bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of Actual Evapotranspiration by Remote Sensing: Application in Thessaly Plain, Greece
Authors: Tsouni Alexia , Kontoes Charalabos , Koutsoyiannis Demetris , Elias Panagiotis , Mamassis Nikos
Published: June 2008

Remote sensing can assist in improving the estimation of the geographical distribution of evapotranspiration, and consequently water demand in large cultivated areas for irrigation purposes and sustainable water resources management. In the direction of these objectives, the daily actual evapotranspiration was calculated in this study during the summer season of 2001 over the Thessaly plain in Greece, a wide irrigated area of great agricultural importance. Three different methods were adapted and applied: the remotesensing methods by Granger (2000) and Carlson and Buffum (1989) that use satellite data in conjunction with ground meteorological measurements and an adapted FAO (Food and Agriculture Organisation) Penman-Monteith method (Allen at al. 1998), which was selected to be the reference method. The satellite data were used in conjunction with ground data collected on the three closest meteorological stations. All three methods, exploit visible channels 1 and 2 and infrared channels 4 and 5 of NOAA-AVHRR (National Oceanic and Atmospheric Administration - Advanced Very High Resolution Radiometer) sensor images to calculate albedo and NDVI (Normalised Difference Vegetation Index), as well as surface temperatures. The FAO Penman-Monteith and the Granger method have used exclusively NOAA-15 satellite images to obtain mean surface temperatures. For the Carlson-Buffum method a combination of NOAA-14 and ΝΟΑΑ-15 satellite images was used, since the average rate of surface temperature rise during the morning was required. The resulting estimations show that both the Carlson-Buffum and Granger methods follow in general the variations of the reference FAO Penman-Monteith method. Both methods have potential for estimating the spatial distribution of evapotranspiration, whereby the degree of the relative agreement with the reference FAO Penman-Monteith method depends on the crop growth stage. In particular, the Carlson- Buffum method performed better during the first half of the crop development stage, while the Granger method performed better during the remaining of the development stage and the entire maturing stage. The parameter that influences the estimations significantly is the wind speed whose high values result in high underestimates of evapotranspiration. Thus, it should be studied further in future.
Free and Forced Rossby Waves in the Western South China Sea Inferred from Jason-1 Satellite Altimetry Data
Authors: Wu Xiangyu , Xie Qiang , He Zhigang , Wang Dongxiao
Published: June 2008

Data from a subsurface mooring deployed in the western South China Sea shows clear intra-seasonal oscillations (ISO) at the period of 40~70 days. Analysis of remotelysensed sea surface height (SSH) anomalies in the same area indicates that these ISO signals propagate both eastward and westward. Time-longitude diagrams of ISO signals in SSH anomalies and wind-stress curl indicate that the eastward propagating SSH anomalies is forced by wind-stress curl. This is also confirmed by lag correlation between SSH anomalies and the wind-stress-curl index (wind stress curl averaged over 109.5ºE -115ºE and 12ºN -13.5ºN). Lag correlation of SSH anomaly suggests that the westward propagating signals are free Rossby waves.
Using Electromyography to Detect the Weightings of the Local Muscle Factors to the Increase of Perceived Exertion During Stepping Exercise
Authors: Chang Ya-Ju , Liu Chin-Chih , Lin Cheng-Hsiang , Tsaih Peih-Ling , Hsu Miao-Ju
Published: June 2008

Rate of perceived exertion (RPE) is a clinically convenient indicator for monitoring exercise intensity in cardiopulmonary rehabilitation. It might not be sensitive enough for clinicians to determine the patients’ physiological status because its association with the cardiovascular system and local muscle factors is unknown. This study used the electromyographic sensor to detect the local muscle fatigue and stabilization of patella, and analyzed the relationship between various local muscle and cardiovascular factors and the increase of RPE during stepping exercise, a common exercise program provided in cardiopulmonary rehabilitation. Ten healthy adults (4 males and 6 females) participated in this study. Each subject used their right bare foot to step up onto a 23-cm-high step at a constant speed until the RPE score reached 20. The RPE, heart rate (HR), and surface EMG of the rectus femoris (RF), vastus medialis, and vastus lateralis were recorded at 1-minute intervals during the stepping exercise. The generalized estimating equations (GEE) analysis indicated that the increase in RPE significantly correlated with the increase in HR, and decrease in median frequency (MF) of the EMG power spectrum of the RF. Experimental results suggest that the increase in RPE during stepping exercise was influenced by the cardiovascular status, localized muscle fatigue in the lower extremities. The weighting of the local muscle factors was more than half of the weighting of the cardiovascular factor.
An Investigation on Micro-Raman Spectra and Wavelet Data Analysis for Pemphigus Vulgaris Follow-up Monitoring.
Authors: Camerlingo Carlo , Zenone Flora , Perna Giuseppe , Capozzi Vito , Cirillo Nicola , Gaeta Giovanni Maria , Lepore Maria
Published: June 2008

A wavelet multi-component decomposition algorithm has been used for data analysis of micro-Raman spectra of blood serum samples from patients affected by pemphigus vulgaris at different stages. Pemphigus is a chronic, autoimmune, blistering disease of the skin and mucous membranes with a potentially fatal outcome. Spectra were measured by means of a Raman confocal microspectrometer apparatus using the 632.8 nm line of a He-Ne laser source. A discrete wavelet transform decomposition method has been applied to the recorded Raman spectra in order to overcome problems related to low-level signals and the presence of noise and background components due to light scattering and fluorescence. This numerical data treatment can automatically extract quantitative information from the Raman spectra and makes more reliable the data comparison. Even if an exhaustive investigation has not been done in this work, the feasibility of the follow-up monitoring of pemphigus vulgaris pathology has been clearly proved with useful implications for the clinical applications.
Disposable E-Tongue for the Assessment of Water Quality in Fish Tanks
Authors: Chang Chew-Cheen , Saad Bahruddin , Surif Misni , Ahmad Mohd Noor , Md Shakaff Ali Yeon
Published: June 2008

A disposable screen-printed e-tongue based on sensor array and pattern recognition that is suitable for the assessment of water quality in fish tanks is described. The characteristics of sensors fabricated using two kinds of sensing materials, namely (i) lipids (referred to as Type 1), and (ii) alternative electroactive materials comprising liquid ion-exchangers and macrocyclic compounds (Type 2) were evaluated for their performance stability, sensitivity and reproducibility. The Type 2 e-tongue was found to have better sensing performance in terms of sensitivity and reproducibility and was thus used for application studies. By using a pattern recognition tool i.e. principal component analysis (PCA), the e-tongue was able to discriminate the changes in the water quality in tilapia and catfish tanks monitored over eight days. E-tongues coupled with partial least squares (PLS) was used for the quantitative analysis of nitrate and ammonium ions in catfish tank water and good agreement were found with the ion-chromatography method (relative error, ±1.04- 4.10 %).
Flow-Injection Coulometric Detection Based on Ion Transfer and Its Application to the Determination of Chlorpromazine
Authors: Ortuño Joaquín A. , Gil Antonio , Sánchez-Pedreño Concepción
Published: June 2008

A flow-injection coulometric method for the determination of chlorpromazine based on ion transfer into a plasticized poly(vinyl chloride) (PVC) membrane, was developed. The detector used consists of a flow-through cell that incorporates a plasticized poly(vinyl chloride) (PVC) membrane which contains tetrabutylammonium tetraphenylborate as electrolyte. The membrane is located between the flowing solution and an inner aqueous electrolyte solution. Two pairs of electrodes, each pair formed by a reference electrode and a working electrode, are used, one pair in each solution. The potential between the reference electrodes was controlled by a four-electrode potentiostat with ohmic drop compensation. A potential step capable of producing the transfer of the chlorpromazine ion into the membrane was applied during the passage of a wide portion of sample plug through the cell and the corresponding quantity of the electricity was measured. In the selected conditions, a linear relationship was observed between the quantity of electricity and chlorpromazine concentrations over a range of 1x10-6 -1x10-4 M. The detection limit was 2 x 10-7 M. Good repeatability and between-day reproducibility was obtained. No interference was observed on the part of some common ions and pharmaceutical excipients. The method proposed was applied satisfactorily to the determination of chlorpromazine in pharmaceuticals and human urine.
Fluorescent Indolizine-b-Cyclodextrin Derivatives for the Detection of Volatile Organic Compounds
Authors: Becuwe Matthieu , Landy David , Delattre François , Cazier Francine , Fourmentin Sophie
Published: June 2008

This paper presents the synthesis, the structural determination and the sensing capabilities toward Volatile Organic Compounds (VOCs) of a new class of fluorescent indolizine-cyclodextrin sensors. Two different pathways, both involving bipyridinium ylides and 6-amino-b-cyclodextrin, have been used to carry out the synthesis of these sensors. The macrocycle structures were dominantly established by 1H-NMR spectra and systematically studied by molecular modelling (MM3, AM1, AM1-COSMO methods). The sensing capabilities of the sensors were evaluated by emission of fluorescence, during the inclusion of the guest (adamantanol or aromatic derivatives) into the cyclodextrin (CD) host cavity. The host/guest complex formation was investigated by formation constant determinations, using experimental methods, coupled with theoretical calculations of formation energies using a specific docking procedure. Both experimental and theoretical results suggest that some compounds would make very attractive sensors for VOC detection. Some compounds could also be taken into consideration as biological markers.
Dynamic Characteristics of Vertically Coupled Structures and the Design of a Decoupled Micro Gyroscope
Authors: Choi Bumkyoo , Lee Seung-Yop , Kim Taekhyun , Baek Seog Soon
Published: June 2008

In a vertical type, vibratory gyroscope, the coupled motion between reference (driving) and sensing vibrations causes the zero-point output, which is the unwanted sensing vibration without angular velocity. This structural coupling leads to an inherent discrepancy between the natural frequencies of the reference and the sensing oscillations, causing curve veering in frequency loci. The coupled motion deteriorates sensing performance and dynamic stability. In this paper, the dynamic characteristics associated with the coupling phenomenon are theoretically analyzed. The effects of reference frequency and coupling factor on the rotational direction and amplitude of elliptic oscillation are determined. Based on the analytical studies on the coupling effects, we propose and fabricate a vertically decoupled vibratory gyroscope with the frequency matching.
Comparative Analysis of EO-1 ALI and Hyperion, and Landsat ETM+ Data for Mapping Forest Crown Closure and Leaf Area Index
Authors: Pu Ruiliang , Gong Peng , Yu Qian
Published: June 2008

In this study, a comparative analysis of capabilities of three sensors for mapping forest crown closure (CC) and leaf area index (LAI) was conducted. The three sensors are Hyperspectral Imager (Hyperion) and Advanced Land Imager (ALI) onboard EO-1 satellite and Landsat-7 Enhanced Thematic Mapper Plus (ETM+). A total of 38 mixed coniferous forest CC and 38 LAI measurements were collected at Blodgett Forest Research Station, University of California at Berkeley, USA. The analysis method consists of (1) extracting spectral vegetation indices (VIs), spectral texture information and maximum noise fractions (MNFs), (2) establishing multivariate prediction models, (3) predicting and mapping pixel-based CC and LAI values, and (4) validating the mapped CC and LAI results with field validated photo-interpreted CC and LAI values. The experimental results indicate that the Hyperion data are the most effective for mapping forest CC and LAI (CC mapped accuracy (MA) = 76.0%, LAI MA = 74.7%), followed by ALI data (CC MA = 74.5%, LAI MA = 70.7%), with ETM+ data results being least effective (CC MA = 71.1%, LAI MA = 63.4%). This analysis demonstrates that the Hyperion sensor outperforms the other two sensors: ALI and ETM+. This is because of its high spectral resolution with rich subtle spectral information, of its short-wave infrared data for constructing optimal VIs that are slightly affected by the atmosphere, and of its more available MNFs than the other two sensors to be selected for establishing prediction models. Compared to ETM+ data, ALI data are better for mapping forest CC and LAI due to ALI data with more bands and higher signal-to-noise ratios than those of ETM+ data.
Fabrication and Characterization of Silicon Micro-Funnels and Tapered Micro-Channels for Stochastic Sensing Applications
Authors: Archer Marie J. , Ligler Frances S.
Published: June 2008

We present a simplified, highly reproducible process to fabricate arrays of tapered silicon micro-funnels and micro-channels using a single lithographic step with a silicon oxide (SiO2) hard mask on at a wafer scale. Two approaches were used for the fabrication. The first one involves a single wet anisotropic etch step in concentrated potassium hydroxide (KOH) and the second one is a combined approach comprising Deep Reactive Ion Etch (DRIE) followed by wet anisotropic etching. The etching is performed through a 500 mm thick silicon wafer, and the resulting structures are characterized by sharp tapered ends with a sub-micron cross-sectional area at the tip. We discuss the influence of various parameters involved in the fabrication such as the size and thickness variability of the substrate, dry and wet anisotropic etching conditions, the etchant composition, temperature, diffusion and micro-masking effects, the quality of the hard mask in the uniformity and reproducibility of the structures, and the importance of a complete removal of debris and precipitates. The presence of apertures at the tip of the structures is corroborated through current voltage measurements and by the translocation of DNA through the apertures. The relevance of the results obtained in this report is discussed in terms of the potential use of these structures for stochastic sensing.
Comparing Different Approaches for Mapping Urban Vegetation Cover from Landsat ETM+ Data: A Case Study on Brussels
Authors: Van de Voorde Tim , Vlaeminck Jeroen , Canters Frank
Published: June 2008

Urban growth and its related environmental problems call for sustainable urban management policies to safeguard the quality of urban environments. Vegetation plays an important part in this as it provides ecological, social, health and economic benefits to a city’s inhabitants. Remotely sensed data are of great value to monitor urban green and despite the clear advantages of contemporary high resolution images, the benefits of medium resolution data should not be discarded. The objective of this research was to estimate fractional vegetation cover from a Landsat ETM+ image with sub-pixel classification, and to compare accuracies obtained with multiple stepwise regression analysis, linear spectral unmixing and multi-layer perceptrons (MLP) at the level of meaningful urban spatial entities. Despite the small, but nevertheless statistically significant differences at pixel level between the alternative approaches, the spatial pattern of vegetation cover and estimation errors is clearly distinctive at neighbourhood level. At this spatially aggregated level, a simple regression model appears to attain sufficient accuracy. For mapping at a spatially more detailed level, the MLP seems to be the most appropriate choice. Brightness normalisation only appeared to affect the linear models, especially the linear spectral unmixing.
Interferometric Synthetic Aperture Microscopy: Computed Imaging for Scanned Coherent Microscopy
Authors: Davis Brynmor J. , Marks Daniel L. , Ralston Tyler S. , Carney P. Scott , Boppart Stephen A.
Published: June 2008

Three-dimensional image formation in microscopy is greatly enhanced by the use of computed imaging techniques. In particular, Interferometric Synthetic Aperture Microscopy (ISAM) allows the removal of out-of-focus blur in broadband, coherent microscopy. Earlier methods, such as optical coherence tomography (OCT), utilize interferometric ranging, but do not apply computed imaging methods and therefore must scan the focal depth to acquire extended volumetric images. ISAM removes the need to scan the focus by allowing volumetric image reconstruction from data collected at a single focal depth. ISAM signal processing techniques are similar to the Fourier migration methods of seismology and the Fourier reconstruction methods of Synthetic Aperture Radar (SAR). In this article ISAM is described and the close ties between ISAM and SAR are explored. ISAM and a simple strip-map SAR system are placed in a common mathematical framework and compared to OCT and radar respectively. This article is intended to serve as a review of ISAM, and will be especially useful to readers with a background in SAR.
Connecting Hazard Analysts and Risk Managers to Sensor Information
Authors: Le Cozannet Gonéri , Hosford Steven , Douglas John , Serrano Jean-Jacques , Coraboeuf Damien , Comte Jérémie
Published: June 2008

Hazard analysts and risk managers of natural perils, such as earthquakes, landslides and floods, need to access information from sensor networks surveying their regions of interest. However, currently information about these networks is difficult to obtain and is available in varying formats, thereby restricting accesses and consequently possibly leading to decision-making based on limited information. As a response to this issue, state-of-the-art interoperable catalogues are being currently developed within the framework of the Group on Earth Observations (GEO) workplan. This article provides an overview of the prototype catalogue that was developed to improve access to information about the sensor networks surveying geological hazards (geohazards), such as earthquakes, landslides and volcanoes.
A Lidar Point Cloud Based Procedure for Vertical Canopy Structure Analysis And 3D Single Tree Modelling in Forest
Authors: Wang Yunsheng , Weinacker Holger , Koch Barbara
Published: June 2008

A procedure for both vertical canopy structure analysis and 3D single tree modelling based on Lidar point cloud is presented in this paper. The whole area of research is segmented into small study cells by a raster net. For each cell, a normalized point cloud whose point heights represent the absolute heights of the ground objects is generated from the original Lidar raw point cloud. The main tree canopy layers and the height ranges of the layers are detected according to a statistical analysis of the height distribution probability of the normalized raw points. For the 3D modelling of individual trees, individual trees are detected and delineated not only from the top canopy layer but also from the sub canopy layer. The normalized points are resampled into a local voxel space. A series of horizontal 2D projection images at the different height levels are then generated respect to the voxel space. Tree crown regions are detected from the projection images. Individual trees are then extracted by means of a pre-order forest traversal process through all the tree crown regions at the different height levels. Finally, 3D tree crown models of the extracted individual trees are reconstructed. With further analyses on the 3D models of individual tree crowns, important parameters such as crown height range, crown volume and crown contours at the different height levels can be derived.
Simultaneous Chronoamperometric Sensing of Ascorbic Acid and Acetaminophen at a Boron-Doped Diamond Electrode
Authors: Cofan Codruţa , Radovan Ciprian
Published: June 2008

Cyclic voltammetry (CV) and chronoamperometry (CA) have been used to sense and determine simultaneously L-ascorbic acid (AA) and acetaminophen (AC) at a boron-doped diamond electrode (BDDE) in a Britton-Robinson buffer solution. The calibration plots of anodic current peak versus concentration obtained from CV and CA data for both investigated compounds in single and di-component solutions over the concentration range 0.01 mM – 0.1 mM proved to be linear, with very good correlation parameters. Sensitivity values and RSD of 2-3% were obtained for various situations, involving both individual and simultaneous presence of AA and AC. The chronoamperometric technique associated with standard addition in sequential one step and/or two successive and continuous chronoamperograms at two characteristic potential levels represented a feasible option for the simultaneous determination of AA and AC in real sample systems such as pharmaceutical formulations. The average values indicated by the supplier were confirmed to a very close approximation from chronoamperomgrams by using several additions with the application of suitable current correction factors.
Detecting Aquatic Vegetation Changes in Taihu Lake, China Using Multi-temporal Satellite Imagery
Authors: Ma Ronghua , Duan Hongtao , Gu Xiaohong , Zhang Shouxuan
Published: June 2008

We have measured the water quality and bio-optical parameters of 94 samples from Taihu Lake in situ and/or in the lab between June 10-18, 2007. A transparencyassisted decision tree was developed to more accurately divide the aquatic vegetation zone into a floating vegetation-dominated zone and a submerged vegetation-dominated zone, whose respective present biomass retrieval models were easily developed with an empirical approach because of the quasi-concurrence of ground field investigations with the satellite sensor flight over the lake. The significant quantitative relationships between the vegetation index NDVI (Normalized Difference Vegetation Index) of different images at different times were used to help develop the past biomass retrieval model on the basis of the present developed model. In Taihu Lake, the total covering area of aquatic vegetations decreased from 454.6 km2 in 2001 to 364.1 km2 in 2007. Correspondingly, the total biomass decreased from 489,000 tons in 2001 to 406,000 tons in 2007, suggesting that a great change in the ecological environment has been taking place in Taihu Lake over this period.
Numerical Deformation Analysis of Bridge Concrete Girders
Authors: Kaklauskas Gintaris , Girdzius Rokas , Bacinskas Darius , Sokolov Aleksandr
Published: July 2008

Present research was aiming at deriving tension stiffening relationship based on EC2 provisions for deformation analysis of bending RC structures. According to the algorithm proposed by the first author, a tension stiffening relationships were derived from moment-curvature diagrams of reinforced concrete beams calculated according to EC2 technique. The obtained tension stiffening relationship was applied in the parametric study, using non-linear finite element software ATENA and layered model. Theoretical results were compared with experimental data of beams reported in the literature. The defined tension stiffening relationship was also applied for calculation of moment-curvature response of reinforced concrete bridge girder. The analyses have shown that the deformations calculated using the derived tension stiffening relationship and the EC2 technique were in good agreement.
Nonheme Iron Halogenases
Authors: Blasiak Leah C , Drennan Catherine L
Published: June 2008

Nonheme iron halogenases require Fe(II), O
2
, α‐ketoglutarate (αKG), and a halide ion and catalyze halogenation at unactivated, aliphatic carbons on their substrates. The nonheme iron halogenase SyrB2, from

Pseudomonas syringae

, catalyzes chlorination of threonine during biosynthesis of the plant toxin syringomycin. The X‐ray crystal structure of SyrB2 revealed a mononuclear iron center coordinated by two histidine residues, bidentate αKG, and a chloride ion. Spectroscopic studies on the nonheme iron halogenase CytC3 from
Streptomyces
sp. RK95‐74 have implicated an iron(IV)‐oxo as a hydrogen atom abstracting species in a mechanism similar to the related nonheme iron dioxygenases.
The Impact of Climate Change and Variability on Heavy Precipitation, Floods, and Droughts
Authors: Trenberth Kevin E
Published: June 2008

There is a direct influence of global warming on changes in precipitation and heavy rains. Increased heating leads to greater evaporation and thus surface drying, thereby increasing intensity and duration of drought. However, the water‐holding capacity of air increases by about 7% per 1 °C warming, which leads to increased water vapor in the atmosphere, and this probably provides the biggest influence on precipitation. Storms, whether individual thunderstorms, extratropical rain or snow storms, or tropical cyclones and hurricanes, supplied by increased moisture, produce more intense precipitation events that are widely observed to be occurring, even in places where total precipitation is decreasing. In turn, this increases the risk of flooding. Patterns of where it rains also have been observed to change, with dry areas becoming drier (generally throughout the subtropics) and wet areas becoming wetter, especially in mid to high latitudes. This pattern is simulated by climate models and is projected to continue into the future. Since more precipitation occurs as rain instead of snow with warming, and snow melts earlier, there is increased runoff and risk of flooding in early spring, but increased risk of drought in deep summer, especially over continental areas.
Boron: Metallacarbaboranes
Authors: Housecroft Catherine E.
Published: June 2008

Metallacarbaboranes comprise carbon, boron, and metal‐atom‐containing clusters. The classes of compounds and their syntheses are described, as well as skeletal isomerism, electrochemistry, and reactivity. The applications of metallacarbaboranes in biosciences, medicinal chemistry, and materials science are gradually becoming more significant.
ResonanceRaman Spectroscopy
Authors: Czernuszewicz Roman S. , Zaczek Marzena B.
Published: June 2008

Resonance Raman (RR) spectroscopy is an invaluable and widely used probe of structure and bonding for chromophoric transition metal centers in proteins and enzymes. The spectacular increase in detection sensitivity and selectivity of RR spectroscopy for vibrations that are localized in the absorbing center(s) of the molecule has revolutionized the vibrational spectroscopic field of bioinorganic systems. In this article, we explain the characteristics of RR spectra, emphasizing the kind of information that can be obtained and the rules for optimal resonance enhancement. We then discuss the applications of RR scattering to the study of structural dynamics of two different mononuclear metal‐cysteinate sites, type‐1 copper in cupredoxins and Fe(S‐Cys)4center in rubredoxins, using a combination of site‐directed mutagenesis, production of isotopically labeled proteins, and cryogenic‐temperature RR methods. These chromophores, involved in biological electron transport, have been very suitable subjects for RR studies because they exhibit strong absorption bands in the visible region due to (Cys)S → Cu(II) (∼625 nm) and (Cys)S → Fe(III) (∼500–570 nm) charge‐transfer electronic transitions that facilitate the observation of resonantly enhanced Cu‐and Fe‐thiolate vibrations.
Receptor Theory
Authors: Kenakin Terry
Published: June 2008

Receptor theory assigns mathematical rules to biological systems in order to quantify drug effects and define what biological systems can and cannot do, leading to the design of experiments that may further modify the model. Drug receptor theory also furnishes the tools for quantifying the activity of drugs in a system‐independent manner, essential because drugs are almost always studied in test systems somewhat removed from the therapeutic system for which they are intended. Since biological systems operate at different set points in the body under different conditions, the ability to predict drug effects under a variety of circumstances is important. This unit provides a historical perspective of classical receptor theory and the currently used operational model of drug effects. The mechanism of drug receptor function is also described in terms of the various iterations of the ternary complex model, the two‐state theory for ion channels, and a probabilistic model of multiple receptor conformations.Curr. Protoc. Pharmacol. 41:1.2.1‐1.2.28. © 2008 by John Wiley & Sons, Inc.
Rodent Model of Attention: The 5‐Choice Serial Reaction Time Task
Authors: Higgins Guy A. , Breysse Nathalie
Published: June 2008

The 5‐choice serial reaction time task (5‐CSRTT) is the most widely used test to measure attentional performance in rodents. The basic test design involves training animals to respond to a brief visual stimulus presented unpredictably in one of five locations. Once trained to stable performance levels, the effects of experimental manipulations on response speed and choice accuracy are measured and each are related to attentional performance. Increasingly, the test is also used to examine aspects of response control. Having been adapted from a human task, the test has also been successfully extended to the mouse and primate, thus highlighting its translational value. Increasingly this test is being applied in drug discovery efforts, primarily to identify novel drug treatments for conditions associated with attention deficits.Curr. Protoc. Pharmacol. 41:5.49.1‐5.49.20. © 2008 by John Wiley & Sons, Inc.
Synthesis of 2′‐Cyclohexenylnucleosides and Corresponding CeNA Building Blocks
Authors: Liu Feng‐Wu , Di Salvo Alberto , Herdewijn Piet
Published: June 2008

A cyclohexene ring has similar structural properties and conformational behavior to a saturated five‐membered furanose ring. In particular, it has good hydrolytic stability. Cyclohexenylnucleosides have been utilized in antiviral drug design, and some nucleosides and oligonucleotides based on the cyclohexene system have been developed. For further investigation of these modified nucleosides and oligonucleotides, synthesis of the chiral cyclohexenylnucleosides in high enantiomeric excess and in bulk quantities is necessary. This unit describes the complete synthesis of four enantiomerically pure 5′‐hydroxy‐4′‐hydroxymethyl‐2′‐cyclohexenylnucleosides (thymine, cytosine, guanine, and adenine) and the four corresponding N‐protected 4′‐(monomethoxytrityl)oxymethyl cyclohexenyl nucleic acids (CeNA) building blocks. The chirality of these compounds is 1′S, 4′R, and 5′S. Curr. Protoc. Nucleic Acid Chem. 33:1.20.1‐1.20.21. © 2008 by John Wiley & Sons, Inc.
Bisulfite Modification for Analysis of DNA Methylation
Authors: Hayatsu Hikoya , Shiraishi Masahiko , Negishi Kazuo
Published: June 2008

Bisulfite is known to deaminate cytosine in nucleic acids, while 5‐methylcytosine resists this bisulfite action. For this reason, bisulfite treatment has been used for detecting 5‐methylcytosine in DNA, a minor component of eukaryotic DNA, presently recognized as playing an important role in the control of gene function. This procedure, called bisulfite genomic sequencing, is a principal method for the analysis of DNA methylation in various biological phenomena, including human diseases such as cancer. This unit describes an efficient procedure utilizing a newly developed high‐concentration bisulfite solution. Protocols for this methodology are supplemented with discussions focused on chemical aspects of the bisulfite treatment. Curr. Protoc. Nucleic Acid Chem. 33:6.10.1‐6.10.15. © 2008 by John Wiley & Sons, Inc.
Cardiac Function Evaluation with Cine MRI of the Heart
Authors: Stillman Arthur E. , Jerosch‐Herold Michael
Published: June 2008

This unit describes how to determine hemodynamic parameters of cardiac function such as ejection fraction (EF), end diastolic volume (EDV), end systolic volume (ESV), stroke volume (SV), and cardiac mass, based on experience using a Siemens 1.5 T Sonata scanner. Briefly, cine loops are acquired over several heartbeats, synchronized with the heart cycle by gating of the encoding steps with the patients electrocardiogram (ECG). Recently, it has become feasible to acquire cine loops in real time, although the temporal resolution is not optimal. Options discussed in this unit include breath hold versus free breathing, prospective triggering versus retrospective gating, and volumetric data sets versus biplanar approaches. Patient parameters such as heart rate or rhythm, degree of functional impairment, the presence of valvular disease, and the need to assess for jets from shunts or valve dysfunction are also treated.
MR Imaging of the Ankle and Hindfoot
Authors: Bencardino Jenny , Rosenberg Zehava S.
Published: June 2008

Magnetic Resonance Imaging (MRI) is the diagnostic modality of choice for evaluation of traumatic ligamentous and tendinous injuries of the ankle and hindfoot. MRI is also valuable in the detection of occult bony trauma, osteochondral injuries, avascular necrosis, osteomyelitis, and a variety of other osseous conditions. This unit presents basic protocols for T1‐ and T2‐weighted sequences and short tau inversion recovery (STIR) imaging. Additional imaging following intravenous gadolinium is indicated in selected cases.
Fluorescence Imaging Techniques for Studying Drosophila Embryo Development
Authors: Mavrakis Manos , Rikhy Richa , Lilly Mary , Lippincott‐Schwartz Jennifer
Published: June 2008

This unit describes fluorescence‐based techniques for noninvasive imaging of development in living Drosophila embryos, discussing considerations for fluorescent imaging within living embryos and providing protocols for generation of flies expressing fluorescently tagged proteins and for preparation of embryos for fluorescent imaging. The unit details time‐lapse confocal imaging of live embryos and discusses optimizing image acquisition and performing three‐dimensional imaging. Finally, the unit provides a variety of specific methods for optical highlighting of specific subsets of fluorescently tagged proteins and organelles in the embryo, including fluorescence recovery after photobleaching (FRAP), fluorescence loss in photobleaching (FLIP), and photoactivation techniques, permitting analysis of specific movements of fluorescently tagged proteins within cells. These protocols, together with the relative ease of generating transgenic animals and the ability to express tagged proteins in specific tissues or at specific developmental times, provide powerful means for examining in vivo behavior of any tagged protein in embryos in myriad mutant backgrounds. Curr. Protoc. Cell Biol. 39:4.18.1‐4.18.43. © 2008 by John Wiley & Sons, Inc.
Visualizing Protease Activity in Living Cells: From Two Dimensions to Four Dimensions
Authors: Jedeszko Christopher , Sameni Mansoureh , Olive Mary B. , Moin Kamiar , Sloane Bonnie F.
Published: June 2008

Proteolytic degradation of extracellular matrix (ECM) components by cells is an important metabolic activity as cells grow, remodel, and migrate through the ECM. The ability to analyze ECM degradation can be valuable in the study of developmental processes as well as pathologies, such as cancer. In this unit we describe an in vitro live cell–based method to image and quantitatively measure the degradation of ECM components by live cells. Cells are grown in the presence of fluorescent dye‐quenched protein substrates (DQ‐gelatin, DQ‐collagen I, and DQ‐collagen IV) that are mixed with protein matrices. Upon proteolytic cleavage, fluorescence is released that directly reflects the level of proteolysis by the cells. Using confocal microscopy and advanced imaging software, the fluorescence is detected and accurate measurements of proteolytic degradation in three and four dimensions can be assessed. Curr. Protoc. Cell Biol. 39:4.20.1‐4.20.15. © 2008 by John Wiley & Sons, Inc.
Visualization and Measurement of DNA Methyltransferase Activity in Living Cells
Authors: Schermelleh Lothar , Spada Fabio , Leonhardt Heinrich
Published: June 2008

In this unit, a live‐cell assay to measure DNA (cytosine‐5) methyltransferase (MTase) activity at the single‐cell level is described. This method takes advantage of the irreversible binding of enzymatically active MTases to genomic DNA substituted with the mechanism‐based inhibitor 5‐aza‐2′‐deoxycytidine (5‐aza‐dC). The procedure comprises incorporation of this nucleoside analog into DNA during replication and quantification of the time‐dependent MTase immobilization by fluorescence recovery after photobleaching (FRAP). This trapping assay monitors kinetic properties and activity‐dependent immobilization of MTases in their native environment and enables direct comparison of mutations and inhibitors that affect MTase regulation and catalytic activity in single living cells. In addition, a simplified protocol to obtain qualitative information on the activity of either endogenously or exogenously expressed MTases is provided. Curr. Protoc. Cell Biol. 39:22.12.1‐22.12.16. © 2008 by John Wiley & Sons, Inc.
Using ZINC to Acquire a Virtual Screening Library
Authors: Irwin John J.
Published: June 2008

The ZINC database of commercially available compounds contains biologically relevant representations of purchasable compounds in ready‐to‐screen formats. ZINC uses catalogs from over 50 compound vendors, changing from time to time to reflect newly available compounds and depleted stock. ZINC is available in subsets that reflect current opinion in the field such as “fragment‐like” and “lead‐like,” and has a facility to create additional small ad hoc subsets. ZINC has a search facility, as well as a service to process molecules that are not in ZINC by uploading them to a server. Curr. Protoc. Bioinform. 22:14.6.1–14.6.23. © 2008 by John Wiley & Sons, Inc.
The Catalytic Asymmetric
S
trecker Reaction
Authors: Shibasaki Masakatsu , Kanai Motomu , Mita Tsuyoshi
Published: June 2008

Alpha‐amino acids are important building blocks for proteins, peptides, and pharmaceuticals. Among a variety of methods to synthesize optically active alpha‐amino acids, the Strecker reaction is one of the simplest and most powerful. This reaction consists of three steps (1) condensation of an aldehyde or ketone with an amine to produce and imine, (2) nucleophilic attack of cyanide on the imine to produce and amino nitrile, and (3) hydrolysis of the amino nitrile to the corresponding alpha‐amino acid. These steps can be conducted in one pot. Conversion of the nitrile group to amide, amine, or aldehyde functionalities is also possible. The catalytic promotion and enantiocontrol of the cyanide addition to the imines is the main focus of the Strecker reaction. Therefore, isolated and purified imines are normally used as substrates. The catalyst turnover efficiency and enantioselectivity of this step are intimately related to the electronic and steric characteristics of the substrate imines, with nitrogen substituent greatly contributing to these factors. However, since optically active alpha‐amino acids are generally the synthetic target of the catalytic asymmetric Strecker reaction, the accessibilty of the starting imines and ease of final deprotection of the product are also important considerations. This chapter focuses on catalytic enantioselective Strecker and Reissert reactions.
Mass Spectrometry of Biological Molecules
Authors: Fuchs Beate , Arnold Klaus , Schiller Jürgen
Published: June 2008

Mass spectrometric methods may serve as powerful analytical methods in life sciences and medicine. Mass spectrometry (MS) is comparable in sensitivity to techniques based on chromatography or electrophoresis but has superior resolution. Although there are a number of suitable ionization methods, allowing the analysis of biological molecules that are of high molecular weight and low volatility, there are mainly two “soft‐ionization” techniques that confer only a minimum of degradation of the analyte: MALDI (matrix‐assisted laser desorption/ionization) and ESI (electrospray ionization).

The following article provides a short overview on the advantages and drawbacks of MALDI analysis of biological samples. Whereas most applications of MALDI are in the field of protein analysis, the analyses of carbohydrates and lipids are also comprehensively discussed. It is shown that MALDI is a useful tool especially in the field of lipid analysis, whereas with carbohydrate analysis, still a number of problems have to be solved. MALDI is a rapid and very sensitive (from the low picomolar to the attomolar range) tool that tolerates high amounts of impurities (in contrast to ESI), which are typically present in biological samples. A further advantage is that mainly singly charged ions are formed; this enables MALDI to be applied even to the analysis of crude mixtures although ion yields may differ significantly in dependence on the molecules of interest. In comparison with ESI, MALDI detects compounds of higher molecular weights more sensitively, whereas ESI is more suitable for labile compounds. Therefore, the combination of both methods is, in many cases, the ideal solution for a number of analytical problems.
Quantitative Structure–Activity Relationships and Computational Methods in Drug Discovery
Authors: Balaban Alexandru T.
Published: June 2008

Quantitative structure–activity relationships (QSARs) are mathematical equations or other types of functions (such as the weights of connections in artificial neural networks) relating chemical structures to their biological activity. The purpose of QSAR studies is to predict novel structures with either beneficial activity as drugs for human or veterinary medicine (bactericides, antiviral or anticancer drugs, and metabolic regulators, such as hypoglycemics, hypotensives, etc.), or selective toxicity for various unwanted higher organisms (pesticides such as fungicides, insecticides, acaricides, weed killers, etc.) Quantitative structure–property relationships (QSPRs) are similar, but the property may be physical or chemical. The main problems involve

finding a mathematical representation of chemical structures (usually organic molecules), represented either as molecular graphs by their constitution or connectivity without considering the three‐dimensional (3‐D) (stereochemical) factors, or as 3‐D objects including stereochemical information;

measuring the biological activities of a series of molecules;

finding the QSAR between each type of biological activity and the most convenient molecular descriptors.

Physicochemical parameters that are closely related to drug transport and ligand binding include lipophilicity, polarity, polarizability, and electronic influence on hydrogen‐donor and hydrogen‐acceptor binding. The next task is to use the QSAR to predict which novel structures to prepare in order to obtain molecules with the desired biological activity. Then the cycle is usually repeated, because a single pass seldom affords the optimal solution.

The main mathematical descriptors and the techniques for obtaining QSARs are reviewed. An important molecular parameter, which may be measured experimentally or computed from the chemical structure, is lipophilicity or hydrophobicity; Hansch introduced then‐octanol–water partition coefficient as a measure of this property, which, to a large extent, determines the ability of molecules to penetrate the lipophilic, bilayer, extra‐ or intracellular membranes. Lipophilicity levels that are too high lead to insolubility in water, i.e. it is difficult to administer the drug orally via the digestive tract. The main constitutional and 3‐D molecular descriptors are described and examples are given. To be statistically valid, correlations must involve orthogonal or orthogonalized descriptors. Linear, multilinear, and nonlinear types of correlations are reviewed. Screening of virtual combinatorial libraries together with high‐throughput combinatorial synthesis and testing provides modern tools for more efficient drug design.
Inductively Coupled Plasma‐Optical Emission Spectrometry
Authors: Hou Xiandeng , Jones Bradley T.
Published: June 2008

Inductively coupled plasma‐optical emission spectrometry (ICP‐OES) is a powerful tool for the determination of metals in a variety of different sample matrices. With this technique, liquid samples are injected into a radiofrequency (RF)‐induced argon plasma using one of a variety of nebulizers or sample introduction techniques. The sample mist reaching the plasma is quickly dried, vaporized, and energized through collisional excitation at high temperature. The atomic emission emanating from the plasma is viewed in either a radial or axial configuration, collected with a lens or mirror, and imaged onto the entrance slit of a wavelength selection device. Single element measurements can be performed cost‐effectively with a simple monochromator‐photomultiplier tube (PMT) combination, and simultaneous multielement determinations are performed for up to 70 elements with the combination of a polychromator and an array detector. The analytical performance of such systems is competitive with most other inorganic analysis techniques, especially with regard to sample throughput and sensitivity.
Cavity Ringdown Laser Absorption Spectroscopy
Authors: Wang Chuji , Miller George P. , Winstead Christopher B.
Published: June 2008

Cavity ringdown spectroscopy (CRDS) has developed rapidly during the last two decades and has been implemented for a variety of applications ranging from fundamental spectroscopic studies, trace chemical detection for environmental monitoring, combustion flame chemistry and plasma diagnostics, elemental and isotopic measurements, breath gas analysis, and fiber ringdown chemical and physical sensor development. A host of chemical species, including atoms, ions, molecules, clusters, and free radicals, have been studied by CRDS. The experimental ringdown scheme has also evolved from an original mirror‐based format to various new forms for detection and analysis of analytes in either gas phase or liquid solutions. Recent research effort has also extended the CRDS approach for fiber optical sensor development. CRDS has become a mature spectrometric technique for a range of prototype and commercial instrumentation. This article provides a review of the latest developments in CRDS applications, specifically emphasizing new trends in elemental and isotopic analysis, plasma diagnostics, breath gas analysis, and new fiber ringdown techniques for sensor development. The introduction of cutting‐edge laser sources into CRDS methods, the combination of CRDS with conventional analytical tools, and current CRDS instrumentation are also briefly discussed.