bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized extract preparation methods and reaction conditions for improved yeast cell‐free protein synthesis
Authors: Hodgman C. Eric , Jewett Michael C. 
Published: April 2013

ABSTRACTCell‐free protein synthesis (CFPS) has emerged as a powerful platform technology to help satisfy the growing demand for simple, affordable, and efficient protein production. In this article, we describe a novel CFPS platform derived from the popular bio‐manufacturing organism Saccharomyces cerevisiae. By developing a streamlined crude extract preparation protocol and optimizing the CFPS reaction conditions we were able to achieve active firefly luciferase synthesis yields of 7.7 ± 0.5 µg mL−1 with batch reactions lasting up to 2 h. This duration of synthesis is the longest ever reported for a yeast CFPS batch reaction. Furthermore, by removing extraneous processing steps and eliminating expensive reagents from the cell‐free reaction, we have increased relative product yield (µg protein synthesized per $ reagent cost) over an alternative commonly used method up to 2000‐fold from ∼2 × 10−4 to ∼4 × 10−1 µg $−1, which now puts the yeast CPFS platform on par with other eukaryotic CFPS platforms commercially available. Our results set the stage for developing a yeast CFPS platform that provides for high‐yielding and cost‐effective expression of a variety of protein therapeutics and protein libraries. Biotechnol. Bioeng. 2013;110: 2643–2654. © 2013 Wiley Periodicals, Inc.
Cost‐effectiveness of full coverage of aromatase inhibitors for Medicare beneficiaries with early breast cancer
Authors: Ito Kouta , Elkin Elena , Blinder Victoria , Keating Nancy , Choudhry Niteesh 
Published: April 2013

BACKGROUNDRates of nonadherence to aromatase inhibitors (AIs) among Medicare beneficiaries with hormone receptor‐positive early breast cancer are high. Out‐of‐pocket drug costs appear to be an important contributor to this and may be addressed by eliminating copayments and other forms of patient cost sharing. The authors estimated the incremental cost‐effectiveness of providing Medicare beneficiaries with full prescription coverage for AIs compared with usual prescription coverage under the Medicare Part D program.METHODSA Markov state‐transition model was developed to simulate AI use and disease progression in a hypothetical cohort of postmenopausal Medicare beneficiaries with hormone receptor‐positive early breast cancer. The analysis was conducted from the societal perspective and considered a lifetime horizon. The main outcome was an incremental cost‐effectiveness ratio, which was measured as the cost per quality‐adjusted life‐year (QALY) gained.RESULTSFor patients receiving usual prescription coverage, average quality‐adjusted survival was 11.35 QALYs, and lifetime costs were $83,002. For patients receiving full prescription coverage, average quality‐adjusted survival was 11.38 QALYs, and lifetime costs were $82,728. Compared with usual prescription coverage, full prescription coverage would result in greater quality‐adjusted survival (0.03 QALYs) and less resource use ($275) per beneficiary. From the perspective of Medicare, full prescription coverage was cost‐effective (incremental cost‐effectiveness ratio, $15,128 per QALY gained) but not cost saving.CONCLUSIONSProviding full prescription coverage for AIs to Medicare beneficiaries with hormone receptor‐positive early breast cancer would both improve health outcomes and save money from the societal perspective.Cancer2013;119:2494‐2502. ©2013 American Cancer Society.
Deriving bio-equivalents from in vitro bioassays: Assessment of existing uncertainties and strategies to improve accuracy and reporting
Authors: Wagner Martin , Vermeirssen Etiënne L.M. , Buchinger Sebastian , Behr Maximilian , Magdeburg Axel , Oehlmann Jörg 
Published: April 2013

Abstract

Bio-equivalents (e.g., 17β-estradiol or dioxin equivalents) are commonly employed to quantify the in vitro effects of complex human or environmental samples. However, there is no generally accepted data analysis strategy for estimating and reporting bio-equivalents. Therefore, the aims of the present study are to 1) identify common mathematical models for the derivation of bio-equivalents from the literature, 2) assess the ability of those models to correctly predict bio-equivalents, and 3) propose measures to reduce uncertainty in their calculation and reporting. We compiled a database of 234 publications that report bio-equivalents. From the database, we extracted 3 data analysis strategies commonly used to estimate bio-equivalents. These models are based on linear or nonlinear interpolation, and the comparison of effect concentrations (ECX). To assess their accuracy, we employed simulated data sets in different scenarios. The results indicate that all models lead to a considerable misestimation of bio-equivalents if certain mathematical assumptions (e.g., goodness of fit, parallelism of dose–response curves) are violated. However, nonlinear interpolation is most suitable to predict bio-equivalents from single-point estimates. Regardless of the model, subsequent linear extrapolation of bio-equivalents generates additional inaccuracy if the prerequisite of parallel dose–response curves is not met. When all these factors are taken into consideration, it becomes clear that data analysis introduces considerable uncertainty in the derived bio-equivalents. To improve accuracy and transparency of bio-equivalents, we propose a novel data analysis strategy and a checklist for reporting Minimum Information about Bio-equivalent ESTimates (MIBEST). Environ Toxicol Chem 2013;32:1906–1917. © 2013 SETAC
Tunable delivery of bioactive peptides from hydroxyapatite biomaterials and allograft bone using variable‐length polyglutamate domains
Authors: Culpepper Bonnie K. , Webb William M. , Bonvallet Paul P. , Bellis Susan L. 
Published: April 2013

AbstractHydroxyapatite (HA) biomaterials and allograft bone are common alternatives to autogenous grafts; however, these materials lack the strong osteoinductive potential of autologous bone. Previous studies have established that polyglutamate domains, which bind selectively to HA, can be engineered onto bioactive peptides as a mechanism for coupling osteoinductive signals onto HA and allograft. In the current investigation, we adapted the polyglutamate approach to tailor delivery of a model collagen‐derived peptide, Asp‐Gly‐Glu‐Ala (DGEA), by manipulating the number of glutamates in the HA binding domain. Specifically, DGEA was modified with diglutamate (E2‐DGEA), tetraglutamate (E4‐DGEA), or heptaglutamate (E7‐DGEA), and it was found that initial peptide binding to HA and allograft was significantly enhanced as the number of glutamates increased. We also determined that the rate of release of polyglutamate‐DGEA from substrates over a 5‐day interval increased proportionally as the number of glutamate residues was decreased. Additionally, we tuned the peptide release rate by creating mixtures of E2‐DGEA, E4‐DGEA, and E7‐DGEA, and observed that release kinetics of the mixtures were distinct from pure solutions of each respective peptide. These collective results suggest that variable‐length polyglutamate domains provide an effective mechanism for controlled delivery of osteoregenerative peptides on HA‐containing bone graft materials. © 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 1008–1016, 2014.
Long‐term starvation in cave salamander effects on liver ultrastructure and energy reserve mobilization
Authors: Bizjak Mali Lilijana , Sepčić Kristina , Bulog Boris 
Published: April 2013

ABSTRACTThe morphological alterations of hepatocytes of cave‐dwelling salamander Proteus anguinus anguinus after food deprivation periods of one and 18 months were investigated and the concentrations of glycogen, lipids, and proteins in the liver were determined. Quantitative analyses of the hepatocyte size, the lipid droplets, the number of mitochondria, and volume densities of M and P in the hepatocytes were completed. After one month of food deprivation, the cytological changes in the hepatocytes are mainly related to the distribution and amount of glycogen, which was dispersed in the cytoplasm and failed to form clumps typical of normal liver tissue. After 18 months of food deprivation hepatocytes were reduced in size, lipid droplets were less numerous, peroxisomes formed clusters with small, spherical mitochondria, and specific mitochondria increased in size and lost cristae. Lysosomes, autophagic vacuoles, and clear vacuoles were numerous. The liver integrity was apparently maintained, no significant loss of cytoplasmic constituents have been observed. Biochemical analysis revealed the utilization of stored metabolic reserves in the liver during food deprivation. Glycogen is rapidly utilized at the beginning of the starvation period, whereas lipids and proteins are utilized subsequently, during prolonged food deprivation. In the Proteus liver carbohydrates are maintained in appreciable amounts and this constitutes a very important energy depot, invaluable in the subterranean environment. J. Morphol. 274:887–900, 2013. © 2013 Wiley Periodicals, Inc.
The entotympanic in late fetal artiodactyla (Mammalia)
Authors: Maier Wolfgang 
Published: April 2013

ABSTRACTThe entotympanic is a neomorphic component of the bulla tympanica of placental mammals. Ontogenetically, its rostral component seems to be derived from the tubal cartilage, whereas its caudal component is normally connected with the sheath of the tympanohyal; the present study indicates additional sources of the caudal entotympanic. The entotympanics develop in late fetal or early postnatal life as cartilaginous structures, but in most taxa they ossifiy endochondrally as “os bullae”. This skeletal element is absent only in a few placental orders, among them the Artiodactyla. Because it is present in their sister taxa within the Scrotifera, it is likely to be reduced secondarily in the even‐toed mammals. The study of histological serial sections of late fetal stages of several artiodactyl species shows that vestigial cartilaginous homologues of the entotympanics are invariably present, contrary to statements in the literature. In a few perinatal stages even secondary ossifications or calcifications of the entotympanic cartilages can be observed. The tubal cartilage of artiodactyls also continues into an anterior tegmen tympani (new term) that forms the floor of the fossa muscularis major. J. Morphol. 274:926–939, 2013. © 2013 Wiley Periodicals, Inc.
Kinetics of the Rapid Base Catalyzed Iodination of Imidazole and 2‐Methylimidazole by Molecular Iodine in Aqueous Medium: pH Effect
Authors: Bonde S. L. , Dangat V. T. , Bhadane R. P. , Joshi V. S. 
Published: April 2013

ABSTRACTThe second‐order kinetics of iodination of imidazole and 2‐methylimidazole in aqueous medium at various pH values and temperatures are studied in the presence and absence of a base catalyst. The reactions being electrophilic substitutions, molecular iodine is the sole iodinating agent, as the reactant solutions used are totally devoid of I− ions. The specific reaction rates of imidazole (I) and 2‐methylimidazole (II) for the catalyzed reactions are found to be 87.00 and 62.92 M−1 s−1 at 27.0°C, respectively, at 7.0 pH. The base component of the buffer used to maintain the pH catalyzes the reactions. The rapidity of the reactions necessitates the use of a rotating platinum electrode to follow the decay of the unreacted iodine. The study provides a quantitative verification of the reactivities of the substrates.
A Shock Tube Study of H2 + OH → H2O + H Using OH Laser Absorption
Authors: Lam King‐Yiu , Davidson David F. , Hanson Ronald K. 
Published: April 2013

ABSTRACTThe rate constant for the reaction of hydroxyl radicals (OH) with molecular hydrogen (H2) was measured behind reflected shock waves using UV laser absorption of OH radicals near 306.69 nm. Test gas mixtures of H2 and tert‐butyl hydroperoxide (TBHP) diluted in argon were shock‐heated to temperatures ranging from 902 to 1518 K at pressures of 1.15–1.52 atm. OH radicals were produced by rapid thermal decomposition of TBHP at high temperatures. The rate constant for the title reaction was inferred by best fitting the measured OH time histories with the simulated profiles from the comprehensive reaction mechanism of Wang et al. (USC‐Mech v2.0) (2007). The measured values can be expressed in the Arrhenius equation as k1(T) = 4.38 × 1013 exp(–3518/T) cm3 mol−1 s−1 over the temperature range studied. A detailed error analysis was performed to estimate the overall uncertainty of the title reaction, and the estimated (2 – σ) uncertainties were found to be ±17% at 972 and 1228 K. The present measurements are in excellent agreement with the previous experimental studies from Frank and Just (Ber Bunsen‐Ges Phys Chem 1985, 89, 181–187), Michael and Sutherland (J Phys Chem 1988, 92, 3853–3857), Davidson et al. (Symp (Int) Combust 1988, 22, 1877–1885), Oldenborg et al. (J Phys Chem 1992, 96, 8426–8430), and Krasnoperov and Michael (J Phys Chem A 2004, 108, 5643–5648).In addition, the measured rate constant is in close accord with the non‐Arrhenius expression from GRI‐Mech 3.0 (http://www.me.berkeley.edu/gri_mech/) and the theoretical calculation using semiclassical transition state theory from Nguyen et al. (Chem Phys Lett 2010, 499, 9–15).
Time‐Varying Flexible Least Squares for Thermal Desorption of Gases
Authors: Miron David J. , Kendell Shane M. , Munshi Alaa M. , Alanazi Abdullah K. , Brown Trevor C. 
Published: April 2013

ABSTRACTTime‐varying linear regression via flexible least squares is used to determine temperature‐dependent kinetic parameters during low‐pressure, steady‐state, temperature‐programmed desorption from catalytic surfaces. The flexible least squares approach optimizes time‐varying parameters by minimizing dynamic and measurement discrepancies between a linear theoretical model and experimental data using linear regression. The effectiveness of this approach is demonstrated by calculation of accurate temperature‐dependent activation energies, preexponential factors, and differential conversion functions for the evolution of 3‐methyl‐2‐oxetanone (β‐lactone) during the selective oxidation of isobutane over aluminum phosphomolybdates.
On the Separation of Timescales in Chemically Activated Reactions
Authors: Pinches Samuel J. , da Silva Gabriel 
Published: April 2013

ABSTRACTChemically activated reactions are important in describing the composition of reactive gases including flames, planetary atmospheres, and the interstellar medium (ISM). In a chemically activated reaction, two reactants combine to populate a vibrationally excited well that can undergo unimolecular transformations (isomerization, dissociation) or be thermalized through collisions with the bath gas. Once a well has been thermalized, it may still have sufficient energy to undergo further unimolecular reaction, in a purely thermal process. If the timescale for the thermally activated process is sufficiently short, such that it approaches that of the chemically activated reaction, the two concurrent processes become inseparable and the value of the phenomenological rate coefficient is no longer obvious. Here, we introduce the thermal decay (TD) procedure to determine phenomenological rate coefficients for chemically activated reactions proceeding on timescales approaching those of thermal reaction, principally for use in stochastic master equation simulations of multiple‐well multiple‐channel unimolecular reaction processes. By fitting the thermal decay of the initially activated well to a first‐order kinetic model, the would‐be thermal yield can be eliminated so as to arrive at the chemically activated component in a reliable and objective fashion. This technique is demonstrated here for the reaction of 1,3,6‐heptatriyne with H using the MultiWell code and a 16‐well 33‐channel C7H5 reaction model. A computer program implementing the TD method and for postprocessing of MultiWell output data, PPM, is provided.
Construction and Activity of a New Catalytic System in the Hydrolysis of Bis(4‐nitrophenyl) Phosphate Ester
Authors: Xie Jiaqing , Li Ci , Wang Min , Jiang Bingying 
Published: April 2013

ABSTRACTA new catalytic system containing an unsaturated heterocyclic nitrogen ligand and lanthanum(III) was constructed and used as a catalyst in the hydrolysis of bis(4‐nitrophenyl) phosphate ester (BNPP) in this work. The results indicated that this catalytic system showed greater catalytic activity in the hydrolysis of BNPP and better reproducibility and stability than other similar lanthanum(III) systems. The catalytic rate of the BNPP hydrolysis was about 107‐fold faster than that of its spontaneous hydrolysis at the same conditions. Compared with the previous Cu(II) or Ni(II) complex containing the same ligand in the water, the activity of the macrocyclic La(III) complex increases ca. 103‐fold for BNPP catalytic hydrolysis. The experimental data showed that the monohydroxy complex made of the heterocyclic nitrogen ligand and lanthanum(III) is the real active species as a catalyst in BNPP catalytic hydrolysis.
Hydrolysis Kinetic Studies of Schiff Bases Derived from Pyrrolic Aldehydes in Buffered Aqueous Ethanol and Sulfuric Acid Solutions: Structural Effects of Substitutes
Authors: Bengharez Zohra , El Bahri Zineb , Mesli Abderrezzak 
Published: April 2013

ABSTRACTTwo series of substituted N‐pyrrolyl‐2‐methylene‐aniline were synthesized and characterized to study their stability in a large domain of pH (0–14) and especially in the H0 domain (–4 to 0). The hydrolysis kinetics of the azomethine group was established in homogeneous media using a thermostated UV–vis spectrophotometer. The hydrolysis mechanism was investigated, and the experimental kinetic constants were calculated. Then, the pH–rate diagram profile was determined and the structural effect of substitutes on the kinetic constants was clarified and discussed.
Numerical modelling of the hydro‐chemo‐mechanical behaviour of geomaterials in the context of CO2 injection
Authors: Vallin V. , Pereira J.M. , Fabbri A. , Wong H. 
Published: April 2013

SUMMARYSafety assessment of geosequestration of CO2 into deep saline aquifers requires a precise understanding of the study of hydro‐chemo‐mechanical couplings occurring in the rocks and the cement well. To this aim, a coupled chemo‐poromechanical model has been developed and implemented into a research code well‐suited to the resolution of fully coupled problems. This code is based on the finite volume methods.In a 1D axisymmetrical configuration, this study aims to simulate the chemo‐poromechanical behaviour of a system composed by the cement well and the caprock during CO2 injection. Major chemical reactions of carbonation occurring into cement paste and rocks are considered in order to evaluate the consequences of the presence of CO2 on the amount of dissolved matrix and precipitated calcium carbonates. The dissolution of the solid matrix is taken into account through the use of a chemical porosity. Matrix leaching and carbonation lead, as expected, to important variations of porosity, permeability and to alterations of transport properties and mechanical stiffness. These results justify the importance of considering a coupled analysis accounting for the main chemical reactions. It is worth noting that the modelling framework proposed in the present study could be extended to model the chemo‐poromechanical behaviour of the reservoir rock and the caprock when subjected to the presence of an acidic pore fluid (CO2‐rich brine). Copyright © 2013 John Wiley & Sons, Ltd.
Dynamic MRI evaluation of urethral hypermobility post‐radical prostatectomy
Authors: Suskind Anne M. , DeLancey John O.L. , Hussain Hero K. , Montgomery Jeffrey S. , Latini Jerilyn M. , Cameron Anne P. 
Published: April 2013

AbstractAimsOne postulated cause of post‐prostatectomy incontinence is urethral and bladder neck hypermobility. The objective of this study was to determine the magnitude of anatomical differences of urethral and bladder neck position at rest and with valsalva in continent and incontinent men post‐prostatectomy based on dynamic MRI.MethodsAll subjects underwent a dynamic MRI protocol with valsalva and non‐valsalva images and a standard urodynamic evaluation. MRI measurements were taken at rest and with valsalva, including (1) bladder neck to sacrococcygeal inferior pubic point line (SCIPP), (2) urethra to pubis, and (3) bulbar urethra to SCIPP. Data were analyzed in SAS using two‐tailed t tests.ResultsA total of 21 subjects (13 incontinent and 8 continent) had complete data and were included in the final analysis. The two groups had similar demographic characteristics. On MRI, there were no statistically significant differences in anatomic position of the bladder neck or urethra either at rest or with valsalva. The amount of hypermobility ranged from 0.8 to 2 mm in all measures. There were also no differences in the amount of hypermobility (position at rest minus position at valsalva) between groups.ConclusionsWe found no statistically significant differences in bladder neck and urethral position or mobility on dynamic MRI evaluation between continent and incontinent men status post‐radical prostatectomy. A more complex mechanism for post‐prostatectomy incontinence needs to be modeled in order to better understand the continence mechanism in this select group of men. Neurourol. Urodynam. 33:312–315, 2014. © 2013 Wiley Periodicals, Inc.
Assessment of bladder and kidney functioning in adult spina bifida patients by Dutch urologists: A survey
Authors: Veenboer Paul W. , Ruud Bosch J.L.H. , de Kort Laetitia M.O. 
Published: April 2013

AbstractAimsTo investigate how urologists generally perform the follow‐up of adult spina bifida (SB) patients and to see to which extent recommendations from guidelines on neurogenic lower urinary tract dysfunction are followed.MethodsA self‐designed electronic multiple choice questionnaire was sent to all 365 urologists in the Netherlands.ResultsOverall 100 urologists (27.4%) responded, of which 96 (26.3%) responses were usable. Of 95 urologists, 18 (18.9%) saw no adult SB patients, 47 (49.5%) saw 1–5 patients/year, 15 (15.8%) saw 6–10, and 15 urologists (15.8%) saw >10 adult SB patients/year. Of 96 urologists, a specialized clinic for adult SB patients was present in only 11 (11.5%) cases. Ultrasonography was performed regularly (at least once every 1–5 years) by 68/74 (91.9%) urologists. Glomerular filtration rate (GFR) was determined at least every 5 years by 66/74 (89.1%) urologists. For determination of GFR, serum creatinine was most often used (94.5%). Renography and video‐urodynamic investigations (UDS) were performed on a regular basis by 8.1% and 24.3%, respectively.ConclusionsIn adult SB patients, the responding Dutch urologists regularly evaluate bladder and kidney function using GFR and ultrasonography, although less frequently than recommended by the guidelines. UDS is performed on indication only, which is not in accordance with the guidelines. Regular UDS might be valuable to detect risk factors for insidious renal damage. The role of renography, as well as the desirability of multidisciplinary teams, has yet to be determined. Neurourol. Urodynam. 33:289–295, 2014. © 2013 Wiley Periodicals, Inc.