bluuebunny/crossref_metadata_2025 huggingface dataset:
Addressing endotoxin issues in bioengineered heparin
Authors: Suwan Jiraporn , Torelli Amanda , Onishi Akihiro , Dordick Jonathan S. , Linhardt Robert J.
Published: October 2012

Heparin is a widely used clinical anticoagulant that is prepared from pig intestine. A contamination of heparin in 2008 has led to a reexamination of animal‐derived pharmaceuticals. A bioengineered heparin prepared by bacterial fermentation and chemical and enzymatic processing is currently under development. This study examines the challenges of reducing or removing endotoxins associated with this process that are necessary to proceed with preclinical in vivo evaluation of bioengineered heparin. The current process is assessed for endotoxin levels, and strategies are examined for endotoxin removal from polysaccharides and enzymes involved in this process.
Four‐peptide‐nanotube bundle formation by self‐assembling of cyclic tetra‐β‐peptide using g‐quartet motif
Authors: Ishihara Yusuke , Kimura Shunsaku
Published: October 2012

A hydrophilic cyclic tetra‐β‐peptide having guanine at the side chain (CPG) was synthesized to construct a four‐peptide‐nanotube bundle with the formation of guanine quadruplex (G‐quartet). CPG was so soluble in water that molecular association of CPG was very limited in water. However, in the presence of potassium ion, circular dichroism spectral change showed initial molecular association due to the G‐quartet formation followed by a slow growth into peptide nanotubes. Transmission electron microscope observation and electron diffraction analysis revealed that CPG self‐assembled into a four‐peptide‐nanotube bundle with a uniform diameter of 7–8 nm. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 141–147, 2013.
Performance of secondary structure prediction methods on proteins containing structurally ambivalent sequence fragments
Authors: Saravanan K. Mani , Selvaraj Samuel
Published: October 2012

Several approaches for predicting secondary structures from sequences have been developed and reached a fair accuracy. One of the most rigorous tests for these prediction methods is their ability to correctly predict identical fragments of protein sequences adopting different secondary structures in unrelated proteins. In our previous work, we obtained 30 identical octapeptide sequence fragments adopting different backbone conformations. It is of interest to find whether the presence of structurally ambivalent fragments in proteins will affect the accuracy of secondary structure prediction methods or not. Hence, in this work, we have made a systematic comparative analysis on secondary structure prediction results of 30 identical octapeptide pairs and 52 identical heptapeptide pairs adopting different conformations with the aid of segment overlap measure. The results reveal the better performance of profile‐based methods such as PSIpred and JPred and misprediction by classical rule‐based methods such as Garnier Osguthorpe Robson Method and Double Prediction Method. The results discussed here insist that modern secondary structure prediction methods are able to better discriminate conformationally ambivalent peptide fragments. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 148–153, 2013.
Matrix metalloproteinase and cytokine expression in Tenon fibroblasts during scar formation after glaucoma filtration or implant surgery in rats
Authors: Nakamura‐Shibasaki Momoko , Ko Ji‐Ae , Takenaka Joji , Chikama Tai‐ichiro , Sonoda Koh‐Hei , Kiuchi Yoshiaki
Published: October 2012

Failure of surgery for glaucoma is usually due to post‐surgical scarring (fibrosis), a process in which fibroblasts play a prominent role. We investigated the molecular mechanisms of such scarring by examining the expression of matrix metalloproteinases and cytokines in Tenon fibroblasts isolated from rats after glaucoma surgery. Filtration surgery was performed in one eye and implant surgery in the other; and Tenon fibroblasts were isolated from the tissue surrounding the bleb after surgery. The cells were cultured and examined for the expression of matrix metalloproteinases (MMPs) by reverse transcription‐polymerase chain reaction, immunoblot and gelatin zymographic analyses. Culture supernatants were also assayed for cytokines with a multiplex array. The amounts of MMP‐1 and MMP‐3 mRNAs and proteins were greater in cells isolated after implant surgery than in those isolated after filtration surgery, with the progression of scar formation being more complete after the former surgery. The secretion of interleukin‐6 (IL‐6) by cells isolated after filtration surgery was greater than that for cells isolated after implant surgery. Depletion of IL‐6 by RNA interference in cells isolated after filtration surgery increased the expression of MMP‐1 and MMP‐3 in these cells. These results thus suggest that the expression of MMP‐1 and MMP‐3 in Tenon fibroblasts is regulated by IL‐6 during, and may play an important role in, scar formation after glaucoma surgery. Copyright © 2012 John Wiley & Sons, Ltd.
Reflections From the Field: Voices of Experience
Authors: McNair Delores E. , Phelan Daniel J.
Published: October 2012

Interviews with current community college presidents showcase their reflections on their pathway to the corner office and review the competencies they have found to be the most valuable in their practice. The presidents also offer insights into what they are doing to help prepare future leaders at their institutions.
Developing Wetland Restoration Scenarios and Modeling Its Ecological Consequences in the Liaohe River Delta Wetlands, China
Authors: Li Xiaowen , Liang Chen , Shi Jianbin
Published: October 2012

The Liaohe River Delta wetlands contains over 80 000 ha of the world's most important and unique natural wetlands, which support a wide range of important biological diversity and act as crucial staging and breeding areas for migratory bird populations, including some globally threatened species. The economic value and social benefits of the Liaohe River Delta wetlands are also enormous both locally and nationally. In the past two decades, however, these wetlands and the biodiversity they support have been under constant threat of degradation, mostly due to human development pressures. To balance the conflicting potential uses of land by humans and nature conservation, we elaborated spatial planning of three land‐use scenarios (i.e., wetland mitigation, habitat management, and agricultural development) in the Liaohe River Delta wetlands, and each scenario included its landscape targets, ecological objectives, spatial strategies, and management types. In order to support this scenarios approach, a landscape ecological decision and evaluation support system (LEDESS) was employed to accommodate the prevalent scenario structures. By using this expert model, we identified the measures to realize the landscape targets, located the spatial areas involved in these measures, and modeled the ecological impacts on habitat suitability and carrying capacities of the indicator species (i.e., red‐crowned crane and Saunders' gull). Our results indicated that a spatial solution might be reached that could mitigate the competing land‐use needs between the ecological conservation and human needs, and to maintain the “no‐net‐loss” of wetland habitats.
Wetland Network Design for Mitigation of Saltwater Intrusion by Transferring Tidal Discharge
Authors: Zhang Zhiming , Cui Baoshan , Ou Bingbing , Fan Xiaoyun
Published: October 2012

With the interactions of river discharge and tide, the balances between water and saline in estuaries are helpful for maintaining biodiversity and landscape diversity. However, the delicate balances have been broken in many estuaries especially in some areas where prosperous cities have been developed. Saltwater intrusion causes serious adverse effects on estuary ecosystems in Pearl River estuary (PRE), China. This paper tries to use a wetland network which is a methodology to divert saltwater to explain how to address the adverse effects of saltwater intrusion and aims to mitigate such intrusion. The existing wetland patches and corridors are connected and form a wetland network with structural and functional connectivity. The patches in the wetland network are assigned to attributes that represent storage capacity of wetlands, and the corridors are assigned to attributes that represent water flow of channels. The results demonstrated that the saltwater intrusion length follows a linear relationship with tidal discharge in the southern part of Guangzhou (SPG, a part of PRE). When the upstream discharge changed slightly, saltwater intrusion cannot be effectively mitigated merely by diverting water from river channels to wetland network during spring tides. This paper provides new insight for management of saltwater intrusion in estuaries.
A computationally efficient framework for the simulation of cardiac perfusion using a multi‐compartment Darcy porous‐media flow model
Authors: Michler C. , Cookson A. N. , Chabiniok R. , Hyde E. , Lee J. , Sinclair M. , Sochi T. , Goyal A. , Vigueras G. , Nordsletten D. A. , Smith N. P
Published: October 2012

We present a method to efficiently simulate coronary perfusion in subject‐specific models of the heart within clinically relevant time frames. Perfusion is modelled as a Darcy porous‐media flow, where the permeability tensor is derived from homogenization of an explicit anatomical representation of the vasculature. To account for the disparity in length scales present in the vascular network, in this study, this approach is further refined through the implementation of a multi‐compartment medium where each compartment encapsulates the spatial scales in a certain range by using an effective permeability tensor. Neighbouring compartments then communicate through distributed sources and sinks, acting as volume fluxes. Although elegant from a modelling perspective, the full multi‐compartment Darcy system is computationally expensive to solve. We therefore enhance computational efficiency of this model by reducing the N‐compartment system of Darcy equations to N pressure equations, and N subsequent projection problems to recover the Darcy velocity. The resulting ‘reduced’ Darcy formulation leads to a dramatic reduction in algebraic‐system size and is therefore computationally cheaper to solve than the full multi‐compartment Darcy system. A comparison of the reduced and the full formulation in terms of solution time and memory usage clearly highlights the superior performance of the reduced formulation. Moreover, the implementation of flux and, specifically, impermeable boundary conditions on arbitrarily curved boundaries such as epicardium and endocardium is straightforward in contrast to the full Darcy formulation. Finally, to demonstrate the applicability of our methodology to a personalized model and its solvability in clinically relevant time frames, we simulate perfusion in a subject‐specific model of the left ventricle. Copyright © 2012 John Wiley & Sons, Ltd.
Cell‐Free Metabolic Engineering: Production of Chemicals by Minimized Reaction Cascades
Authors: Guterl Jan‐Karl , Garbe Daniel , Carsten Jörg , Steffler Fabian , Sommer Bettina , Reiße Steven , Philipp Anja , Haack Martina , Rühmann Broder , Koltermann Andre , Kettling Ulrich , Brück Thomas , Sieber Volker
Published: October 2012

The limited supply of fossil resources demands the development of renewable alternatives to petroleum‐based products. Here, biobased higher alcohols such as isobutanol are versatile platform molecules for the synthesis of chemical commodities and fuels. Currently, their fermentation‐based production is limited by the low tolerance of microbial production systems to the end products and also by the low substrate flux into cell metabolism. We developed an innovative cell‐free approach, utilizing an artificial minimized glycolytic reaction cascade that only requires one single coenzyme. Using this toolbox the cell‐free production of ethanol and isobutanol from glucose was achieved. We also confirmed that these streamlined cascades functioned under conditions at which microbial production would have ceased. Our system can be extended to an array of industrially‐relevant molecules. Application of solvent‐tolerant biocatalysts potentially allows for high product yields, which significantly simplifies downstream product recovery.
Changes in Surface Chemistry of Carbon Materials upon Electrochemical Measurements and their Effects on Capacitance in Acidic and Neutral Electrolytes
Authors: Hulicova‐Jurcakova Denisa , Fiset Erika , Lu Gao Qing Max , Bandosz Teresa J.
Published: October 2012

Four porous carbon samples with very similar porosities but visible differences in their surface chemistry are investigated as supercapacitor electrodes in 1 M H2SO4 and 3 M NaCl. The key objective is to monitor the changes to the oxygen‐ and nitrogen‐containing functionalities in oxygen‐ and nitrogen+oxygen‐rich carbons upon a three‐electrode test and the effect of these changes on the energy storage capacity in a real two‐electrode supercapacitor setup. The carbon samples are thoroughly characterized by nitrogen sorption measurements, Raman spectroscopy, potentiometric titrations, elemental analysis, and synchrotron XPS. The findings presented in this work imply that the pretreatment of the oxygen‐ and nitrogen+oxygen‐rich carbons under the conditions of the three‐electrode test in an acidic electrolyte are beneficial to the overall energy storage capacity as the pores become more accessible to the electrolyte ions and the contribution of pseudocapacitive oxygen‐containing groups increases in the oxygen‐rich carbons, whereas favorable changes to the electronic structure take place in the nitrogen+oxygen‐rich carbons. Thus, the total capacitance increases as a result of the improved double‐layer capacitance as well as pseudocapacitance. Greater capacitance after the three‐electrode test is also measured in a neutral electrolyte for both sets of samples, which is a result of improved double‐layer capacitance upon the removal of some oxygen‐containing functional groups that leads to better accessibility of the pores.
Batchwise and Continuous Nanofiltration of POSS‐Tagged Grubbs–Hoveyda‐Type Olefin Metathesis Catalysts
Authors: Kajetanowicz Anna , Czaban Justyna , Krishnan G. Rajesh , Malińska Maura , Woźniak Krzysztof , Siddique Humera , Peeva Ludmila G. , Livingston Andrew G. , Grela Karol
Published: October 2012

New molecular‐weight‐enlarged metathesis catalysts, which bear polyhedral oligomeric silsesquioxane (POSS) tags, were synthesized and characterized. The catalysts can be recovered from the reaction mixture by using nanofiltration techniques and can be reused. It was found that the membranes Starmem 228 and PuraMem 280 successfully separate the catalyst from the post‐reaction mixtures to below 3 ppm. The application of these POSS‐tagged catalysts in a continuous metathesis reaction was also investigated.
Quantitative assessment of cell viability based on flow cytometry and microscopy
Authors: Kummrow A. , Frankowski M. , Bock N. , Werner C. , Dziekan T. , Neukammer J.
Published: October 2012

We compare flow cytometric and microscopic determination of cell viability by fluorescence labeling using calcein acetoxy‐methyl‐ester and ethidium homodimer‐1 as live and dead stain, respectively. Peripheral blood monocytes served as model system and were accumulated applying density gradients. Subsequently, monocytes were further enriched by magnetic‐activated or fluorescence‐activated cell sorting (MACS, FACS) targeting the antigen CD14. Identical samples were used for flow cytometric and microscopic analysis to allow direct comparison of both analysis methods. More than 1,000 cells were measured for each sample to minimize the measurement uncertainty caused by counting statistics. We observed good agreement of flow cytometric and microscopic viability measurements. On average, the difference in viability measured by flow cytometry and microscopy amounted to (2.7 ± 1.4)% for live staining and (1.7 ± 1.2)% for dead staining. These deviations were similar to the uncertainty of measurement for cell viability, thus demonstrating that both methods delivered equal results. Besides monocytes, comparison of flow cytometric and microscopy viability for MACS enriched CD34‐positive cells also showed consistent results. © 2012 International Society for Advancement of Cytometry
A flow cytometric method for viability assessment of Staphylococcus aureus and Burkholderia cepacia in mixed culture
Authors: Rüger Marc , Bensch Gerald , Tüngler Ralf , Reichl Udo
Published: October 2012

Mixed bacterial communities are commonly encountered in microbial infections of humans. Knowledge on the composition of species and viability of each species in these communities allows for a detailed description of the complexity of interspecies dynamics and contributes to the assessment of the severity of infections. Several assays exist for quantification of specific species in mixed communities, including analysis of quantitative terminal restriction fragment length polymorphisms. While this method allows for species‐specific cell enumeration, it cannot provide viability data. In this study, flow cytometry was applied to assess the viability of Staphylococcus aureus and Burkholderia cepacia in mixed culture by membrane integrity analysis using SYBR® Green I and propidium iodide staining. Both bacteria are relevant to pulmonary infections of cystic fibrosis patients. Fluorescence staining was optimized separately for each species in pure culture due to differences between species in cell wall structure and metabolic capabilities. To determine viability of species in mixed culture, a protocol was established as a compromise between optimum conditions determined before for pure cultures. This protocol allowed the detection of viable and dead cells of both species, exhibiting an intact and a permeabilized membrane, respectively. To discriminate between S. aureus and B. cepacia, the protocol was combined with Gram‐specific fluorescent staining using wheat germ agglutinin. The established three‐color staining method was successfully tested for viability determination of S. aureus and B. cepacia in mixed culture cultivations. In addition, growth of both species was monitored by quantitative terminal restriction fragment length polymorphisms. The obtained data revealed alterations in viability during cultivations for different growth phases and suggest interspecies effects in mixed culture. Overall, this method allows for rapid simultaneous Gram‐differentiation and viability assessment of bacterial mixed cultures and is therefore suitable for the analysis of dynamics of mixed communities of medical, environmental, and biotechnological relevance. © 2012 International Society for Advancement of Cytometry
Short computational Diffie–Hellman‐based proxy signature scheme in the standard model
Authors: Zhang Jianhong , Yu Yong
Published: October 2012

Proxy signature is an important delegation technique. It allows that the original signer delegates his or her signing capability to a proxy signer that can generate valid signatures on behalf of the original signer. Until now, most of proxy signature schemes only were proven secure in the random oracle model. And the length of a proxy signature is usually a sum of the lengths of two signatures in most of the proxy signature schemes. Therefore, the factors make the proxy signature unsuitable for many applications with the constrained space or bandwidth. In this paper, we propose a novel short proxy signature scheme in the standard model. And the scheme is probably secure in the standard model. Compared with all existing proxy signature schemes without random oracles, the scheme achieves the following advantages: stronger security, shorter system parameters, shorter signature length and higher efficiency. To the best of our knowledge, this is the first shortest proxy signature scheme in the standard model, whose length is only 320 b for practical 80‐bit security level and the same as that of Digital Signature Algorithm. Copyright © 2012 John Wiley & Sons, Ltd.
Advances in Computational Medicinal Chemistry: Matched Molecular Pair Analysis
Authors: Wassermann Anne Mai , Dimova Dilyana , Iyer Preeti , Bajorath Jürgen
Published: October 2012

Preclinical Research

Herein we discuss the concept of matched molecular pairs (MMPs) and relevant medicinal chemistry applications. In recent years, this concept has become popular in medicinal chemistry as it provides a formal and general basis to establish structural relationships between compounds, identify chemical changes that transform structurally related compounds into each other, and facilitate a large‐scale analysis of structure–activity relationships. Algorithms have been developed for the systematic computational identification of qualifying pairs in large compound databases. In addition to a number of other areas such as graphical analysis and visualization of structure–activity relationships, systematic MMP analysis has significantly advanced the field of computational medicinal chemistry, providing a basis for many practical applications. Characteristic features of this concept include that it eliminates subjective criteria from structural comparisons, alleviates the need to employ predefined molecular hierarchies in studying structural relationships, and elucidates distinguishing structural features between active compounds in a highly intuitive manner. Hence, the results of computational MMP analysis are readily accessible to medicinal chemists, which makes this type of analysis highly attractive for a variety of applications.
Vaccinology Is Turning into an Omics‐Based Science
Authors: Prachi Prachi , Biagini Massimiliano , Bagnoli Fabio
Published: October 2012

Preclinical Research

Vaccines developed by conventional approaches have significantly reduced global morbidity and mortality associated with infectious diseases. However, efficacious medications are still lacking for several pathogens. With the advent of genomics, vaccine discovery has dramatically changed leading to the establishment of reverse vaccinology, which can predict vaccine candidates prior to experimental testing. Today, antigen selection can be performed through a multifold approach, based on the reverse vaccinology principles, but with the inclusion of information from multiple omics such as proteomics, transcriptomics, immunomics, and structural biology. Once vaccine candidates have been selected, systems biology can be used to interpret host responses to vaccines in clinical trials and identify correlates of protection. We believe that omics‐based vaccine discovery approaches have the potential to develop efficacious vaccines against diseases lacking known protective mechanisms and for which conventional vaccinology failed.
Mass spectrometric analysis of EPO IEF‐PAGE interfering substances in nitrile examination gloves
Authors: Reichel Christian
Published: October 2012

Direct detection of doping with recombinant erythropoietins (rhEPO) is accomplished by isoelectric focusing (IEF) or sodium dodecylsulfate (SDS) polyacrylamide gel electrophoresis (PAGE). In a recent publication, Lasne et al. (Electrophoresis 2011, 32, 1444) showed that improper use of nitrile examination gloves during sample collection, sample preparation, and IEF‐PAGE may lead to distorted or absent EPO IEF‐profiles. In order to clarify which substances are responsible for this observation, a mass spectrometric study on water extractable compounds found in nitrile gloves was performed. Several substance classes were shown to be present, among them polyethylene glycols (PEG), anionic and nonionic surfactants, as well as alcohol ethoxylates and plasticizers. It could be demonstrated that alkylbenzenesulfonates, the main category of detectable anionic detergents, and among them sodium dodecylbenzenesulfonate (SDBS) and its homologs, are the prime reason for the interference of nitrile gloves with EPO IEF‐PAGE. Copyright © 2012 John Wiley & Sons, Ltd.
Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus)
Authors: Elizabeth Alter S. , Rosenbaum Howard C. , Postma Lianne D. , Whitridge Peter , Gaines Cork , Weber Diana , Egan Mary G. , Lindsay Melissa , Amato George , Dueck Larry , Brownell Robert L. , Heide‐Jørgensen Mads‐Peter , Laidre Kristin L. , Caccone Gisella , Hancock Brittany L.
Published: October 2012

Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range‐wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay‐Davis Strait, Hudson Bay‐Foxe Basin, Bering‐Beaufort‐Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.
Synthesis of the BCD‐Ring Substructure of Granaticin A
Authors: Bachmann Janina , Mang Christian , Haustedt Lars Ole , Harms Klaus , Koert Ulrich
Published: October 2012

The BCD‐ring substructure of granaticin A was synthesised following a new approach for the construction of the naphthoquinone moiety. The 2‐oxabicyclo[2.2.2]oct‐5‐ene substructure was accessible stereoselectively using a Sharpless asymmetric dihydroxylation and a diastereoselective ketone reduction in combination with Yoshii's route. The naphthoquinone B‐ring was prepared by addition of an aryllithium intermediate to an anhydride followed by a Friedel–Crafts cyclisation mediated by AlCl3 and Mg(OTf)2. The success of the Friedel–Crafts cyclisation relied on the conversion of the ketone‐carboxylic acid into a lactone acetal.
Proteomic analysis and brain‐specific systems biology in a rodent model of penetrating ballistic‐like brain injury
Authors: Boutté Angela M. , Yao Changping , Kobeissy Firas , May Lu Xi‐Chun , Zhang Zhiqun , Wang Kevin K. , Schmid Kara , Tortella Frank C. , Dave Jitendra R.
Published: October 2012

Proteomics and systems biology have significantly contributed to biomarker discovery in the field of brain injury. This study utilized 2D‐DIGE‐PMF‐MS as a preliminary screen to detect biomarkers in a rat model of penetrating ballistic‐like brain injury (PBBI). Brain‐specific systems biology analysis of brain tissue identified 386 proteins having a fold change of more than 2, of which 321 proteins were increased and 65 were decreased 24 h after PBBI compared to sham controls. The majority of upregulated proteins were cytoskeletal (10.5%), nucleic acid binding (9.3%), or kinases (8.9%). Most proteins were involved in protein metabolism (22.7%), signal transduction (20.4%), and development (9.6%). Pathway analysis indicated that these proteins were involved in neurite outgrowth and cell differentiation. Semiquantitative Western blotting of 6, 24, 48, and 72 h after PBBI indicated ubiquitin carboxyl‐terminal hydrolase isozyme L1 (a proposed traumatic brain injury biomarker in human clinical trials), tyrosine hydroxylase, and syntaxin‐6 were found to be consistently elevated in brain tissue and cerebral spinal fluid after PBBI compared to sham controls. Combining proteomics and brain‐specific systems biology can define underlying mechanisms of traumatic brain injury and provide valuable information in biomarker discovery that, in turn, may lead to novel therapeutic targets.
Recent progress in analytical capillary isotachophoresis
Authors: Malá Zdena , Gebauer Petr , Boček Petr
Published: October 2012

This review brings a survey of the literature on analytical isotachophoresis (ITP) from the years 2010–2012. It confirms the fact that ITP alone is not used for analyses frequently but that its online combinations with other methods are of paramount importance. This review shows that the inherent features of the technique and first of all its concentrating ability are still unique for reaching high sensitivity and efficient sample cleanup in analytical applications. The part devoted to theory is mostly represented by computer simulations and confirms the power and significance of this approach. The section oriented at instrumentation and techniques shows the advantages of ITP in column combinations and microchip techniques. The chapter reviewing the applications is categorized according to the techniques applied, viz., column switching, on line ITP‐CZE and on‐chip analyses. The final part of the review is devoted to the nearly omnipresent electrophoresis principle of transient isotachophoresis, and to the advantages that it may offer for detection and sampling. In all parts, the significance of the operational conditions is also considered and where possible, the electrolyte system is explicitly presented.
Recent advances in preparation and application of hybrid organic‐silica monolithic capillary columns
Authors: Ou Junjie , Lin Hui , Zhang Zhenbin , Huang Guang , Dong Jing , Zou Hanfa
Published: October 2012

Hybrid organic‐silica monolithic columns, regarded as a second generation of silica‐based monoliths, have received much interest due to their unique properties over the pure silica‐based monoliths. This review mainly focuses on development in the fields of preparation of hybrid monolithic columns in a capillary and their application for CEC and capillary liquid chromatography separation, as well as for sample pretreatment of solid‐phase microextraction and immobilized enzyme reactor since July 2010. The preparation approaches are comprehensively summarized with three routes: (i) general sol–gel process using trialkoxysilanes and tetraalkoxysilanes as coprecursors; (ii) “one‐pot” process of alkoxysilanes and organic monomers concomitantly proceeding sol–gel chemistry and free radical polymerization; and (iii) other polymerization approaches of organic monomers containing silanes. The modification of hybrid monoliths containing reactive groups to acquire the desired surface functionality is also described.
Micellar electrokinetic chromatography: A review of methodological and instrumental innovations focusing on practical aspects
Authors: Silva Manuel
Published: October 2012

This review article addresses recent methodological and instrumental innovations in MEKC with emphasis on practical aspects. Like its predecessors, this review is intended to provide an updated overview covering work on the most salient methodological contributions to enhancing sensitivity and resolution in MEKC‐based determinations published over the past two years. The most widespread approaches to enhancing sensitivity, which include improving “classical” online sample concentration techniques, combinations of on‐ and off‐line sample concentration protocols and recent developments are discussed, and so are modifications of existing MEKC systems with various micellar phases, the use of BGE additives (organic modifiers, chiral selectors, gold nanoparticles) and coated capillaries, and the implementation of 2D separations and chemometric methods to enhance resolution. Instrumental approaches such as MS and LIF are also discussed, and proposals for overcoming the problems typically encountered in directly coupling MEKC with MS, and the recent inception of quantum dots with a great potential for LIF detection in MEKC, are also dealt with. Finally, foreseeable developments on potential future directions are also expressed.
Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2010–2012)
Authors: Breadmore Michael C. , Shallan Aliaa I. , Rabanes Heide R. , Gstoettenmayr Daniel , Abdul Keyon Aemi S. , Gaspar Andras , Dawod Mohamed , Quirino Joselito P.
Published: October 2012

CE has been alive for over two decades now, yet its sensitivity is still regarded as being inferior to that of more traditional methods of separation such as HPLC. As such, it is unsurprising that overcoming this issue still generates much scientific interest. This review continues to update this series of reviews, first published in Electrophoresis in 2007, with updates published in 2009 and 2011 and covers material published through to June 2012. It includes developments in the field of stacking, covering all methods from field amplified sample stacking and large volume sample stacking, through to isotachophoresis, dynamic pH junction and sweeping. Attention is also given to online or inline extraction methods that have been used for electrophoresis.
Measuring bluff erosion part 1: terrestrial laser scanning methods for change detection
Authors: Day Stephanie S. , Gran Karen B. , Belmont Patrick , Wawrzyniec Tim
Published: October 2012

Human activities influence watershed sediment dynamics in profound ways, often resulting in excessive loading of suspended sediment to rivers. One of the primary factors limiting our ability to effectively manage sediment at the watershed scale has been our inability to adequately measure relatively small erosion rates (on the order of millimeters to centimeters per year) over annual and sub‐annual time scales on spatially‐extensive landforms, such as river banks and bluffs. Terrestrial laser scanning (TLS) can be employed to address this need. TLS collects high‐resolution data allowing for more accurate monitoring of erosion rates and processes, and provides a new opportunity to make precise measurements of geomorphic change on vertical landforms like banks and bluffs, but challenges remain. This research highlights challenges and limitations of using TLS for change detection on river banks and bluffs including the presence of vegetation, natural surface crenulations, and difficulties with creating benchmarks, and provides solutions developed to overcome these limitations. Results indicate that data processing algorithms for change detection can have a significant impact on the calculated erosion rates, with different methods producing results that can vary by over 100%. The most accurate change detection technique compares a point cloud to a triangulated irregular network (TIN) along a set of vectors that accommodate bluff curvature. This paper outlines a variety of methods used to measure bluff change via TLS and explains the accompanying error analysis that supports these methods. Copyright © 2012 John Wiley & Sons, Ltd.
Numerical prediction of turbulent flows using Reynolds‐averaged Navier–Stokes and large‐eddy simulation with uncertain inflow conditions
Authors: Congedo Pietro Marco , Duprat Cedric , Balarac Guillaume , Corre Christophe
Published: October 2012

Numerous comparisons between Reynolds‐averaged Navier–Stokes (RANS) and large‐eddy simulation (LES) modeling have already been performed for a large variety of turbulent flows in the context of fully deterministic flows, that is, with fixed flow and model parameters. More recently, RANS and LES have been separately assessed in conjunction with stochastic flow and/or model parameters. The present paper performs a comparison of the RANS k − ε model and the LES dynamic Smagorinsky model for turbulent flow in a pipe geometry subject to uncertain inflow conditions. The influence of the experimental uncertainties on the computed flow is analyzed using a non‐intrusive polynomial chaos approach for two flow configurations (with or without swirl). Measured quantities including an estimation of the measurement error are then compared with the statistical representation (mean value and variance) of their RANS and LES numerical approximations in order to check whether experiment/simulation discrepancies can be explained within the uncertainty inherent to the studied configuration. The statistics of the RANS prediction are found in poor agreement with experimental results when the flow is characterized by a strong swirl, whereas the computationally more expensive LES prediction remains statistically well inside the measurement intervals for the key flow quantities.Copyright © 2012 John Wiley & Sons, Ltd.
Performance of a three‐dimensional unstructured mesh compressible flow solver on NVIDIA Fermi‐class graphics processing unit hardware
Authors: Waltz Jacob
Published: October 2012

We describe the performance of Chicoma, a 3D unstructured mesh compressible flow solver, on graphics processing unit (GPU) hardware. The approach used to deploy the solver on GPU architectures derives from the threaded multicore execution model used in Chicoma, and attempts to improve memory performance via the application of graph theory techniques. The result is a scheme that can be deployed on the GPU with high‐level programming constructs, for example, compiler directives, rather than low‐level programming extensions. With an NVIDIA Fermi‐class GPU (NVIDIA Corp., Sta. Clara, CA, USA) and double precision floating point arithmetic, we observe performance gains of 4–5 × on problem sizes of 106– 107 tetrahedra. We also compare GPU performance to threaded multicore performance with OpenMP and demonstrate hybrid multicore‐GPU calculations with adaptive mesh refinement. Published 2012. This article is a US Government work and is in the public domain in the USA.
Regulatory economics: Saved by the carbon tax?
Authors: Barclay Richard A.
Published: October 2012

This year's national election winners will be on the edge of a “fiscal cliff.”1
New Supramolecular Triorganotin(IV) Dithiocarboxylates as Potential Antibacterial Agents
Authors: Zia‐ur‐Rehman  , Muhammad Niaz , Shah Afzal , Ali Saqib , Khan Ezzat
Published: October 2012

Four triorganotin derivatives of general formula C10H10NS2SnR3,, where R = CH3 (1), C4H9 (2), C6H11 (3), and C6H5 (4), have been synthesized by the metathesis reaction of 1,2,3,4‐tetrahydroisoquinolnium salt of ligand with triorganotin(IV) chloride in the 1:1 ratio. These complexes were characterized by elemental analysis, Raman, IR, multinuclear NMR (1H, 13C, and 119Sn), and mass spectrometry. The crystal structure confirmed a supramolecular zig‐zag chain structure mediated by S–H (2.968 Å) for complex 4 with the central Sn atom exists in a distorted trigonal bipyramidal geometry. A subsequent antibacterial study indicates that the compounds are biologically active.
C–N Coupling of 1,2‐Dihydro‐2,2,4‐trimethylquinoline Derivatives via a Silver(I)‐Catalyzed Direct Functionalization of a C–H Bond
Authors: Fotie Jean , Rhodus Jessica L. , Taha Hashem A. , Reid Carolyn S.
Published: October 2012

Two C,N‐linked dimeric 1,2‐dihydro‐2,2,4‐trimethylquinolines, namely 6‐chloro‐1‐(6‐chloro‐1,2‐dihydro‐2,2,4‐trimethylquinolin‐8‐yl)‐1,2‐dihydro‐2,2,4‐trimethylquinoline (3a) and 6‐ethoxy‐1‐(6‐ethoxy‐1,2‐dihydro‐2,2,4‐trimethylquinolin‐8‐yl)‐1,2‐dihydro‐2,2,4‐trimethylquinoline (3b), have been prepared through a silver‐catalyzed dimerization of their corresponding monomers. The effect of different silver salts on the reaction was also investigated, and the obtained results suggest that silver ions effectively catalyzed the formation of a C–N bond under these mild conditions. This represents one of the rare reports on the silver‐catalyzed C–N bond formation through a coupling of a secondary amine and an activated aromatic system, via a direct C–H functionalization. Theoretical studies showed that these dimeric structures favor a conformation in which their monomer units are oriented approximately perpendicular to each other, with an intramolecular hydrogen bond (N–H distance of 2.33 Å) forming between the hydrogen atom of the amine in one of the monomeric units and the tertiary nitrogen atom of the other one.
Applying the Balanced Scorecard approach in teaching hospitals: a literature review and conceptual framework
Authors: Trotta Annarita , Cardamone Emma , Cavallaro Giusy , Mauro Marianna
Published: October 2012

Teaching hospitals (THs) simultaneously serve three different roles: offering medical treatment, teaching future doctors and promoting research. The international literature recognises such organisations as ‘peaks of excellence’ and highlights their economic function in the health system. In addition, the literature describes the urgent need to manage the complex dynamics and inefficiency issues that threaten the survival of teaching hospitals worldwide. In this context, traditional performance measurement systems that focus only on accounting and financial measures appear to be inadequate. Given that THs are highly specific and complex, a multidimensional system of performance measurement, such as the Balanced Scorecard (BSC), may be more appropriate because of the multitude of stakeholders, each of whom seek a specific type of accountability. The aim of the paper was twofold: (i) to review the literature on the BSC and its applications in teaching hospitals and (ii) to propose a scorecard framework that is suitable for assessing the performance of THs and serving as a guide for scholars and practitioners. In addition, this research will contribute to the ongoing debate on performance evaluation systems by suggesting a revised BSC framework and proposing specific performance indicators for THs. Copyright © 2012 John Wiley & Sons, Ltd.
Use of the ecosystem services concept in ecological risk assessment of chemicals
Authors: Forbes Valery E , Calow Peter
Published: October 2012

The reason for expressing ecological protection goals in terms of ecosystem services is to make a connection between ecosystems and what people get out of them in terms of marketed goods and nonmarketed welfare. Here our focus will be on how the ecosystem services framework is and can be applied to the ecological risk assessment (ERA) of chemicals. We provide 2 contrasting examples of how the ecosystem services framework is currently being applied in regulatory risk assessment, and we discuss the challenges and knowledge gaps that need to be addressed if such a framework is to substantially improve ERAs and their ability to inform management decisions. We make the point that formulating protection goals in terms of ecosystem services only makes sense if they can be used in managing environmental impacts and if they are useful in informing the risk assessments behind these. Ecosystem services can make a contribution to management by connecting ecosystem structure and process to what is valued, and analyzing risk in this context is a way of making risk assessment more policy- and value-relevant. Using an ecosystem services framework to its fullest potential to support ERA will require the successful development of a suite of coupled Valuation Methods, Ecological Production Functions, and Mechanistic Effect Models that will require the establishment of strong multidisciplinary collaborations among ecologists, computer scientists, social scientists, and possibly others. In addition, buy-in from environmental decision makers and other stakeholders will be crucial. Some progress is being made on the research front, and the implementation of new legislation is providing incentives for developing risk assessment outputs that are much more directly related to environmental protection goals than those used currently. Integr Environ Assess Manag 2013; 9: 269–275. © 2012 SETAC
From home range dynamics to population cycles: Validation and realism of a common vole population model for pesticide risk assessment
Authors: Wang Magnus
Published: October 2012

Despite various attempts to establish population models as standard tools in pesticide risk assessment, population models still receive limited acceptance by risk assessors and authorities in Europe. A main criticism of risk assessors is that population models are often not, or not sufficiently, validated. Hence the realism of population-level risk assessments conducted with such models remains uncertain. We therefore developed an individual-based population model for the common vole, Microtus arvalis, and demonstrate how population models can be validated in great detail based on published data. The model is developed for application in pesticide risk assessment, therefore, the validation covers all areas of the biology of the common vole that are relevant for the analysis of potential effects and recovery after application of pesticides. Our results indicate that reproduction, survival, age structure, spatial behavior, and population dynamics reproduced from the model are comparable to field observations. Also interannual population cycles, which are frequently observed in field studies of small mammals, emerge from the population model. These cycles were shown to be caused by the home range behavior and dispersal. As observed previously in the field, population cycles in the model were also stronger for longer breeding season length. Our results show how validation can help to evaluate the realism of population models, and we discuss the importance of taking field methodology and resulting bias into account. Our results also demonstrate how population models can help to test or understand biological mechanisms in population ecology. Integr Environ Assess Manag 2013; 9: 294–307. © 2012 SETAC
Differential promoter activities of functional haplotypes in the 5′‐flanking region of human Sulfotransferase 1A1
Authors: Lin Zhong‐Ning , Lin Yu‐Chun , Zhang Xuemei , Kadlubar Susan , Tuo Jingsheng , Green Bridgett , Deng Helen , Ning Baitang
Published: October 2012

Previously, we reported five common single nucleotide polymorphisms (SNPs), −624G>C, −396G>A, −358A>C, −341C>G, and −294T>C, and six common haplotypes (CGACT, GAACT, GGAGC, GGACC, CAACT, and GAACC) in the 5′‐flanking region of the SULT1A1 gene that were associated with altered enzymatic activity. In the present study, we performed in vitro assays to determine the functional impact of these genetic variations on the promoter activity. Dual luciferase reporter assays revealed that these SNPs are located in a negative regulatory fragment of the SULT1A1 gene. Further experiments demonstrated that these SNPs and haplotypes affected promoter activities of SULT1A1. Electrophoretic mobility shift assays showed distinctive binding patterns for the SNPs ‐396G>A and ‐294T>C, due to differential binding affinities of the G/A alleles and the T/C alleles to nuclear proteins extracted from the liver carcinoma cell lines, HepG2 and Huh7. © 2012 Wiley Periodicals, Inc. J Biochem Mol Toxicol 26:422–428, 2012; View this article online at wileyonlinelibrary.com. DOI 10:1002/jbt.21437