bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitivity and identifiability of stream flow generation parameters of the SWAT model
Authors: Cibin R. , Sudheer K. P. , Chaubey I.
Published: January 2010

Implementation of sensitivity analysis (SA) procedures is helpful in calibration of models and also for their transposition to different watersheds. The reported studies on SA of Soil and Water Assessment Tool (SWAT) model were mostly focused on identifying parameters for pruning or modifying during the calibration process. This paper presents a sensitivity and identifiability analysis of model parameters that influence stream flow generation in SWAT. The analysis was focused on evaluating the sensitivity of the parameters in different climatic settings, temporal scales and flow regimes. The global sensitivity analysis (GSA) technique based on classical decomposition of variance, Sobol', was employed in this study. The results of the study indicate that modeled stream flow show varying sensitivity to parameters in different climatic settings. The results also suggest that the identifiability of a parameter for a given watershed is a major concern in calibrating the model for the specific watershed, as it might lead to equifinality of parameters. The SWAT model parameters show varying sensitivity in different years of simulation suggesting the requirement for dynamic updation of parameters during the simulation. The sensitivity of parameters during various flow regimes (low, medium and high flow) is also found to be uneven, which suggests the significance of a multi‐criteria approach for the calibration of models. Copyright © 2010 John Wiley & Sons, Ltd.
Parenting behaviour as a mediator between young children's negative emotionality and their anxiety/depression
Authors: van der Bruggen Corine O. , Stams Geert Jan J. M. , Bögels Susan M. , Paulussen‐Hoogeboom Marja C.
Published: January 2010

The goal of this longitudinal study was to examine observed paternal and maternal control (psychological control and autonomy granting) and support (rejection and emotional warmth) as mediators of the relation between children's negative emotionality at 3.5 years of age and depression and anxiety problems at 4.5 years. For 35 children, 60‐min unstructured parent–child interactions were rated at 4.5 years. Results indicated that maternal rejection mediated the relation between children's negative emotionality and their later anxiety/depression. Higher levels of child negative emotionality predicted more psychological control in mothers, but did not predict any parenting behaviours in fathers. Higher levels of paternal autonomy granting were associated with more child anxiety/depression. Unexpectedly, however, more maternal emotional warmth was related to higher levels of child anxiety/depression. The findings offer new insights to guide future research on the (mediating) role of parenting behaviours in the relation between children's negative emotionality and their internalizing problems. Copyright © 2010 John Wiley & Sons, Ltd.
Radiochemical and biological characteristics of 99mTc‐difloxacin and 99mTc‐pefloxacin for detecting sites of infection
Authors: Motaleb M. A.
Published: January 2010

The optimization of the radiolabeling yield of ciprofloxacin analogous, difloxacin and pefloxacin, with 99mTc was described. At pH 4, difloxacin was labeled with 99mTc with a labeling yield of 95.6% by adding 99mTc to 5 mg difloxacin in the presence of 100 µg SnCl2·2H2O whereas 99mTc‐pefloxacin was labeled (98.1%) by adding 99mTc to 4 mg pefloxacin in the presence of 50 µg SnCl2·2H2O. The radiochemical purity for both labeled compounds was evaluated with ITLC and HPLC system. Biological distribution of 99mTc‐difloxacin and 99mTc‐pefloxacin was carried out in experimentally induced infection rats, in the left thigh, using Staphylococcus aureus. Both thighs of the rats were dissected and counted and the ratio of bacterial infected thigh/contralateral thigh was then evaluated. T/NT for both 99mTc‐difloxacin and 99mTc‐pefloxacin was found to be 5.5±0.5 and 4.9±0.3, respectively, which was higher than that of the commercially available 99mTc‐ciprofloxacin. Copyright © 2010 John Wiley & Sons, Ltd.
Lung size and thoracic morphology in shallow‐ and deep‐diving cetaceans
Authors: Piscitelli Marina A. , McLellan William A. , Rommel Sentiel A. , Blum James E. , Barco Susan G. , Pabst D. Ann
Published: January 2010

Shallow‐diving, coastal bottlenose dolphins (Tursiops truncatus) and deep‐diving, pelagic pygmy and dwarf sperm whales (Kogia breviceps and K. sima) will experience vastly different ambient pressures at depth, which will influence the volume of air within their lungs and potentially the degree of thoracic collapse they experience. This study tested the hypotheses that lung size will be reduced and/or thoracic mobility will be enhanced in deeper divers. Lung mass (T. truncatus, n = 106; kogiids, n = 18) and lung volume (T. truncatus, n = 5; kogiids, n = 4), relative to total body mass, were compared. One T. truncatus and one K. sima were cross‐sectioned to calculate lung, thoracic vasculature, and other organ volumes. Excised thoraxes (T. truncatus, n = 3; kogiids, n = 4) were mechanically manipulated to compare changes in thoracic cavity shape and volume. Kogiid lungs were half the mass and one‐fifth the volume of those of similarly sized T. truncatus. The lungs occupied only 15% of the total thoracic cavity volume in K. sima and 37% in T. truncatus. The kogiid and dolphin thoraxes underwent similar changes in shape and volume, although the width of the thoracic inlet was relatively constrained in kogiids. A broader phylogenetic comparison demonstrated that the ratio of lung mass to total body mass in kogiids, physeterids, and ziphiids was similar to that of terrestrial mammals, while delphinids and phocoenids possessed relatively large lungs. Thus, small lung size in deep‐diving odontocetes may be a plesiomorphic character. The relatively large lung size of delphinids and phocoenids appears to be a derived condition that may permit the lung to function as a site of respiratory gas exchange throughout a dive in these rapid breathing, short‐duration, shallow divers. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.
Topsoil reduction and cereal yields on loess soils of southeast Poland
Authors: Rejman J. , Iglik I.
Published: January 2010

The effect of topsoil reduction on yields of cereals on soils developed from loess was evaluated on the basis of a case study and analysis of regional data. Differentiation of yields depended on climatic conditions, soil erosion class and its location in the landscape. The results showed a tendency towards soil productivity decrease with topsoil losses. The greatest decreases were found on severely eroded (18 per cent), for the case study and on very severely eroded soil developed from calcareous loess (25 per cent), for the regional database. On average, yields decreased by 3–4·3 per cent per 10 cm of topsoil reduction. The yield decrease on eroded soils was partly compensated by its increase in some areas of colluvials. Average changes of productivity were compiled together with percentage share of various soils in four loess catchments. The sites were characterised by various time of agricultural land use, start of tractor tillage and percentage of soils transformed by erosion. Despite the differences, similar levels of decrease of cereals productivity, in the range of 5–7 per cent, were found for all the sites at catchment scale. Copyright © 2010 John Wiley & Sons, Ltd.
Corrosion protection of stainless steel by separate polypyrrole electrode in acid solutions
Authors: Hu J. , Zhu H. , Ma Y. , Yi T. , Mao X. , Lin A. , Gan F.
Published: January 2010

Galvanic anodic protection (GAP) of stainless steels by doped polypyrrole (PPy) was investigated using chemically synthesized PPy. Separate PPy powder‐pressed electrodes with different surface areas were prepared. Electrochemical properties of PPy electrodes were studied by open circuit potentials (OCPs) and potentiostatic polarization. PPy powder‐pressed electrodes were coupled with 410‐stainless steel electrodes in different concentrations of sulfuric acid solutions, 5 M phosphoric acid solution, and industrial phosphoric acid solution (5 M phosphoric acid + 0.05% chloride ion). Remarkable shift of OCP to the positive direction and sharp decrease of corrosion rate were observed during the coupling experiments, which implies that 410‐stainless steel was transferred to passive state. Results also showed that PPy electrode with sufficient surface area can provide corrosion protection to 410‐stainless steel electrode in highly corrosive acid solution. Based on the experiment results, GAP provided by PPy and PANi (synthesized under similar conditions) was compared.
Effect of hydrostatic pressure on the nature of passive film of pure nickel
Authors: Liu B. , Zhang T. , Shao Y. , Meng G. , Wang F.
Published: January 2010

The effect of hydrostatic pressure on the nature of passive film of nickel in 3.5% NaCl solution was investigated by means of polarization curves, electrochemical impedance spectroscopy (EIS), and Mott–Schottky measurement. The experimental results revealed that hydrostatic pressure had two opposite effects on passive film of nickel. On one hand, hydrostatic pressure improved the corrosion resistance of passive film of nickel such as the decreased acceptor density. On the other hand, the passive film became unstable and showed a higher diffusivity of acceptor density with the increasing of hydrostatic pressure, which deteriorated the corrosion resistance of passive film of nickel. The deterioration effect had greater influence on the passive film than the improvement effect, which led to the decreasing corrosion resistance of passive film with the increasing of hydrostatic pressure.
Oxidation kinetics of Y‐doped FeCrAl‐alloys in low and high pO2 gases
Authors: Young D. J. , Naumenko D. , Niewolak L. , Wessel E. , Singheiser L. , Quadakkers W. J.
Published: January 2010

A model Fe‐20Cr‐5Al‐0.05Y alloy was oxidized in Ar‐20%O2 and Ar‐4%H2‐7%H2O at 1200–1300 °C. Two‐stage oxidation experiments using oxygen isotope tracers showed that inward oxygen diffusion was predominant in both gases, but more isotope exchange was observed in the H2/H2O gas reaction. The alumina scales formed in both gases were composed of columnar grains, the lateral size of which increased linearly with depth beneath the scale surface. Thermogravimetric measurement of oxygen uptake revealed kinetics which were intermediate to parabolic and cubic kinetic rate laws. A model based on grain boundary diffusion control coupled with competitive oxide grain growth accounts satisfactorily for the results when the requirement for a divergence‐free flux within the scale is imposed. This treatment shows that the oxide grain boundary diffusion coefficient is lower when H2O is the oxidant. It is concluded that hydrogen slows the grain boundary diffusion process by altering the nature of the diffusing species.
Corrosion behaviour of Mg/Al alloys in high humidity atmospheres
Authors: Arrabal R. , Pardo A. , Merino M. C. , Merino S. , Mohedano M. , Casajús P.
Published: January 2010

The influence of relative humidity (80–90–98% RH) and temperature (25 and 50 °C) on the corrosion behaviour of AZ31, AZ80 and AZ91D magnesium alloys was evaluated using gravimetric measurements. The results were compared with the data obtained for the same alloys immersed in Madrid tap water. The corrosion rates of AZ alloys increased with the RH and temperature and were influenced by the aluminium content and alloy microstructure for RH values above 90%. The initiation of corrosion was localised around the Al–Mn inclusions in the AZ31 alloy and at the centre of the α‐Mg phase in the AZ80 and AZ91D alloys. The β‐Mg17Al12 phase acted as a barrier against corrosion.
Corrosion resistance of stainless steel pipes in soil
Authors: Sjögren L. , Camitz G. , Peultier J. , Jacques S. , Baudu V. , Barrau F. , Chareyre B. , Bergquist A. , Pourbaix A. , Carpentiers P.
Published: January 2010

To be able to give safe recommendations concerning the choice of suitable stainless steel grades for pipelines to be buried in various soil environments, a large research programme, including field exposures of test specimens buried in soil in Sweden and in France, has been performed. Resistance against external corrosion of austenitic, super austenitic, lean duplex, duplex and super duplex steel grades in soil has been investigated by laboratory tests and field exposures. The grades included have been screened according to their critical pitting‐corrosion temperature and according to their time‐to‐re‐passivation after the passive layer has been destroyed locally by scratching. The field exposures programme, being the core of the investigation, uses large specimens: 2 m pipes and plates, of different grades. The exposure has been performed to reveal effects of aeration cells, deposits or confined areas, welds and burial depth. Additionally, investigations of the tendency of stainless steel to corrode under the influence of alternating current (AC) have been performed, both in the laboratory and in the field. Recommendations for use of stainless steels under different soil conditions are given based on experimental results and on operating experiences of existing stainless steel pipelines in soil.
Developments in molecular SIMS depth profiling and 3D imaging of biological systems using polyatomic primary ions
Authors: Fletcher John S. , Lockyer Nicholas P. , Vickerman John C.
Published: January 2010

In principle mass spectral imaging has enormous potential for discovery applications in biology. The chemical specificity of mass spectrometry combined with spatial analysis capabilities of liquid metal cluster beams and the high yields of polyatomic ion beams should present unprecedented ability to spatially locate molecular chemistry in the 100 nm range. However, although metal cluster ion beams have greatly increased yields in the m/z range up to 1000, they still have to be operated under the static limit and even in most favorable cases maximum yields for molecular species from 1 µm pixels are frequently below 20 counts. However, some very impressive molecular imaging analysis has been accomplished under these conditions. Nevertheless although molecular ions of lipids have been detected and correlation with biology is obtained, signal levels are such that lateral resolution must be sacrificed to provide a sufficient signal to image. To obtain useful spatial resolution detection below 1 µm is almost impossible. Too few ions are generated! The review shows that the application of polyatomic primary ions with their low damage cross‐sections offers hope of a new approach to molecular SIMS imaging by accessing voxels rather than pixels to thereby increase the dynamic signal range in 2D imaging and to extend the analysis to depth profiling and 3D imaging. Recent data on cells and tissue analysis suggest that there is, in consequence, the prospect that a wider chemistry might be accessible within a sub‐micron area and as a function of depth. However, these advances are compromised by the pulsed nature of current ToF‐SIMS instruments. The duty cycle is very low and results in excessive analysis times, and maximum mass resolution is incompatible with maximum spatial resolution. New instrumental directions are described that enable a dc primary beam to be used that promises to be able to take full advantage of all the capabilities of the polyatomic ion beam. Some new data are presented that suggest that the aspirations for these new instruments will be realized. However, although prospects are good, the review highlights the continuing challenges presented by the low ionization efficiency and the complications that arise from matrix effects. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:142–174, 2011
Refining oxygen isotope analysis in the Nasca region of Peru: An investigation of water sources and archaeological samples
Authors: Buzon M. R. , Conlee C. A. , Bowen G. J.
Published: January 2010

The development of complex societies, irrigation agriculture and sociopolitical transitions are of interest to researchers working in the Nasca region on the south coast of Peru. Occupied for thousands of years, many questions regarding the circumstances of these changes in the area are being investigated. Oxygen isotope analysis provides a method for exploring residential mobility of past peoples during these transitions. This study presents new δ18O data from water sources that would have been used by the ancient inhabitants, providing important information regarding the oxygen isotope variability in the region and the necessary baseline data for migration studies in this region. Our results suggest that the isotopic composition of water sources in the Nasca region is not highly variable. In addition, archaeological human tooth enamel samples from the sites of La Tiza and Pajonal Alto are analysed. The δ18Oc results of the human enamel samples confirm the local nature of the burial population, as suggested by previous strontium isotope analysis (87Sr/86Sr). Copyright © 2010 John Wiley & Sons, Ltd.

This article was published online on 13 January 2010. An error was subsequently identified. This notice is included in the online and print versions to indicate that both have been corrected 15 January 2010.
Exploring differential prescribing between anti‐epileptic drugs in epilepsy patients with a history of mood disorders
Authors: Ishihara Lianna , Webb David J. , Irizarry Michael , Weil John
Published: January 2010

Purpose

To explore differential prescribing of anti‐epileptic drugs (AEDs) to patients with epilepsy by history of mood disorder.

Methods

Epilepsy was defined as at least one diagnosis code and one AED prescription, and all patients must have been on the database 182 days before and after their first AED prescription. The Integrated HealthCare Information Services (IHCIS) insurance claims database included 44 557 patients with epilepsy between January 1997 and March 2007. The General Practice Research Database (GPRD) included 16 904 patients with epilepsy up to March 2007. Patients were categorized by their first use of specified AEDs. Mood disorders were defined as diagnosis codes for depression and bipolar disorder, or anti‐depressant use. The unadjusted odds ratios and 95% confidence intervals for a history of mood disorder diagnosis ever or within the three months prior to AED use were calculated with carbamazepine and oxcarbazepine (CBZ) as the referent.

Results

In the US IHCIS, a history of mood disorders was significantly more common in new users of most AEDs compared to CBZ new users, indicating differential prescribing. Clonazepam and gabapentin were the most commonly prescribed AEDs in patients with epilepsy and a history of mood disorders.

In the UK GPRD, there was less evidence of differential prescribing of AEDs, although gabapentin was prescribed most often to epilepsy patients with a history of mood disorders.

Conclusions

Any observational studies of AEDs and suicidality would have to consider potential channeling bias by history of mood disorders, which is a major risk factor for suicide. Copyright © 2010 John Wiley & Sons, Ltd.
Medical diagnostic consultation concerning mental retardation: An analogue study of school psychologists' attitudes
Authors: Wodrich David L. , Tarbox Jennifer , Balles John , Gorin Joanna
Published: January 2010

Recent research of relevance to school psychologists suggests that the cause, or etiology, of mental retardation can be established by medical diagnosticians in approximately one‐half of cases. In the current study, 109 practicing school psychologists considered a hypothetical case of an elementary student with mental retardation and indicated their attitudes toward the use of medical consultation. School psychologists were randomly assigned to one of three experimental conditions defined by the amount of information about medical diagnostic consultations they received: (a) no information, (b) guidelines from the American Academy of Neurology (AAN) calling for medical consultation in cases of developmental delay, or (c) AAN guidelines plus a concise summary of research on etiology, prevention, and mental retardation. School psychologists with more than 10 years of experience evidenced a more favorable attitude toward medical diagnostic consultation when provided more information, whereas their less experienced colleagues demonstrated no such pattern. This finding, together with others derived from participants' responses, is discussed regarding school psychologists' practice and training. © 2010 Wiley Periodicals, Inc.
Using Laboratory Information Management Systems as central part of a proteomics data workflow
Authors: Stephan Christian , Kohl Michael , Turewicz Michael , Podwojski Katharina , Meyer Helmut E. , Eisenacher Martin
Published: January 2010

The organization and storage of proteomics data are challenging issues today and even more for the rising amount of information in the future. This review article describes the advantages of using Laboratory Information Management Systems (LIMS) in proteomics laboratories. Seven typical LIMS are explored in detail to describe their role in an even bigger interrelation. They are a central part of the proteomics data workflow, starting with data generation and ending with the publication in journals and repositories. Therefore, they enable community‐wide data utilization and further Systems Biology discoveries.
Human duodenal proteome modulations by glutamine and antioxidants
Authors: Thébault Sandrine , Deniel Nicolas , Galland Alexandra , Lecleire Stéphane , Charlionet Roland , Coëffier Moïse , Tron François , Vaudry David , Déchelotte Pierre
Published: January 2010

Purpose: Glutamine (Gln) has protective, anti‐inflammatory effects in animal models and humans. Antioxidant nutrients may exert synergistic effects on intestinal functions. Therefore, these combined nutrients may have a therapeutic potential during intestinal inflammation. This study was designed to investigate in humans the effects of a supplement composed of Gln and high‐dosed antioxidant micronutrients compared to isomolar Gln only, on duodenal proteome.

Experimental design: Enteral perfusion of Gln (0.8 mmol . kg−1. h−1) or supplement was performed in two groups of six healthy volunteers during 5 h before taking endoscopic duodenal biopsies. Protein expression was analyzed by 2‐DE and the relevant proteins identified by MS/MS.

Results: About 1500 protein spots were revealed in both supplement and Gln conditions. Comparative proteomics analysis indicated that 11 proteins were differentially and significantly (p≤0.05) expressed in response to the supplement. These proteins were essentially implicated in metabolism pathways,e.g.fatty acid binding protein‐1 and 40S ribosomal protein SA expressions were downregulated while manganese superoxide dismutase and retinal dehydrogenase‐1 expressions were upregulated.

Conclusions and clinical relevance: This study provides new information on human duodenal proteome and its nutritional modulation, and supports further clinical investigations designed to evaluate the effects of Gln plus antioxidants during intestinal inflammation and cancer.
Colorectal cancer proteomics, molecular characterization and biomarker discovery
Authors: Barderas Rodrigo , Babel Ingrid , Casal José Ignacio
Published: January 2010

Colorectal cancer (CRC) is a widespread disease, whose major genetic changes and mutations have been well characterized in the sporadic form. Much less is known at the protein and proteome level. Still, CRC has been the subject of multiple proteomic studies due to the urgent necessity of finding clinically relevant markers and to elucidate the molecular mechanisms underlying the progression of the disease. These proteomic approaches have been limited by different technical issues, mainly related with sensitivity and reproducibility. However, recent advances in proteomic techniques and MS systems have rekindled the quest for new biomarkers in CRC and an improved molecular characterization. In this review, we will discuss the application of different proteomic approaches to the identification of differentially expressed proteins in CRC. In particular, we will make a critical assessment about the use of 2‐D DIGE, MS and protein microarray technologies, in their different formats, to identify up‐ or downregulated proteins and/or autoantibodies profiles that could be useful for CRC characterization and diagnosis. Despite a wide list of potential biomarkers, it is clear that more scientific efforts and technical advances are still needed to cover the range of low‐abundant proteins, which may play a key role in CRC diagnostics and progression.
Proteomics of bacterial pathogens: Pseudomonas aeruginosa infections in cystic fibrosis – A case study
Authors: Hare Nathan J. , Cordwell Stuart J.
Published: January 2010

Technology development in the high throughput sciences of genomics, transcriptomics and proteomics, has been driven by bacteriological research. These organisms are excellent models for testing new methodology due to their comparatively small genome size, the relative ease of culturing large amounts of material, and the inherent biomedical, environmental and biotechnological interest in their underlying biology. Techniques developed in prokaryotes have since become applicable to higher organisms and human disease, opening vast research opportunities for understanding complex molecular processes. Pseudomonas aeruginosa is an excellent example of a microbe with fascinating properties suitable for stretching the boundaries of technology, and with underlying biology that remains poorly understood. P. aeruginosa is an opportunistic pathogen in humans and contains one of the largest genetic capabilities for a single‐celled organism (approximately 5500 genes), which allows it to encode a wide variety of surface‐associated and secreted virulence factors, as well as adapt to harsh environments, forming resistance to an array of antibacterial agents. While it is a major threat as a nosocomial pathogen, and particularly in the immunocompromised, it is also the most significant cause of mortality in patients suffering from the genetic disorder, cystic fibrosis. This review examines the role of proteomics in gaining a better understanding of the molecular basis of P. aeruginosa infection and persistence in the lungs of cystic fibrosis patients.
Proteomics in chronic wound research: Potentials in healing and health
Authors: Broadbent James , Walsh Terry , Upton Zee
Published: January 2010

Chronic wounds, such as venous and diabetic leg ulcers, represent a significant health and financial burden to individuals and healthcare systems. In worst‐case scenarios this condition may require the amputation of an affected limb, with significant impact on patient quality of life and health. Presently, there are no clinical biochemical analyses used in the diagnosis and management of this condition; moreover few biochemical therapies are accessible to patients. This presents a significant challenge in the efficient and efficacious treatment of chronic wounds by medical practitioners. A number of protein‐centric investigations have analyzed the wound environment and implicated a suite of molecular species predicted to be involved in the initiation or perpetuation of the condition. However, comprehensive proteomic investigation is yet to be engaged in the analysis of chronic wounds for the identification of molecular diagnostic/prognostic markers of healing or therapeutic targets. This review examines clinical chronic wound research and recommends a path toward proteomic investigation for the discovery of medically significant targets. Additionally, the Supporting Information documents associated with this review provide the first comprehensive summary of protein‐centric, small molecule and elemental analyses in clinical chronic wound research.
Degradative proteomics and disease mechanisms
Authors: Lanucara Francesco , Brownridge Philip , Young Iain S. , Whitfield Phillip D. , Doherty Mary K.
Published: January 2010

Protein degradation is a fundamental biological process, which is essential for the maintenance and regulation of normal cellular function. In humans and animals, proteins can be degraded by a number of mechanisms: the ubiquitin‐proteasome system, autophagy and intracellular proteases. The advances in contemporary protein analysis means that proteomics is increasingly being used to explore these key pathways and as a means of monitoring protein degradation. The dysfunction of protein degradative pathways has been associated with the development of a number of important diseases including cancer, muscle wasting disorders and neurodegenerative diseases. This review will focus on the role of proteomics to study cellular degradative processes and how these strategies are being applied to understand the molecular basis of diseases arising from disturbances in protein degradation.
Glycoproteomics and clinical applications
Authors: Tian Yuan , Zhang Hui
Published: January 2010

Glycosylation is the most structurally complicated and diverse type of protein modifications. Protein glycosylation has long been recognized to play fundamental roles in many biological processes, as well as in disease genesis and progression. Glycoproteomics focuses on characterization of proteins modified by carbohydrates. Glycoproteomic studies normally include strategies to enrich glycoproteins containing particular carbohydrate structures from protein mixtures followed by quantitative proteomic analysis. These glycoproteomic studies determine which proteins are glycosylated, the glycosylation sites, the carbohydrate structures, as well as the abundance and function of the glycoproteins in different biological and pathological processes. Here we review the recent development in methods used in glycoproteomic analysis. These techniques are essential in elucidation of the relationships between protein glycosylation and disease states. We also review the clinical applications of different glycoproteomic methods.
Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions
Authors: Singh Nidhi , Warshel Arieh
Published: January 2010

Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer‐aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic linear response approximation (LRA/β version) and related approaches including the linear interaction energy (LIE) to the more approximated and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S‐LRA version) as well as the less rigorous molecular mechanics Poisson–Boltzmann/surface area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S‐LRA/β, and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the nonelectrostatic term. The PDLD/S‐LRA/β performs effectively without the need of reparameterization. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies because of its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S‐LRA/β appears to offer an appealing option for the final stages of massive screening approaches. Proteins 2010. © 2010 Wiley‐Liss, Inc.
‘Mobile transmigrants’ or ‘unsettled returnees’? myth of return and permanent resettlement among Senegalese migrants
Authors: Sinatti Giulia
Published: January 2010

The importance gained by transnationalism and growing attention for the development potential of migration have recently brought forward a new concern for the issue of return migration. Within this framework, return to the home country is understood as having an increasingly less permanent nature. Transnational movement itself is conceived as a form of return, and the debate on the migration–development nexus considers circulation to foster development as it enhances the flow of financial, social, and cultural capital to countries of origin. Seldom, however, has research taken into account the view of migrants themselves. What are their perceptions of transnationalism and return?

Based on ethnographic research conducted among Senegalese migrants in the home country and in Italy, this paper demonstrates the existence, the logics, and functioning of a transmigrant movement made of people who are regular ‘comers and goers’ between Africa and Europe. I show, however, that in the view of these largely unskilled migrants, successful return is still associated with permanent return. This desire for definitive resettlement in the home society must nonetheless be compromised with aspirations for economic advancement and family obligations. Continually delayed, permanent return acquires the status of a myth. Copyright © 2010 John Wiley & Sons, Ltd.
Analgesic and diuretic properties of α‐santalone fromPolygonum flaccidum
Authors: Mazid Abdul , Datta Bidyut K. , Nahar Lutfun , Rashid Abdur , Bachar Sitesh C. , Bashar S. A. M. Khairul , Sarker Satyajit D.
Published: January 2010

Polygonum flaccidumMeissn. is an annual herb, native to Bangladesh, and well known for its analgesic, anti‐inflammatory, diuretic, purgative and insecticidal properties, and also for its use against snake‐bites. The analgesic and the diuretic properties of α‐santalone (1), isolated from the aerial parts ofPolygonum flaccidum, were assessed by the acetic‐acid‐induced writhing method and the Lipschitz test, respectively. Complete1H and13C NMR data of 1 are also presented. Copyright © 2010 John Wiley & Sons, Ltd.
p‐coumaric acid not only inhibits human tyrosinase activityin vitrobut also melanogenesis in cells exposed to UVB
Authors: An Sang Mi , Koh Jae‐Sook , Boo Yong Chool
Published: January 2010

Tyrosinase (TYR) catalyzes rate‐limiting steps of melanogenesis and thus its inhibitors are potentially useful as hypopigmenting agents. Recently,p‐coumaric acid (p‐CA) has been suggested to interfere with the pro‐melanogenic actions of tyrosine due to its structural similarity with tyrosine (An SMet al.,Br J Dermatol2008. 159: 292). In this study, we compared the inhibitory effects ofp‐CA and two other well known TYR inhibitors used in cosmetics – arbutin and kojic acid – on the catalytic activities of mushroom, murine and human TYRsin vitro, using tyrosine and 3,4‐dihydroxyphenylalanine (DOPA) as substrates. The results showed thatp‐CA is a weaker inhibitor of mushroom TYR but much stronger inhibitor of human or murine TYR in comparison with kojic acid and arbutin. In addition,p‐CA inhibited human TYR at much lower concentrations than those required for the inhibition of murine or mushroom TYRs. Enzyme kinetics analysis indicated thatp‐CA is a mixed type (for tyrosine) or competitive inhibitor (for DOPA) of human TYR. Potent antimelanogenic effects ofp‐CA were observed in human epidermal melanocytes exposed to UVB. The present study demonstrated thatp‐CA is a potent and selective inhibitor of human TYR and is potentially useful as a hypopigmenting agent. Copyright © 2010 John Wiley & Sons, Ltd.
On experimental versus theoretically calculated properties of thiadiazole derivatives
Authors: Vasini Enrique Julio , Mirífico María Virginia , Caram José Alberto
Published: January 2010

The recently published results of a theoretical calculation of the physicochemical properties of acenaphtho[1,2‐c]‐ and phenanthro[9,10‐c]‐1,2,5‐thiadiazole 1,1‐dioxide, using a modified density functional theory (CHIH‐DFT), are compared with our experimental results. The CHIH‐DFT‐calculated IR spectra of both compounds are also compared with those obtained using relatively simple RHF calculations. It is concluded that, in these cases, the improvements claimed for the new model chemistry are marginal. The IR spectra of three new derivatives of 1,2,5‐thiadiazole are also reported and calculated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Liquid chromatography/mass spectrometry analysis revealing preferential occurrence of non‐arachidonate‐containing phosphatidylinositol bisphosphate species in nuclei and changes in their levels during cell cycle
Authors: Ogiso Hideo , Nakamura Kazuhiro , Yatomi Yutaka , Shimizu Takao , Taguchi Ryo
Published: January 2010

Phosphatidylinositol phosphates (PtdInsPs) are present within the nucleus, as well as in the membrane. In this mass spectrometry study, different acyl‐containing species of endonuclear PtdInsPs were analyzed in order to clearly understand the role of individual molecular species. A (34:1) acyl‐containing phosphatidylinositol bisphosphate [PtdInsP2(34:1)] and PtdInsP2(36:1) were preferentially detected in envelope‐less nuclei prepared from various cultured human cells, while PtdInsP2(38:4) was not a major component within these nuclei. A significant amount of PtdInsP2(34:0) was detected in the HeLa cell nucleus, but not in the A431 and THP‐1 cell nuclei. During the cell cycle in HeLa cells, PtdInsP2(34:0) levels increased in the early G1 phase, and then gradually decreased through S phase, while PtdInsP2(34:1) levels tended to decrease only in late G1 phase and PtdInsP2(38:4) did not change significantly. Thus, individual PtdInsP2 species apparently play different roles in nuclear events based on individual regulation of endonuclear levels. The non‐arachidonate‐containing species were also detected in normal human blood and fluids, suggesting that these minor species may have unique functions in the human body. The techniques used in this study will be applied to clinical studies on a PtdInsPs metabolism. Copyright © 2010 John Wiley & Sons, Ltd.
On the design of multi‐rate tracking controllers: Application to rotorcraft guidance and control
Authors: Antunes Duarte , Silvestre Carlos , Cunha Rita
Published: January 2010

This paper presents a new methodology for the design and implementation of gain‐scheduled controllers for multi‐rate systems. The proposed methodology provides a natural way to address the integrated guidance and control problem for autonomous vehicles when the outputs are sampled at different instants of time. A controller structure is first proposed for the regulation of non‐square multi‐rate systems with more measured outputs than inputs. Based on this structure, an implementation for a gain‐scheduled controller is obtained that satisfies an important property known as the linearization property. The implementation resembles the velocity implementation for single‐rate systems. The method is then applied to the problem of steering an autonomous rotorcraft along a predefined trajectory defined in terms of space and time coordinates. By considering a convenient error vector to describe the vehicle's dynamics, the trajectory tracking problem is reduced to that of regulating the error variables to zero. Because of the periodic multi‐rate nature of the onboard sensor suite, the controller synthesis is dealt with under the scope of linear periodic systems theory. Simulation results obtained with a full non‐linear rotorcraft dynamic model are presented and discussed. Copyright © 2010 John Wiley & Sons, Ltd.
Reconstruction of the history of the photoelectric effect and its implications for general physics textbooks
Authors: Niaz Mansoor , Klassen Stephen , McMillan Barbara , Metz Don
Published: January 2010

The photoelectric effect is an important part of general physics textbooks. To study the presentation of this phenomenon, we have reconstructed six essential, history and philosophy of science (HPS)‐related aspects of the events that culminated in Einstein proposing his hypothesis of lightquanta and the ensuing controversy within the scientific community. These aspects are (1) Lenard's trigger hypothesis to explain the photoelectric effect, (2) Einstein's quantum hypothesis to explain the photoelectric effect, (3) lack of acceptance of Einstein's quantum hypothesis in the scientific community, (4) Millikan's experimental determination of the Einstein photoelectric equation and Planck's constant, h, (5) Millikan's presuppositions about the nature of light, and (6) the historical presentation and its interpretation within a history and philosophy of science perspective. Using these aspects as criteria, we analyzed 103 university general physics textbooks. Results obtained reveal that these historical elements are largely ignored or distorted in the textbooks, with only three of the texts obtaining a score of satisfactory and none a score of excellent. It is concluded that inclusion of HPS‐related aspects in general physics textbooks can facilitate a better understanding of the dynamics associated with the initial controversy and final acceptance of Einstein's explanation of the photoelectric effect by the scientific community. © 2010 Wiley Periodicals, Inc. Sci Ed 94:903–931, 2010
Change resistance as the crux of the environmental sustainability problem
Authors: Harich Jack
Published: January 2010

Why, despite over 30 years of prodigious effort, has the human system failed to solve the environmental sustainability problem? Decomposing the problem into two sequential subproblems, (1) how to overcome change resistance and (2) how to achieve proper coupling, opens up a fresh line of attack. A simulation model shows that in problems of this type the social forces favoring resistance will adapt to the forces favoring change. If change resistance is high this adaptation response either prevents proper coupling from ever being achieved or delays it for a long time. From this we conclude that systemic change resistance is the crux of the problem and must be solved first. An example of how this might be done is presented. Copyright © 2010 John Wiley & Sons, Ltd.
Trusted intrusion detection architecture for high‐speed networks based on traffic classification, load balancing and high availability mechanism
Authors: Meharouech Sourour , Bouhoula Adel , Abbes Tarek
Published: January 2010

During this time when Internet provides essential communication between an infinite number of people and is being increasingly used as a tool for commerce, security becomes a tremendously important issue to deal with. However, traditional widely used security methods such as firewalls, cryptography and intrusion detection systems (IDSs) have been unable to provide an effective security mechanism for defending high‐speed networks. In fact, nowadays high‐speed networks are very popular; they play an increasingly important role in the domain of information technology, they provide us with a lot of advantages, but they present a big problem for security tools; as networks are becoming faster there is an emerging need for security analysis techniques that keep up with the increased network throughput. In this paper, we are interested in the network intrusion detection systems (NIDSs). In fact, existing NIDSs can barely keep up with bandwidths of some hundred Mbps, whereas nowadays, the network speed presses forward 10 Gbps. So, in order to protect such installations, we propose a new approach presenting trusted intrusion detection architecture for high‐speed networks. The approach aims at accelerating the intrusion detection operation and it is based on three main steps: traffic classification, load balancing and high availability mechanism. This paper describes the above‐mentioned approaches and presents an experimental evaluation of their effectiveness. Copyright © 2010 John Wiley & Sons, Ltd.
Modeling smoking cessation data with alternating states and a cure fraction using frailty models
Authors: Li Yimei , Wileyto E. Paul , Heitjan Daniel F.
Published: January 2010

We propose a flexible parametric model to describe alternating states recurrent‐event data where there is a possibility of cure with each type of event. We begin by introducing a novel cure model in which a common frailty influences both the cure probability and the hazard function given not cured. We then extend our model to data with recurring events of two alternating types. We assume that each type of event has a gamma frailty, and we link the frailties by a Clayton copula. We illustrate the model with an analysis of data from two smoking cessation trials comparing bupropion and placebo, in which each subject potentially experienced a series of lapse and recovery events. Our analysis suggests that bupropion increases the probability of permanent cure and decreases the hazard of lapse, but does not affect the distribution of time to recovery during a lapse. The data suggest a positive but non‐significant association between the lapse and recovery frailties. A simulation study suggests that the estimates have little bias and that their 95 per cent confidence intervals have nearly nominal coverage in samples of practical size. Copyright © 2010 John Wiley & Sons, Ltd.
Conducting‐Polymer Nanotubes Improve Electrical Properties, Mechanical Adhesion, Neural Attachment, and Neurite Outgrowth of Neural Electrodes
Authors: Abidian Mohammad Reza , Corey Joseph M. , Kipke Daryl R. , Martin David C.
Published: January 2010

An in vitro comparison of conducting‐polymer nanotubes of poly(3,4‐ethylenedioxythiophene) (PEDOT) and poly(pyrrole) (PPy) and to their film counterparts is reported. Impedance, charge‐capacity density (CCD), tendency towards delamination, and neurite outgrowth are compared. For the same deposition charge density, PPy films and nanotubes grow relatively faster vertically, while PEDOT films and nanotubes grow more laterally. For the same deposition charge density (1.44 C cm−2), PPy nanotubes and PEDOT nanotubes have lower impedance (19.5 ± 2.1 kΩ for PPy nanotubes and 2.5 ± 1.4 kΩ for PEDOT nanotubes at 1 kHz) and higher CCD (184 ± 5.3 mC cm−2 for PPy nanotubes and 392 ± 6.2 mC cm−2 for PEDOT nanotubes) compared to their film counterparts. However, PEDOT nanotubes decrease the impedance of neural‐electrode sites by about two orders of magnitude (bare iridium 468.8 ± 13.3 kΩ at 1 kHz) and increase capacity of charge density by about three orders of magnitude (bare iridium 0.1 ± 0.5 mC cm−2). During cyclic voltammetry measurements, both PPy and PEDOT nanotubes remain adherent on the surface of the silicon dioxide while PPy and PEDOT films delaminate. In experiments of primary neurons with conducting‐polymer nanotubes, cultured dorsal root ganglion explants remain more intact and exhibit longer neurites (1400 ± 95 µm for PPy nanotubes and 2100 ± 150 µm for PEDOT nanotubes) than their film counterparts. These findings suggest that conducting‐polymer nanotubes may improve the long‐term function of neural microelectrodes.