bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing endotoxin issues in bioengineered heparin
Authors: Suwan Jiraporn , Torelli Amanda , Onishi Akihiro , Dordick Jonathan S. , Linhardt Robert J. 
Published: October 2012

AbstractHeparin 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.
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

AbstractThe 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

AbstractWith 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

SUMMARYWe 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

AbstractThe 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

AbstractFour 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

AbstractNew 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

AbstractWe 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

AbstractMixed 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

SUMMARYProxy 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

Abstract

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

Abstract

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.
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

AbstractSea 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

AbstractThe 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.
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

ABSTRACTHuman 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.