bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive validity of five comorbidity indices in prostate carcinoma patients treated with curative intent
Authors: Boulos David L. , Groome Patti A. , Brundage Michael D. , Siemens D. Robert , Mackillop William J. , Heaton Jeremy P.W. , Schulze Karleen M. , Rohland Susan L.
Published: March 2006

BACKGROUND

Comorbidity is important to consider in clinical research on curative prostate carcinoma because of the role of competing risks. Five chart‐based comorbidity indices were assessed for their ability to predict survival.

METHODS

This was a case‐cohort study of prostate carcinoma patient cohort treated with curative intent in Toronto and Southeast Cancer Care Ontario regions between 1990 and 1996; the subcohort was drawn from these men, whereas cases were cohort members who died from causes other than prostate carcinoma. Comorbidity data were obtained from medical charts (269 subjects). Vital status, age, area of residence, and socioeconomic status information were available. Predictive validity was quantified by the percent variance explained (PVE) over and above age using proportional hazards modeling.

RESULTS

The Chronic Disease Score (CDS) (PVE = 11.3%; 95% confidence interval [95% CI], 3.5‐22.8%), Index of Coexistent Disease (ICED) (PVE = 9.0%; 95% CI, 2.9‐17.9%), Cumulative Illness Rating Scale (CIRS) (PVE = 7.2%; 95% CI, 1.4‐17.1%), Kaplan‐Feinstein Index (PVE = 4.9%; 95% CI, 0.6‐12.8%), and Charlson Index (PVE = 3.8%; 95% CI, 0.3‐10.9%) each explained some outcome variability beyond age. PVE differences among indices were not statistically significant. A comorbidity identified at the time of cancer diagnosis was the cause of death in 59.2% of cases (75% for cardiac or vascular causes).

CONCLUSIONS

The better‐performing, more comprehensive indices (CDS, ICED, and CIRS) would be useful in measuring and controlling for comorbidity in this setting. The CDS was easiest to apply and explained the most outcome variability. Cancer 2006. © 2006 American Cancer Society.
Phase II trial of oral uracil/tegafur plus leucovorin in patients with hormone‐refractory prostate carcinoma
Authors: Bhandari Manish S. , Pienta Kenneth J. , Fardig Judith , Olson Karin , Smith David C.
Published: March 2006

BACKGROUND

The current study evaluated the efficacy of oral uracil/tegafur (UFT) and leucovorin (LV) in patients with hormone‐refractory metastatic prostrate carcinoma.

METHODS

Twenty‐eight patients with hormone‐refractory metastatic carcinoma of the prostate who had undergone antiandrogen withdrawal and no more than 1 prior chemotherapy treatment were enrolled on a single‐institution Phase II trial. Patients were treated with oral UFT at a dose of 300 mg/m2/d and oral LV at a dose of 90 mg/day for 28 days followed by 7 days off therapy on a 35‐day cycle regimen.

RESULTS

Twenty‐six patients were evaluable for response and toxicity. There was no response by objective criteria in 9 patients with measurable disease. Four responses by prostate‐specific antigen (PSA) criteria (i.e., PSA decrease by > 50%) were noted (15%) lasting a mean of 20.5 weeks. Therapy was generally well tolerated, with 2 patients developing Grade 4 toxicity (1 patient each with diarrhea and hand‐foot syndrome) and 4 patients having significant Grade 3 toxicity (anemia, hyperbilirubinemia, and vomiting) (Toxicity was graded according to the National Cancer Institute Common Toxicity Criteria). Six patients had stable disease by clinical, laboratory, and radiologic criteria for an average of 5 cycles of treatment (25 wks).

CONCLUSIONS

Although UFT and LV are generally well tolerated in the setting of hormone‐refractory metastatic prostate carcinoma, the combination has a low level of activity. Its toxicity and activity is similar to that observed when intravenous 5‐fluorouracil or capecitabine are given alone. It may be an option for further investigations in combination regimens. Cancer 2006. © 2006 American Cancer Society.
Prognostic factors of recurrence in encapsulated Hurthle cell carcinoma of the thyroid gland
Authors: Ghossein Ronald A. , Hiltzik David H. , Carlson Diane L. , Patel Snehal , Shaha Ashok , Shah Jatin P. , Tuttle Robert M. , Singh Bhuvanesh
Published: March 2006

BACKGROUND

Follicular carcinomas of the thyroid gland, including its oncocytic variant (so‐called Hurthle cell carcinoma), are subdivided into the indolent encapsulated (“minimally invasive”) and the clinically aggressive widely invasive tumors. There are, however, cases of encapsulated follicular carcinoma that recur and metastasize. Identifying these cases at the time of diagnosis is crucial for prognostic and therapeutic considerations. Because to the authors' knowledge most studies do not focus exclusively on the encapsulated Hurthle cell carcinoma (EHC), the current study attempted to identify predictors of recurrence in EHC.

METHODS

A tumor was defined as EHC if it was encapsulated, macroscopically well defined with microscopic but no macroscopic evidence of vascular or capsular invasion, and composed of >75% follicular oncocytic cells. Retrospective chart review and microscopic examination identified 50 primary tumors meeting the above criteria at the Memorial Sloan‐Kettering Cancer Center between 1967 and 2005. The cases were analyzed for various histologic and clinical parameters. Each parameter was correlated with recurrence‐free survival (RFS).

RESULTS

Seven of 50 (14%) patients developed disease recurrence. All patients who developed recurrence were found to have a high number of foci of vascular invasion (≥ 4). In univariate analysis, ≥ 4 foci of vascular invasion (P <.0001), tumor size > 4 cm (P = .049), the presence of mitosis (P = .018), and a solid/trabecular growth pattern (P = .009) were found to be correlated with a decreased RFS. Extensive capsular invasion, gender, and age did not confer a statistically higher recurrence rate. The finding of a solid/trabecular growth and mitosis correlated with the presence of numerous foci (≥ 4) of vascular invasion (P = .01 and P = .005, respectively).

CONCLUSIONS

A diligent search for vascular invasion is recommended in EHC that display mitosis or a solid/trabecular growth pattern. The presence of ≥ 4 foci of vascular invasion should alert the pathologist and the clinician to a significantly higher risk of recurrence in EHC. Cancer 2006. © 2006 American Cancer Society.
Expression of the dlx gene family during formation of the cranial bones in the zebrafish (Danio rerio): Differential involvement in the visceral skeleton and braincase
Authors: Verreijdt L. , Debiais‐Thibaud M. , Borday‐Birraux V. , Van der heyden C. , Sire J.‐Y. , Huysseune A.
Published: March 2006

We have used dlx genes to test the hypothesis of a separate developmental program for dermal and cartilage bones within the neuro‐ and splanchnocranium by comparing expression patterns of all eight dlx genes during cranial bone formation in zebrafish from 1 day postfertilization (dPF) to 15 dPF. dlx genes are expressed in the visceral skeleton but not during the formation of dermal or cartilage bones of the braincase. The spatiotemporal expression pattern of all the members of the dlx gene family, support the view that dlx genes impart cellular identity to the different arches, required to make arch‐specific dermal bones. Expression patterns seemingly associated with cartilage (perichondral) bones of the arches, in contrast, are probably related to ongoing differentiation of the underlying cartilage rather than with differentiation of perichondral bones themselves. Whether dlx genes originally functioned in the visceral skeleton only, and whether their involvement in the formation of neurocranial bones (as in mammals) is secondary, awaits clarification. Developmental Dynamics 235:1371–1389, 2006. © 2006 Wiley‐Liss, Inc.
Notch receptor encodes two structurally separable functions in Drosophila: A genetic analysis
Authors: Langdon Tim , Hayward Penelope , Brennan Keith , Wirtz‐Peitz Frederik , Sanders Phil , Zecchini Vincent , Friday Adrian , Balayo Tina , Martinez Arias Alfonso
Published: March 2006

The Notch gene of Drosophila encodes a single transmembrane receptor that plays a central role in the process of lateral inhibition. This process results in the selection of individual mesodermal and neural precurors during the development of the muscular and nervous systems. The activation of Notch during lateral inhibition is mediated by the transmembrane ligand Delta (Dl) and effected by the transcription factor Suppressor of Hairless (Su(H)). The same functional cassette plays a role in other processes, in particular, the development and patterning of the wing. Genetic analysis has suggested that, in addition to the Su(H)‐dependent pathway, Notch can signal in an Su(H)‐independent manner. This process seems to be tightly associated with signalling by Wingless, a member of the Wnt family of signalling molecules. Here, we have analyzed further the possibility that the Notch protein encodes two different functions. To do so, we have studied the activities and genetic properties of different Notch receptors bearing deletions of specific regions of the intracellular and the extracellular domains in different developmental processes, and have sought to correlate the activity of these mutant proteins with those of existing mutants in Notch. Our results support the existence of at least two different activities of Notch each of which can be associated with specific structural domains. Developmental Dynamics 235:998–1013, 2006. © 2006 Wiley‐Liss, Inc.
Deficient morphological processing in adults with developmental dyslexia: another barrier to efficient word recognition?
Authors: Schiff Rachel , Raveh Michal
Published: March 2006

Research on dyslexia has focused on the phonological level of linguistic analysis. Here we extend the investigation of the linguistic competence of individuals with dyslexia to the morphological level of linguistic analysis. We examine whether adult Hebrew readers with dyslexia extract and represent morphemic units similarly to normal readers. Using the priming paradigm in the word fragment completion task, we measured the magnitude of morphological priming and contrasted this effect with the repetition priming effect. Students with normal reading ability showed the typical repetition priming effect. A comparable repetition priming effect was also found for the dyslexic group as a whole. However, when the dyslexics were classified into three subtypes according to their phonological and orthographic decoding skills, repetition priming effects were significant only for the phonological dyslexia subgroup but not for the surface or mixed dyslexia subgroups. Furthermore, students with normal reading ability showed strong morphological priming, comparable in strength to the repetition priming effect. In contrast, the dyslexic readers did not show morphological priming, neither the dyslexia group as a whole, nor any of the subgroups. Our results highlight an additional source for dyslexics' difficulties with word recognition which lie at the level of morphological processing. Copyright © 2006 John Wiley & Sons, Ltd.
Metal Phosphonates Based on {[(Benzimidazol‐2‐ylmethyl)imino]bis(methylene)}bis(phosphonic Acid): Syntheses, Structures and Magnetic Properties of the Chain Compounds [M{(C7H5N2)CH2N(CH2PO3H)2}](M = Mn, Fe, Co, Cu, Cd)
Authors: Cao Deng‐Ke , Xiao Jing , Li Yi‐Zhi , Clemente‐Juan Juan Modesto , Coronado Eugenio , Zheng Li‐Min
Published: March 2006

Five compounds based on {[(benzimidazol‐2‐ylmethyl)imino]bis(methylene)}bis(phosphonic acid) [(C7H5N2)CH2N(CH2PO3H2)2], namely [M{(C7H5N2)CH2N(CH2PO3H)2}] [M = Mn (1), Fe (2), Co (3), Cu (4), Cd (5)] have been synthesized under hydrothermal conditions. These compounds are isostructural, crystallizing in the orthorhombic space groupPbca, witha= 15.331(2),b= 10.7150(16), andc= 16.715(2) Å for1;a= 15.320(3),b= 10.477(2), andc= 16.764(3) Å for2;a= 15.207(2),b= 10.4626(16), andc= 16.794(3) Å for3;a= 15.101(3),b= 10.3517(17), andc= 16.997(3) Å for4; anda= 15.4679(19),b= 10.8923(13), andc= 16.6175(19) for5. Each compound shows a one‐dimensional chain structure where {MO3N2} trigonal bipyramids are connected by {CPO3} tetrahedra through corner‐sharing. The chains are further connected to each other through aromatic stacking of the benzimidazole rings and extensive hydrogen bonds, forming a supramolecular 3D structure. Magnetic susceptibility studies of1–4reveal that weak antiferromagnetic interactions occur between the metal centers. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
A New Bi4Mn1/3W2/3O8Cl Sillén–Aurivillius Intergrowth: Synthesis and Structural Characterisation by Quantitative Transmission Electron Microscopy
Authors: Ávila‐Brande David , Otero‐Díaz L. Carlos , Landa‐Cánovas Ángel R. , Bals Sara , Van Tendeloo Gustaaf
Published: March 2006

The synthesis and structural characterisation of a new phase with nominal composition Bi4Mn1/3W2/3O8Cl is presented. Conventional and analytical transmission electron microscopy are used to determine the composition, unit‐cell symmetry and space group of the compound, whereas a structural model is deducted by exit‐wave reconstruction in the transmission electron microscope. This technique allows the microscope information limit of 1.1 Å to be reached and the (light) oxygen atoms in the presence of heavier atoms (Bi, W, Mn) to be imaged. The average structure is refined from X‐ray powder diffraction data using the Rietveld method yielding an orthorhombic unit cell with lattice parameters a = 5.467(4) Å, b = 5.466(7) Å and c = 14.159(3) Å and space group Cm2m, which could be described as a Sillén–Aurivillius intergrowth. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Synthesis of New Water‐Soluble DNA‐Binding Subunits for Analogues of the Cytotoxic Antibiotic CC‐1065 and Their Prodrugs
Authors: Tietze Lutz F. , Major Felix
Published: March 2006

Novel water‐soluble indole‐2‐carboxylic acid derivatives (7, 13, 21 and 25) bearing a substituent with a tertiary amino functionality at C‐5 have been prepared. These new DNA‐binding subunits can be used for the synthesis of new analogues of the cytotoxic antibiotic CC‐1065 and their corresponding prodrugs for antibody‐directed enzyme prodrug therapy (ADEPT) within a selective treatment of cancer.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Selective Inclusion of Equatorial Isomers of Cyclohexane‐Polyols in Phosphonium Salt Hosts
Authors: Tanaka Koichi , Nakashima Aki , Shimada Yuji , Scott Janet L.
Published: March 2006

Phosphonium salt host compounds 1–3 form inclusion crystals with cyclohexane‐1,3‐diol (4), cyclohexane‐1,4‐diol (5) and cyclohexane‐1,3,5‐triol (6), in which the equatorial conformers are selectively included. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Conjugated Azomethine Ylides
Authors: Pinho e Melo Teresa M. V. D.
Published: March 2006

The 1,3‐dipolar cycloaddition of azomethine ylides is an efficient and versatile tool for the construction of five‐membered nitrogen‐heterocycles. When the azomethine ylide is conjugated with a double bond or a 1,3‐diene moiety, other reactivity pathways are also available, namely 1,5‐electrocyclization or 1,7‐electrocyclization. The present review is focused on the generation and reactivity of this type of dipoles, which offer general strategies for the formation of five‐ and seven‐membered nitrogen‐heterocyclic compounds. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
The Suzuki Coupling of Aryl Chlorides in Aqueous Media Catalyzed by in situ Generated Calix[4]arene‐Based N‐Heterocyclic Carbene Ligands
Authors: Brendgen Thomas , Frank Markus , Schatz Jürgen
Published: March 2006

We report on the use of an in situ system for the catalytic Suzuki cross‐coupling reaction of chlorobenzenes and benzeneboronic acid to yield biphenyls. Calix[4]arene‐based imidazolium salts were used as precursors of N‐heterocyclic carbene ligands and Pd(OAc)2as the palladium source. In dioxane as the organic medium, the steric demands of the substituents on the calixarene skeleton and on the imidazolium moiety parallel the catalytic activity; the best catalytic results were obtained by using dimesityl‐ or 2,6‐diisopropylphenyl‐substituted calixarene‐imidazolium salts. Among the bases tested Cs2CO3and CsF were the most effective. The catalytic protocol established for organic solvents could also be used for the Suzuki cross‐coupling reaction in aqueous solution. In dioxane/water (50:50) the activity is nearly the same as in pure dioxane and in pure water, an environmentally friendly and cheap solvent, a 60 % level of reactivity was maintained; here the calixarene ligand precursor3ashowed the highest activity. Nonmacrocyclic compounds used for comparison showed considerably lower catalytic ability proving that calix[4]arene‐based imidazolium salts are attractive supramolecular skeletons for the N‐heterocyclic carbene ligands used in selective Suzuki cross‐coupling reactions of aryl chlorides in aqueous solution. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Validated capillary electrophoresis assay for the simultaneous enantioselective determination of propafenone and its major metabolites in biological samples
Authors: Afshar Minoo , Thormann Wolfgang
Published: March 2006

A robust, inexpensive, and fully validated CE method for the simultaneous determination of the enantiomers of propafenone (PPF), 5‐hydroxy‐propafenone (5OH‐PPF) and N‐despropyl‐propafenone (NOR‐PPF) in serum and in in vitro media is described. It is based upon liquid–liquid extraction at alkaline pH followed by analysis of the reconstituted extract by CE in presence of a pH 2.0 running buffer composed of 100 mM sodium phosphate, 19% methanol, and 0.6% highly sulfated β‐CD. For each compound, the S‐enantiomers are shown to migrate ahead of their antipodes, and the overall run time is about 30 min. Enantiomer levels between 25 and 1000 ng/mL provide linear calibration graphs, and the LOD for all enantiomers is between 10 and 12 ng/mL. The assay is shown to be suitable for the determination of the enantiomers of PPF and its metabolites in in vitro incubations comprising human liver microsomes or single CYP450 enzymes (SUPERSOMES). Incubations with CYP2D6 SUPERSOMES revealed, for the first time, the simultaneous formation of the enantiomers of 5OH‐PPF and NOR‐PPF with that enzyme. CE data can be used for the evaluation of the enzymatic N‐dealkylation and hydroxylation rates.
Selenium‐binding protein 2, the major hepatic target for acetaminophen, shows sex differences in protein abundance
Authors: Mattow Jens , Demuth Ilja , Haeselbarth Gisela , Jungblut Peter R. , Klose Joachim
Published: March 2006

Liver samples from female and male mice of two subspecies, Mus musculus musculus and Mus musculus domesticus, were investigated by a combination of 2‐DE and MALDI‐MS. The image analysis of the generated 2‐DE patterns revealed several protein spots with significant differences in intensity/abundance between the sexes. Seven protein spots, which were prominent in 2‐DE patterns of male mice, but which showed very low intensities in females, were identified as selenium‐binding protein 2 (SBP2) also known as 56‐kDa acetaminophen‐binding protein. Edman degradation indicated that at least three of these protein spots represent N‐terminally truncated SBP2 variants. Furthermore, it was shown that the observed differences in SBP2 abundance correlate with sex differences in transcription of the gene encoding SBP2, selenbp2, as revealed by RT‐PCR and restriction digest as well as sequence analysis of the products. Since SBP2 has been described as the major target for acetaminophen in mouse liver cytosol, these findings are discussed with respect to their possible relevance for sex differences in acetaminophen‐mediated toxicity, which have been described in a variety of mammals including mice and rats.
Selection of surfactants for cell lysis in chemical cytometry to study protein‐DNA interactions
Authors: Pang Zhulin , Al‐Mahrouki Azza , Berezovski Maxim , Krylov Sergey N.
Published: March 2006

Protein‐DNA interactions play a defining role in many cellular processes. Studying such interactions at the single‐cell level is important and challenging. Here we make the first step toward achieving this goal with chemical cytometry. Chemical cytometry utilizes capillary separation for detailed chemical analyses of single cells. The cell is injected into a capillary, lysed, and its components are analyzed by CE or capillary chromatography with highly sensitive detection. In order to apply chemical cytometry to studies of protein‐DNA interactions, cell lysis must not destroy protein‐DNA complexes. Surfactants represent the most practical means of cell lysis inside the capillary. This work aimed at finding surfactants and lysis conditions that do not destroy protein‐DNA complexes. We studied three groups of surfactants – ionic, zwitterionic, and nonionic – with respect to their ability to lyse the cell membrane without significantly influencing the stability of protein‐DNA complexes. Nonequilibrium CE of equilibrium mixtures with surfactants in the equilibrium mixtures and in the run buffer was used to measure the equilibrium constant, Kd, and rate constant, koff, of protein‐DNA complex dissociation. We found that nonionic surfactants worked best: they lyse the plasma membrane without significantly influencing Kd, koff, or the EOF. This work creates the foundation for studies of protein‐DNA interactions in single cells by chemical cytometry.
Contribution of cell culture additives to the two‐dimensional protein patterns of mouse macrophages
Authors: Miller Ingrid , Radwan Marta , Strobl Birgit , Müller Mathias , Gemeiner Manfred
Published: March 2006

Low levels of fetal calf serum (FCS), used as protein supplement in cell culture medium, were traced in preparations of primary murine macrophages (bone‐marrow‐derived macrophages (BMM) and peritoneal macrophages (PM)). Main components of this common additive were mapped in 2‐DE by means of differential image gel electrophoresis and immunoblotting. Additional washing steps in cell preparation helped to decrease the levels of the four highest abundance foetal serum proteins (serum albumin (SA), α1‐fetoprotein (AFP), α1‐antitrypsin (α1AT) and transferrin (Tf)) to less than 1% of total protein. Macrophage spot pattern was recorded in parallel and showed little variation. Results presented are supposed to be of general interest for cell preparations with similar background.
Rapid quantification of human complement component C4A and C4B genes by capillary gel electrophoresis
Authors: Szilagyi Agnes , Blasko Bernadett , Ronai Zsolt , Fust Gyorgy , Sasvari‐Szekely Maria , Guttman András
Published: March 2006

Complement component 4 (C4) is an important plasma protein playing a major role in the human defense mechanism against infectious diseases and inflammatory processes. The C4A and C4B genes, encoding the two isoforms of complement 4, are located in the nuclear serine/threonine protein kinase‐C4A or B gene‐cytochrome 21‐hydroxylase‐tenascin X module (RP‐C4‐CYP21‐TNX) and manifested by variable copy numbers among individuals between zero to six in the human diploid genome. Quantification of the C4A and C4B genes has great clinical importance since unbalanced production of C4A and C4B proteins might be associated with pathological immune processes. Albeit, high‐throughput analysis methods for C4 gene dosage determination are not yet available. Here we present a novel combination of allele‐specific PCR and CGE separation for rapid quantification of the C4A and C4B genes where a single‐step, single‐tube PCR reaction generates two allele‐specific (C4A and C4B) and two control amplicons, followed by CGE analysis of the four fragments. The method presented in this paper enables automated and high‐throughput gene dosage analysis of large sample cohorts.
Enhanced method performances for conventional and chiral CE‐ESI/MS analyses in plasma
Authors: Schappler Julie , Guillarme Davy , Prat Josiane , Veuthey Jean‐Luc , Rudaz Serge
Published: March 2006

Due to its high efficiency, selectivity, and sensitivity, CE‐ESI/MS has evolved as an efficient technique for the drugs and metabolites analysis in biological matrices. However, a sample preparation is mandatory prior to CE‐ESI/MS analysis. To achieve fast and simplified sample preparation of plasma samples, protein precipitation (PP) and liquid–liquid extraction (LLE) were used with two injection techniques: hydrodynamic (HD) and electrokinetic (EK) injection. CE‐ESI/MS analyses of pharmaceutical compounds and amphetamine derivatives were developed. Detection limits of 1 ppm were reached with PP and HD injection whereas 1 ppb was detected when samples were prepared with LLE and injected by EK. Same experiments were performed for stereoselective determinations in partial‐filling mode and detection limits achieved were equivalent to conventional analysis (0.5 ppb per enantiomer). When complex matrices are analyzed, MS signal suppression or enhancement effects are generally not reproducible and could compromise results with ESI. Therefore, matrix effect was investigated in CE‐ESI/MS with a commercially available coaxial sheath–liquid ESI interface used as postcapillary infusion system to determine MS signal alterations. Matrix effects were differentially evidenced according to the selected sample preparation. With PP, signal suppression was observed out of the analyses migration window, while for LLE no relevant matrix effect occurred in all experiments.
Model study of the relationship between sediment yield and river basin area
Authors: Birkinshaw S. J. , Bathurst J. C.
Published: March 2006

The SHETRAN physically based, spatially distributed model is used to investigate the scaling relationship linking specific sediment yield to river basin area, for two contrasting topographies of upland and more homogeneous terrain and as a function of sediment source, land use and rainfall distribution. Modelling enables the effects of the controls to be examined on a systematic basis, while avoiding the difficulties associated with the use of field data (which include limited data, lack of measurements for nested basins and inability to isolate the effects of individual controls). Conventionally sediment yield is held to decrease as basin area increases, as the river network becomes more remote from the headwater sediment sources (an inverse relationship). However, recent studies have reported the opposite variation, depending on the river basin characteristics. The simulation results are consistent with these studies. If the sediment is supplied solely from hillslope erosion (no channel bank erosion) then, with uniform land use, sediment yield either decreases or is constant as area increases. The downstream decrease is accentuated if rainfall (and thence erosion) is higher in the headwaters than at lower elevations. Introducing a non‐uniform land use (e.g. forest at higher elevations, wheat at lower elevations) can reverse the trend, so that sediment yield increases downstream. If the sediment is supplied solely from bank erosion (no hillslope erosion), the sediment yield increases downstream for all conditions. The sediment yield/basin area relationship can thus be inverse or direct, depending on basin characteristics. There still remains, therefore, considerable scope for defining a universal scaling law for sediment yield. Copyright © 2006 John Wiley & Sons, Ltd.
Coeval biochemical and biophysical weathering processes on Quaternary sandstone terraces south of Rabat (Temara), northwest Morocco
Authors: Duane Michael J.
Published: March 2006

Despite numerous investigations on substrate‐inhabiting microflora, especially lichens, very little is known about the colonization of coastal escarpments by lithobiontic micro‐organisms, inland of a retreating coastline in Africa. Reported herein are the results of a combined field observation and microscopy study focusing on the connection between microrelief of the substrate, colonies of lithobiontic micro‐organisms (in particular the lichen Xanthoria parietina) and microstructures of putative bacterial origin. The occurrence of weathering pits in which the early stages of the biotic development occurs, and the subsequent disintegration of the rock indicate that lichens, mosses and fungi act synergistically by alternating chemical and mechanical weathering. Penetration of grains by expansion and contraction of the hyphae depletes the rock matrix and contributes to the mechanical breakdown of the rock. Calcite rhombs on the weathered surfaces of the calcite‐cemented sandstones are severely etched with well‐developed rhomb‐shaped etch pits (‘spiky calcite’), holes, or has one or more of the faces removed, and their cores exposed and leached. Nanofilaments (c. 100–700 nm) and ‘nanomicrobial’ fruiting bodies (c. 250 nm) emanating from micropores appear to be common on affected crystalline structures. Weddellite present immediately below the thallus is a strong indicator of biomineralization.

Quartz responds differently to chemical weathering by producing peeling structures and microbrecciation features. The dissolution of these crystals appears to be a surface reaction‐controlled process mediated by microbial microfilaments and nanofilaments. A model is proposed, firstly indicating early‐stage biochemical weathering, followed by biophysical weathering. Disintegration of the rock outcrops in due to a complex interplay of several events, probably beginning at the nanoscale with penetration of sites on crystal faces. Copyright © 2006 John Wiley & Sons, Ltd.
A mass movement origin for cirques
Authors: Turnbull Jill M. , Davies Timothy R. H.
Published: March 2006

The glacial process of cirque initiation, whereby small initial hillslope hollows grow by nivation until snow can form glacier ice, and ice motion then enlarges the hollow to a fully developed cirque, appears to have difficulty explaining the creation of large cirques in the time available during Quaternary glaciations, at the rates at which glaciers are reported to erode rock, and in rapidly uplifting mountain ranges. It also has difficulty explaining the striking proliferation of cirques in Fiordland, South Island, New Zealand, an area of harder rock and less glaciation than the nearby cirque‐poor area of South Westland. Here we show that cirques can be initiated as large, deep‐seated, often coseismic rock slope failure source area depressions in which snow may accumulate to form cirque glaciers, which can then remove detritus from, smooth, and enlarge the cirque. We present an example of a classically shaped cirque that has never held a glacier. We show that many similarities between the locations, sizes and shapes of rock slope failure source area depressions and cirques are understandable on this basis, as is the occurrence of cirques in presently aseismic intraplate locations and their relative paucity in actively uplifting ranges. The extent to which cirques may be of mass movement origin has implications for their value as palaeoclimatic indicators. Copyright © 2006 John Wiley & Sons, Ltd.
The multi‐stage centred‐scheme approach applied to a drift‐flux two‐phase flow model
Authors: Munkejord Svend Tollak , Evje Steinar , Flåtten Tore
Published: March 2006

For two‐phase flow models, upwind schemes are most often difficult do derive, and expensive to use. Centred schemes, on the other hand, are simple, but more dissipative. The recently proposed multi‐stage (MUSTA) method is aimed at coming close to the accuracy of upwind schemes while retaining the simplicity of centred schemes. So far, the MUSTA approach has been shown to work well for the Euler equations of inviscid, compressible single‐phase flow. In this work, we explore the MUSTA scheme for a more complex system of equations: the drift‐flux model, which describes one‐dimensional two‐phase flow where the motions of the phases are strongly coupled. As the number of stages is increased, the results of the MUSTA scheme approach those of the Roe method. The good results of the MUSTA scheme are dependent on the use of a large‐enough local grid. Hence, the main benefit of the MUSTA scheme is its simplicity, rather than CPU‐time savings. Copyright © 2006 John Wiley & Sons, Ltd.
A compact finite difference method on staggered grid for Navier–Stokes flows
Authors: Zhang K. K. Q. , Shotorban B. , Minkowycz W. J. , Mashayek F.
Published: March 2006

Compact finite difference methods feature high‐order accuracy with smaller stencils and easier application of boundary conditions, and have been employed as an alternative to spectral methods in direct numerical simulation and large eddy simulation of turbulence. The underpinning idea of the method is to cancel lower‐order errors by treating spatial Taylor expansions implicitly. Recently, some attention has been paid to conservative compact finite volume methods on staggered grid, but there is a concern about the order of accuracy after replacing cell surface integrals by average values calculated at centres of cell surfaces. Here we introduce a high‐order compact finite difference method on staggered grid, without taking integration by parts. The method is implemented and assessed for an incompressible shear‐driven cavity flow at Re = 103, a temporally periodic flow at Re = 104, and a spatially periodic flow at Re = 104. The results demonstrate the success of the method. Copyright © 2006 John Wiley & Sons, Ltd.
NG2 proteoglycan‐expressing microglia as multipotent neural progenitors in normal and pathologic brains
Authors: Yokoyama Akiko , Sakamoto Aiko , Kameda Kenji , Imai Yoshinori , Tanaka Junya
Published: March 2006

Rat primary microglia (MG) acquired a multipotent property to give rise to neuroectodermal cells through two‐step culture in 10 and 70% serum‐supplemented media for 5 days. Such multipotent MG, called promicroglioblasts (ProMGBs), formed cell aggregates, which generated cells with neuroectodermal phenotypes shortly after their transfer into serum‐free medium. As revealed by immunohistochemistry, there were a few MG expressing NG2 chondroitin sulfate proteoglycan (NG2) in the neonatal rat brain. Primary culture from the neonatal brain contained NG2+ MG, which appeared to be the source of NG2+ ProMGB aggregates. The aggregates were MG marker+/NG2+/GFAP+/NCAM+/S‐100β− and had alkaline phosphatase activity. The marked accumulation of NG2+ MG was observed close to stab wounds made in the mature rat brain. The accumulated NG2+ MG in the wound gradually decreased in number, but the cells persisted up to 150 days postlesioning. In addition, GFAP immunoreactivity increased markedly around the wound. The NG2+ MG in the wounds separated with trypsin‐EDTA formed NG2+ aggregates in 70% serum‐supplemented medium and then transformed into cells with neuroectodermal phenotypes in serum‐free medium. Although it is difficult to separate viable neurons from mature brains, cells from stab wounds generated process‐bearing β‐tubulin III+ cells in vitro easily. These data suggest that NG2+ MG in normal developing or pathologic brains are involved in the genesis or regeneration of the brain. © 2006 Wiley‐Liss, Inc.
Localization of aquaporin‐1 water channel in glial cells of the human peripheral nervous system
Authors: Gao Hongwen , He Chengyan , Fang Xuedong , Hou Xia , Feng Xuechao , Yang Hong , Zhao Xuejian , Ma Tonghui
Published: March 2006

The aquaporins (AQPs) are a family of water channel proteins with at least 13 mammalian members (AQPs 0–12) expressed in diverse fluid transporting tissues. AQP1, AQP4, and AQP9 have been identified in the central nervous system and demonstrated or proposed to play important roles in brain water homeostasis. Aquaporin expression in the peripheral nervous system is poorly studied. Here we report that the AQP1 water channel is specifically localized to glial cells of the peripheral nervous system by immunohistochemistry, RT‐PCR, and immunoblotting. Paraffin‐embedded biopsies of human pancreas, esophagus, and sciatic nerves were accessed by immunoperoxidase staining using affinity‐purified AQP1, AQP4, and AQP9 antibodies. Strong AQP1 expression was identified in pancreatic nerve plexuses and in the submucosal and myenteric nerve plexuses in the esophagus. AQP1 was localized to the same cell population expressing glial fibrillary acidic protein (GFAP), but not to the neurons in the plexuses, indicating glial cell‐specific expression. RT‐PCR and immunoblot analysis of microdissected pancreatic ganglia confirmed the expression of AQP1 transcript and protein. Pancreatic and sciatic nerve bundles, which contain nonmyelinating and myelinating Schwann cells, respectively, were also selectively labeled by AQP1 antibody. AQP4 and AQP9, which are broadly expressed in astroglial cells in brain and spinal cord, were not localized in glial cells in the peripheral nerve plexuses. These results suggest that AQPs are differentially expressed in the peripheral versus central nervous system and that channel‐mediated water transport mechanisms may be involved in peripheral neuronal activity by regulating water homeostasis in nerve plexuses and bundles. © 2006 Wiley‐Liss, Inc.
Minocycline affects microglia activation, Aβ deposition, and behavior in APP‐tg mice
Authors: Seabrook Timothy J. , Jiang Liying , Maier Marcel , Lemere Cynthia A.
Published: March 2006

Activated microglia and reactive astrocytes invade and surround cerebral β amyloid (Aβ) plaques in Alzheimer's disease (AD), but the role of microglia in plaque development is still unclear. In this study, minocycline was administered for 3 months, prior to and early in Aβ plaque formation in amyloid precursor protein transgenic mice (APP‐tg). When minocycline was given to younger mice, there was a small but significant increase in Aβ deposition in the hippocampus, concurrent with improved cognitive performance relative to vehicle treated mice. If APP‐tg mice received minocycline after Aβ deposition had begun, microglial activation was suppressed but this did not affect Aβ deposition or improve cognitive performance. In vitro studies demonstrated that minocycline suppressed microglial production of IL‐1β, IL‐6, TNF, and NGF. Thus, minocycline has different effects on Aβ plaque deposition and microglia activation depending on the age of administration. Our data suggest that this may be due to the effects of minocycline on microglial function. Therefore, anti‐inflammatory therapies to suppress microglial activation or function may reduce cytokine production but enhance Aβ plaque formation early in AD. © 2006 Wiley‐Liss, Inc.
Relative risk of a shuffled deck: a generalizable logical consistency criterion for sample selection in health state valuation studies
Authors: Craig Benjamin M. , Ramachandran Sulabha
Published: March 2006

In a health state valuation study, respondents may be asked to rank a deck of cards, with each card representing a particular health state. A logical inconsistency occurs when a more severe health state card is ranked higher than a less severe card. Occasional inconsistencies may be justified by errors in judgment or measurement. However, when respondents return shuffled decks, their responses must be removed from the sample; otherwise, valuation estimates will be biased toward the median. In this paper, we present a logical consistency criterion for sample selection in health state valuation studies. This statistical criterion is based on the relative risk of a shuffled deck and generalizable to all health state classification systems, subsets (or decks) of health states, and valuation techniques. We applied the criterion to secondary data collected from 4048 United States and 3395 United Kingdom respondents. In both studies, respondents evaluated 12‐card decks of EQ‐5D health states using time trade‐off and visual analog scale techniques. Among the UK respondents, a small portion (approximately 5%) did not satisfy the criterion; their exclusion significantly changed the sample characteristics and the mean value estimates of the EQ‐5D health states. Similar results were found among the US respondents. Copyright © 2006 John Wiley & Sons, Ltd.
Causal effects of alcoholism on earnings: estimates from the NLSY
Authors: Jones Alison Snow , Richmond David W.
Published: March 2006

Propensity score matching is used to investigate the causal relationship between alcoholism and earnings in a young cohort of males and females drawn from the 1989 and 1994 National Longitudinal Survey of Youth (NLSY) in order to investigate productivity losses attributed to alcoholism and to quantify these effects. Results suggest that there are productivity losses attributable to alcoholism; that they become more pronounced over the life cycle; and that they differ between men and women. Ways in which estimates from propensity score matching may or may not improve on instrumental variables estimates are discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures
Authors: Wu Li‐Cheng , Horng Jorng‐Tzong , Huang Shir‐Ly , Huang Hsien‐Da , Liu Baw‐Jhiune
Published: March 2006

Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 798–808, 2006
Nuclear‐targeted minicircle to enhance gene transfer with non‐viral vectors in vitro and in vivo
Authors: Vaysse Laurence , Gregory Lisa G. , Harbottle Richard P. , Perouzel Eric , Tolmachov Oleg , Coutelle Charles
Published: March 2006

Background

To develop more efficient non‐viral vectors, we have previously described a novel approach to attach a nuclear localisation signal (NLS) to plasmid DNA, by generating a fusion protein between the tetracycline repressor protein TetR and an SV40 NLS peptide (TetR‐NLS). The high affinity of TetR for the DNA sequence tetO is used to bind the NLS to DNA. We have now investigated the ability of this system displaying the SV40 NLS or HIV‐1 TAT peptide to enhance nuclear import of a minimised DNA construct more suitable for in vivo gene delivery: a minicircle.

Methods

We have produced a new LacZ minicircle compatible with the TetR system. After transfection of the minicircle in combination with TetR‐NLS or TetR‐TAT using different transfection agents, we first measured β‐galactosidase activity in vitro. We then used a special delivery technique, in which DOTAP/cholesterol liposomes and DNA/protein complexes are sequentially injected intravenously, to evaluate the activity of this system in vivo.

Results

In vitro results showed a 30‐fold increase in transfection efficiency of the nuclear‐targeted minicircle compared to normal plasmid lipofection. Results on cell cycle arrested cells seem to indicate a different mechanism between the TetR‐NLS and TetR‐TAT. Finally, we demonstrate a more than 6‐fold increase in β‐galactosidase expression in the mouse lung using the minicircle and the TetR‐TAT protein. This increase is specific for the peptide sequence and is not observed with the control protein TetR.

Conclusions

Our results indicate that the combination of a minicircle DNA construct with a TetR nuclear‐targeting system is able to potentiate gene expression of non‐viral vectors. Copyright © 2006 John Wiley & Sons, Ltd.
Novel two‐stage screening procedure leads to the identification of a new class of transfection enhancers
Authors: Neukamm Birgit , Weimann Andreas , Wu Shuling , Danevad Margrete , Lang Christine , Geßner Reinhard
Published: March 2006

Background

Non‐viral gene transfer efficiency is low as compared to viral vector systems. Here we describe the discovery of new drugs that are capable of enhancing non‐viral gene transfer into mammalian cells using a novel two‐stage screening procedure.

Methods

First, potential candidates are preselected from a molecular library at various concentrations by a semi‐automated yeast transfection screen (YTS). The maximal transfection efficiency of every positive drug is subsequently determined in independent experiments at the optimal concentration and compared to the inhibitory effect of the drug on cell growth (IC50). In a subsequent mammalian cell transfection screen (MTS), the maximal transfection efficiency and the IC50 are determined for all preselected drugs using a human cell line and a luciferase reporter gene construct.

Results

Employing our novel system we have been able to identify a new class of transfection enhancers, the tricyclic antidepressants (i.e. doxepin, maprotiline, desipramine and amoxapine). All positive drugs enhanced gene transfer in both yeast and human cell lines, but lower concentrations were sufficient for mammalian cells. With a triple combination of doxepin, amoxapine and chloroquine we obtained a transfection efficiency that exceeded that of chloroquine, one of the best‐known transfection enhancers of mammalian cells, by nearly one order of magnitude.

Conclusions

Non‐viral gene transfer efficiency can be increased significantly using new transfection enhancers that are identified by a novel, semi‐automated two‐stage screening system employing yeast cells in the first and specific human target cells in the second round. Copyright © 2006 John Wiley & Sons, Ltd.
Specific and efficient targeting of adenovirus vectors to macrophages: application of a fusion protein between an adenovirus‐binding fragment and avidin, linked to a biotinylated oligonucleotide
Authors: Emile Gras J. C. , Verkuijlen Paul , Frants Rune R. , Havekes Louis M. , van Berkel Theo J. C. , Biessen Erik A. L. , van Dijk K. Willems
Published: March 2006

Background

The application of serotype 5 adenoviruses (Ad5) in macrophages is hampered by the absence of the endogenous coxsackie adenovirus receptor (CAR).

Methods

To overcome this limitation, we first generated a linker protein consisting of the virus‐binding domain of CAR and the C‐terminus of avidin. Second, to target macrophages, this linker protein was equipped with the biotinylated (bio) oligonucleotide dA6G10, which was previously shown to display a high affinity for the scavenger receptor A (SR‐A).

Results

As compared to nontargeted virus, the linker protein equipped with bio‐dA6G10 showed a 500‐fold increased reporter gene expression in mouse macrophage RAW264.7 cells. A linker protein equipped with a bio‐dA16 control oligonucleotide was inactive. Moreover, the bio‐dA6G10‐equipped linker showed a 390‐fold increased luciferase expression in the macrophage cell line J774 and 276‐ and 150‐fold increased reporter gene expression in primary peritoneal and bone marrow (BM)‐derived macrophages, respectively. Using BM‐derived macrophages from SR‐A knockout mice, it was shown that the dA6G10‐mediated uptake is predominantly SR‐A‐mediated.

Conclusions

Thus, we have developed a novel tool to link biotinylated ligands to a virus‐binding fragment of CAR and have exploited this linker protein to extend the applicability of Ad5 to infect transformed and primary macrophages. Copyright © 2006 John Wiley & Sons, Ltd.