bluuebunny/crossref_metadata_2025 huggingface dataset:
Contribution of Horizontal Gene Transfer to the Evolution of
Saccharomyces cerevisiae
Authors: Hall Charles , Brachat Sophie , Dietrich Fred S.
Published: June 2005

The genomes of the hemiascomycetes
Saccharomyces cerevisiae
and
Ashbya gossypii
have been completely sequenced, allowing a comparative analysis of these two genomes, which reveals that a small number of genes appear to have entered these genomes as a result of horizontal gene transfer from bacterial sources. One potential case of horizontal gene transfer in
A. gossypii
and 10 potential cases in
S. cerevisiae
were identified, of which two were investigated further. One gene, encoding the enzyme dihydroorotate dehydrogenase (DHOD), is potentially a case of horizontal gene transfer, as shown by sequencing of this gene from additional bacterial and fungal species to generate sufficient data to construct a well-supported phylogeny. The DHOD-encoding gene found in
S. cerevisiae
,
URA1
(YKL216W), appears to have entered the
Saccharomycetaceae
after the divergence of the
S. cerevisiae
lineage from the
Candida albicans
lineage and possibly since the divergence from the
A. gossypii
lineage. This gene appears to have come from the
Lactobacillales
, and following its acquisition the endogenous eukaryotic DHOD gene was lost. It was also shown that the bacterially derived horizontally transferred DHOD is required for anaerobic synthesis of uracil in
S. cerevisiae.
The other gene discussed in detail is
BDS1
, an aryl- and alkyl-sulfatase gene of bacterial origin that we have shown allows utilization of sulfate from several organic sources. Among the eukaryotes, this gene is found in
S. cerevisiae
and
Saccharomyces bayanus
and appears to derive from the alpha-proteobacteria.
Constitutive Signal Transduction by Mutant Ssy5p and Ptr3p Components of the SPS Amino Acid Sensor System in
Saccharomyces cerevisiae
Authors: Poulsen Peter , Wu Boqian , Gaber Richard F. , Kielland-Brandt Morten C.
Published: June 2005

Amino acids in the environment of
Saccharomyces cerevisiae
can transcriptionally activate a third of the amino acid permease genes through a signal that originates from the interaction between the extracellular amino acids and an integral plasma membrane protein, Ssy1p. Two plasma membrane-associated proteins, Ptr3p and Ssy5p, participate in the sensing, which results in cleavage of the transcription factors Stp1p and Stp2p, removing 10 kDa of the N terminus of each of them. This confers the transcription factors with the ability to gain access to the nucleus and activate transcription of amino acid permease genes. To extend our understanding of the role of Ptr3p and Ssy5p in this amino acid sensing process, we have isolated constitutive gain-of-function mutants in these two components by using a genetic screening in which potassium uptake is made dependent on amino acid signaling. Mutants which exhibit inducer-independent processing of Stp1p and activation of the amino acid permease gene
AGP1
were obtained. For each component of the SPS complex, constitutive signaling by a mutant allele depended on the presence of wild-type alleles of the other two components. Despite the signaling in the absence of inducer, the processing of Stp1p was more complete in the presence of inducer. Dose response assays showed that the median effective concentration for Stp1p processing in the mutant cells was decreased; i.e., a lower inducer concentration is needed for signaling in the mutant cells. These results suggest that the three sensor components interact intimately in a complex rather than in separate reactions and support the notion that the three components function as a complex.
Class I and Class II Chitin Synthases Are Involved in Septum Formation in the Filamentous Fungus
Aspergillus nidulans
Authors: Ichinomiya Masayuki , Yamada Emi , Yamashita Shuichi , Ohta Akinori , Horiuchi Hiroyuki
Published: June 2005

The class II and class I chitin synthases of the filamentous fungus
Aspergillus nidulans
are encoded by
chsA
and
chsC
, respectively. Previously, we presented several lines of evidence suggesting that ChsA and ChsC have overlapping functions in maintaining cell wall integrity. In order to determine the functions of these chitin synthases, we employed electron and fluorescence microscopy and investigated in detail the cell wall of a Δ
chsA
Δ
chsC
double mutant (ΔAC mutant) along with the localization of ChsA and ChsC. In the lateral cell wall of the ΔAC mutant, electron-transparent regions were thickened. Septa of the ΔAC mutant were aberrantly thick and had a large pore. Some septa were located abnormally close to adjacent septa. A functional hemagglutinin (HA)-tagged ChsA (HA-ChsA) and a functional FLAG-tagged ChsC (FLAG-ChsC) were each localized to a subset of septation sites. Comparison with the localization pattern of actin, which is known to localize at forming septa, suggested that ChsA and ChsC transiently exist at the septation sites during and shortly after septum formation. Double staining of HA-ChsA and FLAG-ChsC indicated that their localizations were not identical but partly overlapped at the septation sites. Fluorescence of FLAG-ChsC, but not of HA-ChsA, was also observed at hyphal tips. These data indicate that ChsA and ChsC share overlapping roles in septum formation.
Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids
Authors: Marande William , Lukeš Julius , Burger Gertraud
Published: June 2005

Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of
Diplonema papillatum
, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the
cox1
gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous
cox1
mRNA requires
trans
-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of
Diplonema
is not only different from that of kinetoplastids but unique among eukaryotes as a whole.
Eukaryotic UDP-Galactopyranose Mutase (
GLF
Gene) in Microbial and Metazoal Pathogens
Authors: Beverley Stephen M. , Owens Katherine L. , Showalter Melissa , Griffith Cara L. , Doering Tamara L. , Jones Victoria C. , McNeil Michael R.
Published: June 2005

Galactofuranose (Gal

f

) is a novel sugar absent in mammals but present in a variety of pathogenic microbes, often within glycoconjugates that play critical roles in cell surface formation and the infectious cycle. In prokaryotes, Gal

f

is synthesized as the nucleotide sugar UDP-Gal

f

by UDP-galactopyranose mutase (UGM) (gene
GLF
). Here we used a combinatorial bioinformatics screen to identify a family of candidate eukaryotic
GLF
s that had previously escaped detection.
GLF
s from three pathogens, two protozoa (
Leishmania major
and
Trypanosoma cruzi
) and one fungus (
Cryptococcus neoformans
), had UGM activity when expressed in
Escherichia coli
and assayed in vivo and/or in vitro. Eukaryotic
GLF
s are closely related to each other but distantly related to prokaryotic
GLF
s, showing limited conservation of core residues around the substrate-binding site and flavin adenine dinucleotide binding domain. Several eukaryotes not previously investigated for Gal

f

synthesis also showed strong
GLF
homologs with conservation of key residues. These included other fungi, the alga
Chlamydomonas
and the algal phleovirus
Feldmannia irregularis
, parasitic nematodes (
Brugia
,
Onchocerca
, and
Strongyloides
) and
Caenorhabditis elegans
, and the urochordates
Halocynthia
and
Cionia
. The
C. elegans
open reading frame was shown to encode UGM activity. The
GLF
phylogenetic distribution suggests that Gal

f

synthesis may occur more broadly in eukaryotes than previously supposed. Overall,
GLF
/Gal

f

synthesis in eukaryotes appears to occur with a disjunct distribution and often in pathogenic species, similar to what is seen in prokaryotes. Thus, UGM inhibition may provide an attractive drug target in those eukaryotes where Gal

f

plays critical roles in cellular viability and virulence.
The
RIM101/pacC
Homologue from the Basidiomycete
Ustilago maydis
Is Functional in Multiple pH-Sensitive Phenomena
Authors: Aréchiga-Carvajal Elva T. , Ruiz-Herrera José
Published: June 2005

A homologue of the gene encoding the transcription factor Rim101 (PacC), involved in pH signal transduction in fungi, was identified in the pathogenic basidiomycete
Ustilago maydis
. The gene (
RIM101
) encodes a protein of 827 amino acid residues, which shows highest similarity to PacC proteins from
Fusarium oxysporum
and
Aspergillus niger
. The gene had the capacity to restore protease activity to
rim101
mutants from
Yarrowia lipolytica
, confirming its homologous function, and was expressed at both acid and neutral pH. Null
Δrim101
mutants were not affected in the in vitro pH-induced dimorphic transition, their growth rate, resistance to hypertonic sorbitol or KCl stress, and pathogenicity. However, similar to
pacC
(
rim101
) mutants in other fungi, they displayed a pleiotropic phenotype with alterations in morphogenesis, impairment in protease secretion, and increased sensitivity to Na
+
and Li
+
ions. Other phenotypic characteristics not previously reported in fungal
pacC
(
rim101
) mutants (morphological changes, increased sensitivity to lytic enzymes, and augmented polysaccharide secretion) were also observed in
U. maydis
mutants. All these modifications were alleviated by transformation with the wild-type gene, confirming that all were the result of mutation in
RIM101
. These data indicate that the Pal/Rim pathway is functional in
U. maydis
(and probably in other basidiomycetes) and plays complex roles in pH-sensing phenomena, as occurs in ascomycetes and deuteromycetes.
Unraveling the Secret Lives of Bacteria: Use of In Vivo Expression Technology and Differential Fluorescence Induction Promoter Traps as Tools for Exploring Niche-Specific Gene Expression
Authors: Rediers Hans , Rainey Paul B. , Vanderleyden Jos , De Mot René
Published: June 2005

A major challenge for microbiologists is to elucidate the strategies deployed by microorganisms to adapt to and thrive in highly complex and dynamic environments. In vitro studies, including those monitoring genomewide changes, have proven their value, but they can, at best, mimic only a subset of the ensemble of abiotic and biotic stimuli that microorganisms experience in their natural habitats. The widely used gene-to-phenotype approach involves the identification of altered niche-related phenotypes on the basis of gene inactivation. However, many traits contributing to ecological performance that, upon inactivation, result in only subtle or difficult to score phenotypic changes are likely to be overlooked by this otherwise powerful approach. Based on the premise that many, if not most, of the corresponding genes will be induced or upregulated in the environment under study, ecologically significant genes can alternatively be traced using the promoter trap techniques differential fluorescence induction and in vivo expression technology (IVET). The potential and limitations are discussed for the different IVET selection strategies and system-specific variants thereof. Based on a compendium of genes that have emerged from these promoter-trapping studies, several functional groups have been distinguished, and their physiological relevance is illustrated with follow-up studies of selected genes. In addition to confirming results from largely complementary approaches such as signature-tagged mutagenesis, some unexpected parallels as well as distinguishing features of microbial phenotypic acclimation in diverse environmental niches have surfaced. On the other hand, by the identification of a large proportion of genes with unknown function, these promoter-trapping studies underscore how little we know about the secret lives of bacteria and other microorganisms.
The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology
Authors: Sapp Jan
Published: June 2005

Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the “prokaryote,” in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.
The TetR Family of Transcriptional Repressors
Authors: Ramos Juan L. , Martínez-Bueno Manuel , Molina-Henares Antonio J. , Terán Wilson , Watanabe Kazuya , Zhang Xiaodong , Gallegos María Trinidad , Brennan Richard , Tobes Raquel
Published: June 2005

We have developed a general profile for the proteins of the TetR family of repressors. The stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix DNA binding motif and adjacent regions in the three-dimensional structures of TetR, QacR, CprB, and EthR, four family members for which the function and three-dimensional structure are known. We have detected a set of 2,353 nonredundant proteins belonging to this family by screening genome and protein databases with the TetR profile. Proteins of the TetR family have been found in 115 genera of gram-positive, α-, β-, and γ-proteobacteria, cyanobacteria, and archaea. The set of genes they regulate is known for 85 out of the 2,353 members of the family. These proteins are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which the family member is involved can be simple, as in TetR (i.e., TetR bound to the target operator repressestetAtranscription and is released in the presence of tetracycline), or more complex, involving a series of regulatory cascades in which either the expression of the TetR family member is modulated by another regulator or the TetR family member triggers a cell response to react to environmental insults. Based on what has been learned from the cocrystals of TetR and QacR with their target operators and from their three-dimensional structures in the absence and in the presence of ligands, and based on multialignment analyses of the conserved stretch of 47 amino acids in the 2,353 TetR family members, two groups of residues have been identified. One group includes highly conserved positions involved in the proper orientation of the helix-turn-helix motif and hence seems to play a structural role. The other set of less conserved residues are involved in establishing contacts with the phosphate backbone and target bases in the operator. Information related to the TetR family of regulators has been updated in a database that can be accessed atwww.bactregulators.org.
ON THE PROPERTIES OF ∊-SENSITIVITY ANALYSIS FOR LINEAR PROGRAMMING
Authors: PARK CHAN-KYOO , KIM WOO-JE , PARK SOONDAL
Published: June 2005

∊-Sensitivity analysis (∊-SA) is a kind of method to perform sensitivity analysis for linear programming. Its main advantage is that it can be directly applied for interior-point methods with a little computation. In this paper, we discuss the property of ∊-SA analysis and its relationship with other sensitivity analysis methods. First, we present a new property of ∊-SA, from which we derive a simplified formula for finding the characteristic region of ∊-SA. Next, based on the simplified formula, we show that the characteristic region of ∊-SA includes the characteristic region of Yildirim and Todd's method. Finally, we show that the characteristic region of ∊-SA asymptotically becomes a subset of the characteristic region of sensitivity analysis using optimal partition. Our results imply that ∊-SA can be used as a practical heuristic method for approximating the characteristic region of sensitivity analysis using optimal partition.
A PERCENTILE SEARCH HEURISTIC FOR GENERALIZED ASSIGNMENT PROBLEMS WITH A VERY LARGE NUMBER OF JOBS
Authors: HIGGINS A. J.
Published: June 2005

This article presents a new heuristic for generalized assignment problems with a very large number of jobs. The heuristic applies a probabilistic acceptance of a move, based on a percentile threshold, using information from recent moves. This percentile search heuristic (PSH) is compared to tabu search, simulated annealing, and threshold accepting using a rigorous computational experimentation with randomly generated problem instances of up to 50,000 jobs and 40 agents. The PSH did find the best solution among the heuristics for 45% of the instances, particularly larger size problems, versus 30% for tabu search, but required more fine-tuning of the heuristic parameters.
METAHEURISTIC APPROACHES FOR THE MULTILEVEL RESOURCE-CONSTRAINED LOT-SIZING PROBLEM WITH SETUP AND LEAD TIMES
Authors: BERRETTA REGINA , FRANÇA PAULO M. , ARMENTANO VINÍCIUS A.
Published: June 2005

We propose the use of metaheuristics for the resource-capacitated multilevel lot-sizing problem with general product structures, setup costs, setup times, and lead times. Initially, we develop a heuristic which moves production in time in order to obtain feasible solutions with good quality. Strategies for the short-term memory and long-term memory of tabu search are then included to guide the search of the subordinate heuristic for new, feasible, and better solutions. Simulated annealing components are embedded into tabu search in order to improve its performance. For small problems, the solutions provided by tabu search and the hybrid metaheuristic are compared to optimal solutions and for larger problems, the quality of the solutions is evaluated against a lower bound generated by Lagrangean relaxation.
AN ALGORITHM FOR THE GENERALIZED VEHICLE ROUTING PROBLEM WITH BACKHAULING
Authors: MITRA SUBRATA
Published: June 2005

The Vehicle Routing Problem with Backhauling deals with the supply of finished goods from a depot to a number of delivery points, and picking up returnable items and bringing them back to the depot using a fleet of trucks. Traditionally, the objective of the problem has been to determine the truck routes such that the total number of trucks and/or the total distance traveled/total route cost are minimized. Most of the papers available in the literature in this connection deal with problems where the linehaul (having a demand for finished goods) and backhaul (having items to be returned to the depot) customers are different, and a customer may be visited by at most one truck limiting demand and returns at a location by the capacity of the truck. In this paper, we allow the linehaul and backhaul customers to be the same leading to simultaneous delivery and pickup at a customer location, and also there is no restriction on the quantity demanded at (to be returned from) a customer location. As such a customer may be visited by more than one truck and more than once by the same truck. We developed a Mixed Integer Linear programming (MILP) formulation of the problem and a route construction heuristic. The heuristic averaged 80 ms for 110 problems tested, and in 78 of them the heuristic costs were either equal to the optimal costs or at most equal to the upper bounds on the optimal costs obtained after running the optimization package for 30 min. Optimal solutions were obtained for 28 problems at an average time of 295 ms. The heuristic could match the optimal solutions for 22 of these problems at an average time of 71 ms.
ANALYSIS OF A BULK QUEUE WITH FAST AND SLOW SERVICE RATES AND MULTIPLE VACATIONS
Authors: ARUMUGANATHAN R. , RAMASWAMI K. S.
Published: June 2005

We analyze a Mx/G(a,b)/1 queueing system with fast and slow service rates and multiple vacations. The server does the service with a faster rate or a slower rate based on the queue length. At a service completion epoch (or) at a vacation completion epoch if the number of customers waiting in the queue is greater than or equal to N (N > b), then the service is rendered at a faster rate, otherwise with a slower service rate. After finishing a service, if the queue length is less than 'a' the server leaves for a vacation of random length. When he returns from the vacation, if the queue length is still less than 'a' he leaves for another vacation and so on until he finally finds atleast 'a' customers waiting for service. After a service (or) a vacation, if the server finds atleast 'a' customers waiting for service say ξ, then he serves a batch of min (ξ, b) customers, where b ≥ a. We derive the probability generating function of the queue size at an arbitrary time. Various performance measures are obtained. A cost model is discussed with a numerical solution.
THE EFFECT OF CREDIT PERIOD ON THE OPTIMAL LOT SIZE FOR DETERIORATING ITEMS WITH TIME VARYING DEMAND AND DETERIORATION RATES
Authors: CHANG HORNG-JINH , DYE CHUNG-YUAN
Published: June 2005

In this paper, we present an inventory model for deteriorating items with time varying demand and deterioration rates when the credit period depends on the retailer's ordering quantity. We also provide simple solution procedures for finding the optimal replenishment period and show in a rigorous way that the policy suggested is indeed optimal. Further, we use numerical examples to illustrate the model and conclude the paper with suggestions for possible future research.
SEMI-ON-LINE SCHEDULING PROBLEM FOR MAXIMIZING THE MINIMUM MACHINE COMPLETION TIME ON THREE SPECIAL UNIFORM MACHINES
Authors: LUO RUN-ZI , SUN SHI-JIE
Published: June 2005

In this paper, we investigate a semi-on-line version for a special case of three machines M1, M2, M3 where the processing time of the largest job is known in advance. A speed si(s1 = s2 = 1, 1 ≤ s3 = s) is associated with machine Mi. Our goal is to maximize the C min — the minimum workload of three machines. We give a C min 3 algorithm and prove its competitive ratio is [Formula: see text] and the algorithm is the best possible for 1 ≤ s ≤ 2. We also claim the competitive ratio of algorithm C min 3 is tight.
AN INVENTORY SYSTEM WITH PARTIAL BACKLOGGING MODELED ACCORDING TO A LINEAR FUNCTION
Authors: SAN JOSÉ L. A. , SICILIA J. , GARCÍA-LAGUNA J.
Published: June 2005

In this paper, we study an inventory system with partial backlogging, in which the backlogging rate is a continuous and nonincreasing two piece function. The total shortage cost includes three significant costs: the unit backorder cost (depending on the backorder time), the opportunity cost, and the goodwill cost. This model generalizes several inventory systems studied by other authors. The optimal policy is characterized through several results, which depend on the values of the known input parameters. Illustrative examples and a sensitivity analysis, which help us understand the theoretical results, are also given.
STUDIES ON MAGNETIC NANOMATERIALS BY ATOMIC FORCE MICROSCOPY WITH HIGH RESOLUTION
Authors: YANG X. H. , WANG Y. F. , LIU A. P. , XIN H. Z. , LIU J. C.
Published: June 2005

Studies on magnetic nanomaterials by atomic force microscopy (AFM) with high resolution are introduced in this paper. We have developed AFM.IPC-208B to observe the microsurface of magnetic fluid and doped cadmium sulfide (CdS·X) , which are two new types of magnetic nanomaterials. By using scanning tunneling microscope to detect the fluctuation of cantilever, we have obtained AFM three-dimensional images of samples, and analyzed the microstructures of the magnetic materials and their magnetism characteristics.
RIGOROUS ELECTROMAGNETIC ANALYSIS OF THE FOCUSING ACTION OF REFRACTIVE CYLINDRICAL MICROLENS
Authors: LIU JUAN , GU BEN-YUAN , DONG BI-ZHEN , YANG GUO-ZHEN
Published: June 2005

The focusing action of refractive cylindrical microlens is investigated based on the rigorous electromagnetic theory with the use of the boundary element method. The focusing behaviors of these refractive microlenses with continuous and multilevel surface-envelope are characterized in terms of total electric-field patterns, the electric-field intensity distributions on the focal plane, and their diffractive efficiencies at the focal spots. The obtained results are also compared with the ones obtained by Kirchhoff's scalar diffraction theory. The present numerical and graphical results may provide useful information for the analysis and design of refractive elements in micro-optics.
ON THE PHONON POLARITON MODES IN SEMICONDUCTOR SUPERLATTICES
Authors: JOSEPH WILSON K. S. , NAVANEETHAKRISHNAN K.
Published: June 2005

The phonon polariton modes in a semiconductor superlattice system is discussed using GaAs/GaP system as an example. The significance of one of the modes, which had not been paid sufficient attention in the past, is pointed out. Numerical results are presented for both TE and TM modes, both at the superlattice Brillouin zone edge and at the center.
LOCALIZED ENTANGLEMENT IN ONE-DIMENSIONAL ANDERSON MODEL
Authors: LI HAIBIN , WANG XIAOGUANG
Published: June 2005

The entanglement in one-dimensional Anderson model is studied. The pairwise entanglement has a direct relation to the localization length and is reduced by disorder. Entanglement distribution displays the entanglement localization. The pairwise entanglements around localization center exhibit a maximum as the disorder strength increases. The dynamics of entanglement are also investigated.
DEPOSITION OF M—C (M = Cr, Mn, Fe) FILMS BY MAGNETRON SPUTTERING
Authors: HOU Q. R. , ZHANG H. Y.
Published: June 2005

Thin films of M — C ( M = Cr , Mn , Fe ) have been deposited on silicon substrates by magnetron sputtering. It was found that interdiffusion between carbide films and silicon substrates occurred for Mn — C/Si and Fe — C/Si samples. The hardness and elastic modulus of the Cr — C films were around 16 ± 1 GPa and 210 ± 21 GPa , respectively. Mn — C and Fe — C films were not so hard as Cr — C films. The resistivity of these films at room temperature was between 0.267 and 3.40 mΩ cm. The resistivity of Cr — C and Mn — C films changed a little with time at 673 K in air.
VARIABLE RANGE HOPPING CONDUCTION IN NiO/Al2O3 NANOCOMPOSITES
Authors: MAKHLOUF SALAH A. , KHALIL KAMAL M. S.
Published: June 2005

The formation and electrical properties of high surface area NiO/Al2O3 nanocomposite materials with composition ranging from 5 to 30% w/w have been studied. The temperature dependence of the DC electrical resistivity was monitored in the temperature range 350–600 K. The results revealed correlation between electrical resistivity and textural properties. The conductivity results were discussed in terms of variable-range-hopping mechanism.
SELF-CONSISTENT SIMULATION OF QUANTUM DOT FLASH MEMORY DEVICE WITH SiO2 AND HfO2 DIELECTRICS
Authors: CHONG CHEE CHING , ZHOU KAI HONG , BAI PING , LI ER PING , SAMUDRA GANESH S.
Published: June 2005

Flash memory structure in which a silicon quantum dot embedded in the gate dielectric region between the channel and the control gate is considered. A self-consistent simulation for such memory devices is performed and aims to understand the relationship between the device structure and the meaningful quantities, as required for an efficient device operation. In this study, both the traditional SiO2 and HfO2 high-k dielectrics are being explored, and their results are compared and contrasted. In particular, the superiority of HfO2 over the SiO2 is demonstrated through various interlocking investigations on the relationships between the tunneling current, dielectric thickness, barrier height, programming and retention times.
NANOINDENTATION STUDY OF NANOCRYSTALLINE NICKEL
Authors: JAYAGANTHAN R. , MOHANKUMAR K. , TAY A. A. O.
Published: June 2005

The mechanical properties of nanocrystalline (Nc) Ni (electrodeposited, sintered, rolled) and microcrystalline (Mc) Ni were investigated by nanoindentation technique. Force-displacement curves generated during loading and unloading of the nanoindenter tip (Berkovich diamond tip) were used to determine the hardness and elastic properties of the Nc-nickel. The influence of loading rate on the hardness of electrodeposited Nc- Ni and microcrystalline (Mc) Ni were studied in the present work. The electrodeposited Nc-nickel exhibits higher hardness and elastic modulus when compared to sintered Nc-nickel. The higher modulus of elasticity is observed for the rolled Nc-nickel due to the increased defect density and less porosity in the samples. The higher modulus of elasticity is observed for Mc-nickel when compared to that of Nc-nickel (electrodeposited) with varying load rate. The strain rate sensitivity of Nc-nickel is due to the grain boundary affected zone.
SYNTHESIS AND CHARACTERIZATION OF DOUBLE SURFACTANT COATED MAGNETIC PARTICLES
Authors: SHAMIM N. , PENG Z. , HONG L. , HIDAJAT K. , UDDIN M. S.
Published: June 2005

The unique and novel physicochemical features of the nanosized magnetic particles, which are attained due to their size and shape morphology, have aggregated an interest in the fields of nanoscience and nanotechnology. In this work, magnetic particles coated with double-layer surfactants were prepared and characterized. The magnetic particles ( Fe3O4 ) were synthesized by chemical precipitation of Fe2+ and Fe 3+ salts (1:2 ratio) with ammonium hydroxide ( NH4OH ) under inert atmosphere at 80°C followed by resuspension of the nanoparticles in water using thiodiglycolic acid. This procedure produced Fe3O4 nanoparticles stabilized against agglomeration. The primary surfactant coated particles were further treated with 4-vinylaniline at 25°C for about thirty minutes. As –SH group in thiodiglycolic acid has greater affinity formagnetic surface, it is easily attached to the iron particles through bonding. Subsequently, the – NH2 functional group of 4-vinylaniline reacts with the acid group – COOH of the thiodiglycolic acid. The size and the distribution of these magnetic particles, their morphologies and magnetic properties were measured by Transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR) and vibrating sample magnetometer (VSM), respectively. TEM results show the formation of single domain nanoparticles of mean diameter of about 10 nm. The strength of the NH–CO bond was measured by FTIR (Bio-Rad), the vibration observed at a wavelength of 1613–1745 cm-1. Thermo gravimetric analysis (TGA) reveals the existence of two distinct layers of surfactants on the particle surface. These surface-modified nanomagnetic particles can further be coated with thermo-sensitive polymeric materials which may be used in separation and purification of bio-molecules.
NANOCRYSTALLINE DIAMOND FILMS ON HIGH SPEED STEEL BY MICROWAVE PLASMA CHEMICAL VAPOR DEPOSITION
Authors: AMORNKITBAMRUNG VITTAYA , BURINPRAKHON THANUSIT , JARERNBOON WIRAT
Published: June 2005

Nanocrystalline diamond films were deposited on high speed steel substrates by microwave plasma chemical vapor deposition. The best hardness improvement was about 130% of the substrate hardness, using -150 V substrate bias deposition conditions. Raman peaks of nanocrystalline diamond at 1190 cm-1 and of graphite nanoclusters at 1522 cm-1 wereobserved in this sample. Scanning electron microscope images show crystallite grains of different sizes between 25–250 nm.
SYNTHESIS OF POLYSTYRENE ENCAPSULATEDZnS-COATEDCdSeNANOCOMPOSITES MODIFIED WITH PLL–PEI–PEG–FA
Authors: CAI JIANLING , HUANG NING , ZHANG YONG
Published: June 2005

Current cell tags using dyes lose their luminescence quickly and are not suitable for optical barcoding. Semiconductor quantum dots (QDs), on the other hand, can be engineered to emit different wavelengths, thus permitting tagging of various cells at the same time. Core/shell luminescent quantum dots, cadmium selenide ( CdSe ) and zinc sulphide ( ZnS ), were synthesized and incorporated into polystyrene (PS) particles grafted with carboxyl groups using microemulsion polymerization method. Highly luminescent monodispersed PS particles with diameters from 30 nm to 50 nm were chosen for subsequent surface modification. Two series of surface modifications were carried out with PS particles. One was modified with poly(L-Lysine) (PLL), polyethylenimine (PEI), Poly(Ethylene Glycol) (PEG) and folic acid (FA) side chains in sequence through chemical bonding. Another was conjugated with PEG and FA in sequence. The folic acid side chains can enter target cells via folate receptors and assisted in the uptake of the luminescent particles into the cells. This property allows them to be used as fluorescent labels for marking their ingress into cells and also for a cornucopia of biomedical applications.
ALIGNED MULTIPLE-WALLED CARBON NANOTUBES AS BIOSENSORS BY COLORIMETRIC AND AMPEROMETRIC TECHNIQUES
Authors: WU JING-RU , JAHNGEN EDWIN , LI KUANG-PANG , TSE WAN-SUN , CHIANG PING , CHIANG HAI-PANG
Published: June 2005

Vertically oriented multiple-walled carbon nanotubes (MWCNTs) aligned on a silicon substrate were covalently bonded with horseradish peroxidase (HRP) and used as biosensors or electrodes. The modified platform was investigated with Scanning Electron Microscopy (SEM), UV-Vis spectrophotometer and Cyclic Voltammetry (CV). The enzyme catalyzed reaction and the subsequent reduction of the enzymatic products by the platform were carefully investigated. The assay was done by measuring the absorbance of the dye formed from the reaction product of the substrates (phenol) and 4-aminoantipyrine. From the linear response, phenol can be quantitized in the range from 47 ppm to 750 ppm with a detection limit of 19 ppm (based on S/N = 3). The resulting modified aligned MWCNTs still exhibited enzymatic activities after storage of 13 days. The activity of the attached HRP was also demonstrated electrochemically.
SYNTHESIS OF NANOSTRUCTURED POROUS CARBON
Authors: SU FABING , LV LU , ZHAO X. S.
Published: June 2005

In this paper, high-surface-area porous carbons with crumpled nanowalls were synthesized by carbonization of sucrose in the presence of zeolite template. The pore structures of the carbon materials were characterized using physical adsorption of nitrogen. Their surface chemistry was analyzed using X-ray photoelectron spectrometer (XPS). The microscopic structure features of the samples were imaged by field-emission scanning electron microscope (FESEM) and transmission electron microscopy (TEM). The nanostructure of synthesized porous carbon with a combination of micro-, meso- and macropores has been obtained.
THE POSSIBILITY OF GROUP WELFARE FUNCTIONS
Authors: SAATY THOMAS L. , VARGAS LUIS G.
Published: June 2005

This paper gives a brief overview of the well-known impossibility-possibility theorem in constructing a social welfare function from individual functions. The Analytic Hierarchy Process uses a fundamental scale of absolute numbers to represent judgments about dominance in paired comparisons. It is shown that it is possible to derive such a function in two ways. One is from the synthesized functions of the judgments of each of the individuals. The other is obtained by first combining corresponding pairwise comparison judgments made by all the individuals, thus obtaining a matrix of combined judgments for the group and then deriving a welfare function for the group. With consistency the four conditions imposed by Arrow are satisfied. With inconsistency, an additional condition is needed.
AN APPROACH TO PURE LINGUISTIC MULTIPLE ATTRIBUTE DECISION MAKING UNDER UNCERTAINTY
Authors: XU ZESHUI
Published: June 2005

The pure linguistic multiple attribute decision making problems are studied, in which the information about the attribute weights are expressed in the form of linguistic variables or uncertain linguistic variables, and the attribute values take the form of uncertain linguistic variables. The operational laws of uncertain linguistic variables are introduced, and two uncertain linguistic aggregation operators called linguistic weighted aggregation operator and uncertain linguistic weighted aggregation operator are developed based on uncertain linguistic variables and their operational laws. An approach based on the developed operators for pure linguistic multiple attribute decision making under uncertainty is proposed. The prominent characteristic of the proposed approach is that it can compute with uncertain linguistic information directly. Furthermore, the approach is straightforward and does not produce any loss of information. Finally, an illustrative example is given.
MAKING DECISIONS IN AN INTELLIGENT TUTORING SYSTEM
Authors: PEK PENG-KIAT , POH KIM-LENG
Published: June 2005

In computerized tutoring, the pace of instruction is related to the student's mastery levels of the learning objectives. The observable student's behavior that can be used to measure his knowledge is usually his responses to test items. Unobservable variables that are related to learner's motivation can affect learning but are difficult to quantify. In comparison with other decision-theoretic tutoring systems, the novelties of this research are: (1) the efficiency-centric approach to develop the Bayesian networks; (2) the formulation of utility values for different tutoring outcomes that are independent of past actions and to satisfy the separability condition; (3) the development of a common measure for student's mastery levels and item difficulties; and (4) the generation of optimal policies in polynomial time. A prototype web-based tutoring system, known as iTutor, incorporating the novelties has been developed for engineering mechanics. Formative evaluations of iTutor have shown encouraging results.
FINDING OUTLIERS AT MULTIPLE SCALES
Authors: HU TIANMIN , SUNG SAM YUAN
Published: June 2005

Outlier detection targets those exceptional data whose pattern is rare and lie in low density regions. In this paper, under the assumption of complete spatial randomness inside clusters, we propose an MDV (Multi-scale Deviation of the Volume) approach to identifying outliers. In addition to assigning an outlier score for each object, it directly outputs a crisp outlier set. It also offers a plot showing the data structure in every object's vicinity, which is useful in explaining why it may be outlying. Finally, the effectiveness of MDV is demonstrated with both artificial and real datasets.
FUZZY MCDM APPROACH FOR EVALUATION OF EXPATRIATE ASSIGNMENTS
Authors: CHEN MEI-FANG , TZENG GWO-HSHIUNG , TANG TZUNG-I
Published: June 2005

As international corporate activities increase, the staffing of their operations involves more strategic concerns. However, foreign assignments have many differences, and dissatisfaction with host country is a known cause of expatriate failure. This study distinguishes from previous studies, which focused on the expatriate selection process from the viewpoint of the human resource managers. From the view of expatriate candidate's points, this paper describes a fuzzy analytic hierarchy process (fuzzy AHP) to determine the weighting of subjective judgments. When the expatriate assignments are evaluated from various aspects, such as employee personal factors, employee competencies, job characteristics, family factors, environmental factors and organization relocation support activities, it can be regarded as an fuzzy multiple criteria decision making (FMCDM) problem. Since expatriate candidates cannot clearly estimate the relative importance of each considered criterion in terms of numerical values, fuzziness is applicable. Consequently, this paper uses triangular fuzzy numbers by fuzzy AHP to establish weights for expatriate candidates, thus determining the relative importance for criteria of expatriate assignments. From the insights of this study, this article addresses this expatriate problem and offers guidelines for managers concerned with a successful expatriate assignment program.
THE INITIAL VALUE PROBLEM IN NUMERICAL RELATIVITY
Authors: PFEIFFER HARALD P.
Published: June 2005

The conformal method for constructing initial data for Einstein's equations is presented in both the Hamiltonian and Lagrangian picture (extrinsic curvature decomposition and conformal thin sandwich formalism, respectively), and advantages due to the recent introduction of a weight-function in the extrinsic curvature decomposition are discussed. I then describe recent progress in numerical techniques to solve the resulting elliptic equations, and explore innovative approaches toward the construction of astrophysically realistic initial data for binary black hole simulations.
PAK1 induces podosome formation in A7r5 vascular smooth muscle cells in a PAK-interacting exchange factor-dependent manner
Authors: Webb Bradley A. , Eves Robert , Crawley Scott W. , Zhou Shutang , Côté Graham P. , Mak Alan S.
Published: June 2005

Remodeling of the vascular smooth muscle cytoskeleton is essential for cell motility involved in the development of diseases such as arteriosclerosis and restenosis. The p21-activated kinase (PAK), which is an effector of the Rho GTPases Rac and Cdc42, has been shown to be involved in cytoskeletal remodeling and cell motility. We show herein that expression of cytoskeletally active constructs of PAK1 is able to induce the formation of dynamic, podosome-like F-actin columns in the A7r5 vascular smooth muscle cell line. Most of these actin columns appear at the junctions between stress fibers and focal adhesions and contain several known podosomal protein markers, such as cortactin, Arp2/3, α-actinin, and vinculin. The kinase activity of PAK plays a role in the regulation of the turnover rates of these actin columns but is not essential for their formation. The ability of PAK to interact with the PAK-interacting exchange factor (PIX) but not with Rac or Cdc42, however, is required for the formation of the actin columns as well as for the translocation of PIX and G protein-coupled receptor kinase-interacting protein (GIT) to focal adhesions adjacent to the actin columns. These findings suggest that interaction between PAK and PIX, as well as the recruitment of PIX and GIT to focal adhesions, plays an important role in the formation of actin columns that resemble podosomes induced by phorbol ester in vascular smooth muscle cells.
Functional characterization of high-affinity Na+/dicarboxylate cotransporter found in Xenopus laevis kidney and heart
Authors: Oshiro Naomi , Pajor Ana M.
Published: June 2005

The SLC13 gene family includes sodium-coupled transporters for citric acid cycle intermediates and sulfate. The present study describes the sequence and functional characterization of a SLC13 family member from Xenopus laevis, the high-affinity Na+/dicarboxylate cotransporter xNaDC-3. The cDNA sequence of xNaDC-3 codes for a protein of 602 amino acids that is ∼70% identical to the sequences of mammalian NaDC-3 orthologs. The message for xNaDC-3 is found in the kidney, liver, intestine, and heart. The xNaDC-3 has a high affinity for substrate, including a Km for succinate of 4 μM, and it is inhibited by the NaDC-3 test substrates 2,3-dimethylsuccinate and adipate. The transport of succinate by xNaDC-3 is dependent on sodium, with sigmoidal activation kinetics, and lithium can partially substitute for sodium. As with other members of the family, xNaDC-3 is electrogenic and exhibits inward substrate-dependent currents in the presence of sodium. However, other electrophysiological properties of xNaDC-3 are unique and involve large leak currents, possibly mediated by anions, that are activated by binding of sodium or lithium to a single site.
Cell-specific posttranscriptional regulation of CFTR gene expression via influence of MAPK cascades on 3′UTR part of transcripts
Authors: Baudouin-Legros Maryvonne , Hinzpeter Alexandre , Jaulmes Amandine , Brouillard Franck , Costes Bruno , Fanen Pascale , Edelman Aleksander
Published: June 2005

Expression of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, which contains the mutations responsible for CF, is regulated by cytokines (TNF-α and IL-1β) in a cell-specific manner. TNF-α decreases CFTR mRNA in human colon cell lines (HT-29), but not in pulmonary cell lines (Calu-3), and IL-1β increases it only in Calu-3 cells. We looked for the cytokine-induced posttranscriptional regulation of CFTR gene expression and studied the modulation of CFTR mRNA stability linked to its 3′ untranslated sequence (3′UTR) in HT-29 and Calu-3 cells. The stability of CFTR mRNA was analyzed by Northern blot after in vitro incubation of total RNAs from CFTR-expressing cells with cytosolic proteins extracted from control or cytokine-treated HT-29 and Calu-3 cells. CFTR mRNA was degraded only by extracts of TNF-α-treated HT-29 cells and not by cytosolic proteins from untreated or IL-1β-treated HT-29 cells. In contrast, extracts of untreated Calu-3 cells enhanced CFTR mRNA degradation, and IL-1β treatment inhibited this; TNF-α had no significant effect. The 3′UTR part of CFTR mRNA was found to be required for this posttranscriptional regulation. The 5′ part of the 3′UTR (the 217 first bases), which contains two AUUUA sequences, was implicated in CFTR mRNA destabilization and the following 136 bases, containing several C-repeats in U-rich environment, in its protection. The proteins, which reacted with the U- and C-repeats of CFTR mRNA 3′UTR, were mainly controlled by stimulation of the p42/p44 and p38 MAP kinase cascades with interaction between these pathways. This posttranscriptional control of gene expression is a common feature of CFTR and many proteins of inflammation.