bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and implementation of a parallel algorithm for the fast design of oligonucleotide probe sets for diagnostic DNA microarrays
Authors: Meier H. , Krause A. , Kräutner M. , Bode A. 
Published: July 2004

AbstractWe describe an accurate method for the automatic parallel generation of oligonucleotide probe sets for DNA microarrays. This approach includes a component for high‐performance specificity evaluation of designed probes in large data sets. The three main algorithmic components of the method, namely probe preselection, hybridization prediction and probe selection are explained in detail. We introduce new combinatorial techniques for the efficient selection of probe sets of high differentiation capability even from sequence databases of conserved homologous genes. These techniques include the automatic generation of group specific probes as well as the design of excluding probes. A basic prototype has been implemented including a shared memory parallelization. Test runs have been performed on a multiprocessor personal computer with subsets of a small subunit ribosomal ribonucleic acid database, containing very conserved sequence data. The applicability of our program is pointed out by designing a set of oligonucleotide probes that shall allow a comprehensive parallel identification and differentiation of several groups of extremophilic prokaryotes by DNA microarray. The probe set is accessible via the Internet. On applying the parallel version on a dual processor system an efficiency of 80% was achieved. Copyright © 2004 John Wiley & Sons, Ltd.
A hybrid self‐organizing maps and particle swarm optimization approach
Authors: Xiao Xiang , Dow Ernst R. , Eberhart Russell , Ben Miled Zina , Oppelt Robert J. 
Published: July 2004

AbstractGene clustering, the process of grouping related genes in the same cluster, is at the foundation of different genomic studies that aim at analyzing the function of genes. Microarray technologies have made it possible to measure gene expression levels for thousands of genes simultaneously. For knowledge to be extracted from the datasets generated by these technologies, the datasets have to be presented to a scientist in a meaningful way. Gene clustering methods serve this purpose. In this paper, a hybrid clustering approach that is based on self‐organizing maps and particle swarm optimization is proposed. In the proposed algorithm, the rate of convergence is improved by adding a conscience factor to the self‐organizing maps algorithm. The robustness of the result is measured by using a resampling technique. The algorithm is implemented on a cluster of workstations. Copyright © 2004 John Wiley & Sons, Ltd.
A specialized hardware device for the protein similarity search
Authors: Marongiu A. , Palazzari P. , Rosato V. 
Published: July 2004

AbstractThis work presents the architecture of PROSIDIS, a special purpose processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Similarity is determined by means of a weighting matrix which measures the degree of similarity between any two amino acids.The paper recalls the basis of the PHG (Parallel Hardware Generator) tool, developed in the framework of the HADES project (Hardware Design for Scientific Applications). Through PHG it is possible to design, in a nearly automatic way, a parallel hardware which efficiently implements an algorithm described through recurrence equations; PHG is able to generate a synthesizable VHDL which represents a parallel system derived from the System of Affine Recurrence Equations (SARE) describing the problem.In this work we illustrate the advantages derived from designing a special purpose processor to face the protein similarity discovery problem. Some preliminary results are given, reporting the time spent by several conventional computing architectures and by the PROSIDIS processor hosted by a personal computer to solve the same protein analysis problem. The results show that PROSIDIS, implemented on a Xilinx XV1000 FPGA, gives speedup figures ranging from 5.6 up to 55.6. Copyright © 2004 John Wiley & Sons, Ltd.
Parallel divide and conquer approach for the protein threading problem
Authors: Yanev Nicola , Andonov Rumen 
Published: July 2004

AbstractFor the Protein Threading Problem (PTP) we propose a network‐flow like formulation. We also show its equivalence with a generalization of the shortest path problem on a graph with a very particular structure. The underlying Mixed Integer Programming (MIP) model proves to be very appropriate for the PTP—large real‐life instances have been solved much faster by using only the MIP solver CPLEX instead of a known special‐purpose branch and bound algorithm. The properties of the MIP model permit a decomposition of the main problem into a large number of subproblems (tasks). We show that a branch and cut strategy can be efficiently applied for solving these tasks in a parallel manner, which leads to a significant reduction in the total running time. Computational experiments with large problem instances are presented. Copyright © 2004 John Wiley & Sons, Ltd.
The AxML program family for maximum likelihood‐based phylogenetic tree inference
Authors: Stamatakis Alexandros P. , Ludwig Thomas , Meier Harald 
Published: July 2004

AbstractInference of phylogenetic (evolutionary) trees comprising hundreds or thousands of organisms based on the maximum likelihood criterion is a computationally extremely intensive task. This paper describes the evolution of the AxML program family which provides novel algorithmic as well as technical solutions for the maximum likelihood‐based inference of huge phylogenetic trees. Algorithmic optimizations and a new tree building algorithm yield runtime improvements of a factor greater than 4 compared with fastDNAml and parallel fastDNAml, returning equally good trees at the same time. Various parallel, distributed, and Grid‐based implementations of AxML give the program the capability to acquire the large amount of required computational resources for the inference of huge high‐quality trees. Copyright © 2004 John Wiley & Sons, Ltd.
Mice deficient in invariant‐chain and MHC class II exhibit a normal mature B2 cell compartment
Authors: Maehr Rene´ , Kraus Manfred , Ploegh Hidde L. 
Published: July 2004

AbstractThe role of the invariant chain (Ii), an MHC class II‐associated chaperone, in B cell development is controversial. Ii deficient mice (Ii–/– mice) show a defect in B cell development.This defect has been attributed to the absence of a fragment liberated from the Ii by intramembranous proteolysis. It was proposed that this fragment is required for activation of the NF‐κB pathway as a means of controlling B cell maturation. The opposing view holds that defects in the assembly of MHC class II molecules result in impaired B cell development. Here we demonstrate that a lack of Ii indeed causes defects in B cell development, with fewer mature B cells in the periphery as previously reported, but that in a compound‐mutant from which both Ii and all MHC class II subunits are absent, B cell development is normal. We suggest that neither Ii itself, nor the MHC class II products are required for normal B cell development.
Reactions of Group 13 and 14 Hydrides and Group 1, 2, 13 and 14 Organyl Compounds with (tert‐Butylimino)(2,2,6,6‐tetramethylpiperidino)borane
Authors: Braun Ulrike , Böck Barbara , Nöth Heinrich , Schwab Ingo , Schwartz Manfred , Weber Siegfried , Wietelmann Ulrich 
Published: July 2004

Abstract(tert‐Butylimino)(2,2,6,6‐tetramethylpiperidino)borane (1) is a highly reactive species. Its B≡N triple bond inserts into the B−H bond of boranes, R2BH, generating diborylamines of the type tmp−BH−NtBu−BR2 (tmp = 2,2,6,6‐tetramethylpiperidino; R = H, Cl, Br, or organyl). Thexylborane reacts analogously, but only one of its two B−H bonds is used for the hydroboration of 1. However, dihaloboranes HB(Hal)2−SMe2 (Hal = Cl, Br) give B‐haloboration products tmp−B(Hal)−NtBu−BH(Hal), while reactions with H2B(Hal)−SMe2 produce a mixture of two isomers by competing hydroboration and haloboration reactions. Tmp−BH−NtBu−AlH2 was obtained from 1 and AlH3−NMe3. It is a dimer in the solid state with pentacoordinate Al atoms and AlH2Al bridges. Hydrosilylation of 1 was achieved with Me2SiHCl, SiHCl3 or Ph2SiH2 to give the N‐silyl‐substituted diaminoboranes tmp‐BH‐NtBu−SiX3−nRn. Me3SnH and Bu3SnH behave similarly, giving the corresponding N‐stannylated diaminoboranes. However, when Ph3SnH was treated with 1, the stannylborane tmp−B(SnPh3)−NHtBu was formed showing an umpolung of the hydrostannylation. Organyllithium compounds provide access to N‐lithiodiaminoboranes of the type tmp−BR−NtBu−Li. The stability of these compounds depends on the substituent R. The least stable compound was the B−tBu derivative followed by the B‐methyl compound. However, in the presence of TMEDA tmp−BMe−NtBu−Li is sufficiently stable to allow reactions, e.g. with B‐chlorocatecholborane, to produce tmp−BMe−NtBu−BO2C6H4. The most stable lithium compound so far is tmp−BPh−NtBu−Li−OEt2, whose structure has been determined by X‐ray crystallography. MgBu2 behaves like LiR and both of its Mg−C bonds can be used for the insertion reaction. The same is also true of ZnMe2. In contrast, at ambient temperature, only one of the E−C bonds of triorganylalanes, triorganylgallanes and InPh3 is used for the insertion reaction. In the solid state, most of the new compounds show a weak to strong coordinate bond between the electrophilic centre (Li, Mg, Zn, Cd, B, Al, Ga and In) and the nitrogen atom of the tmp group which generates a four‐membered ring. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Polynuclear Rhenium and Manganese Selenido‐Carbonyl Complexes − Reversible Square to Butterfly Conversion of the Re4Se2 Core by CO Loss in [Re4(µ3‐Se)2(CO)16(PPh3)2], and the Crystal Structure of [Mn2(µ2‐Se2)(CO)5(PPh3)2]
Authors: Belletti Daniele , Graiff Claudia , Pattacini Roberto , Predieri Giovanni , Tiripicchio Antonio 
Published: July 2004

AbstractThe reaction of Ph3PSe with [Mn2(CO)10] leads to the formation of [Mn4(μ3‐Se)2(μ‐CO)(CO)14(PPh3)2], which contains a butterfly “Mn2Se2 core”, along with traces of [Mn2(μ2‐Se2)(CO)5(PPh3)2] (1), which contains a tetrahedral Mn2Se2 core. The reaction of Ph3PSe with [Re2(CO)8(NCMe)2] affords two new complexes, [Re4(μ3‐Se)2(CO)16(PPh3)2] (2) and [Re4(μ3‐Se)2(μ‐CO)(CO)14(PPh3)2] (3). Their molecular structures, determined by X‐ray diffraction methods, exhibit a nearly square‐planar Re2Se2 and a butterfly Re2Se2 core, respectively. These air‐stable tetrarhenium selenido‐carbonyl species display a reversible loss/addition of a CO molecule, which is accompanied by the formation/cleavage of a Re−Re bond and the consequent rearrangement of the Re2Se2 core, from square to butterfly and vice versa. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Synthesis, Characterisation, Properties and X‐ray Structures of CuII Coordination Compounds with 5,5′‐Dimethylbipyridine and Various Anions: Control of Stoichiometry and Structure by the Counterions
Authors: van Albada Gerard A. , Mohamadou Aminou , Mutikainen Ilpo , Turpeinen Urho , Reedijk Jan 
Published: July 2004

AbstractThe synthesis, crystal structures, and electronic and magnetic properties of eight new CuII compounds containing the ligand 5,5‐dimethyl‐2,2,′‐bipyridine (dmbpy) with the general formula [CuII(dmbpy)x(L)2] (where L = BF4−, CF3SO3−, NO3−, Br−, NCS−, N3−, HCOO−, and x = 1−3) are reported. The geometries of the CuII ions include a four‐coordinate square‐planar polymeric compound [Cu(dmbpy)(N3)2]n (7), the five‐coordinate compounds, [Cu(dmbpy)2(C2H6O)](CF3SO3)2 (2), [Cu(dmbpy)2(NO3)](NO3) (3), [Cu(dmbpy)2(Br)]Br (5), [Cu(dmbpy)(NCS)2]n (6) and [Cu(dmbpy)2(HCOO)](CF3SO3) (8), which have geometries ranging from square pyramidal to trigonal bipyramidal, and the six‐coordinate compounds [Cu(dmbpy)3](BF4)2(C2H6O) (1) and [Cu(dmbpy)(NO3)2] (4), which adopt an octahedrally based geometry. Except for compounds 3 and 4, with nitrate as the anion, a variation of the copper/ligand ratios in the synthesis has no influence on the stoichiometry. The compounds have been characterised in detail by infrared, ligand field and EPR spectroscopy; the data are consistent with the single‐crystal X‐ray structures. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Structural Characterization of Bismuth(III) and Antimony(III) Chlorotriflates: Key Intermediates in Catalytic Friedel−Crafts Transformations
Authors: Mazières Stéphane , Le Roux Christophe , Peyronneau Magali , Gornitzka Heinz , Roques Nicolas 
Published: July 2004

AbstractChlorotriflates of antimony and bismuth ClnM(OSO2CF3)3−n (n = 1 or 2) are believed to be metallic intermediates of major importance in Friedel−Crafts reactions that use Bi(OSO2CF3)3, Sb(OSO2CF3)3, the systems BiCl3/CF3SO2OH or SbCl3/CF3SO2OH as catalysts. Unknown until now, the compounds ClBi(OSO2CF3)2 (1) and Cl2Sb(OSO2CF3) (2) have been synthesized by reaction of MCl3 (M = Bi, Sb) with triflic acid. After crystallization from THF, 1 and 2 were investigated in the solid state by X‐ray crystallography. Their use as catalysts in benzoylation of toluene, acylation of m‐xylene, and sulfonylation of toluene led to conclusive results, thus giving weight to their key role as intermediates in Friedel−Crafts reactions. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Synthesis, Crystal Structures and Electrical Conductivities of the Ionic Liquid Compounds Butyldimethylimidazolium Tetrafluoroborate, Hexafluorophosphate and Hexafluoroantimonate
Authors: Kölle Philipp , Dronskowski Richard 
Published: July 2004

AbstractSee original Eur. J. Inorg. Chem. 2004, 2313–2320 ( DOI: http://dx.doi.org/10.1002/ejic.200300940).
Molecular “Iron Maidens”: Ultrashort Nonbonded Contacts in Cyclophanes and Other Crowded Molecules
Authors: Pascal Robert A. 
Published: July 2004

AbstractUltrashort nonbonded interactions involving aromatic rings should be the sole province of cyclophane chemists, but it is not always so. In this review, the structures, syntheses, and properties of molecules exhibiting the closest nonbonded contacts of various atoms and functional groups with the faces of aromatic rings are discussed and illustrated. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Catalytic Hydrogen‐Mediated Cross‐Coupling of Enones and Carbonyl Compounds: Aldol Condensation by Hydrogenation
Authors: Jang Hye‐Young , Krische Michael J. 
Published: July 2004

AbstractCatalytic hydrogenation of enones and enals in the presence of aldehyde and ketone partners results in the formation of aldol products. A key feature of such hydrogen‐mediated C−C bond formations relates to the heterolytic activation of elemental hydrogen by cationic rhodium(I) complexes, that enables monohydride‐based catalytic cycles for which direct alkyl‐hydrogen reductive elimination pathways are disabled. Here, a concise overview of catalytic hydrogen‐mediated aldol condensation is presented. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
Analysis of the Voltammetric Response of Electroactive Guests in the Presence of Non‐Electroactive Hosts at Moderate Concentrations
Authors: Mendoza Sandra , Castaño Eduardo , Meas Yunny , Godínez Luis A. , Kaifer Angel E. 
Published: July 2004

AbstractIn this work, we present a method to analyze the voltammetric response of reversible redox systems involving molecules that, bearing m non‐interactive electroactive sites, can undergo fast complexation equilibria with host molecules present at concentrations of the same order of magnitude as those of the electroactive guest. The approach focuses on systems for which the relative values of the binding constants for the oxidized and reduced forms of the guest result in the displacement of the voltammetric response of the electroactive molecule as the concentration of the host is increased in the electrolytic solution. This behavior is commonly known as “one wave shift behavior”. Based on a series of assumptions, the method allows calculation of all the thermodynamic parameters that describe the electrochemical and complexation equilibria of a given host‐guest system. The main strength of the suggested method, however, relies on the fact that it only requires cyclic voltammetry data and that it can be used for systems in which large concentrations of the host can not be employed either due to important changes of the ionic strength or to solubility problems. Although the accuracy of the obtained information is limited by the quality of the data provided by the technique, and by the assumptions employed, it certainly represents an excellent starting point for subsequent refinement either using digital simulations or an independent experimental technique.
Microdimensional Polyaniline: Fabrication and Characterization of Dynamics of Charge Propagation at Microdisk Electrodes
Authors: Caban Karolina , Kulesza Pawel J. , Stojek Zbigniew , Donten Mikolaj , Miecznikowski Krzysztof , Chojak Malgorzata 
Published: July 2004

AbstractWe describe fabrication of microdimensional polyanilne films in a controlled manner by voltammetric potential cycling or controlled potential electrolysis on platinum microdisk electrodes. The film grows in a form of hemispherical microdeposits, and its size largely exceeds the size of a Pt microdisk. Consequently, the film covers both the Pt substrate as well as the surrounding glass seal. Since the adhering polyaniline layer is conducting, the latter situation may lead to an increase in the effective electrode surface area. The lateral growth of polyaniline films outside the microdisk has also been demonstrated by performing diagnostic voltammetric experiments with use of a double microdisk set‐up in which independent polarization of each disk is feasible. Microelectrode‐based chronocoulometry, that involves an uncomplicated well‐defined reduction potential step starting from the emeraldine (conducting) form and ending at leucoemeraldine (nonconducting) form, yields (upon application of a sufficiently short pulse) a well‐defined linear response of charge versus square root of time that is consistent with the linear effective diffusion as the predominant charge propagation mechanism. When describing the system kinetics in terms of the effective (apparent) diffusion coefficient, we expect this parameter to be on the level of 10−8 cm2 s−1 or lower. The relative changes in dynamics of charge transport are discussed with respect to the polyaniline film loading, the size of microdisk electrode, expansion of the active electrode area, and the choice of electrolyte (strong acid) anion. The results are consistent with the view that when Pt microelectrode is modified with PANI deposit exceeding the size of the microdisk substrate, it behaves in a way as if its surface area is effectively much larger than the geometric area of Pt microdisk.
Electrochemical and Spectroelectrochemical Studies on Pyridoxine Hydrochloride Using a Poly(methylene blue) Modified Electrode
Authors: Tan Liang , Xie Qingji , Yao Shouzhuo 
Published: July 2004

AbstractThe electrochemical redox processes of pyridoxine hydrochloride (VB6) at a poly(methylene blue) film modified glass carbon electrode (PMBE) in a phosphate buffer solution (PBS, pH 8.0) were studied by cyclic voltammetry. The VB6 electrode reaction with quasi‐reversible characteristics was diffusion‐controlled at low scan rates and adsorption‐controlled at high scan rates. The anodic peak current positive to 0.6 V (vs. SCE) was found to be proportional to the concentration of VB6 in the range of 0.010 to 1.03 mg⋅mL−1 with a detection limit of 1.34 μg mL−1. Fluorescence and UV‐vis absorption spectroelectrochemical measurements suggest that the pyridine ring was not destroyed over the potential range from −0.8 to 1 V (vs. SCE), and the electrocatalytic generation of pyridoxal was anodically started at 0.57 V.
Biosensor for Hepatitis B Virus DNA PCR Product and Electrochemical Study of the Interaction of Di(2,2′‐bipyridine)osmium(III) with DNA
Authors: Zhao Hongtao , Ju Huangxian 
Published: July 2004

AbstractThe strategy for electrochemical detection of HBV DNA PCR product (181 bps) was designed by covalently immobilizing single‐stranded HBV DNA on preoxidized glassy carbon electrode surface. The immobilization of single stranded DNA was verified by AC impedance spectra. The following hybridization reaction on surface was evidenced by electrochemical methods using [Os(bpy)2Cl2]+ as an electroactive indicator. The interactions of [Os(bpy)2Cl2]+ with calf thymus single and double stranded DNA immobilized on preoxidized glassy carbon electrodes were studied. [Os(bpy)2Cl2]+ could bind preferentially to the duplex DNA by intercalating to base pairs. The intrinsic binding constant of [Os(bpy)2Cl2]+ with calf thymus DNA was calculated to be 1.21×104 M−1. Using [Os(bpy)2Cl2]+ as an electrochemical hybridization indicator, the HBV DNA sensor has been used to detect qualitatively target HBV DNA in solution with high sensitivity and selectivity.
Modelling quality of life variables with non‐parametric mixtures
Authors: Forcina Antonio , Bartolucci Francesco 
Published: July 2004

AbstractWe present a new methodology for modelling the joint distribution of ordered categorical variables with finite mixtures where hypotheses of interest may be expressed by linear equality and inequality constraints on the parameters. The connection with non‐parametric polytomousitem response theorymodels is outlined and an application to the quality of life of asthmatic patients is examined. An algorithm for constrained maximum likelihood estimation is described and an analysis of deviance table for hypotheses testing based on the asymptotic distribution of the likelihood ratio statistic is outlined. Copyright © 2004 John Wiley & Sons, Ltd.
Instrumental variables in Gaussian directed acyclic graph models with an unobserved confounder
Authors: Stanghellini Elena 
Published: July 2004

AbstractWe discuss the problem of identification of relevant parameters in a DAG model for Gaussian variables with one unobserved variable that acts as a counfounder. We first make explicit what we intend for identification and then discuss an example where a modified notion of instrumental variable renders a system with a confounder identifiable. Copyright © 2004 John Wiley & Sons, Ltd.
Environmental burden of disease: HRQoL and statistical perspectives
Authors: Kumar Sen Pranab 
Published: July 2004

AbstractEnvironmental toxicity and pollution mingled with substandard sanitation and public health practice can lead to serious health problems. Some of these toxics can be identified and subjected to preventive measures but together with some other major factors they form the environmental burden of disease, more seriously in developing countries. As a result, in health related quality of life risk assessments, especially relating to cancer of various types, as well as chronic and intestinal diseases, we need to incorporate toxicology as well as environmental epidemiology. Statistical perspectives in this challenging task are appraised with special attention to the arsenite contamination of the groundwater problem. Copyright © 2004 John Wiley & Sons, Ltd.