bluuebunny/crossref_metadata_2025 huggingface dataset:
Implicit finite element discretizations based on the flux‐corrected transport algorithm
Authors: Möller Matthias , Kuzmin D. , Turek S.
Published: January 2005

The flux‐corrected transport (FCT) methodology is generalized to implicit finite element schemes and applied to the Euler equations of gas dynamics. For scalar equations, a local extremum diminishing scheme is constructed by adding artificial diffusion so as to eliminate negative off‐diagonal entries from the high‐order transport operator. To obtain a nonoscillatory low‐order method in the case of hyperbolic systems, the artificial viscosity tensor is designed so that all off‐diagonal blocks of the discrete Jacobians are rendered positive semi‐definite. Compensating antidiffusion is applied within a fixed‐point defect correction loop so as to recover the high accuracy of the Galerkin discretization in regions of smooth solutions. All conservative matrix manipulations are performed edge‐by‐edge which leads to an efficient algorithm for the matrix assembly. Copyright © 2005 John Wiley & Sons, Ltd.
Snow, frozen soils and permafrost hydrology in Canada, 1999–2002
Authors: Woo Ming‐Ko , Marsh Philip
Published: January 2005

An overview is provided of Canadian research on snow, frozen soils and permafrost hydrology for 1999–2002, the period between the 1999 IUGG meeting in Birmingham and the 2003 IUGG in Sapporo. Snow research during this period emphasized the blowing snow and sublimation processes, the role of trees in snow distribution, and melt and the effect of heat advection on snowmelt, from patch to regional scales. Regional‐scale studies, largely in connection with the Mackenzie GEWEX study, examined the snow conditions of the lower Mackenzie basin and developed a coupled land surface scheme–hydrological model that incorporates snow processes. In frost hydrology, the effects of organic soils on runoff generation and flow delivery were given much attention. Field investigations ranged from plot to hillslope scales, and the results indicate that organic layers of high porosity permit the production of quick flow, even when frozen. Highly fractured bedrock in the Canadian Shield has likewise the effect of permitting snowmelt infiltration at below‐freezing temperatures. Finally, changes in snow‐covered areas and in snow equivalent over periods from a decade to a century were examined. The responses of snow and ground ice to the warm year of 1998 were also studied as an indication of hydrological responses to climatic warming. Copyright © 2005 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Advances in Canadian forest hydrology, 1999–2003
Authors: Buttle J. M. , Creed I. F. , Moore R. D.
Published: January 2005

Understanding key hydrological processes and properties is critical to sustaining the ecological, economic, social and cultural roles of Canada's varied forest types. This review examines recent progress in studying the hydrology of Canada's forest landscapes. Work in some areas, such as snow interception, accumulation and melt under forest cover, has led to modelling tools that can be readily applied for operational purposes. Our understanding in other areas, such as the link between runoff‐generating processes in different forest landscapes and hydrochemical fluxes to receiving waters, is much more tentative. The 1999–2003 period saw considerable research examining hydrological and biogeochemical responses to natural and anthropogenic disturbance of forest landscapes, spurred by major funding initiatives at the provincial and federal levels. This work has provided valuable insight; however, application of the findings beyond the experimental site is often restricted by such issues as a limited consideration of the background variability of hydrological systems, incomplete appreciation of hydrological aspects at the experiment planning stage, and experimental design problems that often bedevil studies of basin response to disturbance. Overcoming these constraints will require, among other things, continued support for long‐term hydroecological monitoring programmes, the embedding of process measurement and modelling studies within these programmes, and greater responsiveness to the vagaries of policy directions related to Canada's forest resources. Progress in these and related areas will contribute greatly to the development of hydrological indicators of sustainable forest management in Canada. Copyright © 2005 John Wiley & Sons, Ltd.
Controls on runoff from a partially harvested aspen‐forested headwater catchment, Boreal Plain, Canada
Authors: Devito K. J. , Creed I. F. , Fraser C. J. D.
Published: January 2005

The water balance and runoff regime of a 55 ha aspen‐forested headwater catchment located on the Boreal Plain, Alberta, Canada (55·1°N, 113·8°W) were determined for 5 years following a partial timber harvest. Variability in precipitation provided the opportunity to contrast catchment water balances in relatively dry (<350 mm year−1), wet (>500 mm year−1), and average precipitation years. In most years, the catchment water balance was dominated by soil water storage, evapotranspiration losses, and vertical recharge. In 1997, despite near‐average annual precipitation (486 mm), there was significant runoff (250 mm year−1) with a runoff coefficient of 52%. A wet summer and autumn in the preceding year (1996) and large snow accumulation in the spring (1997) reduced the soil water storage potential, and large runoff occurred in response to a substantial July rainfall event. Maps of the surface saturated areas indicated that runoff was generated from the uplands, ephemeral draws, and valley‐bottom wetlands. Following 1997, evapotranspiration exceeded precipitation and large soil water storage potentials developed, resulting in a reduction in surface runoff to 11 mm in 1998, and <2 mm in 1999–2001. During this time, the uplands were hydrologically disconnected from ephemeral draws and valley‐bottom wetlands. Interannual variability was influenced by the degree of saturation and connectivity of ephemeral draws and valley wetlands. Variability in runoff from tributaries within the catchment was influenced by the soil water storage capacity as defined by the depth to the confining layer. An analysis of the regional water balance over the past 30 years indicated that the potential to exceed upland soil water storage capacity, to connect uplands to low‐lying areas, and to generate significant runoff may only occur about once every 20 years. The spatial and temporal variability of soil water storage capacity in relation to evaporation and precipitation deficits complicates interpretation of forest harvesting studies, and low runoff responses may mask the impacts of harvesting of aspen headwater areas on surface runoff in subhumid climates of the Boreal Plain. Copyright © 2005 John Wiley & Sons, Ltd.
Hydrological processes in major types of Chinese forest
Authors: Wei X. , Liu S. , Zhou G. , Wang C.
Published: January 2005

Overexploitation of forest resources in China has caused serious concerns over its negative impacts on water resources, biodiversity, soil erosion, wildlife habitat and community stability. One key concern is the impact of forestry practices on hydrological processes, particularly the effect of forest harvest on water quality and quantity. Since the mid 1980s, a series of scientific studies on forest hydrology have been initiated in major types of forest across the country, including Korean pine (Pinus koraiensis), Chinese fir (Cunninghamia lanceolata), oak (Quercus mongolica), larch (Larix gmelinii), faber fir (Abies fabri), Chinese pine (Pinus tabulaeformis), armand pine (Pinus arandi), birch (Betula platyphylla) and some tropical forests. These studies measured rainfall interception, streamflow, evapotranspiration and impacts of forest management (clearcutting and reforestation). This paper reviews key findings from these forest hydrological studies conducted over the past 20 years in China.

Forest canopy interception rates varied from 15 to 30% of total rainfall, depending on forest canopy and rainfall characteristics. Stemflow is generally a small percentage (<5%) of total rainfall, but it accounts for 15% in the oak forest in northeast China. The high amounts of stemflow, as well as higher amounts of nutrients contained in stemflow, may allow oak trees to adapt to a dry and nutrient‐poor environment. Evapotranspiration was a significant component of the water budget in these Chinese forests studied, ranging from 80–90% of total rainfall in the northern temperate forests to 40–50% in the southern tropical forests. Forests substantially reduced surface runoff and erosion. However, no consistent response on total streamflows was observed. The reason for the inconsistency may be due to complexities of streamflow processes and the utilization of different methodologies applied at the various spatial scales. Copyright © 2005 John Wiley & Sons, Ltd.
Stereodynamics of bond rotation in tertiary 1‐naphthoic acid amides: A computational study
Authors: Campomanes Pablo , Menéndez M. Isabel , López Ramón , Sordo Tomás L.
Published: January 2005

Computations sho that independent NCO rotation is not possible inN,N‐diethyl‐1‐naphthamide, and that the coalescence signal corresponding to methyl equivalence observed in the VT NMR spectrum of this system is caused by a complex process whose rate‐determining step implies concerted NCO, ArCO, and ethyl rotations. The calculated Gibbs energy barriers for these processes in solution are in good agreement with the experimental values. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 365–373, 2005
Interaction of sodium and potassium ions with sandwiched cytosine‐, guanine‐, thymine‐, and uracil‐base tetrads
Authors: Meyer Michael , Hocquet Alexandre , Sühnel Jürgen
Published: January 2005

Nucleic acid tetraplexes and lipophilic self‐assembling G‐quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum‐chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G‐tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G‐, C‐, U‐, and T‐tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base–base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 352–364, 2005
Posttraining intrahippocampal infusion of a protein kinase AII inhibitor impairs spatial memory retention in rats
Authors: Sharifzadeh Mohammad , Sharifzadeh Kurdistan , Naghdi Nasser , Ghahremani Mohammad H. , Roghani Ali
Published: January 2005

The role of protein kinase AII (PKA II) in spatial memory retention in male rats and its regulation of cholinergic gene expression were explored through the effects of intrahippocampal infusion of H‐89, a selective PKA II inhibitor. Alterations in escape latency, travel distance, and swimming speed in a Morris water maze were measured. Animals were trained for 3 days; each day included two blocks, and each block contained four trials. Stereotaxic surgery was employed for the infusions after the last trial on the third day of training, and the animals were tested 48 hr after surgery. Bilateral intrahippocampal infusion of H‐89 (2.5 or 5 μM) into the CA1 region generated significant alterations in escape latency and traveled distance but not swimming speed. The response was fairly dose dependent, and the maximal effect was obtained with 5 μM H‐89. After behavioral testing, several of the infused animals were transcardially perfused and their brains removed. Brain tissue sections from these rats were subjected to immunohistochemical staining analysis with anticholine acetyltransferase (ChAT) antibodies. These analyses indicated that 5 μM H‐89 infusions qualitatively reduced the density of ChAT‐containing cholinergic nerve terminals in the dorsal hippocampus. The intrahippocampal infusions with 5 μM H‐89 also caused an apparent reduction in the number of ChAT‐containing neurons in the medial septum. Our results suggest that PKA II is involved in regulation of cholinergic gene expression and plays an important role in spatial memory retention in rats. © 2004 Wiley‐Liss, Inc.
Weather regimes and their connection to the winter rainfall in Portugal
Authors: Santos J.A. , Corte‐Real J. , Leite S.M.
Published: January 2005

Wintertime rainfall over Portugal is strongly coupled with the large‐scale atmospheric flow in the Euro‐Atlantic sector. A K‐means cluster analysis, on the space spanned by a subset of the empirical orthogonal functions of the daily mean sea‐level pressure fields, is performed aiming to isolate the weather regimes responsible for the interannual variability of the winter precipitation. Each daily circulation pattern is keyed to a set of five weather regimes (C, W, NAO−, NAO+ and E). The dynamical structure of each regime substantiates the statistical properties of the respective rainfall distribution and validates the clustering technique. The C regime is related to low‐pressure systems over the North Atlantic that induce southwesterly and westerly moist winds over the country. The W regime is characterized by westerly disturbed weather associated with low‐pressure systems mainly located over northern Europe. The NAO− regime is manifested by weak low‐pressure systems near Portugal. The NAO+ regime corresponds to a well‐developed Azores high with generally settled and dry weather conditions. Finally, the E regime is related to anomalous strong easterly winds and rather dry conditions. Although the variability in the frequencies of occurrence of the C and NAO− regimes is largely dominant in the interannual variability of the winter rainfall throughout Portugal, the C regime is particularly meaningful over northern Portugal and the NAO− regime acquires higher relevance over southern Portugal. The inclusion of the W regime improves the description of the variability over northern and central Portugal. Dry weather conditions prevail in both the NAO+ and E regimes, with hardly any exceptions. The occurrence of the NAO+ and the NAO− regimes is also strongly coupled with the North Atlantic oscillation. Copyright © 2005 Royal Meteorological Society
Recent temporal and spatial temperature changes in Egypt
Authors: Domroes Manfred , El‐Tantawi Attia
Published: January 2005

In order to detect and to estimate trends of temperature change in Egypt, trend analyses applying the least‐squares method and the non‐parametric Mann–Kendall test for trends were carried out at six stations for the period 1941–2000 (60 years), and at nine stations for the period 1971–2000 (30 years).

According to the trend computations for the period 1941–2000, variable temperature trends over time and space have been observed. Decreasing trends of the mean annual temperature were observed in northern Egypt and (weakly) increasing trends in southern Egypt. Seasonally, positive trends prevailed in summer compared with negative trends in winter. For the recent period, 1971–2000, positive trends were computed for the mean annual and mean minimum temperatures at all stations except Port Said in northern Egypt, where the annual trend was weakly negative. The mean maximum temperature trends were, however, negative at most stations. Seasonally, a definite trend of warming occurred in summer, in contrast to the observations of a global temperature increase in winter.

A principal component analysis was applied to compute the all‐Egypt temperature trends. For the observation period, 1941–2000, decreasing trends were shown for annual, maximum, winter and autumn temperatures and increasing trends for minimum, winter and spring temperatures. For the recent period, 1971–2000, all trends were positive except maximum temperature. Copyright © 2005 Royal Meteorological Society
1.70 Å X‐ray structure of human apo kallikrein 1: Structural changes upon peptide inhibitor/substrate binding
Authors: Laxmikanthan Gurunathan , Blaber Sachiko I. , Bernett Matthew J. , Scarisbrick Isobel A. , Juliano Maria Aparecida , Blaber Michael
Published: January 2005

Human kallikreins are serine proteases that comprise a recently identified large and closely related 15‐member family. The kallikreins include both regulatory‐ and degradative‐type proteases, impacting a variety of physiological processes including regulation of blood pressure, neuronal health, and the inflammatory response. While the function of the majority of the kallikreins remains to be elucidated, two members are useful biomarkers for prostate cancer and several others are potentially useful biomarkers for breast cancer, Alzheimer's, and Parkinson's disease. Human tissue kallikrein (human K1) is the best functionally characterized member of this family, and is known to play an important role in blood pressure regulation. As part of this function, human K1 exhibits unique dual‐substrate specificity in hydrolyzing low molecular weight kininogen between both Arg‐Ser and Met‐Lys sequences. We report the X‐ray crystal structure of mature, active recombinant human apo K1 at 1.70 Å resolution. The active site exhibits structural features intermediate between that of apo and pro forms of known kallikrein structures. The S2 to S2′ pockets demonstrate a variety of conformational changes in comparison to the porcine homolog of K1 in complex with peptide inhibitors, including the displacement of an extensive solvent network. These results indicate that the binding of a peptide substrate contributes to a structural rearrangement of the active‐site Ser 195 resulting in a catalytically competent juxtaposition with the active‐site His 57. The solvent networks within the S1 and S1′ pockets suggest how the Arg‐Ser and Met‐Lys dual substrate specificity of human K1 is accommodated. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Role of trehalose and heat in the structure of the C‐terminal activation domain of the heat shock transcription factor
Authors: Bulman Amanda L. , Nelson Hillary C.M.
Published: January 2005

The heat shock transcription factor (HSF) is the primary transcriptional regulator of the heat shock response in eukaryotes. Saccharomyces cerevisiae HSF1 has two functional transcriptional activation domains, located N‐ and C‐terminal to the central core of the protein. These activation domains have a low level of transcriptional activity prior to stress, but they acquire a high level of transcriptional activity in response to stresses such as heat. Previous studies on the N‐terminal activation domain have shown that it can be completely disordered.1 In contrast, we show that the C‐terminal activation domain of S. cerevisiae HSF1 does contain a certain amount of secondary structure as measured by circular dichroism (CD) and protease resistance. The α‐helical content of the domain can be increased by the addition of the disaccharide trehalose but not by sucrose. Trehalose, but not sucrose, causes a blue shift in the fluorescence emission spectra, which is suggestive of an increase in tertiary structure. Trehalose, which is known to be a chemical chaperone, also increases proteases' resistance and promotes heat‐induced increases in α‐helicity. The latter is particularly intriguing because of the physiological role of trehalose in yeast. Trehalose levels are increased dramatically after heat shock, and this is thought to protect protein structure prior to the increase of heat shock protein levels. Our results suggest that the dramatic changes in S. cerevisiae HSF1 transcriptional activity in response to stress might be linked to the combined effects of trehalose and elevated temperatures in modifying the overall structure of HSF1's C‐terminal activation domain. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The key role of atom types, reference states, and interaction cutoff radii in the knowledge‐based method: New variational approach
Authors: Ruvinsky A. M. , Kozintsev A. V.
Published: January 2005

We present a variational method to derive knowledge‐based potentials. The method is based on an optimization procedure of objective variables: atom types, reference states, and interaction cutoff radii. We suggest and apply new unsymmetrical reference states. The cutoff radii and atom types are optimized to improve docking accuracy of the corresponding potentials. The atom types are varied along an atom type tree, with 6 root and 49 top atom types, and the set of 18 optimal atom types is obtained. We demonstrate strong dependence between the choice of atom types and the docking accuracy of the potentials derived with these atom types. The averaged root‐mean square deviations (RMSDs) of the ligand docked positions relative to the experimentally determined positions decrease when the elements C, N, O are split into the optimal types. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Prediction of binding modes for ligands in the cytochromes P450 and other heme‐containing proteins
Authors: Kirton Stewart B. , Murray Christopher W. , Verdonk Marcel L. , Taylor Richard D.
Published: January 2005

The cytochromes P450 (P450s) are a family of heme‐containing monooxygenase enzymes involved in a variety of functions, including the metabolism of endogenous and exogenous substances in the human body. During lead optimization, and in drug development, many potential drug candidates are rejected because of the affinity they display for drug‐metabolising P450s. Recently, crystal structures of human enzymes involved in drug metabolism have been determined, significantly augmenting the prospect of using structure‐based design to modulate the binding and metabolizing properties of compounds against P450 proteins. An important step in the application of structure‐based metabolic optimization is the accurate prediction of docking modes in heme binding proteins. In this paper we assess the performance of the docking program GOLD at predicting the binding mode of 45 heme‐containing complexes. We achieved success rates of 64% and 57% for Chemscore and Goldscore respectively; these success rates are significantly lower than the value of 79% observed with both scoring functions for the full GOLD validation set. Re‐parameterization of metal‐acceptor interactions and lipophilicity of planar nitrogen atoms in the scoring functions resulted in a significant increase in the percentage of successful dockings against the heme binding proteins (Chemscore 73%, Goldscore 65%). The modified scoring functions will be useful in docking applications on P450 enzymes and other heme binding proteins. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Energy transfer phenomena in the luminescence of wide band‐gap scintillators
Authors: Nikl M.
Published: January 2005

Luminescence and scintillation dynamics can be extensively influenced by the energy transfer processes, which is demonstrated at three selected scintillator materials: PbWO4, Ce‐doped aluminium garnets and PrF3:Ce single crystals. Charge carrier retrapping processes can delay radiative recombination at the luminescence centers in an extended time scale, which makes a substantial part of generated scintillation light technically unexploitable. Correlated measurements based on time‐resolved emission spectroscopy and thermoluminescence are of great help to evaluate these phenomena and to understand their microscopic origin. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic and atomic relaxation processes in irradiated cryocrystals
Authors: Savchenko E. V. , Bondybey V. E.
Published: January 2005

Relaxation processes and stability of charge centers in preirradiated cryocrystals doped with atomic and molecular species are discussed. The study was performed combining techniques of spectrally resolved thermally stimulated luminescence (TSL), thermally stimulated exoelectron emission (TSEE) and photon‐stimulated exoelectron emission (PSEE). Comparison of the yields of electrons and photons in VUV and visible ranges made it possible to discriminate between reactions of charge carriers and neutral reactive species and find interconnection between atomic and electronic processes of relaxation. The radiative mechanism of electronic relaxation stimulation via an atomic subsystem is verified. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photostimulable defects in nano‐crystallites in fluorozirconate glasses
Authors: Schweizer S. , Spaeth J.‐M. , Secu M. , Edgar A. , Williams G. V. M.
Published: January 2005

The photostimulated luminescence (PSL) from Eu‐doped fluorobromo‐ and fluorochlorozirconate glass‐ceramics is reviewed. The PSL is attributed to the characteristic emission of Eu2+ present in BaX2 (X = Br, Cl) crystallites which form in the glass upon thermal processing. Both the photoluminescence intensity and the PSL efficiency increase with the size of the crystallites in a way that is consistent with a PSL‐inert surface layer surrounding the crystallites. The increasing crystallite sizes also result in decreased optical transparency at the stimulation wavelength due to scattering. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
DFT study of surface reactivity of CX3I (XH and F) with CH2I2 to form CH2CX2 on the Ag(111) surface
Authors: Lin Jyh Shing , Chou Wen‐Chi
Published: January 2005

Recently, Chiang's research group successfully carried out the temperature programmed reaction (TPR) spectroscopy under ultrahigh‐vacuum conditions to probe the reaction pathways of adsorbed methyl (CH3(ads)) and trifluoromethyl (CF3(ads)) with coadsorbed methylene (CH2(ads)) via the CH2 insertion reaction, leading to the formation of adsorbed 1,1,1‐trifluoro‐ethyl (CF3CH2(ads)) and ethyl (CH3CH2(ads)) on the Ag(111) surface. Additionally, the authors found it feasible for CF3CH2(ads) to proceed the subsequent β‐fluoride elimination on the Ag(111) surface to produce 1,1 difluoroethylene (CF2CH2(g)) but difficult for CH3CH2(ads) to proceed β‐hydride elimination to form ethylene (CH2CH2(g)) on the Ag(111) surface. To elaborate on this noticeably different reactivity between β‐hydride and β‐fluoride eliminations on the Ag(111) surface we performed total energy calculations based on density functional theory in connection with ultrasoft pseudopotential and generalized gradient spin‐polarized approximation, and partial structural constraint path minimization to establish the energetically more favorable pathways for the CH2 insertion into AgCX3 (XH and F) bonds followed by β–X elimination to generate an isolated CH2CX2(g) on the Ag(111) surface. Following our proposed reaction pathways, namely, the diffusion of the fcc‐hollow site of CX3(ads) toward the bridge site of CH2(ads) through the CH2 insertion and the subsequent β–X elimination to form both isolated CH2CX2(g) and hcp‐hollow site of X(ads) on the Ag(111) surface, our calculated energy barrier for β‐hydride elimination is significantly larger than (∼0.661 eV) that for β‐fluoride elimination. This unusual high‐energy barrier prohibits β‐hydride elimination of CH2CH3(ads) to form an isolated CH2CH2(g) on the Ag(111) surface and explains what we observed from the TPR experimental data. We also attribute this much higher energy barrier to forming a largely distorted seven‐center ring transition state structure with a larger distortion of the AgC(α)H2C(β)H3Ag and a less stable AgH bond on the Ag(111) surface. Finally, our calculated energy barrier for β‐fluoride elimination to form CH2CF2(g) is 0.687 eV, in very good agreement with the experimental data. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Positive and negative ion chemistry of the anesthetic halothane (1‐bromo‐1‐chloro‐2,2,2‐trifluoroethane) in air plasma at atmospheric pressure
Authors: Marotta Ester , Bosa Elisabetta , Scorrano Gianfranco , Paradisi Cristina
Published: January 2005

The ion chemistry of 1‐bromo‐1‐chloro‐2,2,2‐trifluoroethane (the common anesthetic halothane) in air plasma at atmospheric pressure was investigated by atmospheric pressure chemical ionization mass spectrometry (APCI‐MS). The major positive ion observed at low declustering (API interface) energies is the ionized dimer, M+.M, an unexpectedly abundant species which possibly is stabilized by two H‐bonding interactions. At higher energies [MHF]+. and [MBr]+ prevail; the former, corresponding to ionized olefin [ClBrCCF2]+., appears to originate from M+.M and is quite stable towards fragmentation. The latter fragment ion ([MBr]+) and its analogue, [MCl]+, which is also observed though at much lower abundance, are originally ethyl cations +CHXCF3 (X = Br, Cl) which, upon collisional activation, rearrange and fragment to CHFX+ via elimination of CF2. All of the above described ions are also observed in humid air: in addition, the oxygenated ion [ClBrCCFOH]+. also forms in humid air via water addition to [ClBrCCF2]+. and HF elimination, as observed earlier for ionized trichloroethene. In contrast with similar chloro‐ and fluoro‐substituted ethanes, halothane does not react with H3O+ in the APCI plasma, a result confirmed by selected ion APCI triple‐quadrupole (TQ) experiments. Major negative ions formed from halothane in the air plasma are Br− and, to a lesser extent, Cl−, and their complexes with neutral halothane. APCI‐TQ experiments indicated that Br− and Cl− are formed via reaction of halothane with O, O(H2O) and O, possibly via dissociative electron transfer or nucleophilic substitution. Competing proton transfer was also observed in the reaction with O and, at high halothane pressure, also with O(H2O); at lower pressures the molecular anion M−. was observed instead. The other minor anions of the air plasma, NO, N2O and NO, were found to be unreactive towards halothane. Copyright © 2005 John Wiley & Sons, Ltd.
On the formation of conjugated linoleic acid diagnostic ions with acetonitrile chemical ionization tandem mass spectrometry
Authors: Michaud Anthony L. , Lawrence Peter , Adlof Richard , Brenna J. Thomas
Published: January 2005

Acetonitrile chemical ionization tandem mass spectrometry has recently been shown to be a rapid method for the identification of double‐bond position and geometry in methyl esters of conjugated linoleic acids (CLAs); however, the structures of intermediate and diagnostic ions and their mechanisms of formation are not known. A mechanism is proposed here in which the m/z 54 ion, (1‐methyleneimino)‐1‐ethenylium (MIE), undergoes nucleophilic attack preferentially by the cis double bond in CLAs with mixed geometry (cis/trans, trans/cis), favoring the observed CC cleavage vinylic to the trans double bond. The [M+54]+ addition product intermediate is consistent with a heterocyclic six‐membered ring resulting from the two‐step addition of MIE to the CLA. Experiments with isotopically labeled CLAs and acetonitrile, and from MS/MS/MS experiments, yield data consistent with this proposal. The proposed mechanism is also consistent with known ion—molecule chemistry in smaller compounds, and explains most phenomena associated with MIE‐CLA ion chemistry. Copyright © 2005 John Wiley & Sons, Ltd.
Quantitative Fourier transform ion cyclotron resonance mass spectrometry—the determination of creatinine by isotope dilution mass spectrometry
Authors: Bristow Tony , Stokes Peter , O'Connor Gavin
Published: January 2005

Accurate quantitation has been demonstrated on many different types of mass spectrometer. However, quantitative applications of Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) have been limited. In this study, the quantitative potential of FTICRMS has been investigated using an exact matching isotope dilution method for the determination of creatinine in serum. Creatinine is an important clinical biomarker and its measurement is used as an assessment of renal function. The quantitation of creatinine was selected because a high‐accuracy high‐performance liquid chromatography/mass spectrometry (HPLC/MS) determination using a triple quadrupole mass spectrometer has already been successfully developed in‐house. Therefore, a direct comparison of the quantitative capability of FTICRMS could be made against an established method. The accuracy of the quantitation of creatinine was found to be equivalent to that obtained using LC/MS. However, the expanded measurement uncertainty (k = 2) was larger, at 6%, when using FTICRMS compared with 1% when using HPLC/MS with the triple quadrupole mass spectrometer. Copyright © 2005 John Wiley & Sons, Ltd.
Update on master's genetic counseling training programs: Survey of curriculum content and graduate analysis summary
Authors: Smith Ann C. M.
Published: January 2005

The field of genetic counseling is a recognized specialty in medical genetics with the primary practitioners being masters degree prepared individuals. Since the inception of the first master's degree genetic counseling (MGC) training program in 1969, more than 1000 genetic counselors have graduated from established training programs in United States and Canada. The MGC programs involve a 2‐year academic curriculum of both didactic course work and supervised clinical field work (clinical praticums). A recent survey of 17 existing MGC training programs (16 U.S. and 1 Canadian) reveals that MGC graduates average a total of 1349 actual contact hours (range 854–1952 hours) during their 2‐year degree program course of study. Clinical experience gained through clinical practica accounts for 58% of required coursework, followed by didactic coursework in basic science (21%) and counseling (16%), respectively. A few programs also have requisite laboratory practica, which accounts for 5% of overall content hours. The 17 existing MGC programs produce approximately 100 graduates annually. Although the number of programs has grown since inception of the first MGC program in 1969, the mean number of graduates per program remains fairly constant. By year 2002, the estimated total number of master's degree trained genetic counselors will approach 2200.
Psychological aspects of genetic counseling. VIII. Suffering and countertransference
Authors: Kessler Seymour
Published: January 2005

Two common forms of countertransferential problems seen in genetic counseling, associative and projective, are described and illustrated. Both forms have the potential of reducing the quality of empathy counselors provide counselees. When counselors experience the same problems as the counselees they counsel it is virtually impossible to avoid facing countertransferential reactions which may not always promote the counselees' interests and/or redound to their benefit. Genetic counselors, like other personal counselors and psychotherapists, have a professional responsibility to be aware of, monitor, contain, and learn from their countertransferential experiences.
Major Bronchial Trauma in the Pediatric Age Group
Authors: Heldenberg E. , Vishne T.H. , Pley M. , Simansky D. , Refaeli Y. , Binun A. , Saute M. , Yellin A.
Published: January 2005

Tracheobronchial injuries are rare among all age groups and are extremely rare among the pediatric age group. Yet, the incidence has seemed to increase. Most of these patients die before reaching the hospital from severe associated injuries. Isolated bronchial injury is even more rare than tracheal injury, and it is the focus of the present study. A retrospective national survey was conducted among all tertiary referral and trauma centers in Israel regarding the period between the years 1983 and 1998. Only six cases (3 males and 3 females) of isolated bronchial rupture were found the throughout the country. Ages of the patients ranged from 2 to 14 years; all were involved in motor vehicle accidents, four of them as pedestrians. Ruptures occurred in the bronchus intermedicus (2 cases), left and right main bronchus (2 cases each). All but one patient went through primary repair. We give a full description of the procedure and discuss the literature regarding incidence, diagnosis, treatment, and outcome.
Sequential Changes in Plasma Intact and Whole Parathyroid Hormone Levels during Parathyroidectomy for Secondary Hyperparathyroidism
Authors: Yamashita Hiroyuki , Cantor Tom , Uchino Shinya , Watanabe Shin , Ogawa Takahiro , Moriyama Taiki , Takamatsu Yuji , Fukagawa Masafumi , Noguchi Shiro
Published: January 2005

Most commercial assays for intact parathyroid hormone (iPTH) cross‐react with non‐PTH1‐84 fragments (likely to be PTH7‐84). We aimed to evaluate a whole PTH assay that measured only PTH1‐84 by comparing it with an assay measuring iPTH levels during parathyroidectomy in secondary hyperparathyroidism (HPT). Twenty‐eight patients with secondary HPT who underwent total parathyroidectomy with autotransplantation served as subjects. Blood samples for postoperative assay were drawn after anesthesia; immediately prior to excision of the last parathyroid gland; and at 5, 10, and 15 minutes after excision. The PTH7‐84 level was calculated by subtracting the whole PTH value from the iPTH value. Plasma whole PTH decreased more rapidly than iPTH after parathyroidectomy (p < 0.0001). PTH levels that decreased by 50% or more from levels prior to excision to 10 minutes after excision were used to predict successful parathyroidectomy; decreases in whole PTH substantiated curative surgery for all patients without introducing false‐positive and false‐negative results. iPTH levels decreased by at least 50% in only 16 patients at 10 minutes after excision without false‐positive results. Out of 11 cases in which iPTH decreased less than 50%, two were true‐negatives and nine were false‐negatives. Decreases in whole PTH levels more accurately reflect surgical outcome than do decreases in iPTH levels during parathyroidectomy in secondary HPT patients. Even though the quick iPTH assay is used infrequently during surgery for secondary HPT, our results suggest that a quick whole PTH assay may be more useful than the iPTH assay currently used in parathyroidectomy procedures for secondary HPT.
A Prospective Randomized Comparison of Bilateral Subtotal Thyroidectomy Versus Unilateral Total and Contralateral Subtotal Thyroidectomy for Graves’ Disease
Authors: Chi Shun‐Yu , Hsei Kun‐Chou , Sheen‐Chen Shyr‐Ming , Chou Fong‐Fu
Published: January 2005

To reduce the chance of recurrent hyperthyroidism, two methods of subtotal thyroidectomy were performed and compared. From January 1998 to December 2002, 340 patients were operated on with subtotal thyroidectomy. They were prospectively randomized into two groups. Group A included 166 patients and group B 174 patients. Group A patients had a 2.5 × 1 × 1 cm thyroid remnant on each side and group B patients had a 2.5 ×1 × 1 cm remnant on one side plus total lobectomy on the other side. Thyroid function tests including T3, T4, TSH, and antimicrosomal antibody (AMA) were checked preoperatively and in the follow‐up period of 3 months, and later up to 26.4 ± 1.1 months (mean ± SE). The age, sex, duration of oral medicine, and blood loss of the two groups were not significantly different during surgery and the follow‐up period. The operative time was less in group A (113 ± 3.3 minutes) than that in group B (131 ± 3.2 minutes) (p < 0.001). In the long‐term follow‐up period, recurrent hyperthyroidism was noted in 15 patients in group A and 3 patients in group B. The difference was significant (p = 0.003). Hypothyroidism was noted in 35 of the group A patients and in 46 of the group B patients. The differences between the two groups regarding hypothyroidism was not significant (p = 0.181). Multivariate logistic regression analysis revealed preoperative titers of AMA ≥ 6400, which was the only factor affecting the incidence of hypothyroidism in the later follow‐up period. In consideration of hypothyroidism, recurrent hyperthyroidism, and postoperative complications, subtotal thyroidectomy with total lobectomy plus subtotal lobectomy provides a better outcome than bilateral subtotal lobectomy.
Duodenogastric Reflux after Esophagectomy and Gastric Pull‐up: The Effect of the Route of Reconstruction
Authors: Katsoulis Iraklis E. , Robotis Ioannis , Kouraklis Grigorios , Yannopoulos Panagiotis
Published: January 2005

Duodenogastric reflux (DGR) is a common sequel of subtotal esophagectomy and gastric pull‐up, and it may contribute to mucosal changes of both the gastric conduit and the esophageal remnant. This study investigated the effect of the route of reconstruction on the DGR. 24‐hour ambulatory bilirubin monitoring was performed on patients who underwent transhiatal subtotal esophagectomy and a gastric tube interposition either in the posterior mediastinum (PM group, n = 11), or in the retrosternal space (RS group, n = 8): A Control group of 8 healthy volunteers was also studied. The median percentage of reflux time, the median number of reflux episodes, and the median number of reflux episodes longer than 5 minutes, in PM versus RS groups, were 29.1% versus 0.15% (p < 0.001), 185 versus 8 (p = 0.002) and 10 versus 0 (p = 0.001), respectively. The values of the above variables in PM versus control groups were 29.1% versus 3.95% (p = 0.007), 185 versus 21 (p = 0.02), and 10 versus 2 (p = 0.009), respectively, whereas in RS versus control groups they were 0.15% versus 3.95% (p = 0.01), 8 versus 21 (p = 0.04), and 0 versus 2 (p = 0.05), respectively. Posterior mediastinal gastric interposition is associated with high reflux of duodenal contents, whereas retrosternal interposition minimizes the reflux at levels even lower than those of the healthy individuals. The latter type of reconstruction may be a good alternative from that perspective, especially in patients with long life expectancy.
Heterogeneity of Subvesical Ducts or the Ducts of Luschka: A Study Using Drip‐infusion Cholangiography‐Computed Tomography in Patients and Cadaver Specimens
Authors: Kitami Masahiro , Murakami Gen , Suzuki Daisuke , Takase Kei , Tsuboi Masahiro , Saito Haruo , Takahashi Shoki
Published: January 2005

The objective of this study was to examine the heterogeneity of the subvesical duct or the ducts of Luschka as well as the reliability of drip‐infusion cholangiography with computed tomography (DIC‐CT) for their identification. DIC‐CT was used in 277 consecutive patients (135 men, 142 women) and for the dissection and histologic study of 10 cadaver livers. We found 32 subvesical ducts in 28 (10.1%) of 277 patients. Irrespective of whether the terminals were extra‐ or intraparenchymal, the subvesical ducts often (17/32 ducts, 15/28 patients) drained into a subsegmental duct of S5 or S4. Notably, some displayed an “intermediate” course along the gallbladder fossa with an intraparenchymal origin and terminated at S5. Such ducts tended to be seen in the elderly. Another 15 ducts drained into a thick, centrally located duct, such as the right sectorial or hepatic duct. The anatomic study demonstrated that the subvesical duct likely included the cystic vein‐concomitant duct. A major type of subvesical duct, characterized by an intermediate course along its bed, appeared to result from degenerative exposure of a peripheral duct with aging. The subvesical duct draining into the thick duct included both a “daughter branch,” such as seen in the lung, and the so‐called anomaly. Such ducts can be demonstrated with DIC‐CT, but the incidence might be limited. However, the cystic vein/concomitant duct was difficult to identify radiologically. Consequently, although presurgical radiology is useful for avoiding bile leakage after laparoscopic cholecystectomy, surgeons should be aware of its limitations.
A seasonal change in the distribution of a stream‐dwelling stonefly nymph reflects oxygen supply and water flow
Authors: Genkai‐Kato Motomi , Mitsuhashi Hiromune , Kohmatsu Yukihiro , Miyasaka Hitoshi , Nozaki Kentaro , Nakanishi Masami
Published: January 2005

We examined the effects of oxygen availability, which has been viewed as a minor factor in streams, on the seasonal and spatial microhabitat distribution of a stonefly. Surveys were conducted in winter and summer in a mountain stream by collecting stones from the streambed and determining the presence or absence of the insect. At each stone sampling, we also measured physical conditions. The probability of the stonefly presence increased significantly with current velocity in summer, but not in winter. Because current influences oxygen renewal rates, our results suggest that the distribution of the insect could be restricted by oxygen.
The aggravating role of the ubiquitin–proteasome system in neurodegeneration
Authors: Ardley Helen C , Hung Chao-Chun , Robinson Philip A
Published: January 2005

Association of protein inclusions or aggregates within brain tissues of patients with neurodegenerative disorders has been widely reported. These inclusions are commonly characterised both by the presence of ubiquitylated proteins and the sequestration of components of the ubiquitin–proteasome system (UPS). Such observations have led to the proposition that the UPS has a direct role in their formation. Indeed, the presence of ubiquitylated proteins and UPS components in inclusions may reflect unsuccessful attempts by the UPS to remove aggregating proteins. Whether the physical presence of inclusions causes cell death or, conversely, whether they are non‐toxic and their presence reflects a cellular protective mechanism remains highly controversial.
Misfolding of glycoproteins is a prerequisite for peptide: N‐glycanase mediated deglycosylation
Authors: Joshi Shivanjali , Katiyar Samiksha , Lennarz William J.
Published: January 2005

Peptide:N‐glycanase (PNGase) is a deglycosylating enzyme that catalyzes the hydrolysis of the β‐aspartylglycosylamine bond of aspargine‐linked glycopeptides and glycoproteins. Earlier studies from our laboratory indicated that PNGase catalyzed de‐N‐glycosylation was limited to glycopeptide substrates, but recent reports have demonstrated that it also acts upon full‐length misfolded glycoproteins. In this study, we utilized two glycoprotein substrates, yeast carboxypeptidase and chicken egg albumin (ovalbumin), to study the deglycosylation activity of yeast PNGase and its mutants. Our results provide further evidence that PNGase acts upon full‐length glycoprotein substrates and clearly establish that PNGase acts only on misfolded or denatured glycoproteins.
Physiological stress of intracellular Shigella flexneri visualized with a metabolic sensor fused to a surface‐reporter system
Authors: Guzmán Carlos A. , Cebolla Angel , Beltrametti Fabricio , Staender Lothar H. , de Lorenzo Víctor
Published: January 2005

When deleted of its N‐terminal signal‐reception domain, the broad host range σ54‐dependent transcriptional regulator XylR, along with its cognate promoter Pu, becomes a sensor of the metabolic stress of the carrier bacteria. We have employed a surface reporter system to visualize the physiological status of intracellular Shigella flexneri during infection of Henle 407 cells in culture. To this end, the xylRΔA gene has been engineered adjacent to a bicistronic transcriptional fusion of Pu to a lamB variant tagged with a short viral sequence (cor) and β‐galactosidase (lacZ). The accessibility of the cor epitope to the externalmost medium and the expression of Pu in the bacterial population was confirmed, respectively, with immunomagnetic beads and the sorting of Escherichia coli cells treated with a fluorescent antibody. Intracellular Shigella cells expressed the Pu–lamB/cor–lacZ reporter at high levels, suggesting that infectious cells endure a considerable metabolic constraint during the invasion process.