bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of defense response of wildtype Arabidopsis thaliana and plants with impaired NO‐ homeostasis
Authors: Holzmeister Christian , Fröhlich Andreas , Sarioglu Hakan , Bauer Norbert , Durner Jörg , Lindermayr Christian 
Published: March 2011

AbstractIn recent years, nitric oxide (NO) has been recognized as a signalling molecule of plants, being involved in diverse processes like germination, root growth, stomatal closing, and responses to various stresses. A mechanism of how NO can regulate physiological processes is the modulation of cysteine residues of proteins (S‐nitrosylation) by S‐nitrosoglutathione (GSNO), a physiological NO donor. The concentration of GSNO and the level of S‐nitrosylated proteins are regulated by GSNO reductase, which seems to play a major role in NO signalling. To investigate the importance of NO in plant defense response, we performed a proteomic analysis of Arabidopsis wildtype and GSNO‐reductase knock‐out plants infected with both the avirulent and virulent pathogen strains of Pseudomonas syringae. Using 2‐D DIGE technology in combination with MS, we identified proteins, which are differentially accumulated during the infection process. We observed that both lines were more resistant to avirulent infections than to virulent infections mainly due to the accumulation of stress‐, redox‐, and defense‐related proteins. Interestingly, after virulent infections, we also observed accumulation of defense‐related proteins, but no or low accumulation of stress‐ and redox‐related proteins, respectively. In summary, we present here the first detailed proteomic analysis of plant defense response.
Changes in proteomics profile during maturation of marrow‐derived dendritic cells treated with oxidized low‐density lipoprotein
Authors: Ge Junhua , Yan Hui , Li Shan , Nie Wencheng , Dong Kan , Zhang Li , Zhu Weiguo , Fan Fangyan , Zhu Jianhua 
Published: March 2011

AbstractIncreasing evidence suggests that dendritic cells (DCs) and oxidized low‐density lipoprotein (ox‐LDL) participate in atherosclerosis. However, few data on the molecular mechanisms of this process are available. To address this question, we used iTRAQ labeling followed by LC‐MS/MS analysis to identify many proteins that changed markedly during the maturation of dendritic cells stimulated with ox‐LDL. Among a total of 781 identified proteins, 93 were upregulated and 100 were downregulated. The major and significant changes in upregulated proteins were that ox‐LDL not only affected the levels of intracellular cathepsins G, Z, D and S, but also significantly enhanced cathepsin S secretion by the treated cells. Our results may provide clues for a more comprehensive understanding the pathogenesis of atherosclerosis.
Path lengths in protein–protein interaction networks and biological complexity
Authors: Xu Ke , Bezakova Ivona , Bunimovich Leonid , Yi Soojin V. 
Published: March 2011

AbstractWe investigated the biological significance of path lengths in 12 protein–protein interaction (PPI) networks. We put forward three predictions, based on the idea that biological complexity influences path lengths. First, at the network level, path lengths are generally longer in PPIs than in random networks. Second, this pattern is more pronounced in more complex organisms. Third, within a PPI network, path lengths of individual proteins are biologically significant. We found that in 11 of the 12 species, average path lengths in PPI networks are significantly longer than those in randomly rewired networks. The PPI network of the malaria parasite Plasmodium falciparum, however, does not exhibit deviation from rewired networks. Furthermore, eukaryotic PPIs exhibit significantly greater deviation from randomly rewired networks than prokaryotic PPIs. Thus our study highlights the potentially meaningful variation in path lengths of PPI networks. Moreover, node eccentricity, defined as the longest path from a protein to others, is significantly correlated with the levels of gene expression and dispensability in the yeast PPI network. We conclude that biological complexity influences both global and local properties of path lengths in PPI networks. Investigating variation of path lengths may provide new tools to analyze the evolution of functional modules in biological systems.
Proteomics indicates modulation of tubulin polymerization by L‐menthol inhibiting human epithelial colorectal adenocarcinoma cell proliferation
Authors: Faridi Uzma , Sisodia Brijesh S. , Shukla Ashutosh K. , Shukla Rakesh K. , Darokar Mahendra P. , Dwivedi Upendra N. , Shasany Ajit K. 
Published: March 2011

AbstractMenthol is a naturally occurring cyclic monoterpene used in oral hygiene products, confectionary, pharmaceuticals, cosmetics, pesticides, and as a flavoring agent. In the present study, we analyzed the differentially expressing proteome in L‐menthol‐treated Caco‐2 cell line as it was found to inhibit cell proliferation. Interestingly, free tubulin proteins were observed to be limited after menthol treatment. Semiquantitative RT‐PCR with α‐tubulin primers showed no change in the level of RNA expression in menthol‐treated cell line. However, tubulin polymerization assay with menthol indicated a trend similar to taxol in promoting microtubule assembly. Further, physical counting of apoptotic nuclei and active caspase‐3 assays confirmed onset of apoptosis though the rate was slower as compared with that of taxol treatment. This study is the first report of a monoterpene L‐menthol modulating tubulin polymerization and apoptosis to inhibit cancer cell proliferation.
Tunable poly(hydroxyl urethane) from CO2‐Based intermediates using thiol‐ene chemistry
Authors: Tang Chau N. , Nulwala Hunaid B. , Damodaran Krishnan , Kaur Palwinder , Luebke David R. 
Published: March 2011

AbstractCO2‐based, crosslinked poly(hydroxyl urethane)s (PHUs) are accessed via a set of efficient reactions based on the addition chemistry of thiol‐ene and amines‐cyclic carbonates. This strategy to utilize 5‐membered cyclic carbonates produced from CO2 is robust, facile, modular, and atomically efficient in nature. The thiol‐ene reaction was utilized to access bis(cyclic carbonate), tris(cyclic carbonate), and tetrakis(cyclic carbonate) in quantitative yield from 4‐vinyl‐1,3‐dioxolan‐2‐one and thiols. Multi‐functional cyclic carbonates were simply mixed with diethylenetriamine and/or 1,6‐diaminohexane to generate crosslinked PHUs from 25 to 80 °C. These materials are easy to scale‐up and are potential candidates in many applications such as coatings, binders, and resins. The resulting polymers have glass transition temperatures between −1 and 16 °C and thermal decomposition temperatures from 190 to 230 °C. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Thermal and spectral stability of fluorescent copolymers containing tetraphenylthiophene‐quinoline unit
Authors: Lai Chung‐Tin , Chien Rong‐Hong , Liu Chi‐Wei , Hong Jin‐Long 
Published: March 2011

AbstractFluorescent alternative copolymers containing tetraphenylthiophene‐quinoline (TP‐Qu) moiety were synthesized from Friedländer reaction between o‐aminoketone and acetyl groups. With the wholly aromatic‐quinoline chain structure, the alternative donor–acceptor copolymers of PTPQu and PTPTPQu are rigid materials with high glass transitions (Tg = 245 and 295 °C, respectively) and with high thermal stability (with ≤2% weight loss at 500 °C). The multiple phenyl pendant rings inherited PTPQu and PTPTPQu copolymers with good solubility in common organic solvents, which facilitate the easy fabrications of light‐emitting diode (LED) devices. CV study resulted in the reversible Eox/onset values of 0.78 and 0.75 V for the PTPQu and PTPTPQu copolymers, respectively. With high quantum yields (ϕFs, = 0.59 for PTPQu and 0.74 for PTPTPQu) in the film states, the two copolymers and their devices exhibit stable photoluminescence (PL) and electroluminescence (EL) spectra, respectively, on change of annealing temperatures to at least higher than 250 °C. After annealing at 250 °C (or 300 °C), no change was observed in the respective PL and EL spectra of PTPQu (or PTPTPQu) copolymers. The results indicate that alternative copolymers containing donor–acceptor TP‐Qu unit are promising candidates for LEDs with high efficiency and spectral stability. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
A test purpose‐based approach for testing timed input output automata
Authors: En‐Nouaary Abdeslam 
Published: March 2011

SUMMARYReal‐time applications are those reactive systems whose behavior depends not only on their interactions with the environment but also on the times at which these interactions take place. The timing aspect of such applications makes it hard to test them exhaustively because of the infinite number of possible computations. One way to deal with this difficulty is to have the tester choose some important features of the application and check if they are properly implemented. This paper follows this principle and proposes a method for testing real‐time applications formally modeled as Timed Input Output Automata (TIOA), a variant of Timed Automata of Alur and Dill (Theor. Comp. Sci. 1994; 126:183–235). The method is based on test purposes. A test purpose is a description of a well‐defined testing objective focusing on a single requirement or a set of requirements of the system under test. Test purposes, in this paper, are used to describe the features of the application to be checked by the tester. They are also formally modeled, in this paper, as a TIOA. Since test purposes are a partial behavior of the application under test, they significantly help to reduce the number of test cases to be generated, and consequently minimize the time, effort, and money to spend in testing the application. Basically, the paper proposes an approach, which takes as inputs a test purpose and a specification, and generates test cases, which are able to check if the test purpose is satisfied by an implementation of the specification. The proposed method consists of three main steps. First, the TIOAs of the specification and test purpose are combined together in one TIOA. Second, the resulting TIOA is sampled to construct a sub‐automaton of the system with a finite number of executions for test generation. The sampling of a TIOA is done based on the number of clocks describing the timing behavior of the system. Finally, the sub‐automaton resulting from the second step is traversed to generate test cases. The real‐time applications dealt with in this paper are supposed to be deterministic; i.e. the test results are the same when the same input data are applied to the implementation of the application. Copyright © 2011 John Wiley & Sons, Ltd.
Data mining tools
Authors: Mikut Ralf , Reischl Markus 
Published: March 2011

AbstractThe development and application of data mining algorithms requires the use of powerful software tools. As the number of available tools continues to grow, the choice of the most suitable tool becomes increasingly difficult. This paper attempts to support the decision‐making process by discussing the historical development and presenting a range of existing state‐of‐the‐art data mining and related tools. Furthermore, we propose criteria for the tool categorization based on different user groups, data structures, data mining tasks and methods, visualization and interaction styles, import and export options for data and models, platforms, and license policies. These criteria are then used to classify data mining tools into nine different types. The typical characteristics of these types are explained and a selection of the most important tools is categorized. This paper is organized as follows: the first section Historical Development and State‐of‐the‐Art highlights the historical development of data mining software until present; the criteria to compare data mining software are explained in the second section Criteria for Comparing Data Mining Software. The last section Categorization of Data Mining Software into Different Types proposes a categorization of data mining software and introduces typical software tools for the different types. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 431‐443 DOI: 10.1002/widm.24This article is categorized under:

Application Areas > Data Mining Software Tools
Current trends in nanobiosensor technology
Authors: Bellan Leon M. , Wu Diana , Langer Robert S. 
Published: March 2011

AbstractThe development of tools and processes used to fabricate, measure, and image nanoscale objects has lead to a wide range of work devoted to producing sensors that interact with extremely small numbers (or an extremely small concentration) of analyte molecules. These advances are particularly exciting in the context of biosensing, where the demands for low concentration detection and high specificity are great. Nanoscale biosensors, or nanobiosensors, provide researchers with an unprecedented level of sensitivity, often to the single molecule level. The use of biomolecule‐functionalized surfaces can dramatically boost the specificity of the detection system, but can also yield reproducibility problems and increased complexity. Several nanobiosensor architectures based on mechanical devices, optical resonators, functionalized nanoparticles, nanowires, nanotubes, and nanofibers have been demonstrated in the lab. As nanobiosensor technology becomes more refined and reliable, it is likely it will eventually make its way from the lab to the clinic, where future lab‐on‐a‐chip devices incorporating an array of nanobiosensors could be used for rapid screening of a wide variety of analytes at low cost using small samples of patient material. WIREs Nanomed Nanobiotechnol 2011 3 229–246 DOI: 10.1002/wnan.136This article is categorized under:

Diagnostic Tools > Biosensing
Diagnostic Tools > Diagnostic Nanodevices
Diagnostic Tools > In Vitro Nanoparticle-Based Sensing
Growth Temperature and Salinity Impact Fatty Acid Composition and Degree of Unsaturation in Peanut‐Nodulating Rhizobia
Authors: Paulucci Natalia S. , Medeot Daniela B. , Dardanelli Marta S. , de Lema Mirta García 
Published: March 2011

AbstractGrowth and survival of bacteria depend on homeostasis of membrane lipids, and the capacity to adjust lipid composition to adapt to various environmental stresses. Membrane fluidity is regulated in part by the ratio of unsaturated to saturated fatty acids present in membrane lipids. Here, we studied the effects of high growth temperature and salinity (NaCl) stress, separately or in combination, on fatty acids composition and de novo synthesis in two peanut‐nodulating Bradyrhizobium strains (fast‐growing TAL1000 and slow‐growing SEMIA6144). Both strains contained the fatty acids palmitic, stearic, and cis‐vaccenic + oleic. TAL1000 also contained eicosatrienoic acid and cyclopropane fatty acid. The most striking change, in both strains, was a decreased percentage of cis‐vaccenic + oleic (≥80% for TAL1000), and an associated increase in saturated fatty acids, under high growth temperature or combined conditions. Cyclopropane fatty acid was significantly increased in TAL1000 under the above conditions. De novo synthesis of fatty acids was shifted to the synthesis of a higher proportion of saturated fatty acids under all tested conditions, but to a lesser degree for SEMIA6144 compared to TAL1000. The major adaptive response of these rhizobial strains to increased temperature and salinity was an altered degree of fatty acid unsaturation, to maintain the normal physical state of membrane lipids.
Influence of Turbidity Grade on Color and Appearance of Virgin Olive Oil
Authors: Gordillo Belen , Ciaccheri Leonardo , Mignani Anna G. , Gonzalez‐Miret M. Lourdes , Heredia Francisco J. 
Published: March 2011

AbstractThe appearance of most of the commercialized olive oils involves both their color and turbidity depending on the different technologies used for their elaboration. This research has been carried out to study the filtration impact on the colorimetric changes of virgin olive oils. Naturally turbid olive oils were blended at different proportions (100, 80, 60, 40, 20 and 0%) with their corresponding filtered replicates to obtain a scale of six levels of turbidity and simulating different turbidity grades. Tristimulus colorimetry, particularly the CIELAB uniform color, was used to follow color changes. As turbidity of the oil increased in the blend, yellowish oils, darker, and less saturated were obtained. Univariate correlations between the colorimetric parameters and turbid content were achieved with second degree polynomial equations, being chroma () and hue (hab) the best correlated parameters. The color differences () calculated between turbid oils (100%) and the consecutively decreasing turbid oils blends ranged from 3.18 to 18.72 CIELAB units, revealing differences in color visually perceptible to the human eye.
Congenital dislocation of the knee: A protocol for management based on degree of knee flexion
Authors: Abdelaziz Tarek Hassan , Samir Shady 
Published: March 2011

Purpose Congenital dislocation of the knee (CDK) is a relatively rare condition. It may occur as an isolated deformity, it may be associated with musculoskeletal anomalies such as developmental dysplasia of the hip and clubfoot, or it may occur as part of a syndrome such as arthrogryposis multiplex congenita or Larsen syndrome, or it may occur in paralytic conditions such as meningomyelocele. Treatment options include serial casting, percutaneous quadriceps recession (PQR) and V–Y quadricepsplasty (VYQ). The aim of this study is to evaluate the medium-term results of PQR and VYQ, and to set a protocol of management for CDK based on a modified grading system. Methods Eleven infants with 21 CDK were treated at our unit. Five knees were treated with serial casting, 12 knees with PQR and four knees with VYQ. Follow up averaged 41 months. Results Twelve knees achieved excellent results, seven knees achieved good results and two knees achieved fair results. Conclusion A modified grading system for CDK is introduced. Based on this, we recommend the following. Serial casting is performed in patients with GI CDK. In GII CDK in neonates (babies up to the age of 1 month) serial casting is started. A maximum of four weekly manipulations and castings are attempted. If a range of flexion >90° is achieved, serial casting is continued; if range of flexion remains <90° it is necessary to proceed to PQR. In babies older than 1 month when first seen; PQR is performed from the start. VYQ is indicated in patients with GIII CDK or in recurrent cases.
Modulation of mammary gland development in pre-pubertal mice as affected by soya and milk protein supplements
Authors: Alston-Mills Brenda , Lepri J. J. , Martin C. A. 
Published: March 2011

The objective of the present study was to determine the effects of soya and whey milk protein, α-lactalbumin (α-LA), on mammary gland morphology and the structural support of the gland, in pre-pubertal mice after 7 d of treatment. In Expt 1, weaned (day 21) CD1 mice were given one of the four treatments, three included dietary supplements: (1) control diet, casein, (2) soya, (3) α-LA and (4) subcutaneous injection of 2·5 μg oestradiol benzoate in 20 μl maize oil and fed the control diet. All diets were isoenergetic with equal protein concentrations. All groups that were not treated with oestradiol received the vehicle. Whole-mount analyses were performed to determine longitudinal ductal growth and terminal end bud development. DNA was extracted from the gland and assessed by spectrophotometry (260/280 nm). Tissue extracts for extracellular matrix (ECM) proteins, matrix metalloproteinase-2 (MMP2), tissue inhibitor of MMP2 (TIMP2), and serum oestradiol and mammary tissue epidermal growth factors (EGF) were measured by immunoassays. Expt 2 utilised the Her2/neu transgenic strain, with the same protocols. Statistical significance was determined by one-way ANOVA. From Expt 1 and 2, soya and α-LA significantly increased ductal elongation when compared with the oestrogen and control groups. These results were corroborated by data on total DNA and the ratio of MMP2:TIMP2. The ratio of MMP2:TIMP2 was affected by α-LA. Serum oestradiol was decreased only in the oestradiol-treated groups in both experiments. Soya is known to be oestrogenic and can act on epithelia directly. The mechanism by which α-LA affects glandular development is by modulating the ECM or by promoting the synthesis/activity of EGF.
Thermal maturity of the Upper Triassic–Middle Jurassic Shemshak Group (Alborz Range, Northern Iran) based on organic petrography, geochemistry and basin modelling: implications for source rock evaluation and petroleum exploration
Authors: SHEKARIFARD ALI , BAUDIN FRANÇOIS , SEYED-EMAMI KAZEM , SCHNYDER JOHANN , LAGGOUN-DEFARGE FATIMA , RIBOULLEAU ARMELLE , BRUNET MARIE-FRANÇOISE , SHAHIDI ALIREZA 
Published: March 2011

AbstractOrganic petrography and geochemical analyses have been carried out on shales, carbonaceous shales and coals of the Shemshak Group (Upper Triassic–Middle Jurassic) from 15 localities along the Alborz Range of Northern Iran. Thermal maturity of organic matter (OM) has been investigated using vitrinite reflectance, Rock-Eval pyrolysis and elemental analysis of kerogen. Reflectance of autochthonous vitrinite varies from 0.6 to 2.2% indicating thermally early-mature to over-mature OM in the Shemshak Group, in agreement with other maturity parameters used. The shales of the Shemshak Group are characterized by poor to high residual organic carbon contents (0.13 to 5.84%) and the presence of hydrogen-depleted OM, predominantly as a consequence of oxidation of OM at the time of deposition and the hydrogen loss during petroleum generation. According to light-reflected microscopy results, vitrinite/vitrinite-like macerals are dominant in the kerogen concentrates from the shaly facies. The coals and carbonaceous shales of the Shemshak Group show a wide range in organic carbon concentration (3.5 to 88.6%) and composition (inertinite- and vitrinite-rich types), and thereby different petroleum potentials. Thermal modelling results suggest that low to moderate palaeo-heat flow, ranging from 47 to 79 mW m−2 (57 mW m−2 on average), affected the Central-Eastern Alborz basin during Tertiary time, the time of maximum burial of the Shemshak Group. The maximum temperature that induced OM maturation of the Shemshak Group seems to be related to its deep burial rather than to a very strong heat flow related to an uppermost Triassic–Liassic rifting. The interval of petroleum generation in the most deeply buried part of the Shemshak Group (i.e. Tazareh section) corresponds to Middle Jurassic–Early Cretaceous times. Exhumation of the Alborz Range during Late Neogene time, especially along the axis of the Central-Eastern Alborz, where maximum vitrinite reflectance values are recorded, probably destroyed possible petroleum accumulations. However, on the northern flank of the Central-Eastern Alborz, preservation of petroleum accumulations may be expected. The northern part of the basin therefore seems the best target for petroleum exploration.