bluuebunny/crossref_metadata_2025 huggingface dataset:
REAL-TIME DISPATCHING: SCHEDULING STABILITY AND PRECEDENCE
Authors: KRINGS AXEL W. , DROR MOSHE
Published: January 2003

This paper introduces a new graph theoretical concept called strong precedence which is used to address the problem of scheduling instability is non-preemptive static list scheduling. Scheduling instability occurs when a reduction in task duration of one or more tasks causes other tasks to miss their deadline. This problem has been addressed in the past by introducing additional precedence constraints into the precedence graph representing the workload, or by limiting the depth the dispatchers scan at run-time. We present an alternative stabilization approach based on the concept of strong and weak precedence. By defining a strong precedence relation on selected subgraphs, the workload becomes inherently stable without requiring the introduction of new edges into the graph.
GRAMMARS AND AUTOMATA TO OPTIMIZE CHAIN LOGIC QUERIES
Authors: GRECO SERGIO , SACCÀ DOMENICO , ZANIOLO CARLO
Published: January 2003

The critical problem of finding efficient implementations for recursive queries with bound arguments offers many open challenges of practical and theoretical import. In particular, there is a need to find methods that are effective for the general case, such as non-linear programs, as well as for specialized cases, such as left-recursive linear programs. In this paper, we propose a novel approach that solves this problem for chain queries, i.e., for queries where bindings are propagated from arguments in the head to arguments in the tail of the rules, in a chain-like fashion. The method, called pushdown method, is based on the fact that a chain query can have associated a context-free language and a pushdown automaton recognizing this language can be emulated by rewriting the query as a particular factorized left-linear program. The proposed method generalizes and unifies previous techniques such as the 'counting' and 'right-, left-, mixed-linear' methods. It also succeeds in reducing many non-linear programs to query-equivalent linear ones.
THE FARMER MODEL WITH THE COMPONENT FARMING CONCEPT FOR DEVELOPING TMN SYSTEMS
Authors: PARK SOO-HYUN , BAIK DOO-KWON
Published: January 2003

Since the development of Telecommunication Management Network (TMN) by using different commercial platform tool kits, hardware platforms, and operating systems, there have been several problems with class management. One of the main problems is that all the agents of the TMN system must be duplicated and the software and the data blocks that perform identical function be maintained. Therefore, the standard of the Q3 interface development cannot be defined and the multi-platform cannot be supported in the development of the TMN agent. In order to overcome these problems, the Farming method that is based on the Farmer model has been suggested. The main concept of the Farming method is that the software and the data components that are duplicated and stored in each distributed object are saved in the Platform Independent Class Repository (PICR) by converting them into the format of the independent componentware in the platform, so that the componentwares that are essential for the execution can be loaded and used statically or dynamically from PICR as described in the framework of each distributed object. The distributed TMN agent of the personal communication network is designed and developed by using the Farmer model. The Farmer model is a frame structure model that is used for knowledge representation which introduces the concept of the system entity structure, and it is based on the Entity-Aspect (EA) model that is the knowledge representation model. The main objective of the Farmer model is to separate and extract the component elements that constitutes the agent by analyzing the agent which is actually planned to be designed. As a result of this, the component elements are located on the leaf node of the Farmer model tree, and these component elements are finally stored in PICR. In this paper, the design of TMN agent of Personal Communication Network (PCN) is described by using the Farmer model.
TRANSFER EQUIVALENCE AND REALIZATION OF NONLINEAR HIGHER ORDER INPUT/OUTPUT DIFFERENCE EQUATIONS USING MATHEMATICA
Authors: KOTTA ÜLLE , TÕNSO MARIS
Published: January 2003

This paper presents a contribution to the development of symbolic computation tools for discrete-time nonlinear control systems. A set of functions is developed in Mathematica 3.0 that test if the higher order input/output difference equation is realizable in the classical state-space form, and for simple examples, also find such state equations. The approach relies on a new notion of equivalence of higher order difference equations which yields a minimal (i.e. accessible and observable) realization and generalizes the notion of transfer equivalence to the nonlinear case. The application of the developed functions is demonstrated on three examples obtained via identification.
ON THE ROBUST STABILITY OF DISCRETE-TIME SYSTEMS
Authors: NURGES ÜLO , RÜSTERN ENNU
Published: January 2003

A sufficient stability condition for monic Schur polynomials is obtained via the so-called reflection coefficients of polynomials and the discrete version of Kharitonov's weak theorem. The discrete Kharitonov theorem defines only (n - 1)-dimensional stable hyperrectangle for n-degree monic polynomials. By the use of a linear Schur invariant transformation we put stable line segments through vertices of this hyperrectangle and find an n-dimensional stable polytope with all vertices on the stability boundary.
FAST MOTION ESTIMATION SCHEME FOR VIDEO CODING USING FEATURE VECTOR MATCHING AND MOTION VECTOR'S CORRELATIONS
Authors: ZHAO TINGRONG , YANAGISAWA MASAO , OHTSUKI TATSUO
Published: January 2003

In this paper, we propose a fast block motion estimation scheme by exploiting the correlations of motion vectors (MV) existing in spatially- and temporally-adjacent as well as hierarchically-related blocks. The basic idea is to use the information obtained from the corresponding block at a coarser resolution level and spatio-temporal neighboring blocks at the same level in order to select a good set of initial MV candidates and then perform further local search to find the best matching MV. In order to further reduce computational complexity, the sign pattern vector (SPV) is defined and used for block matching, as opposed to the pixel intensity values used in the conventional block matching methods. By using the SPV definition, a data block can be presented by a mean and a set of binary sign patterns with a much reduced data set. The block matching motion estimation is then divided into mean matching and binary phase matching. The proposed technique enables a significant reduction in computational complexity compared with the conventional block matching motion estimation (ME) because binary phase matching only involves Boolean logic operations. This scheme also significantly reduces the data transfer time between the frame buffer and motion estimator. Our test results indicate that the performance of the proposed scheme is comparable with the full-search block matching under the same search ranges, however, the proposed scheme has a speed-up factor ranging from 250 to 370 in comparison with full search.
A SIMULTANEOUS PLACEMENT AND GLOBAL ROUTING ALGORITHM FOR FPGAS WITH POWER OPTIMIZATION
Authors: TOGAWA NOZOMU , UKAI KAORU , YANAGISAWA MASAO , OHTSUKI TATSUO
Published: January 2003

This paper proposes a simultaneous placement and global routing algorithm for FPGAs with power optimization. The algorithm is based on hierarchical bipartitioning of layout regions and sets of logic-blocks. When bipartitioning a layout region, pseudo-blocks are introduced to preserve connections if there exist connections between bipartitioned logic-block sets. A global route is represented by a sequence of pseudo-blocks. Since pseudo-blocks and logic-blocks can be dealt with equally, placement and global routing are processed simultaneously. The algorithm gives weights to nets with high switching probabilities and attempts to assign the blocks connected by weighted nets to the same region. Thus their length is shortened and the power consumption of a whole circuit can be reduced. The experimental results demonstrate the effectiveness and efficiency of the algorithm.
A TWO LEVEL TRANSMISSION LINE MODEL FOR TRANSIENT ANALYSIS
Authors: HWANGKHUNNATHAM METHEE , LEELARASMEE EKACHAI
Published: January 2003

An efficient approach based on conventional techniques for transient analysis of transmission line circuit initially modelled as large number (N) of segments of lumped components is presented. This technique avoids the simultaneous solution of a large number of variables by computing an equivalent macromodel of each transmission line and splitting the analysis into two levels. The first level deals with a normal circuit analysis in which each transmission line is replaced by a simple lumped equivalent two port companion macromodel having only three resistors and two current sources. However, the initial N-segmented model of transmission line must be separately analyzed at the second level in order to update the transmission line companion macromodel at each timepoint. This latter analysis of the transmission line can be done efficiently using a set of recursive formulae whose complexities depend linearly on N. A simulation result of this technique is presented and compared with SPICE program.
USING PERTURBATION TO IMPROVE ROBUSTNESS OF SOLUTIONS GENERATED BY GENETIC PROGRAMMING FOR ROBOT LEARNING
Authors: CHONGSTITVATANA PRABHAS
Published: January 2003

This paper proposes a method to improve robustness of the robot programs generated by genetic programming. The main idea is to inject perturbation into the simulation during the evolution of the solutions. The resulting robot programs are more robust because they have evolved to tolerate the changes in their environment. We set out to test this idea using the problem of navigating a mobile robot from a starting point to a target in an unknown cluttered environment. The result of the experiments shows the effectiveness of this scheme. The analysis of the result shows that the robustness depends on the "experience" that a robot program acquired during evolution. To improve robustness, the size of the set of "experience" should be increased and/or the amount of reusing the "experience" should be increased.
ID-BASED DIGITAL MULTISIGNATURE SCHEME
Authors: TANG SHAOHUA , WEI GANG
Published: January 2003

By introducing identity-based cryptosystem into the digital multisignature, we propose a new ID-based digital multisignature scheme in this paper, which allows a user to communicate with others by knowing only the identity of his communication partner and the public key of the KAC, and provides an efficient multisignature without any data expansion. Its security is also analyzed.
APPROACHES FOR BLIND SEPARATION OF SOURCES BASED ON MULTIVARIATE DENSITY ESTIMATION
Authors: HE ZHENYA , YANG LUXI , LIU JU , LU ZIYI , HE CHEN , SHI YUHUI
Published: January 2003

A class of learning algorithms is developed for the blind separation of independent source signals from their linear mixtures. The algorithms are based on the Kullback–Leibler distance. A multivariate density estimation technique is used in estimating the probability density function of independent components. Simulations using speech signals and images as sources illustrate the performances of the algorithms.
PROGRAMMABLE CELLULAR AUTOMATA
Authors: KOKOLAKIS I. , ANDREADIS I. , TSALIDES PH.
Published: January 2003

A new architecture of the binary cellular automata (CA), called programmable CA (PCA), is presented for the first time in this letter. The basic properties of the PCA are also studied. The proposed architecture is simple and fast and aims at providing efficient solutions to a variety of CA applications.
IDENTIFICATION OF VOLTAGE-CURRENT OPERATORS SATISFYING TELLEGEN'S THEOREM
Authors: CEL J.
Published: January 2003

Let [Formula: see text] be a directed nonseparable network composed of a finite set ℬ of branches and F(u,i), an operator defined on the set of all ordered pairs of voltages and currents. It is proved that, if [Formula: see text] is neither a cutset nor a loop, and contains both a loop and a cutset with unequal numbers of opposite directed branches, and [Formula: see text] for all branch voltages [Formula: see text] and currents [Formula: see text] satisfying Kirchhoff's voltage and current laws respectively in every loop and cutset of [Formula: see text], then F is biadditive. This substantially strengthens an old theorem of Kishi and Kida in which, [Formula: see text] was allowed to vary over the set of all networks and physically reveals that the power is essentially the only continuous voltage-current operator which, when associated with a branch, yields Tellegen's famous theorem. It is also proved that, conversely, if F is biadditive, then the above sum is zero for an arbitrary network [Formula: see text]. The topological assumptions imposed on [Formula: see text] are thoroughly examined and shown to be necessary. Finally, similar analytic characterizations of eulerian and bipartite networks, respectively in terms of voltage and current operators with zero sums of values over all network branches are given.
DIRECTED USER AUTHENTICATION SCHEME BASED ON DISCRETE LOGARITHM
Authors: TANG SHAOHUA , MA WEIHUA
Published: January 2003

One new concept, "directed" authentication is presented in this letter. By "directed", we mean "of one direction", i.e., only the specified verifier can validate the verifiee's identity, anyone else cannot verify it without the help of this specified verifier. One strong directed authentication scheme based on the discrete logarithm is proposed in this letter, and the security and performance of which are also analyzed. It is shown in this letter that the proposed scheme is secure and the performance is superior to those of the mutual authentication schemes based on ID-based cryptosystems.
NOVEL EMBEDDED CODING TECHNIQUE USING ARRAY CODES AND STATISTICAL CHANNEL EVALUATION
Authors: SOYJAUDAH K. M. S. , JAHMEERBACUS M. I.
Published: January 2003

Previously, the proposed embedded coding techniques based on the row and column array codes, employ a combination of inner codes for error correction and outer codes for error detection. The outer codes involve the addition of further redundant bits. This reduces the overall code rate and hence, the throughput of the system. Furthermore, the decoding of these array codes is not a maximum likelihood decoding. In this paper, we propose a novel embedded coding technique that employs a combination of row and column array codes as well as the generalized array codes, but no outer code. The decoding of these codes is a maximum likelihood decoding and the error detection is done by a new statistical channel evaluation technique that uses the trellises of the component codes embedded in the main block.
AN ADIABATIC 4:2 COMPRESSOR DESIGN FOR LOW POWER VLSI
Authors: NG K. W. , LAU K. T.
Published: January 2003

4:2 compressors are basic components in the design of parallel multipliers. Low power consuming 4:2 compressors can result in a significant reduction of power when realizing power-efficient multipliers in any low power oriented systems. In the area of low power integrated circuit design, adiabatic switching technique has received considerable attention in the recent years. Many adiabatic logic architectures have been reported. In this letter, a low power 4:2 compressor circuit based on the adiabatic switching principle is proposed. When simulated using HSPICE, it was shown that the proposed circuit consumed very much less power than the static CMOS version.
MINIMIZING LATENCY AND JITTER FOR LARGE-SCALE MULTIMEDIA REPOSITORIES THROUGH PREFIX CACHING
Authors: PRABHAKAR SUNIL , CHARI RAHUL
Published: January 2003

Multimedia data poses challenges for efficient storage and retrieval due to its large size and playback timing requirements. For applications that store very large volumes of multimedia data, hierarchical storage offers a scalable and economical alternative to store data on magnetic disks. In a hierarchical storage architecture data is stored on a tape or optical disk based tertiary storage layer with the secondary storage disks serving as a cache or buffer. Due to the need for swapping media on drives, retrieving multimedia data from tertiary storage can potentially result in large delays before playback (startup latency) begins as well as during playback (jitter). In this paper we address the important problem of reducing startup latency and jitter for very large multimedia repositories. We propose that secondary storage should not be used as a cache in the traditional manner — instead, most of the secondary storage should be used to permanently store partial objects. Furthermore, replication is employed at the tertiary storage level to avoid expensive media switching. In particular, we show that by saving the initial segments of documents permanently on secondary storage, and replicating them on tertiary storage, startup latency can be significantly reduced. Since we are effectively reducing the amount of secondary storage available for buffering the data from tertiary storage, an increase in jitter may be expected. However, our results show that the technique also reduces jitter, in contrast to the expected behavior. Our technique exploits the pattern of data access. Advance knowledge of the access pattern is helpful, but not essential. Lack of this information or changes in access patterns are handled through adaptive techniques. Our study addresses both single- and multiple-user scenarios. Our results show that startup latency can be reduced by as much as 75% and jitter practically eliminated through the use of these techniques.
POLYHEDRAL MODEL RETRIEVAL USING WEIGHTED POINT SETS
Authors: TANGELDER JOHAN W. H. , VELTKAMP REMCO C.
Published: January 2003

Due to the recent improvements in laser scanning technology, 3D visualization and modeling, there is an increasing need for tools supporting the automatic search for 3D objects in archives. In this paper we describe a new geometric approach to 3D shape comparison and retrieval for arbitrary objects described by 3D polyhedral models that may contain gaps. In contrast with the existing approaches, our approach takes the overall relative spatial location into account by representing the 3D shape as a weighted point set. To compare two objects geometrically, we enclose each object by a 3D grid and generate a weighted point set, which represents a salient point for each non-empty grid cell. We compare three methods to obtain a salient point and a weight in each grid cell: (1) choosing the vertex in the cell with the highest Gaussian curvature, and choosing a measure as weight for that curvature, (2) choosing the area-weighted mean of the vertices in the cell, and choosing a measure as weight denoting the normal variation of the facets in the cell and (3) choosing the center of mass of all vertices in the cell, and choosing one as weight. Finally, we compute the similarity between two shapes by comparing their weighted point sets using a new shape similarity measure based on weight transportation that is a variation of the Earth Mover's Distance. Unlike the Earth Mover's Distance, the new shape similarity measure satisfies the triangle inequality. This property makes it suitable for use in indexing schemes, that depend on the triangle inequality, such as the one we introduce, based on the so-called vantage objects. The strength of our approach is proven through experimental results using a database consisting of 133 models such as mugs, cars and boats, and a database consisting of 512 models, mostly air planes, classified into conventional air planes, delta-jets, multi-fuselages, biplanes, helicopters and other models. The results show that the retrieval performance is better than related shape matching methods.
Novel Pharmacological Approaches to Manage Interstitial Lung Fibrosis in the Twenty-First Century
Authors: Giri Shri N.
Published: January 2003

Pharmacological agents currently in use to treat interstitial lung fibrosis are either ineffective or too toxic in humans. This review addresses mechanistically based novel approaches that have the potential to minimize the accumulation of collagen in the lung, a hallmark of lung fibrosis. These approaches include maintaining the intracellular levels of NAD+and ATP, blocking the biological activities of TGF-β and integrins, evaluating the effectiveness of PAF-receptor antagonists and NOS inhibitors, and developing a new generation of cysteine pro-drugs with an adequate degree of bioavailabilty. A critical analysis of each approach as it relates to management of IPF in humans is presented.
2,5-Hexanedione-Induced Testicular Injury
Authors: Boekelheide Kim , Fleming Shawna L. , Allio Theresa , Embree-Ku Michelle E. , Hall Susan J. , Johnson Kamin J. , Kwon Eun Ji , Patel Sutchin R. , Rasoulpour Reza J. , Schoenfeld Heidi A. , Thompson Stephanie
Published: January 2003

Now in its third decade of mechanistic investigation, testicular injury caused by 2,5-hexanedione (2,5-HD) exposure is a well-studied model with a rich database. The development of this model reflects the larger changes that have moved biology from a branch of chemistry into the molecular age. Critically examined in this review is the proposed mechanism for 2,5-HD-induced testicular injury in which germ cell maturation is disrupted owing to alterations in Sertoli cell microtubule-mediated functions. The goal is to evaluate the technical and conceptual approaches used to assess 2,5-HD-induced testicular injury, to highlight unanswered questions, and to identify fruitful avenues of future research.
Hormesis: The Dose-Response Revolution
Authors: Calabrese Edward J. , Baldwin Linda A.
Published: January 2003

Hormesis, a dose-response relationship phenomenon characterized by low-dose stimulation and high-dose inhibition, has been frequently observed in properly designed studies and is broadly generalizable as being independent of chemical/physical agent, biological model, and endpoint measured. This under-recognized and -appreciated concept has the potential to profoundly change toxicology and its related disciplines with respect to study design, animal model selection, endpoint selection, risk assessment methods, and numerous other aspects, including chemotherapeutics. This article indicates that as a result of hormesis, fundamental changes in the concept and conduct of toxicology and risk assessment should be made, including (a) the definition of toxicology, (b) the process of hazard (e.g., including study design, selection of biological model, dose number and distribution, endpoint measured, and temporal sequence) and risk assessment [e.g., concept of NOAEL (no observed adverse effect level), low dose modeling, recognition of beneficial as well as harmful responses] for all agents, and (c) the harmonization of cancer and noncancer risk assessment.
Nitric Oxide–Releasing Drugs
Authors: Napoli Claudio , Ignarro Louis J.
Published: January 2003

Pharmacological compounds that release nitric oxide (NO) have been useful tools for evaluating the broad role of NO in physiology and therapeutics. NO deficiency has been implicated in the genesis and evolution of several disease states. Both medical needs and commercial opportunities have fostered attempts to modulate NO in the human body for therapeutic gain. Strategies for NO modulation encompass antiinflammatory, sexual dysfunction, and cardiovascular indications. Apart from newly developed drugs, several commonly used cardiovascular drugs exert their beneficial action, at least in part, by modulating the NO pathway. This review discusses the fundamental pharmacological properties and mechanisms of action of NO-releasing drugs. Some of these compounds may enter in the clinical arena providing important therapeutic benefits in human diseases.
Genetic Polymorphisms of the HumanMDR1Drug Transporter
Authors: Schwab Matthias , Eichelbaum Michel , Fromm Martin F.
Published: January 2003

P-glycoprotein is an ATP-dependent efflux pump that contributes to the protection of the body from environmental toxins. It transports a huge variety of structurally diverse compounds. P-glycoprotein is involved in limiting absorption of xenobiotics from the gut lumen, in protection of sensitive tissues (brain, fetus, testis), and in biliary and urinary excretion of its substrates. P-glycoprotein can be inhibited or induced by xenobiotics, thereby contributing to variable drug disposition and drug interactions. Recently, several SNPs have been identified in the MDR1 gene, some of which can affect P-glycoprotein expression and function. Potential implications of MDR1 polymorphisms for drug disposition, drug effects, and disease risk are discussed.
Retinoid Receptors and Their Coregulators
Authors: Wei Li-Na
Published: January 2003

Retinoids regulate gene transcription by binding to the nuclear receptors, the retinoic acid (RA) receptors (RARs), and the retinoid X receptors (RXRs). RARs and RXRs are ligand-activated transcription factors for the regulation of RA-responsive genes. The actions of RARs and RXRs on gene transcription require a highly coordinated interaction with a large number of coactivators and corepressors. This review focuses on our current understanding of these coregulators known to act in concert with RARs and RXRs. The mechanisms of action of these coregulators are beginning to be uncovered and include the modification of chromatin and the recruitment of basal transcription factors. Challenges remain to understand the specificity of action of RARs and RXRs and the formation of specific transcription complexes consisting of the receptors, coregulators, and other unknown factors.
Sulfenamide-catalyzed Oxidation of Primary and Secondary Alcohols with Molecular Bromine
Authors: Matsuo Jun-ichi , Kawana Asahi , Yamanaka Hiroyuki , Mukaiyama Teruaki
Published: January 2003

Primary and secondary alcohols were smoothly oxidized to the corresponding aldehydes and ketones in high yields at room temperature with 1.1 equiv. of molecular bromine by using a catalytic amount of N-t-butyl-2-nitrobenzenesulfenamide in the coexistence of potassium carbonate and molecular sieves 4A.
Surface Modification of Ordered Mesoporous Silica with an Organosilane Containing Polyethylene Oxide Groups to Retain the Hydrophilic Nature
Authors: Kimura Tatsuo , Suzuki Makiko , Tomura Shinji , Oda Kiichi
Published: January 2003

The ability to adsorb water of ordered mesoporous silica was successfully controlled by organic modification with an organoalkoxysilane containing polyethylene oxide groups.
Higher Water Intrusion Property on Novel Porous Matrix Composed of Bioinspired Polymer Stereocomplex for Tissue Engineering
Authors: Watanabe Junji , Ishihara Kazuhiko
Published: January 2003

A porous matrix composed of bioinspired phospholipid polymers with enantiomeric poly(lactic acid) segments in side chain, were prepared by formation of stereocomplex between them and characterized for use as new cell culture matrix.
TiNxOyFz as a Stable Photocatalyst for Water Oxidation in Visible Light (<570 nm)
Authors: Nukumizu Kohta , Nunoshige Jun , Takata Tsuyoshi , Kondo Junko N , Hara Michikazu , Kobayashi Hisayoshi , Domen Kazunari
Published: January 2003

TiNxOyFz prepared from (NH4)2TiF6 and SiO2 under NH3 flow at 773 K has a bandgap-absorption edge at about 570 nm and functions as a stable photocatalyst for water oxidation.
The 9-Å solution: How mRNA pseudoknots promote efficient programmed −1 ribosomal frameshifting
Authors: PLANT EWAN P. , JACOBS KRISTI L. MULDOON , HARGER JASON W. , MESKAUSKAS ARTURAS , JACOBS JONATHAN L. , BAXTER JENNIFER L. , PETROV ALEXEY N. , DINMAN JONATHAN D.
Published: January 2003

There is something special about mRNA pseudoknots that allows them to elicit efficient levels of programmed −1 ribosomal frameshifting. Here, we present a synthesis of recent crystallographic, molecular, biochemical, and genetic studies to explain this property. Movement of 9 Å by the anticodon loop of the aminoacyl-tRNA at the accommodation step normally pulls the downstream mRNA a similar distance along with it. We suggest that the downstream mRNA pseudoknot provides resistance to this movement by becoming wedged into the entrance of the ribosomal mRNA tunnel. These two opposing forces result in the creation of a local region of tension in the mRNA between the A-site codon and the mRNA pseudoknot. This can be relieved by one of two mechanisms; unwinding the pseudoknot, allowing the downstream region to move forward, or by slippage of the proximal region of the mRNA backwards by one base. The observed result of the latter mechanism is a net shift of reading frame by one base in the 5′ direction, that is, a −1 ribosomal frameshift.
Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA
Authors: McCONNELL TIMOTHY S. , LOKKEN R. PETER , STEITZ JOAN A.
Published: January 2003

Nucleotide analog interference mapping (NAIM) is a powerful method for identifying RNA functional groups involved in protein–RNA interactions. We examined particles assembled on modified U1 small nuclear RNAs (snRNAs) in vitro and detected two categories of interferences. The first class affects the stability of two higher-order complexes and comprises changes in two adenosines, A65 and A70, in the loop region previously identified as the binding site for the U1 small nuclear ribonucleoprotein (snRNP)-specific U1A protein. Addition of an exocyclic amine to position 2 of A65 interferes strongly with protein binding, whereas removal or modification of the exocyclic amine at position 6 makes little difference. Modifications of A70 exhibit the opposite effects: Additions at position 2 are permitted, but modification of the exocyclic amine at position 6 significantly inhibits protein binding. These interactions, critical for U1A-U1 snRNA recognition in the context of in vitro snRNP assembly, are consistent with previous structural studies of the isolated protein with the RNA hairpin containing the U1A binding site. The second category of interferences affects all partially assembled U1-protein complexes by decreasing the stability of Sm core protein associations. Interestingly, most strong interferences occur at phosphates in the terminal stem-loop region of U1, rather than in the Sm binding site. These data argue that interactions with the phosphate backbone of the terminal stem loop are essential for the stable association of Sm core proteins with the U1 snRNA. We suggest that the stem loop of all Sm snRNAs may act as a clamp to hold the ring of Sm proteins in place.
Finding specific RNA motifs: Function in a zeptomole world?
Authors: KNIGHT ROB , YARUS MICHAEL
Published: January 2003

We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif’s rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1–1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1–1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules.
3′-processing of yeast tRNATrp precedes 5′-processing
Authors: KUFEL JOANNA , TOLLERVEY DAVID
Published: January 2003

Previous analyses of eukaryotic pre-tRNAs processing have reported that 5′-cleavage by RNase P precedes 3′-maturation. Here we report that in contrast to all other yeast tRNAs analyzed to date, tRNATrp undergoes 3′-maturation prior to 5′-cleavage. Despite its unusual processing pathway, pre-tRNATrp resembles other pre-tRNAs, showing dependence on the essential Lsm proteins for normal processing and efficient association with the yeast La homolog, Lhp1p. tRNATrp is also unusual in not requiring Lhp1p for 3′ processing and stability. However, other Lhp1p-independent tRNAs, tRNA2Lys and tRNA1Ile, follow the normal pathway of 5′-processing prior to 3-processing.
New microRNAs from mouse and human
Authors: LAGOS-QUINTANA MARIANA , RAUHUT REINHARD , MEYER JUTTA , BORKHARDT ARNDT , TUSCHL THOMAS
Published: January 2003

MicroRNAs (miRNAs) represent a new class of noncoding RNAs encoded in the genomes of plants, invertebrates, and vertebrates. MicroRNAs regulate translation and stability of target mRNAs based on (partial) sequence complementarity. Although the number of newly identified miRNAs is still increasing, target mRNAs of animal miRNAs remain to be identified. Here we describe 31 novel miRNAs that were identified by cloning from mouse tissues and the human Saos-2 cell line. Fifty-three percent of all known mouse and human miRNAs have homologs in Fugu rubripes (pufferfish) or Danio rerio (zebrafish), of which almost half also have a homolog in Caenorhabditis elegans or Drosophila melanogaster. Because of the recurring identification of already known miRNAs and the unavoidable background of ribosomal RNA breakdown products, it is believed that not many more miRNAs may be identified by cloning. A comprehensive collection of miRNAs is important for assisting bioinformatics target mRNA identification and comprehensive genome annotation.
After the ribosome structure: How does translocation work?: FIGURE 1.
Authors: JOSEPH SIMPSON
Published: January 2003

Structures of the ribosomal large and small subunits have been solved to atomic resolution by X-ray crystallography. These structures provide a new foundation to address the complex process of protein biosynthesis by the ribosome. Translocation of the tRNA–mRNA complex is one of the most fascinating tasks performed by the ribosome. The impact of the crystal structures in understanding the molecular mechanism of translocation is highlighted in this review.
Graft copolymerization of nitrile monomers onto sulfonated jute‐cotton blended fabric
Authors: Mondal Ibrahim H.
Published: January 2003

Graft copolymerization of nitrile monomers, such as acrylonitrile and methacrylonitrile, onto bleached sulfonated jute‐cotton blended fabric was carried out in an aqueous medium using potassium permanganate as an initiator under the catalytic influence of sulfuric acid in a nitrogen atmosphere. The effect of concentrations of monomer, permanganate, sulfuric acid, reaction time, and reaction temperature on the percent graft yield was studied. The percent graft yield was found to be dependent on the above‐mentioned variables. On the basis of experimental findings, an optimum condition for effective grafting is suggested. As evidence of polymer grafting, some instrumental analyses, such as thermogravimetric analysis, infrared spectroscopy, and X‐ray diffractometry were carried out. Grafting improved the thermal stability, protected from photo‐oxidative degradation, affected dyeability, and had a positive impact on color fastness. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 2262–2266, 2003
Surface photografting polymerization of vinyl acetate, maleic anhydride, and their charge‐transfer complex. IV. Maleic anhydride
Authors: Jianping Deng , Wantai Yang
Published: January 2003

In general, it has been accepted that maleic anhydride (MAH) cannot be homopolymerized under normal conditions. However, MAH can be grafted onto substrates under UV irradiation rather easily. In this study, the photografting polymerization of MAH was examined with low‐density polyethylene (LDPE) film as a substrate. The initiating performances of different photoinitiators, including benzophenone (BP), Irgacure 651, and benzoyl peroxide (BPO), were examined. The effects of some principal factors, such as the temperature, solvent, and UV intensity, on the grafting polymerization of MAH were also investigated. The results show that MAH can be smoothly grafted onto LDPE film by UV radiation. Enhancing the intensity of UV radiation and elevating the irradiation temperature facilitate the grafting polymerization of MAH. Among BP, Irgacure 651, and BPO, Irgacure 651 can initiate the polymerization of more MAH, but BP is more effective for the initiation of surface grafting polymerization. Solvents of MAH also have a great influence on the grafting polymerization; some of them even seem to take part in the reaction. The occurrence of photografting polymerization was verified with Fourier transform infrared and electron spectroscopy for chemical analysis spectra. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 2318–2325, 2003
Thermal and kinetic study of radical polymerization I. Melt state bulk polymerization of acrylamide by DSC
Authors: Mahdavian Ali‐Reza , Zandi Mojgan
Published: January 2003

Radical‐initiated bulk polymerization of acrylamide in the presence of potassium persulfate in the melt phase has been investigated by differential scanning calorimetry (DSC). The method presented here has been carried out in isothermal condition. This not only saves energy and time but also has some less probable side effects. Side effects such as evaporation and imidization could affect the final yield and properties of the obtained product. Different temperatures have been examined for isothermal polymerization to find out the optimum temperature with complete conversion of acrylamide to its corresponding polymer. During the polymerization process, high‐molecular‐weight polyacrylamide is being produced without any significant loss in total yield. The molecular weight was determined by inherent viscosity measurement. Also, no side reaction such as imidization resulting in partial insolubility or crosslinked product was being observed. It is noteworthy that we believe DSC studies show the existence of living radicals that has not been reported before. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 2335–2340, 2003
Synthesis of butyl rubber in hexane using a mixture of Et2AlCl and EtAlCl2 in the initiating system
Authors: Gronowski Adam A.
Published: January 2003

A method was studied to obtain butyl rubber in hexane at −75 and −60°C using a mixture of a major amount of diethylaluminum chloride and a minor amount of ethylaluminum dichloride in the initiating system. The Jaacks method was used to determine the monomer reactivity ratio of isobutylene in copolymerization with isoprene in hexane at −75°C with the above initiating system; rIB = 1.54 ± 0.06. This value was different from a literature value rIB = 1.08 when just EtAlCl2 was used in hexane at −80°C. The mixture of both alkylaluminum chlorides in the initiating solution was subsequently directly activated with minute amounts of water or methylaluminoxane (MAO). The use of the modified initiators resulted in higher molecular weights, higher degrees of conversion, and higher isoprene contents in the butyl rubber. At the same time, temperature control was good during polymerizations. With modified alkylaluminum halides, the monomer reactivity ratio of isobutylene in copolymerization with isoprene in hexane at −75°C was close to unity, similar to the reported case with just EtAlCl2. The system activated with MAO made it possible to synthesize butyl rubber in hexane at −60°C having main characteristics typical of commercial butyl rubber manufactured in methyl chloride at −95°C. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 87: 2360–2364, 2003
Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem
Authors: Hyrien Olivier , Marheineke Kathrin , Goldar Arach
Published: January 2003

Eukaryotic DNA replication initiates at multiple origins. In early fly and frog embryos, chromosomal replication is very rapid and initiates without sequence specificity. Despite this apparent randomness, the spacing of these numerous initiation sites must be sufficiently regular for the genome to be completely replicated on time. Studies in various eukaryotes have revealed that there is a strict temporal separation of origin “licensing” prior to S phase and origin activation during S phase. This may suggest that replicon size must be already established at the licensing stage. However, recent experiments suggest that a large excess of potential origins are assembled along chromatin during licensing. Thus, a regular replicon size may result from the selection of origins during S phase. We review single molecule analyses of origin activation and other experiments addressing this issue and their general significance for eukaryotic DNA replication. BioEssays 25:116–125, 2003. © 2003 Wiley Periodicals, Inc.
Closing the (Ran)GAP on segregation distortion in Drosophila
Authors: Kusano Ayumi , Staber Cynthia , Chan Ho Yin Edwin , Ganetzky Barry
Published: January 2003

Segregation Distorter (SD) is a meiotic drive system in Drosophila that causes preferential transmission of the SD chromosome from SD/SD+ males owing to induced dysfunction of SD+ spermatids. Since its discovery in 1956, SD and its mode of action have baffled biologists. Recently, substantial progress has been made in elucidating this puzzle. Sd, the primary gene responsible for distortion encodes a mutant RanGAP, a key protein in the Ran signaling pathway required for nuclear transport and other nuclear functions. The mutant protein is enzymatically active but mislocalized to nuclei, which apparently disrupts Ran signaling by reducing intranuclear Ran‐GTP levels. Some evidence suggests that a defect in nuclear transport may be the main cause of sperm dysfunction. Although important questions remain, the basic mechanism of distortion is now understood sufficiently well that specific hypotheses can be formulated and tested. This previously mysterious genetic system may now offer unique insights into novel aspects of regulation by Ran. BioEssays 25:108–115, 2003. © 2003 Wiley Periodicals, Inc.
Proline‐directed phosphorylation and isomerization in mitotic regulation and in Alzheimer's Disease
Authors: Lu Kun Ping , Liou Yih‐Cherng , Vincent Inez
Published: January 2003

The reversible phosphorylation of proteins on serine/threonine residues preceding proline (Ser/Thr‐Pro) is a major regulatory mechanism for the control of a series of cell cycle events. Although phosphorylation is thought to regulate protein function by inducing conformational changes, little is known about most of these conformational changes and their significance. Recent studies indicate that the conformation and function of a subset of these phosphorylated proteins are controlled by the prolyl isomerase Pin1 through isomerization of specific phosphorylated Ser/Thr‐Pro bonds. Furthermore, compelling evidence supports the idea that proline‐directed phosphorylation and subsequent isomerization play a critical role not only in cell cycle control, but also in the development of Alzheimer's disease, where postmitotic neurons display various cell cycle markers, especially mitotic events, prior to degeneration. BioEssays 25:174–181, 2003. © 2003 Wiley Periodicals, Inc.
When parsimony backfires: Neglecting DNA repair may doom neurons in Alzheimer's disease
Authors: Nouspikel Thierry , Hanawalt Philip C.
Published: January 2003

Taking advantage of the fact that they need not replicate their DNA, terminally differentiated neurons only repair their expressed genes and largely dispense with the burden of removing damage from most of their genome. However, they may pay a heavy price for this laxity if unforeseen circumstances, such as a pathological condition like Alzheimer's disease, cause them to re‐enter the cell cycle. The lifetime accumulation of unrepaired lesions in the silent genes of neurons is likely to be significant and may result in aborting the mitotic process and triggering cell death if the cells attempt to express these dormant genes and resume DNA replication. BioEssays 25:168–173, 2003. © 2003 Wiley Periodicals, Inc.
Visualization of molecular and cellular events with green fluorescent proteins in developing embryos: a review
Authors: Yu Yong A. , Oberg Kerby , Wang Gefu , Szalay Aladar A.
Published: January 2003

An Erratum has been published for this article in Luminescence (2003) 18(4) 243

During the past 5 years, green fluorescent protein (GFP) has become one of the most widely used in vivo protein markers for studying a number of different molecular processes during development, such as promoter activation, gene expression, protein trafficking and cell lineage determination. GFP fluorescence allows observation of dynamic developmental processes in real time, in both transiently and stably transformed cells, as well as in live embryos. In this review, we include the most up‐to‐date use of GFP during embryonic development and point out the unique contribution of GFP visualization, which resulted in novel discoveries. Copyright © 2002 John Wiley & Sons, Ltd.
Assessment of training effects on activity levels of alveolar macrophage in matured rats using chemiluminescent technique
Authors: Kumae Takashi , Arakawa Hatsuko
Published: January 2003

Chemiluminescence responses have been used for the evaluation of phagocyte function. In this study, to evaluate effects of training started after maturation on pulmonary immunity, the activity levels of rat alveolar macrophages (AMs) were assessed as reactive oxygen species (ROS) generating capacity, measured by lucigenin‐ and luminol‐dependent chemiluminescence, using a parallel luminometer. One group of male Wistar rats started training at 11 weeks old and another group at 17 weeks old. The experimental period was 12 weeks, and about half of the rats were sacrificed after 6 weeks. The forced and voluntary exercises affect the mean levels of body weights and cell populations in the bronchoalveolar lavage fluid in younger animals; however, the voluntary exercise group in younger animals seemed to adapt after 12 weeks. By contrast, chemiluminescence responses in older rats observed after 6 weeks suggest that AMs are primed, and the maximum releasing activities of ROS are reduced. These changes in AM activity may be caused by the exercise and separation stresses and the rats may adapt to those stressors after 12 weeks. The chemiluminescent technique is thought to be useful to evaluate the changes of AM activity. Copyright © 2002 John Wiley & Sons, Ltd.
Imaging of ultra‐weak bio‐chemiluminescence and singlet oxygen generation in germinating soybean in response to wounding
Authors: Chen Wen Li , Xing Da , Tan ShiCi , Tang YongHong , He Yonghong
Published: January 2003

Ultra‐weak bio‐chemiluminescence (UBC) from germinating soybean (Glycine max L. Merr) cotyledon under mechanical wounding was observed using a high‐sensitivity imaging system based on an ICCD detector and a highly sensitive single photon counter (SPC) device. The UBC imaging showed that the intensity at the injury location on a wounded cotyledon was obviously enhanced as compared with that at the non‐injured point. The UBC intensity of wounded cotyledons was initially very high and reached a stationary state after about 5 min. Wounding‐induced emission could be suppressed by wounding in the presence of sodium azide. Deuterium oxide amplified the emission intensity. It was concluded that singlet oxygen (1O2) was the main cause of the emission during the wounding phase. Copyright © 2002 John Wiley & Sons, Ltd.