bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytometry of DNA replication and RNA synthesis: Historical perspective and recent advances based on “click chemistry”
Authors: Darzynkiewicz Zbigniew , Traganos Frank , Zhao Hong , Halicka H. Dorota , Li Jiangwei
Published: March 2011

This review covers progress in the development of cytometric methodologies designed to assess DNA replication and RNA synthesis. The early approaches utilizing autoradiography to detect incorporation of 3H‐ or 14C‐labeled thymidine were able to identify the four fundamental phases of the cell cycle G1, S, G2, and M, and by analysis of the fraction of labeled mitosis (FLM), to precisely define the kinetics of cell progression through these phases. Analysis of 3H‐uridine incorporation and RNA content provided the means to distinguish quiescent G0 from cycling G1 cells. Subsequent progress in analysis of DNA replication was based on the use of BrdU as a DNA precursor and its detection by the quenching of the fluorescence intensity of DNA‐bound fluorochromes such as Hoechst 33358 or acridine orange as measured by flow cytometry. Several variants of this methodology have been designed and used in studies to detect anticancer drug‐induced perturbations of cell cycle kinetics. The next phase of method development, which was particularly useful in studies of the cell cycle in vivo, including clinical applications, relied on immunocytochemical detection of incorporated halogenated DNA or RNA precursors. This approach however was hampered by the need for DNA denaturation, which made it difficult to concurrently detect other cell constituents for multiparametric analysis. The recently introduced “click chemistry” approach has no such limitation and is the method of choice for analysis of DNA replication and RNA synthesis. This method is based on the use of 5‐ethynyl‐2′deoxyuridine (EdU) as a DNA precursor or 5‐ethynyluridine (EU) as an RNA precursor and their detection with fluorochrome‐tagged azides utilizing a copper (I) catalyzed [3+2] cycloaddition. Several examples are presented that illustrate incorporation of EdU or EU in cells subjected to DNA damage detected as histone H2AX phosphorylation that have been analyzed by flow or laser scanning cytometry. © 2011 International Society for Advancement of Cytometry
Validated stability‐indicating derivative and derivative ratio methods for the determination of some drugs used to alleviate respiratory tract disorders and their degradation products
Authors: Hassib Sonia T. , El‐Zaher Asmaa A. , Fouad Marwa A.
Published: March 2011

Derivative and derivative ratio methods are presented for the determination of butamirate citrate, formoterol fumarate, montelukast sodium, and sodium cromoglycate. Using the second derivative ultraviolet (UV) spectrophotometry, butamirate citrate and formoterol fumarate were determined by measuring the peak amplitude at 260.4 and 261.8 nm, respectively, without any interference of their degradation products. Butamirate citrate degradation product, 2‐phenyl butyric acid, was determined by the measurement of its second derivative amplitude at 246.7 nm where butamirate citrate displays zero crossing. Formoterol fumarate degradation product, desformyl derivative, could be evaluated through the use of the first derivative at peak amplitude of 264.8 nm where interference of formoterol fumarate is negligible. In the first mode, the zero‐crossing technique was applied at 305 nm for the determination of montelukast sodium in the presence of its photodegradation product, cis‐isomer. The derivative of ratio spectra of montelukast sodium and its cis‐ isomer were used to determine both isomers using the first derivative of the ratio spectra by measuring the amplitudes of the trough at 305 nm and the peak at 308 nm, respectively. The later technique was also used for the determination of a ternary mixture of sodium cromoglycate and its two degradation products using zero‐crossing method. In the derivative ratio spectra of the ternary mixture, trough depths were measured at 271.6, 302.8 and 302.2 nm, using the second, the first, and the second mode to evaluate sodium cromoglycate, degradation product (1) and degradation product (2), respectively. All the methods were applied successfully to the pharmaceutical preparation and were validated according to ICH guidelines. Copyright © 2011 John Wiley & Sons, Ltd.
Straightforward Access to (Imidazol‐2‐yl)acetates by Reaction of 2‐Unsubstituted Imidazole 3‐Oxides with Dimethyl Acetylenedicarboxylate
Authors: Mlostoń Grzegorz , Jasiński Marcin , Heimgartner Heinz
Published: March 2011

A new method for the preparation of 1,4,5‐trisubstituted (imidazol‐2‐yl)acetates, based on the reaction of the corresponding imidazole 3‐oxides with dimethyl acetylenedicarboxylate (DMAD) is described. Formation of the products is rationalized by a formal 1,3‐dipolar cycloaddition and subsequent oxaloyl cleavage.
In‐channel amperometric detection for microchip electrophoresis using a wireless isolated potentiostat
Authors: Gunasekara Dulan B. , Hulvey Matthew K. , Lunte Susan M.
Published: March 2011

The combination of microchip electrophoresis with amperometric detection leads to a number of analytical challenges that are associated with isolating the detector from the high voltages used for the separation. While methods such as end‐channel alignment and the use of decouplers have been employed, they have limitations. A less common method has been to utilize an electrically isolated potentiostat. This approach allows placement of the working electrode directly in the separation channel without using a decoupler. This paper explores the use of microchip electrophoresis and electrochemical detection with an electrically isolated potentiostat for the separation and in‐channel detection of several biologically important anions. The separation employed negative polarity voltages and tetradecyltrimethylammonium bromide (as a buffer modifier) for the separation of nitrite (NO), glutathione, ascorbic acid, and tyrosine. A half‐wave potential shift of approximately negative 500 mV was observed for NO and H2O2 standards in the in‐channel configuration compared to end‐channel. Higher separation efficiencies were observed for both NO and H2O2 with the in‐channel detection configuration. The limits of detection were approximately two‐fold lower and the sensitivity was approximately two‐fold higher for in‐channel detection of nitrite when compared to end‐channel. The application of this microfluidic device for the separation and detection of biomarkers related to oxidative stress is described.
Grain size and topographical differences between static and mobile armour layers
Authors: Mao Luca , Cooper James R. , Frostick Lynne E.
Published: March 2011

A series of laboratory flume experiments under conditions of sediment starvation (zero sediment feeding) and recirculation were conducted in order to identify the temporal evolution and surface properties of static and mobile armour layers. The experiments were carried out in an 8 m long flume using a bimodal grain‐size mixture (D50 = 6·2 mm) and a range of shear stresses ranging from 4·0 to 8·6 N m–2. The results confirm that a static armour layer is coarser than a mobile one, and that the grain size of a mobile armour layer is rather insensitive to changes in the imposed flow strength. An analysis of laser scan bed surveys revealed the highly structured and imbricated nature of the static armour layer. Under these conditions the vertical roughness length scale of the bed diminished and it became topographically less complex at higher forming discharges. The topography of mobile armour layers created by rising discharges differed. They exhibited a greater roughness length scale and were less organized, despite the fact that the grain size of the surface material maintained an approximately constant value during recirculation. Also, the mobile armour tended to create larger cluster structures than static armour layers when formed by higher discharges. These differences were mainly due to the transport of the coarser fraction of bed sediments, which diminished to zero over the static armour because of being hidden within the bed, whereas in the mobile armour the coarser particles protruded into the flow and were actively transported, increasing the vertical roughness length scale. Overall, the results show that an examination of the grain size characteristics of armour layers cannot be used to infer sediment mobility and bed roughness. Detailed elevation models of exposed surfaces of gravel‐bed rivers are required to provide critical insight on the sediment availability and sedimentation processes. Copyright © 2011 John Wiley & Sons, Ltd.
Lateral plucking as a mechanism for elongate erosional glacial bedforms: explaining megagrooves in Britain and Canada
Authors: Krabbendam Maarten , Bradwell Tom
Published: March 2011

Megagrooves are kilometre‐scale linear topographic lows carved in bedrock, separated by ridges, typically in areas of largely devoid of till. They have been reported from several areas covered by Pleistocene glaciations, such as Canadian Northwest (NW) Territories, Michigan and NW Scotland. Here we report two previously undocumented megagroove fields from Ungava, Canada, and northern England, and present new analyses of the megagrooves from NW Scotland. This paper seeks to determine the nature of the lithological and structural controls on the occurrence and formation of megagrooves. Analysis of both geomorphological and bedrock properties shows that megagrooves are generally:

confined to well stratified or layered bedrock, such as (meta)sedimentary rocks with closely spaced joints, and tend not to occur on massive rocks such as gneiss or granite, or thick‐bedded sedimentary rocks;

subparallel to palaeo‐ice flow and the strike of the strata; and tend not to occur where palaeo‐ice flow is at high angles to the strike of strata;

produced by significant glacial erosion by sustained unidirectional ice flow.

Detailed analysis of megagrooves in NW Scotland shows that neither glacio‐fluvial erosion, nor differential abrasion was the dominant mechanism of formation. A mechanism, here termed ‘lateral plucking’, is suggested that involves block plucking on rock steps parallel to ice flow. Removal of joint‐bounded blocks from such rock steps involves a component of rotation along a vertical axis. Block removal may be enhanced by a direct component of shear stress onto the vertical stoss sides. The lateral plucking mechanism results in horizontal erosion at right angles to the ice flow, and enhances the groove/ridge topography. Megagrooves are potentially useful as palaeo‐ice flow indicators in areas devoid of till, and can thus complement the palaeo‐ice stream datasets which are presently largely based on soft‐sediment landform studies. British Geological Survey © NERC 2011
A fast WT‐based algorithm to distinguish between transformer internal faults and inrush currents
Authors: Rahmati A. , Sanaye‐Pasand M.
Published: March 2011

This paper presents a novel algorithm for power transformer differential protection which differentiates internal faults from magnetizing inrush currents and saturation of current transformers using wavelet transform. The technique is based on pattern recognition of the instantaneous differential currents using the high‐frequency components generated during the disturbance. These components are extracted using a wavelet‐based processor stage. In this method, an appropriate criterion at a suitable frequency range is developed. Using the developed criterion for three phases, internal faults are correctly detected in about 1/8th cycle after occurrence of the disturbance. The proposed algorithm is evaluated using generated data from simulation of a model power system using Electromagnetic Transients Program software. The performance of the proposed algorithm is tested in many different cases and promising results are obtained. Copyright © 2011 John Wiley & Sons, Ltd.
Optimal least squares support vector machines for SMES controller design using wide area phasor measurements
Authors: Pahasa Jonglak , Ngamroo Issarachai
Published: March 2011

In this paper, the least squares support vector machines (LS‐SVMs) based design of superconducting magnetic energy storage (SMES) controller is proposed for wide area stability control. The LS‐SVMs for SMES controllers are trained by local and inter‐area data based on synchronized phasor measurements considering time delay. A large amount of training data set of a multi‐machine power system is reduced by the measurement of similarity among samples. The LS‐SVM parameters and the similarity threshold are optimized by a particle swarm optimization. Subsequently, the redundant data in the training set can be discarded while the reduced data are the optimal support vectors in the LS‐SVM model. The LS‐SVM control signals can be adapted by various operating conditions and different disturbances. Simulation results in a six‐area West Japan interconnected power system demonstrate that the proposed LS‐SVM for SMES controller is robust to various disturbances under wide range of operating conditions in comparison to the conventional SMES. Copyright © 2011 John Wiley & Sons, Ltd.
Negative and positive predictive values of nerve monitoring in thyroidectomy
Authors: Cernea Claudio R. , Brandão Lenine G. , Hojaij Flavio C. , De Carlucci Dorival , Brandão José , Cavalheiro Beatriz , Sondermann Adriana
Published: March 2011

Background

Recurrent nerve injury is 1 of the most important complications of thyroidectomy. During the last decade, nerve monitoring has gained increasing acceptance in several centers as a method to predict and to document nerve function at the end of the operation. We evaluated the efficacy of a nerve monitoring system in a series of patients who underwent thyroidectomy and critically analyzed the negative predictive value (NPV) and positive predictive value (PPV) of the method.

Methods

NIM System efficacy was prospectively analyzed in 447 patients who underwent thyroidectomy between 2001 and 2008 (366 female/81 male; 420 white/47 nonwhite; 11 to 82 years of age; median, 43 years old). There were 421 total thyroidectomies and 26 partial thyroidectomies, leading to 868 nerves at risk. The gold standard to evaluate inferior laryngeal nerve function was early postoperative videolaryngoscopy, which was repeated after 4 to 6 months in all patients with abnormal endoscopic findings.

Results

At the early evaluation, 858 nerves (98.8%) presented normal videolaryngoscopic features after surgery. Ten paretic/paralyzed nerves (1.2%) were detected (2 unexpected unilateral paresis, 2 unexpected bilateral paresis, 1 unexpected unilateral paralysis, 1 unexpected bilateral paralyses, and 1 expected unilateral paralysis). At the late videolaryngoscopy, only 2 permanent nerve paralyses were noted (0.2%), with an ultimate result of 99.8% functioning nerves. Nerve monitoring showed absent or markedly reduced electrical activity at the end of the operations in 25/868 nerves (2.9%), including all 10 endoscopically compromised nerves, with 15 false‐positive results. There were no false‐negative results. Therefore, the PPV was 40.0%, and the NPV was 100%.

Conclusions

In the present series, nerve monitoring had a very high PPV but a low NPV for the detection of recurrent nerve injury. © 2011 Wiley Periodicals, Inc. Head Neck, 2012
In vitro toxicity of aflatoxin B1 and its photodegradation products in HepG2 cells
Authors: Liu Ruijie , Jin Qingzhe , Huang Jianhua , Liu Yuanfa , Wang Xingguo , Zhou Xinglong , Mao Wenyue , Wang Shanshan
Published: March 2011

The effects of aflatoxin B1 (AFB1) were studied using the HepG2 cell line. Cytotoxicity, apoptosis and p53 expression were assessed after exposure to different concentrations of AFB1 (0–100 μm) and its two types of degradation products, namely the mixtures of photodegradation products in water (Pw) and the mixtures of photodegradation products in peanut oil (Po) for different time periods (0, 24, and 48 h). After exposure of the HepG2 cells to these compounds for different times and concentrations, the cytotoxicity of Pw and Po decreased approximately 40 and 100% compared with AFB1, respectively. The expression of p53 protein decreased significantly in AFB1‐exposed cells, decreased slightly in Pw‐treated cells and did not decrease compared to the untreated cells. The results of the in vitro cytotoxicity assay indicate that Pw is less toxic than AFB1, and Po has almost no toxicity, which can be explained by the differences in the chemical nature of the various kinds of the test compounds. Copyright © 2011 John Wiley & Sons, Ltd.
Histone acetylation is essential for ANG‐II‐induced IGF‐IIR gene expression in H9c2 cardiomyoblast cells and pathologically hypertensive rat heart
Authors: Chu Chun‐Hsien , Lo Jeng‐Fan , Hu Wei‐Syun , Lu Ru‐Band , Chang Mu‐Hsin , Tsai Fuu‐Jen , Tsai Chang‐Hai , Weng Yueh‐Shan , Tzang Bor‐Show , Huang Chih‐Yang
Published: March 2011

The IGF‐II/mannose 6‐phosphate receptor (IGF‐IIR/Man‐6‐P) up‐regulation correlates with heart disease progression and its signaling cascades directly trigger pathological cardiac hypertrophy, fibrosis, and cardiomyocytes apoptosis. IGF‐IIR gene expression/ suppression is able to prevent myocardial remodeling. However, the regulating mechanisms for the IGF‐IIR gene remain unclear. This study performed reverse transcriptase PCR (RT‐PCR) and methylation‐specific PCR (MS‐PCR) to detect expression and DNA methylation of CpG islands within the IGF‐IIR genomic DNA region. Our finding revealed that the IGF‐IIR gene was up‐regulated both in H9c2 cells treated with tumor necrosis factor‐alpha (TNF‐α), lipopolysaccharide (LPS), angiotensin II (ANGII) and inomycin, and age‐dependently in spontaneously hypertensive rat (SHR) heart. For the DNA methylation study, although there were four CpG islands within IGF‐IIR genomic regions, the DNA methylation distribution showed no change either in cells treated with ANGII or in the SHR heart. Using chemical inhibitors to individually block histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity, we found that histone acetylation was essential for ANGII‐induced IGF‐IIR gene expression using RT‐PCR and luciferase assay. The Chromatin immuno‐precipitation assay indicated that acetyl‐Histone H3 and acetyl‐Histone H4 associated with the IGF‐IIR promoter increased in the presence of ANGII, otherwise methyl‐CpG binding domain protein 2 (MeCP2) is disassociated with this. Taken together, this study demonstrates that histone acetylation plays a critical role in IGF‐IIR up‐regulation during pathological cardiac diseases and might provide a targeting gene in transcriptional therapies for the failing heart. J. Cell. Physiol. 227: 259–268, 2012. © 2011 Wiley Periodicals, Inc.
Case report: A case of light chain deposition disease involving liver and stomach with chronic hepatitis C virus infection and hepatocellular carcinoma
Authors: Kwon Jung Hee , Jeong Sook‐Hyang , Kim Jin‐Wook , Bang Soo‐Mee , Kim Haeryoung , Kim Young Hoon , Song Sang Hoon
Published: March 2011

Light chain deposition disease (LCDD) is a rare, plasma cell proliferative disorder characterized by mainly abnormal light chain deposition in various organs. Hepatitis C virus (HCV) is a hepatotrophic and lymphotrophic virus and significantly related to B‐cell proliferation. This is a case report of systemic LCDD involving liver, stomach, bone marrow, and probably kidney, in a patient with HCV‐related hepatocellular carcinoma (HCC). A 62‐year‐old man with chronic HCV infection who presented with a small HCC in segment 8 of the liver and nephrotic syndrome showed kappa typed immunoglobulin light chain depositions in biopsy specimens of bone marrow, stomach, and non‐tumorous liver parenchyma. After treatment of the HCC with transarterial chemoembolization, antiviral therapy for chronic hepatitis C was started. The patient showed early virologic response at 12 weeks of treatment; however, antiviral therapy was discontinued due to adverse effects and he was lost to follow‐up. This is the first case of LCDD involving the liver and stomach in a patient with chronic HCV infection and HCC, which may represent LCDD as a rare HCV‐associated B cell proliferative disease. J. Med. Virol. 83:810–814, 2011. © 2011 Wiley‐Liss, Inc.
A 2000‐year lipid biomarker record preserved in a stalagmite from north‐west Scotland
Authors: Blyth Alison J. , Baker Andy , Thomas Louise E. , Van Calsteren Peter
Published: March 2011

Previous studies on lipid biomarkers preserved in Chinese stalagmites have indicated that ratios of low‐molecular‐weight (LMW) to high‐molecular‐weight (HMW) n‐alkanes, n‐alkan‐2‐ones, n‐alkanols and n‐alkanoic acids can be used as an index of vegetation versus microbial organic matter input to the system and, by extension, a marker of climatic changes, with increases in the proportion of LMW compounds coinciding with colder periods. Here we test whether this hypothesis is equally applicable to a different geographical region (north‐west Scotland), by examining a stalagmite record of the past 200 years, and a wider range of lipid markers. We also test the applicability of other lipid proxies in this context, including the use of n‐alkane ratios, to interpret vegetation changes, and unsaturated alkanoic acid ratios as climatic indicators. The results show that lipid proxies preserved in stalagmites, and especially those related to vegetation, are potentially extremely useful in palaeoenvironmental research. Of particular value is the use of C27/C31 n‐alkane ratios as a proxy for vegetation change, clearly indicating variations between herbaceous and arboreal cover. This proxy has now been successfully applied to samples from diverse environments, and can be considered sufficiently robust to be of use in analysing future stalagmite records. It will be of particular value in areas where reliable pollen records are not available, as is often the case with deeper cave deposits. However, the division between LMW and HMW aliphatic compounds is not a clear‐cut case of microbial versus plant activity, with the changes in LMW compounds relating more closely to those in their HMW analogues than in specific bacterial biomarkers. The use of unsaturated alkanoic acid ratios here gives conflicting results, with the observed variation through time depending on the isomer measured. The discrepancies between the findings of this study and previous work are likely to be due to the varying controls on the lipids (original organic matter input, and compound degradation), which in turn will be affected by whether the main climatic limiting factor on the soil is temperature or precipitation. This suggests that lipid proxies preserved in stalagmites must be interpreted with care, particularly in the case of bacterial compounds which may be derived from within the cave or from the soil. However, many of these issues can be resolved by the use of multi‐proxy studies. Copyright © 2011 John Wiley & Sons, Ltd.
Elmendorf Tear Test of Polyethylene Films: Mechanical Interpretation and Model
Authors: Kissin Yury V.
Published: March 2011

A physical model of one of the principal end‐use tests of film manufactured from linear low‐density and low‐density PE resins, the Elmendorf tear test (ASTM D1922, ISO 6383‐2), is described. According to this model, the tear test of film is a special case of a high‐speed stress/strain measurement performed on a polymer sample with a varying cross‐section. The tear resistance of film is a function of all the parameters that characterize the stress/strain curve of the resin: stresses and strains at the yield, the necking, and the breaking points. The model affords estimations of tear resistance of semi‐crystalline PE film and provides explanations for differences between tear strength of film manufactured from different types of resins.

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The best constant in a fractional Hardy inequality
Authors: Bogdan Krzysztof , Dyda Bartłomiej
Published: March 2011

We prove an optimal Hardy inequality for the fractional Laplacian on the half‐space. © 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim
The pivotal role of mass spectrometry in determining the presence of chemical contaminants in food raw materials
Authors: Mohamed Rayane , Guy Philippe A.
Published: March 2011

During recent years, a rising interest from consumers and various governmental organizations towards the quality of food has continuously been observed. Human intervention across the different stages of the food supply chain can lead to the presence of several types of chemical contaminants in food‐based products. On a normal daily consumption basis, some of these chemicals are not harmful; however, for those that present a risk to consumers, legislation rules were established to specify tolerance levels or in some cases the total forbiddance of these specific contaminants. Hence, the use of appropriate analytical tools is recommended to properly identify chemical contaminants. In that context, mass spectrometry (MS)‐based techniques coupled or not to chromatography offer a vast panel of features such as sensitivity, selectivity, quantification at trace levels, and/or structural elucidation. Because of the complexity of food‐based matrices, sample preparation is a crucial step before final detection. In the present manuscript, we review the contribution and the potentialities of MS‐based techniques to ensure the absence of chemical contaminants in food‐based products. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:1073–1095, 2011
Hexamethyldisiloxane‐based nanoprobes for 1H MRI oximetry
Authors: Gulaka Praveen K. , Rastogi Ujjawal , McKay Madalyn A. , Wang Xianghui , Mason Ralph P. , Kodibagkar Vikram D.
Published: March 2011

Quantitative in vivo oximetry has been reported using 19F MRI in conjunction with reporter molecules, such as perfluorocarbons, for tissue oxygenation (pO2). Recently, hexamethyldisiloxane (HMDSO) has been proposed as a promising alternative reporter molecule for 1H MRI‐based measurement of pO2. To aid biocompatibility for potential systemic administration, we prepared various nanoemulsion formulations using a wide range of HMDSO volume fractions and HMDSO to surfactant ratios. Calibration curves (R1 versus pO2) for all emulsion formulations were found to be linear and similar to neat HMDSO for low surfactant concentrations (< 10% v/v). A small temperature dependence in the calibration curves was observed, similar to previous reports on neat HMDSO, and was characterized to be approximately 1 Torr/ °C under hypoxic conditions. To demonstrate application in vivo, 100 µL of this nanoemulsion was administered to healthy rat thigh muscle (Fisher 344, n = 6). Dynamic changes in mean thigh tissue pO2 were measured using the PISTOL (proton imaging of siloxanes to map tissue oxygenation levels) technique in response to oxygen challenge. Changing the inhaled gas to oxygen for 30 min increased the mean pO2 significantly (p < 0.001) from 39 ± 7 to 275 ± 27 Torr. When the breathing gas was switched back to air, the tissue pO2 decreased to a mean value of 45 ± 6 Torr, not significantly different from baseline (p > 0.05), in 25 min. A first‐order exponential fit to this part of the pO2 data (i.e. after oxygen challenge) yielded an oxygen consumption‐related kinetic parameter k = 0.21 ± 0.04 min−1. These results demonstrate the feasibility of using HMDSO nanoemulsions as nanoprobes of pO2 and their utility to assess oxygen dynamics in vivo, further developing quantitative 1H MRI oximetry. Copyright © 2011 John Wiley & Sons, Ltd.
Efficient generation of pareto‐optimal topologies for compliance optimization
Authors: Turevsky Inna , Suresh Krishnan
Published: March 2011

In multi‐objective optimization, a design is defined to beit pareto‐optimal if no other design exists that is better with respect to one objective, and as good with respect to other objectives. In this paper, we first show that if a topology is pareto‐optimal, then it must satisfy certain properties associated with the topological sensitivity field, i.e. no further comparison is necessary. This, in turn, leads to a deterministic, i.e. non‐stochastic, method for efficiently generating pareto‐optimal topologies using the classic fixed‐point iteration scheme. The proposed method is illustrated, and compared against SIMP‐based methods, through numerical examples. In this paper, the proposed method of generating pareto‐optimal topologies is limited to bi‐objective optimization, namely compliance–volume and compliance–compliance. The future work will focus on extending the method to non‐compliance and higher dimensional pareto optimization. Copyright © 2011 John Wiley & Sons, Ltd.
Folic acid‐conjugated depolymerized quaternized chitosan as potential targeted gene delivery vector
Authors: Morris Viola B , Pillai Chennakkattu K S , Sharma Chandra P
Published: March 2011

Ligand‐conjugated delivery vectors that target over‐expressed cell surface receptors have a potential impact on gene therapy. In the study reported, high‐molecular‐weight chitosan was depolymerized to medium and low molecular weight and trimethylated to render the polymer soluble over a wider pH range. Folate conjugation was introduced to the quarternized derivative to improve gene transfection efficiency. Complexes of the folic acid‐conjugated trimethylated depolymerized chitosan (FTMC) with plasmid DNA (pDNA) formed core–shell nanostructured particles. Gel electrophoretic band retardation showed efficient condensation of DNA. These derivatives and their complexes with pDNA were tested for toxicity and haemocompatibility and were found to be significantly less toxic and haemocompatible than polyethyleneimine. Transfection efficiency and nuclear uptake properties were tested in the human KB oral epidermoid cell line, which over‐expresses the folate receptor in the presence of 10% serum. Among the four FTMC derivatives investigated, folic acid‐conjugated chitosan having low molecular weight and medium folate conjugation was found to be a potential vector for gene delivery applications with good transfection and nuclear uptake properties, as proved by YOYO labelling of pDNA. Copyright © 2011 Society of Chemical Industry
Chitosan nanoparticles: a contribution to nanomedicine
Authors: Peniche Hazel , Peniche Carlos
Published: March 2011

Chitosan is a cationic polysaccharide that finds diverse applications in medicine and pharmacy because of its excellent biological qualities: it is biocompatible, biodegradable, mucoadhesive and non‐toxic, and exhibits antimicrobial, antiviral and immunoadjuvant properties. It can be easily processed in diverse forms, such as films, threads, tablets, membranes and microparticles/nanoparticles, allowing the design of a variety of medical and pharmacological devices adaptable to end purposes. In particular, chitosan nanoparticles have become of great interest as polymeric platforms for the development of new pharmacological and therapeutic drug release systems with improved biodistribution and increased specificity and sensitivity, and reduced pharmacological toxicity. Chitosan nanoparticles have been found appropriate for non‐invasive routes of drug administration: oral, nasal, pulmonary and ocular routes. These applications are facilitated by the absorption‐enhancing effect of chitosan. Additionally, chitosan nanoparticles have been proposed as non‐viral vectors in gene therapy and have shown adjuvant effect in vaccines. This paper reviews the main procedures developed for preparing chitosan nanoparticles. Moreover, it illustrates the state of the art of chitosan nanoparticle applications in drug delivery. Copyright © 2011 Society of Chemical Industry
Elevated expression levels of ANXA11, integrins β3 and α3, and TNF‐α contribute to a candidate proteomic signature in urine for kidney allograft rejection
Authors: Srivastava Meera , Eidelman Ofer , Torosyan Yelizaveta , Jozwik Catherine , Mannon Roslyn B. , Pollard Harvey B.
Published: March 2011

Purpose: Kidney transplantation is the treatment of choice for end stage renal disease, with long‐term allograft loss being the major obstacle, and for which potential treatments are based on a histological diagnosis. The problem is that markers for predicting graft rejection are limited in number, are invasive, and are quite non‐specific. We have hypothesized that protein biomarkers might be discovered in the urine of patients when acute or chronic rejection might be occurring.

Experimental design: We have established a workflow in which initial screening for candidate biomarkers is first performed using urine samples on large‐scale antibody microarrays. This approach generated several dozen candidates. The next step is to qualify some of the strongest signals using the high‐throughput Reverse Capture Protein Microarray platform.

Results: Four top candidates including ANXA11, Integrin α3, Integrin β3 and TNF‐α, initially identified by the antibody microarray platform, were all qualified using Reverse Capture Protein Microarrays. We also used receiver operating condition (ROC) curves to independently quantify the specificity and sensitivity of these four analytes.

Conclusions and clinical relevance: The present data suggest that these novel four analytes in the urine, together or independently, may contribute to a robust and quantitative urine proteomic signature for diagnosing acute or chronic rejection of renal allografts.
Constraining local structure can speed up folding by promoting structural polarization of the folding pathway
Authors: Buck Patrick M. , Bystroff Christopher
Published: March 2011

The pathway which proteins take to fold can be influenced from the earliest events of structure formation. In this light, it was both predicted and confirmed that increasing the stiffness of a beta hairpin turn decreased the size of the transition state ensemble (TSE), while increasing the folding rate. Thus, there appears to be a relationship between conformationally restricting the TSE and increasing the folding rate, at least for beta hairpin turns. In this study, we hypothesize that the enormous sampling necessary to fold even two‐state folding proteins in silico could be reduced if local structure constraints were used to restrict structural heterogeneity by polarizing folding pathways or forcing folding into preferred routes. Using a Gō model, we fold Chymotrypsin Inhibitor 2 (CI‐2) and the src SH3 domain after constraining local sequence windows to their native structure by rigid body dynamics (RBD). Trajectories were monitored for any changes to the folding pathway and differences in the kinetics compared with unconstrained simulations. Constraining local structure decreases folding time two‐fold for 41% of src SH3 windows and 45% of CI‐2 windows. For both proteins, folding times are never significantly increased after constraining any window. Structural polarization of the folding pathway appears to explain these rate increases. Folding rate enhancements are consistent with the goal to reduce sampling time necessary to reach native structures during folding simulations. As anticipated, not all constrained windows showed an equal decrease in folding time. We conclude by analyzing these differences and explain why RBD may be the preferred way to constrain structure.
Development of an organic vapor sensor based on functionalized porous silicon
Authors: Badilla J. P. , Rojas D. C. , López V. , Fahlman B. D. , Ramírez‐Porras A.
Published: March 2011

Functionalization of hydrofluoric acid‐etched crystalline silicon surfaces were performed using 4‐aminopyridine. This treatment was employed to perform an organic interface with the exterior ambient. The obtained treated surfaces were exposed to different organic vapors while keeping track of their electric conductance to assess their sensing abilities. Results for these tests are provided.
Growth of AlGaN/GaN heterostructure on vicinal m‐plane free‐standing GaN substrates prepared by the Na flux method
Authors: Isobe Yasuhiro , Iida Daisuke , Sakakibara Tatsuyuki , Iwaya Motoaki , Takeuchi Tetsuya , Kamiyama Satoshi , Akasaki Isamu , Amano Hiroshi , Imade Mamoru , Kitaoka Yasuo , Mori Yusuke
Published: March 2011

We fabricated and characterized AlGaN/GaN heterostructure growth by MOVPE on vicinal m‐plane free‐standing GaN substrates prepared by the Na flux method. The miscut angle in the LPE‐GaN substrate has a great influence on the surface morphology and crystalline quality of epitaxial GaN and AlGaN films. In particular, AlGaN/GaN on a 4° miscut‐angle LPE‐GaN substrate shows large step bunching, small‐miscut‐angle LPE GaN substrate is essential for fabricating on FET structure with a flat surface.
Structural and mechanical properties of dolomite rock under high pressure conditions: A first‐principles study
Authors: Bakri Z. , Zaoui A.
Published: March 2011

The structural behaviour of carbonate minerals under lower mantle pressures, experimentally investigated by means of X‐ray diffraction and infrared spectra measurements can be interpreted and difficulties surmounted by first principles quantum mechanical simulations based on density functional theory (DFT). This work is devoted to structural and mechanical properties of CaMg(CO3)2–dolomite mineral. From Birch–Murnaghan equation of state (BM‐EoS) applied to the energy–volume data of the dolomite polymorph, we obtain a bulk modulus of 93.7 GPa with a pressure derivative of 4.7, which show suitable agreement with experimental data. Under hydrostatic pressure the mineral system shows an anisotropic compression behaviour and is found to be more compressible in the z direction. The investigation of dolomite mineral structural phase stability under hydrostatic pressure has confirmed previously range‐determined but still debated values of structural phase transition. Two phases transitions were encountered when increasing pressure. The first one occurring from dolomite to the orthorhombic calcite‐III‐like structure was predicted at ∼34 GPa; and the second one between the calcite III and the aragonite II at ∼52.5 GPa. This approach overestimates the transition pressure value when confronted to experimental findings. On the other hand the mechanical behaviour of this mineral under ambient and high pressure conditions was studied. To this end we used a stress–strain ab initio based model to calculate the elastic constants of CaMg(CO3)2–dolomite. Based on the trigonal symmetry (space group R3) we found 196.6, 64.4, 54.7, 22.4, 110 and 41.6 GPa for C11, C12, C13, C14, C33 and C44, respectively.
A Tool to Estimate Land‐Surface Emissivities at Microwave frequencies (TELSEM) for use in numerical weather prediction
Authors: Aires Filipe , Prigent Catherine , Bernardo Frédéric , Jiménez Carlos , Saunders Roger , Brunel Pascal
Published: March 2011

A Tool to Estimate Land Surface Emissivities at Microwave frequencies (TELSEM) has been developed for use with the Radiative Transfer for the Television and infrared Observation satellite operational Vertical Sounder (RTTOV) model. Its objective is to provide a good estimate of the microwave surface emissivity to improve the retrieval of atmospheric profiles or the direct assimilation of radiances in numerical weather prediction (NWP) models using microwave sounder data over land. TELSEM provides emissivity estimates and error‐covariance matrices for all land surfaces between 19 and 100 GHz and for all angles and linear polarizations. It is based on a pre‐calculated monthly‐mean emissivity climatology derived from Special Sensor Microwave/Imager (SSM/I) observations. Results show that when TELSEM is used, radiative‐transfer simulations are closer to real observations. This is important when RTTOV is used to generate simulated datasets, to analyze new instrument concepts or for assimilation schemes. Experiments also show that TELSEM can be applied to provide a first guess for the surface emissivity down to 6 GHz and up to 190 GHz (extrapolating the SSM/I emissivities). These emissivities are essential for atmospheric profile retrievals over land: results for water‐vapour retrieval show that surface‐contaminated channels can be utilized and that the retrieval is improved, in particular for the lower troposphere. Furthermore, TELSEM emissivity first guesses can be improved in emissivity‐retrieval schemes. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office
DFT and Ab Initio calculations of spectroscopic properties of tetramethyltin and of its cation
Authors: Dhouib A. , Abderrabba M. , Essalah K. , Brites V. , Hochlaf M.
Published: March 2011

DFT and ab initio calculations are performed on tetramethyltin (SnMe4, TMSn) and its cation. A set of spectroscopic constants for both species are derived. They include equilibrium geometries, rotational constants and vibrational wavenumbers. All quantities are in close agreement with the available experimental data. For the cation, our calculations confirm the C3v charge transfer structure proposed earlier through the analysis of electron paramagnetic resonance (EPR) experimental data. Using multi reference configuration interaction and time dependant density functional theory (TD‐DFT) methodologies, the vertical electronic excitation energies of TMSn and TMSn+ are determined. For the singlet‐singlet neutral molecule, our calculated transition energies are distinctly lower than those previously computed. For the TMSn (
$\tilde X$1A1 → 11T2) absorption transition, our computed excitation energy coincides, however, with the experimental value. Predictive data are also given for the TMSn triplets. At the best level of theory, the vertical and the adiabatic ionization energies of TMSn are computed 9.86 eV and 8.74 eV, respectively. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
POST‐DAMMING FLOW REGIME DEVELOPMENT IN A LARGE LOWLAND RIVER (VOLGA, RUSSIAN FEDERATION): IMPLICATIONS FOR FLOODPLAIN INUNDATION AND FISHERIES
Authors: Górski K. , van den Bosch L. V. , van de Wolfshaar K. E. , Middelkoop H. , Nagelkerke L. A. J. , Filippov O. V. , Zolotarev D. V. , Yakovlev S. V. , Minin A. E. , Winter H. V. , De Leeuw J. J. , Buijse A. D. , Verreth J. A. J.
Published: March 2011

Periodic flooding plays a key role in the ecology of floodplain rivers. Damming of such rivers can disturb flooding patterns and have a negative impact on commercial fish yield. The Volga River, the largest river in Europe, has a regulated flow regime after completion of a cascade of dams. Here, we study effects of damming on long‐term discharge variability and flood pulse characteristics. In addition, we evaluate the effects of the altered flood pulse on floodplain ecosystem functioning and commercial fish yields. Our results indicate that both flood pulse and fish populations of the Volga–Akhtuba floodplain have varied considerably over the past decades. After damming, annual maximum peak discharges have decreased, minimum discharges increased, but average discharges remained similar to pre‐damming conditions. Moreover, because of bed level incision of over 1.5 m, a higher discharge is needed to reach bankfull level and inundate the floodplains. Despite this significantly altered hydrological regime and subsequent morphological changes, current discharge management still provides significant spring flooding. However, commercial fish catches did decrease after damming, both in the main channel and in the floodplain lakes. All catches were dominated by species with a eurytopic flow preference, although catches from the main channel contained more rheophilic species, and floodplain catches contained more limnophilic and phytophilic species. The strong increase of opportunistic gibel carp (Carassius gibelio) around 1985 was apparent in the main channel and the floodplain lakes. Despite the hydrological changes, the decrease in overall catches, and the upsurge of gibel, we found a strong positive effect of flood magnitude in the previous year on commercial fish yield in the floodplain lakes. This suggests that under the current discharge management there still is an increased fish growth and/or survival during high floods and that functioning of the floodplain is at least partly intact. Copyright © 2011 John Wiley & Sons, Ltd.
The use of search‐based optimization techniques to schedule and staff software projects: an approach and an empirical study
Authors: Di Penta Massimiliano , Harman Mark , Antoniol Giuliano
Published: March 2011

Allocating resources to a software project and assigning tasks to teams constitute crucial activities that affect project cost and completion time. Finding a solution for such a problem is NP‐hard; this requires managers to be supported by proper tools for performing such an allocation. This paper shows how search‐based optimization techniques can be combined with a queuing simulation model to address these problems. The obtained staff and task allocations aim to minimize the completion time and reduce schedule fragmentation. The proposed approach allows project managers to run multiple simulations, compare results and consider trade‐offs between increasing the staffing level and anticipating the project completion date and between reducing the fragmentation and accepting project delays. The paper presents results from the application of the proposed search‐based project planning approach to data obtained from two large‐scale commercial software maintenance projects. Copyright © 2011 John Wiley & Sons, Ltd.
Peer educators in learning assistance programs: Best practices for new programs
Authors: Wilson Wendy L. , Arendale David R.
Published: March 2011

Starting a new peer education program in learning assistance requires attention to critical program components. What steps need to be taken, and what resources are available?
Numerical validation of a finite element thin‐walled beam model of a composite wind turbine blade
Authors: Cárdenas Diego , Escárpita Alejandro A. , Elizalde Hugo , Aguirre Juan José , Ahuett Horacio , Marzocca Piergiovanni , Probst Oliver
Published: March 2011

This paper presents a numerical validation of a thin‐walled beam (TWB) finite element (FE) model of a realistic wind turbine rotor blade. Based on the theory originally developed by Librescu et al. and later extended to suit FE modelling by Phuong, Lee and others, this computationally efficient yet accurate numerical model is capable of capturing most of the features found in large blades including thin‐walled hollow cross section with variable thickness along the section's contour, inner reinforcements, arbitrary material layup and non‐linear anisotropic fibre‐reinforced composites; the present application is, for the time being, restricted to linearity. This one‐dimensional (1D) FE model allows retaining information of different regions of the blade's shell and therefore approximates the behaviour of more complex three‐dimensional (3D) shell or solid FE models more accurately than typical 1D FE beam models. A 9.2 m rotor blade, previously reported in specialized literature, was chosen as a case study to validate the static and dynamic behaviour predicted by a TWB model against an industry‐standard 3D shell model built in a commercial software tool. Given the geometric and material complexities involved, an excellent agreement was found for static deformation curves, as well as a good prediction of the lowest frequency modes in terms of resonance frequencies, mode shapes and frequency response functions; the highest (sixth) frequency mode shows only a fair agreement as expected for an FE model. It is concluded that despite its simplicity, a TWB FE model is sufficiently accurate to serve as a design tool for the recursive analyses required during design and optimization stages of wind turbines using only readily available computational tools. Copyright © 2011 John Wiley & Sons, Ltd.