bluuebunny/crossref_metadata_2025_split huggingface dataset:
Method for calculating the scattering matrix of arbitrary microwave networks giving both internal and external scattering
Authors: Hallbjörner Paul 
Published: May 2003

AbstractA general method for calculating the scattering matrix of an arbitrary microwave networks is presented. Compared to existing methods, it uses a simplified algorithm that makes no distinction between external and internal ports. It thereby achieves algorithmic simplicity, and provides waves internally in the network as well as scattered waves at the ports. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 99–102, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10983
An accurate tuning method for dual‐mode cavity filters
Authors: Lee Juseop , Uhm Man Seok , Yom In‐Bok , Lee Seong Pal 
Published: May 2003

AbstractAn accurate tuning method using a short‐ended dummy cavity is presented for dual‐mode cavity filters. Tuning is based on the match of the computed and measured phase responses of the reflection coefficient. An equivalent circuit model is adopted for computing the required phase response of the reflection coefficient. This method is applied to a 4‐pole longitudinal dual‐mode filter for demonstration. Good agreement is found between the experimental and computed responses. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 123–125, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10991
A reconfigurable Yagi antenna for wireless communications
Authors: Wahid P. F. , Ali M. A. , DeLoach B. C. 
Published: May 2003

AbstractThe design of a reconfigurable Yagi antenna that can operate at two frequencies, 2.4 GHz and 5.78 GHz, for use in wireless communications is presented. The Yagi can be reconfigured through the use of appropriate switches placed on the elements of the antenna. This paper shows the feasibility of this antenna and presents simulated and measured results at the two frequencies. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 38: 140–141, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10997
Characterization of polo‐like kinase‐1 in rat oocytes and early embryos implies its functional roles in the regulation of meiotic maturation, fertilization, and cleavage
Authors: Fan Heng‐Yu , Tong Chao , Teng Chun‐Bo , Lian Li , Li Shi‐Wen , Yang Zeng‐Ming , Chen Da‐Yuan , Schatten Heide , Sun Qing‐Yuan 
Published: May 2003

AbstractPolo‐like kinase 1 (Plk1) is a family of serine/threonine protein kinases that play important regulatory roles during mitotic cell cycle progression. In this study, Plk1 expression, subcellular localization, and possible functions during rat oocyte meiotic maturation, fertilization, and embryonic cleavages were studied by using RT‐PCR, Western blot, confocal microscopy, drug‐treatments, and antibody microinjection. Both the mRNA and protein of this kinase were detected in rat maturing oocytes and developing embryos. Confocal microscopy revealed that Plk1 distributed abundantly in the nucleus at the germinal vesicle (GV) stage, was associated with spindle poles during the formation of M‐phase spindle, and was translocated to the spindle mid‐zone at anaphase. In fertilized eggs, Plk1 was strongly stained in the cytoplasm between the apposing male and female pronuclei, from where microtubules radiated. Throughout cytokinesis, Plk1 was localized to the division plane, both during oocyte meiosis and embryonic mitosis. The specific subcellular distribution of Plk1 was distorted after disrupting the M‐phase spindle, while additional aggregation dots could be induced in the cytoplasm by taxol, suggesting its intimate association with active microtubule assembly. Plk1 antibody microinjection delayed the meiotic resumption and blocked the emission of polar bodies. In conclusion, Plk1 may be a multifunctional kinase that plays pivotal regulatory roles in microtubule assembly during rat oocyte meiotic maturation, fertilization, and early embryonic mitosis. Mol. Reprod. Dev. 65: 318–329, 2003. © 2003 Wiley‐Liss, Inc.
Nongenetic causes of hearing loss
Authors: Roizen Nancy J. 
Published: May 2003

AbstractNongenetic as well as genetic etiologies must be explored in the child with identified hearing loss. Graduates of the neonatal intensive care unit are at increased risk for developing hearing loss due to hypoxia, hyperbilirubinemia, very low birth weight, and ototoxic medications. Although meningitis has decreased in frequency, it is still a risk factor for hearing loss. Cytomegalovirus remains the most common congenital infection and a relatively common etiology of hearing loss, which can be progressive. Preventable causes of hearing loss include those caused by head trauma, noise, and ototoxic medications. Identification of the etiology of hearing loss can facilitate the development of a treatment and management plan. MRDD Research Reviews 2003;9:120–127. © 2003 Wiley‐Liss, Inc.
Proposed amino acid sequence and the 1.63 Å X‐ray crystal structure of a plant cysteine protease, ervatamin B: Some insights into the structural basis of its stability and substrate specificity
Authors: Biswas Sampa , Chakrabarti Chandana , Kundu Suman , Jagannadham Medicherla V. , Dattagupta Jiban K. 
Published: May 2003

AbstractThe crystal structure of a cysteine protease ervatamin B, isolated from the medicinal plant Ervatamia coronaria, has been determined at 1.63 Å. The unknown primary structure of the enzyme could also be traced from the high‐quality electron density map. The final refined model, consisting of 215 amino acid residues, 208 water molecules, and a thiosulfate ligand molecule, has a crystallographic R‐factor of 15.9% and a free R‐factor of 18.2% for F > 2σ(F). The protein belongs to the papain superfamily of cysteine proteases and has some unique properties compared to other members of the family. Though the overall fold of the structure, comprising two domains, is similar to the others, a few natural substitutions of conserved amino acid residues at the interdomain cleft of ervatamin B are expected to increase the stability of the protein. The substitution of a lysine residue by an arginine (residue 177) in this region of the protein may be important, because Lys → Arg substitution is reported to increase the stability of proteins. Another substitution in this cleft region that helps to hold the domains together through hydrogen bonds is Ser36, replacing a conserved glycine residue in the others. There are also some substitutions in and around the active site cleft. Residues Tyr67, Pro68, Val157, and Ser205 in papain are replaced by Trp67, Met68, Gln156, and Leu208, respectively, in ervatamin B, which reduces the volume of the S2 subsite to almost one‐fourth that of papain, and this in turn alters the substrate specificity of the enzyme. Proteins 2003;51:489–497. © 2003 Wiley‐Liss, Inc.
Endogenous tryptophan residues of cAPK regulatory subunit type IIβ reveal local variations in environments and dynamics
Authors: Zawadzki Kerri M. , Pan Chia‐Pin , Barkley Mary D. , Johnson David , Taylor Susan S. 
Published: May 2003

AbstractThe amino terminal dimerization/docking domain and the two‐tandem, carboxy‐terminal cAMP‐binding domains (A and B) of cAMP‐dependent protein kinase regulatory (R) subunits are connected by a variable linker region. In addition to providing a docking site for the catalytic subunit, the linker region is a major source of sequence diversity between the R‐subunit isoforms. The RIIβ isoform uniquely contains two endogenous tryptophan residues, one at position 58 in the linker region and the other at position 243 in cAMP‐binding domain A, which can act as intrinsic reporter groups of their dynamics and microenvironment. Two single‐point mutations, W58F and W243F, allowed the local environment of each Trp to be probed using steady‐state and time‐resolved fluorescence techniques. We report that: (a) the tryptophan fluorescence of the wild‐type protein largely reflects Trp243 emission; (2) cAMP selectively quenches Trp243 and thus acts as a cAMP sensor; (3) Trp58 resides in a highly solvated, unstructured, and mobile region of the protein; and (4) Trp243 resides in a stable, folded domain and is relatively buried and rigid within the domain. The use of endogenous Trp residues presents a non‐perturbing method for studying R‐subunit subdomain characteristics in addition to providing the first biophysical data on the RIIβ linker region. Proteins 2003;51:552–561. © 2003 Wiley‐Liss, Inc.
Insights into nonspecific binding of homeodomains from a structure of MATα2 bound to DNA
Authors: Aishima Jun , Wolberger Cynthia 
Published: May 2003

AbstractThe 2.1‐Å resolution crystal structure of the MATα2 homeodomain bound to DNA reveals the unexpected presence of two nonspecifically bound α2 homeodomains, in addition to the two α2 homeodomains bound to canonical α2 binding sites. One of the extra homeodomains makes few base‐specific contacts, while the other extra homeodomain binds to DNA in a previously unobserved manner. This unusually bound homeodomain is rotated on the DNA, making possible major groove contacts by side‐chains that normally do not contact the DNA. This alternate docking may represent one way in which homeodomains sample nonspecific DNA sequences. Proteins 2003;51:544–551. © 2003 Wiley‐Liss, Inc.
Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2
Authors: Ritchie David W. 
Published: May 2003

AbstractThis article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein–protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e.g., Lactobacillus HPr kinase, hemagglutinin, bovine rotavirus VP6). Here we describe several enhancements to our original spherical polar Fourier docking correlation algorithm. For example, a novel surface sphere smothering algorithm is introduced to generate multiple local coordinate systems around the surface of a large receptor molecule, which may be used to define a small number of initial ligand‐docking orientations distributed over the receptor surface. High‐resolution spherical polar docking correlations are performed over the resulting receptor surface patches, and candidate docking solutions are refined by using a novel soft molecular mechanics energy minimization procedure. Overall, this approach identified two good solutions at rank 5 or less for two of the seven CAPRI complexes. Subsequent analysis of our results shows that Hex 3.1 is able to place good solutions within a list of ≤20 for four of the seven targets. This finding shows that useful in silico protein–protein docking predictions can now be made with increasing confidence, even for very large macromolecular complexes. Proteins 2003;52:98–106. © 2003 Wiley‐Liss, Inc.
A soft docking algorithm for predicting the structure of antibody‐antigen complexes
Authors: Li Chun Hua , Ma Xiao Hui , Chen Wei Zu , Wang Cun Xin 
Published: May 2003

AbstractAn efficient soft docking algorithm is described for predicting the mode of binding between an antibody and its antigen based on the three‐dimensional structures of the molecules. The basic tools are the “simplified protein” model and the docking algorithm of Wodak and Janin. The side‐chain flexibility of Arg, Lys, Asp, Glu, and Met residues on the protein surface is taken into account. A combined filtering technique is used to select candidate binding modes. After energy minimization, we calculate a scoring function, which includes electrostatic and desolvation energy terms. This procedure was applied to targets 04, 05, and 06 of CAPRI, which are complexes of three different camelid antibody VHH variable domains with pig α‐amylase. For target 06, two native‐like structures with a root‐mean‐square deviation < 4.0 Å relative to the X‐ray structure were found within the five top ranking structures. For targets 04 and 05, our procedure produced models where more than half of the antigen residues forming the epitope were correctly predicted, albeit with a wrong VHH domain orientation. Thus, our soft docking algorithm is a promising tool for predicting antibody‐antigen recognition. Proteins 2003;52:47–50. © 2003 Wiley‐Liss, Inc.
Protein–protein docking predictions for the CAPRI experiment
Authors: Gray Jeffrey J. , Moughon Stewart E. , Kortemme Tanja , Schueler‐Furman Ora , Misura Kira M.S. , Morozov Alexandre V. , Baker David 
Published: May 2003

AbstractWe predicted structures for all seven targets in the CAPRI experiment using a new method in development at the time of the challenge. The technique includes a low‐resolution rigid body Monte Carlo search followed by high‐resolution refinement with side‐chain conformational changes and rigid body minimization. Decoys (∼106 per target) were discriminated using a scoring function including van der Waals and solvation interactions, hydrogen bonding, residue–residue pair statistics, and rotamer probabilities. Decoys were ranked, clustered, manually inspected, and selected. The top ranked model for target 6 predicted the experimental structure to 1.5 Å RMSD and included 48 of 65 correct residue–residue contacts. Target 7 was predicted at 5.3 Å RMSD with 22 of 37 correct residue–residue contacts using a homology model from a known complex structure. Using a preliminary version of the protocol in round 1, target 1 was predicted within 8.8 Å although few contacts were correct. For targets 2 and 3, the interface locations and a small fraction of the contacts were correctly identified. Proteins 2003;52:118–122. © 2003 Wiley‐Liss, Inc.
GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1
Authors: Gardiner Eleanor J. , Willett Peter , Artymiuk Peter J. 
Published: May 2003

AbstractAs part of the first Critical Assessment of PRotein Interactions, round 1, we predict the structure of two protein–protein complexes, by using a genetic algorithm, GAPDOCK, in combination with surface complementarity, buried surface area, biochemical information, and human intervention. Among the five models submitted for target 1, HPr phosphocarrier protein (B. subtilis) and the hexameric HPr kinase (L. lactis), the best correctly predicts 17 of 52 interprotein contacts, whereas for target 2, bovine rotavirus VP6 protein‐monoclonal antibody, the best model predicts 27 of 52 correct contacts. Given the difficult nature of the targets, these predictions are very encouraging and compare well with those obtained by other methods. Nevertheless, it is clear that there is a need for improved methods for distinguishing between “correct” and “plausible but incorrect” complexes. Proteins 2003;52:10–14. © 2003 Wiley‐Liss, Inc.
ZDOCK: An initial‐stage protein‐docking algorithm
Authors: Chen Rong , Li Li , Weng Zhiping 
Published: May 2003

AbstractThe development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody‐antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near‐native structure within the top 2000 predictions at the 6° rotational sampling density, with an average of 52 near‐native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/∼rong/dock. Proteins 2003;52:80–87. © 2003 Wiley‐Liss, Inc.
United States Department of Agriculture–Agricultural Research Service research programs in biological control of plant diseases
Authors: Roberts Daniel P , Lohrke Scott M 
Published: May 2003

AbstractA number of USDA–ARS programs directed at overcoming impediments to the use of biocontrol agents on a commercial scale are described. These include improvements in screening techniques, taxonomic studies to identify beneficial strains more precisely, and studies on various aspects of the large‐scale production of biocontrol agents. Another broad area of studies covers the ecological aspects of biocontrol agents—their interaction with the pathogen, with the plant and with other aspects of the environmental complex. Examples of these studies are given and their relevance to the further development and expansion of biocontrol agents is discussed. Published in 2003 for SCI by John Wiley & Sons, Ltd.
Invasive species research in the United States Department of Agriculture–Agricultural Research Service
Authors: Carruthers Raymond I 
Published: May 2003

AbstractInvasive pests cause huge losses both to agricultural production systems and to the natural environment through displacing native species and decreasing biodiversity. It is now estimated that many thousand exotic insect, weed and pathogen species have been established in the USA and that these invasive species are responsible for a large portion of the $130 billion losses estimated to be caused by pests each year. The Agricultural Research Service (ARS) has responded with extensive research and action programs aimed at understanding these problems and developing new management approaches for their control. This paper provides an overview of some of the ARS research that has been conducted on invasive species over the past few years and addresses both different categories of research and some specific pest systems of high interest to the US Department of Agriculture. Published in 2003 for SCI by John Wiley & Sons, Ltd.
United States Department of Agriculture–Agricultural Research Service research on veterinary pests
Authors: Hogsette Jerome A 
Published: May 2003

AbstractAn overview of ARS research in the field of veterinary pests is presented. Results of research from the past three years on ticks, fire ants, nuisance flies, mosquitoes, sand flies and black flies, among others, are included. Where applicable, significance of research is discussed. Published in 2003 for SCI by John Wiley & Sons, Ltd.
United States Department of Agriculture–Agricultural Research Service research on pest biology: weeds
Authors: Forcella Frank 
Published: May 2003

AbstractOver 125 permanent full‐time scientists conduct research within the USDA Agricultural Research Service (ARS) on issues related to weeds. The research emphasis of most of these scientists involves ecology and management or biological control of weeds. Many scientists perform research on weed biology as components of their primary projects on weed control and integrated crop and soil management. Describing all ARS projects involved with weed biology is impossible, and consequently only research that falls within the following arbitrarily chosen topics is highlighted in this article: dormancy mechanisms; cell division; diversity of rangeland weeds; soil resources and rangeland weeds; poisonous rangeland plants; horticultural weeds; weed traits limiting chemical control; aquatic and semi‐aquatic weeds; weed/transgenic wheat hybrids; seedbanks, seedling emergence and seedling populations; and weed seed production. Within these topics, and others not highlighted, the desire of ARS is that good information on weed biology currently translates or eventually will translate into practical advice for those who must manage weeds. Published in 2003 for SCI by John Wiley & Sons, Ltd.
United States Department of Agriculture–Agricultural Research Service research on natural products for pest management
Authors: Duke Stephen O , Baerson Scott R , Dayan Franck E , Rimando Agnes M , Scheffler Brian E , Tellez Mario R , Wedge David E , Schrader Kevin K , Akey David H , Arthur Frank H , De Lucca Anthony J , Gibson Donna M , Harrison Howard F , Peterson Joseph K , Gealy David R , Tworkoski Thomas , Wilson Charles L , Morris J Brad 
Published: May 2003

AbstractRecent research of the Agricultural Research Service of USDA on the use of natural products to manage pests is summarized. Studies of the use of both phytochemicals and diatomaceous earth to manage insect pests are discussed. Chemically characterized compounds, such as a saponin from pepper (Capsicum frutescens L), benzaldehyde, chitosan and 2‐deoxy‐D‐glucose are being studied as natural fungicides. Resin glycosides for pathogen resistance in sweet potato and residues of semi‐tropical leguminous plants for nematode control are also under investigation. Bioassay‐guided isolation of compounds with potential use as herbicides or herbicide leads is underway at several locations. New natural phytotoxin molecular target sites (asparagine synthetase and fructose‐1,6‐bisphosphate aldolase) have been discovered. Weed control in sweet potato and rice by allelopathy is under investigation. Molecular approaches to enhance allelopathy in sorghum are also being undertaken. The genes for polyketide synthases involved in production of pesticidal polyketide compounds in fungi are found to provide clues for pesticide discovery. Gene expression profiles in response to fungicides and herbicides are being generated as tools to understand more fully the mode of action and to rapidly determine the molecular target site of new, natural fungicides and herbicides. Published in 2003 for SCI by John Wiley & Sons, Ltd.
United States Department of Agriculture–Agricultural Research Service research on improving host‐plant resistance to pests
Authors: Lynch Robert E , Guo Baozhu , Timper Patricia , Wilson Jeffrey P 
Published: May 2003

AbstractHost‐plant resistance is an efficient, economical and environmentally benign approach used to manage many pests and diseases of agricultural crops. After nearly a century of research, the resources and tools have become more refined, but the basic tasks in breeding for resistance have not changed. Resistance must be identified, incorporated into elite germplasm, and deployed in a form useful to growers. In some instances, biotechnology has expedited this process through incorporating a foreign gene(s) for resistance into elite germplasm. The USDA Agricultural Research Service (ARS) has made significant contributions in the development of germplasm with resistance to insects, nematodes and plant diseases. Because resistant plant varieties are an essential component of sustainable production systems, ARS is committed to developing techniques and germplasm to help meet this goal. Published in 2003 for SCI by John Wiley & Sons, Ltd.