bluuebunny/crossref_metadata_2025 huggingface dataset:
Water mass analysis of the Coral Sea through an Optimum Multiparameter method
Authors: Gasparin Florent , Maes Christophe , Sudre Joel , Garcon Veronique , Ganachaud Alexandre
Published: August 2014

A water mass analysis of the Coral Sea thermocline waters provides a description of their distribution, pathways and mixture based on recent oceanographic cruises in this region of strong western boundary currents. The Optimum Multiparameter method is used to determine the relative contribution of core water masses based on their measured temperature, salinity and dissolved oxygen. The thermocline waters, carried by the broad South Equatorial Current (SEC), are essentially composed of four core water masses of different origins. Coming from the south, the South Pacific Tropical Water South (SPTWS, σ = 25.3 kg m−3) and the Western South Pacific Central Water (WSPCW, σ = 26.3 kg m−3) enter the Coral Sea by the channel between the island of New Caledonia and the Vanuatu archipelago. Coming from the north, the South Pacific Tropical Water North (SPTWN, σ = 24.5 kg m−3) and the Pacific Equatorial Water (PEW, σ = 26.3 kg m−3) flow north of Vanuatu. The upper thermocline water that exits the Coral Sea equatorward, is mainly composed of SPTWN carried by the New Guinea Coastal Undercurrent. In contrast, upper thermocline waters exiting the Coral Sea poleward, in the East Australian Current, is dominated by SPTWS. The relative contributions are different in the lower thermocline where WSPCW dominates both western boundary currents. This refined description is consistent with the dynamics of the main currents, with a very strong depth dependence in the partitioning of incoming SEC waters.
Estimating ice particle scattering properties using a modified Rayleigh‐Gans approximation
Authors: Lu Yinghui , Clothiaux Eugene E. , Aydin Kültegin , Verlinde Johannes
Published: August 2014

A modification to the Rayleigh‐Gans approximation is made that includes self‐interactions between different parts of an ice crystal, which both improves the accuracy of the Rayleigh‐Gans approximation and extends its applicability to polarization‐dependent parameters. This modified Rayleigh‐Gans approximation is both efficient and reasonably accurate for particles with at least one dimension much smaller than the wavelength (e.g., dendrites at millimeter or longer wavelengths) or particles with sparse structures (e.g., low‐density aggregates). Relative to the Generalized Multiparticle Mie method, backscattering reflectivities at horizontal transmit and receive polarization (HH) (ZHH) computed with this modified Rayleigh‐Gans approach are about 3 dB more accurate than with the traditional Rayleigh‐Gans approximation. For realistic particle size distributions and pristine ice crystals the modified Rayleigh‐Gans approach agrees with the Generalized Multiparticle Mie method to within 0.5 dB for ZHH whereas for the polarimetric radar observables differential reflectivity (ZDR) and specific differential phase (KDP) agreement is generally within 0.7 dB and 13%, respectively. Compared to the A‐DDA code, the modified Rayleigh‐Gans approximation is several to tens of times faster if scattering properties for different incident angles and particle orientations are calculated. These accuracies and computational efficiencies are sufficient to make this modified Rayleigh‐Gans approach a viable alternative to the Rayleigh‐Gans approximation in some applications such as millimeter to centimeter wavelength radars and to other methods that assume simpler, less accurate shapes for ice crystals. This method should not be used on materials with dielectric properties much different from ice and on compact particles much larger than the wavelength.
Rapid photochemical equilibration of isotope bond ordering in O2
Authors: Yeung Laurence Y. , Ash Jeanine L. , Young Edward D.
Published: August 2014

The abundances of 18O18O and 17O18O in the atmosphere were recently found to be enriched relative to the stochastic distribution of isotopes in O2. The enrichment is believed to arise from O(3P) + O2 isotope exchange reactions, which reorder the isotopes in O2 to a distribution that favors bonds between heavy isotopes. Theoretical predictions and laboratory experiments suggest that the reordered distribution of isotopes should reflect internal isotopic equilibrium, but a laboratory test of this hypothesis for the complete O2 isotopologue system has not yet been realized. Here we use a simple photochemical experiment that reorders the isotopes in O2 at temperatures between 200 K and 350 K. Using simultaneous measurements of five O2 isotopologues, we show that O(3P) + O2 reorders the isotopes in O2 to isotopic equilibrium. Furthermore, we use this scheme to calibrate measurements of isotopic ordering in samples of O2, obtaining Δ36 and Δ35 values within ±0.1‰. Measurements of atmospheric O2 sampled at the University of California, Los Angeles, from 2012 to 2014 have mean values of Δ36 = 1.97 ± 0.07‰ and Δ35 = 1.0 ± 0.1‰ (2 SE; n = 23), with no detectable long‐term trend. These measurements are consistent with values for air reported earlier, but with a threefold to fourfold improvement in precision. Together, the experiments and observations support the case that isotopic ordering in tropospheric O2 is altered by O(3P) + O2; however, they also suggest that tropospheric Δ36 and Δ35 values do not reflect complete isotopic equilibration in the troposphere. Isotopic ordering in atmospheric O2 likely reflects the decadal‐scale balance of stratospheric and tropospheric air masses modulated by variations in tropospheric photochemistry and convection.
Mathematical analysis of the Saint‐Venant‐Hirano model for mixed‐sediment morphodynamics
Authors: Stecca G. , Siviglia A. , Blom A.
Published: August 2014

Sediment of different size are transported in rivers under the action of flow. The first and still most popular sediment continuity model able to deal with mixed sediment is the so‐called active layer model proposed by Hirano (1971, 1972). In this paper, we consider the one‐dimensional hydromorphodynamic model given by the Saint‐Venant equations for free‐surface flow coupled with the active layer model. We perform a mathematical analysis of this model, extending the previous analysis by Ribberink (1987), including full unsteadiness and grainsize selectivity of the transported load by explicitly considering multiple sediment fractions. The presence of multiple fractions gives rise to distinct waves traveling in the downstream direction, for which we provide an analytical approximation of propagation velocity under any Froude regime. We finally investigate the role of different waves in advecting morphodynamic changes through the domain. To this aim, we implement an analytical linearized solver to analyze the propagation of small‐amplitude perturbations of the bed elevation and grainsize distribution of the active layer as described by the system of governing equations. We find that initial gradients in the grainsize distribution of the active layer are able to trigger significant bed variations, which propagate in the downstream direction at faster pace than the “bed” wave arising from the unisize‐sediment Saint‐Venant‐Exner model. We also verify that multiple “sorting” waves carry multiple associated bed perturbations, traveling at different speeds.
Regulating Water Adhesion on Superhydrophobic TiO2 Nanotube Arrays
Authors: Hu Ziying , Zhang Xuming , Liu Zhaoyue , Huo Kaifu , Chu Paul K , Zhai Jin , Jiang Lei
Published: August 2014

Bioinspired surfaces with special wettability have attracted a significant attention in recent years because of their potential applications for no loss liquid transfer, anti‐icing, and self‐cleaning. Herein, the realization of two extreme superhydrophobic states on 1H, 1H, 2H, 2H–perfluorooctyltriethoxysilane‐modified TiO2 nanotube arrays (NTAs) is described by changing the structural characteristics of nanotubes while keeping the surface chemical composition constant. The water adhesive force is regulated in a wide range from ≈4.4 to ≈89.6 μN by the nanotubular diameter, length, density, and surface roughness. The cooperation effect between the negative pressures induced by the volume change of sealed air‐pockets and the van der Waals' attraction at solid–liquid interface contributes to the water adhesion. The superhydrophobic TiO2 NTAs with a high adhesive force is used as a “mechanical hand” to transfer water microdroplets without any loss, and the one with extremely low adhesive force is utilized as a self‐cleaning and anti‐icing surface.
Systematic Investigation of Side‐Chain Branching Position Effect on Electron Carrier Mobility in Conjugated Polymers
Authors: Dou Jin‐Hu , Zheng Yu‐Qing , Lei Ting , Zhang Shi‐Ding , Wang Zhi , Zhang Wen‐Bin , Wang Jie‐Yu , Pei Jian
Published: August 2014

Recently, polymer field‐effect transistors have gone through rapid development. Nevertheless, charge transport mechanism and structure‐property relationship are less understood. Here we use strong electron‐deficient benzodifurandione‐based poly(p‐phenylene vinylene) (BDPPV) as polymer backbone and develop six BDPPV‐based polymers (BDPPV‐C1 to C6) with various side‐chain branching positions to systematically study the side‐chain effect on device performance. All the polymers exhibited ambient‐stable n‐type transporting behaviors with the highest electron mobility of up to 1.40 cm2 V−1 s−1. The film morphologies and microstructures of all the six polymers were systematically investigated. Our results demonstrate that the interchain π–π stacking distance decreases as moving the branching position away from polymer backbones, and an unprecedentedly close π–π stacking distance down to 3.38 Å is obtained for BDPPV‐C4 to C6. Nonetheless, closer π–π stacking distance does not always correlate with higher electron mobility. Polymer crystallinity, thin film disorder, and polymer packing conformation, which all influenced by side‐chain branching position, are proved to show significant influence on device performance. Our study not only reveals that π–π stacking distance is not the decisive factor on carrier mobility in conjugated polymers but also demonstrates that side‐chain branching position engineering is a powerful strategy to modulate and balance these factors in conjugated polymers.
Brief Communication: Lactase persistence and dairy intake in Mapuche and Mestizo populations from southern Chile
Authors: Fernández Catalina I. , Flores Sergio V.
Published: August 2014

Lactase persistence (LP) occurs at a very low frequency in indigenous populations from Latin America, offering an opportunity to understand the relationship between this genetic trait and patterns of dairy consumption. Here, the frequency of LP is analyzed from Mapuche and ‐an adjacent‐ mestizo population inhabiting the Araucanía region. In addition to genotyping for LP, participants were surveyed in relation to general perception and consumption habits of dairy products. Low LP frequency (10%) and very low dairy intake was found among the Mapuche population as compared with Mestizo populations inhabiting Chile. The survey reported that the main reasons for avoidance of dairy were the gastrointestinal symptoms after dairy intake and cultural dietary habits. The interaction between low LP genotype frequency, low dairy intake, and sociocultural determinants is here discussed in the light of their potential health outcomes. Am J Phys Anthropol 155:482–487, 2014. © 2014 Wiley Periodicals, Inc.
Isotopic studies of the diet of the people of the coast of British Columbia
Authors: Schwarcz Henry P. , Chisholm Brian S. , Burchell Meghan
Published: August 2014

In 1982, Chisholm et al. used δ13C data for human burials from shell midden sites widely distributed on the coast of British Columbia (BC) to show the extreme dependence of these individuals on high trophic level marine consumers, principally salmon and marine mammals. Here, we present previously unpublished analyses of δ15N for some of the same individuals as well as δ13C data for additional individuals. Nitrogen isotope data show that the diet was dominated by high trophic level marine fauna including carnivorous fish and marine mammals. Although most burials were found in shell middens, marine mollusks made up of only a minor component of diet. The data for δ13C demonstrate that terrestrial faunal foods are undetectable in the diet of the majority of individuals, and seldom constitute more than 10% of the dietary protein of individuals living on the coast although terrestrial fauna were widely available as a potential source of protein. This dietary pattern of exclusion of land‐based animals from their diet persisted for almost 6,000 years along a wide expanse of coastline. In contrast, people from the BC interior (100 km or more from the coast) consumed a mixed diet of terrestrial and marine foods including spawning salmon. Am J Phys Anthropol 155:460–468, 2014. © 2014 Wiley Periodicals, Inc.
Bioarcheology has a “health” problem: Conceptualizing “stress” and “health” in bioarcheological research
Authors: Temple Daniel H. , Goodman Alan H.
Published: August 2014

This article provides a critical historical overview of the stress concept in bioarcheological research and critically evaluates the term “health” in reference to skeletal samples. Stress has a considerable history in 20th century physiological research, and the term has reached a critical capacity of meaning. Stress was operationalized around a series of generalized physiological responses that were associated with a deviation from homeostasis. The term was incorporated into anthropological research during the mid‐20th century, and further defined in bioarcheological context around a series of skeletal indicators of physiological disruption and disease. Emphases on stress became a predominate area of research in bioarcheology, and eventually, many studies utilized the terms “health” and “stress” interchangeably as part of a broader, problem‐oriented approach to evaluating prehistoric population dynamics. Use of the term “health” in relation to skeletal samples is associated with the intellectual history of bioarcheological research, specifically influences from cultural ecology and processualist archeology and remains problematic for two reasons. First, health represents a comprehensive state of well‐being that includes physiological status and individual perception, factors that cannot be readily observed in skeletal samples. Second, the categorization of populations into relative levels of health represents a typological approach, however unintentional. This article advocates for the integration of methodological and theoretical advances from human biology and primatology, while simultaneously incorporating the theoretical constructs associated with social epidemiology into bioarcheological research. Such an approach will significantly increase the applicability of bioarcheological findings to anthropological and evolutionary research, and help realize the goal of a truly relevant bioarcheological paradigm. Am J Phys Anthropol 155:186–191, 2014. © 2014 Wiley Periodicals, Inc.
Phosphonated Near‐Infrared Fluorophores for Biomedical Imaging of Bone
Authors: Hyun Hoon , Wada Hideyuki , Bao Kai , Gravier Julien , Yadav Yogesh , Laramie Matt , Henary Maged , Frangioni John V. , Choi Hak Soo
Published: August 2014

The conventional method for creating targeted contrast agents is to conjugate separate targeting and fluorophore domains. A new strategy is based on the incorporation of targeting moieties into the non‐delocalized structure of pentamethine and heptamethine indocyanines. Using the known affinity of phosphonates for bone minerals in a model system, two families of bifunctional molecules that target bone without requiring a traditional bisphosphonate are synthesized. With peak fluorescence emissions at approximately 700 or 800 nm, these molecules can be used for fluorescence‐assisted resection and exploration (FLARE) dual‐channel imaging. Longitudinal FLARE studies in mice demonstrate that phosphonated near‐infrared fluorophores remain stable in bone for over five weeks, and histological analysis confirms their incorporation into the bone matrix. Taken together, a new strategy for creating ultra‐compact, targeted near‐infrared fluorophores for various bioimaging applications is described.
Reconfigurable Swarms of Nematic Colloids Controlled by Photoactivated Surface Patterns
Authors: Hernàndez‐Navarro Sergi , Tierno Pietro , Farrera Joan Anton , Ignés‐Mullol Jordi , Sagués Francesc
Published: August 2014

Different phoretic driving mechanisms have been proposed for the transport of solid or liquid microscopic inclusions in integrated chemical processes. It is now shown that a substrate that was chemically modified with photosensitive self‐assembled monolayers enables the direct control of the assembly and transport of large ensembles of micrometer‐sized particles and drops that were dispersed in a thin layer of anisotropic fluid. This strategy separates particle driving, which was realized by AC electrophoresis, and steering, which was achieved by elastic modulation of the nematic host fluid. Inclusions respond individually or in collective modes following arbitrary reconfigurable paths that were imprinted by irradiation with UV or blue light. Relying solely on generic material properties, the proposed procedure is versatile enough for the development of applications that involve either inanimate or living materials.
Copper‐Mediated C6‐Selective Dehydrogenative Heteroarylation of 2‐Pyridones with 1,3‐Azoles
Authors: Odani Riko , Hirano Koji , Satoh Tetsuya , Miura Masahiro
Published: August 2014

A copper‐mediated C6‐selective dehydrogenative heteroarylation of 2‐pyridones with 1,3‐azoles has been developed. The reaction proceeded smoothly by twofold CH cleavage even in the absence of noble‐metal catalysts. The observed site selectivity was directed by a pyridyl substituent on the nitrogen atom of the pyridone ring. This directing group was readily removed after the coupling event, thus leading to 2‐pyridone derivatives with a free NH group. Moreover, in some cases, catalytic turnover of the Cu salt was also possible with the ideal terminal oxidant: molecular oxygen in air.
Progress towards Bioorthogonal Catalysis with Organometallic Compounds
Authors: Völker Timo , Dempwolff Felix , Graumann Peter L. , Meggers Eric
Published: August 2014

The catalysis of bioorthogonal transformations inside living organisms is a formidable challenge—yet bears great potential for future applications in chemical biology and medicinal chemistry. We herein disclose highly active organometallic ruthenium complexes for bioorthogonal catalysis under biologically relevant conditions and inside living cells. The catalysts uncage allyl carbamate protected amines with unprecedented high turnover numbers of up to 270 cycles in the presence of water, air, and millimolar concentrations of thiols. By live‐cell imaging of HeLa cells and with the aid of a caged fluorescent probe we could reveal a rapid development of intense fluorescence within the cellular cytoplasm and therefore support the proposed bioorthogonality of the catalysts. In addition, to illustrate the manifold applications of bioorthogonal catalysis, we developed a method for catalytic in‐cell activation of a caged anticancer drug, which efficiently induced apoptosis in HeLa cells.
Revealing the Distribution of the Atoms within Individual Bimetallic Catalyst Nanoparticles
Authors: Felfer Peter , Benndorf Paul , Masters Anthony , Maschmeyer Thomas , Cairney Julie M.
Published: August 2014

To be able to correlate the catalytic properties of nanoparticles with their structure, detailed knowledge about their make‐up on the atomic level is required. Herein, we demonstrate how atom‐probe tomography (APT) can be used to quantitatively determine the three‐dimensional distribution of atoms within a Au@Ag nanoparticle with near‐atomic resolution. We reveal that the elements are not evenly distributed across the surface and that this distribution is related to the surface morphology and residues from the particle synthesis.
Double‐Clicking Peptides onto Phosphorothioate Oligonucleotides: Combining Two Proapoptotic Agents in One Molecule
Authors: Abendroth Frank , Seitz Oliver
Published: August 2014

Described here is a method for the conjugation of phosphorothioate oligonucleotides (PSOs) with peptides. PSOs are key to antisense technology. Peptide–PSO conjugates may improve target specificity, tissue distribution, and cellular uptake of PSOs. However, the highly nucleophilic phosphorothioate structure poses a challenge to conjugation chemistry. Herein, we introduce a new method which involves a sequence of oxime ligation and strain‐promoted [2+3] cycloaddition. The usefulness of the method was demonstrated in the synthesis of peptide–PSO conjugates that targeted two suppressors of both the intrinsic and the extrinsic pathway of apoptosis. It is shown that the activity of a PSO sequence targeted against mRNA from c‐Flip can be enhanced by conjugation with a peptide mimetic designed to inhibit the X‐linked inhibitor of apoptosis protein (XIAP).
1‐Acetyl‐3,5‐diaryl‐4,5‐dihydro(1H)pyrazoles: Exhibiting Anticancer Activity through Intracellular ROS Scavenging and the Mitochondria‐Dependent Death Pathway
Authors: Alex Jimi M. , Singh Sandeep , Kumar Raj
Published: August 2014

A series of 17 analogs of 1‐acetyl‐4,5‐dihydro(1H)pyrazoles (JP‐1toJP‐17) bearing two aromatic rings at positions 3 and 5, either of which ought to be heterocyclic, were synthesized and evaluated for their anti‐proliferative potential against breast cancer (MCF‐7 and T‐47D) and lung cancer (H‐460 and A‐549) cell lines for the first time.JP‐1–7, ‐10, ‐11, ‐14, and ‐15were observed to exhibit significant anti‐proliferative activity against MCF‐7 cells. Some notions about structure–activity relationships are reported. The investigated compounds were found to lower the intracellular reactive oxygen species in the H2DCFDA assay and also caused mitochondria‐dependent cell death in the MCF‐7 cell line, indicating a plausible mechanism of their anticancer effect.
Hierarchical Self‐Assembly of Supramolecular Hydrophobic Metallacycles into Ordered Nanostructures
Authors: Zhang Jing , Marega Riccardo , Chen Li‐Jun , Wu Nai‐Wei , Xu Xing‐Dong , Muddiman David C. , Bonifazi Davide , Yang Hai‐Bo
Published: August 2014

We describe herein the hierarchical self‐assembly of discrete supramolecular metallacycles into ordered fibers or spherical particles through multiple noncovalent interactions. A new series of well‐defined metallacycles decorated with long alkyl chains were obtained through metal–ligand interactions, which were capable of aggregating into ordered fibroid or spherical nanostructures on the surface, mostly driven by hydrophobic interactions. In‐depth studies indicated that the morphology diversity was originated from the structural information encoded in the metallacycles, including the number of alkyl chains and their spatial orientation. Interestingly, the morphology of the metallacycle aggregates could be tuned by changing the solvent polarity. These findings are of special significance since they provide a simple yet highly controllable approach to prepare ordered and tunable nanostructures from small building blocks by means of hierarchical self‐assembly.
Time efficient way to calculate oxygen transfer areas and power input in cylindrical disposable shaken bioreactors
Authors: Klöckner Wolf , Lattermann Clemens , Pursche Franz , Büchs Jochen , Werner Sören , Eibl Dieter
Published: August 2014

Disposable orbitally shaken bioreactors are a promising alternative to stirred or wave agitated systems for mammalian and plant cell cultivation, because they provide a homogeneous and well‐defined liquid distribution together with a simple and cost‐efficient design. Cultivation conditions in the surface‐aerated bioreactors are mainly affected by the size of the volumetric oxygen transfer area (a) and the volumetric power input (P∕VL) that both result from the liquid distribution during shaking. Since Computational Fluid Dynamics (CFD)—commonly applied to simulate the liquid distribution in such bioreactors—needs high computing power, this technique is poorly suited to investigate the influence of many different operating conditions in various scales. Thus, the aim of this paper is to introduce a new mathematical model for calculating the values of a and P∕VL for liquids with water‐like viscosities. The model equations were derived from the balance of centrifugal and gravitational forces exerted during shaking. A good agreement was found among calculated values for a and P∕VL, CFD simulation values and empirical results. The newly proposed model enables a time efficient way to calculate the oxygen transfer areas and power input for various shaking frequencies, filling volumes and shaking and reactor diameters. All these parameters can be calculated fast and with little computing power. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1441–1456, 2014
Characterization of an organic solvent‐tolerant thermostable glucoamylase from a halophilic isolate, Halolactibacillus sp. SK71 and its application in raw starch hydrolysis for bioethanol production
Authors: Yu Hui‐Ying , Li Xin
Published: August 2014

A halophilic bacterium Halolactibacillus sp. SK71 producing extracellular glucoamylase was isolated from saline soil of Yuncheng Salt Lake, China. Enzyme production was strongly influenced by the salinity of growth medium with maximum in the presence of 5% NaCl. The glucoamylase was purified to homogeneity with a molecular mass of 78.5 kDa. It showed broad substrate specificity and raw starch hydrolyzing activity. Analysis of hydrolysis products from soluble starch by thin‐layer chromatography revealed that glucose was the sole end‐product, indicating the enzyme was a true glucoamylase. Optimal enzyme activity was found to be at 70°C, pH 8.0, and 7.5% NaCl. In addition, it was highly active and stable over broad ranges of temperature (0–100°C), pH (7.0–12.0), and NaCl concentration (0–20%), showing excellent thermostable, alkali stable, and halotolerant properties. Furthermore, it displayed high stability in the presence of hydrophobic organic solvents. The purified glucoamylase was applied for raw corn starch hydrolysis and subsequent bioethanol production using Saccharomyces cerevisiae. The yield in terms of grams of ethanol produced per gram of sugar consumed was 0.365 g/g, with 71.6% of theoretical yield from raw corn starch. This study demonstrated the feasibility of using enzymes from halophiles for further application in bioenergy production. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1262–1268, 2014
Potential application of aqueous two‐phase systems and three‐phase partitioning for the recovery of superoxide dismutase from a clarified homogenate of Kluyveromyces marxianus
Authors: Simental‐Martínez Jesús , Rito‐Palomares Marco , Benavides Jorge
Published: August 2014

Superoxide dismutase (SOD; EC 1.15.1.1) is an antioxidant enzyme that represents the primary cellular defense against superoxide radicals and has interesting applications in the medical and cosmetic industries. In the present work, the partition behavior of SOD in aqueous two‐phase systems (ATPS) (using a standard solution and a complex extract from Kluyveromyces marxianus as sample) was characterized on different types of ATPS (polymer–polymer, polymer–salt, alcohol–salt, and ionic liquid (IL)–salt). The systems composed of PEG 3350‐potassium phosphate, 45% TLL, 0.5 M NaCl (315 U/mg, 87% recovery, and 15.1‐fold purification) and t‐butanol‐20% ammonium sulfate (205.8 U/mg, 80% recovery and 9.8‐fold purification), coupled with a subsequent 100 kDa ultrafiltration stage, allowed the design of a prototype process for the recovery and partial purification of the product of interest. The findings reported herein demonstrate the potential of PEG‐salt ATPS for the potential recovery of SOD. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1326–1334, 2014
In silico model‐based inference: A contemporary approach for hypothesis testing in network biology
Authors: Klinke David J.
Published: August 2014

Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model‐based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model‐based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1247–1261, 2014
Development and scale‐up of a commercial fed batch refolding process for an anti‐CD22 two chain immunotoxin
Authors: Linke Thomas , Aspelund Matthew T. , Thompson Christopher , Xi Guoling , Fulton Andrew , Wendeler Michaela , Pabst Timothy M. , Wang Xiangyang , Wang William K. , Ram Kripa , Hunter Alan K.
Published: August 2014

We describe the development and scale‐up of a novel two chain immunotoxin refolding process. This work provides a case study comparing a clinical manufacturing process and the commercial process developed to replace it. While the clinical process produced high quality material, it suffered from low yield and high yield variability. A systematic approach to process development and understanding led to a number of improvements that were implemented in the commercial process. These include a shorter inclusion body recovery process, limiting the formation of an undesired deamidated species and the implementation of fed batch dilution refolding for increased refold titers. The use of a combination of urea, arginine and DTT for capture column cleaning restored the binding capacity of the capture step column and resulted in consistent capture step yields compared to the clinical process. Scalability is shown with data from 250 L and 950 L scale refolding processes. Compared to the clinical process it replaces, the commercial process demonstrated a greater than fivefold improvement in volumetric productivity at the 950 L refolding scale. © 2014 American Institute of Chemical EngineersBiotechnol. Prog., 30:1380–1389, 2014
Chemoenzymatic Synthesis of Trehalose Analogues: Rapid Access to Chemical Probes for Investigating Mycobacteria
Authors: Urbanek Bailey L. , Wing Douglas C. , Haislop Krystal S. , Hamel Chelsey J. , Kalscheuer Rainer , Woodruff Peter J. , Swarts Benjamin M.
Published: August 2014

Trehalose analogues are emerging as valuable tools for investigating Mycobacterium tuberculosis, but progress in this area is slow due to the difficulty in synthesizing these compounds. Here, we report a chemoenzymatic synthesis of trehalose analogues that employs the heat‐stable enzyme trehalose synthase (TreT) from the hyperthermophile Thermoproteus tenax. By using TreT, various trehalose analogues were prepared quickly (1 h) in high yield (up to >99 % by HPLC) in a single step from readily available glucose analogues. To demonstrate the utility of this method in mycobacteria research, we performed a simple “one‐pot metabolic labeling” experiment that accomplished probe synthesis, metabolic labeling, and imaging of M. smegmatis in a single day with only TreT and commercially available materials.
Superparamagnetic CuFeO2 Nanoparticles in Deep Eutectic Solvent: an Efficient and Recyclable Catalytic System for the Synthesis of Imidazo[1,2‐a]pyridines
Authors: Lu Jun , Li Xiao‐Tang , Ma Er‐Qian , Mo Li‐Ping , Zhang Zhan‐Hui
Published: August 2014

Superparamagnetic CuFeO2 nanoparticles were prepared and characterized by XRD, SEM, TEM, FRIR spectroscopy, and vibrating sample magnetometry techniques. The catalytic activity of CuFeO2 nanoparticles was investigated in the one‐pot, three‐component reaction of 2‐aminopyridines, aldehydes, and alkynes using citric acid–dimethylurea melt as a green solvent. An array of imidazo[1,2‐a]pyridines were obtained in good to excellent yields. The catalytic system can be successfully reused six times with keeping its catalytic performance.
Greenhouse Gas Mitigation Costs of Synthetic Methane and Methanol from Biomass and Coal
Authors: Rönsch S. , Zeymer M. , Majer S.
Published: August 2014

Zur Bereitstellung von Sekundärenergieträgern wie Methan und Methanol ist die gemeinsame Nutzung von Kohle und Biomasse in Co‐Vergasungsanlagen eine Alternative zu Erdöl. Trotz der anfallenden Mehrkosten könnte die Einsparung von CO2‐Zertifikaten beim Einsatz von Biomasse einen wirtschaftlichen Anreiz bieten. Hier werden daher die CO2‐Zertifikatepreise abgeschätzt, bei denen die Produktion von Methanol und Methan in Europa ökonomisch wettbewerbsfähig ist. Dazu werden Massen‐ und Energiebilanzen berechnet und die Treibhausgasvermeidungskosten ausgewiesen.
Modelling of particulate matter transformations and capture efficiency
Authors: Sjöblom Jonas , Kannan Ananda Subramani , Ojagh Houman , Ström Henrik
Published: August 2014

In the current work, a comprehensive computational fluid dynamics (CFD) model is developed for an accurate description of the transport and transformation of automotive particulate matter (PM) in monolithic reactors. The model accounts for the developing gas flow, the evaporation of hydrocarbons (HCs) from the particles, and the adsorption of HCs in the washcoat, as well as motion, shrinkage, and deposition of particles in the channel. The comprehensive CFD model is used to validate a simplified tanks‐in‐series approach with a conceptual model for PM transformations. In the development of more detailed and accurate chemical kinetics for the reactions of PM in filters, it will be necessary to also predict the time‐resolved properties of the particles collected in the filter (e.g., reactivity, amount of adsorbed HCs). It is shown in this work how the data necessary to construct such models can be obtained in situ with the aid of the conceptual model and PM measurements over an inert open substrate.
Chemometric Interpretation on the Occurrence of Endocrine Disruptors in Source Water from Malaysia
Authors: Santhi Veerasingan Armugam , Juahir Hafizan , Retnam Ananthy , Mustafa Ali Mohd
Published: August 2014

Multivariate statistical techniques comprising of hierarchical cluster analysis (HACA), discriminant analysis (DA), and principal component analysis (PCA) were used to evaluate and interpret a large dataset for the rivers in Selangor, Malaysia. The dataset consists of analytical results for three physical parameters and nine endocrine disrupting compounds from 25 sampling sites representing source water in the state. HACA successfully grouped the sampling sites to three major clusters (low, moderate, and high pollution) while DA identified eight of the most significant variables that contributed to the high spatial variation to afford 94% correct assignations. Moreover, the application of DA to confirm the seasonal classification to dry and rainy season afforded 88% correct assignations using three variables. In addition, DA offers insight on the inadequacies of the current classification of river water by the Department of Environment based on physical variables. Meanwhile, PCA identified eleven variables to point out 67% of spatial variability. While significant data reduction was not achieved using PCA, it allowed grouping of the variables according to common features which was useful in identifying sources of contamination. This study highlights the usefulness of chemometric techniques for the effective management of source water and identifying appropriate pollution control strategies.
Chance Constrained Optimization of Booster Chlorination in Water Distribution Networks
Authors: Köker Ezgi , Altan‐Sakarya A. Burcu
Published: August 2014

Quality of municipal water is sustained by addition of disinfectant, generally chlorine, to the water distribution network. Because of health problems, chlorine concentration in the network is limited between maximum and minimum limits. Carcinogenic disinfectant by‐products start to occur at high concentrations so it is desired to have minimum amount of chlorine without violating the limit. In addition to the health issues, minimum injection amount is favorable concerning cost. Hence, an optimization problem which covers all of these considerations should be modeled. However, there are uncertain factors as chlorine is reactive and decays both over time and space. Thus, probabilistic approach is necessary to obtain reliable and realistic results from the model. In this study, a linear programming model is developed for the chance constrained optimization of the water distribution network. The objective is to obtain minimum amount of injection mass subjected to maintaining more uniformly distributed chlorine concentrations within the limits, while considering the randomness of chlorine concentration by probability distributions. Network hydraulics and chlorine concentration are computed by the network simulation software, EPANET.
Diagnostic and prognostic value of preoperative combined GFAP, IGFBP‐2, and YKL‐40 plasma levels in patients with glioblastoma
Authors: Gállego Pérez‐Larraya Jaime , Paris Sophie , Idbaih Ahmed , Dehais Caroline , Laigle‐Donadey Florence , Navarro Soledad , Capelle Laurent , Mokhtari Karima , Marie Yannick , Sanson Marc , Hoang‐Xuan Khê , Delattre Jean‐Yves , Mallet Alain
Published: August 2014

BACKGROUND

Circulating proteins released by tumor cells have recently been investigated as potential single surrogate biomarkers for glioblastoma multiforme (GBM). The aim of the current hypothesis‐generating study was to evaluate the diagnostic and prognostic role of preoperative insulin‐like growth factor‐binding protein 2 (IGFBP‐2), chitinase‐3‐like protein 1 (YKL‐40), and glial fibrillary acidic protein (GFAP) plasma levels in patients with GBM, both as single markers and as a combined profile.

METHODS

Plasma samples from 111 patients with GBM and a subset of 40 patients with nonglial brain tumors were obtained preoperatively. Plasma from 99 healthy controls was also analyzed. IGFBP‐2, YKL‐40, and GFAP levels were determined using enzyme‐linked immunoadsorbent assay tests. Their association with histological and radiological variables was assessed.

RESULTS

Circulating levels of all 3 proteins were found to be significantly higher in patients with GBM compared with healthy controls (P < .01). Only YKL‐40 and GFAP were found to demonstrate significant differences between patients with GBM and nonglial brain tumors (P = .04). GFAP was undetectable (<0.02 ng/mL) in all patients without GBM. A receiver operating characteristic analysis accounting for a 2‐step diagnostic procedure including the 3 biomarkers afforded an area under the curve of 0.77 for differentiating patients with GBM from those with nonglial brain tumors. There was a significant correlation between tumor volume and plasma IGFBP‐2 level (Spearman Rho correlation coefficient, 0.22; P = .025) and GFAP (Spearman Rho correlation coefficient, 0.36; P < .001) among patients with GBM. Preoperative plasma IGFBP‐2 levels were found to be independently associated with worse overall survival among patients with GBM (hazard ratio, 1.3; P = .05).

CONCLUSIONS

A combined profile of preoperative IGFBP‐2, GFAP, and YKL‐40 plasma levels could serve as an additional diagnostic tool for patients with inoperable brain lesions suggestive of GBM. In addition, IGFBP‐2 levels appear to constitute an independent prognostic factor in patients with GBM. Cancer 2014;120:3972–3980. © 2014 American Cancer Society.
Investigating the Thermostability of Succinate: Quinone Oxidoreductase Enzymes by Direct Electrochemistry at SWNTs‐Modified Electrodes and FTIR Spectroscopy
Authors: Melin Frederic , Noor Mohamed R. , Pardieu Elodie , Boulmedais Fouzia , Banhart Florian , Cecchini Gary , Soulimane Tewfik , Hellwig Petra
Published: August 2014

Succinate: quinone reductases (SQRs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. Herein, we compare the temperature‐dependent activity and structural stability of two SQRs, the first from the mesophilic bacterium Escherichia coli and the second from the thermophilic bacterium Thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. Direct electron transfer was achieved with full membrane protein complexes at single‐walled carbon nanotube (SWNT)‐modified electrodes. The possible structural factors that contribute to the temperature‐dependent activity of the enzymes and, in particular, to the thermostability of the Thermus thermophilus SQR are discussed.
Diglycerol‐Based Polyesters: Melt Polymerization with Hydrophobic Anhydrides
Authors: Dakshinamoorthy Deivasagayam , Weinstock Allison K. , Damodaran Krishnan , Iwig David F. , Mathers Robert T.
Published: August 2014

The melt polymerization of diglycerol with bicyclic anhydride monomers derived from a naturally occurring monoterpene provides an avenue for polyesters with a high degree of sustainability. The hydrophobic anhydrides are synthesized at ambient temperature via a solvent‐free Diels–Alder reaction of α‐phellandrene with maleic anhydride. Subsequent melt polymerizations with tetra‐functional diglycerol are effective under a range of [diglycerol]/[anhydride] ratios. The hydrophobicity of α‐phellandrene directly impacts the swelling behavior of the resulting polyesters. The low E factors (<2), large amount of bio‐based content (>75 %), ambient temperature monomer synthesis, and polymer degradability represent key factors in the design of these sustainable polyesters.
Tethering Metal Ions to Photocatalyst Particulate Surfaces by Bifunctional Molecular Linkers for Efficient Hydrogen Evolution
Authors: Yu Weili , Isimjan Tayirjan , Gobbo Silvano Del , Anjum Dalaver H. , Abdel‐Azeim Safwat , Cavallo Luigi , Garcia‐Esparza Angel T. , Domen Kazunari , Xu Wei , Takanabe Kazuhiro
Published: August 2014

A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S‐Na2SO3‐containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials.
Efficient Water‐Splitting Device Based on a Bismuth Vanadate Photoanode and Thin‐Film Silicon Solar Cells
Authors: Han Lihao , Abdi Fatwa F. , van de Krol Roel , Liu Rui , Huang Zhuangqun , Lewerenz Hans‐Joachim , Dam Bernard , Zeman Miro , Smets Arno H. M.
Published: August 2014

A hybrid photovoltaic/photoelectrochemical (PV/PEC) water‐splitting device with a benchmark solar‐to‐hydrogen conversion efficiency of 5.2 % under simulated air mass (AM) 1.5 illumination is reported. This cell consists of a gradient‐doped tungsten–bismuth vanadate (W:BiVO4) photoanode and a thin‐film silicon solar cell. The improvement with respect to an earlier cell that also used gradient‐doped W:BiVO4 has been achieved by simultaneously introducing a textured substrate to enhance light trapping in the BiVO4 photoanode and further optimization of the W gradient doping profile in the photoanode. Various PV cells have been studied in combination with this BiVO4 photoanode, such as an amorphous silicon (a‐Si:H) single junction, an a‐Si:H/a‐Si:H double junction, and an a‐Si:H/nanocrystalline silicon (nc‐Si:H) micromorph junction. The highest conversion efficiency, which is also the record efficiency for metal oxide based water‐splitting devices, is reached for a tandem system consisting of the optimized W:BiVO4 photoanode and the micromorph (a‐Si:H/nc‐Si:H) cell. This record efficiency is attributed to the increased performance of the BiVO4 photoanode, which is the limiting factor in this hybrid PEC/PV device, as well as better spectral matching between BiVO4 and the nc‐Si:H cell.
Electron Beam‐Induced CVD of Nanoalloys for Nanoelectronics
Authors: Shawrav Mostafa Moonir , Belić Domagoj , Gavagnin Marco , Wachter Stefan , Schinnerl Markus , Wanzenboeck Heinz D. , Bertagnolli Emmerich
Published: August 2014

Among various multi‐metal combinations, Au‐Fe nanoalloys are envisaged as prospective materials for data storage applications. Here we report on the first successful achievement of Au‐Fe nanoalloys using focused electron beam‐induced deposition (FEBID), exploiting the possibility of directly writing nanostructures at nanometer resolution. Gaseous organometallic precursors are injected simultaneously into the deposition chamber to co‐deposit Fe and Au within the same nanostructure. Fabricated nanostructures show a spatially uniform elemental ratio of iron to gold that can be tailored by experimental conditions.
Genome size estimates for crustaceans using Feulgen image analysis densitometry of ethanol‐preserved tissues
Authors: Jeffery Nicholas W. , Gregory T. Ryan
Published: August 2014

Crustaceans are enormously diverse both phylogenetically and ecologically, but they remain substantially underrepresented in the existing genome size database. An expansion of this dataset could be facilitated if it were possible to obtain genome size estimates from ethanol‐preserved specimens. In this study, two tests were performed in order to assess the reliability of genome size data generated using preserved material. First, the results of estimates based on flash‐frozen versus ethanol‐preserved material were compared across 37 species of crustaceans that differ widely in genome size. Second, a comparison was made of specimens from a single species that had been stored in ethanol for 1–14 years. In both cases, the use of gill tissue in Feulgen image analysis densitometry proved to be a very viable approach. This finding is of direct relevance to both new studies of field‐collected crustaceans as well as potential studies based on existing collections. © 2014 International Society for Advancement of Cytometry