bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical identification of differentially labeled peptides from liquid chromatography tandem mass spectrometry
Authors: Cho HyungJun , Smalley David M. , Theodorescu Dan , Ley Klaus , Lee Jae K.
Published: September 2007

LC‐MS/MS with certain labeling techniques such as isotope‐coded affinity tag (ICAT) enables quantitative analysis of paired protein samples. However, current identification and quantification of differentially expressed peptides (and proteins) are not reliable for large proteomics screening of complex biological samples. The number of replicates is often limited because of the high cost of experiments and the limited supply of samples. Traditionally, a simple fold change cutoff is used, which results in a high rate of false positives. Standard statistical methods such as the two‐sample t‐test are unreliable and severely underpowered due to high variability in LC‐MS/MS data, especially when only a small number of replicates are available. Using an advanced error pooling technique, we propose a novel statistical method that can reliably identify differentially expressed proteins while maintaining a high sensitivity, particularly with a small number of replicates. The proposed method was applied both to an extensive simulation study and a proteomics comparison between microparticles (MPs) generated from platelet (platelet MPs) and MPs isolated from plasma (plasma MPs). In these studies, we show a significant improvement of our statistical analysis in the identification of proteins that are differentially expressed but not detected by other statistical methods. In particular, several important proteins – two peptides for β‐globin and three peptides for von Willebrand Factor (vWF) – were identified with very small false discovery rates (FDRs) by our method, while none was significant when other conventional methods were used. These proteins have been reported with their important roles in microparticles in human blood cells: vWF is a platelet and endothelial cell product that binds to P‐selectin, GP1b, and GP IIb/IIIa, and β‐globin is one of the peptides of hemoglobin involved in the transportation of oxygen by red blood cells.
Synthesis, structural, and retrostructural analysis of helical dendronized poly(1‐naphthylacetylene)s
Authors: Percec Virgil , Rudick Jonathan G. , Peterca Mihai , Aqad Emad , Imam Mohammad R. , Heiney Paul A.
Published: September 2007

Structural and retrostructural analysis of chiral, nonracemic (poly [(3,4,5)dm8G1‐1EN]), and achiral (poly[(3,4,5)12G1‐1EN]) poly(1‐naphthylacetylene)s demonstrates new design principles for helical dendronized polyarylacetylenes. The oblate cylindrical dendronized polymers self‐organize in a c2mm centered rectangular columnar (Φr‐c) lattice. An all cis‐polyene backbone microstructure with very high cisoid character is introduced to rationalize features from small‐ and wide‐angle X‐ray diffraction experiments. More compact helical conformations are ideal for efficient communication or amplification of chirality over long distances. Peripheral chiral tails select a preferred helical screw sense of the polyene backbone. In solution, the preferred helical conformation persists over a wide temperature range. In bulk, the naphthyl moiety facilitates a longer correlation length for helical order compared to an analogous minidendritic poly(phenylacetylene). These attributes suggest that the naphthyl moiety may be better suited for expressing helical chirality in monolayer domains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4974–4987, 2007
Factors that influence cancer patients' and relatives' anxiety following a three‐person medical consultation: impact of a communication skills training program for physicians
Authors: Lienard Aurore , Merckaert Isabelle , Libert Yves , Delvaux Nicole , Marchal Serge , Boniver Jacques , Etienne Anne‐Marie , Klastersky Jean , Reynaert Christine , Scalliet Pierre , Slachmuylder Jean‐Louis , Razavi Darius
Published: September 2007

Background: No study has yet assessed the impact of physicians' skills acquisition after a communication skills training program on changes in patients' and relatives' anxiety following a three‐person medical consultation. This study aimed at comparing, in a randomized study, the impact, on patients' and relatives' anxiety, of a basic communication skills training program and the same program consolidated by consolidation workshops and at investigating physicians' communication variables associated with patients' and relatives' anxiety.

Methods: Consultations with a cancer patient and a relative were recorded and analyzed by the Cancer Research Campaign Workshop Evaluation Manual. Patients' and relatives' anxiety were assessed with the State‐Trait Anxiety Inventory—State.

Results: No statistically significant change over time and between groups was observed. Mixed‐effects modeling of changes in patients' and relatives' anxiety showed that decreases in both patients' and relatives' anxiety were linked with patients' and relatives' self‐reported distress (p = 0.031 and 0.005), and that increases in both patients' and relatives' anxiety were linked with physicians' breaking bad news (p = 0.028 and 0.005).

Conclusion: No impact of the training program was observed. Results indicate the need to further study communication skills which may help reduce patients' and relatives' anxiety especially when breaking bad news. Copyright © 2007 John Wiley & Sons, Ltd.
Antibody and T‐cell responses specific for the androgen receptor in patients with prostate cancer
Authors: Olson Brian M. , McNeel Douglas G.
Published: September 2007

BACKGROUND

The androgen receptor (AR) is a steroid hormone receptor that is an essential regulator of prostate development, and the primary molecular target for the treatment of metastatic prostate cancer. In this report, we evaluated whether patients with prostate cancer have pre‐existing immune responses specific for the AR as evidence that the AR also might be pursued as an immunological target antigen.

METHODS

The detection of auto‐antibodies specific for the AR in patient sera was evaluated by ELISA and Western blotting. Peripheral blood mononuclear cells were analyzed for the presence of AR‐specific T‐cells, as measured by T‐cell proliferation, interferon gamma (IFNγ) and interleukin‐10 secretion.

RESULTS

We found that a significantly higher frequency of prostate cancer patients have AR LBD‐specific antibody responses than do healthy male volunteers [18/105 cancer patients (17.1%) vs. 0/41 healthy volunteers, P = 0.0049], and that these responses were present regardless of the patients' disease stage [8/46 organ‐confined prostate cancer patients (17.4%), 3/22 metastatic androgen‐dependent patients (13.6%), and 7/37 metastatic, androgen‐independent patients (18.9%)]. These antibodies were pre‐dominantly of the IgG isotype, and furthermore of the IgG2 sub‐isotype. In addition, we found that patients with antibody responses also had concurrent antigen‐specific CD4+ and CD8+ T‐cell proliferation and IFNγ secretion when compared to patients without antibody responses.

CONCLUSIONS

These data demonstrate that some patients with prostate cancer have pre‐existing humoral and cellular immune responses specific for the AR, suggesting that tolerance against the AR is not absolute and that the AR may be a potential immunotherapeutic target antigen. Prostate 67: 1729–1739, 2007. © 2007 Wiley‐Liss, Inc.
Prostatic basal cells in the peripheral and transitional zones: Zonal variation in morphology and in immunophenotype
Authors: Garcia Fernando U. , Haber Marian M. , Chen Xiaoli
Published: September 2007

BACKGROUND

Benign prostatic hyperplasia and prostatic adenocarcinoma exhibit prominent zonal predilections. Basal cells from the transitional zone and from the peripheral zone are postulated to have different underlying biological properties. We studied basal cells in both prostatic zones.

METHODS

Tissue microarrays (TMA) were prepared from 65 whole‐mounted prostatectomy specimens with prostatic adenocarcinoma. The transitional zone and peripheral zone were sampled from each prostate. TMA sections were stained with a basal cell cocktail (CK 34βE12 + p63). The immunostaining pattern and the morphology of basal cells were recorded.

RESULTS

Triangular‐shaped basal cells were highlighted by CK 34βE12 cytoplasmic and p63 nuclear staining. These basal cells had their long axis oriented perpendicular to the basement membrane and their apex toward the lumen interdigited between secretory luminal cells. This morphology was seen in the majority of peripheral zone benign prostatic glands (92.0%) but only a minority of transitional zone benign prostatic glands (18.0%). Basal cells of the transitional zone showed weak or absent CK 34βE12 staining in 65.9% of glands while maintaining p63. All glands with high‐grade prostatic intraepithelial neoplasia (HGPIN) contained the triangular basal cells. In addition, basal cell clusters were identified in 8.7% of peripheral zone glands and 5.2% of HGPIN glands.

CONCLUSIONS

Our results indicate that the basal cell morphology and the basal cell immunophenotype have a zonal variation. The finding of a unique morphology of basal cells and the presence of basal cell clusters in the peripheral zone suggests that the peripheral zone might be the stem/progenitor cell‐rich area in the human prostates. Prostate 67: 1686–1692, 2007. © 2007 Wiley‐Liss, Inc.
Structure of 2‐deoxy‐scyllo‐inosose synthase, a key enzyme in the biosynthesis of 2‐deoxystreptamine‐containing aminoglycoside antibiotics, in complex with a mechanism‐based inhibitor and NAD+
Authors: Nango Eriko , Kumasaka Takashi , Hirayama Toshifumi , Tanaka Nobuo , Eguchi Tadashi
Published: September 2007

A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2‐deoxy‐scyllo‐inosose synthase (DOIS), which catalyzes carbocycle formation from D‐glucose‐6‐phosphate to 2‐deoxy‐scyllo‐inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3‐deoxy‐D‐arabino‐heputulosonate‐7‐phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose‐6‐phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N‐terminal and C‐terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn‐elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A chirality index for investigating protein secondary structures and their time evolution
Authors: Pietropaolo Adriana , Muccioli Luca , Berardi Roberto , Zannoni Claudio
Published: September 2007

We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly‐L‐proline II left‐handed helices, often not detected by secondary structure assignment algorithms.

Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Impact of alpha‐cypermethrin on honey bees foraging on spring oilseed rape (Brassica napus) flowers in field conditions
Authors: Karise Reet , Viik Eneli , Mänd Marika
Published: September 2007

BACKGROUND: Cruciferous oil‐bearing crops have gained in importance worldwide. The expansion of the growing area of these crops has caused a proliferation of pests. Exposure to organophosphate, carbamate and pyrethroid insecticides has been associated with bee poisoning in food crops. This study examines the repellent effect of alpha‐cypermethrin on the number of foraging honey bees, Apis mellifera L., on fields of spring oilseed rape, Brassica napus L. var. oleifera.

RESULTS: The first experiment was conducted on differently sprayed 10 m2 experimental plots where alpha‐cypermethrin was applied at different times. Another experiment was conducted on a 4 ha seed production field divided into two parts: one part was treated with alpha‐cypermethrin and the other was not treated with this insecticide. The results show that there was no difference in the number of honey bees between alpha‐cypermethrin‐treated and untreated patches. The result persisted through three observation years, regardless of varying flower and honey bee densities.

CONCLUSION: No repellent effect of the insecticide on honey bees was found even 24 h after spraying. The density of oilseed rape flowers most likely played a major role in choosing the foraging area. Copyright © 2007 Society of Chemical Industry
Pesticide residues in beeswax samples collected from honey bee colonies (Apis mellifera L.) in France
Authors: Chauzat Marie‐Pierre , Faucon Jean‐Paul
Published: September 2007

In 2002 a field survey was initiated in French apiaries in order to monitor the health of honey bee colonies (Apis mellifera L.). Studied apiaries were evenly distributed across five sites located in continental France. Beeswax samples were collected once a year over 2 years from a total of 125 honey bee colonies. Multiresidue analyses were performed on these samples in order to identify residues of 16 insecticides and acaricides and two fungicides. Residues of 14 of the searched‐for compounds were found in samples. Tau‐fluvalinate, coumaphos and endosulfan residues were the most frequently occurring residues (61.9, 52.2 and 23.4% of samples respectively). Coumaphos was found in the highest average quantities (792.6 µg kg−1). Residues of cypermethrin, lindane and deltamethrin were found in 21.9, 4.3 and 2.4% of samples respectively. Statistical tests showed no difference between years of sampling, with the exception of the frequency of pyrethroid residues. Beeswax contamination was the result of both in‐hive acaricide treatments and, to a much lesser extent, environmental pollution. Copyright © 2007 Society of Chemical Industry
The incidence of honey bee pests and diseases in England and Wales
Authors: Wilkins Selwyn , Brown Mike A , Cuthbertson Andrew GS
Published: September 2007

The Central Science Laboratory (CSL) National Bee Unit (NBU) has been responsible for maintaining the Integrated Bee Health Programme in England and Wales since the early 1990s. The role of the Bee Health Programme is to protect the honey bee, a major pollinator of agricultural and horticultural crops and wild flora, and to provide up‐to‐date technical support to beekeepers. The Bee Health Programme is funded in England by the Department for Environment, Food and Rural Affairs (Defra) and in Wales by the Welsh Assembly Government (WAG). The work includes inspection of honey bee colonies, disease and pest diagnosis, development of contingency plans for emerging threats, minimising the risk of introduction of potentially serious exotic pests and diseases through importation by import risk analysis and related extension work and consultancy services to both government and industry. There is also an underpinning programme of research and development. © Crown copyright 2007. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Risk assessment to honey bees: a scheme developed in France for non‐sprayed systemic compounds
Authors: Alix Anne , Vergnet Christine
Published: September 2007

BACKGROUND: Directive 91/414/EEC envisages that the systemic properties of active substances, if any, are taken into account in evaluating the risk posed to the environment by plant protection products. Among others, honey bees may be exposed to substances via this route, which may pose problems when substances with high toxicity are ingested through pollen or nectar. The guidance documents in support of the risk assessment to bees within the framework of Directive 91/414/EEC do not provide detailed technical guidance on how to proceed in a risk assessment for substances with systemic properties.

RESULTS: A stepwise approach aiming specifically to assess the risk posed by non‐sprayed systemic substances to bees is therefore proposed. This approach first identifies substances with systemic properties, which should be quantified in plant material as pollen and nectar. Exposure estimates calculated for different categories of bees (e.g. foraging bees), based on expected concentrations of the product in pollen or nectar, may be compared with several toxicity endpoints for acute or chronic effects on adults and/or larvae with a toxicity/exposure ratio, which is a measurement of potential risks.

CONCLUSION: Such a ratio is proposed to be used as a trigger for any further refined assessment that would focus on the measurement of effects at the colony level. Copyright © 2007 Society of Chemical Industry
Comparative study of unscreened and screened molecular static linear polarizability in the Hartree–Fock, hybrid‐density functional, and density functional models
Authors: Zope Rajendra R. , Baruah Tunna , Pederson Mark R. , Dunlap B. I.
Published: September 2007

The sum‐over‐states (SOS) polarizabilities are calculated within approximate mean‐field electron theories such as the Hartree–Fock approximation and density functional models using the eigenvalues and orbitals obtained from the self‐consistent solution of the single‐particle equations. The SOS polarizabilities are then compared with those calculated using the finite‐field (FF) method. Three widely used mean‐field models are as follows: (1) the Hartree–Fock (HF) method, (2) the three parameter hybrid generalized gradient approximation (GGA) (B3LYP), and (3) the parameter‐free generalized gradient approximation due to Perdew–Burke–Ernzerhof (PBE). The comparison is carried out for polarizabilities of 142 molecules calculated using the 6‐311++G(d,p) basis set at the geometries optimized at the B3LYP/6‐311G** level. The results show that the SOS method almost always overestimates the FF polarizabilities in the PBE and B3LYP models. This trend is reversed in the HF method. A few exceptions to these trends are found. The mean absolute errors (MAE) in the screened (FF) and unscreened (SOS) polarizability are 0.78, 1.87, and 3.44 Å3 for the HF, B3LYP, and PBE‐GGA methods, respectively. Finally, a simple scheme is devised to obtain FF quality polarizability from the SOS polarizability. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Compound‐specific 81Br/79Br analysis by capillary gas chromatography/multicollector inductively coupled plasma mass spectrometry
Authors: Sylva Sean P. , Ball Lary , Nelson Robert K. , Reddy Christopher M.
Published: September 2007

Brominated organic compounds (BOCs) are of great interest in atmospheric chemistry, natural products, geochemistry, and marine chemistry. The Br isotope ratios (81Br and 79Br; average 81Br/79Br = 0.97277) have significant potential for the study of the source, transport, and fate of these compounds. Currently, there is no published method for determining the Br isotopic content of BOCs in complex mixtures. To measure the ratios of stable Br in BOCs on a compound‐specific basis, we assembled a gas chromatography/multicollector inductively coupled plasma mass spectrometry (GC/MCICPMS) system. Background signals, the formation of Ar dimers from organic hydrogen, and the solvent peak did not affect the results. The analysis of three brominated benzenes revealed that 0.3‰ precision can be attained when 0.3 nmol of Br are injected. For samples larger than 0.3 nmol Br, the isotopic precision was within a factor of 3 of the shot‐noise limit, which is the best possible statistical precision attainable avoiding all other sources of noise. Copyright © 2007 John Wiley & Sons, Ltd.
Analysis of low molecular weight acids by negative mode matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Shroff Rohit , Muck Alexander , Svatoš Aleš
Published: September 2007

Free 9‐aminoacridine base is demonstrated to be a suitable matrix for negative mode matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometric (MALDI‐TOFMS) analysis of a wide range of low molecular weight organic acids including aliphatic (from acetic to palmitic acid), aromatic acids, phytohormones (e.g. jasmonic and salicylic acids), and amino acids. Low limits of quantitation in the femtomolar range (jasmonic – 250 fmol; caffeic – 160 fmol and salicylic – 12.5 fmol) and linear detector response over two concentration orders in the pico‐ and femtomolar range are extremely encouraging for the direct study of such acids in complex biological matrices. Copyright © 2007 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the detection of hemoglobins as the protein biomarkers for fecal occult blood
Authors: Lin Shu‐Yao , Shih Shu‐Hung , Wu Deng‐Chyang , Lee Yi‐Chern , Wu Chen‐I , Lo Li‐Hua , Shiea Jentaie
Published: September 2007

In this study, we discover that hemoglobins (Hb), highly water‐soluble globular proteins that are the most predominant proteins detected by matrix‐assisted laser desorption ionization/time‐of‐flight (MALDI‐TOF) mass spectrometry in blood, can be used as protein biomarkers for fecal occult blood (FOB). Hemoglobins were extracted from the feces with pure water and separated from the solids in feces through centrifugation. Singly charged molecular ions of Hb‐related α chains (theoretical MW: 15 126) and β chains (theoretical MW: 15 867) were detected by MALDI‐TOF operated in linear mode using 4‐hydroxy‐α‐cyanocinnamic acid (α‐CHC) as the matrix (with a volumetric ratio of 1:1). The detection limit of FOB using this method is estimated to be lower than 0.1 µg blood per mg of feces, which is approximately 10 to 100 times lower than that of the conventional chemical approaches. The foods and dietary supplements that commonly interfere with the conventional chemical assays of FOB – such as animal blood food products and tablets containing iron and vitamin C – do not interfere with the detection of Hb biomarkers during MALDI‐TOF analysis. Copyright © 2007 John Wiley & Sons, Ltd.
An ion optics for effective ion detection in single particle mass spectrometry
Authors: Cho Sung‐Woo , Lee Donggeun
Published: September 2007

Recently, we reported that significant ion loss occurs prior to detection in conventional single particle mass spectrometry. A more serious type of loss is ion‐kinetic‐energy‐dependent loss. This leads to significant errors in the measured chemical composition of nanoparticles, especially when they have a core‐shell structure. In this paper, a novel ion optics for effective detection of ions generated from a single nanoparticle is designed. Using the commercial software SIMION, the trajectories of ions launched at different speeds inside a single particle mass spectrometer are simulated. The effects of changes are investigated with different repelling plates, Einzel lens additions, and substitutions of the tube electrode between extraction and acceleration grids on the ion flight. The best design was found when assembling the trials in the present condition. It was demonstrated experimentally that the new ion optics works well not only in theory, but also in practice. Copyright © 2007 John Wiley & Sons, Ltd.
Experimental investigation of mass analysis using an island of stability with a quadrupole with 2.0% added octopole field
Authors: Moradian Annie , Douglas D. J.
Published: September 2007

We describe experimental investigations of mass analysis using an island of stability with a linear quadrupole with a 2.0% added octopole field. The island is formed by auxiliary quadrupole excitation. The experiments confirm the results of previous computer simulations (Konenkov et al., J. Am. Soc. Mass Spectrom. 2007; 18: 826–834). With the resolving direct current (dc) applied to the quadrupole so that the Mathieu parameter a > 0, conventional mass analysis with applied radio‐frequency (rf) and dc and no auxiliary excitation is possible. In this case, use of an island of stability yields similar peak shape and resolution. However, with the polarity of the resolving dc reversed, so that a < 0, only very low resolution can be obtained; the added octopole prevents conventional mass analysis. By using a stability island when a < 0, the resolution is substantially improved. In this case the use of an island allows mass analysis under conditions where the added octopole field severely degrades conventional analysis. The experiments also confirm the position of the island predicted by the simulations. Copyright © 2007 John Wiley & Sons, Ltd.
Cross‐layer approach for an air interface of GEO satellite communication networks
Authors: Kota Sastri , Giambene Giovanni , Candio Nico Liberato
Published: September 2007

Satellite communications play a significant role in supporting next‐generation IP‐based networks. To deploy state‐of‐the‐art satellite technologies supporting media‐rich applications, efficient utilization of radio resources and end‐to‐end Quality of Service support are mandatory requirements. The study of satellite communication constraints such as attenuation, propagation delays, fading is very critical to support user service level agreements. Adaptive resource management, advanced modulation and coding techniques and congestion control algorithms must be jointly conceived. Transport protocols need to address the impact on end‐to‐end system performance due to lower layer protocols. In this paper, we focus on cross‐layer adaptation and interaction analysis. In particular, we refer to TCP and lower layers in a geostationary‐based network architecture, assuming transport protocol enhancements such as TCP NewReno, SACK, Westwood+ and Hybla. At the physical layer, modulations and coding considered include BPSK and QPSK with convolutional coder/Viterbi decoder. The interest of this study is in evaluating the impact of two different transmission mode selection techniques: one scheme selects between the two modes on the basis of the layer 2 packer error rate performance (non‐cross‐layer method); while, the other technique selects the transmission mode on the basis of the TCP goodput performance (cross‐layer method). Our simulation results demonstrate that the second scheme permits the significant improvement of the end‐to‐end performance. Copyright © 2007 John Wiley & Sons, Ltd.
Experimental verification of optical backhaul links for high‐altitude platform networks: Atmospheric turbulence and downlink availability
Authors: Horwath Joachim , Perlot Nicolas , Knapek Markus , Moll Florian
Published: September 2007

Optical backhaul downlinks from high‐altitude platforms (HAPs) are investigated. An experiment demonstrated the advantages of optical links: a small and lightweight terminal with low power consumption was launched to the stratosphere and data transmitted down to a ground station at a rate of 1.25 Gbit/s. Owing to the chosen system parameters and the high budget margin, disturbing turbulence effects did not decrease the link performance.

The scientific aspect of the experiment was to study turbulence effects in order to design future systems with higher transmission performance. On the day of the experiment, measured scintillation and wavefront distortions were minimal in the morning. The best atmospheric conditions were observed about 3 h after sunrise with a peak of the atmospheric coherence length r0 at 16 cm. An r0 of 4 cm was measured as the worst case before sunrise and later during the day. This trend could also be observed for power‐ ($ {\sigma _P^2} $) and intensity scintillation index ($ {\sigma _I^2} $). The latter $ {\sigma _I^2} $ changed from 0.28 (best case) to 1.12. For small $ {\sigma _I^2} $, a lognormal intensity probability density function was measured.

Apart from the robust intensity modulation scheme with direct detection which was used for the trial, future improved systems could benefit from a coherent transmission scheme. According to the r0 measurements and further simulations on heterodyne efficiency it turned out that the aperture size can be decreased from 40 to 10 cm without any significant change in the link margin.

Future stratospheric optical links between HAPs or links from platforms to satellites will not suffer from cloud blockage but it remains an issue for up/downlinks to a ground station. This can be mitigated by ground‐station diversity. Four optical ground stations in the southern part of Europe can lead to an availability of over 98%. The separation distance of the ground stations is about 900 km with a negligible correlation of cloud cover. A change of wavelength from the employed 1.55 to a wavelength around 11‐µm with minimum cloud attenuation would increase the link availability for thin clouds. Copyright © 2007 John Wiley & Sons, Ltd.
Multiuser detection for S‐UMTS and GMR‐1 mobile systems
Authors: Neri Massimo , Casadei Marika , Vanelli‐Coralli Alessandro , Corazza Giovanni E.
Published: September 2007

In this paper, we dwell on the applicability of successive interference cancellation (SIC) and turbo spatial minimum mean‐squared error joint to parallel interference cancellation (turbo SMMSE‐PIC) to a CDMA and a TDMA mobile satellite system (MSS), i.e. Satellite Universal Mobile Telecommunication System (S‐UMTS) and Geo Mobile Radio (GMR‐1), which provide seamless service and coverage extension to their terrestrial counterparts: UMTS and GSM. The adoption of MUD techniques for the return link of these two systems turns out to be instrumental in achieving the required high spectral efficiency but is also very challenging due to the peculiarities of the MSS environment. The theoretical capacity is computed for the considered scenarios, and is then compared with the system performance in real conditions, considering correlated Rician fading, non‐linear distortion introduced by high‐power amplifiers, and residual parameter estimation errors. Physical layer results are used to perform a link budget study and assess the potential system throughput increase. Our results show that MUD techniques allow to largely increase MSS throughput: in S‐UMTS the gain exceeds 50%, while full frequency reuse can be adopted in GMR‐1, compared with the three or more frequency reuse patterns adopted in currently operating systems. In S‐UMTS, the additional antenna gain in the beam centre is exploited to further boost the achievable capacity. Copyright © 2007 John Wiley & Sons, Ltd.
Taurine and zoo felids: considerations of dietary and biological tissue concentrations
Authors: Hedberg Gail E. , Dierenfeld Ellen S. , Rogers Quinton R.
Published: September 2007

Taurine (TAU) is an essential amino acid required in the diets of Felidae at concentrations ranging between 0.04 and 0.2% on a dry matter (DM) basis (in purified, highly digestible diets, and canned diets, respectively). Although the domestic cat seems to be an appropriate physiologic model for zoo felids, it is sometimes difficult to assess TAU status in zoo feeding programs owing to scattered information on feed ingredient TAU content as well as a lack of normal ranges for assessment of TAU in biological tissues. Knowing that TAU is required in the formulation of hand‐rearing diets for exotic felids, the TAU content of 38 ingredients or products used in zoo carnivore feeding or hand‐rearing programs was summarized, including 21 new feedstuffs for which TAU data were previously lacking. The kitten milk replacer contained a lower than expected value for TAU. Commercially prepared frozen or canned meat products, seafood products, whole rodent prey, and most strained meat jarred baby foods contained adequate TAU; chunk meats, and some specific types of jarred baby food meats were considerably lower in TAU content (≤0.10% DM) than other foodstuffs. TAU concentrations in plasma and whole blood of eight spp. of zoo felids sampled opportunistically fell within reference ranges for domestic cats (80–120 and 300–600 nmol/ml in plasma and whole blood, respectively). Plasma concentrations are a useful measure of dietary impact, whereas whole blood concentrations seem to reflect tissue storage of this nutrient. Zoo Biol 26:517–531, 2007. © 2007 Wiley‐Liss, Inc.
The Campaign to End Fistula: What have we learned? Findings of facility and community needs assessments
Authors: Velez A. , Ramsey K. , Tell K.
Published: September 2007

Objective

To present a summary of the findings of the fistula needs assessments that have been conducted through the Campaign to End Fistula in 25 countries in Africa and Asia to expand knowledge on the issue related to causes and impact, country capacity to manage the problem and clinical and programmatic gaps.

Method

The methodology of the assessments was qualitative and quantitative, and included focus group discussions; in‐depth interviews/narratives; key informant interviews; and review of medical records, with slight variations by country.

Results

Analysis of 20 of these assessments provides insight into the capacities, gaps, and perspectives specific to each country regarding fistula prevention and treatment and the social reintegration of treated women.

Conclusion

Needs assessment findings have been key tools to spark action and guide the implementation of national programs to eliminate obstetric fistulas throughout Africa and Asia.
Special Issue: Design Computing and Cognition
Authors: Dong Andy , Gero John S.
Published: September 2007

How can we characterize the promulgation of computing in design? At the outset, computing was conceived predominantly in terms of design automation. It was quickly realized that this medium offered a great deal more than automation, and computing rapidly become a mode of conception for designing. At the juncture of art, design, and computing, however, we recognize computing as becoming loaded with cultural meanings that are enacted through designed works, and designed works that reinterpret a range of assumptions about computing. Design and computing are intervening and lending each other ever-accruing layers of possibilities. The arena of design and computing is producing a new object of knowledge from which they effect: a mode of inquiry, a form of critique, a constitution of practices of subjectivities, and an articulation of objective and subjective investigations. The four papers selected for publication in this Special Issue triangulate these perspectives, providing a new vision for the direction of design and computing and emerging research themes.
Unveiling the structure of the Marrakech Medina: A shape grammar and an interpreter for generating urban form
Authors: Duarte José P. , Rocha João M. , Soares Gonçalo Ducla
Published: September 2007

This paper describes research carried out to develop a parametric urban shape grammar for the Zaouiat Lakhdar quarter of the Medina of Marrakech in Morocco. The goal is to create the basis for a system that could capture some features of the existing urban fabric and apply them in contemporary urban planning and architectural design. The methodology used is described, from the initial historical analysis and fieldwork to the identification of three subgrammars necessary to encode the complexity of the urban preexistences: the urban grammar, the negotiation grammar, and the housing grammar. Top-down and bottom-up approaches to grammar design are analyzed and compared. The bottom-up urban grammar developed is then described, and a hand derivation of the existing urban fabric is proposed. Visual, symbolic, and tagged computer implementations of shape grammars are briefly discussed and a novel design generated by the tagged interpreter is presented.
A function–behavior–structure ontology of processes
Authors: Gero John S. , Kannengiesser Udo
Published: September 2007

This paper presents how the function–behavior–structure (FBS) ontology can be used to represent processes despite its original focus on representing objects. The FBS ontology provides a uniform framework for classifying processes, and includes higher level semantics in their representation. We show that this ontology supports a situated view of processes based on a model of three interacting worlds. The situated FBS framework is then used to describe the situated design of processes.
Moderate psallendo: Musical participation in worship among Gilbertine nuns
Authors: JOSSELYN-CRANSON HEATHER
Published: September 2007

The Gilbertine Order, a monastic community for both sexes founded by Gilbert of Sempringham, attracted the attention of contemporaries because of the close proximity of the men and women who made up its members. Although Gilbertine canons, nuns, lay brothers and lay sisters were strictly separated by gender, the possibility of scandal aroused the suspicion of twelfth-century observers. Modern scholars seem to share the same fascination, even as this applies to the musical history of the order. Many Gilbertine scholars assume that the nuns of the Order of Sempringham did not participate musically in Mass or the Office, lest the canons of the Order fall into sin at the sound of their alluring, feminine voices. This article re-examines the texts that have prompted such assumptions, including the Gilbertine Institutiones, two papal bulls directed at the Order, and works by John Capgrave, John of Salisbury, Gerald of Wales and Nigel de Longchamps. The reassessment of these texts provides evidence that the Gilbertine nuns did sing in worship, albeit in a restricted fashion.
Liturgical chant bibliography 16
Authors: PAUCKER GÜNTHER MICHAEL
Published: September 2007

Liturgical chant bibliography 16 maintains the previously established subdivisions: (1) Editions and facsimile editions, (2) Books and reprints, (3) Congress reports, (4) Chant journals, (5) Collections of essays and dictionaries, (6) Articles in periodicals and Festschriften. Additions to previous bibliographies, mostly reviews, will be found immediately following this introduction.
Social Capital and Political Participation: Understanding the Dynamics of Young People's Political Disengagement in Contemporary Britain
Authors: Henn Matt , Weinstein Mark , Hodgkinson Sarah
Published: September 2007

Only 37 per cent of young people voted at the 2005 British General Election, seemingly confirming the oft-cited view that this generation is becoming increasingly disconnected from the political process. Results from a nationwide survey, however, indicate that their withdrawal from formal politics is more a result of their scepticism of the way the political system operates, than apathy. Furthermore, they are diverse in their political (dis)engagement. Results from an examination of the relative effects of socio-economic location and social capital are inconclusive, although the data indicate that government social policy aimed at mobilising social capital and addressing socio-economic issues may increase civic engagement.
Civic Labour or Doulia? Care, Reciprocity and Welfare
Authors: Deacon Alan
Published: September 2007

This article discusses the grounds on which those who provide informal social care for dependent adults and children can be held to warrant public support, and what obligations they should accept in return. It outlines two interpretations of the rights and responsibilities of such care workers: Stuart White's notion of care as civic labour and Eva Feder Kittay's principle of doulia. It shows that these interpretations reflect different understandings of the self and of reciprocity. The conclusion is that Kittay's writings better reflect the relationality of care, but that it is still possible to justify some forms of welfare conditionality.
Turkey, the EU and Social Policy
Authors: Manning Nick
Published: September 2007

This paper considers what we might expect to be the effect on social policy of Turkish accession to the EU by reviewing the impact of EU membership on social policy in other new member and candidate countries. This effect begins long before membership is finalised, and continues long after membership has been achieved. The patterns of impact can be divided along a number of dimensions: between ‘accession’ and ‘enlargement’; state and civil society; centre and periphery; formal and substantive; and different welfare institutions. In the course of reviewing these variations, the paper reflects upon the nature of social policy itself, and in particular the nature of the European Social Model.
Building Alliances: Incentives and Impediments in the UK Health Consumer Group Sector
Authors: Jones Kathryn
Published: September 2007

This paper addresses the incentives and impediments to alliance formation in the UK health consumer group sector. Research funded by the Economic and Social Research Council shows that links between groups are extensive and highly valued. However, they take place in the context of competition for resources and influence within New Labour's reform agenda. Drawing on theories from sociology and political science this paper shows how in recent years the working environment of groups has shaped cooperation. However, alliance working carries opportunity costs and doubts remain about their ability to survive once these external stimuli disappear.
Time and Change: A Review of the Qualitative Longitudinal Research Literature for Social Policy
Authors: Corden Anne , Millar Jane
Published: September 2007

The four earlier articles in this themed section are based on presentations at a workshop convened to explore challenges in using qualitative longitudinal methods for policy-related research, with particular focus on data analysis and interpretation. Together, they provide useful pointers to the scope of qualitative longitudinal approaches, and extensive discussion of management and analysis of the particular and complex data produced. Readers who are interested in pursuing themselves a qualitative longitudinal approach to policy-related social research will want also to look to a wider literature to enhance their understanding of issues to be taken into consideration, and to explore the range of methods and options. The aim of this review article is to provide some ideas about the kind of literature likely to prove helpful. The bibliographic references for this review article are supplemented by the guide to sources which completes this themed section.
Some Useful Sources
Authors: Corden Anne , Millar Jane
Published: September 2007

There are many key references in the articles in this themed section, including the review article. Rather than repeating those, here we give some web references and also some specific references to the topic of archiving and secondary analysis of qualitative data (with thanks to Rachel Thomson who provided these). This is not a topic that we have covered in any depth in this themed section but it is an important area for anyone thinking of adopting this methodology. We also provide some references on ethical issues.
Baroclinic effects and tides on the Cape Hatteras continental shelf
Authors: Savidge Dana K. , Edwards Catherine R. , Santana Mark
Published: September 2007

Seasonal variability has been identified on the shelf near Cape Hatteras in the semidiurnal and diurnal frequency bands. Large summertime semidiurnal currents appear to be an M2 internal tide whose propagation shoreward is supported by strong Middle Atlantic Bight (MAB) seasonal stratification. At the southern limit of the MAB, strong MAB stratification gives way to weaker seasonal stratification in the South Atlantic Bight (SAB), and the M2 internal tide propagates shoreward less effectively. Strong diurnal variability appears in K1 and O1 components in summer, achieving magnitudes as large as the M2. The diurnal components are typically much smaller than M2 in winter. However, this summer signal is unlikely to be a diurnal internal tide since at these latitudes (34.5–36.5N) the diurnal frequency is subinertial. Coastally trapped waves (CTWs) are presented as a mechanism to explain the increased variability in the diurnal band under summertime stratification. Alongshore southward propagation of the diurnal variability is evident from moorings on the middle and outer shelf (phase speed of 2.1–2.6 m/s along the 60‐m isobath) as far south as Cape Hatteras, but little energy in this band propagates past Cape Hatteras. While diurnal band CTW propagation will not occur at this latitude under well‐mixed conditions, stratification could cause those frequencies to become available for a given wave number, as described in the work of Brink (1990). Estimates of the Huthnance (1978) stratification and slope parameter A, and the Burger number S, suggest the summertime diurnal signal is consistent with baroclinic CTWs. If so, these are the first observations of diurnal CTWs at Cape Hatteras.
Advective transport caused by intraseasonal Rossby waves: A key player of the high chlorophyll variability off the Peru upwelling region
Authors: Bonhomme C. , Aumont O. , Echevin V.
Published: September 2007

The upwelling region off Peru between 5°S and 12°S is characterized by high offshore intraseasonal variability in sea‐surface productivity due to westward propagating chlorophyll anomalies, whose magnitude can reach half the variance of total chlorophyll variations. Spectral analyses of SSH, SST and chlorophyll satellite data show that these events are generated by intraseasonal Rossby waves. The almost constant phase shift between chlorophyll and altimetric signals suggests a physical mechanism dominated by horizontal advection, which is confirmed by the use of a simple conceptual model. Furthermore, an increase from the north to the south in the detected Rossby wave periods, correlated with a decrease in the wavelengths and phase velocities of the wave, suggests the presence of a second baroclinic mode north of 8°S and of a first baroclinic mode south of this latitude. The latitude of this transition is consistent with the theory of critical latitudes, which specifies that at a given latitude, only Rossby wave with periods below a threshold period, depending on the baroclinic structure of the wave, can propagate offshore. According to this theory, second baroclinic mode Rossby waves with periods greater than 130 days are supposed to propagate off the South American coast north of 8°S, the corresponding critical latitude.