NNSA, Contract No. DE-AC04-94AL85000.

Mutation in Cyclophilin B That Causes Hyperelastosis Cutis in American Quarter Horse Does Not Affect Peptidylprolyl cis-trans Isomerase Activity but Shows Altered Cyclophilin B-Protein Interactions and Affects Collagen Folding*

PubMed Central

Ishikawa, Yoshihiro; Vranka, Janice A.; Boudko, Sergei P.; Pokidysheva, Elena; Mizuno, Kazunori; Zientek, Keith; Keene, Douglas R.; Rashmir-Raven, Ann M.; Nagata, Kazuhiro; Winand, Nena J.; Bächinger, Hans Peter

2012-01-01

The rate-limiting step of folding of the collagen triple helix is catalyzed by cyclophilin B (CypB). The G6R mutation in cyclophilin B found in the American Quarter Horse leads to autosomal recessive hyperelastosis cutis, also known as hereditary equine regional dermal asthenia. The mutant protein shows small structural changes in the region of the mutation at the side opposite the catalytic domain of CypB. The peptidylprolyl cis-trans isomerase activity of the mutant CypB is normal when analyzed in vitro. However, the biosynthesis of type I collagen in affected horse fibroblasts shows a delay in folding and secretion and a decrease in hydroxylysine and glucosyl-galactosyl hydroxylysine. This leads to changes in the structure of collagen fibrils in tendon, similar to those observed in P3H1 null mice. In contrast to cyclophilin B null mice, where little 3-hydroxylation was found in type I collagen, 3-hydroxylation of type I collagen in affected horses is normal. The mutation disrupts the interaction of cyclophilin B with the P-domain of calreticulin, with lysyl hydroxylase 1, and probably other proteins, such as the formation of the P3H1·CypB·cartilage-associated protein complex, resulting in less effective catalysis of the rate-limiting step in collagen folding in the rough endoplasmic reticulum. PMID:22556420

Running retraining to treat lower limb injuries: a mixed-methods study of current evidence synthesised with expert opinion.

PubMed

Barton, C J; Bonanno, D R; Carr, J; Neal, B S; Malliaras, P; Franklyn-Miller, A; Menz, H B

2016-05-01

Running-related injuries are highly prevalent. Synthesise published evidence with international expert opinion on the use of running retraining when treating lower limb injuries. Mixed methods. A systematic review of clinical and biomechanical findings related to running retraining interventions were synthesised and combined with semistructured interviews with 16 international experts covering clinical reasoning related to the implementation of running retraining. Limited evidence supports the effectiveness of transition from rearfoot to forefoot or midfoot strike and increase step rate or altering proximal mechanics in individuals with anterior exertional lower leg pain; and visual and verbal feedback to reduce hip adduction in females with patellofemoral pain. Despite the paucity of clinical evidence, experts recommended running retraining for: iliotibial band syndrome; plantar fasciopathy (fasciitis); Achilles, patellar, proximal hamstring and gluteal tendinopathy; calf pain; and medial tibial stress syndrome. Tailoring approaches to each injury and individual was recommended to optimise outcomes. Substantial evidence exists for the immediate biomechanical effects of running retraining interventions (46 studies), including evaluation of step rate and strike pattern manipulation, strategies to alter proximal kinematics and cues to reduce impact loading variables. Our synthesis of published evidence related to clinical outcomes and biomechanical effects with expert opinion indicates running retraining warrants consideration in the treatment of lower limb injuries in clinical practice. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding.

PubMed Central

Woenckhaus, J; Köhling, R; Thiyagarajan, P; Littrell, K C; Seifert, S; Royer, C A; Winter, R

2001-01-01

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique. PMID:11222312

Inhibiting renin angiotensin system in rate limiting step by aliskiren as a new approach for preventing indomethacin induced gastric ulcers.

PubMed

Halici, Zekai; Polat, Beyzagul; Cadirci, Elif; Topcu, Atilla; Karakus, Emre; Kose, Duygu; Albayrak, Abdulmecit; Bayir, Yasin

2016-10-25

Previously blocking the renin angiotensin system (RAAS) has been effective in the prevention of gastric damage. Therefore, the aim of this study was to investigate the effects of aliskiren, and thus, direct renin blockage, in indomethacin-induced gastric damage model. Effects of aliskiren were evaluated in indomethacin-induced gastric damage model on Albino Wistar rats. Effects of famotidine has been investigated as standard antiulcer agent. Stereological analyses for ulcer area determination, biochemical analyses for oxidative status determination and molecular analyses for tissue cytokine and cyclooxygenase determination were performed on stomach tissues. In addition, to clarify antiulcer effect mechanism of aliskiren pylorus ligation-induced gastric acid secretion model was applied on rats. Aliskiren was able to inhibit indomethacin-induced ulcer formation. It also inhibited renin, and thus, decreased over-produced Angiotensin-II during ulcer formation. Aliskiren improved the oxidative status and cytokine profile of the stomach, which was most probably impaired by increased Angiotensin II concentration. Aliskiren also increased gastroprotective prostaglandin E2 concentration. Finally, aliskiren did not change the gastric acidity in pylorus ligation model. Aliskiren exerted its protective effects on stomach tissue by decreasing inflammatory cytokines and oxidative stress as a result of inhibiting the RAAS, at a rate-limiting step, as well as its end product, angiotensin II. Aliskiren also significantly increased protective factors such as PGE2, but not affect aggressive factors such as gastric acidity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Design and status of the RF-digitizer integrated circuit

NASA Technical Reports Server (NTRS)

Rayhrer, B.; Lam, B.; Young, L. E.; Srinivasan, J. M.; Thomas, J. B.

1991-01-01

An integrated circuit currently under development samples a bandpass-limited signal at a radio frequency in quadrature and then performs a simple sum-and-dump operation in order to filter and lower the rate of the samples. Downconversion to baseband is carried out by the sampling step itself through the aliasing effect of an appropriately selected subharmonic sampling frequency. Two complete RF digitizer circuits with these functions will be implemented with analog and digital elements on one GaAs substrate. An input signal, with a carrier frequency as high as 8 GHz, can be sampled at a rate as high as 600 Msamples/sec for each quadrature component. The initial version of the chip will sign-sample (1-bit) the input RF signal. The chip will contain a synthesizer to generate a sample frequency that is a selectable integer multiple of an input reference frequency. In addition to the usual advantages of compactness and reliability associated with integrated circuits, the single chip will replace several steps required by standard analog downconversion. Furthermore, when a very high initial sample rate is selected, the presampling analog filters can be given very large bandwidths, thereby greatly reducing phase and delay instabilities typically introduced by such filters, as well as phase and delay variation due to Doppler changes.

Dissolution-modulating mechanism of pH modifiers in solid dispersion containing weakly acidic or basic drugs with poor water solubility.

PubMed

Tran, Phuong Ha-Lien; Tran, Thao Truong-Dinh; Lee, Kyoung-Ho; Kim, Dong-Jin; Lee, Beom-Jin

2010-05-01

Although the solid dispersion method has been known to increase the dissolution rate of poorly water-soluble drugs by dispersing them in hydrophilic carriers, one obstacle of the solid dispersion method is its limited solubilization capacity, especially for pH-dependent soluble drugs. pH-modified solid dispersion, in which pH modifiers are incorporated, may be a useful method for increasing the dissolution rate of weakly acidic or basic drugs. Sufficient research, including the most recent reports, was undertaken in this review. How could the inclusion of the pH the pH modifiers in the solid dispersion system change drug structural behaviors, molecular interactions, microenvironmental pH, and/or release rate of pH modifiers, relating with the enhanced dissolution of weakly acidic or weakly basic drugs with poor water solubility? These questions have been investigated to determine the dissolution-modulating mechanism of pH modifiers in solid dispersion containing weakly acidic or basic drugs. It is believed that step-by-step mechanistic approaches could provide the ultimate solution for solubilizing several poorly water-soluble drugs with pH-dependent solubility from a solid dispersion system, as well as provide ideas for developing future dosage systems.

Correlation between cross-bridge kinetics obtained from Trp fluorescence of myofibril suspensions and mechanical studies of single muscle fibers in rabbit psoas.

PubMed

Candau, Robin; Kawai, Masataka

2011-12-01

Our goal is to correlate kinetic constants obtained from fluorescence studies of myofibril suspension with those from mechanical studies of skinned muscle fibers from rabbit psoas. In myofibril studies, the stopped-flow technique with tryptophan fluorescence was used; in muscle fiber studies, tension transients with small amplitude sinusoidal length perturbations were used. All experiments were performed using the equivalent solution conditions (200 mM ionic strength, pH 7.00) at 10°C. The concentration of MgATP was varied to characterize kinetic constants of the ATP binding step 1 (K (1): dissociation constant), the binding induced cross-bridge detachment step 2 (k (2), k (-2): rate constants), and the ATP cleavage step 3 (k (3), k (-3)). In myofibrils we found that K (1) = 0.52 ± 0.08 mM (±95% confidence limits), k (2) = 242 ± 24 s(-1), and k (-2) ≈ 0; in muscle fibers, K (1) = 0.46 ± 0.06 mM, k (2) = 286 ± 32 s(-1), and k (-2) = 57 ± 21 s(-1). From these results, we conclude that myofibrils and muscle fibers exhibit nearly equal ATP binding step, and nearly equal ATP binding induced cross-bridge detachment step. Consequently, there is a good correlation between process C (phase 2 of step analysis) and the cross-bridge detachment step. The reverse detachment step is finite in fibers, but almost absent in myofibrils. We further studied partially cross-linked myofibrils and found little change in steps 2 and 3, indicating that cross-linking does not affect these steps. However, we found that K (1) is 2.5× of native myofibrils, indicating that MgATP binding is weakened by the presence of the extra load. We further studied the phosphate (Pi) effect in myofibrils, and found that Pi is a competitive inhibitor of MgATP, with the inhibitory dissociation constant of ~9 mM. Similar results were also deduced from fiber studies. To characterize the ATP cleavage step in myofibrils, we measured the slow rate constant in fluorescence, and found that k (3) + k (-3) = 16 ± 1 s(-1).

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cannon, William; Zucker, Jeremy; Baxter, Douglas

We report the application of a recently proposed approach for modeling biological systems using a maximum entropy production rate principle in lieu of having in vivo rate constants. The method is applied in four steps: (1) a new ODE-based optimization approach based on Marcelin’s 1910 mass action equation is used to obtain the maximum entropy distribution, (2) the predicted metabolite concentrations are compared to those generally expected from experiment using a loss function from which post-translational regulation of enzymes is inferred, (3) the system is re-optimized with the inferred regulation from which rate constants are determined from the metabolite concentrationsmore » and reaction fluxes, and finally (4) a full ODE-based, mass action simulation with rate parameters and allosteric regulation is obtained. From the last step, the power characteristics and resistance of each reaction can be determined. The method is applied to the central metabolism of Neurospora crassa and the flow of material through the three competing pathways of upper glycolysis, the non-oxidative pentose phosphate pathway, and the oxidative pentose phosphate pathway are evaluated as a function of the NADP/NADPH ratio. It is predicted that regulation of phosphofructokinase (PFK) and flow through the pentose phosphate pathway are essential for preventing an extreme level of fructose 1, 6-bisphophate accumulation. Such an extreme level of fructose 1,6-bisphophate would otherwise result in a glassy cytoplasm with limited diffusion, dramatically decreasing the entropy and energy production rate and, consequently, biological competitiveness.« less

Reactivity of chemisorbed oxygen atoms and their catalytic consequences during CH4-O2 catalysis on supported Pt clusters.

PubMed

Chin, Ya-Huei Cathy; Buda, Corneliu; Neurock, Matthew; Iglesia, Enrique

2011-10-12

Kinetic and isotopic data and density functional theory treatments provide evidence for the elementary steps and the active site requirements involved in the four distinct kinetic regimes observed during CH(4) oxidation reactions using O(2), H(2)O, or CO(2) as oxidants on Pt clusters. These four regimes exhibit distinct rate equations because of the involvement of different kinetically relevant steps, predominant adsorbed species, and rate and equilibrium constants for different elementary steps. Transitions among regimes occur as chemisorbed oxygen (O*) coverages change on Pt clusters. O* coverages are given, in turn, by a virtual O(2) pressure, which represents the pressure that would give the prevalent steady-state O* coverages if their adsorption-desorption equilibrium was maintained. The virtual O(2) pressure acts as a surrogate for oxygen chemical potentials at catalytic surfaces and reflects the kinetic coupling between C-H and O═O activation steps. O* coverages and virtual pressures depend on O(2) pressure when O(2) activation is equilibrated and on O(2)/CH(4) ratios when this step becomes irreversible as a result of fast scavenging of O* by CH(4)-derived intermediates. In three of these kinetic regimes, C-H bond activation is the sole kinetically relevant step, but occurs on different active sites, which evolve from oxygen-oxygen (O*-O*), to oxygen-oxygen vacancy (O*-*), and to vacancy-vacancy (*-*) site pairs as O* coverages decrease. On O*-saturated cluster surfaces, O*-O* site pairs activate C-H bonds in CH(4) via homolytic hydrogen abstraction steps that form CH(3) groups with significant radical character and weak interactions with the surface at the transition state. In this regime, rates depend linearly on CH(4) pressure but are independent of O(2) pressure. The observed normal CH(4)/CD(4) kinetic isotope effects are consistent with the kinetic-relevance of C-H bond activation; identical (16)O(2)-(18)O(2) isotopic exchange rates in the presence or absence of CH(4) show that O(2) activation steps are quasi-equilibrated during catalysis. Measured and DFT-derived C-H bond activation barriers are large, because of the weak stabilization of the CH(3) fragments at transition states, but are compensated by the high entropy of these radical-like species. Turnover rates in this regime decrease with increasing Pt dispersion, because low-coordination exposed Pt atoms on small clusters bind O* more strongly than those that reside at low-index facets on large clusters, thus making O* less effective in H-abstraction. As vacancies (*, also exposed Pt atoms) become available on O*-covered surfaces, O*-* site pairs activate C-H bonds via concerted oxidative addition and H-abstraction in transition states effectively stabilized by CH(3) interactions with the vacancies, which lead to much higher turnover rates than on O*-O* pairs. In this regime, O(2) activation becomes irreversible, because fast C-H bond activation steps scavenge O* as it forms. Thus, O* coverages are set by the prevalent O(2)/CH(4) ratios instead of the O(2) pressures. CH(4)/CD(4) kinetic isotope effects are much larger for turnovers mediated by O*-* than by O*-O* site pairs, because C-H (and C-D) activation steps are required to form the * sites involved in C-H bond activation. Turnover rates for CH(4)-O(2) reactions mediated by O*-* pairs decrease with increasing Pt dispersion, as in the case of O*-O* active structures, because stronger O* binding on small clusters leads not only to less reactive O* atoms, but also to lower vacancy concentrations at cluster surfaces. As O(2)/CH(4) ratios and O* coverages become smaller, O(2) activation on bare Pt clusters becomes the sole kinetically relevant step; turnover rates are proportional to O(2) pressures and independent of CH(4) pressure and no CH(4)/CD(4) kinetic isotope effects are observed. In this regime, turnover rates become nearly independent of Pt dispersion, because the O(2) activation step is essentially barrierless. In the absence of O(2), alternate weaker oxidants, such as H(2)O or CO(2), lead to a final kinetic regime in which C-H bond dissociation on *-* pairs at bare cluster surfaces limit CH(4) conversion rates. Rates become first-order in CH(4) and independent of coreactant and normal CH(4)/CD(4) kinetic isotope effects are observed. In this case, turnover rates increase with increasing dispersion, because low-coordination Pt atoms stabilize the C-H bond activation transition states more effectively via stronger binding to CH(3) and H fragments. These findings and their mechanistic interpretations are consistent with all rate and isotopic data and with theoretical estimates of activation barriers and of cluster size effects on transition states. They serve to demonstrate the essential role of the coverage and reactivity of chemisorbed oxygen in determining the type and effectiveness of surface structures in CH(4) oxidation reactions using O(2), H(2)O, or CO(2) as oxidants, as well as the diversity of rate dependencies, activation energies and entropies, and cluster size effects that prevail in these reactions. These results also show how theory and experiments can unravel complex surface chemistries on realistic catalysts under practical conditions and provide through the resulting mechanistic insights specific predictions for the effects of cluster size and surface coordination on turnover rates, the trends and magnitude of which depend sensitively on the nature of the predominant adsorbed intermediates and the kinetically relevant steps.

Influence of calcium on microbial reduction of solid phase uranium(VI).

PubMed

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M; Wang, Zheming

2007-08-15

The effect of calcium on the dissolution and microbial reduction of a representative solid phase uranyl [U(VI)], sodium boltwoodite (NaUO(2)SiO(3)OH . 1.5H(2)O), was investigated to evaluate the rate-limiting step of microbial reduction of the solid phase U(VI). Microbial reduction experiments were performed in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1, in a bicarbonate medium with lactate as electron donor at pH 6.8 buffered with PIPES. Calcium increased the rate of Na-boltwoodite dissolution and U(VI) bioavailability by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) collectively revealed that microbial reduction of solid phase U(VI) was a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. Under studied experimental conditions, the overall rate of microbial reduction of solid phase U(VI) was limited by U(VI) dissolution reactions in solutions without calcium and limited by microbial reduction in solutions with calcium. Generally, the overall rate of microbial reduction of solid phase U(VI) was determined by the coupling of solid phase U(VI) dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) that were all affected by calcium. (c) 2007 Wiley Periodicals, Inc.

5 CFR 531.405 - Waiting periods for within-grade increase.

Code of Federal Regulations, 2010 CFR

2010-01-01

... step 4-52 calendar weeks of creditable service; (ii) Rate of basic pay equal to or greater than the... creditable service; and (iii) Rate of basic pay equal to or greater than the rate of basic pay at step 7-156... step 4-260 days of creditable service in a pay status over a period of not less than 52 calendar weeks...

Modeling the formation of N-nitrosodimethylamine (NDMA) from the reaction of natural organic matter (NOM) with monochloramine.

PubMed

Chen, Zhuo; Valentine, Richard L

2006-12-01

This paper presents mechanistic studies on the formation of NDMA, a newly identified chloramination disinfection byproduct, from reactions of monochloramine with natural organic matter. A kinetic model was developed to validate proposed reactions and to predict NDMA formation in chloraminated water during the time frame of 1-5 days. This involved incorporating NDMA formation reactions into an established comprehensive model describing the oxidation of humic-type natural organic matter by monochloramine. A rate-limiting step involving the oxidation of NOM is theorized to control the rate of NDMA formation which is assumed to be proportional to the rate of NOM oxidized by monochloramine. The applicability of the model to describe NDMA formation in the presence of three NOM sources over a wide range in water quality (i.e., pH, DOC, and ammonia concentrations) was evaluated. Results show that with accurate measurement of monochloramine demand for a specific supply, NDMA formation could be modeled over an extended range of experimental conditions by considering a single NOM source-specific value of thetaNDMA, a stoichiometric coefficient relating the amount of NDMA produced to the amount of NOM oxidized, and several kinetic parameters describing NOM oxidation. Furthermore, the oxidation of NOM is the rate-limiting step governing NDMA formation. This suggests that NDMA formation over a 1-5 day time frame may be estimated from information on the chloramine or free chlorine demand of the NOM and the source-specific linear relationship between this demand and NDMA formation. Although the proposed model has not yet been validated for shorter time periods that may better characterize the residence time in some distribution systems, the improved understanding of the important reactions governing NDMA formation and the resulting model should benefit the water treatment industry as a tool in developing strategies that minimize NDMA formation.

Phase-field modeling of two-dimensional crystal growth with anisotropic diffusion.

PubMed

Meca, Esteban; Shenoy, Vivek B; Lowengrub, John

2013-11-01

In the present article, we introduce a phase-field model for thin-film growth with anisotropic step energy, attachment kinetics, and diffusion, with second-order (thin-interface) corrections. We are mainly interested in the limit in which kinetic anisotropy dominates, and hence we study how the expected shape of a crystallite, which in the long-time limit is the kinetic Wulff shape, is modified by anisotropic diffusion. We present results that prove that anisotropic diffusion plays an important, counterintuitive role in the evolving crystal shape, and we add second-order corrections to the model that provide a significant increase in accuracy for small supersaturations. We also study the effect of different crystal symmetries and discuss the influence of the deposition rate.

Stability limits of unsteady open capillary channel flow

NASA Astrophysics Data System (ADS)

Grah, Aleksander; Haake, Dennis; Rosendahl, Uwe; Klatte, J.?Rg; Dreyer, Michael E.

This paper is concerned with steady and unsteady flow rate limitations in open capillary channels under low-gravity conditions. Capillary channels are widely used in Space technology for liquid transportation and positioning, e.g. in fuel tanks and life support systems. The channel observed in this work consists of two parallel plates bounded by free liquid surfaces along the open sides. The capillary forces of the free surfaces prevent leaking of the liquid and gas ingestion into the flow.In the case of steady stable flow the capillary pressure balances the differential pressure between the liquid and the surrounding constant-pressure gas phase. Increasing the flow rate in small steps causes a decrease of the liquid pressure. A maximum steady flow rate is achieved when the flow rate exceeds a certain limit leading to a collapse of the free surfaces due to the choking effect. In the case of unsteady flow additional dynamic effects take place due to flow rate transition and liquid acceleration. The maximum flow rate is smaller than in the case of steady flow. On the other hand, the choking effect does not necessarily cause surface collapse and stable temporarily choked flow is possible under certain circumstances.To determine the limiting volumetric flow rate and stable flow dynamic properties, a new stability theory for both steady and unsteady flow is introduced. Subcritical and supercritical (choked) flow regimes are defined. Stability criteria are formulated for each flow type. The steady (subcritical) criterion corresponds to the speed index defined by the limiting longitudinal small-amplitude wave speed, similar to the Mach number. The unsteady (supercritical) criterion for choked flow is defined by a new characteristic number, the dynamic index. It is based on pressure balances and reaches unity at the stability limit.The unsteady model based on the Bernoulli equation and the mass balance equation is solved numerically for perfectly wetting incompressible liquids. The unsteady model and the stability theory are verified by comparison to results of a sounding rocket experiment (TEXUS 41) on capillary channel flows launched in December 2005 from ESRANGE in north Sweden. For a clear overview of subcritical, supercritical, and unstable flow, parametric studies and stability diagrams are shown and compared to experimental observations.

Analysis of reaction schemes using maximum rates of constituent steps

PubMed Central

Motagamwala, Ali Hussain; Dumesic, James A.

2016-01-01

We show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, rmax,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of rmax,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of rmax,i can be used to predict the rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. This approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps. PMID:27162366

Analysis of reaction schemes using maximum rates of constituent steps

DOE PAGES

Motagamwala, Ali Hussain; Dumesic, James A.

2016-05-09

In this paper, we show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, r max,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of r max,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of r max,i can be used to predict themore » rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. Finally, this approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps.« less

Action mechanism of tyrosinase on meta- and para-hydroxylated monophenols.

PubMed

Fenoll, L G; Rodríguez-López, J N; Varón, R; García-Ruiz, P A; García-Cánovas, F; Tudela, J

2000-04-01

The relationship between the structure and activity of meta- and para-hydroxylated monophenols was studied during their tyrosinase-catalysed hydroxylation and the rate-limiting steps of the reaction mechanism were identified. The para-hydroxylated substrates permit us to study the effect of a substituent (R) in the carbon-1 position (C-1) of the benzene ring on the nucleophilic attack step, while the meta group permits a similar study of the effect on the electrophilic attack step. Substrates with a -OCH3 group on C-1, as p-hydroxyanisol (4HA) and m-hydroxyanisol (3HA), or with a -CH2OH group, as p-hydroxybenzylalcohol (4HBA) and m-hydroxybenzylalcohol (3HBA), were used because the effect of the substituent (R) size was assumed to be similar. However, the electron-donating effect of the -OCH3 group means that the carbon-4 position (C-4) is favoured for nucleophilic attack (para-hydroxylated substrates) or for electrophilic attack (meta-hydroxylated substrates). The electron-attracting effect of the -CH2OH group has the opposite effect, hindering nucleophilic (para) or electrophilic (meta) attack of C-4. The experimental data point to differences between the maximum steady-state rate (V(M)Max) of the different substrates, the value of this parameter depends on the nucleophilic and electrophilic attack. However, differences are greatest in the Michaelis constants (K(M)m), with the meta-hydroxylated substrates having very large values. The catalytic efficiency k(M)cat/K(M)m is much greater for thepara-hydroxylated substrates although it varies greatly between one substrate and the other. However, it varies much less in the meta-hydroxylated substrates since this parameter describes the power of the nucleophilic attack, which is weaker in the meta OH. The large increase in the K(M)m of the meta-hydroxylated substrates might suggest that the phenolic OH takes part in substrate binding. Since this is a weaker nucleophil than the para-hydroxylated substrates, the binding constant decreases, leading to an increase in K(M)m. The catalytic efficiency of tyrosinase on a monophenol (para or meta) is directly related to the nucleophilic power of the oxygen of the phenolic OH. The oxidation step is not limiting since if this were the case, the para and meta substrates would have the same V(M)max. The small difference between the absolute values of V(M)max suggests that the rate constants of the nucleophilic and electrophilic attacks are on the same order of magnitude.

Optimization of a one-step heat-inducible in vivo mini DNA vector production system.

PubMed

Nafissi, Nafiseh; Sum, Chi Hong; Wettig, Shawn; Slavcev, Roderick A

2014-01-01

While safer than their viral counterparts, conventional circular covalently closed (CCC) plasmid DNA vectors offer a limited safety profile. They often result in the transfer of unwanted prokaryotic sequences, antibiotic resistance genes, and bacterial origins of replication that may lead to unwanted immunostimulatory responses. Furthermore, such vectors may impart the potential for chromosomal integration, thus potentiating oncogenesis. Linear covalently closed (LCC), bacterial sequence free DNA vectors have shown promising clinical improvements in vitro and in vivo. However, the generation of such minivectors has been limited by in vitro enzymatic reactions hindering their downstream application in clinical trials. We previously characterized an in vivo temperature-inducible expression system, governed by the phage λ pL promoter and regulated by the thermolabile λ CI[Ts]857 repressor to produce recombinant protelomerase enzymes in E. coli. In this expression system, induction of recombinant protelomerase was achieved by increasing culture temperature above the 37°C threshold temperature. Overexpression of protelomerase led to enzymatic reactions, acting on genetically engineered multi-target sites called "Super Sequences" that serve to convert conventional CCC plasmid DNA into LCC DNA minivectors. Temperature up-shift, however, can result in intracellular stress responses and may alter plasmid replication rates; both of which may be detrimental to LCC minivector production. We sought to optimize our one-step in vivo DNA minivector production system under various induction schedules in combination with genetic modifications influencing plasmid replication, processing rates, and cellular heat stress responses. We assessed different culture growth techniques, growth media compositions, heat induction scheduling and temperature, induction duration, post-induction temperature, and E. coli genetic background to improve the productivity and scalability of our system, achieving an overall LCC DNA minivector production efficiency of ∼ 90%.We optimized a robust technology conferring rapid, scalable, one-step in vivo production of LCC DNA minivectors with potential application to gene transfer-mediated therapeutics.

Role of protein conformational mobility in enzyme catalysis: acylation of alpha-chymotrypsin by specific peptide substrates.

PubMed

Hengge, Alvan C; Stein, Ross L

2004-01-27

To probe the mechanistic origins of convex Eyring plots that have been observed for alpha-chymotrypsin (alpha-CT)-catalyzed hydrolysis of specific p-nitroanilide substrates [Case, A., and Stein, R. L. (2003) Biochemistry 42, 3335-3348], we determined the temperature-dependence of (15)N-kinetic isotope effects for the alpha-CT-catalyzed hydrolysis of N-succinyl-Phe p-nitroanilide (Suc-Phe-pNA). To provide an interpretational context for these enzymatic isotope effects, we also determined 15N-KIE for alkaline hydrolysis of p-nitroacetanilide. In 0.002 and 2 N hydroxide (30 degrees C), 15N-KIE values are 1.035 and 0.995 (+/-0.001), respectively, and are consistent with the reported [HO-]-dependent change in rate-limiting step from leaving group departure from an anionic tetrahedral intermediate in dilute base, to hydroxide attack in concentrated base. For the alpha-CT-catalyzed hydrolysis of Suc-Phe-pNA, 15N-KIE is on kc/Km and thus reflects structural features of transition states for all reaction steps up to and including acylation of the active site serine. The isotope effect at 35 degrees C is 1.014 (+/-0.001) and suggests that in the transition state for this reaction, departure of leaving group from the tetrahedral intermediate is well advanced. Significantly, 15N-KIE does not vary over the temperature range 5-45 degrees C. This result eliminates one of the competing hypotheses for the convex Eyring plot observed for this reaction, that is, a temperature-dependent change in rate-limiting step within the chemical manifold of acylation, but supports a mechanism in which an isomerization of enzyme conformation is coupled to active site chemistry. We finally suggest that the near absolute temperature-independence of 15N-KIE may point to a unique transition state for this process.

Optimization of a One-Step Heat-Inducible In Vivo Mini DNA Vector Production System

PubMed Central

Wettig, Shawn; Slavcev, Roderick A.

2014-01-01

While safer than their viral counterparts, conventional circular covalently closed (CCC) plasmid DNA vectors offer a limited safety profile. They often result in the transfer of unwanted prokaryotic sequences, antibiotic resistance genes, and bacterial origins of replication that may lead to unwanted immunostimulatory responses. Furthermore, such vectors may impart the potential for chromosomal integration, thus potentiating oncogenesis. Linear covalently closed (LCC), bacterial sequence free DNA vectors have shown promising clinical improvements in vitro and in vivo. However, the generation of such minivectors has been limited by in vitro enzymatic reactions hindering their downstream application in clinical trials. We previously characterized an in vivo temperature-inducible expression system, governed by the phage λ pL promoter and regulated by the thermolabile λ CI[Ts]857 repressor to produce recombinant protelomerase enzymes in E. coli. In this expression system, induction of recombinant protelomerase was achieved by increasing culture temperature above the 37°C threshold temperature. Overexpression of protelomerase led to enzymatic reactions, acting on genetically engineered multi-target sites called “Super Sequences” that serve to convert conventional CCC plasmid DNA into LCC DNA minivectors. Temperature up-shift, however, can result in intracellular stress responses and may alter plasmid replication rates; both of which may be detrimental to LCC minivector production. We sought to optimize our one-step in vivo DNA minivector production system under various induction schedules in combination with genetic modifications influencing plasmid replication, processing rates, and cellular heat stress responses. We assessed different culture growth techniques, growth media compositions, heat induction scheduling and temperature, induction duration, post-induction temperature, and E. coli genetic background to improve the productivity and scalability of our system, achieving an overall LCC DNA minivector production efficiency of ∼90%.We optimized a robust technology conferring rapid, scalable, one-step in vivo production of LCC DNA minivectors with potential application to gene transfer-mediated therapeutics. PMID:24586704

Physiological stratification in electricity-producing biofilms of Geobacter sulfurreducens.

PubMed

Schrott, Germán David; Ordoñez, María Victoria; Robuschi, Luciana; Busalmen, Juan Pablo

2014-02-01

The elucidation of mechanisms and limitations in electrode respiration by electroactive biofilms is significant for the development of rapidly emerging clean energy production and wastewater treatment technologies. In Geobacter sulfurreducens biofilms, the controlling steps in current production are thought to be the metabolic activity of cells, but still remain to be determined. By quantifying the DNA, RNA, and protein content during the long-term growth of biofilms on polarized graphite electrodes, we show in this work that current production becomes independent of DNA accumulation immediately after a maximal current is achieved. Indeed, the mean respiratory rate of biofilms rapidly decreases after this point, which indicates the progressive accumulation of cells that do not contribute to current production or contribute to a negligible extent. These results support the occurrence of physiological stratification within biofilms as a consequence of respiratory limitations imposed by limited biofilm conductivity. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Suppressed expression of choline monooxygenase in sugar beet on the accumulation of glycine betaine.

PubMed

Yamada, Nana; Takahashi, Hiroyuki; Kitou, Kunihide; Sahashi, Kosuke; Tamagake, Hideto; Tanaka, Yoshito; Takabe, Teruhiro

2015-11-01

Glycine betaine (GB) is an important osmoprotectant and synthesized by two-step oxidation of choline. Choline monooxygenase (CMO) catalyzes the first step of the pathway and is believed to be a rate limiting step for GB synthesis. Recent studies have shown the importance of choline-precursor supply for GB synthesis. In order to investigate the role of CMO for GB accumulation in sugar beet (Beta vulgaris), transgenic plants carrying the antisense BvCMO gene were developed. The antisense BvCMO plants showed the decreased activity of GB synthesis from choline compared to wild-type (WT) plants which is well related to the suppressed level of BvCMO protein. However, GB contents were similar between transgenic and WT plants with the exception of young leaves and storage roots. Transgenic plants showed enhanced susceptibility to salt stress than WT plants. These results suggest the importance of choline-precursor-supply for GB accumulation, and young leaves and storage root are sensitive sites for GB accumulation. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Limitations for current production in Geobacter sulfurreducens biofilms.

PubMed

Bonanni, P Sebastian; Bradley, Dan F; Schrott, Germán D; Busalmen, Juan Pablo

2013-04-01

Devices that exploit electricity produced by electroactive bacteria such as Geobacter sulfurreducens have not yet been demonstrated beyond the laboratory scale. The current densities are far from the maximum that the bacteria can produce because fundamental properties such as the mechanism of extracellular electron transport and factors limiting cell respiration remain unclear. In this work, a strategy for the investigation of electroactive biofilms is presented. Numerical modeling of the response of G. sulfurreducens biofilms cultured on a rotating disk electrode has allowed for the discrimination of different limiting steps in the process of current production within a biofilm. The model outputs reveal that extracellular electron transport limits the respiration rate of the cells furthest from the electrode to the extent that cell division is not possible. The mathematical model also demonstrates that recent findings such as the existence of a redox gradient in actively respiring biofilms can be explained by an electron hopping mechanism but not when considering metallic-like conductivities. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aerospace technology development of three types of solid state remote power controllers for 120VDC with current ratings of five, and thirty amperes, one type having current limiting

NASA Technical Reports Server (NTRS)

Baker, D. E.

1975-01-01

The first generation of remote power controllers (RPC) developed included: a 5-ampere design (Type 1), capable of limiting maximum overload current to 15 amperes for .1 sec; and 5-ampere noncurrent (Type 2) and 30-ampere noncurrent (Type 3) limiting designs, both with selectable instant trip levels for high-current overload. Each design provides overcurrent protection through an inverse I squared T trip-out function with an automatic reset option and demonstrates step-applied fault capability with a 4000-ampere surge, fast-risetime (low-inductance) power source. They also meet MIL - STD - 461A specification for electromagnetic interference. The second generation RPCs traded off specification compliance for reduction in cost and complexity for the Type 1 and 2 designs and give comparable or improved performance in most areas. The noncurrent limiting RPC proved to be a more economical and feasible method of overload protection for certain load types.

Enhanced poly(3-hydroxybutyrate) production in transgenic tobacco BY-2 cells using engineered acetoacetyl-CoA reductase.

PubMed

Yokoo, Toshinori; Matsumoto, Ken'ichiro; Ooba, Takashi; Morimoto, Kenjiro; Taguchi, Seiichi

2015-01-01

Highly active mutant of NADPH-dependent acetoacetyl-CoA reductase (PhaB) was expressed in Nicotiana tabacum cv. Bright Yellow-2 cultured cells to produce poly(3-hydroxybutyrate) [P(3HB)]. The mutated PhaB increased P(3HB) content by three-fold over the control, indicating that the mutant was a versatile tool for P(3HB) production. Additionally, the PhaB-catalyzed reaction was suggested to be a rate-limiting step of P(3HB) biosynthesis in tobacco BY-2 cells.

Millstone: software for multiplex microbial genome analysis and engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Stereoconvergent Amine-Directed Alkyl–Alkyl Suzuki Reactions of Unactivated Secondary Alkyl Chlorides

PubMed Central

Lu, Zhe; Wilsily, Ashraf; Fu, Gregory C.

2011-01-01

A new family of stereoconvergent cross-couplings of unactivated secondary alkyl electrophiles has been developed, specifically, arylamine-directed alkyl–alkyl Suzuki reactions. This represents the first such investigation to be focused on the use of alkyl chlorides as substrates. Structure-enantioselectivity studies are consistent with the nitrogen, not the aromatic ring, serving as the primary site of coordination of the arylamine to the catalyst. The rate law for this asymmetric cross-coupling is compatible with transmetalation being the turnover-limiting step of the catalytic cycle. PMID:21553917

Security of coherent-state quantum cryptography in the presence of Gaussian noise

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heid, Matthias; Luetkenhaus, Norbert

2007-08-15

We investigate the security against collective attacks of a continuous variable quantum key distribution scheme in the asymptotic key limit for a realistic setting. The quantum channel connecting the two honest parties is assumed to be lossy and imposes Gaussian noise on the observed quadrature distributions. Secret key rates are given for direct and reverse reconciliation schemes including post-selection in the collective attack scenario. The effect of a nonideal error correction and two-way communication in the classical post-processing step is also taken into account.

Laser cooling of 85Rb atoms to the recoil-temperature limit

NASA Astrophysics Data System (ADS)

Huang, Chang; Kuan, Pei-Chen; Lan, Shau-Yu

2018-02-01

We demonstrate the laser cooling of 85Rb atoms in a two-dimensional optical lattice. We follow the two-step degenerate Raman sideband cooling scheme [Kerman et al., Phys. Rev. Lett. 84, 439 (2000), 10.1103/PhysRevLett.84.439], where a fast cooling of atoms to an auxiliary state is followed by a slow cooling to a dark state. This method has the advantage of independent control of the heating rate and cooling rate from the optical pumping beam. We operate the lattice at a Lamb-Dicke parameter η =0.45 and show the cooling of spin-polarized 85Rb atoms to the recoil temperature in both dimensions within 2.4 ms with the aid of adiabatic cooling.

Generalization of improved step length symmetry from treadmill to overground walking in persons with stroke and hemiparesis†

PubMed Central

Savin, Douglas N.; Morton, Susanne M.; Whitall, Jill

2013-01-01

Objectives Determine whether adaptation to a swing phase perturbation during gait transferred from treadmill to overground walking, the rate of overground deadaptation, and whether overground aftereffects improved step length asymmetry in persons with hemiparetic stroke and gait asymmetry. Methods Ten participants with stroke and hemiparesis and 10 controls walked overground on an instrumented gait mat, adapted gait to a swing phase perturbation on a treadmill, then walked overground on the gait mat again. Outcome measures, primary: overground step length symmetry, rates of treadmill step length symmetry adaptation and overground step length symmetry deadaptation; secondary: overground gait velocity, stride length, and stride cycle duration. Results Step length symmetry aftereffects generalized to overground walking and adapted at a similar rate on the treadmill in both groups. Aftereffects decayed at a slower rate overground in participants with stroke and temporarily improved overground step length asymmetry. Both groups’ overground gait velocity increased post adaptation due to increased stride length and decreased stride duration. Conclusions Stroke and hemiparesis do not impair generalization of step length symmetry changes from adapted treadmill to overground walking, but prolong overground aftereffects. Significance Motor adaptation during treadmill walking may be an effective treatment for improving overground gait asymmetries post-stroke. PMID:24286858

Super-sensitive time-resolved fluoroimmunoassay for thyroid-stimulating hormone utilizing europium(III) nanoparticle labels achieved by protein corona stabilization, short binding time, and serum preprocessing.

PubMed

Näreoja, Tuomas; Rosenholm, Jessica M; Lamminmäki, Urpo; Hänninen, Pekka E

2017-05-01

Thyrotropin or thyroid-stimulating hormone (TSH) is used as a marker for thyroid function. More precise and more sensitive immunoassays are needed to facilitate continuous monitoring of thyroid dysfunctions and to assess the efficacy of the selected therapy and dosage of medication. Moreover, most thyroid diseases are autoimmune diseases making TSH assays very prone to immunoassay interferences due to autoantibodies in the sample matrix. We have developed a super-sensitive TSH immunoassay utilizing nanoparticle labels with a detection limit of 60 nU L -1 in preprocessed serum samples by reducing nonspecific binding. The developed preprocessing step by affinity purification removed interfering compounds and improved the recovery of spiked TSH from serum. The sensitivity enhancement was achieved by stabilization of the protein corona of the nanoparticle bioconjugates and a spot-coated configuration of the active solid-phase that reduced sedimentation of the nanoparticle bioconjugates and their contact time with antibody-coated solid phase, thus making use of the higher association rate of specific binding due to high avidity nanoparticle bioconjugates. Graphical Abstract We were able to decrease the lowest limit of detection and increase sensitivity of TSH immunoassay using Eu(III)-nanoparticles. The improvement was achieved by decreasing binding time of nanoparticle bioconjugates by small capture area and fast circular rotation. Also, we applied a step to stabilize protein corona of the nanoparticles and a serum-preprocessing step with a structurally related antibody.

Gold Nanoparticle Labels and Heterogeneous Immunoassays: The Case for the Inverted Substrate.

PubMed

Crawford, Alexis C; Young, Colin C; Porter, Marc D

2018-06-15

This paper examines how the difference in the spatial orientation of the capture substrate influences the analytical sensitivity and limits of detection for immunoassays that use gold nanoparticle labels (AuNPs) and rely on diffusion in quiet solution in the antigen capture and labeling steps. Ideally, the accumulation of both reactants should follow a dependence governed by the rate in which diffusion delivers reactants to the capture surface. In other words, the accumulation of reactants should increase with the square root of the incubation time, i.e., t1/2. The work herein shows, however, that this expectation is only obeyed when the capture substrate is oriented to direct the gravity-induced sedimentation of the AuNP labels away from the substrate. Using an assay for human IgG, the results show that circumventing the sedimentation of the gold nanoparticle labels by substrate inversion enables the dependence of the labeling step on diffusion, reduces nonspecific label adsorption, and improves the estimated detection limit by ~30×. High-density maps of the signal across the two types of substrates also demonstrate that inversion in the labeling step results in a more uniform distribution of AuNP labels across the surface, which translates to a greater measurement reproducibility. These results, which are supported by model simulations via the Mason-Weaver sedimentation-diffusion equation, and their potential implications when using other nanoparticle labels and related materials in diagnostic tests and other applications, are briefly discussed.

A model for the pyrolysis of unfilled and filled polymers and comparisons with NBS smoke-density chamber data

NASA Technical Reports Server (NTRS)

Kumar, R. N.

1976-01-01

This paper considers a model for the pyrolysis of polymers for use in mass loss and smoke density predictions in a fire situation. It is based on the fundamental postulate that the overall rate-limiting reactions are in the relatively low temperature condensed phase; the rate limiting step is the polymer degradation to a vaporizable state. The state of the polymer (chain length) at the surface is specified by the vapor pressure equilibrium criterion. For the case of polymers with inert fillers, like alumina trihydrate, the further assumption is made that the linear regression rate of the material is identical to the unfilled material's at the same surface temperature. The fraction of polymer mass loss converted to smoke is inferred from the literature. The smoke density in the NBS-smoke density chamber is predicted for a polyester and the same polyester with two different loads of alumina trihydrate filler. Diffusional effects in the smoke spreading are considered in an elementary manner. The comparisons with experimental data are encouraging. The overall fire characteristics are predicted using only the fundamental physicochemical property values of ingredients.

Moving beyond the limits of mass transport in liquid absorbent microfilms through the implementation of surface-induced vortices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bigham, S; Yu, DZ; Chugh, D

2014-02-01

The slow diffusion of an absorbate molecule into an absorbent often makes the absorption process a rate-limiting step in many applications. In cases involving an absorbate with a high heat of phase change, such as water absorption into a LiBr (lithium bromide) solution, the absorption rate is further slowed due to significant heating of the absorbent. Recently, it has been demonstrated that constraining a LiBr solution film by a hydrophobic porous structure enables manipulation of the solution flow thermohydraulic characteristics. Here, it is shown that mass transport mode in a constrained laminar solution flow can be changed from diffusive tomore » advective. This change in mode is accomplished through stretching and folding the laminar streamlines within the solution film via the implementation of micro-scale features on the flow channel surface. The process induces vortices within the solution film, which continuously bring concentrated solution from the bottom and middle of the solution channel to its interface with the vapor phase, thus leading to a significant enhancement in the absorption rate. The detailed physics of the involved transport processes is elucidated using the LBM (Lattice Boltzmann Method). Published by Elsevier Ltd.« less

The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy

PubMed Central

Kötting, Carsten; Kallenbach, Angela; Suveyzdis, Yan; Wittinghofer, Alfred; Gerwert, Klaus

2008-01-01

Members of the Ras superfamily of small G proteins play key roles in signal transduction pathways, which they control by GTP hydrolysis. They are regulated by GTPase activating proteins (GAPs). Mutations that prevent hydrolysis cause severe diseases including cancer. A highly conserved “arginine finger” of GAP is a key residue. Here, we monitor the GTPase reaction of the Ras·RasGAP complex at high temporal and spatial resolution by time-resolved FTIR spectroscopy at 260 K. After triggering the reaction, we observe as the first step a movement of the switch-I region of Ras from the nonsignaling “off” to the signaling “on” state with a rate of 3 s−1. The next step is the movement of the “arginine finger” into the active site of Ras with a rate of k2 = 0.8 s−1. Once the arginine points into the binding pocket, cleavage of GTP is fast and the protein-bound Pi intermediate forms. The switch-I reversal to the “off” state, the release of Pi, and the movement of arginine back into an aqueous environment is observed simultaneously with k3 = 0.1 s−1, the rate-limiting step. Arrhenius plots for the partial reactions show that the activation energy for the cleavage reaction is lowered by favorable positive activation entropy. This seems to indicate that protein-bound structured water molecules are pushed by the “arginine finger” movement out of the binding pocket into the bulk water. The proposed mechanism shows how the high activation barrier for phosphoryl transfer can be reduced by splitting into partial reactions separated by a Pi-intermediate. PMID:18434546

Understanding the Relationship Between Kinetics and Thermodynamics in CO 2 Hydrogenation Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeletic, Matthew S.; Hulley, Elliott B.; Helm, Monte L.

Linear free-energy relationships have been identified that link the kinetic activity for catalytic hydrogenation of CO2 to formate with the thermodynamic driving force for the rate-limiting steps of catalysis. Cobalt and rhodium bis(diphosphine) complexes with different hydricities (G°H-), acidities (pKa), and free energies for H2 addition (G°H2) were examined. Catalytic CO2 hydrogenation was studied under 1.8 and 20 atm of pressure (1:1 CO2:H2) at room temperature in tetrahydrofuran with a spread of turnover frequencies (TOF) ranging from 0 to 74,000 h-1. The catalysis was followed by 1H and 31P NMR in real time under all conditions to yield information aboutmore » the rate determining step. Catalysts exhibiting the highest activities were found to have hydride transfer and hydrogen addition steps that were each downhill by approximately 6 to 7 kcal/mol, and the deprotonation step was thermoneutral. The research by M.S.J., A.M.A., E.S.W., and J.C.L. was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The research by E.B.H., M.L.H., and M.T.M. (X-ray crystallography, synthesis) was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. The authors thank Dr. Samantha A. Burgess for assistance in collecting cyclic voltammetry data. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Improving oxygen therapy for children and neonates in secondary hospitals in Nigeria: study protocol for a stepped-wedge cluster randomised trial.

PubMed

Graham, Hamish R; Ayede, Adejumoke I; Bakare, Ayobami A; Oyewole, Oladapo B; Peel, David; Gray, Amy; McPake, Barbara; Neal, Eleanor; Qazi, Shamim; Izadnegahdar, Rasa; Falade, Adegoke G; Duke, Trevor

2017-10-27

Oxygen is a life-saving, essential medicine that is important for the treatment of many common childhood conditions. Improved oxygen systems can reduce childhood pneumonia mortality substantially. However, providing oxygen to children is challenging, especially in small hospitals with weak infrastructure and low human resource capacity. This trial will evaluate the implementation of improved oxygen systems at secondary-level hospitals in southwest Nigeria. The improved oxygen system includes: a standardised equipment package; training of clinical and technical staff; infrastructure support (including improved power supply); and quality improvement activities such as supportive supervision. Phase 1 will involve the introduction of pulse oximetry alone; phase 2 will involve the introduction of the full, improved oxygen system package. We have based the intervention design on a theory-based analysis of previous oxygen projects, and used quality improvement principles, evidence-based teaching methods, and behaviour-change strategies. We are using a stepped-wedge cluster randomised design with participating hospitals randomised to receive an improved oxygen system at 4-month steps (three hospitals per step). Our mixed-methods evaluation will evaluate effectiveness, impact, sustainability, process and fidelity. Our primary outcome measures are childhood pneumonia case fatality rate and inpatient neonatal mortality rate. Secondary outcome measures include a range of clinical, quality of care, technical, and health systems outcomes. The planned study duration is from 2015 to 2018. Our study will provide quality evidence on the effectiveness of improved oxygen systems, and how to better implement and scale-up oxygen systems in resource-limited settings. Our results should have important implications for policy-makers, hospital administrators, and child health organisations in Africa and globally. Australian New Zealand Clinical Trials Registry: ACTRN12617000341325 . Retrospectively registered on 6 March 2017.

Compliance With WHO/UNICEF BFHI Standards in Croatia After Implementation of the BFHI.

PubMed

Zakarija-Grković, Irena; Boban, Marija; Janković, Sunčana; Ćuže, Anamarija; Burmaz, Tea

2018-02-01

The primary goal of the Baby-Friendly Hospital Initiative (BFHI) is to create conditions in maternity facilities that enable women to initiate and sustain the practice of breastfeeding exclusively. Research aim: This study aimed to determine hospital practices and breastfeeding rates before and after BFHI implementation and assess compliance with UNICEF/World Health Organization (WHO) standards for seven of the BFHI's Ten Steps to Successful Breastfeeding ( Ten Steps). Mothers of healthy, term infants ( N = 1,115) were recruited from the postnatal ward of the University Hospital of Split, Croatia, between February 2008 and July 2011 and followed for 12 months in a repeated-measures, prospective, longitudinal, three-group, nonequivalent, cohort study. Breastfeeding rates, hospital practices-including seven of the Ten Steps-and maternal sociodemographic data were collected. Parts of all seven Ten Steps that were assessed improved significantly post-BFHI. Step 3 ("antenatal education") showed the least improvement, whereas Step 7 ("rooming-in"; 2.6% pre-BFHI vs. 98.5% post-BFHI) and Step 9 ("no pacifiers/teats"; 21.8% pre-BFHI vs. 99.4% post-BFHI) showed the greatest improvement. Six months after Baby-Friendly designation, only Steps 7 and 9 were in full compliance with UNICEF/WHO standards. In-hospital, exclusive-breastfeeding rates rose markedly ( p < .001), but no change occurred in breastfeeding rates at 3, 6, or 12 months. Full implementation of the BFHI was associated with significant improvement in hospital practices and in-hospital, exclusive-breastfeeding rates, but it did not affect breastfeeding rates postdischarge, emphasizing the vital role of community support. Baby-Friendly Hospital Initiative standards declined rapidly post-hospital designation, indicating the need for regular monitoring and reassessment as well as ongoing, effective training for hospital staff.

Kinetics and mechanisms of iron sulfide reductions in hydrogen and in carbon monoxide

USGS Publications Warehouse

Wiltowski, T.; Hinckley, C.C.; Smith, Gerard V.; Nishizawa, T.; Saporoschenko, Mykola; Shiley, R.H.; Webster, J.R.

1987-01-01

The reduction of iron sulfides by hydrogen and by carbon monoxide has been studied using plug flow and thermogravimetric methods. The reactions were studied in the 523-723??K temperature range and were found to be first-order processes. Plug flow studies were used to correlate reaction rates between pyrite and the gases as a function of the surface area of the pyrite. The rate of H2S formation increases with the surface area of the pyrite sample. The results of thermogravimetric experiments indicate that the reactions consist of several steps. Rate constants for the pyrite reduction by H2 and by CO were obtained. The activation energies increased with degree of reduction. Values of Ea were 113.2 (step I) and 122.5 kJ/mole (step II) for pyrite reduction with CO and 99.4 (step I), 122.4 (step II), 125.2 (step III), and 142.6 kJ/mole (step IV) for pyrite reduction with hydrogen. ?? 1987.

Novel ex vivo model for hands-on teaching of and training in EUS-guided biliary drainage: creation of "Mumbai EUS" stereolithography/3D printing bile duct prototype (with videos).

PubMed

Dhir, Vinay; Itoi, Takao; Fockens, Paul; Perez-Miranda, Manuel; Khashab, Mouen A; Seo, Dong Wan; Yang, Ai Ming; Lawrence, Khek Yu; Maydeo, Amit

2015-02-01

EUS-guided biliary drainage (EUS-BD) has emerged as an alternative rescue method in patients with failed ERCP. Opportunities for teaching and training are limited because of a low case volume at most centers. To evaluate a stereolithography/3-dimensional (3D) printing bile duct prototype for teaching and training in EUS-BD. Prospective observational feasibility study. Tertiary referral center. Twenty endosonographers attending an interventional EUS workshop. A prototype of a dilated biliary system was prepared by computer-aided design and 3D printing. The study participants performed guidewire manipulation and EUS-BD procedures (antegrade procedure and/or choledochoduodenostomy) on the prototype. Participants were scored with the device on a scale of 1 to 5 via a questionnaire. Participants' success rate for various steps of the EUS-BD procedure was noted. Subjective and objective evaluation of the prototype regarding its overall applicability, quality of radiographic and EUS images, and 4 steps of EUS-BD procedure (needle puncture, guidewire manipulation, tract dilation, stent placement). Fifteen participants returned the questionnaire, and 10 completed all 4 steps of EUS-BD. The median score for overall utility was 4, whereas that for EUS and US views was 5. Participants with experience in performing more than 20 EUS-BD procedures scored the prototype significantly lower for stent placement (P = .013) and equivalent for needle puncture, tract dilation, and wire manipulation. The success rate of various steps was 100% for needle puncture and tract dilation, 82.35% for wire manipulation, and 80% for stent placement. The mean overall procedure time was 18 minutes. Small number of participants. The 3D printing bile duct prototype appears suitable for teaching of and training in the various steps of EUS-BD. Further studies are required to elucidate its role. Copyright © 2015 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis

PubMed Central

Wright, Jaden R.; Keffer-Wilkes, Laura C.; Dobing, Selina R.; Kothe, Ute

2011-01-01

Pseudouridine synthases catalyze formation of the most abundant modification of functional RNAs by site-specifically isomerizing uridines to pseudouridines. While the structure and substrate specificity of these enzymes have been studied in detail, the kinetic and the catalytic mechanism of pseudouridine synthases remain unknown. Here, the first pre-steady-state kinetic analysis of three Escherichia coli pseudouridine synthases is presented. A novel stopped-flow absorbance assay revealed that substrate tRNA binding by TruB takes place in two steps with an overall rate of 6 sec−1. In order to observe catalysis of pseudouridine formation directly, the traditional tritium release assay was adapted for the quench-flow technique, allowing, for the first time, observation of a single round of pseudouridine formation. Thereby, the single-round rate constant of pseudouridylation (kΨ) by TruB was determined to be 0.5 sec−1. This rate constant is similar to the kcat obtained under multiple-turnover conditions in steady-state experiments, indicating that catalysis is the rate-limiting step for TruB. In order to investigate if pseudouridine synthases are characterized by slow catalysis in general, the rapid kinetic quench-flow analysis was also performed with two other E. coli enzymes, RluA and TruA, which displayed rate constants of pseudouridine formation of 0.7 and 0.35 sec−1, respectively. Hence, uniformly slow catalysis might be a general feature of pseudouridine synthases that share a conserved catalytic domain and supposedly use the same catalytic mechanism. PMID:21998096

Quick and Easy Rate Equations for Multistep Reactions

ERIC Educational Resources Information Center

Savage, Phillip E.

2008-01-01

Students rarely see closed-form analytical rate equations derived from underlying chemical mechanisms that contain more than a few steps unless restrictive simplifying assumptions (e.g., existence of a rate-determining step) are made. Yet, work published decades ago allows closed-form analytical rate equations to be written quickly and easily for…

DOCKTITE-a highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment.

PubMed

Scholz, Christoph; Knorr, Sabine; Hamacher, Kay; Schmidt, Boris

2015-02-23

The formation of a covalent bond with the target is essential for a number of successful drugs, yet tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare and limited in use. In this work we present DOCKTITE, a highly versatile workflow for covalent docking in the Molecular Operating Environment (MOE) combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking, and a novel consensus scoring approach. The comprehensive validation study includes pose predictions of 35 protein/ligand complexes which resulted in a mean RMSD of 1.74 Å and a prediction rate of 71.4% with an RMSD below 2 Å, a virtual screening with an area under the curve (AUC) for the receiver operating characteristics (ROC) of 0.81, and a significant correlation between predicted and experimental binding affinities (ρ = 0.806, R(2) = 0.649, p < 0.005).

Anaerobic digestion of microalgal biomass: Challenges, opportunities and research needs.

PubMed

Gonzalez-Fernandez, Cristina; Sialve, Bruno; Molinuevo-Salces, Beatriz

2015-12-01

Integration of anaerobic digestion (AD) with microalgae processes has become a key topic to support economic and environmental development of this resource. Compared with other substrates, microalgae can be produced close to the plant without the need for arable lands and be fully integrated within a biorefinery. As a limiting step, anaerobic hydrolysis appears to be one of the most challenging steps to reach a positive economic balance and to completely exploit the potential of microalgae for biogas and fertilizers production. This review covers recent investigations dealing with microalgae AD and highlights research opportunities and needs to support the development of this resource. Novel approaches to increase hydrolysis rate, the importance of the reactor design and the noteworthiness of the microbial anaerobic community are addressed. Finally, the integration of AD with microalgae processes and the potential of the carboxylate platform for chemicals and biofuels production are reviewed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cooperative catalysis by tertiary amino-thioureas: mechanism and basis for enantioselectivity of ketone cyanosilylation.

PubMed

Zuend, Stephan J; Jacobsen, Eric N

2007-12-26

The mechanism of the enantioselective cyanosilylation of ketones catalyzed by tertiary amino-thiourea derivatives was investigated using a combination of experimental and theoretical methods. The kinetic analysis is consistent with a cooperative mechanism in which both the thiourea and the tertiary amine of the catalyst are involved productively in the rate-limiting cyanide addition step. Density functional theory calculations were used to distinguish between mechanisms involving thiourea activation of ketone or of cyanide in the enantioselectivity-determining step. The strong correlation obtained between experimental and calculated ee's for a range of substrates and catalysts provides support for the most favorable calculated transition structures involving amine-bound HCN adding to thiourea-bound ketone. The calculations suggest that enantioselectivity arises from direct interactions between the ketone substrate and the amino-acid derived portion of the catalyst. On the basis of this insight, more enantioselective catalysts with broader substrate scope were prepared and evaluated experimentally.

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Mapping the ecological networks of microbial communities.

PubMed

Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

2017-12-11

Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

Airborne Microalgae: Insights, Opportunities, and Challenges

PubMed Central

Skjøth, Carsten Ambelas; Šantl-Temkiv, Tina; Löndahl, Jakob

2016-01-01

Airborne dispersal of microalgae has largely been a blind spot in environmental biological studies because of their low concentration in the atmosphere and the technical limitations in investigating microalgae from air samples. Recent studies show that airborne microalgae can survive air transportation and interact with the environment, possibly influencing their deposition rates. This minireview presents a summary of these studies and traces the possible route, step by step, from established ecosystems to new habitats through air transportation over a variety of geographic scales. Emission, transportation, deposition, and adaptation to atmospheric stress are discussed, as well as the consequences of their dispersal on health and the environment and state-of-the-art techniques to detect and model airborne microalga dispersal. More-detailed studies on the microalga atmospheric cycle, including, for instance, ice nucleation activity and transport simulations, are crucial for improving our understanding of microalga ecology, identifying microalga interactions with the environment, and preventing unwanted contamination events or invasions. PMID:26801574

Free-Energy Landscape of the Dissolution of Gibbsite at High pH.

PubMed

Shen, Zhizhang; Kerisit, Sebastien N; Stack, Andrew G; Rosso, Kevin M

2018-04-05

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.

Speeding up biomolecular interactions by molecular sledding

DOE PAGES

Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; ...

2015-10-07

In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptidemore » and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.« less

Assay Methods for ACS Activity and ACS Phosphorylation by MAP Kinases In Vitro and In Vivo.

PubMed

Han, Xiaomin; Li, Guojing; Zhang, Shuqun

2017-01-01

Ethylene, a gaseous phytohormone, has profound effects on plant growth, development, and adaptation to the environment. Ethylene-regulated processes begin with the induction of ethylene biosynthesis. There are two key steps in ethylene biosynthesis. The first is the biosynthesis of 1-aminocyclopropane-1-carboxylic acid (ACC) from S-Adenosyl-Methionine (SAM), a common precursor in many metabolic pathways, which is catalyzed by ACC synthase (ACS). The second is the oxidative cleavage of ACC to form ethylene under the action of ACC oxidase (ACO). ACC biosynthesis is the committing and generally the rate-limiting step in ethylene biosynthesis. As a result, characterizing the cellular ACS activity and understanding its regulation are important. In this chapter, we detail the methods used to measure, (1) the enzymatic activity of both recombinant and native ACS proteins, and (2) the phosphorylation of ACS protein by mitogen-activated protein kinases (MAPKs) in vivo and in vitro.

Sequential control of step-bunching during graphene growth on SiC (0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, Jianfeng; Kusunoki, Michiko; Yasui, Osamu

2016-08-22

We have investigated the relation between the step-bunching and graphene growth phenomena on an SiC substrate. We found that only a minimum amount of step-bunching occurred during the graphene growth process with a high heating rate. On the other hand, a large amount of step-bunching occurred using a slow heating process. These results indicated that we can control the degree of step-bunching during graphene growth by controlling the heating rate. We also found that graphene coverage suppressed step bunching, which is an effective methodology not only in the graphene technology but also in the SiC-based power electronics.

Evaluating Validity Evidence for USMLE Step 2 Clinical Skills Data Gathering and Data Interpretation Scores: Does Performance Predict History-Taking and Physical Examination Ratings for First-Year Internal Medicine Residents?

PubMed

Cuddy, Monica M; Winward, Marcia L; Johnston, Mary M; Lipner, Rebecca S; Clauser, Brian E

2016-01-01

To add to the small body of validity research addressing whether scores from performance assessments of clinical skills are related to performance in supervised patient settings, the authors examined relationships between United States Medical Licensing Examination (USMLE) Step 2 Clinical Skills (CS) data gathering and data interpretation scores and subsequent performance in history taking and physical examination in internal medicine residency training. The sample included 6,306 examinees from 238 internal medicine residency programs who completed Step 2 CS for the first time in 2005 and whose performance ratings from their first year of residency training were available. Hierarchical linear modeling techniques were used to examine the relationships among Step 2 CS data gathering and data interpretation scores and history-taking and physical examination ratings. Step 2 CS data interpretation scores were positively related to both history-taking and physical examination ratings. Step 2 CS data gathering scores were not related to either history-taking or physical examination ratings after other USMLE scores were taken into account. Step 2 CS data interpretation scores provide useful information for predicting subsequent performance in history taking and physical examination in supervised practice and thus provide validity evidence for their intended use as an indication of readiness to enter supervised practice. The results show that there is less evidence to support the usefulness of Step 2 CS data gathering scores. This study provides important information for practitioners interested in Step 2 CS specifically or in performance assessments of medical students' clinical skills more generally.

Specific effects of background electrolytes on the kinetics of step propagation during calcite growth

NASA Astrophysics Data System (ADS)

Ruiz-Agudo, Encarnación; Putnis, Christine V.; Wang, Lijun; Putnis, Andrew

2011-07-01

The mechanisms by which background electrolytes modify the kinetics of non-equivalent step propagation during calcite growth were investigated using Atomic Force Microscopy (AFM), at constant driving force and solution stoichiometry. Our results suggest that the acute step spreading rate is controlled by kink-site nucleation and, ultimately, by the dehydration of surface sites, while the velocity of obtuse step advancement is mainly determined by hydration of calcium ions in solution. According to our results, kink nucleation at acute steps could be promoted by carbonate-assisted calcium attachment. The different sensitivity of obtuse and acute step propagation kinetics to cation and surface hydration could be the origin of the reversed geometries of calcite growth hillocks (i.e., rate of obtuse step spreading < rate of acute step spreading) observed in concentrated (ionic strength, IS = 0.1) KCl and CsCl solutions. At low IS (0.02), ion-specific effects seem to be mainly associated with changes in the solvation environment of calcium ions in solution. With increasing electrolyte concentration, the stabilization of surface water by weakly paired salts appears to become increasingly important in determining step spreading rate. At high ionic strength (IS = 0.1), overall calcite growth rates increased with increasing hydration of calcium in solution (i.e., decreasing ion pairing of background electrolytes for sodium-bearing salts) and with decreasing hydration of the carbonate surface site (i.e., increasing ion pairing for chloride-bearing salts). Changes in growth hillock morphology were observed in the presence of Li +, F - and SO42-, and can be interpreted as the result of the stabilization of polar surfaces due to increased ion hydration. These results increase our ability to predict crystal reactivity in natural fluids which contain significant amounts of solutes.

True cadence and step accumulation are not equivalent: the effect of intermittent claudication on free-living cadence.

PubMed

Stansfield, B; Clarke, C; Dall, P; Godwin, J; Holdsworth, R; Granat, M

2015-02-01

'True cadence' is the rate of stepping during the period of stepping. 'Step accumulation' is the steps within an epoch of time (e.g. 1min). These terms have been used interchangeably in the literature. These outcomes are compared within a population with intermittent claudication (IC). Multiday, 24h stepping activity of those with IC (30) and controls (30) was measured objectively using the activPAL physical activity monitor. 'True cadence' and 'step accumulation' outcomes were calculated. Those with IC took fewer steps/d 6531±2712 than controls 8692±2945 (P=0.003). However, these steps were taken within approximately the same number of minute epochs (IC 301±100min/d; controls 300±70min/d, P=0.894) with only slightly lower true cadence (IC 69 (IQ 66,72) steps/min; controls 72 (IQ 68,76) steps/min, P=0.026), giving substantially lower step accumulation (IC 22 (IQ 19,24) steps/min; controls 30 (IQ 23,34) steps/min) (P<0.001). However, the true cadence of stepping within the blocks of the 1, 5, 20, 30 and 60min with the maximum number of steps accumulated was lower for those with IC than controls (P<0.05). Those with IC took 1300 steps fewer per day above a true cadence of 90 steps/min. True cadence and step accumulation outcomes were radically different for the outcomes examined. 'True cadence' and 'step accumulation' were not equivalent in those with IC or controls. The measurement of true cadence in the population of people with IC provides information about their stepping rate during the time they are stepping. True cadence should be used to correctly describe the rate of stepping as performed. Copyright © 2014 Elsevier B.V. All rights reserved.

A comparative meta-analysis of maximal aerobic metabolism of vertebrates: implications for respiratory and cardiovascular limits to gas exchange.

PubMed

Hillman, Stanley S; Hancock, Thomas V; Hedrick, Michael S

2013-02-01

Maximal aerobic metabolic rates (MMR) in vertebrates are supported by increased conductive and diffusive fluxes of O(2) from the environment to the mitochondria necessitating concomitant increases in CO(2) efflux. A question that has received much attention has been which step, respiratory or cardiovascular, provides the principal rate limitation to gas flux at MMR? Limitation analyses have principally focused on O(2) fluxes, though the excess capacity of the lung for O(2) ventilation and diffusion remains unexplained except as a safety factor. Analyses of MMR normally rely upon allometry and temperature to define these factors, but cannot account for much of the variation and often have narrow phylogenetic breadth. The unique aspect of our comparative approach was to use an interclass meta-analysis to examine cardio-respiratory variables during the increase from resting metabolic rate to MMR among vertebrates from fish to mammals, independent of allometry and phylogeny. Common patterns at MMR indicate universal principles governing O(2) and CO(2) transport in vertebrate cardiovascular and respiratory systems, despite the varied modes of activities (swimming, running, flying), different cardio-respiratory architecture, and vastly different rates of metabolism (endothermy vs. ectothermy). Our meta-analysis supports previous studies indicating a cardiovascular limit to maximal O(2) transport and also implicates a respiratory system limit to maximal CO(2) efflux, especially in ectotherms. Thus, natural selection would operate on the respiratory system to enhance maximal CO(2) excretion and the cardiovascular system to enhance maximal O(2) uptake. This provides a possible evolutionary explanation for the conundrum of why the respiratory system appears functionally over-designed from an O(2) perspective, a unique insight from previous work focused solely on O(2) fluxes. The results suggest a common gas transport blueprint, or Bauplan, in the vertebrate clade.

The Kinetic Mechanism for DNA Unwinding by Multiple Molecules of Dda Helicase Aligned on DNA†

PubMed Central

Eoff, Robert L.; Raney, Kevin D.

2010-01-01

Helicases catalyze the separation of double-stranded nucleic acids to form single-stranded intermediates. Using transient state kinetic methods we have determined the kinetic properties of DNA unwinding under conditions that favor a monomeric form of the Dda helicase as well as conditions that allow multiple molecules to function on the same substrate. Multiple helicase molecules can align like a train on the DNA track. The number of base pairs unwound in a single binding event for Dda is increased from ~19 bp for the monomeric form to ~64 bp when as many as four Dda molecules are aligned on the same substrate, while the kinetic step-size (3.2 ± 0.7 bp) and unwinding rate (242 ± 25 bp s−1) appear to be independent of the number of Dda molecules present on a given substrate. The data support a model in which the helicase molecules bound to the same substrate move along the DNA track independently during DNA unwinding. The observed increase in processivity arises from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. These results are in contrast to previous reports in which multiple Dda molecules on the same track greatly enhanced the rate and amplitude for displacement of protein blocks on the track. Therefore, only when the progress of the lead molecule in the train is impeded by some type of block, such as a protein bound to DNA, do the trailing molecules interact with the lead molecule in order to overcome the block. The fact that trailing helicase molecules have little impact on the lead molecule in the train during routine DNA unwinding suggests that the trailing molecules are moving at similar rates as the lead molecule. This result implicates a step in the translocation mechanism as contributing greatly to the overall rate-limiting step for unwinding of duplex DNA. PMID:20408588

29 CFR 1926.1053 - Ladders.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) SAFETY AND HEALTH REGULATIONS FOR CONSTRUCTION Stairways and Ladders § 1926.1053 Ladders. Link to an... structural defects, such as, but not limited to, broken or missing rungs, cleats, or steps, broken or split..., such as, but not limited to, broken or missing rungs, cleats, or steps, broken or split rails, or...

16 CFR 701.3 - Written warranty terms.

Code of Federal Regulations, 2010 CFR

2010-01-01

... in compliance with part 703 of this subchapter; (7) Any limitations on the duration of implied... warranty duration; (5) A step-by-step explanation of the procedure which the consumer should follow in... following statement: Some States do not allow limitations on how long an implied warranty lasts, so the...

Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination

PubMed Central

Tao, Zhimin; Raffel, Ryan A.; Souid, Abdul-Kader; Goodisman, Jerry

2009-01-01

The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 ± 0.7) ×104 M−1s−1 at 37°C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37°C and well above unity at 25°C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s−1 and 0.090 s−1 respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain. PMID:19348778

Wearable Devices for Classification of Inadequate Posture at Work Using Neural Networks

PubMed Central

Barkallah, Eya; Freulard, Johan; Otis, Martin J. -D.; Ngomo, Suzy; Ayena, Johannes C.; Desrosiers, Christian

2017-01-01

Inadequate postures adopted by an operator at work are among the most important risk factors in Work-related Musculoskeletal Disorders (WMSDs). Although several studies have focused on inadequate posture, there is limited information on its identification in a work context. The aim of this study is to automatically differentiate between adequate and inadequate postures using two wearable devices (helmet and instrumented insole) with an inertial measurement unit (IMU) and force sensors. From the force sensors located inside the insole, the center of pressure (COP) is computed since it is considered an important parameter in the analysis of posture. In a first step, a set of 60 features is computed with a direct approach, and later reduced to eight via a hybrid feature selection. A neural network is then employed to classify the current posture of a worker, yielding a recognition rate of 90%. In a second step, an innovative graphic approach is proposed to extract three additional features for the classification. This approach represents the main contribution of this study. Combining both approaches improves the recognition rate to 95%. Our results suggest that neural network could be applied successfully for the classification of adequate and inadequate posture. PMID:28862665

Toward intensifying design of experiments in upstream bioprocess development: An industrial Escherichia coli feasibility study.

PubMed

von Stosch, Moritz; Hamelink, Jan-Martijn; Oliveira, Rui

2016-09-01

In this study, step variations in temperature, pH, and carbon substrate feeding rate were performed within five high cell density Escherichia coli fermentations to assess whether intraexperiment step changes, can principally be used to exploit the process operation space in a design of experiment manner. A dynamic process modeling approach was adopted to determine parameter interactions. A bioreactor model was integrated with an artificial neural network that describes biomass and product formation rates as function of varied fed-batch fermentation conditions for heterologous protein production. A model reliability measure was introduced to assess in which process region the model can be expected to predict process states accurately. It was found that the model could accurately predict process states of multiple fermentations performed at fixed conditions within the determined validity domain. The results suggest that intraexperimental variations of process conditions could be used to reduce the number of experiments by a factor, which in limit would be equivalent to the number of intraexperimental variations per experiment. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1343-1352, 2016. © 2016 American Institute of Chemical Engineers.

How we treat chronic active Epstein-Barr virus infection.

PubMed

Sawada, Akihisa; Inoue, Masami; Kawa, Keisei

2017-04-01

Chronic active Epstein-Barr virus infection (CAEBV) is a prototype of the EBV-associated T- or NK-cell lymphoproliferative diseases, which also include hypersensitivity to mosquito bites and severe-type hydroavacciniforme. The manifestations of CAEBV are often self-limiting with minimum supportive care or only prednisolone and cyclosporine A with or without etoposide. However, allogeneic hematopoietic stem cell transplantation (HSCT) is the only cure, without which patients with CAEBV die within several years. A severe hypercytokinemia and hemophagocytic syndrome, which may occur suddenly, often results in a fatal clinical course. At out institute, we have established a 3-step strategy, including allogeneic HSCT, for the treatment of CAEBV. Seventy-nine patients with CAEBV and related diseases have been treated to date. The 3-year overall survival rate (3y-OS) is currently 87.3 ± 4.2% after planned allogeneic HSCT. However, 3y-OS in patients with uncontrolled active disease is only 16.7 ± 10.8%. To maximize survival rates with minimized late sequelae, we recommend earlier initiation and completion of the 3-step treatment without watchful waiting. We present six illustrative and difficult cases (including severe hypercytokinemia or emergent HSCT) and discuss them together with 73 residual cases.

Shutdown Dose Rate Analysis Using the Multi-Step CADIS Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ibrahim, Ahmad M.; Peplow, Douglas E.; Peterson, Joshua L.

2015-01-01

The Multi-Step Consistent Adjoint Driven Importance Sampling (MS-CADIS) hybrid Monte Carlo (MC)/deterministic radiation transport method was proposed to speed up the shutdown dose rate (SDDR) neutron MC calculation using an importance function that represents the neutron importance to the final SDDR. This work applied the MS-CADIS method to the ITER SDDR benchmark problem. The MS-CADIS method was also used to calculate the SDDR uncertainty resulting from uncertainties in the MC neutron calculation and to determine the degree of undersampling in SDDR calculations because of the limited ability of the MC method to tally detailed spatial and energy distributions. The analysismore » that used the ITER benchmark problem compared the efficiency of the MS-CADIS method to the traditional approach of using global MC variance reduction techniques for speeding up SDDR neutron MC calculation. Compared to the standard Forward-Weighted-CADIS (FW-CADIS) method, the MS-CADIS method increased the efficiency of the SDDR neutron MC calculation by 69%. The MS-CADIS method also increased the fraction of nonzero scoring mesh tally elements in the space-energy regions of high importance to the final SDDR.« less

Two-Step Production of Phenylpyruvic Acid from L-Phenylalanine by Growing and Resting Cells of Engineered Escherichia coli: Process Optimization and Kinetics Modeling.

PubMed

Hou, Ying; Hossain, Gazi Sakir; Li, Jianghua; Shin, Hyun-Dong; Liu, Long; Du, Guocheng; Chen, Jian

2016-01-01

Phenylpyruvic acid (PPA) is widely used in the pharmaceutical, food, and chemical industries. Here, a two-step bioconversion process, involving growing and resting cells, was established to produce PPA from l-phenylalanine using the engineered Escherichia coli constructed previously. First, the biotransformation conditions for growing cells were optimized (l-phenylalanine concentration 20.0 g·L-1, temperature 35°C) and a two-stage temperature control strategy (keep 20°C for 12 h and increase the temperature to 35°C until the end of biotransformation) was performed. The biotransformation conditions for resting cells were then optimized in 3-L bioreactor and the optimized conditions were as follows: agitation speed 500 rpm, aeration rate 1.5 vvm, and l-phenylalanine concentration 30 g·L-1. The total maximal production (mass conversion rate) reached 29.8 ± 2.1 g·L-1 (99.3%) and 75.1 ± 2.5 g·L-1 (93.9%) in the flask and 3-L bioreactor, respectively. Finally, a kinetic model was established, and it was revealed that the substrate and product inhibition were the main limiting factors for resting cell biotransformation.

Kinetic characterization of the critical step in HIV-1 protease maturation.

PubMed

Sadiq, S Kashif; Noé, Frank; De Fabritiis, Gianni

2012-12-11

HIV maturation requires multiple cleavage of long polyprotein chains into functional proteins that include the viral protease itself. Initial cleavage by the protease dimer occurs from within these precursors, and yet only a single protease monomer is embedded in each polyprotein chain. Self-activation has been proposed to start from a partially dimerized protease formed from monomers of different chains binding its own N termini by self-association to the active site, but a complete structural understanding of this critical step in HIV maturation is missing. Here, we captured the critical self-association of immature HIV-1 protease to its extended amino-terminal recognition motif using large-scale molecular dynamics simulations, thus confirming the postulated intramolecular mechanism in atomic detail. We show that self-association to a catalytically viable state requires structural cooperativity of the flexible β-hairpin "flap" regions of the enzyme and that the major transition pathway is first via self-association in the semiopen/open enzyme states, followed by enzyme conformational transition into a catalytically viable closed state. Furthermore, partial N-terminal threading can play a role in self-association, whereas wide opening of the flaps in concert with self-association is not observed. We estimate the association rate constant (k(on)) to be on the order of ∼1 × 10(4) s(-1), suggesting that N-terminal self-association is not the rate-limiting step in the process. The shown mechanism also provides an interesting example of molecular conformational transitions along the association pathway.

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

DOE PAGES

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; ...

2017-06-09

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order tomore » achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.« less

Fabrication of 3D surface structures using grayscale lithography

NASA Astrophysics Data System (ADS)

Stilson, Christopher; Pal, Rajan; Coutu, Ronald A.

2014-03-01

The ability to design and develop 3D microstructures is important for microelectromechanical systems (MEMS) fabrication. Previous techniques used to create 3D devices included tedious steps in direct writing and aligning patterns onto a substrate followed by multiple photolithography steps using expensive, customized equipment. Additionally, these techniques restricted batch processing and placed limits on achievable shapes. Gray-scale lithography enables the fabrication of a variety of shapes using a single photolithography step followed by reactive ion etching (RIE). Micromachining 3D silicon structures for MEMS can be accomplished using gray-scale lithography along with dry anisotropic etching. In this study, we investigated: using MATLAB for mask designs; feasibility of using 1 μm Heidelberg mask maker to direct write patterns onto photoresist; using RIE processing to etch patterns into a silicon substrate; and the ability to tailor etch selectivity for precise fabrication. To determine etch rates and to obtain desired etch selectivity, parameters such as gas mixture, gas flow, and electrode power were studied. This process successfully demonstrates the ability to use gray-scale lithography and RIE for use in the study of micro-contacts. These results were used to produce a known engineered non-planer surface for testing micro-contacts. Surface structures are between 5 μm and 20 μm wide with varying depths and slopes based on mask design and etch rate selectivity. The engineered surfaces will provide more insight into contact geometries and failure modes of fixed-fixed micro-contacts.

Accelerating FRET between Near-Infrared Emitting Quantum Dots Using a Molecular J-Aggregate as an Exciton Bridge.

PubMed

Wang, Chen; Weiss, Emily A

2017-09-13

Fast energy transfer (EnT) among quantum dots (QDs) with near-infrared (NIR) emission is essential for fully exploiting their light harvesting and photon downconversion (multiexciton generation) abilities. This paper demonstrates a relayed EnT mechanism that accelerates the migration of NIR excitons between PbS QDs by a factor of 20 from that of one-step EnT through a polyelectrolyte and even a factor of ∼2 from that of one-step EnT between QDs in direct contact, by employing a J-aggregate (J-agg) of a cyanine dye as an exciton bridge. The donor QDs, acceptor QDs, and J-agg are electrostatically assembled into a sandwich structure with layer-by-layer deposition. Estimates of EnT rate and yield from transient and steady-state absorption and photoluminescence spectroscopies show that the rate-limiting step in the relay is EnT from the donor QD to the J-agg, while EnT from the J-agg to the acceptor QD occurs in <10 ps. A comparison of this system to the analogous solution-phase system suggests that the overall donor-to-acceptor EnT yield in the relay (18%) can be improved by depositing the J-agg with more intermolecular order. This work demonstrates the viability of relayed EnT through a molecular bridge as a strategy for accelerating long-distance exciton migration in assemblies of QDs, in particular in the near-infrared.

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Savara, Aditya

2017-10-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of "KMC stiffness" (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps/CPU time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events-allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm is designed for use in achieving and simulating steady-state conditions in KMC simulations. As shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Biocatalytic oxidation by chloroperoxidase from Caldariomyces fumago in polymersome nanoreactors.

PubMed

de Hoog, H M; Nallani, M; Cornelissen, J J L M; Rowan, A E; Nolte, R J M; Arends, I W C E

2009-11-21

The encapsulation of chloroperoxidase from Caldariomyces fumago (CPO) in block copolymer polymersomes is reported. Fluorescence and electron microscopy show that when the encapsulating conditions favour self-assembly of the block copolymer, the enzyme is incorporated with concentrations that are 50 times higher than the enzyme concentration before encapsulation. The oxidation of two substrates by the encapsulated enzyme was studied: i) pyrogallol, a common substrate used to assay CPO enzymatic activity and ii) thioanisole, of which the product, (R)-methyl phenyl sulfoxide, is an important pharmaceutical intermediate. The CPO-loaded polymersomes showed distinct reactivity towards these substrates. While the oxidation of pyrogallol was limited by diffusion of the substrate into the polymersome, the rate-limiting step for the oxidation of thioansiole was the turnover by the enzyme.

Erosion of stereochemical control with increasing nucleophilicity: O-glycosylation at the diffusion limit.

PubMed

Beaver, Matthew G; Woerpel, K A

2010-02-19

Nucleophilic substitution reactions of 2-deoxyglycosyl donors indicated that the reactivity of the oxygen nucleophile has a significant impact on stereoselectivity. Employing ethanol as the nucleophile resulted in a 1:1 (alpha:beta) ratio of diastereomers under S(N)1-like reaction conditions. Stereoselective formation of the 2-deoxy-alpha-O-glycoside was only observed when weaker nucleophiles, such as trifluoroethanol, were employed. The lack of stereoselectivity observed in reactions of common oxygen nucleophiles can be attributed to reaction rates of the stereochemistry-determining step that approach the diffusion limit. In this scenario, both faces of the prochiral oxocarbenium ion are subject to nucleophilic addition to afford a statistical mixture of diastereomeric products. Control experiments confirmed that all nucleophilic substitution reactions were performed under kinetic control.

Sustainable development goals and the human resources crisis.

PubMed

Freer, Joseph

2017-01-01

Achieving universal health coverage by 2030 requires that lessons from the Millennium Development Goals must be heeded. The most important lesson is that the workforce underpins every function of the health system, and is the rate-limiting step. The three dimensions that continue to limit the success of the development agenda are availability, distribution and performance of health workers - and the Sustainable Development Goals cannot be achieved without addressing all three. Hence, the traditional response of scaling up supply is inadequate: a paradigm shift is required in the design of systems that can properly identify, train, allocate and retain health workers. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The wireless Web and patient care.

PubMed

Bergeron, B P

2001-01-01

Wireless computing, when integrated with the Web, is poised to revolutionize the practice and teaching of medicine. As vendors introduce wireless Web technologies in the medical community that have been used successfully in the business and consumer markets, clinicians can expect profound increases in the amount of patient data, as well as the ease with which those data are acquired, analyzed, and disseminated. The enabling technologies involved in this transformation to the wireless Web range from the new generation of wireless PDAs, eBooks, and wireless data acquisition peripherals to new wireless network protocols. The rate-limiting step in the application of this technology in medicine is not technology per se but rather how quickly clinicians and their patients come to accept and appreciate the benefits and limitations of the application of wireless Web technology.

The relationship between communication scores from the USMLE Step 2 Clinical Skills examination and communication ratings for first-year internal medicine residents.

PubMed

Winward, Marcia L; Lipner, Rebecca S; Johnston, Mary M; Cuddy, Monica M; Clauser, Brian E

2013-05-01

This study extends available evidence about the relationship between scores on the Step 2 Clinical Skills (CS) component of the United States Medical Licensing Examination and subsequent performance in residency. It focuses on the relationship between Step 2 CS communication and interpersonal skills scores and communication skills ratings that residency directors assign to residents in their first postgraduate year of internal medicine training. It represents the first large-scale evaluation of the extent to which Step 2 CS communication and interpersonal skills scores can be extrapolated to examinee performance in supervised practice. Hierarchical linear modeling techniques were used to examine the relationships among examinee characteristics, residency program characteristics, and residency-director-provided ratings. The sample comprised 6,306 examinees from 238 internal medicine residency programs who completed Step 2 CS for the first time in 2005 and received ratings during their first year of internal medicine residency training. Although the relationship is modest, Step 2 CS communication and interpersonal skills scores predict communication skills ratings for first-year internal medicine residents after accounting for other factors. The results of this study make a reasonable case that Step 2 CS communication and interpersonal skills scores provide useful information for predicting the level of communication skill that examinees will display in their first year of internal medicine residency training. This finding demonstrates some level of extrapolation from the testing context to behavior in supervised practice, thus providing validity-related evidence for using Step 2 CS communication and interpersonal skills scores in high-stakes decisions.

The potential role of sea spray droplets in facilitating air-sea gas transfer

NASA Astrophysics Data System (ADS)

Andreas, E. L.; Vlahos, P.; Monahan, E. C.

2016-05-01

For over 30 years, air-sea interaction specialists have been evaluating and parameterizing the role of whitecap bubbles in air-sea gas exchange. To our knowledge, no one, however, has studied the mirror image process of whether sea spray droplets can facilitate air-sea gas exchange. We are therefore using theory, data analysis, and numerical modeling to quantify the role of spray on air-sea gas transfer. In this, our first formal work on this subject, we seek the rate-limiting step in spray-mediated gas transfer by evaluating the three time scales that govern the exchange: τ air , which quantifies the rate of transfer between the atmospheric gas reservoir and the surface of the droplet; τ int , which quantifies the exchange rate across the air-droplet interface; and τ aq , which quantifies gas mixing within the aqueous solution droplet.

Redox Chemistry in Laccase-Catalyzed Oxidation of N-Hydroxy Compounds

PubMed Central

Xu, Feng; Kulys, Juozas J.; Duke, Kyle; Li, Kaichang; Krikstopaitis, Kastis; Deussen, Heinz-Josef W.; Abbate, Eric; Galinyte, Vilija; Schneider, Palle

2000-01-01

1-Hydroxybenzotriazole, violuric acid, and N-hydroxyacetanilide are three N-OH compounds capable of mediating a range of laccase-catalyzed biotransformations, such as paper pulp delignification and degradation of polycyclic hydrocarbons. The mechanism of their enzymatic oxidation was studied with seven fungal laccases. The oxidation had a bell-shaped pH-activity profile with an optimal pH ranging from 4 to 7. The oxidation rate was found to be dependent on the redox potential difference between the N-OH substrate and laccase. A laccase with a higher redox potential or an N-OH compound with a lower redox potential tended to have a higher oxidation rate. Similar to the enzymatic oxidation of phenols, phenoxazines, phenothiazines, and other redox-active compounds, an “outer-sphere” type of single-electron transfer from the substrate to laccase and proton release are speculated to be involved in the rate-limiting step for N-OH oxidation. PMID:10788380

Engagement and Retention of Suicide Attempters in Clinical Research

PubMed Central

Gibbons, Carly J.; Stirman, Shannon Wiltsey; Brown, Gregory K.; Beck, Aaron T.

2010-01-01

Background High attrition rates in longitudinal research can limit study generalizability, threaten internal validity, and decrease statistical power. Research has demonstrated that there can be significant differences between participants who complete a research study and those who drop out prematurely, and that treatment outcomes may be dependent on retention in a treatment protocol. Aims The current paper describes the challenges encountered when implementing a randomized controlled trial of cognitive therapy for the prevention of suicide attempts and the solutions developed to overcome these problems. Methods Problems unique to suicide attempters are discussed, and strategies successfully implemented to boost retention rates are provided. Results The methods implemented appeared to increase retention rates in the randomized controlled trial. Conclusions Many steps can be taken to work with this difficult population, and researchers are encouraged to be as involved and flexible with participants as possible. PMID:20418211

Evaluation of a Rapid One-step Real-time PCR Method as a High-throughput Screening for Quantification of Hepatitis B Virus DNA in a Resource-limited Setting.

PubMed

Rashed-Ul Islam, S M; Jahan, Munira; Tabassum, Shahina

2015-01-01

Virological monitoring is the best predictor for the management of chronic hepatitis B virus (HBV) infections. Consequently, it is important to use the most efficient, rapid and cost-effective testing systems for HBV DNA quantification. The present study compared the performance characteristics of a one-step HBV polymerase chain reaction (PCR) vs the two-step HBV PCR method for quantification of HBV DNA from clinical samples. A total of 100 samples consisting of 85 randomly selected samples from patients with chronic hepatitis B (CHB) and 15 samples from apparently healthy individuals were enrolled in this study. Of the 85 CHB clinical samples tested, HBV DNA was detected from 81% samples by one-step PCR method with median HBV DNA viral load (VL) of 7.50 × 10 3 lU/ml. In contrast, 72% samples were detected by the two-step PCR system with median HBV DNA of 3.71 × 10 3 lU/ml. The one-step method showed strong linear correlation with two-step PCR method (r = 0.89; p < 0.0001). Both methods showed good agreement at Bland-Altman plot, with a mean difference of 0.61 log 10 IU/ml and limits of agreement of -1.82 to 3.03 log 10 IU/ml. The intra-assay and interassay coefficients of variation (CV%) of plasma samples (4-7 log 10 IU/ml) for the one-step PCR method ranged between 0.33 to 0.59 and 0.28 to 0.48 respectively, thus demonstrating a high level of concordance between the two methods. Moreover, elimination of the DNA extraction step in the one-step PCR kit allowed time-efficient and significant labor and cost savings for the quantification of HBV DNA in a resource limited setting. Rashed-Ul Islam SM, Jahan M, Tabassum S. Evaluation of a Rapid One-step Real-time PCR Method as a High-throughput Screening for Quantification of Hepatitis B Virus DNA in a Resource-limited Setting. Euroasian J Hepato-Gastroenterol 2015;5(1):11-15.

Evaluation of a Rapid One-step Real-time PCR Method as a High-throughput Screening for Quantification of Hepatitis B Virus DNA in a Resource-limited Setting

PubMed Central

Jahan, Munira; Tabassum, Shahina

2015-01-01

Virological monitoring is the best predictor for the management of chronic hepatitis B virus (HBV) infections. Consequently, it is important to use the most efficient, rapid and cost-effective testing systems for HBV DNA quantification. The present study compared the performance characteristics of a one-step HBV polymerase chain reaction (PCR) vs the two-step HBV PCR method for quantification of HBV DNA from clinical samples. A total of 100 samples consisting of 85 randomly selected samples from patients with chronic hepatitis B (CHB) and 15 samples from apparently healthy individuals were enrolled in this study. Of the 85 CHB clinical samples tested, HBV DNA was detected from 81% samples by one-step PCR method with median HBV DNA viral load (VL) of 7.50 × 103 lU/ml. In contrast, 72% samples were detected by the two-step PCR system with median HBV DNA of 3.71 × 103 lU/ml. The one-step method showed strong linear correlation with two-step PCR method (r = 0.89; p < 0.0001). Both methods showed good agreement at Bland-Altman plot, with a mean difference of 0.61 log10 IU/ml and limits of agreement of -1.82 to 3.03 log10 IU/ml. The intra-assay and interassay coefficients of variation (CV%) of plasma samples (4-7 log10 IU/ml) for the one-step PCR method ranged between 0.33 to 0.59 and 0.28 to 0.48 respectively, thus demonstrating a high level of concordance between the two methods. Moreover, elimination of the DNA extraction step in the one-step PCR kit allowed time-efficient and significant labor and cost savings for the quantification of HBV DNA in a resource limited setting. How to cite this article Rashed-Ul Islam SM, Jahan M, Tabassum S. Evaluation of a Rapid One-step Real-time PCR Method as a High-throughput Screening for Quantification of Hepatitis B Virus DNA in a Resource-limited Setting. Euroasian J Hepato-Gastroenterol 2015;5(1):11-15. PMID:29201678

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gavva, S.R.; Harris, B.G.; Cook, P.F.

A thiol group at the malate-binding site of the NAD-malic enzyme from Ascaris suum has been modified to thiocyanate. The modified enzyme generally exhibits slight increases in K{sub NAD} and K{sub i metal} and decreases in V{sub max} as the metal size increases from Mg{sup 2+} to Mn{sup 2+} to Cd{sup 2+}, indicative of crowding in the site. The K{sub malate} value increases 10- to 30-fold, suggesting that malate does not bind optimally to the modified enzyme. Deuterium isotope effects on V and V/K{sub malate} increase with all three metal ions compared to the native enzyme concomitant with a decreasemore » in the {sup 13}C isotope effect, suggesting a switch in the rate limitation of the hydride transfer and decarboxylation steps with hydride transfer becoming more rate limiting. The {sup 13}C effect decreases only slightly when obtained with deuterated malate, suggestive of the presence of a secondary {sup 13}C effect in the hydride transfer step, similar to data obtained with non-nicotinamide-containing dinucleotide substrates for the native enzyme (see the preceding paper in this issue). The native enzyme is inactivated in a time-dependent manner by Cd{sup 2+}. This inactivation occurs whether the enzyme alone is present or whether the enzyme is turning over with Cd{sup 2+} as the divalent metal activator. Upon inactivation, only Cd{sup 2+} ions are bound at high stoichiometry to the enzyme, which eventually becomes denatured. Conversion of the active-site thiol to thiocyanate makes it more difficult to inactivate the enzyme by treatment with Cd{sup 2+}.« less

Contribution of first- versus second-generation products to secondary organic aerosols formed in the oxidation of biogenic hydrocarbons.

PubMed

Ng, Nga L; Kroll, Jesse H; Keywood, Melita D; Bahreini, Roya; Varutbangkul, Varuntida; Flagan, Richard C; Seinfeld, John H; Lee, Anita; Goldstein, Allen H

2006-04-01

Biogenic hydrocarbons emitted by vegetation are important contributors to secondary organic aerosol (SOA), but the aerosol formation mechanisms are incompletely understood. In this study, the formation of aerosols and gas-phase products from the ozonolysis and photooxidation of a series of biogenic hydrocarbons (isoprene, 8 monoterpenes, 4 sesquiterpenes, and 3 oxygenated terpenes) are examined. By comparing aerosol growth (measured by Differential Mobility Analyzers, DMAs) and gas-phase concentrations (monitored by a Proton Transfer Reaction Mass Spectrometer, PTR-MS), we study the general mechanisms of SOA formation. Aerosol growth data are presented in terms of a "growth curve", a plot of aerosol mass formed versus the amount of hydrocarbon reacted. From the shapes of the growth curves, it is found that all the hydrocarbons studied can be classified into two groups based entirely on the number of double bonds of the hydrocarbon, regardless of the reaction systems (ozonolysis or photooxidation) and the types of hydrocarbons studied: compounds with only one double bond and compounds with more than one double bond. For compounds with only one double bond, the first oxidation step is rate-limiting, and aerosols are formed mainly from low volatility first-generation oxidation products; whereas for compounds with more than one double bond, the second oxidation step may also be rate-limiting and second-generation products contribute substantially to SOA growth. This behavior is characterized by a vertical section in the growth curve, in which continued aerosol growth is observed even after all the parent hydrocarbon is consumed.

Accuracy of the Garmin 920 XT HRM to perform HRV analysis.

PubMed

Cassirame, Johan; Vanhaesebrouck, Romain; Chevrolat, Simon; Mourot, Laurent

2017-12-01

Heart rate variability (HRV) analysis is widely used to investigate autonomous cardiac drive. This method requires periodogram measurement, which can be obtained by an electrocardiogram (ECG) or from a heart rate monitor (HRM), e.g. the Garmin 920 XT device. The purpose of this investigation was to assess the accuracy of RR time series measurements from a Garmin 920 XT HRM as compared to a standard ECG, and to verify whether the measurements thus obtained are suitable for HRV analysis. RR time series were collected simultaneously with an ECG (Powerlab system, AD Instruments, Castell Hill, Australia) and a Garmin XT 920 in 11 healthy subjects during three conditions, namely in the supine position, the standing position and during moderate exercise. In a first step, we compared RR time series obtained with both tools using the Bland and Altman method to obtain the limits of agreement in all three conditions. In a second step, we compared the results of HRV analysis between the ECG RR time series and Garmin 920 XT series. Results show that the accuracy of this system is in accordance with the literature in terms of the limits of agreement. In the supine position, bias was 0.01, - 2.24, + 2.26 ms; in the standing position, - 0.01, - 3.12, + 3.11 ms respectively, and during exercise, - 0.01, - 4.43 and + 4.40 ms. Regarding HRV analysis, we did not find any difference for HRV analysis in the supine position, but the standing and exercise conditions both showed small modifications.

Magnesite Step Growth Rates as a Function of the Aqueous Magnesium:Carbonate Ratio

DOE PAGES

Bracco, Jacquelyn N.; Stack, Andrew G.; Higgins, Steven R.

2014-10-01

Step velocities of monolayer-height steps on the (101 ⁻4) magnesite surface have been measured as functions of the aqueous magnesium-to-carbonate ratio and saturation index (SI) using a hydrothermal atomic force microscope (HAFM). At SI ≤ 1.9 and 80-90 °C, step velocities were found to be invariant with changes in the magnesium-to-carbonate ratio, an observation in contrast with standard models for growth and dissolution of ionically-bonded, multi-component crystals. However, at high saturation indices (SI = 2.15), step velocities displayed a ratio dependence, maximized at magnesium-to-carbonate ratios slightly greater than 1:1. Traditional affinity-based models were unable to describe growth rates at themore » higher saturation index. Step velocities also could not be modeled solely through nucleation of kink sites, in contrast to other minerals whose bonding between constituent ions is also dominantly ionic in nature, such as calcite and barite. Instead, they could be described only by a model that incorporates both kink nucleation and propagation. Based on observed step morphological changes at these higher saturation indices, the step velocity maximum at SI = 2.15 is likely due to the rate of attachment to propagating kink sites overcoming the rate of detachment from kink sites as the latter becomes less significant under far from equilibrium conditions.« less

Development and validation of an affinity chromatography step using a peptide ligand for cGMP production of factor VIII.

PubMed

Kelley, Brian D; Tannatt, Molly; Magnusson, Robert; Hagelberg, Sigrid; Booth, James

2004-08-05

An affinity chromatography step was developed for purification of recombinant B-Domain Deleted Factor VIII (BDDrFVIII) using a peptide ligand selected from a phage display library. The peptide library had variegated residues, contained both within a disulfide bond-constrained ring and flanking the ring. The peptide ligand binds to BDDrFVIII with a dissociation constant of approximately 1 microM both in free solution and when immobilized on a chromatographic resin. The peptide is chemically synthesized and the affinity resin is produced by coupling the peptide to an agarose matrix preactivated with N-hydroxysuccinimide. Coupling conditions were optimized to give consistent and complete ligand incorporation and validated with a robustness study that tested various combinations of processing limits. The peptide affinity chromatographic operation employs conditions very similar to an immunoaffinity chromatography step currently in use for BDDrFVIII manufacture. The process step provides excellent recovery of BDDrFVIII from a complex feed stream and reduces host cell protein and DNA by 3-4 logs. Process validation studies established resin reuse over 26 cycles without changes in product recovery or purity. A robustness study using a factorial design was performed and showed that the step was insensitive to small changes in process conditions that represent normal variation in commercial manufacturing. A scaled-down model of the process step was qualified and used for virus removal studies. A validation package addressing the safety of the leached peptide included leaching rate measurements under process conditions, testing of peptide levels in product pools, demonstration of robust removal downstream by spiking studies, end product testing, and toxicological profiling of the ligand. The peptide ligand affinity step was scaled up for cGMP production of BDDrFVIII for clinical trials.

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

40 CFR 35.909 - Step 2+3 grants.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ASSISTANCE Grants for Construction of Treatment Works-Clean Water Act § 35.909 Step 2+3 grants. (a) Authority... design (step 2) and construction (step 3) of a waste water treatment works. (b) Limitations. The Regional... Water and Waste Management finds to have unusually high costs of construction, the Regional...

40 CFR 35.909 - Step 2+3 grants.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ASSISTANCE Grants for Construction of Treatment Works-Clean Water Act § 35.909 Step 2+3 grants. (a) Authority... design (step 2) and construction (step 3) of a waste water treatment works. (b) Limitations. The Regional... Water and Waste Management finds to have unusually high costs of construction, the Regional...

40 CFR 35.909 - Step 2+3 grants.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ASSISTANCE Grants for Construction of Treatment Works-Clean Water Act § 35.909 Step 2+3 grants. (a) Authority... design (step 2) and construction (step 3) of a waste water treatment works. (b) Limitations. The Regional... Water and Waste Management finds to have unusually high costs of construction, the Regional...

40 CFR 35.909 - Step 2+3 grants.

Code of Federal Regulations, 2011 CFR

2011-07-01

... design (step 2) and construction (step 3) of a waste water treatment works. (b) Limitations. The Regional... ASSISTANCE Grants for Construction of Treatment Works-Clean Water Act § 35.909 Step 2+3 grants. (a) Authority... Water and Waste Management finds to have unusually high costs of construction, the Regional...

Formation mechanism of the secondary building unit in a chromium terephthalate metal-organic framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu Cantu, David; McGrail, B. Peter; Glezakou, Vassiliki Alexandra

2014-09-18

Based on density functional theory calculations and simulation, a detailed mechanism is presented on the formation of the secondary building unit (SBU) of MIL-101, a chromium terephthalate metal-organic framework (MOF). SBU formation is key to MOF nucleation, the rate-limiting step in the formation process of many MOFs. A series of reactions that lead to the formation of the SBU of MIL-101 is proposed in this work. Initial rate-limiting reactions form the metal cluster with three chromium (III) atoms linked to a central bridging oxygen. Terephthalate linkers play a key role as chromium (III) atoms are joined to linker carboxylate groupsmore » prior to the placement of the central bridging oxygen. Multiple linker addition reactions, which follow in different paths due to structural isomers, are limited by the removal of water molecules in the first chromium coordination shell. The least energy path is identified were all linkers on one face of the metal center plane are added first. A simple kinetic model based on transition state theory shows the rate of secondary building unit formation similar to the rate metal-organic framework nucleation. The authors are thankful to Dr. R. Rousseau for a critical reading of the manuscript. This research would not have been possible without the support of the Office of Fossil Energy, U.S. Department of Energy. This research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and the PNNL Institutional Computing (PIC) program located at Pacific Northwest National Laboratory.« less

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

PubMed

Harris, Michael E; Piccirilli, Joseph A; York, Darrin M

2015-11-01

The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

Quantum chemical investigation on photodegradation mechanisms of sulfamethoxypyridazine with dissolved inorganic matter and hydroxyl radical.

PubMed

Shah, Shaheen; Hao, Ce

2017-07-01

Sulfamethoxypyridazine (SMP) is one of the commonly used sulfonamide antibiotics (SAs). SAs are mainly studied to undergo triplet-sensitized photodegradation in water under natural sunlight with other coexisting aquatic environmental organic pollutants. In this work, SMP was selected as a representative of SAs. We studied the mechanisms of triplet-sensitized photodegradation of SMP and the influence of selected dissolved inorganic matter, i.e., anions (Br - , Cl - , and NO 3 - ) and cations ions (Ca 2+ , Mg 2+ , and Zn 2+ ) on SMP photodegradation mechanism by quantum chemical methods. In addition, the degradation mechanisms of SMP by hydroxyl radical (OH) were also investigated. The creation of SO 2 extrusion product was accessed with two different energy pathways (pathway-1 and pathway-2) by following two steps (step-I and step-II) in the triplet-sensitized photodegradation of SMP. Due to low activation energy, the pathway-1 was considered as the main pathway to obtain SO 2 extrusion product. Step-II of pathway-1 was measured to be the rate-limiting step (RLS) of SMP photodegradation mechanism and the effect of the selected anions and cations was estimated for this step. All selected anions and cations promoted photodegradation of SMP by dropping the activation energy of pathway-1. The estimated low activation energies of different degradation pathways of SMP with OH radical indicate that OH radical is a very powerful oxidizing agent for SMP degradation via attack through benzene derivative and pyridazine derivative ring. Copyright © 2016. Published by Elsevier B.V.

In-vitro development of vitrified-warmed bovine oocytes after activation may be predicted based on mathematical modelling of cooling and warming rates during vitrification, storage and sample removal.

PubMed

Sansinena, Marina; Santos, Maria Victoria; Chirife, Jorge; Zaritzky, Noemi

2018-05-01

Heat transfer during cooling and warming is difficult to measure in cryo-devices; mathematical modelling is an alternative method that can describe these processes. In this study, we tested the validity of one such model by assessing in-vitro development of vitrified and warmed bovine oocytes after parthenogenetic activation and culture. The viability of oocytes vitrified in four different cryo-devices was assessed. Consistent with modelling predictions, oocytes vitrified using cryo-devices with the highest modelled cooling rates had significantly (P < 0.05) better cleavage and blastocyst formation rates. We then evaluated a two-step sample removal process, in which oocytes were held in nitrogen vapour for 15 s to simulate sample identification during clinical application, before being removed completely and warmed. Oocytes exposed to this procedure showed reduced developmental potential, according to the model, owing to thermodynamic instability and devitrification at relatively low temperatures. These findings suggest that cryo-device selection and handling, including method of removal from nitrogen storage, are critical to survival of vitrified oocytes. Limitations of the study include use of parthenogenetically activated rather than fertilized ova and lack of physical measurement of recrystallization. We suggest mathematical modelling could be used to predict the effect of critical steps in cryopreservation. Copyright © 2018 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Intraprotein electron transfer between the FMN and heme domains in endothelial nitric oxide synthase holoenzyme

PubMed Central

Feng, Changjian; Taiakina, Valentina; Ghosh, Dipak K.; Guillemette, J. Guy; Tollin, Gordon

2011-01-01

Intraprotein electron transfer (IET) from flavin mononucleotide (FMN) to heme is an essential step in nitric oxide (NO) synthesis by NO synthase (NOS). The IET kinetics in neuronal and inducible NOS (nNOS and iNOS) holoenzymes have been previously determined in our laboratories by laser flash photolysis [reviewed in: C.J. Feng, G. Tollin, Dalton Trans., (2009) 6692-6700]. Here we report the kinetics of the IET in a bovine endothelial NOS (eNOS) holoenzyme in the presence and absence of added calmodulin (CaM). The IET rate constant in the presence of CaM is estimated to be ~ 4.3 s-1. No IET was observed in the absence of CaM, indicating that CaM is the primary factor in controlling the FMN–heme IET in the eNOS enzyme. The IET rate constant value for the eNOS holoenzyme is approximately 10 times smaller than those obtained for the iNOS and CaM-bound nNOS holoenzymes. Possible mechanisms underlying the difference in IET kinetics among the NOS isoforms are discussed. Because the rate-limiting step in the IET process in these enzymes is the conformational change from input state to output state, a slower conformational change (than in the other isoforms) is most likely to cause the slower IET in eNOS. PMID:21864726

Decomposition behavior of hemicellulose and lignin in the step-change flow rate liquid hot water.

PubMed

Zhuang, Xinshu; Yu, Qiang; Wang, Wen; Qi, Wei; Wang, Qiong; Tan, Xuesong; Yuan, Zhenhong

2012-09-01

Hemicellulose and lignin are the main factors limiting accessibility of hydrolytic enzymes besides the crystallinity of cellulose. The decomposition behavior of hemicellulose and lignin in the step-change flow rate hot water system was investigated. Xylan removal increased from 64.53% for batch system (solid concentration 4.25% w/v, 18 min, 184°C) to 83.78% at high flow rates of 30 ml/min for 8 min, and then 10 ml/min for 10 min. Most of them (80-90%) were recovered as oligosaccharide. It was hypothesized that the flowing water could enhance the mass transfer to improve the sugars recovery. In addition, the solubilization mechanism of lignin in the liquid hot water was proposed according to the results of Fourier transform-infrared spectroscopy and scanning electron microscopy of the water-insoluble fraction and gas chromatography-mass spectrometry of the water-soluble fraction. It was proposed that lignin in the liquid hot water first migrated out of the cell wall in the form of molten bodies, and then flushed out of the reactor. A small quantity of them was further degraded into monomeric products such as vanillin, syringe aldehyde, coniferyl aldehyde, ferulic acid, and p-hydroxy-cinnamic acid. All of these observations would provide important information for the downstream processing, such as purification and concentration of sugars and the enzymatic digestion of residual solid.

Reconstruction of Jakobshavn Isbrae's calving dynamics from 1985 to 2017 and sensitivity to future ocean forcing

NASA Astrophysics Data System (ADS)

Bondzio, J. H.; Morlighem, M.; Seroussi, H. L.

2017-12-01

Oceanic forcing is likely to have triggered the breakup of Jakobshavn Isbræ's floating ice tongue in the late 1990s, which led to ongoing dynamic changes such as widespread flow acceleration and mass loss. Our understanding of the link between ice dynamics, oceanic forcing, and calving is limited, yet crucial for prognostic simulations of Jakobshavn Isbræ. Here, we first reconstruct Jakobshavn's calving dynamics from 1985 to 2017, by relying on the model from Bondzio et al. 2017, but with a freely evolving ice front. We test different calving rate parameterizations implemented in the Ice Sheet System Model (ISSM) and determine the best law by comparing the modeled retreat to observations. We then identify the controls on calving rate and ice front retreat by varying the submarine melting rate and frontal melt rates as a function of subglacial water discharge and ocean thermal forcing. This sensitivity analysis is an important step toward performing prognostic simulations of JI and provides pathways for future data acquisition.

Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Shirong; Davis, Michael J.; Skodje, Rex T.

2015-11-12

The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of howmore » that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H-2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux« less

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE PAGES

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi; ...

2016-12-30

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

In VIVO tracer kinetics of plant function using positron emission technology

NASA Astrophysics Data System (ADS)

Fares, Y.; Goeschl, J. D.; Magnuson, C. E.; Mckinney, C. J.; Musser, R. L.; Strain, B. R.

1989-04-01

A 11CO 2 storage and dispensing system was developed and used successfully to deliver constant activity levels for 2 h plant tracer experiments. Using tracer kinetics of a step input function the relationships between diurnal patterns of carbon partitioning and gas exchange properties of leaves in C 3 and C 4 plants were studied. We also studied the immediate and long term effects of the abrupt changes in CO 2 concentrations on carbon partitioning of these species. Results indicate that raising the CO 2 concentration above ambient immediately increases 11C storage over export rates, while lowering the CO 2 concentration immediately decreases storage more than export rates. This long term accumulation of starch may depend as much on the biochemistry of partitioning within the leaf as on limitations in the sink capacity of plants. Although gas exchange remained constant during the photoperiod, the photosynthate storage rate increased and the export rate decreased. These changes were more pronounced in C 4 plants.

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Daily step count predicts acute exacerbations in a US cohort with COPD.

PubMed

Moy, Marilyn L; Teylan, Merilee; Weston, Nicole A; Gagnon, David R; Garshick, Eric

2013-01-01

COPD is characterized by variability in exercise capacity and physical activity (PA), and acute exacerbations (AEs). Little is known about the relationship between daily step count, a direct measure of PA, and the risk of AEs, including hospitalizations. In an observational cohort study of 169 persons with COPD, we directly assessed PA with the StepWatch Activity Monitor, an ankle-worn accelerometer that measures daily step count. We also assessed exercise capacity with the 6-minute walk test (6MWT) and patient-reported PA with the St. George's Respiratory Questionnaire Activity Score (SGRQ-AS). AEs and COPD-related hospitalizations were assessed and validated prospectively over a median of 16 months. Mean daily step count was 5804±3141 steps. Over 209 person-years of observation, there were 263 AEs (incidence rate 1.3±1.6 per person-year) and 116 COPD-related hospitalizations (incidence rate 0.56±1.09 per person-year). Adjusting for FEV1 % predicted and prednisone use for AE in previous year, for each 1000 fewer steps per day walked at baseline, there was an increased rate of AEs (rate ratio 1.07; 95%CI = 1.003-1.15) and COPD-related hospitalizations (rate ratio 1.24; 95%CI = 1.08-1.42). There was a significant linear trend of decreasing daily step count by quartiles and increasing rate ratios for AEs (P = 0.008) and COPD-related hospitalizations (P = 0.003). Each 30-meter decrease in 6MWT distance was associated with an increased rate ratio of 1.07 (95%CI = 1.01-1.14) for AEs and 1.18 (95%CI = 1.07-1.30) for COPD-related hospitalizations. Worsening of SGRQ-AS by 4 points was associated with an increased rate ratio of 1.05 (95%CI = 1.01-1.09) for AEs and 1.10 (95%CI = 1.02-1.17) for COPD-related hospitalizations. Lower daily step count, lower 6MWT distance, and worse SGRQ-AS predict future AEs and COPD-related hospitalizations, independent of pulmonary function and previous AE history. These results support the importance of assessing PA in patients with COPD, and provide the rationale to promote PA as part of exacerbation-prevention strategies.

Investigating calcite growth rates using a quartz crystal microbalance with dissipation (QCM-D)

NASA Astrophysics Data System (ADS)

Cao, Bo; Stack, Andrew G.; Steefel, Carl I.; DePaolo, Donald J.; Lammers, Laura N.; Hu, Yandi

2018-02-01

Calcite precipitation plays a significant role in processes such as geological carbon sequestration and toxic metal sequestration and, yet, the rates and mechanisms of calcite growth under close to equilibrium conditions are far from well understood. In this study, a quartz crystal microbalance with dissipation (QCM-D) was used for the first time to measure macroscopic calcite growth rates. Calcite seed crystals were first nucleated and grown on sensors, then growth rates of calcite seed crystals were measured in real-time under close to equilibrium conditions (saturation index, SI = log ({Ca2+}/{CO32-}/Ksp) = 0.01-0.7, where {i} represent ion activities and Ksp = 10-8.48 is the calcite thermodynamic solubility constant). At the end of the experiments, total masses of calcite crystals on sensors measured by QCM-D and inductively coupled plasma mass spectrometry (ICP-MS) were consistent, validating the QCM-D measurements. Calcite growth rates measured by QCM-D were compared with reported macroscopic growth rates measured with auto-titration, ICP-MS, and microbalance. Calcite growth rates measured by QCM-D were also compared with microscopic growth rates measured by atomic force microscopy (AFM) and with rates predicted by two process-based crystal growth models. The discrepancies in growth rates among AFM measurements and model predictions appear to mainly arise from differences in step densities, and the step velocities were consistent among the AFM measurements as well as with both model predictions. Using the predicted steady-state step velocity and the measured step densities, both models predict well the growth rates measured using QCM-D and AFM. This study provides valuable insights into the effects of reactive site densities on calcite growth rate, which may help design future growth models to predict transient-state step densities.

Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland.

PubMed

Wild, Birgit; Schnecker, Jörg; Bárta, Jiří; Capek, Petr; Guggenberger, Georg; Hofhansl, Florian; Kaiser, Christina; Lashchinsky, Nikolaj; Mikutta, Robert; Mooshammer, Maria; Santrůčková, Hana; Shibistova, Olga; Urich, Tim; Zimov, Sergey A; Richter, Andreas

2013-12-01

Turbic Cryosols (permafrost soils characterized by cryoturbation, i.e., by mixing of soil layers due to freezing and thawing) are widespread across the Arctic, and contain large amounts of poorly decomposed organic material buried in the subsoil. This cryoturbated organic matter exhibits retarded decomposition compared to organic material in the topsoil. Since soil organic matter (SOM) decomposition is known to be tightly linked to N availability, we investigated N transformation rates in different soil horizons of three tundra sites in north-eastern Siberia and Greenland. We measured gross rates of protein depolymerization, N mineralization (ammonification) and nitrification, as well as microbial uptake of amino acids and NH 4 + using an array of 15 N pool dilution approaches. We found that all sites and horizons were characterized by low N availability, as indicated by low N mineralization compared to protein depolymerization rates (with gross N mineralization accounting on average for 14% of gross protein depolymerization). The proportion of organic N mineralized was significantly higher at the Greenland than at the Siberian sites, suggesting differences in N limitation. The proportion of organic N mineralized, however, did not differ significantly between soil horizons, pointing to a similar N demand of the microbial community of each horizon. In contrast, absolute N transformation rates were significantly lower in cryoturbated than in organic horizons, with cryoturbated horizons reaching not more than 32% of the transformation rates in organic horizons. Our results thus indicate a deceleration of the entire N cycle in cryoturbated soil horizons, especially strongly reduced rates of protein depolymerization (16% of organic horizons) which is considered the rate-limiting step in soil N cycling.

A WENO-Limited, ADER-DT, Finite-Volume Scheme for Efficient, Robust, and Communication-Avoiding Multi-Dimensional Transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norman, Matthew R

2014-01-01

The novel ADER-DT time discretization is applied to two-dimensional transport in a quadrature-free, WENO- and FCT-limited, Finite-Volume context. Emphasis is placed on (1) the serial and parallel computational properties of ADER-DT and this framework and (2) the flexibility of ADER-DT and this framework in efficiently balancing accuracy with other constraints important to transport applications. This study demonstrates a range of choices for the user when approaching their specific application while maintaining good parallel properties. In this method, genuine multi-dimensionality, single-step and single-stage time stepping, strict positivity, and a flexible range of limiting are all achieved with only one parallel synchronizationmore » and data exchange per time step. In terms of parallel data transfers per simulated time interval, this improves upon multi-stage time stepping and post-hoc filtering techniques such as hyperdiffusion. This method is evaluated with standard transport test cases over a range of limiting options to demonstrate quantitatively and qualitatively what a user should expect when employing this method in their application.« less

Effects of a mutation on the folding mechanism of a beta-hairpin.

PubMed

Juraszek, Jarek; Bolhuis, Peter G

2009-12-17

The folding mechanism of a protein is determined by its primary sequence. Yet, how the mechanism is changed by a mutation is still poorly understood, even for basic secondary structures such as beta-hairpins. We perform an extensive simulation study of the effects of mutating the GB1 beta-hairpin into Trpzip4 (Y5W, F12W, V14W) on the folding mechanism. While Trpzip4 has a much more stable native state due to very strong hydrophobic interactions of the side chains, its folding rate does not differ significantly from the wild type beta-hairpin. We sample the free-energy landscapes of both hairpins with Replica Exchange Molecular Dynamics (REMD) and identify the four (meta)stable states (U, H, F, and N). Using Transition Path Sampling (TPS), we then harvest ensembles of unbiased pathways between the H and F states and between the F and N states to investigate the unbiased folding mechanisms. In both hairpins, the hydrophobic collapse (U-H) is followed by the middle hydrogen bond formation (H-F), and finally a closing of the strands in a zipper-like fashion (F-N). For the Trpzip4, the path ensembles indicate that the final F-N step is much more difficult than for GB1 and involves partial unfolding, rezipping of hydrogen bonds, and rearrangement of the Trp-14 side chain. For the rate-limiting (H-F) step, the path ensembles show that in GB1 desolvation and strand closure go hand in hand, while in Trpzip4 desolvation is decoupled from strand closure. Nevertheless, likelihood maximization shows that the reaction coordinate for both hairpins remains the interstrand distance. We conclude that the folding mechanism of both hairpins is a combination of hydrophobic collapse and zipping of hydrogen bonds but that the zipper mechanism is more visible in Trpzip4. A major difference between the two hairpins is that in the transition state of the rate-limiting step for Trpzip4 one tryptophan is exposed to the solvent due to steric hindrance, making the folding mechanism more complex and leading to an increased F-N barrier. Thus, our results show in atomistic detail how a mutation leads to a different folding mechanism and results in a more frustrated folding free-energy landscape.

Force-related neuronal activity in two regions of the primate ventral premotor cortex.

PubMed

Hepp-Reymond, M C; Hüsler, E J; Maier, M A; Ql, H X

1994-05-01

Neuronal activity was recorded in the ventral premotor cortex of one monkey (Macaca fascicularis) trained to exert finely graded forces with thumb and index finger on a force sensor in a visuomotor step-tracking paradigm. Trials with two or three consecutive ramp-and-hold force steps were presented randomly. Most neurons displayed similar discharge patterns in the two- and three-step trials and were assigned to one of the following classes: phasic, phasic-tonic, tonic, decreasing, and mixed. For more than 50% of the neurons with tonic activity, positive or negative correlations between firing rate and force were statistically significant. The indices of force sensitivity were on average higher for the two-step than for the three-step trials, indicating that the correlations yielded linearity over only a limited force range. The force-related cells were located in two regions of the ventral premotor cortex. One group was ying rostrally within the inferior limb of the arcuate sulcus, from which microstimulation elicited movements of fingers and hand. In the other more caudal region, adjacent to the finger region of primary motor cortex, microstimulation was rarely effective, but all neurons had clear peripheral receptive fields on finger and hand. The data indicate that two populations of neurons, located in the ventral premotor cortex, are related to movement execution. Effective microstimulation also suggests that one of the populations has fairly direct access to the spinal motor apparatus.

Automatic segmentation of the optic nerve head for deformation measurements in video rate optical coherence tomography

NASA Astrophysics Data System (ADS)

Hidalgo-Aguirre, Maribel; Gitelman, Julian; Lesk, Mark Richard; Costantino, Santiago

2015-11-01

Optical coherence tomography (OCT) imaging has become a standard diagnostic tool in ophthalmology, providing essential information associated with various eye diseases. In order to investigate the dynamics of the ocular fundus, we present a simple and accurate automated algorithm to segment the inner limiting membrane in video-rate optic nerve head spectral domain (SD) OCT images. The method is based on morphological operations including a two-step contrast enhancement technique, proving to be very robust when dealing with low signal-to-noise ratio images and pathological eyes. An analysis algorithm was also developed to measure neuroretinal tissue deformation from the segmented retinal profiles. The performance of the algorithm is demonstrated, and deformation results are presented for healthy and glaucomatous eyes.

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

Rapid method for measuring rotenone in water at piscicidal concentrations

USGS Publications Warehouse

Dawson, V.K.; Harman, P.D.; Schultz, D.P.; Allen, J.L.

1983-01-01

A high-performance liquid chromatography (HPLC) procedure that is rapid, specific, and sensitive (limit of detection <0.005 mg/liter) was developed for monitoring application and degradation rates of rotenone. For analysis, a water sample is buffered to pH 5 and injected through a Sep Pak(R) C18 disposable cartridge. The cartridge adsorbs and retains the rotenone which then can be eluted quantitatively from the cartridge with a small volume of methanol. This step effectively concentrates the sample and provides sample cleanup. The methanol extract is analyzed directly by HPLC on an MCH 10 reverse-phase column; methanol: water (75:25, volume : volume) is the mobile phase and flow rate is 1.5 ml/minute. The rotenone is detected by ultraviolet spectrophotometry at a wavelength of 295 nm.

5 CFR 532.203 - Structure of regular wage schedules.

Code of Federal Regulations, 2011 CFR

2011-01-01

... grade; (3) NA means a nonappropriated fund nonsupervisory grade; and (4) NL means a nonappropriated fund... schedule for the area, plus 20 percent of the rate for step 2 of NA-8; (2) For grades NS-9 through NS-15... percent, respectively, above the step 2 rate of NA-15; (f) The number of within-grade steps and the...

Clinical Effectiveness of a Resin-modified Glass Ionomer Cement and a Mild One-step Self-etch Adhesive Applied Actively and Passively in Noncarious Cervical Lesions: An 18-Month Clinical Trial.

PubMed

Jassal, M; Mittal, S; Tewari, S

2018-05-21

To evaluate the clinical effectiveness of two methods of application of a mild one-step self-etch adhesive and composite resin as compared with a resin-modified glass ionomer cement (RMGIC) control restoration in noncarious cervical lesions (NCCLs). A total of 294 restorations were placed in 56 patients, 98 in each one of the following groups: 1) G-Bond active application combined with Solare-X composite resin (A-1SEA), 2) G-Bond passive application combined with Solare-X composite resin (P-1SEA), and 3) GC II LC RMGIC. The restorations were evaluated at baseline and after six, 12, and 18 months according to the FDI criteria for fractures/retention, marginal adaptation, marginal staining, postoperative sensitivity, and secondary caries. Cumulative failure rates were calculated for each criterion at each recall period. The effect of adhesive, method of application, and recall period were assessed. The Kruskal-Wallis test for intergroup comparison and Friedman and Wilcoxon signed ranks tests for intragroup comparison were used for each criterion ( α=0.05). The retention rates at 18 months were 93.26% for the A-1SEA group, 86.21% for the P-1SEA group, and 90.91% for the RMGIC group. The active application improved the retention rates compared with the passive application of mild one-step self-etch adhesive; however, no statistically significant difference was observed between the groups. Marginal staining was observed in 13 restorations (1 in A-1SEA, 4 in P-1SEA, and 8 in RMGIC) with no significant difference between the groups. The RMGIC group showed a significant increase in marginal staining at 12 and 18 months from the baseline. There was no significant difference between the groups for marginal adaptation, secondary caries, or postoperative sensitivity. Within the limitations of the study, we can conclude that mild one-step self-etch adhesive followed by a resin composite restoration can be an alternative to RMGIC with similar retention and improved esthetics in restoration of NCCLs. Agitation could possibly benefit the clinical performance of mild one-step self-etch adhesives, but this study did not confirm that the observed benefit was statistically significant.

Multi-application controls: Robust nonlinear multivariable aerospace controls applications

NASA Technical Reports Server (NTRS)

Enns, Dale F.; Bugajski, Daniel J.; Carter, John; Antoniewicz, Bob

1994-01-01

This viewgraph presentation describes the general methodology used to apply Honywell's Multi-Application Control (MACH) and the specific application to the F-18 High Angle-of-Attack Research Vehicle (HARV) including piloted simulation handling qualities evaluation. The general steps include insertion of modeling data for geometry and mass properties, aerodynamics, propulsion data and assumptions, requirements and specifications, e.g. definition of control variables, handling qualities, stability margins and statements for bandwidth, control power, priorities, position and rate limits. The specific steps include choice of independent variables for least squares fits to aerodynamic and propulsion data, modifications to the management of the controls with regard to integrator windup and actuation limiting and priorities, e.g. pitch priority over roll, and command limiting to prevent departures and/or undesirable inertial coupling or inability to recover to a stable trim condition. The HARV control problem is characterized by significant nonlinearities and multivariable interactions in the low speed, high angle-of-attack, high angular rate flight regime. Systematic approaches to the control of vehicle motions modeled with coupled nonlinear equations of motion have been developed. This paper will discuss the dynamic inversion approach which explicity accounts for nonlinearities in the control design. Multiple control effectors (including aerodynamic control surfaces and thrust vectoring control) and sensors are used to control the motions of the vehicles in several degrees-of-freedom. Several maneuvers will be used to illustrate performance of MACH in the high angle-of-attack flight regime. Analytical methods for assessing the robust performance of the multivariable control system in the presence of math modeling uncertainty, disturbances, and commands have reached a high level of maturity. The structured singular value (mu) frequency response methodology is presented as a method for analyzing robust performance and the mu-synthesis method will be presented as a method for synthesizing a robust control system. The paper concludes with the author's expectations regarding future applications of robust nonlinear multivariable controls.

Comparative evaluation of heart rate-based monitors: Apple Watch vs Fitbit Charge HR.

PubMed

Bai, Yang; Hibbing, Paul; Mantis, Constantine; Welk, Gregory J

2018-08-01

The purpose of this investigation was to examine the validity of energy expenditure (EE), steps, and heart rate measured with the Apple Watch 1 and Fitbit Charge HR. Thirty-nine healthy adults wore the two monitors while completing a semi-structured activity protocol consisting of 20 minutes of sedentary activity, 25 minutes of aerobic exercise, and 25 minutes of light intensity physical activity. Criterion measures were obtained from an Oxycon Mobile for EE, a pedometer for steps, and a Polar heart rate strap worn on the chest for heart rate. For estimating whole-trial EE, the mean absolute percent error (MAPE) from Fitbit Charge HR (32.9%) was more than twice that of Apple Watch 1 (15.2%). This trend was consistent for the individual conditions. Both monitors accurately assessed steps during aerobic activity (MAPE Apple : 6.2%; MAPE Fitbit : 9.4%) but overestimated steps in light physical activity. For heart rate, Fitbit Charge HR produced its smallest MAPE in sedentary behaviors (7.2%), followed by aerobic exercise (8.4%), and light activity (10.1%). The Apple Watch 1 had stronger validity than the Fitbit Charge HR for assessing overall EE and steps during aerobic exercise. The Fitbit Charge HR provided heart rate estimates that were statistically equivalent to Polar monitor.

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

PubMed Central

Chakravorty, Dhruva K.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2009-01-01

Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme. PMID:19799395

Limits of thermochemical and photochemical syntheses of gaseous fuels: a finite-time thermodynamic analysis. Annual report, September 1983-February, 1985

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berry, R.S.

The objectives of this project are to develop methods for the evaluation of syntheses of gaseous fuels in terms of their optimum possible performance, particularly when they are required to supply those fuels at nonzero rates. The first objective is entirely in the tradition of classical thermodynamics, the processes, given the characteristics and constraints that define them. The new element which this project introduces is the capability to set limits more realistic than those from classical thermodynamics, by the inclusion of the influence of the rate or duration of a process on its performance. The development of these analyses ismore » a natural step in the evolution represented by the evaluative papers of Appendix IV, e.g., by Funk et al., Abraham, Shinnar, Bilgen and Fletcher. A second objective is to determine how any given process should be carried out, within its constraints, in order to yield its optimum performance and to use this information whenever possible to help guide the design of that process.« less

Atomic layer confined vacancies for atomic-level insights into carbon dioxide electroreduction

NASA Astrophysics Data System (ADS)

Gao, Shan; Sun, Zhongti; Liu, Wei; Jiao, Xingchen; Zu, Xiaolong; Hu, Qitao; Sun, Yongfu; Yao, Tao; Zhang, Wenhua; Wei, Shiqiang; Xie, Yi

2017-02-01

The role of oxygen vacancies in carbon dioxide electroreduction remains somewhat unclear. Here we construct a model of oxygen vacancies confined in atomic layer, taking the synthetic oxygen-deficient cobalt oxide single-unit-cell layers as an example. Density functional theory calculations demonstrate the main defect is the oxygen(II) vacancy, while X-ray absorption fine structure spectroscopy reveals their distinct oxygen vacancy concentrations. Proton transfer is theoretically/experimentally demonstrated to be a rate-limiting step, while energy calculations unveil that the presence of oxygen(II) vacancies lower the rate-limiting activation barrier from 0.51 to 0.40 eV via stabilizing the formate anion radical intermediate, confirmed by the lowered onset potential from 0.81 to 0.78 V and decreased Tafel slope from 48 to 37 mV dec-1. Hence, vacancy-rich cobalt oxide single-unit-cell layers exhibit current densities of 2.7 mA cm-2 with ca. 85% formate selectivity during 40-h tests. This work establishes a clear atomic-level correlation between oxygen vacancies and carbon dioxide electroreduction.

Shock wave lithotripsy: advances in technology and technique

PubMed Central

Lingeman, James E.; McAteer, James A.; Gnessin, Ehud; Evan, Andrew P.

2010-01-01

Shock wave lithotripsy (SWL) is the only noninvasive method for stone removal. Once considered as a primary option for the treatment of virtually all stones, SWL is now recognized to have important limitations that restrict its use. In particular, the effectiveness of SWL is severely limited by stone burden, and treatment with shock waves carries the risk of acute injury with the potential for long-term adverse effects. Research aiming to characterize the renal response to shock waves and to determine the mechanisms of shock wave action in stone breakage and renal injury has begun to suggest new treatment strategies to improve success rates and safety. Urologists can achieve better outcomes by treating at slower shock wave rate using a step-wise protocol. The aim is to achieve stone comminution using as few shock waves and at as low a power level as possible. Important challenges remain, including the need to improve acoustic coupling, enhance stone targeting, better determine when stone breakage is complete, and minimize the occurrence of residual stone fragments. New technologies have begun to address many of these issues, and hold considerable promise for the future. PMID:19956196

Influence of temperature on the hydrolysis, acidogenesis and methanogenesis in mesophilic anaerobic digestion: parameter identification and modeling application.

PubMed

Donoso-Bravo, A; Retamal, C; Carballa, M; Ruiz-Filippi, G; Chamy, R

2009-01-01

The effect of temperature on the kinetic parameters involved in the main reactions of the anaerobic digestion process was studied. Batch tests with starch, glucose and acetic acid as substrates for hydrolysis, acidogenesis and methanogenesis, respectively, were performed in a temperature range between 15 and 45 degrees C. First order kinetics was assumed to determine the hydrolysis rate constant, while Monod and Haldane kinetics were considered for acidogenesis and methanogenesis, respectively. The results obtained showed that the anaerobic process is strongly influenced by temperature, with acidogenesis exerting the highest effect. The Cardinal Temperature Model 1 with an inflection point (CTM1) fitted properly the experimental data in the whole temperature range, except for the maximum degradation rate of acidogenesis. A simple case-study assessing the effect of temperature on an anaerobic CSTR performance indicated that with relatively simple substrates, like starch, the limiting reaction would change depending on temperature. However, when more complex substrates are used (e.g. sewage sludge), the hydrolysis might become more quickly into the limiting step.

A mathematical model of the mevalonate cholesterol biosynthesis pathway.

PubMed

Pool, Frances; Currie, Richard; Sweby, Peter K; Salazar, José Domingo; Tindall, Marcus J

2018-04-14

We formulate, parameterise and analyse a mathematical model of the mevalonate pathway, a key pathway in the synthesis of cholesterol. Of high clinical importance, the pathway incorporates rate limiting enzymatic reactions with multiple negative feedbacks. In this work we investigate the pathway dynamics and demonstrate that rate limiting steps and negative feedbacks within it act in concert to tightly regulate intracellular cholesterol levels. Formulated using the theory of nonlinear ordinary differential equations and parameterised in the context of a hepatocyte, the governing equations are analysed numerically and analytically. Sensitivity and mathematical analysis demonstrate the importance of the two rate limiting enzymes 3-hydroxy-3-methylglutaryl-CoA reductase and squalene synthase in controlling the concentration of substrates within the pathway as well as that of cholesterol. The role of individual feedbacks, both global (between that of cholesterol and sterol regulatory element-binding protein 2; SREBP-2) and local internal (between substrates in the pathway) are investigated. We find that whilst the cholesterol SREBP-2 feedback regulates the overall system dynamics, local feedbacks activate within the pathway to tightly regulate the overall cellular cholesterol concentration. The network stability is analysed by constructing a reduced model of the full pathway and is shown to exhibit one real, stable steady-state. We close by addressing the biological question as to how farnesyl-PP levels are affected by CYP51 inhibition, and demonstrate that the regulatory mechanisms within the network work in unison to ensure they remain bounded. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effective rate constants for nanostructured heterogeneous catalysts

NASA Astrophysics Data System (ADS)

Hendy, Shaun; Gaston, Nicola; Zhang, Philip; Lund, Nat

2012-02-01

There is currently a high level of interest in the use of nanostructured materials for catalysis. For instance, gold, which is largely inert in the bulk, can exhibit strong catalytic activity when in nanoparticle form. With precious metal catalysts such as Pt and Pd in high demand, the use of these materials in nanoparticle form can also substantially reduce costs by exposure of more surface area for the same volume of material. When reactants are plentiful, the effective activity of a nanoparticulate catalyst will increase roughly with its surface area. However, under diffusion-limited conditions, the reactant must diffuse to active sites on the catalyst, so a high surface area and a high density of active sites may bring diminishing returns if reactant is consumed faster than it arrives. Here we apply a mathematical homogenisation approach to derive simple expressions for the effective reactivity of a nanostructured catalyst under diffusion limited conditions that relate the intrinsic rate constants of the surfaces presented by the catalyst to an effective rate constant. When highly active catalytic sites, such as step edges or other defects are present, we show that distinct limiting cases emerge depending on the degree of overlap of the reactant depletion zone about each site. In gases, the size of this depletion zone is approximately the mean free path, so the effective reactivity will depend on the structure of the catalyst on that scale. We discuss implications for the optimal design of nanoparticle catalysts.

Carbothermal Reduction of Quartz with Carbon from Natural Gas

NASA Astrophysics Data System (ADS)

Li, Fei; Tangstad, Merete

2017-04-01

Carbothermal reaction between quartz and two different carbons originating from natural gas were investigated in this paper. One of two carbons is the commercial carbon black produced from natural gas in a medium thermal production process. The other carbon is obtained from natural gas cracking at 1273 K (1000 °C) deposited directly on the quartz pellet. At the 1923 K (1650 °C) and CO atmosphere, the impact of carbon content, pellet structure, gas transfer, and heating rate are investigated in a thermo-gravimetric furnace. The reaction process can be divided into two steps: an initial SiC-producing step followed by a SiO-producing step. Higher carbon content and increased gas transfer improves the reaction rate of SiC-producing step, while the thicker carbon coating in carbon-deposited pellet hinders reaction rate. Better gas transfer of sample holder improves reaction rate but causes more SiO loss. Heating rate has almost no influence on reaction. Mass balance analysis shows that mole ratios between SiO2, free carbon, and SiC in the SiC-producing step and SiO-producing step in CO and Ar fit the reaction SiO2(s) + 3 C(s) = SiC(s) + 2 CO(g). SiC-particle and SiC-coating formation process in mixed pellet and carbon-deposited pellet are proposed. SiC whiskers formed in the voids of these two types of pellets.

Selenium Assimilation and Volatilization from Dimethylselenoniopropionate by Indian Mustard1

PubMed Central

de Souza, Mark P.; Lytle, C. Mel; Mulholland, Maria M.; Otte, Marinus L.; Terry, Norman

2000-01-01

Earlier work from our laboratory on Indian mustard (Brassica juncea L.) identified the following rate-limiting steps for the assimilation and volatilization of selenate to dimethyl selenide (DMSe): (a) uptake of selenate, (b) activation of selenate by ATP sulfurylase, and (b) conversion of selenomethionine (SeMet) to DMSe. The present study showed that shoots of selenate-treated plants accumulated very low concentrations of dimethylselenoniopropionate (DMSeP). Selenonium compounds such as DMSeP are the most likely precursors of DMSe. DMSeP-supplied plants volatilized Se at a rate 113 times higher than that measured from plants supplied with selenate, 38 times higher than from selenite, and six times higher than from SeMet. The conversion of SeMet to selenonium compounds such as DMSeP is likely to be rate-limiting for DMSe production, but not the formation of DMSe from DMSeP because DMSeP was the rate of Se volatilization from faster than from SeMet and SeMet (but no DMSeP) accumulated in selenite- or SeMet-supplied wild-type plants and in selenate-supplied ATP-sulfurylase transgenic plants. DMSeP-supplied plants absorbed the most Se from the external medium compared with plants supplied with SeMet, selenate, or selenite; they also accumulated more Se in shoots than in roots as an unknown organic compound resembling a mixture of DMSeP and selenocysteine. PMID:10759525

Homoepitaxial and Heteroepitaxial Growth on Step-Free SiC Mesas

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Powell, J. Anthony

2004-01-01

This article describes the initial discovery and development of new approaches to SiC homoepitaxial and heteroepitaxial growth. These approaches are based upon the previously unanticipated ability to effectively supress two-dimensional nucleation of 3C-SiC on large basal plane terraces that form between growth steps when epitaxy is carried out on 4H- and 6H-SiC nearly on-axis substrates. After subdividing the growth surface into mesa regions, pure stepflow homoeptixay with no terrace nucleation was then used to grow all existing surface steps off the edges of screw-dislocation-free mesas, leaving behind perfectly on-axis (0001) basal plane mesa surfaces completely free of atomic-scale steps. Step-free mesa surfaces as large as 0.4 mm x 0.4 mm were experimentally realized, with the yield and size of step-free mesas being initally limited by substrate screw dislocations. Continued epitaxial growth following step-free surface formation leads to the formation of thin lateral cantilevers that extend the step-free surface area from the top edge of the mesa sidewalls. By selecting a proper pre-growth mesa shape and crystallographic orientation, the rate of cantilever growth can be greatly enhanced in a web growth process that has been used to (1) enlarge step-free surface areas and (2) overgrow and laterally relocate micropipes and screw dislocations. A new growth process, named step-free surface heteroepitaxy, has been developed to achieve 3C-SiC films on 4H- and 6H-SiC substrate mesas completely free of double positioning boundary and stacking fault defects. The process is based upon the controlled terrace nucleation and lateral expansion of a single island of 3C-SiC across a step-free mesa surface. Experimental results indicate that substrateepilayer lattice mismatch is at least partially relieved parallel to the interface without dislocations that undesirably thread through the thickness of the epilayer. These results should enable realization of improved SiC homojunction and heterojunction devices. In addition, these experiments offer important insights into the nature of polytypism during SiC crystal growth.

Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration

PubMed Central

Hatakeyama, Tetsuhiro S.; Kaneko, Kunihiko

2012-01-01

Circadian clocks—ubiquitous in life forms ranging from bacteria to multicellular organisms—often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations have shown that the amplitude of the oscillation depends on the temperature but the period does not; this suggests that although not every reaction step is temperature independent, the total system comprising several reactions still exhibits compensation. Here we present a general mechanism for such temperature compensation. Consider a system with multiple activation energy barriers for reactions, with a common enzyme shared across several reaction steps. The steps with the highest activation energy rate-limit the cycle when the temperature is not high. If the total abundance of the enzyme is limited, the amount of free enzyme available to catalyze a specific reaction decreases as more substrates bind to the common enzyme. We show that this change in free enzyme abundance compensates for the Arrhenius-type temperature dependence of the reaction coefficient. Taking the example of circadian clocks with cyanobacterial proteins KaiABC, consisting of several phosphorylation sites, we show that this temperature compensation mechanism is indeed valid. Specifically, if the activation energy for phosphorylation is larger than that for dephosphorylation, competition for KaiA shared among the phosphorylation reactions leads to temperature compensation. Moreover, taking a simpler model, we demonstrate the generality of the proposed compensation mechanism, suggesting relevance not only to circadian clocks but to other (bio)chemical oscillators as well. PMID:22566655

Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration.

PubMed

Hatakeyama, Tetsuhiro S; Kaneko, Kunihiko

2012-05-22

Circadian clocks--ubiquitous in life forms ranging from bacteria to multicellular organisms--often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations have shown that the amplitude of the oscillation depends on the temperature but the period does not; this suggests that although not every reaction step is temperature independent, the total system comprising several reactions still exhibits compensation. Here we present a general mechanism for such temperature compensation. Consider a system with multiple activation energy barriers for reactions, with a common enzyme shared across several reaction steps. The steps with the highest activation energy rate-limit the cycle when the temperature is not high. If the total abundance of the enzyme is limited, the amount of free enzyme available to catalyze a specific reaction decreases as more substrates bind to the common enzyme. We show that this change in free enzyme abundance compensates for the Arrhenius-type temperature dependence of the reaction coefficient. Taking the example of circadian clocks with cyanobacterial proteins KaiABC, consisting of several phosphorylation sites, we show that this temperature compensation mechanism is indeed valid. Specifically, if the activation energy for phosphorylation is larger than that for dephosphorylation, competition for KaiA shared among the phosphorylation reactions leads to temperature compensation. Moreover, taking a simpler model, we demonstrate the generality of the proposed compensation mechanism, suggesting relevance not only to circadian clocks but to other (bio)chemical oscillators as well.

An Ai Chi-based aquatic group improves balance and reduces falls in community-dwelling adults: A pilot observational cohort study.

PubMed

Skinner, Elizabeth H; Dinh, Tammy; Hewitt, Melissa; Piper, Ross; Thwaites, Claire

2016-11-01

Falls are associated with morbidity, loss of independence, and mortality. While land-based group exercise and Tai Chi programs reduce the risk of falls, aquatic therapy may allow patients to complete balance exercises with less pain and fear of falling; however, limited data exist. The objective of the study was to pilot the implementation of an aquatic group based on Ai Chi principles (Aquabalance) and to evaluate the safety, intervention acceptability, and intervention effect sizes. Pilot observational cohort study. Forty-two outpatients underwent a single 45-minute weekly group aquatic Ai Chi-based session for eight weeks (Aquabalance). Safety was monitored using organizational reporting systems. Patient attendance, satisfaction, and self-reported falls were also recorded. Balance measures included the Timed Up and Go (TUG) test, the Four Square Step Test (FSST), and the unilateral Step Tests. Forty-two patients completed the program. It was feasible to deliver Aquabalance, as evidenced by the median (IQR) attendance rate of 8.0 (7.8, 8.0) out of 8. No adverse events occurred and participants reported high satisfaction levels. Improvements were noted on the TUG, 10-meter walk test, the Functional Reach Test, the FSST, and the unilateral step tests (p < 0.05). The proportion of patients defined as high falls risk reduced from 38% to 21%. The study was limited by its small sample size, single-center nature, and the absence of a control group. Aquabalance was safe, well-attended, and acceptable to participants. A randomized controlled assessor-blinded trial is required.

Flash crystallization kinetics of methane (sI) hydrate in a thermoelectrically-cooled microreactor.

PubMed

Chen, Weiqi; Pinho, Bruno; Hartman, Ryan L

2017-09-12

The crystallization kinetics of methane (sI) hydrate were investigated in a thermoelectrically-cooled microreactor with in situ Raman spectroscopy. Step-wise and precise control of the temperature allowed acquisition of reproducible data within minutes, while the nucleation of methane hydrates can take up to 24 h in traditional batch reactors. The propagation rates of methane hydrate (from 3.1-196.3 μm s -1 ) at the gas-liquid interface were measured for different Reynolds' numbers (0.7-68.9), pressures (30.0-80.9 bar), and sub-cooling temperatures (1.0-4.0 K). The precise measurement of the propagation rates and their subsequent analyses revealed a transition from mixed heat-transfer-crystallization-rate-limited to mixed heat-transfer-mass-transfer-crystallization-rate-limited kinetics. A theoretical model, based on heat transfer, mass transfer, and intrinsic crystallization kinetics, was derived for the first time to understand the non-linear relationship between the propagation rate and sub-cooling temperature. The molecular diffusivity of methane within a stagnant film (ahead of the propagation front) was discovered to follow Stokes-Einstein, while calculated Hatta (0.50-0.68), Lewis (128-207), and beta (0.79-116) numbers also confirmed that the diffusive flux influences crystal growth. Understanding methane hydrate crystal growth is important to the atmospheric, oceanic, and planetary sciences and to energy production, storage, and transportation. Our discoveries could someday advance the science of other multiphase, high-pressure, and sub-cooled crystallizations.

Compressed Secret Key Agreement:Maximizing Multivariate Mutual Information per Bit

NASA Astrophysics Data System (ADS)

Chan, Chung

2017-10-01

The multiterminal secret key agreement problem by public discussion is formulated with an additional source compression step where, prior to the public discussion phase, users independently compress their private sources to filter out strongly correlated components for generating a common secret key. The objective is to maximize the achievable key rate as a function of the joint entropy of the compressed sources. Since the maximum achievable key rate captures the total amount of information mutual to the compressed sources, an optimal compression scheme essentially maximizes the multivariate mutual information per bit of randomness of the private sources, and can therefore be viewed more generally as a dimension reduction technique. Single-letter lower and upper bounds on the maximum achievable key rate are derived for the general source model, and an explicit polynomial-time computable formula is obtained for the pairwise independent network model. In particular, the converse results and the upper bounds are obtained from those of the related secret key agreement problem with rate-limited discussion. A precise duality is shown for the two-user case with one-way discussion, and such duality is extended to obtain the desired converse results in the multi-user case. In addition to posing new challenges in information processing and dimension reduction, the compressed secret key agreement problem helps shed new light on resolving the difficult problem of secret key agreement with rate-limited discussion, by offering a more structured achieving scheme and some simpler conjectures to prove.

5 CFR 531.406 - Creditable service.

Code of Federal Regulations, 2010 CFR

2010-01-01

... pay is equal to or greater than the rate of basic pay for step 4 of the applicable grade and less than... period for an employee whose rate of basic pay is equal to or greater than the rate of basic pay for step....406 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER THE...