bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refinement of the wetted perimeter breakpoint method for setting cease‐to‐pump limits or minimum environmental flows
Authors: Reinfelds Ivars , Haeusler Tim , Brooks Andrew J. , Williams Simon 
Published: July 2004

AbstractAnalysis of inflections or breakpoints apparent in relationships between measures of wetted perimeter and discharge can be used to assist in the determination of minimum environmental flows for perennial rivers. This paper suggests refinements and provides an example application of the wetted perimeter method for the determination of cease‐to‐pump limits in a perennial, unregulated gravel‐bed river subject to increasing levels of surface water extraction. HEC‐GeoRAS modelling outputs of riffle wetted area are used to illustrate that the magnitude of the discharge selected to represent 100% habitat availability is of crucial importance to the breakpoint method. Because of the dependence of the technique on this assumption, we suggest that it is prudent to use an upper and lower limiting discharge based on an assessment of the degree of flow variability to develop a flow range around the zone of diminishing return in the wetted perimeter to discharge relationship. For rivers exhibiting a low degree of flow variability, the mean and median daily flows are likely to provide appropriate discharges for representation of 100% habitat availability. For perennial rivers with a higher degree of flow variability and considerable differences between the mean and median daily flows we suggest use of the 50th and 80th flow duration percentiles. Wetted perimeter breakpoint results are also influenced by the degree to which areas of non‐riffle habitat are included in the analysis. Inclusion of excessive pool areas can lead to significant reductions in resultant recommendations for cease‐to‐pump limits or minimum environmental flows. Integration of hydraulic model outputs with GIS for wetted perimeter analysis of riffles provides a useful, rapid, field‐based approach that can assist with determination of cease‐to‐pump limits or minimum environmental flows in gravel‐bed rivers. However, care is needed in its application and interpretation as the technique is prone to numerous subjective choices that have a substantial influence on results. Copyright © 2004 John Wiley & Sons, Ltd.
A general momentum theory applied to an energy‐extracting actuator disc
Authors: Sharpe D. J. 
Published: July 2004

AbstractA general momentum theory for an energy‐extracting actuator disc modelling a rotor with a multiplicity of blades having radially uniform circulation is presented that includes the effects of wake rotation and expansion. A parallel theory directed at the propeller has been published elsewhere, but not one intended for the wind turbine. The rotation of the wake is shown to be accompanied by a fall in static pressure that is additional to that which occurs across the actuator disc and accounts for the energy extraction from the wind. Energy extraction is recognized in the fully developed wake by the flow regaining the static pressure of the undisturbed wind at the expense of the kinetic energy in the wake. Because the wake is still rotating in the fully developed wake, the additional fall in static pressure appears there also and so does not augment the energy extraction. However, the additional fall in pressure would cause a discontinuity in pressure across the fully developed wake but is prevented by a further slowing down of the wake. The additional slowing down extracts a little more energy from the flow than that predicted by the simple momentum theory, which does not include wake rotation. The overall effect of wake rotation on energy extraction is very small for wind turbines operating at high tip speed ratios but can significantly increase the predicted power output for turbines operating at low tip speed ratios. Copyright © 2004 John Wiley & Sons, Ltd.
Aeroelastic stability predictions for a MW‐sized blade
Authors: Lobitz Don W. 
Published: July 2004

AbstractClassical aeroelastic flutter instability historically has not been a driving issue in wind turbine design. In fact, rarely has this issue even been addressed in the past. Commensurately, among the wind turbines that have been built, rarely has classical flutter ever been observed. However, with the advent of larger turbines fitted with relatively softer blades, classical flutter may become a more important design consideration. In addition, innovative blade designs involving the use of aeroelastic tailoring, wherein the blade twists as it bends under the action of aerodynamic loads to shed load resulting from wind turbulence, may increase the blade's proclivity for flutter. With these considerations in mind it is prudent to revisit aeroelastic stability issues for a MW‐sized blade with and without aeroelastic tailoring. Focusing on aeroelastic stability associated with the shed wake from an individual blade turning in still air, the frequency domain technique developed by Theodorsen for predicting classical flutter in fixed wing aircraft has been adapted for use with a rotor blade. Results indicate that the predicted flutter speed of a MW‐sized blade is slightly greater than twice the operational speed of the rotor. When a moderate amount of aeroelastic tailoring is added to the blade, a modest decrease (12%) in the flutter speed is predicted. By comparison, for a smaller rotor with relatively stiff blades the predicted flutter speed is approximately six times the operating speed. When frequently used approximations to Theodorsen's method are implemented, drastic underpredictions result, which, while conservative, may adversely impact blade design. These underpredictions are also evident when this MW‐sized blade is analysed using time domain methods. Published in 2004 by John Wiley & Sons, Ltd.
Novel high‐resolution silicon drift detectors
Authors: Lechner P. , Pahlke A. , Soltau H. 
Published: July 2004

AbstractSilicon drift detectors (SDDs) are used as energy‐dispersive detectors for x‐ray fluorescence analysis in commercial systems. Because of the low capacitance of the readout anode, achieved by the device topology and by the integration of the first FET on the chip, noise contributions are very small, allowing good energy resolution at low shaping times and high count rates. Typical energy resolution is better than 147 eV FWHM at 5.9 keV (Mn Kα), at −10°C. This allows the chips to be cooled with a thermoelectric element, avoiding the use of liquid nitrogen. SDD chips are produced at MPI‐Halbleiterlabor in Munich with different geometries and areas. Recently, a new SDD has been developed which places the anode and the integrated JFET at the margin of the chip where it can easily be shielded from direct irradiation with the use of a collimator. The new layout allows the design of a readout anode with smaller area and therefore reduces the capacitance to values of about 120 fF compared with 200–250 fF with standard SDDs. The result is an improvement in energy resolution down to 128 eV at −15°C. A second effect is the enhancement of the peak‐to‐background values to 6000 homogeneously across the active area of the detector. Copyright © 2004 John Wiley & Sons, Ltd.
Extending the quantitative analytical capabilities of the EDXRF technique for plant‐based samples
Authors: Bamford S. A. , Jaksic M. , Medunic Z. , Wegrzynek D. , Chinea‐Cano E. , Markowicz A. 
Published: July 2004

AbstractThe energy‐dispersive x‐ray fluorescence (EDXRF) technique has limitations in the quantitative analysis of light elements (low‐Z analytes with Z < 10), for many reasons. This work, however, circumvents the problem through an a priori determination of low‐Z analytes, representative of plant‐based samples. The main purpose of this work was to characterize the major elements in the dark matrix of some plant‐based samples (including biomonitors) using Rutherford backscattering spectrometry (RBS), and the results provided as a generalized input for EDXRF analysis. The derived stoichiometry and mass ratio for the moss, lichen, and cotton cellulose samples analyzed were found to be similar and close to C7H10O5, with an average matrix of C = 49.8%, H = 4.0% and O = 45.8%. Quantitative analysis of plant‐based reference material IAEA‐336 (lichen) was subsequently carried out. Use of the a priori determined dark matrix elements (from one‐time RBS spectrometry) extended the scope of applicability of the EDXRF quantitative methods used, and improved accuracy in the elemental analysis of plant‐based samples. The results obtained were in good agreement with the reference values. Copyright © 2004 John Wiley & Sons, Ltd.
Characterization of x‐rays emerging from between reflector and sample carrier in reflector‐assisted TXRF analysis
Authors: Tsuji Kouichi , Delalieux Filip 
Published: July 2004

AbstractThe possible application of an Si reflector, which is placed just above the sample carrier in total reflection x‐ray fluorescence (TXRF) analysis, was investigated. The x‐rays that were emitted from an Mo tube and passed between the Si reflector and the Si sample carrier were analyzed with an Si drift detector. In our experimental setup, the angle between the reflector and the sample carrier can be changed by adjusting the inclination of the reflector. The intensity of the x‐rays that emerged from between the two Si surfaces drastically changed depending on the reflector angle. At a proper reflector angle, this intensity showed a maximum and, in addition, the Compton peak in the x‐ray spectrum was suppressed. When this x‐ray beam was used for excitation of TXRF signals, the highest intensity of x‐ray fluorescence emitted from the sample was detected, indicating that these experimental conditions are useful for the enhancement of TXRF intensities. Copyright © 2004 John Wiley & Sons, Ltd.
XRF analysis of arsenic‐doped skin phantoms
Authors: Studinski R. C. N. , McNeill F. E. , Chettle D. R. , O'Meara J. M. 
Published: July 2004

AbstractChronic arsenic poisoning can lead to serious health problems including vascular disorders and cancer. Therefore, the development of a system to measure arsenicin vivowould be useful in monitoring exposure. In particular, as skin is one of the tissues in which arsenic has health consequences and is stored for a prolonged period of time, anin vivomeasure of skin arsenic content would be a clinically useful measure of chronic exposure. The preliminary development of an x‐ray fluorescence system to measure arsenicin vivois reported. Standard addition arsenic‐ doped polyester resin phantoms were prepared, and the fluorescence induced by silver K x‐rays from a109Cd source was measured. Preliminary estimates of detection limits for an 8 mm thick phantom and an effective dose of ∼0.3 µSv are 3.5 ± 0.2 and 10.3 ± 0.5 ppm in 90 and 180° measurement geometries, respectively, for a measurement time of 30 min. Copyright © 2004 John Wiley & Sons, Ltd.
Cation–π interactions studied in a model coiled‐coil peptide
Authors: Slutsky Morris M. , Marsh E. Neil G. 
Published: July 2004

AbstractCation–π interactions between aromatic amino acids and the positively charged residues lysine and arginine have been proposed to play an important role in stabilizing protein structure. We have used a peptide that adopts a coiled coil structure as a model system to evaluate the energetic contribution of cation–π interactions to protein folding. Peptides were designed in which phenylalanine, tyrosine, and tryptophan were placed at a solvent‐exposed position of the helix, one turn removed from an arginine residue that could provide a favorable cation–π interaction. Only the arginine–phenylalanine pairing provided significant stabilization of the peptide structure and it appears that hydrophobic packing, rather than the cation–π effect, is more likely to be responsible for the stability of this peptide. We conclude that any stabilizing effect of cation–π interactions in these peptides is much smaller than that predicted from computational studies.
Biophysical characterization of ZSPA‐1—A phage‐display selected binder to protein A
Authors: Lendel Christofer , Dincbas‐Renqvist Vildan , Flores Alexander , Wahlberg Elisabet , Dogan Jakob , Nygren Per‐Åke , Härd Torleif 
Published: July 2004

AbstractAffibodies are a novel class of binding proteins selected from phagemid libraries of the Z domain from staphylococcal protein A. The ZSPA‐1 affibody was selected as a binder to protein A, and it binds the parental Z domain with micromolar affinity. In earlier work we determined the structure of the Z:ZSPA‐1 complex and noted that ZSPA‐1 in the free state exhibits several properties characteristic of a molten globule. Here we present a more detailed biophysical investigation of ZSPA‐1 and four ZSPA‐1 mutants with the objective to understand these properties. The characterization includes thermal and chemical denaturation profiles, ANS binding assays, size exclusion chromatography, isothermal titration calorimetry, and an investigation of structure and dynamics by NMR. The NMR characterization of ZSPA‐1 was facilitated by the finding that trimethylamine N‐oxide (TMAO) stabilizes the molten globule conformation in favor of the fully unfolded state. All data taken together lead us to conclude the following: (1) The topology of the molten globule conformation of free ZSPA‐1 is similar to that of the fully folded structure in the Z‐bound state; (2) the extensive mutations in helices 1 and 2 destabilize these without affecting the intrinsic stability of helix 3; (3) stabilization and reduced aggregation can be achieved by replacing mutated residues in ZSPA‐1 with the corresponding wild‐type Z residues. This stabilization is better correlated to changes in helix propensity than to an expected increase in polar versus nonpolar surface area of the fully folded state.
In vivo folding of recombinant metallo‐β‐lactamase L1 requires the presence of Zn(II)
Authors: Periyannan Gopalraj , Shaw Patrick J. , Sigdel Tara , Crowder Michael W. 
Published: July 2004

AbstractMetallo‐β‐lactamase L1, secreted by pathogenic Stenotrophomonas maltophilia, is a dinuclear Zn(II)‐containing enzyme that hydrolyzes almost all known penicillins, cephalosporins, and carbapenems. The presence of Zn(II) ions in both metal binding sites is essential for full enzymatic activity; however, the mechanism of physiological metal incorporation is unknown. To probe metal incorporation, L1 was over‐expressed in minimal media with (mmL1+Zn) and without (mmL1−Zn) Zn(II) added to the media, and the resulting proteins were purified and characterized. The mmL1+Zn sample was bound by a Q‐Sepharose column, exhibited steady‐state kinetic properties, bound Zn(II), existed as a tetramer, and yielded fluorescence emission and CD spectra similar to L1 overexpressed in rich media. On the other hand, the mmL1−Zn sample did not bind to a Q‐Sepharose column, and gel filtration studies demonstrated that this protein was monomeric. The mmL1−Zn sample exhibited a lower kcat value, bound less Zn(II), and yielded fluorescence emission and CD spectra consistent with this enzyme being folded improperly. Taken together, these data demonstrate that the proper folding of L1 requires the presence of Zn(II) and suggest that in vitro, thermodynamic metal binding studies do not accurately reflect physiological metal incorporation into L1.
H‐bonding in protein hydration revisited
Authors: Petukhov Michael , Rychkov Georgy , Firsov Leonid , Serrano Luis 
Published: July 2004

AbstractH‐bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water–protein H‐bonding at any given protein conformation. The free energy of water–protein H‐bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.
Solution NMR structure of the C‐terminal domain of the human protein DEK
Authors: Devany Matthew , Kotharu N. Prasad , Matsuo Hiroshi 
Published: July 2004

AbstractThe chromatin‐associated protein DEK was first identified as a fusion protein in patients with a subtype of acute myelogenous leukemia. It has since become associated with diverse human ailments ranging from cancers to autoimmune diseases. Despite much research effort, the biochemical basis for these clinical connections has yet to be explained. We have identified a structural domain in the C‐terminal region of DEK [DEK(309–375)]. DEK(309–375) implies clinical importance because it can reverse the characteristic abnormal DNA‐mutagen sensitivity in fibroblasts from ataxia‐telangiectasia (A‐T) patients. We determined the solution structure of DEK(309–375) by nuclear magnetic resonance spectroscopy, and found it to be structurally homologous to the E2F/DP transcription factor family. On the basis of this homology, we tested whether DEK(309–375) could bind DNA and identified the DNA‐interacting surface. DEK presents a hydrophobic surface on the side opposite the DNA‐interacting surface. The structure of the C‐terminal region of DEK provides insights into the protein function of DEK.
Evolutionary trace analysis of the α‐D‐phosphohexomutase superfamily
Authors: Shackelford Grant S. , Regni Catherine A. , Beamer Lesa J. 
Published: July 2004

AbstractThe α‐D‐phosphohexomutase superfamily is composed of four related enzymes that catalyze a reversible, intramolecular phosphoryl transfer on their sugar substrates. The enzymes in this superfamily play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Recent structural and mechanistic studies of one member of this superfamily, phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa, have provided new insights into enzyme mechanism and substrate recognition. Here we use sequence–sequence and sequence–structure comparisons via evolutionary trace analysis to examine 71 members of the α‐D‐phosphohexomutase superfamily. These analyses show that key residues in the active site, including many of those involved in substrate contacts in the P. aeruginosa PMM/PGM complexes, are conserved throughout the enzyme family. Several important regions show class‐specific differences in sequence that appear to be correlated with differences in substrate specificity exhibited by subgroups of the family. In addition, we describe the translocation of a 20‐residue segment containing the catalytic phosphoserine of phosphoacetylglucosamine mutase, which uniquely identifies members of this subgroup.
Effect of hypoxia on the auditory system of goat fetuses during extrauterine incubation
Authors: Nishioka Nobuko , Nishina Hidenori , Yoshida Koyo , Kinoshita Katsuyuki , Ehara Yoshiro 
Published: July 2004

J Obstet Gynaecol Res 2002; 2: 109–114Aim:  To investigate the effect of hypoxia on the auditory system in fetuses, we attempted to analyze the auditory brainstem response, the middle latency response, and changes of several physiological parameters of goat fetuses during extrauterine incubation.Methods:  We conducted extrauterine incubation of five goat fetuses at around 127 days of gestation (term = 148 days). Their physiological parameters, such as fetal heart rate, mean blood pressure, flow rate of carotid artery, as well as the auditory brainstem response and middle latency response, were recorded prior to and during hypoxia, and the two sets of data were compared with each other.Results:  In all five cases, the fetal heart rate decreased from 178 ± 12.2 b.p.m. to 144 ± 15.2 b.p.m. during hypoxia, while mean blood pressure and flow rate of carotid artery increased from 37.3 ± 3.7 mmHg to 43.2 ± 5.1 mmHg, and from 38.5 ± 5.5 mL/min to 47.0 ± 5.1 mL/min, respectively. The latency of the auditory brainstem response's wave V and of the middle latency response's Pa wave elongated from 5.24 ± 0.24 ms to 5.69 ± 0.20 ms, and from 19.2 ± 1.6 ms to 20.9 ± 1.4 ms, respectively.Conclusion:  Although fetal compensatory reactions, such as increases in mean blood pressure and flow rate of carotid artery during hypoxia were recognized, elongation of latency, and decrement of amplitude were observed in the auditory brainstem response and middle latency response. These results suggest that hypoxia itself influences the auditory system of the fetus.
Resection of local recurrence of renal cell carcinoma in a hemodialysis patient 6 years after radical nephrectomy
Authors: IRIE KYOKO , ISHIZUKA OSAMU , YOKOYAMA HITOSHI , KINEBUCHI YOSHIAKI , SATOH TOMOYA , NISHIZAWA OSAMU 
Published: July 2004

Abstract  Left radical nephrectomy was performed on a 39‐year‐old‐man because of renal cell carcinoma (grade 1, clear cell and granular cell carcinoma: pT3b pN0 pM0), 6 years after the beginning of hemodialysis. The second surgical intervention for local recurrence was performed 6 years after the first operation (grade 2 > 3, clear cell and granular cell carcinoma).This is the second published case report of the resection of a local recurrence of renal cell carcinoma after nephrectomy in a hemodialysis patient. Even after the curative operation, follow up for local recurrence should be continued in hemodialysis patients, especially for high stage renal cell carcinoma.
Laparoscopic pyeloplasty for ureteropelvic junction obstruction: Outcome of initial 12 procedures
Authors: IWAMURA MASATSUGU , SOH SHIGEHIRO , IRIE AKIRA , KADOWAKI KAZUOMI , MATSUSITA YASUSHI , FUJIOKA TOMOAKI , BABA SHIRO 
Published: July 2004

Abstract  Background:  Open pyeloplasty has been the gold standard for surgical treatment of ureteropelvic junction (UPJ) obstruction, enjoying a long‐term success rate exceeding 90%. Unfortunately, this procedure requires a muscle incision that entails some degree of morbidity. We have, therefore, investigated the feasibility of laparoscopic pyeloplasty for UPJ obstruction and report here the outcomes of our early cases. The median follow up is 25 months (range, 12–42 months).Methods:  Between March 1999 and September 2001 we performed laparoscopic pyeloplasty on 12 ureters in 11 patients presenting with symptomatic hydronephrosis, secondary to a short stenosis of the UPJ or to ventrally crossing vessels; bilateral pyeloplasty was performed as a single procedure in one patient. We performed dismembered Anderson–Hynes pyeloplasty, Fenger plasty and Y‐V plasty in eight, two and two ureters, respectively. All procedures were carried out transperitoneally.Results:  The procedure was completed successfully in all cases. Crossing vessels were noted in six of 12 ureters (50.0%). Mean operative time and blood loss in 11 patients (including one bilateral case) were 272.8 min (range, 175–480 min) and 96.4 mL (range, 20–340 mL), respectively. Postoperative complications were noted in two patients (18.2%): one instance of prolonged urine leakage and one anastomotic re‐stricture. Eleven of 12 ureters (91.6%) demonstrated a patent UPJ on excretory urography and/or improvement of renal function on diuretic renography at a minimum follow up of 12 months.Conclusion:  Although the procedure requires advanced laparoscopic skills, it can be safely and successfully completed as frequently as the conventional open procedure. Laparoscopic pyeloplasty seems to be a valuable alternative to open pyeloplasty for UPJ obstruction.