bluuebunny/crossref_metadata_2025 huggingface dataset:
Functionalization of heterocyclic compounds using polyfunctional magnesium and zinc reagents
Authors: Knochel Paul , Schade Matthias A , Bernhardt Sebastian , Manolikakes Georg , Metzger Albrecht , Piller Fabian M , Rohbogner Christoph J , Mosrin Marc
Published: September 2011

In this review we summarize the most important procedures for the preparation of functionalized organzinc and organomagnesium reagents. In addition, new methods for the preparation of polyfunctional aryl- and heteroaryl zinc- and magnesium compounds, as well as new Pd-catalyzed cross-coupling reactions, are reported herein. Experimental details are given for the most important reactions in the Supporting Information File 1 of this article.
Governance Structures
Authors: Gottschalk P.
Published: September 2011

The overall objective of this chapter is to concentrate on the important issues of strategy, structure, and management of IT outsourcing arrangements. Using well-known theoretical perspectives described earlier in this book and experience earned from several business case studies in this book, we present a governance model for successful management of IT outsourcing relationships.
Sequential Release of BMP-7 and VEGF from the PLGA/AK-Gelatin Composite Scaffolds
Authors: Liu Gang , Fan W. , Miao X. , Xiao Yin , Good David , Wei M.Q.
Published: September 2011

Vascular endothelial growth factor (VEGF) and bone morphogenetic proteins (BMP-7) are key regulators of angiogenesis and osteogenesis during bone regeneration. The aim of this study was to investigate the possibility of realizing sequential release of the two growth factors using a novel composite scaffold. Poly(lactic-co-glycolic acid) (PLGA)-Akermanite (AK) microspheres were used to make the composite scaffold, which was then loaded with BMP-7, followed by embedding in a gelatin hydrogel matrix loaded with VEGF. The release profiles of the growth factors were studied and selected osteogenic related markers of bone marrow stromal cells (BMSCs) were analysed. It was shown that the composite scaffolds exhibited a fast initial burst release of VEGF within the first 3 days and a sustained slow release of BMP-7 over the full period of 20 days. The in vitro proliferation and differentiation of the BMSCs cultured in the osteogenic medium were enhanced by 1 to 2 times, resulting from the additionally and sequentially release of growth factors from the PLGA-AK/gelatin composite scaffolds.
Cohesin Regulates MHC Class II Genes through Interactions with MHC Class II Insulators
Authors: Majumder Parimal , Boss Jeremy M.
Published: September 2011

Cohesin is a multiprotein, ringed complex that is most well-known for its role in stabilizing the association of sister chromatids between S phase and M. More recently, cohesin was found to be associated with transcriptional insulators, elements that are associated with the organization of chromatin into regulatory domains. The human MHC class II (MHC-II) locus contains 10 intergenic elements, termed MHC-II insulators, which bind the transcriptional insulator protein CCCTC-binding factor. MHC-II insulators interact with each other, forming a base architecture of discrete loops and potential regulatory domains. When MHC-II genes are expressed, their proximal promoter regulatory regions reorganize to the foci established by the interacting MHC-II insulators. MHC-II insulators also bind cohesin, but the functional role of cohesin in regulating this system is not known. In this article, we show that the binding of cohesin to MHC-II insulators occurred irrespective of MHC-II expression but was required for optimal expression of the HLA-DR and HLA-DQ genes. In a DNA-dependent manner, cohesin subunits interacted with CCCTC-binding factor and the MHC-II–specific transcription factors regulatory factor X and CIITA. Intriguingly, cohesin subunits were important for DNA looping interactions between the HLA-DRA promoter region and a 5′ MHC-II insulator but were not required for interactions between the MHC-II insulators themselves. This latter observation introduces cohesin as a regulator of MHC-II expression by initiating or stabilizing MHC-II promoter regulatory element interactions with the MHC-II insulator elements, events that are required for maximal MHC-II transcription.
Impact of the isoprene photochemical cascade on tropical ozone
Authors: Paulot F. , Henze D. K. , Wennberg P. O.
Published: September 2011

Abstract. Tropical tropospheric ozone affects Earth's radiative forcing and the oxidative capacity of the atmosphere. Considerable work has been devoted to the study of the processes controlling its budget. Yet, large discrepancies between simulated and observed tropical tropospheric ozone remain. Here, we characterize some of the mechanisms by which the photochemistry of isoprene impacts the budget of tropical ozone. At the regional scale, we find that isoprene nitrates can account for up to 70% of the local NOx sink. Using forward sensitivity simulations, we show that the modulation of Ox by isoprene nitrates photochemistry can be characterized by their net impact on NOx. We use adjoint sensitivity simulations to demonstrate that the oxidation of isoprene can affect ozone outside of continental regions through the transport of NOx over near-shore regions (e.g., South Atlantic) and the oxidation of isoprene outside of the boundary layer far from its emissions regions. The latter mechanism is promoted by the simulated low boundary-layer oxidative conditions. In our simulation, ~20% of the isoprene is oxidized above the boundary layer in the tropics. Changes in the interplay between regional and global effect are discussed in light of the forecasted increase in anthropogenic emissions in tropical regions.
Comparison of HDO measurements from Envisat/MIPAS with observations by Odin/SMR and SCISAT/ACE-FTS
Authors: Lossow S. , Steinwagner J. , Urban J. , Dupuy E. , Boone C. D. , Kellmann S. , Linden A. , Kiefer M. , Grabowski U. , Glatthor N. , Höpfner M. , Röckmann T. , Murtagh D. P. , Walker K. A. , Bernath P. F. , von Clarmann T. , Stiller G. P.
Published: September 2011

Abstract. Measurements of thermal emission in the mid-infrared by Envisat/MIPAS allow the retrieval of HDO information roughly in the altitude range between 10 km and 50 km. From June 2002 to March 2004 MIPAS performed measurements in the full spectral resolution mode. To assess the quality of the HDO data set obtained during that period comparisons with measurements by Odin/SMR and SCISAT/ACE-FTS were performed. Comparisons were made on profile-to-profile basis as well as using seasonal and monthly averages. All in all the comparisons yield favourable results. The largest deviations between MIPAS and ACE-FTS are observed below 15 km, where relative deviations can occasionally exceed 100%. Despite these deviations in the absolute amount of HDO the latitudinal structures observed by both instruments are consistent in this altitude range. Between 15 km and 20 km there is less good agreement, in particular in the Antarctic during winter and spring. Also in the tropics some deviations are found. Above 20 km there is a high consistency in the structures observed by all three instruments. MIPAS and ACE-FTS typically agree within 10%, with MIPAS mostly showing higher abundances than ACE-FTS. Both data sets show considerably more HDO than SMR. This bias can be explained basically by uncertainties in spectroscopic parameters. Above 40 km, where the MIPAS HDO retrieval reaches its limits, still good agreement with the structures observed by SMR is found for most seasons. This puts some confidence in the MIPAS data at these altitudes.
A laboratory experiment of intact polar lipid degradation in sandy sediments
Authors: Logemann J. , Graue J. , Köster J. , Engelen B. , Rullkötter J. , Cypionka H.
Published: September 2011

Abstract. Intact polar lipids (IPLs) are considered biomarkers for living biomass. Their degradation in marine sediments, however, is poorly understood and complicates interpretation of their occurrence in geological samples. To investigate the turnover of IPLs, a degradation experiment with anoxic sandy sediments from the North Sea was conducted. Intact cells of two organisms that do not naturally occur in North Sea sediments were chosen as IPL sources: (i) Saccharomyces cerevisiae, representative for ester-bound acyl lipids that also occur in Bacteria, and (ii) the archaeon Haloferax volcanii, representative for ether-bound isoprenoid lipids. Surprisingly, IPLs with phosphoester-bound head groups showed approximately the same degradation rate as IPLs with glycosidic head groups. Furthermore, the results indicate a relatively fast degradation of S. cerevisiae IPLs with ester-bound moieties (analogs of bacterial membrane lipids) and no significant degradation of archaeal IPLs with ether-bound moieties. Pore water and 16S rRNA-based DGGE analysis showed only a minor influence of the IPL source on microbial metabolism and community profiles. Due to our results, the IPL-based quantification of Archaea and Bacteria should be interpreted with caution.
Development of a Biomimetic Enzyme‐linked Immunosorbent Assay Method for the Determination of Methimazole in Urine Sample
Authors: Wang Jun‐Ping , Tang Wei‐Wei , Fang Guo‐Zhen , Pan Ming‐Fei , Wang Shuo
Published: September 2011

A fast and direct competitive biomimetic enzyme‐linked immunosorbent assay (BELISA) method was developed for the determination of methimazole (MMZ) in urine sample based on a molecularly imprinted film as an artificial antibody. This is the first example to monitor methimazole with a direct competitive biomimetic enzyme‐linked immunosorbent assay (BELISA) method. The imprinted film was directly synthesized on the well surface of MaxiSorp polystyrene 96‐well plate and characterized. The results showed that it exhibited an antibody‐like binding ability, rapid adsorption speed, high stability, which was particularly advantageous and suitable for BELISA development. The BELISA method established in this paper had a higher selectivity for MMZ than for the structurally related compounds and the IC50 (calculated as the concentration giving 50% inhibition of color development) and the detection limit values under optimized experimental conditions were 70 ± 4 μg L‐1 and 0.9 ± 0.04 μg L‐1, respectively. The method was applied to the determination of MMZ in spiked urine sample with excellent recoveries ranging from 90% to 95%, and the imprinted film was able to be reused for 20 times without loss of sensitivity. The results obtained by BELISA correlated well with that obtained by the high performance liquid chromatography (HPLC) method.
Determination of Nonylphenol Polyethoxylates in Industrial Water Effluents by Liquid Chromatography/Linear Ion Trap Mass Spectrometry
Authors: Lee Ren‐Jye , Hsu Kuo‐En , Chu Ching‐Ping , Chung Yu‐Jen , Lee Maw‐Rong
Published: September 2011

In this study, liquid chromatography/mass spectrometry was used to analyze the trace amounts of nonylphenol polyethoxylates (NPnEOs) in industrial water effluents. The modifier of acetic acid added in mobile phase and the atmospheric pressure chemical ionization (APCI) coupled with linear ion trap mass spectrometry were adopted to improve the sensitivity of NPnEOs analysis. The modification extraction technique of NIEA W801.50B method announced by Taiwan Environmental Protection Agency was used as sample preparation. The analytical results show that the LODs of NPnEO analytes were 0.02‐10 ng/mL. The proposed method has been successfully applied to monitor trace NPnEOs in real industrial water effluents.
Study on the Interaction of Nd3+ with Human Serum Albumin at Molecular Level
Authors: Yuan Dong , Shen Zhong‐Lan , Liu Ru‐Tao , Wei Pei‐Hai , Gao Can‐Zhu
Published: September 2011

Neodymium is applied widely in agriculture to improve crop nutrition and incidentally in fertilizers, yet little is known of its effect on the biological function of human serum albumin (HSA). The interaction of Nd3+ to HSA has been investigated mainly by fluorescence spectra, UV–vis absorption spectra and circular dichroism (CD) under simulative physiological conditions. Fluorescence data revealed that the quenching mechanism of HSA by Nd3+ was a static quenching process and the binding constant is 5.71 × 104 L mol‐1 and the number of binding sites is 1 at 292 K. The thermodynamic parameters (ΔH0 = ‐20.79 kJ mol‐1, ΔG0 = ‐26.58 kJ mol‐1, and ΔS0 = 19.85 J mol‐1 K‐1) indicate that electrostatic effect between the protein and Nd3+ is the main binding force. The distance r = 2.91 nm between donor (HSA) and acceptor (Nd3+) was obtained according to Förster's nonradiative energy transfer. In addition, UV–vis, CD and synchronous fluorescence results showed that the addition of Nd3+ changed the conformation of HSA.
Nonlinear backward Raman scattering in the short laser pulse interaction with a cold underdense transversely magnetized plasma
Authors: Paknezhad Alireza , Dorranian Davoud
Published: September 2011

Raman backward scattering is investigated in the interaction of linearly polarized ultra short laser pulse with a homogenous cold underdense magnetized plasma by taking into account the relativistic effect and the effect of nonlinearity up to third order. The plasma is embedded in a uniform magnetic field perpendicular to both of propagation direction and electric vector of the radiation field. Nonlinear wave equation is set up and differential equations, which model the instability, are derived. Using of the Fourier transformation, analytical solutions are obtained for a set of physically relevant initial conditions and the temporal growth rate of instability is calculated. Results are significantly different in comparison with lower order computations. The growth rate of backward Raman scattering shows an increase due to the presence of external magnetic field as well as nonlinear effects.
Persistent multiferroicity without magnetoelectric effects in CuO
Authors: Wang Fen , Zou Tao , Liu Yi , Yan Li-Qin , Sun Young
Published: September 2011

Multiferroicity and magnetoelectric effects in CuO have been investigated by measurements of magnetization, dielectric constant, and electric polarization with and without magnetic fields. Dielectric anomalies which indicate ferroelectric transitions were observed at two magnetic transition temperatures. Ferroelectric polarization was well detected in the incommensurate spiral phase. However, both dielectric constant and polarization have little changes in a 7 T magnetic field. Our study suggests that although with a high multiferroic temperature, the spiral spin structure in CuO is very stable and the induced ferroelectricity sustains even in a high magnetic field, which results in little magnetoelectric effects.
Genetic diversity between ex situ and in situ samples of Agropyron cristatum (L.) Gaertn. based on simple sequence repeat molecular markers
Authors: Che Y. H. , Yang Y. P. , Yang X. M. , Li X. Q. , Li L. H.
Published: September 2011

Fifty-five populations of Agropyron cristatum (L.) Gaertn., both ex situ conserved and in situ collected and originating from northern China, were analysed using 29 polymorphic simple sequence repeat (SSR) primers mapped on the wheat genome. The study showed ex situ and in situ populations had different numbers of alleles and allelic frequencies in 17 of the 29 primer pairs. The SSR markers revealed significant genetic differences between gene bank-conserved and in situ recollected populations from similar ecogeographical regions. AMOVA analysis indicated 15% of the total variation resided between groups, and 85% resided within groups. According to a dendrogram generated by unweighted pair group method with arithmetic average cluster analysis based on Nei’s genetic distance matrix and principal coordinate analysis, recollected and gene bank-conserved populations from the same regions were distinguished. The results indicate that both in situ and ex situ conservation play complementary roles in the conservation of A. cristatum.
Thermoluminescence as a probe in bioactivity studies; the case of 58S sol–gel bioactive glass
Authors: Polymeris George S , Goudouri Ourania Menti , Kontonasaki Eleana , Paraskevopoulos Konstantinos M , Tsirliganis Nestor C , Kitis George
Published: September 2011

The formation of a carbonated hydroxyapatite (HCAp) layer on the surface of bioactive materials is the main reaction that takes place upon their immersion in physiological fluids. To date, all techniques used for the identification of this HCAp formation are rather time consuming and not well suited to detailed and rapid monitoring of changes in the bioactivity response of the material. The aim of this work is to explore the possibility of using thermoluminescence (TL) for the discrimination between different bioactive responses in the case of the 58S bioactive glass. Results provided strong indications that the 110 °C TL peak of quartz can be used effectively in the study of the bioactive behaviour of 58S bioactive glass, since it is unambiguously present in all samples and does not require deconvolution analysis. Furthermore, the intensity of the 110 °C TL peak is proven to be very sensitive to the different bioactive responses, identifying the loss of silica which takes place at the first stages of the sequence. The discontinuities of the 110 °C TL peak intensity plot versus immersion time at 8 and 1440 min provide experimental indications regarding the timescale for both the beginning of amorphous CaP formation as well as the end of crystalline hydroxyl-apatite formation respectively, while the spike in the sensitization of the 110 °C TL peak, which was observed for immersion times ranging between 20 and 40 min, could be an experimental feature indicating the beginning of the crystalline HCAp formation.
Pension Funds’ Asset Allocation and Participant Age: A Test of the Life‐Cycle Model
Authors: Bikker Jacob A. , Broeders Dirk W. G. A. , Hollanders David A. , Ponds Eduard H. M.
Published: September 2011

Abstract

This article examines the impact of participants’ age distribution on the asset allocation of Dutch pension funds, using a unique data set of pension fund investment plans for 2007. Theory predicts a negative effect of age on (strategic) equity exposures. We observe that a 1‐year higher average age in active participants leads to a significant and robust reduction of the strategic equity exposure by around 0.5 percentage point. Larger pension funds show a stronger age‐equity exposure effect. The average age of active participants influences investment behavior more strongly than the average age of all participants, which is plausible as retirees no longer possess any human capital.
Individual‐based trait analyses reveal assembly patterns in tree sapling communities
Authors: Carlucci Marcos B. , Streit Helena , Duarte Leandro D.S. , Pillar Valério D.
Published: September 2011

Question

Are trait‐convergence assembly patterns (TCAP) and/or trait‐divergence assembly patterns (TDAP) of tree sapling communities related to microhabitat gradients in forest patches? If so, which traits are related to such patterns? What are the niche mechanisms potentially responsible for community assembly?

Location

Grassland–forest mosaic in Serra do Sudeste region, southern Brazil (ca. 30.8°S, 53.1°W).

Methods

We used individual‐based trait information of 1132 tree saplings in 40 plots along gradients of canopy openness and grazing intensity in forest patches in southern Brazil. We used a trait‐based approach, bypassing taxonomic identification, as a first assessment of sapling community assembly in forest patches.

Results

Both TCAP and TDAP indicate niche mechanisms underlying assembly of tree sapling communities. Specific leaf area (SLA), mean leaf area (LA) and relative abundance of toothed leaf margin (TLM) maximized TCAP. SLA and TLM tended to increase under more closed canopies, whereas LA had higher values at intermediate canopy openness. SLA and LA maximized TDAP and tended to vary more in more closed canopies, whereas SLA and presence of spines, which also maximized TDAP, showed higher variation under lower grazing intensity.

Conclusion

The taxon‐free approach was very useful to infer niche mechanisms of tree sapling assembly in forest patches. By adopting an individual‐based trait approach, we assumed that both intra‐specific and intra‐population trait variability were relevant for revealing assembly patterns. We highlight that the use of individual‐based trait data in a metacommunity framework is an excellent way to evaluate TCAP and TDAP at the metacommunity scale, since it takes into account the entire variation of traits throughout communities.
West Nile virus: North American experience
Authors: HOFMEISTER Erik K.
Published: September 2011

West Nile virus, a mosquito‐vectored flavivirus of the Japanese encephalitis serogroup, was first detected in North America following an epizootic in the New York City area in 1999. In the intervening 11 years since the arrival of the virus in North America, it has crossed the contiguous USA, entered the Canadian provinces bordering the USA, and has been reported in the Caribbean islands, Mexico, Central America and, more recently, South America. West Nile virus has been reported in over 300 species of birds in the USA and has caused the deaths of thousands of birds, local population declines of some avian species, the clinical illness and deaths of thousands of domestic horses, and the clinical disease in over 30 000 Americans and the deaths of over 1000. Prior to the emergence of West Nile virus in North America, St. Louis encephalitis virus and Dengue virus were the only other known mosquito‐transmitted flaviviruses in North America capable of causing human disease. This review will discuss the North American experience with mosquito‐borne flavivirus prior to the arrival of West Nile virus, the entry and spread of West Nile virus in North America, effects on wild bird populations, genetic changes in the virus, and the current state of West Nile virus transmission.
Drivers’ Perception of Loss of Adherence in Bends: Influence of Motion Rendering
Authors: Denoual Thomas , Mars Franck , Petiot Jean-François , Reymond Gilles , Kemeny Andras
Published: September 2011

This paper investigated drivers’ perception during situations of loss of adherence (LOA) in static and dynamic driving simulators. The intensity and duration of the LOA were manipulated. Results show that drivers were able to correctly discriminate the different conditions of LOA in both simulators. They also highlight the importance of nonvisual information, with steering wheel haptic cues predominating for the static simulator and both the steering wheel and motion platform predominating for the dynamic simulator. This study is a first step in developing an evaluation method for electronic stability control (ESC) handling in high-performance simulator experiments.
Fimbrial Profiles Predict Virulence of Uropathogenic Escherichia coli Strains: Contribution of Ygi and Yad Fimbriae
Authors: Spurbeck Rachel R. , Stapleton Ann E. , Johnson James R. , Walk Seth T. , Hooton Thomas M. , Mobley Harry L. T.
Published: September 2011

Escherichia coli
, a cause of ∼90% of urinary tract infections (UTI), utilizes fimbrial adhesins to colonize the uroepithelium. Pyelonephritis isolate
E. coli
CFT073 carries 12 fimbrial operons, 5 of which have never been studied. Using multiplex PCR, the prevalence of these 12 and 3 additional fimbrial types was determined for a collection of 303
E. coli
isolates (57 human commensal, 32 animal commensal, 54 asymptomatic bacteriuria, 45 complicated UTI, 38 uncomplicated cystitis, and 77 pyelonephritis). The number of fimbrial types per
E. coli
isolate was distributed bimodally: those with low (3.2 ± 1.1) and those with high (8.3 ± 1.3) numbers of fimbrial types (means ± standard errors of the means). The fimbrial genes
ygiL
,
yadN
,
yfcV
, and
c2395
were significantly more prevalent among urine isolates than human commensal isolates. The effect of deletion of Ygi and Yad fimbrial operons on growth, motility, biofilm formation, adherence to immortalized human epithelial cells, and pathogenesis in the mouse model of UTI was examined. Yad fimbriae were necessary for wild-type levels of adherence to a bladder epithelial cell line and for biofilm formation. Deletion of these fimbrial genes increased motility. Ygi fimbriae were necessary for wild-type levels of adherence to a human embryonic kidney cell line, biofilm formation, and
in vivo
fitness in the urine and kidneys. Complementation of each fimbrial mutant restored wild-type levels of motility, biofilm formation, adherence and, for
ygi
,
in vivo
fitness. A double deletion strain, Δ
ygi Δyad
, was attenuated in the urine, bladder, and kidneys in the mouse model, demonstrating that these fimbriae contribute to uropathogenesis.
Inhibition of Indoleamine 2,3-Dioxygenase Activity by Levo-1-Methyl Tryptophan Blocks Gamma Interferon-Induced Chlamydia trachomatis Persistence in Human Epithelial Cells
Authors: Ibana Joyce A. , Belland Robert J. , Zea Arnold H. , Schust Danny J. , Nagamatsu Takeshi , AbdelRahman Yasser M. , Tate David J. , Beatty Wandy L. , Aiyar Ashok A. , Quayle Alison J.
Published: September 2011

Gamma interferon (IFN-γ) induces expression of the tryptophan-catabolizing enzyme indoleamine 2,3-dioxygenase (IDO1) in human epithelial cells, the permissive cells for the obligate intracellular bacterium
Chlamydia trachomatis
. IDO1 depletes tryptophan by catabolizing it to kynurenine with consequences for
C. trachomatis
, which is a tryptophan auxotroph.
In vitro
studies reveal that tryptophan depletion can result in the formation of persistent (viable but noncultivable) chlamydial forms. Here, we tested the effects of the IDO1 inhibitor, levo-1-methyl-tryptophan (L-1MT), on IFN-γ-induced
C. trachomatis
persistence. We found that addition of 0.2 mM L-1MT to IFN-γ-exposed infected HeLa cell cultures restricted IDO1 activity at the mid-stage (20 h postinfection [hpi]) of the chlamydial developmental cycle. This delayed tryptophan depletion until the late stage (38 hpi) of the cycle. Parallel morphological and gene expression studies indicated a consequence of the delay was a block in the induction of
C. trachomatis
persistence by IFN-γ. Furthermore, L-1MT addition allowed
C. trachomatis
to undergo secondary differentiation, albeit with limited productive multiplication of the bacterium. IFN-γ-induced persistent infections in epithelial cells have been previously reported to be more resistant to doxycycline than normal productive infections
in vitro
. Pertinent to this observation, we found that L-1MT significantly improved the efficacy of doxycycline in clearing persistent
C. trachomatis
forms. It has been postulated that persistent forms of
C. trachomatis
may contribute to chronic chlamydial disease. Our findings suggest that IDO1 inhibitors such as L-1MT might provide a novel means to investigate, and potentially target, persistent chlamydial forms, particularly in conjunction with conventional therapeutics.
Complete Genome Sequence of Alicyclobacillus acidocaldarius Strain Tc-4-1
Authors: Chen Yaping , He Yongzhi , Zhang Bing , Yang Jin , Li Wenjie , Dong Zhiyang , Hu Songnian
Published: September 2011

Alicyclobacillus acidocaldarius
strain Tc-4-1 was initially isolated from a hot spring in Tengchong, China. This organism is both thermophilic and acidophilic. It can produce heat- and acid-stable enzymes, such as amylase and esterase, which may be important in industry. Here we report the whole genome sequence of the strain.
Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1
Authors: Kim Byung Kwon , Jung Man-Young , Yu Dong Su , Park Soo-Je , Oh Tae Kwang , Rhee Sung-Keun , Kim Jihyun F.
Published: September 2011

Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, “
Candidatus
Nitrosopumilus koreensis” MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.
ANALYTICAL MODEL FOR OPTICAL BISTABILITY IN LASER WITH SATURABLE ABSORBER
Authors: DJABI S. , BOUDOUKHA H. , MEGUELLATI S.
Published: September 2011

In this paper, we develop a theoretical model that accurately describes the nonlinear phenomenon of optical bistability in Fabry-Perot laser containing a saturable absorber "LSA". We present an analytical model for optical bistability in a LSA. The physics of optical bistability in a classical optical resonant system such as Fabry-Perot etalon has been well-established, and can be described by simple analytical models. The photon intensities were determined as a function of the pumping rate of the active medium, and we analyzed the linear stability of the stationary solutions obtained.
Heterogeneous network-based trust analysis
Authors: Gupta Manish , Han Jiawei
Published: September 2011

Different information sources publish information with different degrees of correctness and originality. False information can often result in considerable damage. Hence, trustworthinessof information is an important issue in this datadriven world economy. Reputation of different agents in a network has been studied earlier in a variety of domains like e-commerce, social sciences, sensor networks, and P2P networks. Recently there has been work in the data mining community on performing trust analysis based on the data provided by multiple information providers for different objects, and such agents and their provided information about data objects form a multi-typed heterogeneous network. The trust analysis under such a framework is considered as heterogeneous network-based trust analysis. This paper will survey heterogeneous network-based trust analysis models and their applications. We would conclude with a summary and some thoughts on future research in the area.
Friendship Dynamics: Modelling Social Relationships through a Fuzzy Agent‐Based Simulation
Authors: Hassan Samer , Salgado Mauricio , Pavón Juan
Published: September 2011

Social relationships such as friendship and partner choice are ruled by the proximity principle, which states that the more similar two individuals are, the more likely they will become
friends. However, proximity, similarity, and friendship are concepts with blurred edges and imprecise grades of membership.
This study shows how to simulate these friendship dynamics in an agent‐based model that applies fuzzy sets theory to implement agent attributes, rules, and social relationships, explaining the process in detail. Although in principle it may be thought that the use of fuzzy sets theory makes agent‐based modelling more elaborated, in practice it saves the modeller from taking some arbitrary decisions on how to use crisp values for representing properties that are inherently fuzzy. The consequences of applying fuzzy sets and operations to define a fuzzy friendship relationship are compared with a simpler implementation, with crisp values. By integrating agent computational models and fuzzy set theory, this paper provides useful insights into scholars and practitioners to tackle the uncertainty inherent to social relationships in a systematic way.
Fuzzy‐Fated Filters of R0‐Algebras
Authors: Han Jeong Soon , Jun Young Bae , Kim Hee Sik
Published: September 2011

Fuzzy set theory of fated filters in R0‐algebras is considered. A characterization
of a fuzzy‐fated filter is established, and conditions for a fuzzy filter to
be a fuzzy‐fated filter are provided. The notion of an (∈, ∈∨q)‐fuzzy‐fated
filter is introduced. Characterizations of an (∈, ∈∨q)‐fuzzy‐fated filter are provided. Implication‐based fuzzy‐fated filters are discussed.
Inhibition of SAPK2/p38 Enhances Sensitivity to mTORC1 Inhibition by Blocking IRES-Mediated Translation Initiation in Glioblastoma
Authors: Cloninger Cheri , Bernath Andrew , Bashir Tariq , Holmes Brent , Artinian Nicholas , Ruegg Teresa , Anderson Lauren , Masri Janine , Lichtenstein Alan , Gera Joseph
Published: September 2011

A variety of mechanisms confer hypersensitivity of tumor cells to the macrolide rapamycin, the prototypic mTORC1 inhibitor. Several studies have shown that the status of the AKT kinase plays a critical role in determining hypersensitivity. Cancer cells in which AKT activity is elevated are exquisitely sensitive to mTORC1 inhibitors while cells in which the kinase is quiescent are relatively resistant. Our previous work has shown that a transcript-specific protein synthesis salvage pathway is operative in cells with quiescent AKT levels, maintaining the translation of crucial mRNAs involved in cell-cycle progression in the face of global eIF-4E–mediated translation inhibition. The activation of this salvage pathway is dependent on SAPK2/p38-mediated activation of IRES-dependent initiation of the cyclin D1 and c-MYC mRNAs, resulting in the maintenance of their protein expression levels. Here, we show that both genetic and pharmacologic inhibition of SAPK2/p38 in glioblastoma multiforme cells significantly reduces rapamycin-induced IRES-mediated translation initiation of cyclin D1 and c-MYC, resulting in increased G1 arrest in vitro and inhibition of tumor growth in xenografts. Moreover, we observed that the AKT-dependent signaling alterations seen in vitro are also displayed in engrafted tumors cells and were able to show that combined inhibitor treatments markedly reduced the mRNA translational state of cyclin D1 and c-MYC transcripts in tumors isolated from mice. These data support the combined use of SAPK2/p38 and mTORC1 inhibitors to achieve a synergistic antitumor therapeutic response, particularly in rapamycin-resistant quiescent AKT-containing cells. Mol Cancer Ther; 10(12); 2244–56. ©2011 AACR.
SDF-1α Induces PDGF-B Expression and the Differentiation of Bone Marrow Cells into Pericytes
Authors: Hamdan Randala , Zhou Zhichao , Kleinerman Eugenie S.
Published: September 2011

Platelet-derived growth factor B (PDGF-B) and its receptor, PDGFR-β, play a critical role in pericyte maturation; however, the mechanisms by which PDGF-B is upregulated in the tumor microenvironment remain unclear. We previously showed that upregulating stromal-derived factor, SDF-1α, in VEGF165-inhibited Ewing's sarcoma tumors (TC/siVEGF7-1) induced PDGF-B mRNA expression, increased infiltration and differentiation of bone marrow cells (BMC) into pericytes and, rescued tumor growth. The purpose of this study was to investigate the mechanism by which SDF-1α increased PDGF-B expression and the role of this pathway in BM-derived pericyte differentiation. We showed that SDF-1α induced expression of PDGF-B mRNA and protein both in vitro and in vivo. In contrast, inhibiting SDF-1α downregulated PDGF-B. We cloned the 2-kb pdgf-b promoter fragment and showed that SDF-1α activates PDGF-B via a transcriptional mechanism. Chromatin immunoprecipitation showed that the ELK-1 transcription factor binds to the pdgf-b promoter in response to SDF-1α. We confirmed the correlation between the SDF-1α/PDGF-B pathway and the differentiation of PDGFR-β+ BMCs into mature pericytes using an in vitro assay. These findings show that SDF-1α regulates PDGF-B expression and that this regulation plays a critical role in the differentiation of PDGFR-β+ BMCs into mature pericytes. Mol Cancer Res; 9(11); 1462–70. ©2011 AACR.
The appropriateness of single page of activation of the cardiac catheterization laboratory by emergency physician for patients with suspected ST-segment elevation myocardial infarction: a cohort study
Authors: Kim Soo Hyun , Oh Sang Hoon , Choi Seung Pill , Park Kyu Nam , Kim Young Min , Youn Chun Song
Published: September 2011

Background

The early use of reperfusion therapy has a significant effect on the prognosis of patients with ST-segment elevation myocardial infarction (STEMI), and it is recommended that emergency department (ED) physicians activate the cardiac catheterization laboratory (CCL) as soon as possible to treat these patients. The aim of this study was to examine the appropriateness of emergency physician activation of the CCL for patients with suspected STEMI. Inappropriate activations (i.e., false positive activations) were identified according to a variety of criteria.

Methods

All patients with emergency physician CCL activations between August 2009 and April 2011 were included in the study. False positive cases were defined according to ECG criteria and cardiologists' reviews of patients' initial clinical information.

Results

ED physicians used a STEMI page to activate the CCL 117 times. According to reviews by cardiologists, this activation was appropriate 89.8% of the time (in 105/117 cases). Truly unnecessary activation (i.e., cases in which STEMI was not identified by the cardiologists, no clear culprit coronary artery was present, no significant coronary artery disease and cardiac biomarkers were negative) occurred 5.1% of the time (in 6/117 cases).

Conclusions

CCL activation was appropriate for most patients and was unnecessary in a relatively small percentage of cases. This result supports the current recommendation for CCL activation by emergency physicians. Such early activation is a key strategy in the reduction of door-to-balloon time.
Blurred line between chemotactic chase and phagocytic consumption: an immunophysical single-cell perspective
Authors: Heinrich Volkmar , Lee Cheng-Yuk
Published: September 2011

An innate immune cell can sense a pathogen, either from a distance by recognizing chemoattractant stimuli or by direct physical contact. The pathogen is subsequently neutralized, which usually occurs through its phagocytic internalization. By investigating chemotaxis and phagocytosis from an immunophysical single-cell perspective, it now appears that the demarcation between these two processes is less distinct than originally thought. Several lines of evidence support this notion. First, chemotactic stimulation does not cease at the moment of initial contact between the cell and the pathogenic target. Second, even when classical chemotaxis of neutrophils is suppressed, the early cell response to contact with typical chemoattractant targets, such as zymosan, fungal spores or chemokine-coated particles, can still involve morphological attributes of chemotaxis. Recognizing that the changing morphology of motile cells is inextricably linked to physical cell behavior, this Commentary focuses on the mechanical aspects of the early response of innate immune cells to chemotactic and phagocytic stimuli. On the basis of this perspective, we propose that the combined study of chemotaxis and phagocytosis will, potentially, not only advance our grasp of the mechanisms underlying immune-cell motility but also open new lines of research that will promote a deeper understanding of the innate recognition of pathogens.
Policy Watch: Congressional Campaign Finance Reform
Authors: Levitt Steven D
Published: September 2011

While campaign finance reform attracts a lot of attention, it seems unlikely that such reform, at least in it current guise, will have a large impact on the functioning of the American political system. Recent studies have called into question the conventional wisdom that challenger campaign spending is especially effective, suggesting that attempts to close the gap between incumbent and challenger spending will have a smaller-than-expected impact on election outcomes. While it is safe to conclude that PACs wield some influence, it is not clear that limiting cash contributions will have a substantial effect.
Fuzzy Relational Clustering Based on Knowledge Mesh and its Application
Authors: Yang Ren Zi , Yan Hong Sen
Published: September 2011

A selection method of knowledge meshes based on fuzzy relational clustering is proposed. Considering the perfection degree, the matching degree among knowledge meshes and the level frame of knowledge mesh, the similarity function is defined. Its properties are proved. The similarity values between knowledge meshes are regarded as clustering data. The fuzzy relational matrix is constructed and decomposed. The knowledge meshes with high membership in each class are regarded as referenced knowledge meshes. Or the knowledge meshes in the class are further chosen according to user’s needs. Finally the example shows that the method is effective.
Root Node Vaccines for Bayesian Network Structure Learning Based on Immune Algorithm
Authors: Cai Zhi Qiang , Sun Shu Dong , Si Shu Bin , Wang Ning
Published: September 2011

To facilitate the application of Bayesian network in engineering fields, learning proper structure from dataset is one of the most efficiency Bayesian network modeling technique. In this paper, the description and characteristics of Bayesian networks and immune algorithms are discussed at first. Then, the extraction method of root node vaccines is proposed to accelerate the model structure learning process. Thirdly, the immune algorithm based method is also applied to search the best Bayesian network structure. Finally, the simulation studies based on a car start BN model are carried out and the results verify that the proposed Bayesian network structure learning method can build the objective structure from dataset more effectively and more efficiently with the root node vaccines.
Comparison of the Consumption of Resources between HTTP and SIP
Authors: Ravonimanantsoa N.Manda Vy , Randriamitantsoa P. Auguste
Published: September 2011

Currently, the development of research around VoIP experiences a tremendous growth. In the community of open source Asterisk represents a reliable alternative for a lower cost solution. In this same community as the SIP protocol is a supplement to the more asterisk PBX. To share the benefits claimed by proponents of free software co-existence with other Asterisk server is not yet proven. In this context this paper we show a comparison of the use of simplified resource material for the apache server using the HTTP protocol and server that uses the asterisk SIP.
Mining Implied Semantics of Database
Authors: Qu Zhen Xin
Published: September 2011

To mine richer semantics from relational database data, method of mining was discussed. Aiming at specific type of semantics, thirteen rules were proposed. Applying these rules some implied semantics was found naturally. The research shows that these rules have good maneuverability and high efficiency.
Mechanical Properties of Silicon-Germanium Nanotubes under Tensile and Compressive Loadings
Authors: Setoodeh A. , Attariani H. , Jahanshahi M.
Published: September 2011

The mechanical response of single-walled zigzag silicon-germanium nanotubes (SiGeNTs) under tensile and compressive loadings is modeled via atomistic simulation method. The inter-atomic forces are described using the Tersoff's empirical bond-order potential. Initially, the comparative simulations of the bond lengths are presented and quite accurate behavior of the model is demonstrated. Afterwards, the results of the total strain energy are used to establish an expression for evaluating Young's modulus of the nanotubes. Since different choices of wall thickness significantly affect the calculation of Young's modulus, the effective modulus of elasticity is introduced. This procedure provides an accurate means for predicting the elastic modulus of the nanotubes. Numerical simulations were also performed to investigate the buckling behavior of SiGeNTs. Dependence of the critical buckling load on diameter and length of the nanotubes is shown. Finally, the effect of temperature on the axial compressive load of SiGeNTs is also discussed.
Esophageal tissue engineering: An in‐depth review on scaffold design
Authors: Tan J.Y. , Chua C.K. , Leong K.F. , Chian K.S. , Leong W.S. , Tan L.P.
Published: September 2011

Treatment of esophageal cancer often requires surgical procedures that involve removal. The current approaches to restore esophageal continuity however, are known to have limitations which may not result in full functional recovery. In theory, using a tissue engineered esophagus developed from the patient's own cells to replace the removed esophageal segment can be the ideal method of reconstruction. One of the key elements involved in the tissue engineering process is the scaffold which acts as a template for organization of cells and tissue development. While a number of scaffolds range from traditional non‐biodegradable tubing to bioactive decellularized matrix have been proposed to engineer the esophagus in the past decade, results are still not yet favorable with many challenges relating to tissue quality need to be met improvements. The success of new esophageal tissue formation will ultimately depend on the success of the scaffold being able to meet the essential requirements specific to the esophageal tissue. Here, the design of the scaffold and its fabrication approaches are reviewed. In this paper, we review the current state of development in bioengineering the esophagus with particular emphasis on scaffold design. Biotechnol. Bioeng. 2012;109: 1–15. © 2011 Wiley Periodicals, Inc.
A monolithic lipase reactor for biodiesel production by transesterification of triacylglycerides into fatty acid methyl esters
Authors: Urban Jiri , Svec Frantisek , Fréchet Jean M.J.
Published: September 2011

An enzymatic reactor with lipase immobilized on a monolithic polymer support has been prepared and used to catalyze the transesterification of triacylglycerides into the fatty acid methyl esters commonly used for biodiesel. A design of experiments procedure was used to optimize the monolithic reactor with variables including control of the surface polarity of the monolith via variations in the length of the hydrocarbon chain in alkyl methacrylate monomer, time of grafting of 1‐vinyl‐4,4‐dimethylazlactone used to activate the monolith, and time used for the immobilization of porcine lipase. Optimal conditions involved the use of a poly(stearyl methacrylate‐co‐ethylene dimethacrylate) monolith, grafted first with vinylazlactone, then treated with lipase for 2 h to carry out the immobilization of the enzyme. Best conditions for the transesterification of glyceryl tributyrate included a temperature of 37°C and a 10 min residence time of the substrate in the bioreactor. The reactor did not lose its activity even after pumping through it a solution of substrate equaling 1,000 reactor volumes. This enzymatic reactor was also used for the transesterification of triacylglycerides from soybean oil to fatty acid methyl esters thus demonstrating the ability of the reactor to produce biodiesel. Biotechnol. Bioeng. 2012; 109:371–380. © 2011 Wiley Periodicals, Inc.
Facilitated diffusion of myoglobin and creatine kinase and reaction–diffusion constraints of aerobic metabolism under steady‐state conditions in skeletal muscle
Authors: Dasika S.K. , Kinsey S.T. , Locke B.R.
Published: September 2011

The roles of creatine kinase (CK) and myoglobin (Mb) on steady‐state facilitated diffusion and temporal buffering of ATP and oxygen, respectively, are assessed within the context of a reaction–diffusion model of muscle energetics. Comparison of the reaction–diffusion model with experimental data from a wide range of muscle fibers shows that the experimentally observed skeletal muscle fibers are generally not limited by diffusion, and the model further indicates that while some muscle fibers operate near the edge of diffusion limitation, no detectable effects of Mb and CK on the effectiveness factor, a measure of diffusion constraints, are observed under steady‐state conditions. However, CK had a significant effect on average ATP concentration over a wide range of rates and length scales within the reaction limited regime. The facilitated diffusion functions of Mb and CK become observable in the model for larger size cells with low mitochondrial volume fraction and for low boundary O2 concentration and high ATP demand, where the fibers may be limited by diffusion. From the transient analysis it may be concluded that CK primarily functions to temporally buffer ATP as opposed to facilitating diffusion while Mb has a small temporal buffering effect on oxygen but does not play any significant role in steady‐state facilitated diffusion in skeletal muscle fibers under most physiologically relevant regions. Biotechnol. Bioeng. 2012; 109:545–558. © 2011 Wiley Periodicals, Inc.