bluuebunny/crossref_metadata_2025 huggingface dataset:
Improvements to the PhytoDOAS method for identification of major phytoplankton groups using hyper-spectral satellite data
Authors: Sadeghi A. , Dinter T. , Vountas M. , Taylor B. , Peeken I. , Bracher A.
Published: December 2011

Abstract. The goal of this study was to improve PhytoDOAS, which is a new retrieval method for quantitative identification of major Phytoplankton Functional Types (PFTs) using hyper-spectral satellite data. PhytoDOAS is an extension of the Differential Optical Absorption Spectroscopy (DOAS, a method for detection of atmospheric trace gases), developed for remote identification of oceanic phytoplankton groups. Thus far, PhytoDOAS has been successfully exploited to identify cyanobacteria and diatoms over the global ocean from SCIAMACHY (SCanning Imaging Absorption spectroMeter for Atmospheric CartograpHY) hyper-spectral data. The main challenge for retrieving more PFTs by PhytoDOAS is to overcome the correlation effects between different PFTs' absorption spectra. Different PFTs are composed of different types and amounts of pigments, but also have pigments in common, e.g., chl-a, causing correlation effects in the usual performance of the PhytoDOAS retrieval. Two ideas have been implemented to improve PhytoDOAS for the PFT retrieval of more phytoplankton groups. Firstly, using the fourth-derivative spectroscopy, the peak positions of the main pigment components in each absorption spectrum have been derived. After comparing the corresponding results of major PFTs, the optimized fit-window for the PhytoDOAS retrieval of each PFT was determined. Secondly, based on the results from derivative spectroscopy, simultaneous fit of PhytoDOAS has been proposed and tested for a selected set of PFTs (coccolithophores, diatoms and dinoflagllates) within an optimized fit-window. The method was then applied to the processing of SCIAMACHY data over the year 2005. Comparisons of the PhytoDOAS PFT retrievals in 2005 with the modeled PFT data from the NASA Ocean Biochemical Model (NOBM) showed similar patterns in their seasonal distributions for diatoms and coccolithophores, especially in the northern parts of the global ocean. The seasonal patterns of the PhytoDOAS coccolithophores indicated very good agreement with the global distributions of Particulate Inorganic Carbon (PIC) provided by MODIS (MODerate resolution Imaging Spectroradiometer)-Aqua level-3 products. Since PIC is known as a proxy for the abundance of coccolithophores (in open ocean), the latter agreement indicates the basic functionality of the method in retrieving coccolithophores. Moreover, as a case study, the simultaneous mode of PhytoDOAS has been applied to SCIAMACHY data for detecting a coccolithophore bloom around New Zealand (reported by NASA from MODIS imagery in December 2009); the result was quite consistent with the MODIS RGB image and the MODIS PIC map of the bloom, indicating the functionality of the method in short-term retrievals.
Allosteric Activation of Kinases: Design and Application of RapR Kinases
Authors: Karginov Andrei V. , Hahn Klaus M.
Published: December 2011

Here we describe a method for the engineered regulation of protein kinases in living cells, the design and application of RapR (rapamycin regulated) kinases. The RapR kinase method enables activation of kinases with high specificity and precise temporal control. Insertion of an engineered allosteric switch, the iFKBP domain, at a structurally conserved position within the kinase catalytic domain makes the modified kinase inactive. Treatment with rapamycin or its non‐immunosuppressive analogs triggers interaction with a small FKBP‐rapamycin‐binding domain (FRB), restoring the activity of the kinase. The reagents used in this method are genetically encoded or membrane permeable, enabling ready application in many systems. Based on the structural similarity of kinase catalytic domains, this method is likely applicable to a wide variety of kinases. Successful regulation has already been demonstrated for three kinases representing both tyrosine and serine/threonine kinase families (p38, FAK, Src). Procedures for designing and testing RapR kinases are discussed. Curr. Protoc. Cell Biol. 53:14.13.1‐14.13.16. © 2011 by John Wiley & Sons, Inc.
Installation and Use of LabKey Server for Proteomics
Authors: Eckels Joshua , Hussey Peter , Nelson Elizabeth K. , Myers Tamra , Rauch Adam , Bellew Matthew , Connolly Brian , Law Wendy , Eng Jimmy K. , Katz Jonathan , McIntosh Martin , Mallick Parag , Igra Mark
Published: December 2011

LabKey Server (formerly CPAS, the Computational Proteomics Analysis System) provides a Web‐based platform for mining data from liquid chromatography–tandem mass spectrometry (LC‐MS/MS) proteomic experiments. This open source platform supports systematic proteomic analyses and secure data management, integration, and sharing. LabKey Server incorporates several tools currently used in proteomic analysis, including the X! Tandem search engine, the ProteoWizard toolkit, and the PeptideProphet and ProteinProphet data mining tools. These tools and others are integrated into LabKey Server, which provides an extensible architecture for developing high‐throughput biological applications. The LabKey Server analysis pipeline acts on data in standardized file formats, so that researchers may use LabKey Server with other search engines, including Mascot or SEQUEST, that follow a standardized format for reporting search engine results. Supported builds of LabKey Server are freely available at http://www.labkey.com/. Documentation and source code are available under the Apache License 2.0 at http://www.labkey.org. Curr. Protoc. Bioinform. 36:13.5.1‐13.5.25. © 2011 by John Wiley & Sons, Inc.
Adaptive consensus seeking of multiple nonlinear systems
Authors: Dong Wenjie
Published: December 2011

This paper considers two consensus problems of multiple nonlinear systems. In the first consensus problem, distributed control laws for multiple nonlinear systems are proposed such that the state of each system converges to a constant agreement vector with the aid of communications between systems. In the second consensus problem, distributed robust/adaptive control laws for multiple nonlinear systems are proposed such that the state of each system converges to the state of a reference system whose state is available to a portion of multiple systems. Simulation results show the effectiveness of the proposed control laws. Copyright © 2011 John Wiley & Sons, Ltd.
Kilogram‐Scale Asymmetric Ruthenium‐Catalyzed Hydrogenation of a Tetrasubstituted Fluoroenamide
Authors: Stumpf Andreas , Reynolds Mark , Sutherlin Daniel , Babu Srinivasan , Bappert Erhard , Spindler Felix , Welch Michael , Gaudino John
Published: December 2011

Ruthenium‐catalyzed asymmetric homogeneous hydrogenation (AHH) is used as the key step of a multi‐kilogram scale synthesis of an enantiomeric fluoropiperidine. The AHH of a tetrasubstituted β‐fluoroenamide is carried out under mild conditions using a Ru/Josiphos catalyst with high ee (98%).
The Efficient Copper(I) (Hexabenzyl)tren Catalyst and Dendritic Analogues for Green “Click” Reactions between Azides and Alkynes in Organic Solvent and in Water: Positive Dendritic Effects and Monometallic Mechanism
Authors: Liang Liyuan , Ruiz Jaime , Astruc Didier
Published: December 2011

An easily synthesized, copper(I) (hexabenzyl)tren complex 1 is an efficient catalyst for the copper(I)‐catalyzed Huisgen‐type 1,3‐cycloaddition between azides and alkynes (CuAAC) reaction in toluene. Alternatively, a convenient procedure involves mixing copper(I) bromide (CuBr) with hexabenzyltren and the substrates in toluene which gives, for instance, 100% yield of triazole in 10 min using 0.1 equiv. catalyst with phenylacetylene and benzyl azide at room temperature. The toluene‐soluble catalyst 1 is recyclable and is applied, for example, to the CuAAC synthesis of an 81‐branched dendrimer that previously required the use of a stoichiometric amount of copper(II) sulfate (CuSO4)+sodium ascorbate “catalyst”. Dendritic copper(I)‐centered analogues 2 and 3 of the first and second generations (G1 and G2, respectively) containing respectively 18 and 54 branch termini, including a 54‐branched water‐soluble metallodendrimer 5, are also very efficient catalysts for the CuAAC reaction. With the metallodendritic Cu(I) derivatives 2 and 3, the dendritic frame brings about steric protection against the well‐known inner‐sphere aerobic oxidation of Cu(I) to bis(μ‐oxo)‐bis‐Cu(II). The metallodendrimers 2 and 3 are also sometimes more efficient than the parent catalyst, as shown by kinetic studies. Catalysis in water without co‐solvent of the CuAAC reactions of water‐insoluble substrates was achieved under ambient conditions in good yields with the recyclable catalyst 5. Efficient catalysis of the CuAAC reaction by these bulky Cu(I) metallodendrimers emphasizes the monometallic mechanism. The difference of kinetic behavior between 1 and CuBr+hexabenzyltren suggests, however, that whereas a monometallic mechanism is working for 1, the mixture of CuBr+hexabenzyltren might involve the bimetallic mechanism proposed by Fokin and Finn.
Genetic and environmental contributions to self‐reported thoughts of self‐harm and suicide
Authors: Althoff Robert R. , Hudziak James J. , Willemsen Gonneke , Hudziak Vicenta , Bartels Meike , Boomsma Dorret I.
Published: December 2011

Thoughts of self‐harm and suicidal behavior are thought to be influenced by both genetics and environment. Molecular genetic studies are beginning to address the question of which genes may be involved and whether different genes may be expressed in men and women. We examined thoughts of self‐harm and suicidal behavior in a large general population twin sample including male and female same‐ and opposite‐sex twins. In this study, data on self‐reported thoughts of self‐harm and suicide were obtained from self‐report questionnaires (Beck Depression Inventory and Youth or Adult Self Report forms) in 6,265 twin pairs (11,008 individuals) aged 11–90 (62% female) from the Netherlands Twin Registry. Liability threshold models were compared including sex and age (linear and quadratic) effects. Models were compared using measures of parsimony to calculate the simplest model to the data. A model with additive genetic and unique environmental contributions fitted the data for both males and females. There were no qualitative sex differences, but the relative contributions differed between men and women. Heritability was higher in women (0.74, 95% CI 0.65–0.81) than men (0.45, 95% CI 0.28–0.61). The remaining variance was accounted for by environmental influence unique to an individual. These results suggest contributions from additive genetic factors to self‐reported thoughts of self‐harm and suicide and support the continued study of both molecular genetic and individual‐specific environmental risk factors. © 2011 Wiley Periodicals, Inc.
Ätiologie potentiell primordialer Biomolekül‐Strukturen: Vom Vitamin B12zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens – ein Rückblick
Authors: Eschenmoser Albert
Published: December 2011

“Wir werden es nie wissen können” ist ein Truismus, der zu Resignation gegenüber jeglicher experimenteller Investition in eine Suche nach der Chemie der Entstehung des Lebens verführt. Doch widerspricht solche Resignation radikal der Herausforderung, die der Chemie als Naturwissenschaft auferlegt ist. Ungeachtet der Prognose, wonach der kürzeste Weg zum Verständnis der Metamorphose des Chemischen ins Biologische über die experimentelle Modellierung “künstlichen chemischen Lebens” führt, wird die naturwissenschaftliche Suche nach dem von der Natur begangenen Weg der Entstehung des Lebens, das wir kennen, wohl nie wirklich enden. Denn sie ist Teil der Suche nach unserem eigenen Ursprung.
Preparation and in vitro characterization of poly(sebacic acid‐co‐ricinoleic acid)‐based tamoxifen citrate‐loaded microparticles for breast cancer
Authors: Hiremath J. G. , Rudani C.G. , Domb A. J. , Suthar R. V. , Khamar N. S.
Published: December 2011

This study was aimed to develop an injectable polymeric drug delivery system for tamoxifen citrate (TC) using poly(sebacic acid‐co‐ricinoleic acid) [poly(SA‐RA) 70 : 30 w/w] as a drug carrier for the treatment of estrogen receptor positive breast cancer. Injectable biodegradable microparticles of TC were produced by solvent displacement technique of microencapsulation and were characterized by surface morphology (scanning electron microscopy), particle size, size distribution, physical and chemical interaction (Fourier transform infrared), nature and physical state of drug [DSC and X‐ray diffraction (XRD)], and in vitro release studies. TC loading over different concentrations was analyzed by high performance liquid chromatography (HPLC) technique. Polyanhydride microparticles obtained after lyophilization were nearly spherical in shape with smooth surface and size less than 2.5 μm. TC was dispersed in the form of amorphous state, and TC remains intact and stable during the process of microencapsulation. In vitro drug release studies demonstrated prolonged controlled release of TC with zero‐order kinetics. Stability studies revealed that the production process of microparticles itself did not affect the chemical stability of the drug and polymer forming the particle matrix. Significant difference in drug release capacity was observed in microparticles with different drug loadings, and the drug release was more sustained in microparticles prepared with high TC. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Synthesis and characterization of poly(2‐hydroxyethyl methacrylate)‐functionalized Fe‐Au/core‐shell nanoparticles
Authors: Bach Long Giang , Rafiqul Islam Md. , Kim Jin Ho , Kim Hyun Gyu , Lim Kwon Taek
Published: December 2011

Disulfide‐bearing poly(2‐hydroxyethyl methacrylate) (DT‐PHEMA) was synthesized by atom transfer radical polymerization technique, which was subsequently immobilized onto core‐shell structured Fe‐Au nanoparticles (Fe‐AuNPs) by applying a “grafting to” protocol to afford new PHEMA‐grafted Fe‐AuNPs (PHEMA‐g‐Fe‐AuNPs). The Fe‐AuNPs having the iron core of 20–22 nm and the gold layer of 1–2 nm were initially prepared by inverse micelle technique and characterized by XRD and high‐resolution transmission electron microscopy (HR‐TEM). The grafting of DT‐PHEMA on the Fe‐AuNPs was confirmed by Fourier transformed infrared spectrophotometer, thermogravimetric (TGA), X‐ray photoelectron spectroscopy, and energy dispersive X‐ray analyses. The average diameter of polymer coated Fe‐AuNPs was determined to be 28 nm by HR‐TEM analysis. The amount of the polymer on the surface of Fe‐AuNPs was calculated to be about 50% by TGA analysis. The studies of magnetic property by the superconducting quantum interference devices indicate the superparamagnetic property of Fe‐AuNPs and PHEMA‐g‐Fe‐AuNPs. The optical property of the PHEMA‐g‐Fe‐AuNPs was recorded by UV–visible absorption spectroscopy, and a redshift in the absorption was observed, which further suggests the PHEMA attachment on the surface of Fe‐AuNPs. The magnetic nanocomposites demonstrate good dispersibility in common polar solvents. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Working mechanism of a high temperature (200°C) synthetic cement retarder and its interaction with an AMPS®‐based fluid loss polymer in oil well cement
Authors: Tiemeyer Constantin , Plank Johann
Published: December 2011

A copolymer comprising of 2‐acrylamido‐2‐methyl propane sulfonic acid (AMPS®) and itaconic acid (molar ratio 1 : 0.32) was synthesized by aqueous free radical polymerization and probed as high temperature retarder for oil well cement. Characteristic properties of the copolymer including molar masses (Mw and Mn), polydispersity index and anionic charge amount were determined. The copolymer possesses a Mw of ∼ 2 × 105 g/mol and is highly anionic. HT/HP consistometer tests confirmed effectiveness of the retarder at temperatures up to 200°C. The working mechanism of NaAMPS®‐co‐itaconic acid was found to rely exclusively on its huge calcium binding capacity (5 g calcium/g copolymer). It reduces the amount of freely dissolved, nonbound calcium ions present in cement pore solution and thus hinders the growth of cement hydrates because of lack of calcium. The value for the calcium binding capability is 46 times higher than the stoichiometric amount per COO− functionality. Consequently, calcium also coordinates to other donor atoms present in the retarder. NaAMPS®‐co‐itaconic acid also adsorbs onto cement, as was evidenced by TOC analysis of cement filtrates, zeta potential measurement and decreased rheology of cement pastes. However, adsorption plays no role in the retarding mechanism of this copolymer. Combination of NaAMPS®‐co‐itaconic acid retarder with a common CaAMPS®‐co‐NNDMA fluid loss additive (FLA) revealed that competitive adsorption on cement between these two admixtures occurs. The retarder fills interstitial adsorption sites on cement located between those occupied by the larger FLA molecules. In consequence, fewer amounts of CaAMPS®‐co‐NNDMA can adsorb and its effectiveness is reduced. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Preparation of electrospun polycaprolactone nanofibers with water‐soluble eggshell membrane and catechin
Authors: Kang Jian , Chen Long , Okubayashi Satoko , Sukigara Sachiko
Published: December 2011

The process of incorporating water‐soluble eggshell membrane (S‐ESM) into polycaprolactone (PCL) electrospun nanofibers was investigated using the interaction between S‐ESM and catechin. Electrospinning of the nontoxic natural catechin with PCL was examined, and S‐ESM was introduced into the resulting PCL/catechin nanofibers through hydrogen bonding. S‐ESM was added into PCL/catechin electrospun fibers by immersing the as‐spun fibers in an S‐ESM solution that was prepared by dissolving S‐ESM powder in water with a dimethylformamide cosolvent. Morphological observation suggested that S‐ESM was incorporated with catechin and formed S‐ESM/catechin nanoparticles, distributed in the nanofiber webs. Analysis of Fourier transform infrared spectra indicated that hydrogen bonding interactions were generated between PCL and catechin as well as between S‐ESM and catechin. Water contact angle tests suggested that the presence of S‐ESM/catechin improved the wettability of PCL nanofiber webs. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Effect of Al2O3 fibers on the thermal conductivity and mechanical properties of high density polyethylene with the absence and presence of compatibilizer
Authors: Zhang Shuai , Ke Yucai , Cao Xinyu , Ma Yongmei , Wang Fosong
Published: December 2011

Alumina (Al2O3) fiber/high density polyethylene (HDPE) composites were prepared by molding injection with or without compatibilizer, in which, maleic anhydride‐grafted polyethylene (PE‐g‐MA) and acrylic acid‐grafted polyethylene (PE‐g‐AA) were used as the compatibilizers. The thermal conductivities of the composites were anisotropic and the conductivities in the injection direction of the samples were higher than those in perpendicular direction of the injection. The anisotropic thermal conductivity for Al2O3/PE‐g‐AA/HDPE was the most obvious and this composite also gave the best mechanical performance. The SEM and DMA test revealed that PE‐g‐AA was more effective than PE‐g‐MA in improving the matrix–filler interaction. The high interfacial interaction was more favorable for the viscous flow‐induced fiber orientation, which resulted in the largest anisotropic degree of thermal conductivity of the Al2O3/PE‐g‐AA/HDPE among the studied composite. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Influence of a density mismatch on TMPTMA shells nonconcentricity
Authors: Lattaud Cecile , Guillot Lyonel , Brachais Claire‐Hélène , Fleury Emmanuel , Legaie Olivier , Couvercelle Jean‐Pierre
Published: December 2011

Some laser target designs require low‐density organic foam shells to study fusion on the French high‐power laser laser mega joule. Low‐density trimethylolpropane trimethacrylate foam shells composed of C, H, and O, 2 mm diameter, 100‐μm wall thickness, and 250 mg cm−3 density are synthesized by a microencapsulation technique using a droplet generator. These shells have to reach a sphericity higher than 99.9% and a nonconcentricity (NC) lower than 1%. The wall thickness variation is one of the most difficult specifications to meet. An important factor in reducing this defect is the density matching between the three phases of the emulsion at polymerization temperature. The influence of a density mismatch between the internal water phase and the organic phase on the NC of TMPTMA foam shells was studied. The best NC results and yields of shells are obtained with a density gap between the internal water phase and the organic phase of 0.078 g cm−3 at 60°C, with an average NC around 2%. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Poly(propylene‐co‐ethylene) produced with a conventional and a self‐supported ziegler–natta catalyst: Effect of ethylene and hydrogen concentration on activity and polymer structure
Authors: Vestberg Torvald , Parkinson Matthew , Fonseca Isa , Wilén Carl‐Eric
Published: December 2011

A novel self‐supported emulsion‐based catalyst and a conventional MgCl2‐supported Ziegler–Natta catalyst were used in the copolymerization of propylene and ethylene under industrial conditions using triethyl aluminium as cocatalyst and dicyclopentyl dimethoxy silane as external donor. The effects of the concentration of ethylene and hydrogen on the polymerization behaviors and polymer properties were investigated. The combined effect of both ethylene and hydrogen increased the relative activity of the novel catalyst more than for the conventional catalyst. This trend was consistent with our earlier observed higher degree of dormancy, due to 2,1 insertions, found with the novel catalyst. More importantly, the work has uncovered that the self‐supported catalyst incorporates ethylene in a more random fashion and produces copolymers with relatively narrow molecular weight distribution (MWD). These results in combination with polymer microstructure studies using Fourier transform infrared spectroscopy, 13C‐NMR spectroscopy, and differential scanning calorimetry all indicated that the novel catalyst has a narrower distribution of active site types than the conventional reference catalyst. The narrow composition of active site structures, the narrow MWD, and the random incorporation of ethylene into the polymer chain indicated that the emulsion‐based catalyst possesses features that to a certain degree tend to be more indicative for a single‐site‐like catalyst structure and behavior. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Synthesis and Biological Evaluation of New Tetra‐aza Macrocyclic Scaffold Constrained Oxadiazole, Thiadiazole and Triazole Rings
Authors: Vinay Kumar B. , Naik H. S. Bhojya , Girija D. , Sharath N. , Sudeep H. V. , Joy Hoskeri H.
Published: December 2011

A new series of N,N′‐(benzene‐1,3‐diyldi‐1,3,4‐oxadiazole‐5,2‐diyl)bis{2‐[(5‐benzene‐1,3‐diyl‐1,3,4‐oxadiazol‐2‐yl)amino]acetamide}(macrocycle 1), N,N′‐(benzene‐1,3‐diyldi‐1,3,4‐thiadiazole‐5,2‐diyl)bis{2‐[(5‐benzene‐1,3‐diyl‐1,3,4‐thiadiazol‐2‐yl)amino]acetamide} (macrocycle 2) and S,S′‐[benzene‐1,3‐diylbis(4H‐1,2,4‐triazole‐5,3‐diyl)]bis{[(5‐benzene‐1,3‐diyl‐4H‐1,2,4‐triazol‐3‐yl)sulfanyl]ethanethioate}(macrocycle 3) was synthesized from isophthalic dihydrazide (4) through a multistep reaction sequence. All the synthesized compounds were screened for their inhibitory effect against four different bacterial strains: P. aeruginosa ATCC‐20852, K. pneumoniae MTCC‐618, S. aureus ATCC‐ 29737, S. typhi MTCC‐ 3214. The synthesized compounds showed a significant zone of inhibition and the results were comparable with that of the standard drug ciprofloxacin. The synthesized compounds were further studied for their possible in vitro antioxidant effects by DPPH scavenging, total antioxidant capacity, total reductive capacity and H2O2 scavenging activity. The results indicated that the in vitro antioxidant activity for all the three molecules was efficient when compared to the standards. The DNA interaction behavior of macrocycles 1–3 with CT‐DNA was investigated by the absorption spectra obtained (Kb constant for 1 is 4.53 × 104 M−1, for 2 is 5.75 × 104 M−1 and for 3 is 5.86 × 104 M−1). Based on the results it can be interpreted that the reducing power effect of the newly synthesized compounds demonstrates a direct effect on DNA binding and hence inhibiting the bacterial growth through their action on DNA by inhibiting DNA replication or DNA transcription.
Ultrasound‐Assisted Synthesis of Novel α‐Aminophosphonates and Their Biological Activity
Authors: Rasheed Syed , Venkataramana Katla , Chandrasekhar Kuruva , Fareeda Gemmalamadugu , Raju Chamarthi Naga
Published: December 2011

The synthesis of a series of novel α‐aminosubstituted phosphonates was accomplished by the reaction of various substituted aldehydes with an amine amlodipine (3‐ethyl 5‐methyl (±)2‐((2‐aminoethoxy)methyl)‐4‐(2‐chlorophenyl)‐6‐methyl‐1,4‐dihydropyridene‐3,5‐dicarboxylate) followed by diethylphosphite/dibutylphosphite in ethanol using SnCl2.2H2O as a Lewis acid catalyst, under conventional and ultrasonic irradiation. Their structures were established by analytical and spectral data. The title compounds showed good antibacterial, antifungal and antiviral activity depending on the nature of the bioactive groups at the α‐carbon.
Synthesis and Antioxidant Properties of (3,4‐Dihydroxyphenyl)(2,3,4‐trihydroxyphenyl)methanone and Its Derivatives
Authors: Çetinkaya Yasin , Göçer Hülya , Menzek Abdullah , Gülçin İlhami
Published: December 2011

(3,4‐Dihydroxyphenyl)(2,3,4‐trihydroxyphenyl)methanone (5) and its two derivatives with bromine were synthesized from reactions such as bromination and demethylation of (3,4‐dimethoxyphenyl)(2,3,4‐trimethoxyphenyl)methanone (6). The Wolf‐Kishner reduction product (9) of 6 and its three derivatives with bromine were obtained. 4‐(3,4‐Dihydroxybenzyl)benzene‐1,2,3‐triol and its dibromide derivative (16) were also synthesized from 9 and the corresponding dibromide derivative. The in vitro antioxidant activities of nine new compounds synthesized in these reactions were determined by analyzing the radical scavenging activities of bromophenols for 2,2′‐azino‐bis(3‐ethylbenzthiazoline‐6‐sulfonic acid) (ABTS), 1,1‐diphenyl‐2‐picryl‐hydrazyl (DPPH), N,N‐dimethyl‐p‐phenylenediamine (DMPD), and the superoxide anion radical (${\rm O}_{2}^{\bullet - } $) and examining the total reducing power through Fe3+‐Fe2+ transformation, FRAP and CUPRAC assays and the ferrous ions (Fe2+) chelating activities. Moreover, the results of these activities were compared to those of standard antioxidant compounds such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), α‐tocopherol, and trolox. The results showed that the synthesized bromophenols had effective antioxidant power. The phenol 5 with two phenolic rings and five phenolic hydroxyl groups was the most potent antioxidant and radical scavenger. In conclusion, the new compounds are promising molecules to be used owing to their potential antioxidant properties.
4H‐1,4‐Benzothiazine, Dihydro‐1,4‐benzothiazinones and 2‐Amino‐5‐fluorobenzenethiol Derivatives: Design, Synthesis and in vitro Antimicrobial Screening
Authors: Armenise Domenico , Muraglia Marilena , Florio Marco Antonio , De Laurentis Nicolino , Rosato Antonio , Carrieri Antonio , Corbo Filomena , Franchini Carlo
Published: December 2011

As part of our studies focused on the design and synthesis of new antimicrobial agents a series of 7‐fluoro‐3,4‐dihydro‐2H‐1,4‐benzothiazine derivatives (4a–4f, 4h) and 7‐fluoro‐2H‐1,4‐benzothiazin‐3(4H)‐one analogues (4j–4o) were synthesized and evaluated for their in vitro inhibitory activity against a representative panel of Gram‐positive and Gram‐negative bacteria strains and also toward selected fungi species. These compounds were prepared in one step from chloro‐substituted‐2‐amino‐5‐fluorobenzenethiol 6a–6c. The biological screening identified in compounds 4a, 4j and 4l the most promising results of both series showing an interesting antimicrobial activity. Our antibiotic investigation was also completed by testing the key intermediates 6a–6c. Surprisingly, 6a–6c emerged as the compounds exhibiting the highest antimicrobial activity by possessing a remarkable antibacterial effect against the Gram‐positive strains with MIC (minimal inhibitory concentration) values between 2 and 8 µg/mL and the fungi panel with MIC values between 2 and 8 µg/mL. These results may prove useful in the design of a novel pool of antimicrobial agents.
Quantifying and measuring metadata completeness
Authors: Margaritopoulos Merkourios , Margaritopoulos Thomas , Mavridis Ioannis , Manitsaris Athanasios
Published: December 2011

Completeness of metadata is one of the most essential characteristics of their quality. An incomplete metadata record is a record of degraded quality. Existing approaches to measure metadata completeness limit their scope in counting the existence of values in fields, regardless of the metadata hierarchy as defined in international standards. Such a traditional approach overlooks several issues that need to be taken into account. This paper presents a fine‐grained metrics system for measuring metadata completeness, based on field completeness. A metadata field is considered to be a container of multiple pieces of information. In this regard, the proposed system is capable of following the hierarchy of metadata as it is set by the metadata schema and admeasuring the effect of multiple values of multivalued fields. An application of the proposed metrics system, after being configured according to specific user requirements, to measure completeness of a real‐world set of metadata is demonstrated. The results prove its ability to assess the sufficiency of metadata to describe a resource and provide targeted measures of completeness throughout the metadata hierarchy.
Audiovisual speech integration in autism spectrum disorders: ERP evidence for atypicalities in lexical‐semantic processing
Authors: Megnin Odette , Flitton Atlanta , R.G. Jones Catherine , de Haan Michelle , Baldeweg Torsten , Charman Tony
Published: December 2011

In typically developing (TD) individuals, behavioral and event‐related potential (ERP) studies suggest that audiovisual (AV) integration enables faster and more efficient processing of speech. However, little is known about AV speech processing in individuals with autism spectrum disorders (ASD). This study examined ERP responses to spoken words to elucidate the effects of visual speech (the lip movements accompanying a spoken word) on the range of auditory speech processing stages from sound onset detection to semantic integration. The study also included an AV condition, which paired spoken words with a dynamic scrambled face in order to highlight AV effects specific to visual speech. Fourteen adolescent boys with ASD (15–17 years old) and 14 age‐ and verbal IQ‐matched TD boys participated. The ERP of the TD group showed a pattern and topography of AV interaction effects consistent with activity within the superior temporal plane, with two dissociable effects over frontocentral and centroparietal regions. The posterior effect (200–300?ms interval) was specifically sensitive to lip movements in TD boys, and no AV modulation was observed in this region for the ASD group. Moreover, the magnitude of the posterior AV effect to visual speech correlated inversely with ASD symptomatology. In addition, the ASD boys showed an unexpected effect (P2 time window) over the frontocentral region (pooled electrodes F3, Fz, F4, FC1, FC2, FC3, FC4), which was sensitive to scrambled face stimuli. These results suggest that the neural networks facilitating processing of spoken words by visual speech are altered in individuals with ASD. Autism Res2011,4:xxx–xxx. © 2011 International Society for Autism Research, Wiley Periodicals, Inc.
Microarray expression profiling identifies genes regulating sustained cell specific productivity (S‐Qp) in CHO K1 production cell lines
Authors: Doolan Padraig , Barron Niall , Kinsella Paula , Clarke Colin , Meleady Paula , O'Sullivan Finbarr , Melville Mark , Leonard Mark , Clynes Martin
Published: December 2011

Fed batch culture processes are often characterized by decreasing cell culture performance as the process continues, presumably through the depletion of vital nutrients and the accumulation of toxic byproducts. We have similarly observed that cellular productivity (Qp) often declines during the course of a fed batch process; however, it is not clear why some cell lines elicit this behavior, while others do not. We here present a transcriptomic profiling analysis of a phenotype of sustained Qp (S‐Qp) in production Chinese hamster ovary (CHO) culture, in which a marked drop in Qp levels (“non‐sustained” (NS) phenotype) in two cell lines irrespective of viability levels was compared to two cell lines that consistently displayed high Qp throughout the culture (“sustained” (S) phenotype). Statistical analysis of the microarray data resulted in the identification of 22 gene transcripts whose expression patterns were either significantly negatively or positively correlated with long‐term maintenance of Qp over the culture lifespan. qPCR analysis of four of these genes on one of each (NS2, S2) of the cell lines examined by microarray analysis confirmed that two genes (CRYAB and MGST1) both replicated the microarray results and were differentially regulated between the NS and S phenotypes.
Characterization of the acylglycerols and resulting biodiesel derived from vegetable oil and microalgae (Thalassiosira pseudonana and Phaeodactylum tricornutum)
Authors: Zendejas Frank J. , Benke Peter I. , Lane Pamela D. , Simmons Blake A. , Lane Todd W.
Published: December 2011

Algal biofuels are a growing interest worldwide due to their potential in terms of sustainable greenhouse gas displacement and energy production. This article describes a comparative survey of biodiesel production and conversion yields of biodiesel via alkaline transesterification of acylglycerols extracted from the microalgae Thalassiosira pseudonana and Phaeodactylum tricornutum, grown under silicate or nitrate limitation, and that of model vegetable oils: soybean, and rapeseed oil. Acylglycerols were extracted with n‐hexane and the total yield per biomass was determined by gravimetric assay. Under our conditions, the total acylglycerol yield from the microalgae studied was 13–18% of total dry weight. The biodiesel samples were analyzed using gas chromatography–flame ionization detector to determine quantitative information of residual glycerol, mono‐, di‐, and tri‐acylglycerol concentrations in the biodiesel. All of the algal‐based biodiesel demonstrated less mono‐, di‐, and tri‐acylglycerol concentrations than the vegetable‐based biodiesel under identical transesterification conditions. The fatty acid compositions of all the feedstock oils and their resultant biodiesel were also analyzed and reported. Based on the fatty acid methyl ester compositions of our samples we qualitatively assessed the suitability of the algal‐derived biodiesel in terms of cetane number (CN), cold‐flow properties, and oxidative stability. Biotechnol. Bioeng. 2012;109: 1146–1154. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.
Executive deficits detected in mild Alzheimer's disease using the antisaccade task
Authors: Kaufman Liam D. , Pratt Jay , Levine Brian , Black Sandra E.
Published: December 2011

The antisaccade task, a hands‐ and language‐free metric, may provide a functional index of the dorsolateral prefrontal cortex (DLPFC), a region damaged in the later stages of Alzheimer's disease (AD). Our objective was to determine if patients with mild AD made more errors relative to age‐matched controls. Thirty patients with mild AD (Mini Mental Status Exam [MMSE] ≥ 17) and 31 age‐matched controls completed a laptop version of the prosaccades and antisaccades tasks. Patients with AD made more antisaccade errors, and corrected fewer errors, than age‐matched controls. Error rates, corrected or uncorrected, were not correlated with AD MMSE or Dementia Rating Scale scores. Our findings indicate that antisaccade impairments exist in mild AD, suggesting clinically detectable DLPFC pathology may be present earlier than suggested by previous studies.
An automated microscale platform for evaluation and optimization of oxidative bioconversion processes
Authors: Baboo Jasmin Z. , Galman James L. , Lye Gary J. , Ward John M. , Hailes Helen C. , Micheletti Martina
Published: December 2011

In this work an integrated robotic platform has been used for the development of a fully automated microscale process sequence comprising fermentation and bioconversion using E. coli TOP10 [pQR210] expressing cyclohexanone monooxygenase (CHMO). Ninety six‐Deep Square Well (96‐DSW) microtiter plates were used for microbial culture and enzyme‐catalyzed conversion, where plate preparation, reagent addition, and sampling were all carried out without manual intervention. The adoption of automated robotic procedures has enabled the rapid collection of kinetic data for whole process optimization at the microscale. This high‐throughput approach enabled a range of amino acid sources for media formulation and well fill volumes to be investigated highlighting when nutritional limitation and oxygen limitations took place. The automated process sequence has been applied to test six CHMO substrates including norcamphor and cycloheptanone all of which to the best of our knowledge have yet to be tested with E. coli TOP10 [pQR210]. Substrate specificity and product selectivity were effectively demonstrated and compared to both the natural substrate cyclohexanone and the model substrate bicyclo[3.2.0]hept‐2‐en‐6‐one used to demonstrate asymmetric synthesis. The results obtained using the developed process sequence could be reproduced at 75 L scale when a matched oxygen transfer coefficient kLa approach was used. The study demonstrates how automated microscale processing enables the rapid collection of kinetic quantitative data in a robust manner with clear implications for accelerating bioprocess development, optimization, and scale‐up. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012
NBS1 deficiency promotes genome instability by affecting DNA damage signaling pathway and impairing telomere integrity
Authors: Hou Yan Yan , Toh Meng Tiak , Wang Xueying
Published: December 2011

Studies revealed that Nijmegen Breakage Syndrome protein 1 (NBS1) plays an important role in maintaining genome stability, but the underlying mechanism is controversial and elusive. Our results using clinical samples showed that NBS1 was involved in ataxia‐telangiectasia mutated (ATM)‐dependent pathway. NBS1 deficiency severely affected the phosphorylation of ATM as well as its downstream targets. BrdU proliferation assay revealed a delay of NBS cells in inhibiting DNA synthesis after Doxorubicin (Dox) treatment. In addition, under higher concentrations of Dox, NBS cells exhibited a much lower level of apoptosis compared to their normal counterparts, indicating a resistance to Dox treatment. Accelerated telomere shortening was also observed in NBS fibroblasts, consistent with an early onset of cellular replicative senescence in vitro. This abnormality may be due to the shelterin protein telomeric binding factor 2 (TRF2) which was found to be upregulated in NBS fibroblasts. The dysregulation of telomere shortening rate and of TRF2 expression level leads to telomere fusions and cellular aneuploidy in NBS cells. Collectively, our results suggest a possible mechanism that NBS1 deficiency simultaneously affects ATM‐dependent DNA damage signaling and TRF2‐regulated telomere maintenance, which synergistically lead to genomic abnormalities. Copyright © 2011 John Wiley & Sons, Ltd.
Fluorinated Metal–Organic Frameworks: Advantageous for Higher H2 and CO2 Adsorption or Not?
Authors: Pachfule Pradip , Chen Yifei , Jiang Jianwen , Banerjee Rahul
Published: December 2011

The synthesis, structure, and gas adsorption properties of three new metal–organic frameworks (MOFs) designed from isonicotinic acid (INA) and its fluorinated analogue 3‐fluoroisonicotinic acid (FINA) along with CoII as the metal center have been reported. Co‐INA‐1 ([Co3(INA)4(O)(C2H5OH)3][NO3]⋅C2H5OH⋅3 H2O; INA=isonicotinic acid) and Co‐INA‐2 ([Co(INA)2]⋅DMF) are structural isomers as are Co‐FINA‐1 ([Co3(FINA)4(O)(C2H5OH)2]⋅H2O; FINA=3‐fluoroisonicotinic acid) and Co‐FINA‐2 ([Co(FINA)2]⋅H2O), but the most important thing to note here is that Co‐INA‐1 and Co‐FINA‐1 are isostructural as are Co‐INA‐2 and Co‐FINA‐2. The effect of partial introduction of fluorine atoms into the framework on the gas uptake properties of MOFs having similar structures has been analyzed experimentally and computationally in isostructural MOFs.
Synthesis of Bis‐indole Carboxamides as G‐Quadruplex Stabilizing and Inducing Ligands
Authors: Dash Jyotirmayee , Nath Das Rabindra , Hegde Nagaratna , Pantoş G. Dan , Shirude Pravin S. , Balasubramanian Shankar
Published: December 2011

The design and synthesis of a series of bis‐indole carboxamides with varying amine containing side chains as G‐quadruplex DNA stabilising small molecules are reported. Their interactions with quadruplexes have been evaluated by means of Förster resonance energy transfer (FRET) melting analysis, UV/Vis spectroscopy, circular dichroism spectroscopy and molecular modelling studies. FRET analysis indicates that these ligands exhibit significant selectivity for quadruplex over duplex DNA, and the position of the carboxamide side chains is of paramount importance in G‐quadruplex stabilisation. UV/Vis titration studies reveal that bis‐indole ligands bind tightly to quadruplexes and show a three‐ to fivefold preference for c‐kit2 over h‐telo quadruplex DNA. CD studies revealed that bis‐indole carboxamide with a central pyridine ring induces the formation of a single, antiparallel, conformation of the h‐telo quadruplex in the presence and absence of added salt. The chirality of h‐telo quadruplex was transferred to the achiral ligand (induced CD) and the formation of a preferred atropisomer was observed.
ChemInform Abstract: Cyclopropyl Carbinol Rearrangement for Benzo‐Fused Nitrogen Ring Synthesis.
Authors: Kothandaraman Prasath , Huang Chuhui , Susanti Dewi , Rao Weidong , Chan Philip Wai Hong
Published: December 2011

Two types of products are chemoselectively formed by the gold/silver catalyzed reaction.
Crystallisation of ferrous sulphate heptahydrate: Experiments and modelling
Authors: Shaikh Latif , Pandit Aniruddha , Ranade Vivek
Published: December 2011

Crystallisation is an industrially important unit operation for purifying and separating chemical mixtures. A generic crystallisation modelling framework has been implemented in the general process modelling system (gPROMS) software (of PSE, UK). This framework can be used to model the batch cooling crystallisation of ferrous sulphate heptahydrate (FSH). The parameter estimation and sensitivity of the predicted results with various numerical parameters was studied for batch crystalliser. An Excel “front‐end” to the gPROMS model was developed to facilitate the interactive use of the model. © 2011 Canadian Society for Chemical Engineering
An optical platform for cell tracking in adult zebrafish
Authors: Zhang Li , Alt Clemens , Li Pulin , White Richard M. , Zon Leonard I. , Wei Xunbin , Lin Charles P.
Published: December 2011

Adult zebrafish are being increasingly used as a model in cancer and stem cell research. Here we describe an integrated optical system that combines a laser scanning confocal microscope (LSCM) and an in vivo flow cytometer (IVFC) for simultaneous visualization and cell quantification. The system is set up specifically for non‐invasive tracking of both stationary and circulating cells in adult zebrafish (casper) that have been engineered to be optically transparent. Confocal imaging in this instrument serves the dual purpose of visualizing fish tissue microstructure and an imaging‐based guide to locate a suitable vessel for quantitative analysis of circulating cells by IVFC. We demonstrate initial testing of this novel instrument by imaging the transparent adult zebrafish casper vasculature and tracking circulating cells in CD41‐GFP/Gata1‐DsRed transgenic fish whose thrombocytes/erythrocytes express the green and red fluorescent proteins. In vivo measurements allow cells to be tracked under physiological conditions in the same fish over time, without drawing blood samples or sacrificing animals. We also discuss the potential applications of this instrument in biomedical research. © 2011 International Society for Advancement of Cytometry
Di(2‐ethylhexyl) phthalate metabolites as markers for blood transfusion in doping control: Intra‐individual variability of urinary concentrations
Authors: Solymos E. , Guddat S. , Geyer H. , Thomas A. , Thevis M. , Schänzer W.
Published: December 2011

To indicate homologous or autologous blood transfusion in sports drug testing, quantification of increased urinary concentrations of di(2‐ethylhexyl) phthalate (DEHP) metabolites presents a promising approach; however, the possible intra‐individual variation of the metabolite concentrations over time has not been well characterized.

The aim of this study was to explore the intra‐individual variability of urinary DEHP metabolites among seven volunteers without special occupational exposure to DEHP during one week (n = 253) in order to investigate the possibility of increased urinary concentrations of the metabolites caused by, for example, residential, dietary, or environmental exposure.

Quantification of three DEHP metabolites – mono(2‐ethylhexyl) phthalate, mono(2‐ethyl‐5‐oxohexyl) phthalate, and mono(2‐ethyl‐5‐hydroxyhexyl) phthalate – was accomplished after enzymatic hydrolysis of urinary glucuronide conjugates and direct injection using isotope‐dilution liquid chromatography‐tandem mass spectrometry.

Although urinary concentrations of DEHP metabolites showed considerable intra‐individual variation, no increased values were observed comparable to the concentrations measured in urine specimens collected after blood transfusion. Copyright © 2011 John Wiley & Sons, Ltd.
Simulated climate change conditions unveil the toxic potential of the fungicide pyrimethanil on the midge Chironomus riparius: a multigeneration experiment
Authors: Müller Ruth , Seeland Anne , Jagodzinski Lucas S. , Diogo Joao B. , Nowak Carsten , Oehlmann Jörg
Published: December 2011

Although it has been suggested that temperature increase may alter the toxic potential of environmental pollutants, few studies have investigated the potential risk of chemical stressors for wildlife under Global Climate Change (GCC) impact. We applied a bifactorial multigeneration study in order to test if GCC conditions alter the effects of low pesticide concentrations on life history and genetic diversity of the aquatic model organism Chironomus riparius. Experimental populations of the species were chronically exposed to a low concentration of the fungicide pyrimethanil (half of the no‐observed‐adverse‐effect concentration: NOAEC/2) under two dynamic present‐day temperature simulations (11.0–22.7°C; 14.0–25.2°C) and one future scenario (16.5–28.1°C). During the 140‐day multigeneration study, survival, emergence, reproduction, population growth, and genetic diversity of C. riparius were analyzed. Our results reveal that high temperature and pyrimethanil act synergistically on the midge C. riparius. In simulated present‐day scenarios, a NOAEC/2 of pyrimethanil as derived from a life‐cycle toxicity test provoked only slight‐to‐moderate beneficial or adverse effects on C. riparius. In contrast, exposure to a NOAEC/2 concentration of pyrimethanil at a thermal situation likely for a summer under GCC conditions uncovered adverse effects on mortality and population growth rate. In addition, genetic diversity was considerably reduced by pyrimethanil in the future scenario, but only slightly under current climatic conditions. Our multigeneration study under near‐natural (climatic) conditions indicates that not only the impact of climate change, but also low concentrations of pesticides may pose a reasonable risk for aquatic insects in future.