bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calcium/calmodulin‐dependent kinase II is involved in the facilitating effect of clozapine on NMDA‐ and electrically evoked responses in the medial prefrontal cortical pyramidal cells
Authors: Ninan Ipe , Jardemark Kent E. , Liang Xiaofu , Wang Rex Y. 
Published: January 2003

AbstractUsing the method of intracellular recording in in vitro brain slices, we investigated whether calcium/calmodulin‐dependent kinase II (CaMKII) is involved in the facilitating action produced by the atypical antipsychotic drug (APD) clozapine on N‐methyl‐D‐aspartate (NMDA)‐induced inward currents and electrically evoked excitatory postsynaptic currents (EPSCs) in pyramidal cells of the medial prefrontal cortex (mPFC). The CaMKII inhibitor, KN‐93 (N‐[2‐(N‐(4‐Chlorocinnamyl)‐N‐methylaminomethyl)phenyl]‐N‐[2‐hydroxyethyl]‐4‐methoxybenzenesulfonamide), but not the inactive isomer, KN‐92 (2‐[N‐(4‐Methoxybenzenesulfonyl)]amino‐N‐(4‐chlorocinnamyl)‐N‐methylbenzylamine, phosphate), blocked clozapine's augmenting effect on NMDA‐evoked responses in pyramidal cells of the rat mPFC. KN‐93 also inhibited the facilitatory effect of clozapine on electrically evoked responses in the pyramidal cells, while KN‐92 did not show any effect. Similarly, the calmodulin antagonist W‐7 (N‐(6‐Aminohexyl)‐5‐chloro‐1‐naphthalenesulfonamide) inhibited the augmenting effect of clozapine on NMDA‐ and electrically evoked responses in the pyramidal cells. To further test the role of CaMKII in mediating the augmenting action of clozapine, we performed experiments in alpha‐CaMKII mutant and wild‐type mice. In contrast to results in pyramidal cells from rats or wild‐type mice, clozapine was not able to potentiate NMDA‐induced currents in the mPFC pyramidal cells from the CaMKII mutant mouse. Both KN‐93 and W‐7, but not KN‐92, inhibited the augmenting action of clozapine in the pyramidal cells of wild‐type mice. Taken together, these results suggest that the facilitating action of clozapine on the NMDA‐ and electrically evoked responses in pyramidal cells of the mPFC requires activation of CaMKII enzyme. Synapse 47:285–294, 2003. © 2003 Wiley‐Liss, Inc.
Identification and quantification of in vitro adduct formation between protein reactive xenobiotics and a lysine‐containing model peptide
Authors: Reichardt Peter , Schreiber André , Wichmann Gunnar , Metzner Gerhard , Efer Juergen , Raabe Ferdinand 
Published: January 2003

AbstractFormation of in vitro adducts between different classes of xenobiotics and the lysine‐containing peptide Lys‐Tyr was monitored by high‐performance liquid chromatography and electrospray ionization mass spectrometry. The molecular structures of the main resulting products could be sensitively analyzed by mass spectrometry (flow injection analysis), enabling the detection of characteristic binding formations. Aldehydes such as formaldehyde, acetaldehyde, and benzaldehyde were shown to form stable linkages to lysine amino groups via Schiff bases. Other electrophilic substances (e.g., toluene‐2,4‐diisocyanate, 2,4‐dinitro‐1‐fluorobenzene, 2,4,6‐trinitrobenzene sulfonic acid, dansyl chloride, and phthalic acid anhydride) also formed covalent adducts with lysine residues. The reactivity of the compounds was quantified by measuring the amount of peptide that remained unchanged after incubation for a certain period with the xenobiotic. Although reactivity levels within this group of aldehydes varied only to a small extent, as would be expected, extreme differences were seen among the structurally heterogeneous group of nonaldehyde xenobiotics. These results support the hypothesis that simple chemical reactions may lead to the adduction of nucleophilic macromolecules such as peptides or proteins. Such reactions, in particular, Schiff base formation of aldehydes, have previously been shown to be capable of specifically interfering with costimulatory signaling on T cells. Our results suggest that electrophilic xenobiotics of other classes may also inherit the capacity to exert similar effects. Forming covalent linkage to peptides may represent a possible molecular mechanism of electrophilic xenobiotics in vivo, yielding immunotoxic effects. The model utilized in this study is appropriate for monitoring the adduction of xenobiotics to basic peptides and for analyzing the resulting molecular structures. © 2003 Wiley Periodicals, Inc. Environ Toxicol 18: 29–36, 2003.
An empirical taxonomy for quality management systems: a study of the Hong Kong electronics industry
Authors: Yeung A.C.L , Chan L.Y , Lee T.S 
Published: January 2003

AbstractThis study investigates the existence of different patterns of quality management systems (QMS) and the relationship between such patterns and organizational performance by conducting a quantitative and qualitative study of 225 international and local firms in the electronics industry in Hong Kong. A cluster analysis of the survey data results in the identification of four patterns of QMS, which are labeled as undeveloped, frame, accommodating and strategic, respectively, according to the characteristics that each pattern displays. These four types of QMS were found to be associated with various organizational performance measures according to the stage of their development. The study suggests that organizations can improve their time‐based operational performance by establishing a frame quality system. However, the overall performance of an electronics company can be enhanced only by the establishment of a strategic quality system (SQS), which requires the involvement of top management. Our investigation further suggests that the development of a QMS is influenced by top management’s view on quality management. If quality management is viewed as an assurance system or a defensive strategy for answering customer requirements, a more advanced system will not be developed. The taxonomy developed here also enables researchers to understand the differences of major functions of quality systems at various stages of their development, the obstacles that management faces in the transformation process, and the corresponding strategies to be adopted.
The impact of human resource management practices on operational performance: recognizing country and industry differences
Authors: Ahmad Sohel , Schroeder Roger G. 
Published: January 2003

AbstractThe interest in strategic human resource management (HRM) has spawned a number of empirical research studies that investigated the impact of HRM practices on organizational performance. However, very little attention has been paid to address the impact of HRM practices on operations management and to generalize the findings across countries and industries. Success of some business decisions (e.g. globalization and merger and acquisition) necessitates recognition and reconciliation of the differences among HRM practices in different countries and industries. This study attempts to generalize the efficacy of seven HRM practices proposed by Pfeffer in the context of country and industry, focusing primarily on the effects of these practices on operations. The findings provide overall support for Pfeffer’s seven HRM practices and empirically validate an ideal‐type HRM system for manufacturing plants.
Binding of an ankyrin-1 isoform to obscurin suggests a molecular link between the sarcoplasmic reticulum and myofibrils in striated muscles
Authors: Bagnato Paola , Barone Virigina , Giacomello Emiliana , Rossi Daniela , Sorrentino Vincenzo 
Published: January 2003

Assembly of specialized membrane domains, both of the plasma membrane and of the ER, is necessary for the physiological activity of striated muscle cells. The mechanisms that mediate the structural organization of the sarcoplasmic reticulum with respect to the myofibrils are, however, not known. We report here that ank1.5, a small splice variant of the ank1 gene localized on the sarcoplasmic reticulum membrane, is capable of interacting with a sequence of 25 aa located at the COOH terminus of obscurin. Obscurin is a giant sarcomeric protein of ∼800 kD that binds to titin and has been proposed to mediate interactions between myofibrils and other cellular structures. The binding sites and the critical aa required in the interaction between ank1.5 and obscurin were characterized using the yeast two-hybrid system, in in vitro pull-down assays and in experiments in heterologous cells. In differentiated skeletal muscle cells, a transfected myc-tagged ank1.5 was found to be selectively restricted near the M line region where it colocalized with endogenous obscurin. The M line localization of ank1.5 required a functional obscurin-binding site, because mutations of this domain resulted in a diffused distribution of the mutant ank1.5 protein in skeletal muscle cells. The interaction between ank1.5 and obscurin represents the first direct evidence of two proteins that may provide a direct link between the sarcoplasmic reticulum and myofibrils.
In keeping with the proposed role of obscurin in mediating an interaction with ankyrins and sarcoplasmic reticulum, we have also found that a sequence with homology to the obscurin-binding site of ank1.5 is present in the ank2.2 isoform, which in striated muscles has been also shown to associate with the sarcoplasmic reticulum. Accordingly, a peptide containing the COOH terminus of ank2.2 fused with GST was found to bind to obscurin. Based on reported evidence showing that the COOH terminus of ank2.2 is necessary for the localization of ryanodine receptors and InsP3 receptors in the sarcoplasmic reticulum, we propose that obscurin, through multiple interactions with ank1.5 and ank2.2 isoforms, may assemble a large protein complex that, in addition to a structural function, may play a role in the organization of specific subdomains in the sarcoplasmic reticulum.
Bones of Contention: The Repatriation of the Remains of Roger Casement
Authors: Grant Kevin 
Published: January 2003

This is a history of life after death—not the life of a disembodied soul, but of the body left behind in a prison yard, buried in quicklime. It is a history composed of family members, friends, politicians, and bureaucrats drawn into cooperation and conflict by the politics of rebellion, partition, and sexuality in Ireland and Great Britain. The deceased in dispute, Roger Casement, had been a controversial figure during the later years of his life, knighted by the British Crown in 1911 for his advocacy of humanitarian causes in Africa and South America and then hanged by the British government on 3 August 1916 for conspiring with Germany to mobilize and arm Irish separatists. Casement had requested that his body be buried at Murlough Bay, near his family's home in County Antrim in the province of Ulster. Instead, Casement's body was buried at Pentonville Prison in London, and for almost fifty years the British government rejected the appeals of Casement's family and supporters for the repatriation of his body to Ireland. In 1965, the body was finally exhumed and reinterred at Glasnevin Cemetery in Dublin, following a state funeral.Why did the British government take over fifty years to disinter Casement's body from Pentonville, and why was his request to be buried at Murlough Bay not honored? In exploring the answers to these questions, I focus on negotiations between the British and Irish governments, and the terms of their final agreement over the present location of Casement's remains.
A comparison of normalization methods for high density
oligonucleotide array data based on variance and bias
Authors: Bolstad B.M. , Irizarry R.A , Åstrand M. , Speed T.P. 
Published: January 2003

Abstract
Motivation: When running experiments that involve multiple high density oligonucleotide arrays, it is important to remove sources of variation between arrays of non-biological origin. Normalization is a process for reducing this variation. It is common to see non-linear relations between arrays and the standard normalization provided by Affymetrix does not perform well in these situations.
Results: We present three methods of performing normalization at the probe intensity level. These methods are called complete data methods because they make use of data from all arrays in an experiment to form the normalizing relation. These algorithms are compared to two methods that make use of a baseline array: a one number scaling based algorithm and a method that uses a non-linear normalizing relation by comparing the variability and bias of an expression measure. Two publicly available datasets are used to carry out the comparisons. The simplest and quickest complete data method is found to perform favorably.
Availability: Software implementing all three of the complete data normalization methods is available as part of the R package Affy, which is a part of the Bioconductor project http://www.bioconductor.org.
Contact: bolstad@stat.berkeley.edu.
Supplementary information: Additional figures may be found at http://www.stat.berkeley.edu/~bolstad/normalize/index.html
* To whom correspondence should be addressed.
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments
Authors: Wang Lusheng , Xu Ying 
Published: January 2003

Abstract
Summary: SEGID is a tool for finding conserved regions (regions of high scores) for a given (multiple) sequence alignment. It takes a (multiple) sequence alignment as its input and converts the alignment into a sequence of numbers, where each number is the alignment score of a column. Three algorithms are used to identify regions of high scores. A graphical interface is provided to present those identified regions.
Availability: Free from http://www.cs.cityu.edu.hk/~lwang/segid/subject to copyright restrictions.
Contact: cswangl@cityu.edu.hk
* To whom correspondence should be addressed.
r8s: inferring absolute rates of molecular evolution and
divergence times in the absence of a molecular clock
Authors: Sanderson Michael J. 
Published: January 2003

Abstract
Summary: Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions.
Results:
Availability: The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.
Contact: mjsanderson@ucdavis.edu
Chimera: construction of chimeric sequences for
phylogenetic analysis
Authors: Leunissen Jack A.M. 
Published: January 2003

Abstract
Summary: Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output file in PHYLIP or NEXUS formats.
Availability: The computer program, including supporting files and example files, is available from http://www.dalicon.com/chimera/.
Contact: jackl@dalicon.com
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining
Authors: Arakawa K. , Mori K. , Ikeda K. , Matsuzaki T. , Kobayashi Y. , Tomita M. 
Published: January 2003

Abstract
Summary: G-language Genome Analysis Environment (G-language GAE) is an open source generic software package aimed for higher efficiency in bioinformatics analysis. G-language GAE has an interface as a set of Perl libraries for software development, and a graphical user interface for easy manipulation. Both Windows and Linux versions are available.
Availability: From http://www.g-language.org/ under GNU General Public License. CD-ROMs are distributed freely in major conferences.
Contact: info@g-language.org
* To whom correspondence should be addressed.
A profile hidden Markov model for signal peptides generated by HMMER
Authors: Zhang Zemin , Wood William I. 
Published: January 2003

Abstract
Summary: Although the HMMER package is widely used to produce profile hidden Markov models (profile HMMs) for protein domains, it has been difficult to create a profile HMM for signal peptides. Here we describe an approach for building a complex model of eukaryotic signal peptides by the standard HMMER package. Signal peptide prediction with this model gives a 95.6% sensitivity and 95.7% specificity.
Availability: The profile HMM for signal peptides, data sets, and the scripts for analyzing data are available for non-commercial use at http://share.gene.com/.
Contact: zemin@gene.com
* To whom correspondence should be addressed.
MPID: MHC-Peptide Interaction Database for
sequence-structure-function information on peptides binding to
MHC molecules
Authors: Govindarajan Kunde Ramamoorthy , Kangueane Pandjassarame , Tan Tin Wee , Ranganathan Shoba 
Published: January 2003

Abstract
Summary: Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the first step in T-cell mediated immune response. To understand the structural principles governing MHC-specific peptide recognition and binding, we have developed the MHC-Peptide Interaction Database (MPID), containing sequence-structure-function information. MPID (version 1.2) contains curated x-ray crystallographic data on 86 MHC peptide complexes, with precomputed interaction parameters (solvent accessibility, hydrogen bonds, gap volume and gap index). A user-friendly web interface and query tools will facilitate the development of predictive algorithms for MHC-peptide binding from a structural viewpoint.
Availability: Freely accessible from http://surya.bic.nus.edu.sg/mpid.
Contact: shoba@bic.nus.edu.sg
* To whom correspondence should be addressed.
DPX: for the analysis of the protein core
Authors: Pintar Alessandro , Carugo Oliviero , Pongor Sándor 
Published: January 2003

Abstract
Summary: In order to obtain an accurate description of the protein interior, we describe a simple and fast algorithm that measures the depth of each atom in a protein (dpx), defined as its distance (Å) from the closest solvent accessible atom. The program reads a PDB file containing the atomic solvent accessibility in the B-factor field, and writes a file in the same format, where the B-factor field now contains the dpx value. Output structure files can be thus directly displayed with molecular graphics programs like RASMOL, MOLMOL, Swiss-PDB View and colored according to dpx values.
Availability: The algorithm is implemented in a standalone program written in C and its source is freely available at ftp.icgeb.trieste.it/pub/DPX or on request from the authors.
Contact: pintar@icgeb.org; carugo@icgeb.org; pongor@icgeb.org
* To whom correspondence should be addressed.
A reinterpretation of the dimerization interface of the N‐terminal Domains of STATs
Authors: Chen Xiaomin , Bhandari Rashna , Vinkemeier Uwe , van den Akker Focco , Darnell James E. , Kuriyan John 
Published: January 2003

AbstractThe crystal structures of the N‐terminal domain (N‐domain) and the core region of the STAT family of transcription factors have been determined previously. STATs can form cooperative higher order structures (tetramers or higher oligomers) while bound to DNA. The crystal packing in the STAT4 N‐domain crystal structure, determined at 1.5 Å resolution, suggests two alternate organizations of the N‐domain dimer. We now present the results of site directed mutagenesis of residues predicted to be involved at each dimer interface. Our results indicate that the dimer interface suggested earlier as being physiologically relevant is, in fact, unlikely to be so. Given the alternative model for the N‐domain dimer, the ability of the N‐domain to mediate interactions of two STAT dimers on DNA remains unchanged.
Directing the mode of nitrite binding to a copper‐containing nitrite reductase from Alcaligenes faecalis S‐6: Characterization of an active site isoleucine
Authors: Boulanger Martin J. , Murphy Michael E.P. 
Published: January 2003

AbstractUnlike the heme cd1‐based nitrite reductase enzymes, the molecular mechanism of copper‐containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from Alcaligenes faecalis S‐6. The activities of these six variants span nearly two orders of magnitude with one variant, I257V, the only observed natural substitution for Ile257, showing greater activity than the native enzyme. High‐resolution (> 1.8 Å) nitrite‐soaked crystal structures of these variants display different modes of nitrite binding that correlate well with the altered activities. These studies identify for the first time that the highly conserved Ile257 in the native enzyme is a key molecular determinant in directing a catalytically competent mode of nitrite binding in the active site. The O‐coordinate bidentate binding mode of nitrite observed in native and mutant forms with high activity supports a catalytic model distinct from the heme cd1 NiRs.(The atomic coordinates for I257V[NO2−], I257L[NO2−], I257A[NO2−], I257T[NO2−], I257M[NO2−] and I257G[NO2−] AfNiR have been deposited in the Protein Data Bank [PDB identification codes are listed in Table 2].)
Protein conformational changes studied by diffusion NMR spectroscopy: Application to helix‐loop‐helix calcium binding proteins
Authors: Weljie Aalim M. , Yamniuk Aaron P. , Yoshino Hidenori , Izumi Yoshinobu , Vogel Hans J. 
Published: January 2003

AbstractPulsed‐field gradient (PFG) diffusion NMR spectroscopy studies were conducted with several helix‐loop‐helix regulatory Ca2+‐binding proteins to characterize the conformational changes associated with Ca2+‐saturation and/or binding targets. The calmodulin (CaM) system was used as a basis for evaluation, with similar hydrodynamic radii (Rh) obtained for apo‐ and Ca2+‐CaM, consistent with previously reported Rh data. In addition, conformational changes associated with CaM binding to target peptides from myosin light chain kinase (MLCK), phosphodiesterase (PDE), and simian immunodeficiency virus (SIV) were accurately determined compared with small‐angle X‐ray scattering results. Both sets of data demonstrate the well‐established collapse of the extended Ca2+‐CaM molecule into a globular complex upon peptide binding. The Rh of CaM complexes with target peptides from CaM‐dependent protein kinase I (CaMKI) and an N‐terminal portion of the SIV peptide (SIV‐N), as well as the anticancer drug cisplatin were also determined. The CaMKI complex demonstrates a collapse analogous to that observed for MLCK, PDE, and SIV, while the SIV‐N shows only a partial collapse. Interestingly, the covalent CaM–cisplatin complex shows a near complete collapse, not expected from previous studies. The method was extended to related calcium binding proteins to show that the Rh of calcium and integrin binding protein (CIB), calbrain, and the calcium‐binding region from soybean calcium‐dependent protein kinase (CDPK) decrease on Ca2+‐binding to various extents. Heteronuclear NMR spectroscopy suggests that for CIB and calbrain this is likely because of shifting the equilibrium from unfolded to folded conformations, with calbrain forming a dimer structure. These results demonstrate the utility of PFG‐diffusion NMR to rapidly and accurately screen for molecular size changes on protein–ligand and protein–protein interactions for this class of proteins.