bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of ethanolysis products of poly(dimethylsiloxane) species by electrospray ionization tandem mass spectrometry
Authors: Fouquet Thierry , Bour Jérôme , Toniazzo Valérie , Ruch David , Charles Laurence 
Published: July 2012

RATIONALEThe partial and controlled degradation of insoluble cross‐linked silicon‐based polymers is a promising approach to enable their characterization by mass spectrometry. Providing that the chemolysis reaction specifically proceeds at cross‐linking sites, the size of linear poly(dimethylsiloxane)s (PDMS) produced during the treatment should reflect the length of linear segments between branching points in the original network. In this context, the specificity of ethanol to act as a nucleophilic agent towards tri‐functional silicon atoms in a D3TDnTD3 model was evaluated.METHODSTandem mass spectrometry (MS/MS) combined with accurate mass measurements, MS3 experiments and collision‐induced dissociation of authentic compounds was used for structural characterization of D3TDnTD3 ethanolysis products. All MS/MS data were obtained from electrosprayed ammonium adducts, previously reported to provide the most informative data for silicon‐based polymers.RESULTSSince the expected ethanolysis products were hydroxy‐ and ethoxy‐terminated PDMS, the dissociation behavior of such polymeric species was established, using electrosprayed ammonium adducts as the precursor ions. Diagnostic product ions were identified, allowing four main D3TDnTD3 ethanolysis products to be structurally characterized. End‐group analysis of these polymeric distributions clearly indicated that ethanolysis was mostly occurring on tri‐functional silicon atoms but also, to a lesser extent, on those D atoms close to T silicons.CONCLUSIONSThe size of the linear skeleton located between two tri‐functional silicon atoms could be accurately determined by mass spectrometric analyses of a polymeric model submitted to ethanolysis. This soft and rapid pre‐treatment is thus a promising approach for determining the length of linear segments between branching points in the original network of cross‐linked silicon‐based polymers. Copyright © 2012 John Wiley & Sons, Ltd.
The oscillations killer: a mechanism to eliminate undesired limit cycles in a class of nonlinear systems
Authors: Canudas‐de‐Wit C. , Aracil J. , Gordillo F. , Salas F. 
Published: July 2012

SUMMARYIn this paper, we present a mechanism, calledoscillation killer, intended to eliminate limit cycles that may occur as a consequence of unexpected external disturbances, interactions with the environment, changes in systems set‐points, physical parameters, and so on. Examples range from controlled systems with friction to electrical networks with varying loads and impedances. The proposed mechanisms is shown to be particulary appropriate for nonlinear systems displaying a locally asymptotically equilibrium point surrounded by a locally asymptotically stable limit set outside this local domain. Copyright © 2012 John Wiley & Sons, Ltd.
Nanometrical evaluation of direct laser implant surface
Authors: Ricci M. , Mangano F. , Tercio T. , Tonelli P. , Barone A. , Raspanti M. , Covani U. 
Published: July 2012

The present study was designed to evaluate the characteristics and the topography of a new implant surface. Titanium discs were manufactured using master alloy powder (Ti‐6Al‐4V) with a particle size of 25–45 µm as the basic material (Leader Implants, Milan, Italy). We acquired images in three different dimensional ranges of decreasing dimensions: 30 (dimensional class A), 10 (dimensional class B), and 5 µm2 (dimensional class C). For each dimensional range, we collected five (dimensional classes A and B) to ten (dimensional classes C) different images, belonging both to the center and to the edge of the slideResultsIn dimensional class A, implant surface showed an average roughness value (Ra) of 0.6 µm, whereas the root mean square roughness (Rrms) value was 0.78 µm. In the dimensional class B, value of Ra was 133.4 µm and value of Rrms was 161.7 µm. Finally, at a smaller level as in dimensional class C, value of Ra was 68.5 µm and Rrms was 81.05 µm. Moreover, the peak to peak value was 369.5 µm and the average height value was 187.3 µmDiscussionThe surface which results from direct laser fabrication process has an ideal nano‐roughness to enhance protein adsorption and to facilitate precursor osteoblast adhesion. In conclusion, direct laser forming surface seems to be a promising technique for forming dental implants from titanium alloys. Copyright © 2012 John Wiley & Sons, Ltd.
Comparison of methods for imputing ordinal data using multivariate normal imputation: a case study of non‐linear effects in a large cohort study
Authors: Lee Katherine J. , Galati John C. , Simpson Julie A. , Carlin John B. 
Published: July 2012

BackgroundMultiple imputation is becoming increasingly popular for handling missing data, with Markov chain Monte Carlo assuming multivariate normality (MVN) a commonly used approach. Imputing categorical variables (which are clearly non‐normal) using MVN imputation is challenging, and several approaches have been suggested. However, it remains unclear which approach should be preferred.MethodsWe explore methods for imputing ordinal variables using MVN imputation, including imputing as a continuous variable and as a set of indicators, and various methods for assigning imputed values to the possible categories (rounding), for estimating a non‐linear association between an ordinal exposure and binary outcome. We introduce a new approach where we impute as continuous and assign imputed values into categories based on the mean indicators imputed in a separate round of imputation. We compare these approaches in a simple setting where we make 50% of data in an ordinal exposure missing completely at random, within an otherwise complete real dataset.ResultsMethods that impute the ordinal exposure as continuous distorted the non‐linear exposure–outcome association by biasing the relationship towards linearity irrespective of the rounding method. In contrast, imputing using indicators preserved the non‐linear association but not the marginal distribution of the ordinal variable.ConclusionsImputing ordinal variables as continuous can bias the estimation of the exposure–outcome association in the presence of non‐linear relationships. Further work is needed to develop optimal methods for handling ordinal (and nominal) variables when using MVN imputation. Copyright © 2012 John Wiley & Sons, Ltd.
The ghosts of departed quantities: approaches to dealing with observations below the limit of quantitation
Authors: Senn Stephen , Holford Nick , Hockey Hans 
Published: July 2012

A common but not necessarily logical requirement in drug development is that a ‘limit of quantitation’ be set for chemical assays and that observations that fall below the limit should not be treated as real data but should be labelled as below the limit and set aside for special treatment.We examine five of seven approaches to analysing such data considered by Beal in 2001, concentrating in particular on two: one that treats the data as a truncated sample and another that treats them as a censored sample. In fact, using a pattern‐mixture framework, one can show that the former consists of using the conditional distribution of the ‘acceptable values’ and the latter adds the information from the marginal mixing distribution.We illustrate these approaches with a real example, concentrating in particular on the two likelihood‐based methods, provide various formulae that may be used to compare these and other approaches, check these formulae using simulations and make some recommendations as to which approach one should use. Copyright © 2012 John Wiley & Sons, Ltd.
Control of Cell Adhesion and Neurite Outgrowth by Patterned Gold Nanoparticles with Tunable Attractive or Repulsive Surface Properties
Authors: Gilles Sandra , Winter Silke , Michael Kristin E. , Meffert Simone H. , Li Pinggui , Greben Kyrylo , Simon Ulrich , Offenhäusser Andreas , Mayer Dirk 
Published: July 2012

AbstractGuiding of neuronal cells on surfaces is required for the investigation of fundamental aspects of neurobiology, for tissue engineering, and for numerous bioelectronic applications. A modular method to establish nanostructured chemical templates for local deposition of gold nanoparticles is presented. A process comprising nanoimprint lithography, silanization, lift‐off, and gold nanoparticle immobilization is used to fabricate the particle patterns. The chemical composition of the surface can be modified by in situ adsorption of cell‐binding ligands to locally addressed particles. The versatility of this approach is demonstrated by inverting the binding affinity between rat cortical neurons and nanopatterned surfaces via wet‐chemical means and thereby reversing the pattern of guided neurons.
Tuning the Doping Type and Level of Graphene with Different Gold Configurations
Authors: Wu Yaping , Jiang Wei , Ren Yujie , Cai Weiwei , Lee Wi Hyoung , Li Huifeng , Piner Richard D. , Pope Cody W. , Hao Yufeng , Ji Hengxing , Kang Junyong , Ruoff Rodney S. 
Published: July 2012

AbstractAu nanoparticles and films are deposited onto clean graphene surfaces to study the doping effect of different Au configurations. Micro‐Raman spectra show that both the doping type and level of graphene can be tuned by fine control of the Au deposition. The morphological structures of Au on graphene are imaged by transmission electron microscopy, which indicate a size‐dependent electrical characteristic: isolated Au nanoparticles produce n‐type doping of graphene, while continuous Au films produce p‐type doping. Accordingly, graphene field‐effect transistors are fabricated, with the in situ measurements suggesting the tunable conductivity type and level by contacting with different Au configurations. For interpreting the experimental observations, the first‐principles approach is used to simulate the interaction within graphene–Au systems. The results suggest that, different doping properties of Au–graphene systems are induced by the chemical interactions between graphene and the different Au configurations (isolated nanoparticle and continuous film).
Smart grid sensor data collection, communication, and networking: a tutorial
Authors: Kayastha Nipendra , Niyato Dusit , Hossain Ekram , Han Zhu 
Published: July 2012

ABSTRACTThe smart grid is an innovative energy network that will improve the conventional electrical grid network to be more reliable, cooperative, responsive, and economical. Within the context of the new capabilities, advanced data sensing, communication, and networking technology will play a significant role in shaping the future of the smart grid. The smart grid will require a flexible and efficient framework to ensure the collection of timely and accurate information from various locations in power grid to provide continuous and reliable operation. This article presents a tutorial on the sensor data collection, communications, and networking issues for the smart grid. First, the applications of data sensing in the smart grid are reviewed. Then, the requirements for data sensing and collection, the corresponding sensors and actuators, and the communication and networking architecture are discussed. The communication technologies and the data communication network architecture and protocols for the smart grid are described. Next, different emerging techniques for data sensing, communications, and sensor data networking are reviewed. The issues related to security of data sensing and communications in the smart grid are then discussed. To this end, the standardization activities and use cases related to data sensing and communications in the smart grid are summarized. Finally, several open issues and challenges are outlined. Copyright © 2012 John Wiley & Sons, Ltd.
Enhanced production of poly(3-hydroxybutyrate) in a novel airlift reactor with in situ cell retention using Azohydromonas australica
Authors: Gahlawat Geeta , Sengupta Bedoshree , Srivastava Ashok K 
Published: July 2012

Abstract
Economic production of biodegradable plastics is a challenge particularly because of high substrate and energy cost inputs for its production. Research efforts are being directed towards innovations to minimize both of the above costs to economize polyhydroxybutyrate (PHB) production. A novel airlift reactor (ALR) with outer aeration and internal settling was utilized in this investigation. Although it featured no power consumption for agitation, it facilitated increased oxygen transfer rate and better cell retention than stirred tank reactor (STR), thereby resulting in enhanced PHB productivity. ALR with in situ cell retention demonstrated a significant improvement in biomass concentration and biopolymer accumulation. The total PHB production rate, specific biomass, and product yield in the ALR were observed to be 0.84 g/h, 0.43 g/g, and 0.32 g/g, respectively. The studies revealed that the volumetric oxygen mass transfer rate and mixing time for ALR were 0.016 s−1 and 3.73 s, respectively, at 2.0 vvm as compared with corresponding values of 0.005 s−1 and 4.95 s, respectively, in STR. This demonstrated that ALR has better oxygen mass transfer and mixing efficiency than STR. Hence, ALR with cell retention would serve as a better bioreactor design for economic biopolymer production than STR, particularly due to its lower cost of operation and simplicity along with its enhanced oxygen and heat transfer rates.
Engineering ofRhodococcuscell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition
Authors: Ma Yuchao , Yu Huimin 
Published: July 2012

AbstractTolerance to various stresses is a key phenotype for cell catalysts, which are used widely in bioproduction of diverse valuable chemicals. Using the Rhodococcus ruber TH strain, which exhibits high nitrile hydratase activity, as the target cell catalyst for acrylamide production, we established a method to improve cell tolerance by stably introducing global transcription perturbation. The σ70 gene (sigA) of R. ruber was cloned and randomly mutated. An R. ruber TH3/pNV-sigAM library containing additional sigA mutants was constructed and used for survival selection. The TH3/M4N1-59 mutant was selected by acrylonitrile/acrylamide double stress and exhibited a 160 % extension of the half-life of nitrile hydratase upon exposure to 40 % acrylamide. A redesigned parDEM gene was introduced to Rhodococcus to accomplish stable inheritance of plasmids. A two-batch acrylonitrile hydration reaction was performed using the engineered cells as a catalyst. Compared to TH3, the acrylamide productivity of TH3/M4N1-59DEM catalysis increased by 27.8 and 37.5 % in the first and second bioreaction batches, respectively. These data suggest a novel method for increasing the bioconversion productivity of target chemicals through sigA mutation of the cell catalyst.
Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics
Authors: Huang Eric L , Lefsrud Mark G 
Published: July 2012

Abstract
Proteomics and fermentation technology have begun to integrate to investigate fermentation organisms in bioprocess development. This is the first shotgun proteomics study employed to monitor the proteomes of Scheffersomyces stipitis during xylose fermentation under oxygen limitation. We identified 958 nonredundant proteins and observed highly similar proteomes from exponential to early stationary phases. In analyzing the temporal proteome, we identified unique expression patterns in biological processes and metabolic pathways, including alternative respiration salicylhydroxamic acid (SHAM) pathway, activation of glyoxylate cycle, expression of galactose enzymes, and secondary zinc-containing alcohol dehydrogenase and O-glycosyl hydrolases. We identified the expression of a putative, high-affinity xylose sugar transporter Xut1p, but low-affinity xylose transporters were absent. Throughout cell growth, housekeeping processes included oxidative phosphorylation, glycolysis, nonoxidative branch of the pentose phosphate pathway, gluconeogenesis, biosynthesis of amino acids and aminoacyl total RNA (tRNA), protein synthesis and proteolysis, fatty acid metabolism, and cell division. This study emphasized qualitative analysis and demonstrated that shotgun proteomics is capable of monitoring S. stipitis fermentation and identifying physiological states, such as nutrient deficiency.
Optimization of fermentation parameters in phage production using response surface methodology
Authors: Grieco Sung-Hye H , Wong Ann Y K , Dunbar W Scott , MacGillivray Ross T A , Curtis Susan B 
Published: July 2012

Abstract
Previously, we used computer-controlled fermentation technology to improve the yield of filamentous phage produced in Escherichia coli by 10-fold (Grieco et al., Bioprocess Biosyst Eng 32:773–779, 2009). In the current study, three major fermentation parameters (temperature, dissolved oxygen [DO], and pH) were investigated using design of experiments (DOE) methodology. Response surface methodology (RSM) was employed to create a process model and determine the optimal conditions for maximal phage production. The experimental data fitted best to a quadratic model (p &lt; 0.0001). Temperature and pH, but not DO, proved to be significant variables. The model predicted a theoretical optimal condition for maximal bacteriophage production at temperature of 28.1 °C and pH 6.9. A validation run resulted in phage production [3.49 × 1011 transducing units (TU)/mL] comparable to the predicted value (2.86 × 1011 TU/mL). This represented a 7-fold increase in phage production above that obtained without optimization, resulting in a 70-fold increase above that achieved by shake flask culture alone.
Engineering a homobutanol fermentation pathway inEscherichia coliEG03
Authors: Garza Erin , Zhao Jinfang , Wang Yongze , Wang Jinhua , Iverson Andrew , Manow Ryan , Finan Chris , Zhou Shengde 
Published: July 2012

AbstractA homobutanol fermentation pathway was engineered in a derivative of Escherichia coli B (glucose [glycolysis] =&gt; 2 pyruvate + 2 NADH; pyruvate [pyruvate dehydrogenase] =&gt; acetyl-CoA + NADH; 2 acetyl-CoA [butanol pathway enzymes] + 4 NADH =&gt; butanol; summary stoichiometry: glucose =&gt; butanol). Initially, the native fermentation pathways were eliminated from E. coli B by deleting the genes encoding for lactate dehydrogenase (ldhA), acetate kinase (ackA), fumarate reductase (frdABCD), pyruvate formate lyase (pflB), and alcohol dehydrogenase (adhE), and the pyruvate dehydrogenase complex (aceEF-lpd) was anaerobically expressed through promoter replacement. The resulting strain, E. coli EG03 (ΔfrdABCD ΔldhA ΔackA ΔpflB Δ adhE ΔpdhR ::pflBp6-aceEF-lpd ΔmgsA), could generate 4 NADH for every glucose oxidized to two acetyl-CoA through glycolysis and the pyruvate dehydrogenase complex. However, EG03 lost its ability for anaerobic growth due to the lack of NADH oxidation pathways. When the butanol pathway genes that encode for acetyl-CoA acetyltransferase (thiL), 3-hydroxybutyryl-CoA dehydrogenase (hbd), crotonase (crt), butyryl-CoA dehydrogenase (bcd, etfA, etfB), and butyraldehyde dehydrogenase (adheII) were cloned from Clostridium acetobutylicum ATCC 824, and expressed in E. coli EG03, a balanced NADH oxidation pathway was established for homobutanol fermentation (glucose =&gt; 4 NADH + 2 acetyl-CoA =&gt; butanol). This strain was able to convert glucose to butanol (1,254 mg l−1) under anaerobic condition.
Enhanced archaeal laccase production in recombinant Escherichia coli by modification of N-terminal propeptide and twin arginine translocation motifs
Authors: Uthandi Sivakumar , Prunetti Laurence , De Vera Ian Mitchelle S , Fanucci Gail E , Angerhofer Alexander , Maupin-Furlow Julie A 
Published: July 2012

Abstract
Laccases are multicopper oxidases that couple the oxidation of phenolic polymers to the reduction of molecular oxygen. While an archaeal laccase has only recently been described (LccA from the culture broth of Haloferax volcanii), this enzyme appears promising for biotechnology applications based on its robust bilirubin oxidase and laccase activities as well as its ability to withstand prolonged exposure to extreme conditions. To further optimize LccA productivity and develop an option for LccA purification from whole cells, the encoding gene was modified through deletion of the twin-arginine translocation motif and N-terminal propeptide, and the modified genes were expressed in Escherichia coli. With this approach, LccA was readily purified (overall yield up to 54 %) from the soluble fraction of E. coli as a 74-kDa monomer with syringaldazine oxidizing activity as high as 33 U mg−1. LccA proteins prepared from H. volcanii culture broth and the soluble fraction of E. coli cells were compared by ICP-AES, EPR, DSC, CD, and UV–Vis spectroscopy and found to have a similar folding pattern with T m values and a rich β-sheet structure analogous to other multicopper oxidases. However, in contrast to the H. volcanii-purified LccA, which was loaded with copper, copper was not fully incorporated into the type-I Cu center of E. coli purified LccA, thus, providing insight into avenues for further optimization.
Effect of transport proteins on l-isoleucine production with the l-isoleucine-producing strain Corynebacterium glutamicum YILW
Authors: Xie Xixian , Xu Lanlan , Shi Jianming , Xu Qingyang , Chen Ning 
Published: July 2012

Abstract
Previous studies have shown that the deletion of brnQ from the Corynebacterium glutamicum chromosome results in a significant reduction in l-isoleucine uptake rates, while overexpression of brnFE leads to enhanced l-isoleucine export rates. Given that net excretion rates would be an important factor for high titers of l-isoleucine accumulation, we have tested the notion that decreased l-isoleucine uptake combined with increased l-isoleucine excretion will further improve high-yield strains that are currently used for the industrial-scale production of l-isoleucine. To examine the effect of the two carriers on l-isoleucine accumulation in l-isoleucine producer C. glutamicum YILW, we constructed a brnQ deletion mutant (C. glutamicum YILW∆brnQ) and two brnFE overexpressors (C. glutamicum YILWpXMJ19brnFE and C. glutamicum YILW∆brnQpXMJ19brnFE). Compared to the original strain, the efflux rate of the brnQ mutant increased from 19.0 to 23.6 nmol min−1 mg (dry wt)−1 and its l-isoleucine titer increased from 154.3 mM (20.2 g l−1) to 170.3 mM (22.3 g l−1). The efflux rates of C. glutamicum YILWpXMJ19brnFE and C. glutamicum YILW∆brnQpXMJ19brnFE were 33.5 and 39.1 nmol min−1 mg (dry wt)−1, and their l-isoleucine production titers were 197.2 mM (25.9 g l−1) and 221.0 mM (29.0 g l−1), respectively. Our results suggest that modifications of the transport system could provide a promising avenue for further increasing l-isoleucine yield in the l-isoleucine producer.