bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved protein identification efficiency by mass spectrometry using N‐terminal chemical derivatization of peptides from Angiostrongylus costaricensis, a nematode with unknown genome
Authors: León Ileana R. , Neves‐Ferreira Ana G. C. , Valente Richard H. , Mota Ester M. , Lenzi Henrique L. , Perales Jonas
Published: September 2007

Matrix‐assisted laser desorption ionization (MALDI), Peptide Mass Fingerprinting (PMF) and MALDI‐MS/MS ion search (using MASCOT) have become the preferred methods for high‐throughput identification of proteins. Unfortunately, PMF can be ambiguous, mainly when the genome of the organism under investigation is unknown and the quality of spectra generated is poor and does not allow confident identification. The post‐source decay (PSD) fragmentation of singly charged tryptic peptide ions generated by MALDI‐TOF/TOF typically results in low fragmentation efficiency and/or complex spectra, including backbone fragmentation ions (series b and y), internal fragmentation etc. Interpreting these data either manually and/or using de novo sequencing software can frequently be a challenge. To overcome this limitation when studying the proteome of adult Angiostrongylus costaricensis, a nematode with unknown genome, we have used chemical N‐terminal derivatization of the tryptic peptides with 4‐sulfophenyl isothiocyanate (SPITC) prior to MALDI‐TOF/TOF MS. This methodology has recently been reported to enhance the quality of MALDI‐TOF/TOF‐PSD data, allowing the obtainment of complete sequence of most of the peptides and thus facilitating de novo peptide sequencing. Our approach, consisting of SPITC derivatization along with manual spectra interpretation and Blast analysis, was able to positively identify 76% of analyzed samples, whereas MASCOT analysis of derivatized samples, MASCOT analysis of nonderivatized samples and PMF of nonderivatized samples yielded only 35, 41 and 12% positive identifications, respectively. Moreover, de novo sequencing of SPITC modified peptides resulted in protein sequences not available in NCBInr database paving the way to the discovery of new protein molecules. Copyright © 2007 John Wiley & Sons, Ltd.
A novel hybrid electrical/mechanical optimization technique using time‐domain modeling, finite element method and statistical tools for co‐design and optimization of RF‐integrated mechanical structures
Authors: You Chisang , Staiculescu Daniela , Martin Lara , Tentzeris Manos M.
Published: September 2007

The successful use of a design of experiments (DOE) and response surface methods (RSM) approaches in a simultaneous electrical and mechanical optimization study is presented for RF‐integrated mechanical structures. The basic geometry is a mechanically used composite structure consisting of composites facesheets and honeycomb core, in which a microstrip antenna is embedded. The antenna is electromagnetically modeled in time domain and it is found that, for the chosen geometry, the integrated composite structure improves the gain of the antenna without affecting the bandwidth. The structure is then optimized using the same experiment that integrates both the electrical and mechanical parameters of the system. The simple factorial design is very simple to implement and gives a clear understanding of the system behavior, including the interaction between the mechanical changes and electrical performance thus allowing the engineer to integrate, for the first time, both the electrical and mechanical features of the integrated system in the same optimization technique. Copyright © 2007 John Wiley & Sons, Ltd.
Temperature change signals in northern Canada: convergence of statistical downscaling results using two driving GCMs
Authors: Gachon Philippe , Dibike Yonas
Published: September 2007

Coarse resolution global climate models (GCMs) have inherent difficulty simulating a reliable climate regime in coastal areas, as in northern Canada, where sea ice and snow cover are highly sensitive to fine‐scale climate forcings. As a result, strong biases are present in GCM temperature regimes in this region, and the direct use of raw‐GCM climate change signals at the local scale is problematic. However, fine resolution climate change information for use in impact studies can be obtained via statistical downscaling (SD) methods. This study investigates the regression‐based SDSM model with respect to its potential to simulate reliable and plausible changes in mean values as well as probabilities of extreme temperatures, in some specific locations in northern Canada. Four sets of independent climate predictors, from the outputs of two GCMs (i.e. CGCM2 and HadCM3) and using two SRES emission scenarios (i.e. A2 and B2), are used by the SDSM model to construct climate scenario information for this region over the period 2070–2099. The results demonstrate that the SD model is able to capture the major part of the temperature change signal, with a plausible climatic regime for higher warming in winter than in summer and in A2 than in B2 runs. The combination of relevant atmospheric predictors in the SD process is able to take into account most key factors of the temperature change signal, with strong convergence in the magnitude and the timing of the changes in all results. The downscaling signals are more consensual and physically‐plausible in comparison with the raw GCM anomalies, with relatively better skill using HadCM3 predictors than those from CGCM2. The study also confirms that scrupulous analysis of the climate change regime and its temporal and spatial distribution at the scale of interest is essential for it to be useful in impact studies. Copyright © 2007 Crown in the right of Canada. Published by John Wiley & Sons, Ltd
Comparison and evaluation of regional climate scenarios for hydrological impact analysis: General scheme and application example
Authors: Bronstert Axel , Kolokotronis Vassilios , Schwandt Daniel , Straub Helmut
Published: September 2007

We present a scheme and application example for evaluating simulations of possible future conditions of regional climate (‘regional climate change scenarios’) concerning their suitability for hydrological impact studies. The procedure is based on expert knowledge about the impacts of anthropogenic climate change on varying hydrological processes and different hydrological catchment status. A method to evaluate regional climate change scenarios for hydrological impact analysis is presented first, which consists basically of a two‐step knowledge‐based decision and evaluation procedure. The first step (‘climatic evaluation’) evaluates the capability of the climate scenarios to represent regional climate and the plausibility of the future climate conditions. The first step establishes the basis for the second step (‘hydrological evaluation’), which evaluates hydrologically relevant information of the climate scenarios to qualify information about the hydrological processes possibly altered by climate change. From this evaluation of the hydrological processes, an evaluation of regional catchment conditions is derived, such as long‐term water availability, drought conditions or floods.

In the second part of the paper, this method is applied systematically to three different regional climate change scenarios, which have been provided for south Germany. This evaluation results in different levels of adequacy, depending on the hydrological process under question. In general, processes which are governed by temperature conditions (e.g. evaporation, snowmelt) are evaluated as ‘more useful’ than the processes governed by precipitation characteristics (e.g. runoff generation, floods). All regional climate change scenario methods investigated are of rather limited value for extreme hydrological conditions. The proposed method can serve to systematically evaluate the usefulness of climate change scenarios for hydrological impact analysis. It becomes apparent that regional climate scenarios should only be applied for hydrological application if the spatial‐temporal scale of variations of the governing hydrological processes is represented by the scenarios. Copyright © 2007 Royal Meteorological Society
Synoptic evolution of Midwestern US extreme dew point events
Authors: Bentley Mace L. , Stallins J. Anthony
Published: September 2007

Eight Midwestern extremely high dew point events were examined with respect to their synoptic characteristics and evolution. Individual and composite analyses of events suggest that there exists three predominant features associated with extreme dew point events. In nearly all cases, the evolution of the synoptic environment includes the development and propagation of low pressure from the high plains through the upper Great Lakes. The low pressure increases and backs the surface winds acting to advect low‐level moisture from eastern Nebraska, Iowa, Missouri eastward into Illinois and Indiana. The progression of the low pressure and attendant frontal boundaries also acts to modulate the length of the extreme low‐level dew point event. Healthy crops and sufficient soil moisture content throughout this large agricultural region were also evident during the periods of extreme low‐level moisture. Finally, the vertical thermal profile of the atmosphere during extreme dew point events supports previous findings and highlights the importance of restricted low‐level mixing as instrumental in allowing near‐surface moisture to become trapped and increased. Copyright © 2007 Royal Meteorological Society
Preponderance of sensory versus sympathetic nerve fibers and increased cellularity in the infrapatellar fat pad in anterior knee pain patients after primary arthroplasty
Authors: Lehner Birgit , Koeck Franz X. , Capellino Silvia , Schubert Thomas E. O. , Hofbauer Raphael , Straub Rainer H.
Published: September 2007

Sensory nerve fibers transmit pain perception and secrete pro‐inflammatory substance P (SP). Sympathetic nerve fibers secrete anti‐inflammatory norepinephrine and endogenous opioids, which inhibit pain perception in a bidirectional crosstalk with sensory fibers. In patients with anterior knee pain after primary arthroplasty of the knee (AKP), this study investigated in parallel the innervation of the infrapatellar fat pad by sensory and sympathetic nerve fibers. A total of 32 patients with osteoarthritis (OA) of the knee (n = 10), AKP after primary knee joint replacement (n = 7), and OA of the hip (n = 15) were included. Sensory nerve fibers were semiquantitatively detected by immunohistochemistry against SP, and sympathetic nerve fibers were stained with an antibody against tyrosine hydroxylase. Cellular density of the tissue was investigated by counting cell nuclei. The density of sympathetic nerve fibers in the fat tissue was similar in knee OA as compared to AKP. In the fat tissue, density of sensory substance P–positive nerve fibers was higher in AKP than in knee OA, which was not observed in the fibrosis capsule of the fat pad. The preponderance of sensory over sympathetic nerve fibers was accompanied by an increased cellular density in fat tissue in patients with AKP compared to knee OA. A positive correlation existed between cellularity and sensory nerve fiber density in fat tissue. This study revealed a preponderance of sensory over sympathetic innervation in the infrapatellar fat pad in AKP after primary arthroplasty of the knee, which possibly leads to aggravation and continuation of AKP and local inflammation. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:342–350, 2008
Absence of toll-Like Receptor 4 (TLR4) Signaling in the Donor Organ Reduces Ischemia and Reperfusion Injury in a Murine Liver Transplantation Model
Authors: Shen Xiu-Da , Ke Bibo , Zhai Yuan , Gao Feng , Tsuchihashi Sei-Ichiro , Lassman Charles R. , Busuttil Ronald W. , Kupiec-Weglinski Jerzy W.
Published: September 2007

This study analyzes how toll-like receptor 4 (TLR4) signaling in the donor organ affects the ischemia and reperfusion injury (IRI) sequel following liver transplantation. Isogenic orthotopic liver transplantations (OLTs) with rearterialization were performed in groups of wild-type (WT) and TLR4 knockout (KO) mice after donor liver preservation in University of Wisconsin solution at 4°C for 24 hours. Unlike WT OLTs, TLR4-deficient OLTs transplanted to either WT or TLR4 KO recipients suffered significantly less hepatocellular damage, as evidenced by serum alanine aminotransferase levels, and histological Suzuki's grading of liver IRI. Disruption of TLR4 signaling in OLTs decreased local neutrophil sequestration, CD4+ T cell infiltration, interferon (IFN)-γ-inducible protein 10 (CXCL10) and an intercellular adhesion molecule (ICAM-1), as well as tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-2, and IFN-γ, yet increased IL-4 and IL-10 expression. The well-functioning OLTs from TLR4 KO donors revealed attenuated activity of capase-3, and enhanced heme oygenase-1 (HO-1) expression, along with decreased levels of apoptotic endothelial cells/hepatocytes, as compared with WT OLTs with intact TLR4 signaling. Thus, the functional sentinel TLR4 complex in the donor organ plays a key role in the mechanism of hepatic IRI after OLT. Disruption of TLR4 pathway downregulated the early proinflammatory responses and ameliorated hepatic IRI. These results provide the rationale to locally modify innate TLR4 signaling in the donor organ to more efficiently control the adaptive posttransplantation IRI-dependent responses. Liver Transpl 13:1435–1443, 2007. © 2007 AASLD.
Clinical Characteristics of Thrombotic Microangiopathy Following ABO Incompatible Living Donor Liver Transplantation
Authors: Miyata Ryohei , Shimazu Motohide , Tanabe Minoru , Kawachi Shigeyuki , Hoshino Ken , Wakabayashi Go , Kawai Yoko , Kitajima Masaki
Published: September 2007

Thrombotic microangiopathy (TMA) may develop after living donor liver transplantation (LDLT), but the mechanism is not fully understood. We retrospectively analyzed all patients undergoing LDLT at our center, including TMA patients, to elucidate the clinical characteristics and presentation and to determine which patients have a higher risk of occurrence of TMA. In all, 57 adult patients were reviewed after LDLT at our institution. TMA was diagnosed by sudden and severe thrombocytopenia, followed by hemolytic anemia with fractionated erythrocytes in the blood smear. Clinical features were compared between the TMA group and the non-TMA group. Of the 57 patients, 4 were diagnosed with posttransplantation TMA. ABO blood group (ABO)-incompatibility, cyclophosphamide (CPA), and recipient blood group (type O) were closely correlated with the occurrence of TMA. Thrombocytopenia appeared 1 to 5 days before hemolytic anemia. Coagulative function markers stayed at the same level after TMA, while marked elevation was shown in fibrinolytic function markers such as plasminogen activator inhibitor type 1 (PAI-1). TMA occurred at a higher prevalence in ABO-incompatible graft recipients. Additional factors associated with ABO-incompatible transplantation, such as an overdose of immunosuppressants, may affect the likelihood of TMA. Sudden and severe thrombocytopenia presented before hemolytic anemia and the serum levels of PAI-1 correlated well with the clinical course of TMA. In conclusion, early recognition of thrombocytopenia and elevation of PAI-1 is crucial to diagnose TMA especially in ABO-incompatible LDLT. Liver Transpl 13:1455–1462, 2007. © 2007 AASLD.
An Assessment of Interactions Between Hepatitis C Virus and Herpesvirus Reactivation in Liver Transplant Recipients Using Molecular Surveillance
Authors: Humar Atul , Washburn Kenneth , Freeman Richard , Paya Carlos V. , Mouas Houria , Alecock Emma , Razonable Raymund R.
Published: September 2007

Hepatitis C virus (HCV) has been proposed to have immunomodulatory effects in transplant recipients and may promote herpesvirus reactivation. To assess this, we compared the incidence of herpesvirus reactivation in HCV-positive and HCV-negative liver transplant recipients. Quantitative viral load testing was performed at regular intervals posttransplantation for cytomegalovirus (CMV), Epstein-Barr virus (EBV), human herpesviruses (HHV) 6, 7, and 8, and varicella zoster virus (VZV) in 177 liver transplant patients who were HCV-positive (n = 60) or HCV-negative (n = 117). The incidence of CMV disease, CMV viremia, and the peak CMV viral load was not significantly different in HCV-positive vs. HCV-negative patients. Similarly, no differences in HHV-6 or EBV reactivation were observed. HHV-8 or VZV viremia was not detected in any patient in the study. A lower incidence of HHV-7 infection occurred in HCV-positive patients vs. HCV-negative patients (47.6% vs. 72.7%; P = 0.006). In conclusion, these results suggest that HCV infection does not appear to promote herpesvirus reactivation after liver transplantation. Liver Transpl 13:1422–1427, 2007. © 2007 AASLD.
Incidence of Severe Ventricular Arrhythmias During Pulmonary Artery Catheterization in Liver Allograft Recipients
Authors: Gwak Mi Sook , Kim Jie Ae , Kim Gaab Soo , Choi Soo Joo , Ahn Hyun , Lee Jeong Jin , Lee Sang , Kim Myung
Published: September 2007

Liver allograft recipients may develop a hyperdynamic circulation and cardiac electrophysiologic abnormalities. The incidence of severe ventricular arrhythmias in liver allograft recipients during pulmonary artery (PA) catheterization was determined. One hundred five liver allograft recipients were studied prospectively; 5 of the patients with preexisting valvular heart disease, ischemic heart disease, or arrhythmias were excluded. Severe ventricular arrhythmia, defined as 3 or more consecutive ventricular premature beats occurring at a rate of >100 per minute, was observed in 37.0% of the patients during insertion of the catheter and in 25.0% of the patients during removal of the catheter. Two patients developed ventricular tachycardia, and 2 developed ventricular fibrillation; the arrhythmias in these 4 patients did not respond to appropriate pharmacological treatment but resolved promptly after removal of the PA catheter. The catheter transit time from the right ventricle to the pulmonary capillary wedge position was longer in patients with severe ventricular arrhythmia than in those without this arrhythmia (91.6 ± 103.6 s versus 53.3 ± 18.4 s, P < 0.05). In conclusion, patients undergoing liver transplantation have a high risk of developing a ventricular arrhythmia during PA catheterization. Liver Transpl 13:1451–1454. 2007. © 2007 AASLD.
A facile method of shielding from UV damage by polymer photonic crystals
Authors: Wang Jingxia , Liang Jie , Wu Huimeng , Yuan Wenfang , Wen Yongqiang , Song Yanlin , Jiang Lei
Published: September 2007

BACKGROUND: UV radiation is a potent and ubiquitous carcinogen, which is responsible for most of the skin cancer in the human population. General UV protection materials may produce dangerous degradation products under UV irradiation; therefore, safe, nontoxic and simple UV protection approaches are urgent requirements.

RESULTS: A series of photonic crystals with stopband covering the range 200–400 nm have been fabricated which can shield radiation from the whole UV range. Both UV‐visible and 1H NMR results confirm the effective protection from UV light of 254 nm.

CONCLUSIONS: A facile method for UV protection has been demonstrated by utilizing the unusual optical properties of photonic crystals that can inhibit light propagation at a given frequency without specific requirement of chemical composition. This approach opens a new way to protect from UV damage using safe materials, which is of great significance for extending the practical applications of photonic crystals. Copyright © 2007 Society of Chemical Industry
No differences in physical activity in (un)diagnosed asthma and healthy controls
Authors: van Gent René , van der Ent Cornelis K. , van Essen‐Zandvliet Liesbeth E.M. , Rovers Maroeska M. , Kimpen Jan L.L. , de Meer Gea , Klijn Peter H.C.
Published: September 2007

To establish whether asthma affects physical activity levels in children (aged 7–10 years) we evaluated physical activity levels in children with undiagnosed asthma (UDA), diagnosed asthma (DA), and healthy controls (HCs). A cross‐sectional community‐based study was performed which included a parental questionnaire on their child's respiratory health, and testing of airway reversibility and bronchial hyperresponsiveness (BHR). DA was defined as the parents' confirmation of a physician's diagnosis of asthma in the past 12 months. UDA was defined by asthma symptoms combined with airway reversibility or BHR in children without a physician's diagnosis of asthma. Physical activity was measured during 5 days with an accelerometer and a diary, and with the habitual activity estimation scale which reviews the physical activity during the past 2 weeks. The final study population comprised 1614 children of whom 81 (5%) had DA, 130 (8%) UDA, and 202 HCs. Baseline FEV1 % was lowest in children with UDA (UDA FEV1 94% predicted, DA FEV1 98% predicted, HCs FEV1 100% predicted). Using the three methods, no differences were found in the physical activity between children with UDA, DA, and HCs. Childhood asthma does not appear to be associated with a decreased level of daily physical activity in our study population. Pediatr Pulmonol. 2007; 42:1018–1023. © 2007 Wiley‐Liss, Inc.
Evolution of CFTR protein distribution in lung tissue from normal and CF human fetuses
Authors: Marcorelles Pascale , Montier Tristan , Gillet Danièle , Lagarde Nicole , Ferec Claude
Published: September 2007

In order to determine whether or not CFTR protein distribution differs between the airways of fetuses with Cystic Fibrosis (CF) from the airways of normal fetuses we studied the distribution pattern of the CFTR protein in lung. Cases of normal and CF human fetuses as well as cases of normal neonates were examinated. Our aim was to establish whether CFTR expression during pregnancy could be correlated with the maturation of the airways, and to compare normal and CF samples. We hypothesized that any difference between normal and CF fetal lung in CFTR protein expression could be related to a functional change appearing in early development even if no morphological differences could be detected at the light microscopic level. The distribution of CFTR protein progressively increased from 10 weeks of gestation (WG) to mid‐gestation, but thereafter decreased until term. The CFTR protein was first detected in the cytoplasm of undifferentiated epithelial cells. Before mid‐gestation, the immunostaining was strongly positive in bronchi, in sub‐mucosal glands, and in lung parenchyma. Then, it became localized to the apical zone of the epithelial cells. This pattern correlated with differentiation during the second half of gestation. The main difference observed between normal and CF fetuses was a 3‐week delay in detectability of the CFTR protein expression in the latter until 15 weeks of gestation. These results support the hypothesis of an early functional change. Abnormal fetal lung CFTR protein regulation could give rise to a predisposition to the post‐natal inflammatory changes of the airways that characterize CF disease. 2007;42:1032–1040. © 2007 Wiley‐Liss, Inc.
Relationship between pediatric primary provider visits and acute asthma ED visits
Authors: Smith Sharon R. , Wakefield Dorothy B. , Cloutier Michelle M.
Published: September 2007

Objective

The purpose of this study is to evaluate the relationship between primary care provider visits and emergency department (ED) asthma visits for urban, minority children.

Design

This is a retrospective review of eligibility files and Medicaid claims for children with asthma from 1999 to 2001.

Participants

Children 24 months through 17 years of age with Medicaid or state health insurance, who resided in Hartford, Connecticut, and had persistent asthma, were included.

Outcome Measures

The primary outcome was the number of ICD‐9 asthma‐related primary care visits in the 12‐month period before asthma ED visits. Secondary outcomes included the number of filled prescriptions for controller medications 3 and 12 months before emergency asthma visits.

Results

One thousand four hundred seventy‐four children met study criteria. Children with a greater number of asthma‐related primary care visits during the previous 12 months were less likely to have asthma‐related ED visits in 2000 and 2001 (both years P < 0.001). Children with an asthma‐related ED visit had fewer primary care visits (for any reason) in 2000 but not in 2001 (P < 0.01). In 2000, the odds that children with 3 or more asthma‐related primary care visits and a filled inhaled corticosteroid (ICS) had an asthma ED visit were 1/5 those of children with fewer asthma‐related PCP visits or no filled ICS (OR = 0.20, 95% CI (0.06, 0.65)). Fewer than 17% of all children with asthma‐related ED visits filled any prescription for controller medications in the 3 months before these visits.

Conclusion

Asthma‐related primary care visits are associated with fewer asthma‐related ED visits in urban children. 2007;42:1041–1047. © 2007 Wiley‐Liss, Inc.
Safety culture factors, group differences, and risk perception in five petrochemical plants
Authors: Kao Chen‐Shan , Lai Wei Hunq , Chuang Tien Fu , Lee Jin‐Chuan
Published: September 2007

This paper was retracted for necessary author revisions. It later appeared in the June 2008 issue, Vol 27, Issue 2, pp 145 to 152. DOI 10.1002/prs.10246
Luminescence in Si/SiO2/Si structure formed by oxygen implantation
Authors: Shen Zhonghan , Wu Changliang , Lu Qian , Zhang Xin , Wu Xiao‐Jing
Published: September 2007

Luminescent phenomenon, especially electroluminescence (EL), is studied for two samples with a structure of Si/SiO2/Si prepared by oxygen implantation. The asymmetry of EL found in this structure is attributed to the electrical asymmetry of these samples. Several luminescent spots can be observed at the exact same positions under both positive and negative bias, and their area density is about 102/cm2 in these samples. Photoemission microscope (PEM) and optical beam induced resistance change (OBIRCH) are used for the study of EL phenomenon before and after electrical breakdown of the samples, while transmission electron microscope (TEM) is used for the study of the sample's structure. Nc‐Si (nanocrystal silicon) related peaks cannot be found in photoluminescence (PL) spectra for the sample containing Si islands, while oxygen defect related peaks between 350–650 nm can be found for all samples. Luminescence mechanism is discussed based on the model of defect luminescent center (DLC). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of pelletization pressure on the structural and transport properties of TlCaBaCuO superconductors
Authors: Topal U.
Published: September 2007

An investigation is reported of the effects of pelletization pressure on the structural and transport properties of polycrystalline TlCaBaCuO samples with nominal composition of Tl2Ba2Ca2Cu3O10–x. The measurements reveal the following interesting results as the pelletization pressure increases: (1) the volume fraction of self‐formed Tl‐2212 phase decreases and the amount of target Tl‐2223 phase increases; and (2) the links between grains become stronger. Consequently, energy dissipation on grain boundaries decreases and critical current increases. The paper also discusses the applicability of thallium samples as magnetic field sensors. It was found that the samples pelletized at low pressures become more sensitive to a magnetic field compared to those pelletized at high pressures. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photovoltaic effects in InGaN structures with p–n junctions
Authors: Yang Cuibai , Wang Xiaoliang , Xiao Hongling , Ran Junxue , Wang Cuimei , Hu Guoxin , Wang Xinhua , Zhang Xiaobin , Li Jianping , Li Jinmin
Published: September 2007

InGaN photovoltaic structures with p–n junctions have been fabricated by metal organic chemical vapour deposition. Using double‐crystal X‐ray diffraction measurements, it was found that the room temperature band gaps of p‐InGaN and n‐InGaN films were 2.7 and 2.8 eV, respectively. Values of 3.4 × 10–2 mA cm–2 short‐circuit current, 0.43 V open‐circuit voltage and 0.57 fill factor have been achieved under ultraviolet illumination (360 nm), which were related to p–n junction connected back‐to‐back with a Schottky barrier and many defects of the p‐InGaN film. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of hydrogen on electronic structure of fcc iron in relation to hydrogen embrittlement of austenitic steels
Authors: Teus S. M. , Shivanyuk V. N. , Shanina B. D. , Gavriljuk V. G.
Published: September 2007

The total structural energy per primitive lattice cell, density of electron states, spatial distribution of electrons and elastic modulus in fcc Fe–H solid solutions are studied using the density functional theory and Wien2k program package. It is shown that hydrogen increases the density of electron states at the Fermi level. The density of conduction electrons is increased in the vicinity of hydrogen atoms, which suggests that the latter migrate over the crystal lattice surrounded by the clouds of conduction electrons. Calculations of elastic modulus show that hydrogen decreases the shear modulus c44. The consequences for mechanical properties of hydrogen‐charged austenitic steels are analysed taking into account the stress for activation of dislocation sources, the line tension of dislocations and the distance between dislocations in pile‐ups. It is concluded that hydrogen‐induced brittleness of austenitic steels can be satisfactorily interpreted in terms of the hydrogen effect on the electronic structure. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Software component composition: a subdomain‐based testing‐theory foundation
Authors: Hamlet Dick
Published: September 2007

Composition of software elements into assemblies (systems) is a fundamental aspect of software development. It is an important strength of formal mathematical specification that the descriptions of elements can be precisely composed into the descriptions of assemblies. Testing, on the other hand, is usually thought to be ‘non‐compositional.’ Testing provides information about any executable software element, but testing descriptions have not been combined to describe assemblies of elements. The underlying reason for the compositional deficiency of testing is that tests are samples. When two elements are composed, the input samples (test points) for the first lead to an output sample, but it does not match the input test points of the second, following element. The current interest in software components and component‐based software development (CBSD) provides an ideal context for investigating elements and assemblies. In CBSD, the elements (components) are analysed without knowledge of the system(s) to be later assembled. A fundamental testing theory of component composition must use measured component properties (test results) to predict system properties. This paper proposes a testing‐based theory of software component composition based on subdomains. It shows how to combine subdomain tests of components into testing predictions for arbitrarily complex assemblies formed by sequence, conditional, and iteration constructions. The basic construction of the theory applies to functional behaviour, but the theory can also predict the system's non‐functional properties from component subdomain tests. Compared with the alternative of actually building and testing a system, theoretical predictions are computationally more efficient. The theory can also be described as an exercise in modelling. Components are replaced by abstractions derived from testing them, and these models are manipulated to model system behaviour. This article replaces a previously published version. DOI:10.1002/stvr.368. Copyright © 2007 John Wiley & Sons, Ltd.
Optical reflection and mechanical rebound: the shift from analogy to axiomatization in the seventeenth century. Part 1
Authors: SMITH RUSSELL
Published: September 2007

This paper aims to show that the seventeenth-century conception of mechanics as the science of particles in motion founded on universal laws of motion owes much to the employment of a new conceptual resource – the physics of motion developed within optics. The optical analysis of reflection was dynamically interpreted through the mechanical analogy of rebound. The kinematical and dynamical principles so employed became directly applicable to natural phenomena after the eventual transformation of light's ontological status from that of an Aristotelian ‘quality’ to a corpuscular phenomenon, engendered by the rise of atomism during the first half of the seventeenth century. The mechanization of light led to a conceptual shift from the analogical employment of dynamical principles in the physical interpretation of reflection to the mechanical generalization of optical principles – the direct application of kinematical and dynamical principles of reflection to mechanical collisions. This first part of the paper traces out the first conceptual shift from Aristotle's original analogy of reflection as rebound to its full concretization. A second part will trace out the second conceptual shift, from the full concretization of this analogy to the axiomatization of already generalized kinematical and dynamical principles of reflection into laws of nature and of motion.
Storm phase dependence of ion outflow: Statistical signatures obtained by IMAGE/LENA
Authors: Kunori T. , Nosé M. , Taguchi S. , Hosokawa K. , Collier M. R. , Moore T. E.
Published: September 2007

The low‐energy neutral atom (LENA) imager on board the Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE) spacecraft can observe energetic neutral atoms (ENA) of 10 eV to a few keV generated by upflowing ions through charge exchange with the Earth's exosphere. Using IMAGE/LENA data, we statistically analyzed behaviors of the ion outflow in the main and recovery phases of the magnetic storms from June 2000 to December 2001. Results show that during the main phase, most of ENA emissions from the Earth's direction are accompanied by the solar wind dynamic pressure (Pdy) enhancements. For the recovery phase, there are no such tendencies. Instead, the ENA flux shows large values at the beginning of the recovery phase, and then decreases with the storm recovery. These results suggest that the dominant mechanism responsible for the ion outflow during the magnetic storms can be totally different between the two phases.
Abrupt seasonal variation of the ITCZ and the Hadley circulation
Authors: Hu Yongyun , Li Dawei , Liu Jiping
Published: September 2007

Using Global Precipitation Climatology Project (GPCP) daily data, we show that the seasonal migration of the global zonal‐mean intertropical convergence zone (ITCZ) is not smooth, but jumps from the winter hemisphere to the summer hemisphere. The abrupt migration is within 10 days. Detailed analyses reveal that the phenomenon of the abrupt seasonal migration of the ITCZ mainly exists over particular tropical domains, such as Indian Ocean, western and central Pacific, and South America, which gives the rise of the jump of the global zonal‐mean ITCZ. Because the ITCZ constitutes the ascending branch of the Hadley circulation, we also examine whether there exists such an abrupt seasonal change in the Hadley circulation. It is found that the intensity of the Hadley cells evolves smoothly with time. However, the horizontal scales of the Hadley cells demonstrate abrupt seasonal changes, corresponding to the abrupt seasonal migration of the global ITCZ. The winter cell extends rapidly across the equator, while the summer cell rapidly narrows. This suggests that the solsticial cell is the dominant component of the Hadley circulation, and that the equinoctial symmetric pattern is ephemeral.
Generation of a ULF wave resonator in the magnetosphere by neutral gas release
Authors: Mithaiwala Manish , Rudakov Leonid , Ganguli Gurudas
Published: September 2007

ULF waves generated by the release of a neutral gas in the equatorial plane of the Earth's magnetosphere will be trapped between two turning points forming a resonator. This effectively prolongs the lifetime of the ensuing turbulence making it more useful for pitch angle scattering trapped energetic electrons. In the multispecies plasma environment of the magnetosphere, the presence of a small amount of helium causes the waves to reflect when their frequency matches the Buchsbaum frequency as they travel along field lines away from the equator. For a proton‐electron‐helium plasma, the Buchsbaum frequency is near the helium cyclotron frequency. With typical abundances of helium in the inner radiation belts, there is virtually no loss of wave energy by cyclotron damping at the turning points as the waves reflect between conjugate Buchsbaum points. Wave energy is eventually dissipated by collisional effects and radial convection.
Decadal to multidecadal variability and the climate change background
Authors: Parker David , Folland Chris , Scaife Adam , Knight Jeff , Colman Andrew , Baines Peter , Dong Buwen
Published: September 2007

Three prominent quasi‐global patterns of variability and change are observed using the Met Office's sea surface temperature (SST) analysis and almost independent night marine air temperature analysis. The first is a global warming signal that is very highly correlated with global mean SST. The second is a decadal to multidecadal fluctuation with some geographical similarity to the El Niño–Southern Oscillation (ENSO). It is associated with the Pacific Decadal Oscillation (PDO), and its Pacific‐wide manifestation has been termed the Interdecadal Pacific Oscillation (IPO). We present model investigations of the relationship between the IPO and ENSO. The third mode is an interhemispheric variation on multidecadal timescales which, in view of climate model experiments, is likely to be at least partly due to natural variations in the thermohaline circulation. Observed climatic impacts of this mode also appear in model simulations. Smaller‐scale, regional atmospheric phenomena also affect climate on decadal to interdecadal timescales. We concentrate on one such mode, the winter North Atlantic Oscillation (NAO). This shows strong decadal to interdecadal variability and a correspondingly strong influence on surface climate variability which is largely additional to the effects of recent regional anthropogenic climate change. The winter NAO is likely influenced by both SST forcing and stratospheric variability. A full understanding of decadal changes in the NAO and European winter climate may require a detailed representation of the stratosphere that is hitherto missing in the major climate models used to study climate change.
Cargo-dependent cytotoxicity and delivery efficacy of cell-penetrating peptides: a comparative study
Authors: El-Andaloussi Samir , Järver Peter , Johansson Henrik J. , Langel Ülo
Published: September 2007

The use of CPPs (cell-penetrating peptides) as delivery vectors for bioactive molecules has been an emerging field since 1994 when the first CPP, penetratin, was discovered. Since then, several CPPs, including the widely used Tat (transactivator of transcription) peptide, have been developed and utilized to translocate a wide range of compounds across the plasma membrane of cells both in vivo and in vitro. Although the field has emerged as a possible future candidate for drug delivery, little attention has been given to the potential toxic side effects that these peptides might exhibit in cargo delivery. Also, no comprehensive study has been performed to evaluate the relative efficacy of single CPPs to convey different cargos. Therefore we selected three of the major CPPs, penetratin, Tat and transportan 10, and evaluated their ability to deliver commonly used cargos, including fluoresceinyl moiety, double-stranded DNA and proteins (i.e. avidin and streptavidin), and studied their effect on membrane integrity and cell viability. Our results demonstrate the unfeasibility to use the translocation efficacy of fluorescein moiety as a gauge for CPP efficiency, since the delivery properties are dependent on the cargo used. Furthermore, and no less importantly, the toxicity of CPPs depends heavily on peptide concentration, cargo molecule and coupling strategy.
The linker region plays a key role in the adaptation to cold of the cellulase from an Antarctic bacterium
Authors: Sonan Guillaume K. , Receveur-Brechot Véronique , Duez Colette , Aghajari Nushin , Czjzek Mirjam , Haser Richard , Gerday Charles
Published: September 2007

The psychrophilic cellulase, Cel5G, from the Antarctic bacterium Pseudoalteromonas haloplanktis is composed of a catalytic module (CM) joined to a carbohydrate-binding module (CBM) by an unusually long, extended and flexible linker region (LR) containing three loops closed by three disulfide bridges. To evaluate the possible role of this region in cold adaptation, the LR was sequentially shortened by protein engineering, successively deleting one and two loops of this module, whereas the last disulfide bridge was also suppressed by replacing the last two cysteine residue by two alanine residues. The kinetic and thermodynamic properties of the mutants were compared with those of the full-length enzyme, and also with those of the cold-adapted CM alone and with those of the homologous mesophilic enzyme, Cel5A, from Erwinia chrysanthemi. The thermostability of the mutated enzymes as well as their relative flexibility were evaluated by differential scanning calorimetry and fluorescence quenching respectively. The topology of the structure of the shortest mutant was determined by SAXS (small-angle X-ray scattering). The data indicate that the sequential shortening of the LR induces a regular decrease of the specific activity towards macromolecular substrates, reduces the relative flexibility and concomitantly increases the thermostability of the shortened enzymes. This demonstrates that the long LR of the full-length enzyme favours the catalytic efficiency at low and moderate temperatures by rendering the structure not only less compact, but also less stable, and plays a crucial role in the adaptation to cold of this cellulolytic enzyme.
Theory of the microelectronic traveling wave klystron amplifier with field-emission cathode array
Authors: Ryskin N. M. , Han S. T. , Jang K. H. , Park G. S.
Published: September 2007

A nonlinear theory is developed to predict the gain of a distributed vacuum amplifier employed with field-emitter arrays. Contrary to conventional expectation, it is shown that density modulation of the electrons in the emitting structure is limited by high resistive losses and electronic damping. Therefore, a modified schematic is suggested with the high-frequency modulator separated from the emitter that only dc bias voltage is applied to. Small-signal calculation shows that 15–25dB gain (with 3dB bandwidth over 200GHz) at 100–400GHz frequency band can be obtained within 1–2cm drift space length with currently available parameters of field emitters and microstrip transmission lines. Nonlinear calculations predict promising performances of good linearity and 13–20dBm saturated output power. The suggested distributed vacuum amplifier fully based on microelectromechanical systems technologies would open a new era for the devices operating at the border of millimeter and submillimeter bands.
Experimental observation of the effect of aftercavity interaction in a depressed collector gyrotron oscillator
Authors: Choi E. M. , Shapiro M. A. , Sirigiri J. R. , Temkin R. J.
Published: September 2007

This paper presents the experimental observation of the effect of an aftercavity interaction (ACI) in a depressed collector gyrotron oscillator. The gyrotron generates an output power of 1.5MW at 110GHz in 3μs pulses with a 96kV and 40A electron beam and has a single-stage depressed collector. The ACI arises from an unintended cyclotron resonant interaction between the microwave beam traveling out from the cavity and the gyrating electron beam. The interaction occurs in the uptaper of the launcher, immediately downstream from the cavity, where the magnetic field is slightly lower than its value in the cavity region. The ACI results in a reduction in efficiency since the electron beam tends to extract power from the wave. There is also a broadening of the spent beam energy profile, which reduces the effectiveness of the depressed collector and in turn limits the overall efficiency of a gyrotron. Measurements of the maximum depression voltage of the collector vs beam current at 96kV are compared with simulations from the MAGY code [M. Botton et al., IEEE Trans. Plasma Sci. 26, 882 (1998)]. Excellent agreement is obtained between theory and experiment but only if the ACI is included. In the present experiment, it is estimated that the observed efficiency of 50% would have been about 60% in the absence of the ACI. These results verify the role of the ACI in reducing the efficiency of the gyrotron interaction.
Size dependent fluorescence spectroscopy of nanocolloids of ZnO
Authors: Irimpan Litty , Nampoori V. P. N. , Radhakrishnan P. , Deepthy A. , Krishnan Bindu
Published: September 2007

In this article we present size dependent spectroscopic observations of nanocolloids of ZnO. ZnO is reported to show two emission bands, an ultraviolet (UV) emission band and another in the green region. Apart from the known band gap 380 nm and impurity 530 nm emissions, we have found some peculiar features in the fluorescence spectra that are consistent with the nanoparticle size distribution. Results show that additional emissions at 420 and 490 nm are developed with particle size. The origin of the visible band emission is discussed. The mechanism of the luminescence suggests that UV luminescence of ZnO colloid is related to the transition from conduction band edge to valence band, and visible luminescence is caused by the transition from deep donor level to valence band due to oxygen vacancies and by the transition from conduction band to deep acceptor level due to impurities and defect states. A correlation analysis between the particle size and spectroscopic observations is also discussed.
Molecular beam optical Stark study of the [18.1]Π1∕22-XΣ1∕2−4 band system of rhodium monosulfide
Authors: Ma Tongmei , Wang Hailing , Steimle Timothy C.
Published: September 2007

The optical Stark effect in the R13R(0.5) branch feature of the [18.1]Π1∕22-XΣ1∕2−4 (v′,v″=0) band of rhodium monosulfide (RhS) has been recorded and analyzed to determine the permanent electric dipole moment μe of 3.40(2)D for the ground XΣ1∕2−4 (v=0) state and an upper limit of 1.5D for the [18.1]Π1∕22 state. Molecular orbital correlation diagrams are used to interpret the relative values of μe for RhN, RhO, and RhS. The Rh103(I=1∕2) magnetic hyperfine interaction in the XΣ1∕2−4 and [18.1]Π1∕22 states is analyzed.