bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron-Catalyzed Dechlorination of Aryl Chlorides
Authors: Guo Haiqing , Kanno Ken-ichiro , Takahashi Tamotsu
Published: September 2004

Electron-rich aryl chlorides such as chloroanisole, chloroaniline, and chlorotoluene were dechlorinated by Grignard reagents in the presence of a catalytic amount of iron chlorides. This is in sharp contrast to the cross-coupling reactions of electron-poor aryl chlorides with Grignard reagents.
Allylimidazolium Halides as Novel Room Temperature Ionic Liquids
Authors: Mizumo Tomonobu , Marwanta Edy , Matsumi Noriyoshi , Ohno Hiroyuki
Published: September 2004

Liquid state halide salts composed of imidazolium cations having allyl groups were prepared. Their ionic conductivity, viscosity, and thermal properties were investigated. Introduction of allyl group on N-position effectively suppressed the crystallization of the corresponding salts. 1,3-diallyl imidazolium halides therefore showed considerably lower viscosity and higher ionic conductivity than other halide salts.
Preparation of Protected Nanoparticles of Bismuth Telluride by Laser Ablation in Solution
Authors: Watanabe Norihisa , Kawamata Jun , Toshima Naoki
Published: September 2004

Bismuth telluride (Bi2Te3) nanoparticles were prepared by laser ablation in the presence and absence of protective agents. Addition of protective agents could decrease the size of particles, and improve the particle size distribution as well as the colloidal dispersion stability. XRD and HR-TEM have clarified that the Bi2Te3 nanoparticles, thus prepared, have a rhombohedral structure.
Ab initio Studies on Synthetic Routes of Glycine from Simple Molecules via Ammonolysis of Acetolactone: Applications of the Scaled Hypersphere Search Method
Authors: Maeda Satoshi , Ohno Koichi
Published: September 2004

New synthetic routes of glycine, the simplest amino acid molecule, have been discovered by theoretical search of ab initio potential energy surfaces. One step reaction of an acetolactone molecule with an ammonia molecule can produce a glycine molecule without byproducts, and its activation energy is only 1.6 kcal·mol−1. Acetolactone can be produced from either carbon dioxide and singlet methylene (CO2 + CH2) or carbon monoxide and formaldehyde (CO + HCHO) with respective activation energies of 3.2 and 36.3 kcal·mol−1.
Fast and effective prediction of microRNA/target duplexes
Authors: REHMSMEIER MARC , STEFFEN PETER , HÖCHSMANN MATTHIAS , GIEGERICH ROBERT
Published: September 2004

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more complex secondary structures of miRNA/target duplexes. Here, we present a program, RNA-hybrid, that predicts multiple potential binding sites of miRNAs in large target RNAs. In general, the program finds the energetically most favorable hybridization sites of a small RNA in a large RNA. Intramolecular hybridizations, that is, base pairings between target nucleotides or between miRNA nucleotides are not allowed. For large targets, the time complexity of the algorithm is linear in the target length, allowing many long targets to be searched in a short time. Statistical significance of predicted targets is assessed with an extreme value statistics of length normalized minimum free energies, a Poisson approximation of multiple binding sites, and the calculation of effective numbers of orthologous targets in comparative studies of multiple organisms. We applied our method to the prediction of Drosophila miRNA targets in 3′UTRs and coding sequence. RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/).
Multiple links between transcription and splicing
Authors: KORNBLIHTT ALBERTO R. , DE LA MATA MANUEL , FEDEDA JUAN PABLO , MUÑOZ MANUEL J. , NOGUÉS GUADALUPE
Published: September 2004

Transcription and pre-mRNA splicing are extremely complex multimolecular processes that involve protein–DNA, protein–RNA, and protein–protein interactions. Splicing occurs in the close vicinity of genes and is frequently cotranscriptional. This is consistent with evidence that both processes are coordinated and, in some cases, functionally coupled. This review focuses on the roles of cis- and trans-acting factors that regulate transcription, on constitutive and alternative splicing. We also discuss possible functions in splicing of the C-terminal domain (CTD) of the RNA polymerase II (pol II) largest subunit, whose participation in other key pre-mRNA processing reactions (capping and cleavage/polyadenylation) is well documented. Recent evidence indicates that transcriptional elongation and splicing can be influenced reciprocally: Elongation rates control alternative splicing and splicing factors can, in turn, modulate pol II elongation. The presence of transcription factors in the spliceosome and the existence of proteins, such as the coactivator PGC-1, with dual activities in splicing and transcription can explain the links between both processes and add a new level of complexity to the regulation of gene expression in eukaryotes.
The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAProcmo5UGG promotes reading of all four proline codons in vivo
Authors: NÄSVALL S. JOAKIM , CHEN PENG , BJÖRK GLENN R.
Published: September 2004

In Salmonella enterica serovar Typhimurium five of the eight family codon boxes are decoded by a tRNA having the modified nucleoside uridine-5-oxyacetic acid (cmo5U) as a wobble nucleoside present in position 34 of the tRNA. In the proline family codon box, one (tRNAProcmo5UGG) of the three tRNAs that reads the four proline codons has cmo5U34. According to theoretical predictions and several results obtained in vitro, cmo5U34 should base pair with A, G, and U in the third position of the codon but not with C. To analyze the function of cmo5U34 in tRNAProcmo5UGG in vivo, we first identified two genes (cmoA and cmoB) involved in the synthesis of cmo5U34. The null mutation cmoB2 results in tRNA having 5-hydroxyuridine (ho5U34) instead of cmo5U34, whereas the null mutation cmoA1 results in the accumulation of 5-methoxyuridine (mo5U34) and ho5U34 in tRNA. The results suggest that the synthesis of cmo5U34 occurs as follows: U34 →? ho5U →CmoB mo5U →CmoA? cmo5U. We introduced the cmoA1 or the cmoB2 null mutations into a strain that only had tRNAProcmo5UGG and thus lacked the other two proline-specific tRNAs normally present in the cell. From analysis of growth rates of various strains and of the frequency of +1 frameshifting at a CCC-U site we conclude: (1) unexpectedly, tRNAProcmo5UGG is able to read all four proline codons; (2) the presence of ho5U34 instead of cmo5U34 in this tRNA reduces the efficiency with which it reads all four codons; and (3) the fully modified nucleoside is especially important for reading proline codons ending with U or C.
A membrane transporter for tryptophan composed of RNA
Authors: JANAS TERESA , JANAS TADEUSZ , YARUS MICHAEL
Published: September 2004

We have incorporated an RNA binding site for the biological amino acid tryptophan within an RNA complex with affinity for phospholipid bilayer membranes. The resulting RNA (9:10Trp) creates a selective route through the bilayer for the amino acid. Binding and enhanced tryptophan permeability are nonlinear in RNA concentration, suggesting that RNA aggregation is required for both. Tryptophan permeability saturates with increased concentration, though at ~1000-fold greater level than when binding a free aptamer. The RNA (9:10Trp) complex, bound at a mean of two per liposome, halves the activation energy for tryptophan transport (to 46 kJ/mole), specifically increasing tryptophan entry to a maximal velocity of 0.5 sec-1 per liposome with little or no accompanying increase in general permeability. Individual RNAs turn over tens of thousands of times at high tryptophan concentration. Thus, a specific passive membrane transporter whose properties overlap those of single-molecule transporter proteins, can be made of RNA alone. Permeability changes probably rely on disturbances in lipid conformation as well as on an advantageous low free energy position for tryptophan at the membrane. Other RNA activities may yield other RNA-membrane nanosystems via this route.
Computation of Minimum-Volume Covering Ellipsoids
Authors: Sun Peng , Freund Robert M.
Published: September 2004

We present a practical algorithm for computing the minimum-volume n-dimensional ellipsoid that must contain m given points a 1,…,am ∈ ℝ n . This convex constrained problem arises in a variety of applied computational settings, particularly in data mining and robust statistics. Its structure makes it particularly amenable to solution by interior-point methods, and it has been the subject of much theoretical complexity analysis. Here we focus on computation. We present a combined interior-point and active-set method for solving this problem. Our computational results demonstrate that our method solves very large problem instances (m = 30,000 and n = 30) to a high degree of accuracy in under 30 seconds on a personal computer.
Lost-Sales Problems with Stochastic Lead Times: Convexity Results for Base-Stock Policies
Authors: Janakiraman Ganesh , Roundy Robin O.
Published: September 2004

We consider a single-location inventory system with periodic review and stochastic demand. It places replenishment orders to raise the inventory position—that is, inventory on hand plus inventory in transit—to exactly S at the beginning of every period. The lead time associated with each of these orders is random. However, the lead-time process is such that these orders do not cross. Demand that cannot be met with inventory available on hand is lost permanently. We state and prove some sample-path properties of lost sales, inventory on hand at the end of a period, and inventory position at the end of a period as functions of S. The main result is the convexity of the expected discounted sum of holding and lost-sales costs as a function of S. This result justifies the use of common search procedures or linear programming methods to determine optimal base-stock levels for inventory systems with lost sales and stochastic lead times. It should be noted that the class of base-stock policies is suboptimal for such systems, and we are primarily interested in them because of their widespread use.
Optimal Policies for a Capacitated Two-Echelon Inventory System
Authors: Parker Rodney P. , Kapuscinski Roman
Published: September 2004

This paper demonstrates optimal policies for capacitated serial multiechelon production/inventory systems. Extending the Clark and Scarf (1960) model to include installations with production capacity limits, we demonstrate that a modified echelon base-stock policy is optimal in a two-stage system when there is a smaller capacity at the downstream facility. This is shown by decomposing the dynamic programming value function into value functions dependent upon individual echelon stock variables. We show that the optimal structure holds for both stationary and nonstationary stochastic customer demand. Finite-horizon and infinite-horizon results are included under discounted-cost and average-cost criteria.
A Brownian Approximation of a Production-Inventory System with a Manufacturer That Subcontracts
Authors: Bradley James R.
Published: September 2004

This paper considers a production-inventory problem where a manufacturer fulfills stochastic, stationary demand for a single product from a finished-goods inventory. The inventory can be replenished by two production resources, in-house production and a subcontractor, which both have finite capacity. We construct a Brownian approximation of the optimal control problem, assuming that the manufacturer uses a “dual base-stock” policy to control replenishment from the two sources and that her objective is to minimize average cost. A closed-form expression is obtained for one optimal base-stock policy and an analytical expression is derived from which the other optimal base stock can be computed numerically. We show conditions under which the objective is convex in capacity, and the unique globally optimal capacity can be computed numerically. We thus provide a tractable approximation to the two-source problem, which is generally intractable. We demonstrate the accuracy of this approximation for an M/M/1 model. We also draw managerial insight from the Brownian optimal base-stock results into how the optimal base-stock policies control the inventory distribution and under what conditions the contingent source is used to build inventory or to resolve backorders.
Description of X-ray powder pattern of turbostratically disordered layer structures with a Rietveld compatible approach
Authors: Ufer Kristian , Roth Georg , Kleeberg Reinhard , Stanjek Helge , Dohrmann Reiner , Bergmann Jörg
Published: September 2004

We address the problem of the quantitative description of X-ray powder pattern of turbostratically disordered layer compounds. The Debye formula is used, which allows the aperiodic description of any arrangement of atoms. With the extension of Yang and Frindt (1996) for the ideal turbostratic case, these calculations are used to generate reference data that are subsequently treated by the Rietveld method. We are able to show that the case of uncorrelated turbostratic disorder can be modelled equally well in a periodic supercell approach with a single layer in the supercell that is suitable for the Rietveld technique. A brief introduction of this new model was given as an oral contribution at EUROCLAY 2003 (Ufer et al., 2003). The fundamental principles are described in this article because of its complexity. The applicability of this approach to real systems is demonstrated for smectite and corundum mixtures.
On the crystal parameters of some representatives of the NiAs family containing platinum group metals and gold
Authors: Ellner Martin
Published: September 2004

Unit cell parameters were investigated for the palladium/platinum and the B13…B16 element-containing representatives of the Ni2In, NiAs and CdI2 types in the whole range of homogeneity. For phases belonging to the defect Ni2In type, macroscopic density was also measured to determinate the number of atoms in the unit cell. For the homologous phases Pd2Sn(h) and Pd5Pb3(h2), it has been found that the tin-containing compound shows (at the same Pd/B metal stoichiometry) a higher number of atoms in the unit cell than the lead-containing phase. The d electron concentration of the late transition metals controls predominantly the values of the axial ratio c/a: rhodium and iridium-containing representatives of the NiAs family (possessing the same B element) show a higher c/a ratio than corresponding palladium and platinum-containing phases. Comparing the quasihomologous stannides IrSn, PtSn and AuSn, the largest difference between the sum of atomic radii and the measured shortest atomic distance, Δd = (r
A + r
B) – d
A–B, is observed for IrSn and the smallest one for AuSn. Regarding this, the iridium and platinum-containing stannides possess obviously a larger charge transfer as well as a stronger bond energy than the gold containing compound.
Crystal structure determination of In3(H3O)(H2PO4)6(HPO4)2 · 4H2O from X-ray powder diffraction
Authors: Ivashkevich Ludmila S. , Lyakhov Alexander S. , Selevich Anatoly F. , Lesnikovich Anatoly I.
Published: September 2004

The crystal structure of indium hydrogen phosphate hydrate, In3(H3O)(H2PO4)6(HPO4)2 · 4H2O, has been determined from X-ray powder diffraction data by using direct methods (EXPO program), and refined by FULLPROF package to R
Bragg value of 5.6%. The structure is monoclinic, space group C2/c (No. 15), unit cell dimensions a = 17.0835(5), b = 9.6795(3), c = 17.8776(4) Å, β = 90.301(2)°, V = 2956.2(1) Å3, Z = 4, Dx
= 2.73 g/cm3. Hydrogen atoms were placed on calculated positions. There are two unique indium atoms in the crystal structure. InO6 octahedra are connected together via the corners of PO4 tetrahedra to form layers parallel to the xy plane. The layers are linked together by water molecules, located in the interlayer space, through their hydrogen bonds. Within the layers there are hollows occupied by oxonium cations. The compound was found to be isostructural with salts of the composition M III
3MI(H2PO4)6(HPO4)2 · 4H2O, where M III-trivalent metal, M I-monovalent metal, oxonium or ammonium.
Orthorhombic ε-phases and transitional structures in Al—Pd—(Fe)
Authors: Balanetskyy Sergiy , Grushko Benjamin , Velikanova Tamara Ya.
Published: September 2004

The results of an investigation of the structures formed in the range of about Al73Pd27 to Al76Pd14Fe10 by electron diffraction and high-resolution transmission microscopy are reported. The orthorhombic ε
6, ε
16, ε
22 and ε
28 phases were observed in specific compositional sub-ranges. Their lattice parameters a ≈ 2.34 and b ≈ 1.62 nm are essentially the same while the c parameters are ≈1.23, 3.24, 4.49 and 5.70 nm, respectively. Apart from these regular structures, also structures aperiodic along the c-direction are revealed at intermediate compositions. Thus, inside the wide ε-phase range only slight continuous variations of the orthorhombic a and b cell parameters are accompanied by complicated modulations of the c cell parameter.
Structure and characterization of methyl (±)-1-(2-aminophenyl)-2-hydroxy-4-(4-methoxybenzoyl)-5-(4-methoxyphenyl)-3-oxo-2,3-dihydro-1H-pyrrole-2-acetate
Authors: Arıcı Cengiz , Ülkü Dinçer , Üngören S. Hakan , Saçmacı Mustafa , Akçamur Yunus
Published: September 2004

The stoichiometry of 1 was derived from the results of elemental analysis, IR, 1H, 13C-NMR, UV-Vis and mass spectroscopic techniques. The structure derived from physico-chemical methods is consistent with that of the X-ray diffraction. The compound crystallizes in the triclinic system, space group P1̅, with a = 9.3895(12), b = 11.3759(11), c = 12.8077(14)Å, α = 103.290(3)° β = 98.110(4)°, γ = 105.545(3)°, V = 1252.4(2)Å3, Z = 2. The molecule has a non-planar configuration. The methoxy carbonylmethyl group exhibits an E-configuration. The crystal structure is stabilized by intermolecular C—H…O, N—H…O and O—H…O contacts.
Structure analysis and the existence of light-induced long-lived metastable states in Xn[Fe(CN)5NO] with inorganic and organic cations: X
n = Pb, (H3O+CH6N+), (C2N2H7)2 and (C16H36N)2
Authors: Woike Theo , Dahaoui Slimane , Schaniel Dominik , Ponou Simeon , Hansen Niels K. , Petricek Václav
Published: September 2004

The crystal structures of four compounds X
n[Fe(CN)5NO] with the different inorganic and organic cations X
n = Pb, (H3O+CH6N+), (C2N2H7)2 and (C16H36N)2 were determined. (H3O+CH6N+)[Fe(CN)5NO] and (C2N2H7)2[Fe(CN)5NO] crystallize in the non-centrosymmetric space groups Cmc21 and Pca21, respectively. Two metastable states can be excited by irradiation with light in each of these two compounds. Pb[Fe(CN)5NO] and (C16H36N)2[Fe(CN)5NO] crystallize in the centrosymmetric space groups Pnma and P21/n, respectively, but only one metastable state can be obtained at 110 K. In (H3O+CH6N+)[Fe(CN)5NO] and (C2N2H7)2[Fe(CN)5NO] the cations are disordered. The disorder is produced by symmetry related hydrogen bonds. The hydrogen bonds are established for all organic cations, but they are weak in (C16H36N)2[Fe(CN)5NO]. The donor-acceptor relation is fulfilled between the hydrogen atoms of the cations and the nitrogen atoms of the cyanide ligands. The light-induced metastable states, created by irradiation with light in the spectral range Δλ = 410–500 nm at 110 K, were investigated by Differential Scanning Calorimetry. The isothermal measurements show that the decay of the metastable states is purely exponential. From the dynamical measurements of heat flow versus temperature the activations energies and frequency factors of the metastable states are obtained.
Study on β-sheet packing, stabilized by aromatic interactions in a tri-peptide crystal
Authors: Rathore Ravindranath S.
Published: September 2004

The role of unconventional aromatic interactions in the β-sheet packing, inside the crystal, has been highlighted. Crystal structure of terminally blocked tri-peptide, Z-L-Ala-L-Ala-L-Leu-pNA has been determined. There are four different conformers of tri-peptide inside the unit-cell, in space group P1. All the four independent molecules are described by semi-extended backbone conformations which form an anti-parallel β-sheet. The inter β-sheet packing is predominantly stabilized by C—H…π and π…π interactions. In π…π interactions, the center-to-center distance between aromatic rings varies from 3.8 Å to 4.6 Å while the closest distance of approach ranges from 3.4 Å to 3.8 Å. The associations of aromatic-aromatic rings are described by either face-to-face or inclined arrangements.
High-pressurein-situcrystallization, structure and phase transitions in 1,2-dichloroethane
Authors: Bujak Maciej , Budzianowski Armand , Katrusiak Andrzej
Published: September 2004

The single crystal of 1,2-dichloroethane, C2H4Cl2wasin-situcrystallized in a Merrill-Bassett diamond-anvil cell, and its structure determined at 0.7 GPa and 280 K. The crystals are monoclinic, space groupP21/c. The C2H4Cl2molecules in thes-transconformation are located at the inversion centers. The —H2C—CH2—ethylene group is disordered in two sites, with equal occupancies, one rotated by 180° to the other about the Cl⋯Cl axis of the molecule. The crystal cohesion forces have been attributed mainly to Cl⋯Cl intermolecular interactions, and their role in the mechanism of the phase transition at 177 K has been analysed. It was found that the order-disorder phase transition in the structure of 1,2-dichloroethane is associated with the breaking of the Cl⋯Cl intermolecular interactions in the disordered phase. The crystal amorphization under non-homogeneous strain and subsequent transition to a new pressure-induced polymorph at 1.5 GPa has been observed.
Low-temperature crystal structure of RS-thiocamphor
Authors: Robins E. Louise R. , Brunelli Michela , Mora Asiloé J. , Fitch Andrew N.
Published: September 2004

DSC and high-resolution powder X-ray diffraction measurements in the range 295 K–100 K show that RS-thiocamphor undergoes two phase transitions. The first, at around 260 K on cooling, is from the room-temperature body-centred-cubic phase to a short-lived intermediate. At 258 K the low-temperature form starts to appear. The crystal structure of the latter is orthorhombic, space group Pbnm, with a = 9.0643(4) Å, b = 14.6714(8) Å, c = 7.2878(4) Å, Z = 4, ρ
calc = 1.15 g cm–3 at 100 K. The structure is two-fold disordered, with the enantiomers superimposed in the average structure, related by the mirror plane.
Early Kinetics of Infectious Hematopoietic Necrosis Virus (IHNV) Infection in Rainbow Trout
Authors: Ogut Hamdi , Reno P. W.
Published: September 2004

A series of experiments was carried out with infectious hematopoietic necrosis virus (IHNV; 193-110 isolate) in rainbow trout Oncorhynchus mykiss (weight, ∼1.2 g) to determine the duration of the patent period and the timing of onset of the infectious periods. We first attempted to transmit IHNV to recipient fish from infected rainbow trout 2–3 d after they had been exposed. No infection transfer occurred despite high titers (104.79 to 104.91 plaque-forming units 5–8 d postexposure (dpe). To determine the number of secondary cases produced by one infectious individual, we exposed approximately 50 rainbow trout (weight, ∼1.5 g) in each of seven replicate tanks to a donor fish that had been infected with virus by bath exposure 3 d earlier. The prevalence of infection in recipient fish rose from 0.84% at 2 dpe to 7.9% at 6 dpe. Maximum incidence (22 cases) occurred between 2 and 4 dpe. No disease-specific mortalities occurred in recipient fish during the experiment. The titer of virus in both recipient and donor fish increased from 2 to 4 dpe. There was a positive correlation between the level of infection among donors and prevalence values among recipient fish (r2 = 0.60). The level of challenge by one infectious fish under the conditions provided was enough for infection transfer from sick cohabitant to susceptible fish but was not enough for initiation of a full-scale epizootic among recipients.
Effectiveness of Praziquantel Bath Treatments against Bothriocephalus acheilognathi in Grass Carp
Authors: Mitchell Andrew J.
Published: September 2004

Many states ban the importation of fish infected with the Asian tapeworm Bothriocephalus acheilognathi. Treatment with an effective tapeworm parasiticide prior to shipment would allow fish to be imported that might otherwise be rejected. In this study, extended praziquantel bath treatments of infected grass carp Ctenopharyngodon idella were tested to determine their efficacy against Asian tapeworms. Preliminary praziquantel treatments of 0.7 mg/L or more for an exposure period of 24 h at grass carp densities of 69 g/L were effective in eliminating all tapeworms from 22-g fish. When the treatment duration was lowered to 12 h, a praziquantel concentration of 2.8 mg/L was required for effective treatment. In replicated studies, significantly reduced tapeworm numbers (0–5 tapeworms per treated fish compared with 30+ tapeworms per control fish) were observed following 24-h exposures to praziquantel at 0.5, 0.7, 1.0, and 1.5 mg/ L. Tapeworm elimination occurred only at the maximum concentration of 1.5 mg/L when 88-g grass carp were stocked at a density of approximately 6 g/L. When fish density was raised to 60 g/L, the 1.5-mg/L treatment did not eliminate all tapeworms: 4 of 30 fish contained a single tapeworm.
Discriminating between a Neurotropic Myxobolus sp. and M. cerebralis, the Causative Agent of Salmonid Whirling Disease
Authors: Hogge Carla , Campbell Matthew , Johnson Keith
Published: September 2004

While screening salmonids for Myxobolus cerebralis, the causative agent of whirling disease, we detected a neurotropic Myxobolus sp. that is morphologically similar to the M. cerebralis spore in brain and other nervous tissue. We developed a polymerase chain reaction (PCR)–based diagnostic technique to differentiate the two species of Myxobolus. Primers were designed for a 277-base-pair (bp) sequence within the 18S ribosomal DNA (rDNA) gene, and the restriction enzyme Mse-I was chosen to cut the amplified product into diagnostic fragments. When electrophoresed in an acrylamide gel, M. cerebralis yielded a two-band pattern while the neurotropic Myxobolus sp. yielded a three-band pattern. This diagnostic method has resolved cases in which the pepsin–trypsin digest screening test indicated Myxobolus spores but histological examination or PCR was negative for M. cerebralis. We were also able to eliminate M. kisutchi as the neurotropic Myxobolus sp. using spores from infected coho salmon Oncorhynchus kisutch obtained from Minter Creek, Washington (the type host and type location for M. kisutchi), by designing primers to amplify a larger 683-bp amplicon within the 18S rDNA gene. Sequencing of this 683-bp product from the neurotropic Myxobolus sp. and M. kisutchi was then performed. Sequence alignment and phylogenetic analysis on the neurotropic Myxobolus sp. and M. kisutchi as well as M. cerebralis, M. arcticus, M. neurobius, M. insidiosus, and M. squamalis suggest that the neurotropic Myxobolus sp. is a new species.
Exposure to Perchlorate Induces the Formation of Macrophage Aggregates in the Trunk Kidney of Zebrafish and Mosquitofish
Authors: Capps Tim , Mukhi Sandeep , Rinchard Jacques J. , Theodorakis Chris W. , Blazer Vicki S. , Patiño Reynaldo
Published: September 2004

Environmental contamination of ground and surface waters by perchlorate, derived from ammonium perchlorate (AP) and other perchlorate salts, is of increasing concern. Exposure to perchlorate can impair the thyroid endocrine system, which is thought to modulate renal and immune function in vertebrates. This study with zebrafish Danio rerio and eastern mosquitofish Gambusia holbrooki examined the histological effects of perchlorate on the trunk kidney, which in teleosts serves excretory and hemopoietic functions and therefore may be a target of perchlorate effects. Adult zebrafish of both sexes were exposed in the laboratory to waterborne, AP-derived perchlorate at measured concentrations of 18 mg/L for 8 weeks. Adult male mosquitofish were exposed to waterborne sodium perchlorate at measured perchlorate concentrations of 1–92 mg/L for 8 weeks. Control fish were kept in untreated water. The region of the body cavity containing the trunk kidney was processed from each fish for histological analysis. Macrophage aggregates (MAs), possible markers of contaminant exposure or immunotoxic effect, were present in the hemopoietic region of the kidney in both species exposed to perchlorate. The estimated percent area of kidney sections occupied by MAs was greater in zebrafish exposed to perchlorate at 18 mg/L (P < 0.05) than in controls. In male mosquitofish, the incidence of renal MAs increased proportionally with sodium perchlorate concentration and was significantly different from that of controls at 92 mg/L (P < 0.05). These observations confirm that in fish the kidney is affected by exposure to perchlorate. The concentrations of perchlorate at which the effects were noted are relatively high but within the range reported in some contaminated habitats.
On the use and value of new media and how medical students assess their effectiveness in learning anatomy
Authors: Jastrow Holger , Hollinderbäumer Anke
Published: September 2004

The new media have become widely used tools in medical instruction today. But are they regarded as useful by students training to become medical doctors? What are students' most important criteria for a good CD‐ROM or valuable Internet resources? To answer these questions, and to obtain definite data on the use of new media, we distributed a questionnaire to preclinical medical and dental students of the Johannes Gutenberg University in Mainz, Germany. The evaluation of 397 questionnaires demonstrates that 94.9% of the students use personal computers; 91.6% of the 85.8% who own a computer have access to the Internet. The Internet is used at least once a week by 70.1% of students for private and by 59.9% for study purposes. Offers of course‐relevant material (Workshop Anatomy for the Internet) are of major interest. CD‐ROMs with anatomy applications are used by 58.9% of the students. The subjective effectiveness regarding various aspects of learning using books versus CD‐ROMs is compared and the students' views of the importance of different features of electronic media are outlined, including course‐relevant high‐resolution and quality material, key word search, state‐of‐the‐art information, and clearly laid‐out tables. The findings of this survey demonstrate high student demand for computer‐aided instruction and anatomy applications offered on the Internet and on CD‐ROMs. The students' main focus of interest was found to be examination‐relevant material and supplemental study material for courses offered locally. The present results may serve as a basis for the development of valuable educational aids. Anat Rec (Part B: New Anat) 280B:20–29, 2004. © 2004 Wiley‐Liss, Inc.
Perspective on the vestibular cortex throughout history
Authors: Duque‐Parra Jorge Eduardo
Published: September 2004

The human vestibular organ transmits sensory information to various components of the central nervous system related to head movement and, obviously, among these components, to its terminal region(s) in the vestibular parts of the cerebral cortex. Study of vestibular structures dates back to historical epochs when primitive considerations on cerebral global function were made without knowledge of a cerebral cortical region related to vestibular function. At the time of Menière in the 19th century, patients with vertigo were defined as having cerebral congestion. Cerebral mapping and computational anatomy in the 20th century significantly expanded our knowledge of cerebral structure and its function and the concept of cerebral processing of a variety of types of information, including that generated by the vestibular system. These modern techniques include nuclear magnetic resonance imaging, functional magnetic resonance imaging, and positron emission tomography. These techniques have allowed researchers to define the cortical representation of the vestibular system in human beings and in other species, a representation generally assumed to be located in various cerebral temporal and parietal regions. Although vestibular activation has been recorded in frontal lobe regions, the main vestibular cortical zone has been defined as being located in the parietal lobe; others have recognized a vestibular cortical function in the insula. Anat Rec (Part B: New Anat) 280B:15–19, 2004. © 2004 Wiley‐Liss, Inc.
Worldwide use and impact of the NASA Astrophysics Data System digital library
Authors: Kurtz Michael J. , Eichhorn Guenther , Accomazzi Alberto , Grant Carolyn , Demleitner Markus , Murray Stephen S.
Published: September 2004

The NASA Astrophysics Data System (ADS), along with astronomy's journals and data centers (a collaboration dubbed URANIA), has developed a distributed online digital library which has become the dominant means by which astronomers search, access, and read their technical literature. Digital libraries permit the easy accumulation of a new type of bibliometric measure: the number of electronic accesses (“reads”) of individual articles. By combining data from the text, citation, and reference databases with data from the ADS readership logs we have been able to create second‐order bibliometric operators, a customizable class of collaborative filters that permits substantially improved accuracy in literature queries. Using the ADS usage logs along with membership statistics from the International Astronomical Union and data on the population and gross domestic product (GDP), we have developed an accurate model for worldwide basic research where the number of scientists in a country is proportional to the GDP of that country, and the amount of basic research done by a country is proportional to the number of scientists in that country times that country's per capita GDP. We introduce the concept of utility time to measure the impact of the ADS/URANIA and the electronic astronomical library on astronomical research. We find that in 2002 it amounted to the equivalent of 736 full‐time researchers, or $250 million, or the astronomical research done in France.
Effects of β‐estradiol and propofol on the 4‐methylumbelliferone glucuronidation in recombinant human UGT isozymes 1A1, 1A8 and 1A9
Authors: Mano Yuji , Usui Takashi , Kamimura Hidetaka
Published: September 2004

The effects of β‐estradiol and propofol on human UGT1A1, 1A8 and 1A9 activities were investigated using 4‐methylumbelliferone (4‐MU) as a substrate for glucuronidation. The formation of 4‐MU glucuronide (4‐MUG) from 4‐MU, in recombinant human UGT 1A1, 1A8 and 1A9 was determined using HPLC with fluorescence detection. The glucuronidation activity of 4‐MU was the highest in UGT1A9 with an apparent Km value of 8.3 µM, while that in UGT1A1 and 1A8 was linear to at least 100 µM. β‐estradiol had potent inhibitory effects on UGT1A9 as well as on UGT1A1 with IC50 values of 2.1 and 7.2 µM, respectively. Propofol inhibited UGT1A9 activity with an IC50 of 55 µM, while the IC50 value was much higher for UGT1A8. In contrast, β‐estradiol and propofol activated 4‐MU glucuronidation in UGT1A1 and 1A8, respectively. This study therefore indicates that the use of β‐estradiol as a specific inhibitor for UGT1A1 should be used with care in the identification of UGT isozymes responsible for glucuronidation in human liver microsomes. Copyright © 2004 John Wiley & Sons, Ltd.
The somatic mutation theory of cancer: growing problems with the paradigm?
Authors: Soto Ana M. , Sonnenschein Carlos
Published: September 2004

The somatic mutation theory has been the prevailing paradigm in cancer research for the last 50 years. Its premises are: (1) cancer is derived from a single somatic cell that has accumulated multiple DNA mutations, (2) the default state of cell proliferation in metazoa is quiescence, and (3) cancer is a disease of cell proliferation caused by mutations in genes that control proliferation and the cell cycle. From this compelling simplicity, an increasingly complicated picture has emerged as more than 100 oncogenes and 30 tumor suppressor genes have been identified. To accommodate this complexity, additional ad hoc explanations have been postulated. After a critical review of the data gathered from this perspective, an alternative research program has been proposed. It is based on the tissue organization field theory, the premises of which are that carcinogenesis represents a problem of tissue organization, comparable to organogenesis, and that proliferation is the default state of all cells. The merits of these competing theories are evaluated herein. BioEssays 26:1097–1107, 2004. © 2004 Wiley Periodicals, Inc.
The evolution of arthropod segmentation mechanisms
Authors: Peel Andrew
Published: September 2004

The fruit fly, Drosophila melanogaster, patterns its segments rapidly and simultaneously, via a mechanism that relies on the ability of transcription factors to diffuse between blastoderm nuclei. Ancestral arthropods patterned posterior segments sequentially in a cellular environment, where free diffusion was likely to have been inhibited by the presence of cell membranes. Understanding how the Drosophila paradigm evolved is a problem that has interested evolutionary developmental biologists for some time. In this article, I review what is known about arthropod segmentation mechanisms, and present a model for the evolution of the Drosophila paradigm. The model predicts that the primary pair‐rule genes of Drosophila ancestrally functioned within and/or downstream of a Notch‐dependent segmentation clock, their striped expression gradually coming under the control of gap genes as the number of segments patterned simultaneously in the anterior increased and the number patterned sequentially via a segmentation clock mechanism in the posterior correspondingly decreased. BioEssays 26:1108–1116, 2004. © 2004 Wiley Periodicals, Inc.
Lysine acetylation and the bromodomain: a new partnership for signaling
Authors: Yang Xiang‐Jiao
Published: September 2004

Lysine acetylation has been shown to occur in many protein targets, including core histones, about 40 transcription factors and over 30 other proteins. This modification is reversible in vivo, with its specificity and level being largely controlled by signal‐dependent association of substrates with acetyltransferases and deacetylases. Like other covalent modifications, lysine acetylation exerts its effects through “loss‐of‐function” and “gain‐of‐function” mechanisms. Among the latter, lysine acetylation generates specific docking sites for bromodomain proteins. For example, bromodomains of Gcn5, PCAF, TAF1 and CBP are able to recognize acetyllysine residues in histones, HIV Tat, p53, c‐Myb or MyoD. In addition to the acetyllysine moiety, the flanking sequences also contribute to efficient recognition. The relationship between acetyllysine and bromodomains is reminiscent of the specific recognition of phosphorylated residues by phospho‐specific binding modules such as SH2 domains and 14‐3‐3 proteins. Therefore, lysine acetylation forges a novel signaling partnership with bromodomains to govern the temporal and spatial regulation of protein functions in vivo. BioEssays 26:1076–1087, 2004. © 2004 Wiley Periodicals, Inc.
The calpain‐system of Drosophila melanogaster: coming of age
Authors: Friedrich Peter , Tompa Peter , Farkas Attila
Published: September 2004

Drosophila melanogaster is one of the most popular and powerful model organisms that helpour understanding of mammalian (human) life processes at the molecular level. Calpains are Ca2+‐activated cytoplasmic proteases thought to play multiple roles in intracellular signal processing by limited proteolysis of target substrate proteins, thereby changing their function. The calpain superfamily consists of 14 genes in mammals, but only 4 genes in Drosophila. One may assume that the calpain system, i.e. recognizing calpain‐dependent life processes and identifying the substrates cleaved while exerting their functions, would prove easier to solve in Drosophila than in mammals. Recently, major progress has been made in characterizing Drosophila Calpain A, Calpain B and Calpain C. The fourth member, Calpain D (or SOL), was analyzed earlier. At this juncture, it seems justifiable to summarize our knowledge about the Drosophila enzymes, in comparison to the ubiquitous mammalian ones, as regards structure–function relations, mode of activation by Ca2+ and other factors, inhibition, potential targeting, expression pattern in vivo, etc. Equipped with all this information, we may now embark on the genetic modification of family members, interpreting mutant phenotypes in terms of the cell biology of calpains. BioEssays 26:1088–1096, 2004. © 2004 Wiley Periodicals, Inc.
Hop: more than an Hsp70/Hsp90 adaptor protein
Authors: Odunuga O.O. , Longshaw V.M. , Blatch G.L.
Published: September 2004

Molecular chaperones facilitate the correct folding of other proteins under physiological and stress conditions. Recently it has become evident that various co‐chaperone proteins regulate the cellular functions of these chaperones, particularly Hsp70 and Hsp90. Hop is one of the most extensively studied co‐chaperones that is able to directly associate with both Hsp70 and Hsp90. The current dogma proposes that Hop functions primarily as an adaptor that directs Hsp90 to Hsp70‐client protein complexes in the cytoplasm. However, recent evidence suggests that Hop can also modulate the chaperone activities of these Hsps, and that it is not dedicated to Hsp70 and Hsp90. While the co‐chaperone function of Hop within the cytoplasm has been extensively studied, its association with nuclear complexes and prion proteins remains to be elucidated. This article will review the structural features of Hop, and the evidence that its biological function is considerably broader than previously envisaged. BioEssays 26:1058–1068, 2004. © 2004 Wiley Periodicals, Inc.
The continuing challenge of early mortality in acute pancreatitis
Authors: McKay C J , Imrie C W
Published: September 2004

Local networks may aid decision making
Randomized clinical trial of four-layer and short-stretch compression bandages for venous leg ulcers (VenUS I)
Authors: Nelson E A , Iglesias C P , Cullum N , Torgerson D J
Published: September 2004

Background

A randomized clinical trial was undertaken to determine the relative effectiveness of four-layer and short-stretch bandaging for venous ulceration.

Methods

A total of 387 adults with a venous ulcer, who were receiving leg ulcer treatment either in primary care or as a hospital outpatient, were recruited to this parallel-group open study and randomized to either four-layer or short-stretch bandages. Follow-up continued until the patient's reference leg was ulcer free or for a minimum of 12 months. The primary endpoint was time to complete healing of all ulcers on the reference leg. Secondary outcomes included proportion of ulcers healed, health-related quality of life, withdrawals and adverse events. Analysis was by intention to treat.

Results

Unadjusted analysis identified no statistically significant difference in median time to healing: 92 days for four-layer and 126 days for short-stretch bandages. However, when prognostic factors were included in a Cox proportional hazards regression model, ulcers treated with the short-stretch bandage had a lower probability of healing than those treated with the four-layer bandage: hazard ratio 0·72 (95 per cent confidence interval 0·57 to 0·91). More adverse events and withdrawals were reported with the short-stretch bandage.

Conclusion

Venous leg ulcers treated using a four-layer bandage healed more quickly than those treated with a short-stretch bandage.
Economic analysis of VenUS I, a randomized trial of two bandages for treating venous leg ulcers
Authors: Iglesias C P , Nelson E A , Cullum N , Torgerson D J
Published: September 2004

Background

The study investigated the cost-effectiveness of four-layer and short-stretch compression bandages for treating venous leg ulcers.

Methods

Cost-effectiveness and cost-utility analyses were performed using patient-level data collected alongside the VenUS I leg ulcer study. The perspective for the economic analysis was that of the UK National Health Service (NHS) and Personal Social Service. The time horizon for the analysis was 1 year after recruitment. Health benefit was measured as differences in ulcer-free days and quality-adjusted life years (QALYs).

Results

The mean healing time for ulcers treated with four-layer bandages was 10·9 (95 per cent confidence interval (c.i.) −6·8 to 29·1) days less than that for ulcers treated with short-stretch bandages. Mean average difference in QALYs between compression systems was −0·02 (95 per cent c.i. −0·08 to 0·04). The four-layer bandage cost a mean of £227·32 (95 per cent c.i. £16·53 to £448 ·30) less per patient per year than the short-stretch bandage.

Conclusion

On average, four-layer bandaging was associated with greater health benefits and lower costs than short-stretch bandaging.
Perianal Crohn's disease (Br J Surg 2004; 91: 801-814)
Authors: Olaison G , Almer S , Anderson P
Published: September 2004

The Editors welcome topical correspondence from readers relating to articles published in the Journal. Responses can be sent electronically via the BJS website (www.bjs.co.uk) or by post. All letters will be reviewed and, if approved, appear on the website. A selection of these will be edited and published in the Journal. Letters must be no more than 250 words in length. Letters submitted by post should be typed on A4-sized paper in double spacing and should be accompanied by a disk.
Phase‐Transfer Agents as Catalysts for a Nucleophilic Substitution Reaction in Microemulsions
Authors: Häger Maria , Holmberg Krister
Published: September 2004

The reaction between 4‐tert‐butylbenzyl bromide and potassium iodide was carried out in microemulsions based on different nonionic surfactants, and the reaction rates were compared with those obtained in two‐phase systems with added phase‐transfer agent, either a quaternary ammonium salt or a crown ether. The reactions were relatively fast in the microemulsions and extremely sluggish in the two‐phase systems without additional phase‐transfer agent. Addition of a phase‐transfer agent did not accelerate the reaction when a hydrocarbon was used as organic solvent, neither in the two‐phase system nor in the microemulsion. When a chlorinated hydrocarbon was used as solvent, phase‐transfer catalysis became effective and the rate obtained in the two‐phase system with an equimolar amount of phase‐transfer agent added was higher than that obtained in the microemulsion. When a catalytic amount of phase‐transfer agent was used, the rate in the two‐phase system was about the same as the rate obtained in the microemulsion without the phase‐transfer agent. The combined approach, that is, use of a microemulsion as the reaction medium and addition of a phase‐transfer agent, gave the highest reaction rate. The quaternary ammonium salt (tetrabutylammonium hydrogen sulfate) was a more efficient catalyst in the microemulsion system than the crown ether ([18]crown‐6).
A Convenient Synthetic Route to Benz[cd]azulenes: Versatile Ligands with the Potential To Bind Metals in an η5, η6, or η7 Fashion
Authors: Balduzzi Sonya , Müller‐Bunz Helge , McGlinchey Michael J.
Published: September 2004

A facile method for preparing the 2H‐benz[cd]azulene system, based upon an elaboration of the guaiazulene framework, is presented. Aerial oxidation to the corresponding 8‐(2‐propylidene)‐benz[cd]azulene, and also cycloaddition reactions with tetracyanoethylene (TCNE), are described. The first X‐ray crystal structure of a 2H‐benz[cd]azulene, as an η6‐coordinated Cr(CO)3 complex, is reported.