bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome analysis in the study of the bacterial heat‐shock response
Authors: Rosen Ran , Ron Eliora Z. 
Published: January 2003

Abstract

I.
Introduction
245

II.
Global Regulatory Networks
245

III.
Heat‐Shock Response
247

A. Control Elements in Gram‐Positive Bacteria
247

1.  Sigma B‐Controlled Genes
247

2.  HrcA‐CIRCE Controlled Genes
249

3.  Genes Controlled by Additional Repressors
250

B. Control Elements in Gram‐Negative Bacteria
250

1.  Sigma 32‐Controlled Genes
250

2.  Genes Controlled by Other Minor Sigma Factors
252

3.  HrcA‐CIRCE‐Controlled Genes
252

4.  Minor Regulatory Elements
252

C. Networks of Positive and Negative Regulators
253

IV.
Proteome Studies of Heat‐Shock Regulons
253

V.
Mass Spectrometry in The Analysis of Heat‐Shock‐Induced Post‐Translational Modifications of Proteins
256

A. Phosphorylation
256

B. Other Post‐Translational Modifications
258

1.  Protein Oxidation
258

2.  Sulfoxidation
258

3.  Acetylation
258

VI.
Potential Significance of Proteome Studies for Analysis of Regulons
258

Acknowledgments
259

References
259

In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat‐shock response. The heat‐shock response is characterized by the induction of a large set of proteins (heat‐shock proteins—HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat‐shock response is universal and many of the heat‐shock proteins are highly conserved among species. In bacteria, the heat‐shock response has been studied extensively in several Gram‐positive bacteria (Bacillus subtilis) and in the Gram‐negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat‐shock proteins took place with the introduction of high‐resolution two‐dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two‐dimensional gels, followed by mass spectrometry, were used to define the heat‐shock stimulons in several bacteria, and to study the regulatory elements that control the heat‐shock response. Here, we review the heat‐shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:244–265, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10031
Modern strategies for protein quantification in proteome analysis: Advantages and limitations
Authors: Hamdan Mahmoud , Righetti Pier Giorgio 
Published: January 2003

Abstract

I.
Introduction
287

II.
Sample Preparation
289

A. Influence of Alkylation
289

B. Influence of Surfactants
289

III.
MS‐Based Strategies for Protein Quantification
290

A. Isotope‐Coded Affinity Tags (ICAT)
291

B. Mass‐Coded Abundance Tagging (MCAT)
293

C. Stable Isotope‐Labeling of Proteins/Peptides
294

D. Global Internal Standard Strategy (GIST)
294

E. Two‐D Gel or Column Electrophoresis/MALDI‐TOF‐MS
295

F. Fluorescence, Two‐Dimensional Differential in‐Gel Electrophoresis (DIGE) for Quantitative Proteomics
296

IV.
Discussion
299

V.
Concluding Remarks
300

Acknowledgments
300

References
300

Over the last 3 years, a number of mass spectrometry‐based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two‐step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy‐isotope‐labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi‐protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:287–302, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10032
Slowly progressive cerebellar ataxia and cervical dystonia: Clinical presentation of a new form of spinocerebellar ataxia?
Authors: Kuoppamäki Mikko , Giunti Paula , Quinn Niall , Wood Nicholas W. , Bhatia Kailash P. 
Published: January 2003

AbstractWe describe 5 cases with a rare combination of young‐onset, slowly progressive cerebellar ataxia and cervical dystonia. Two were sporadic, whereas the other 3 were familial, including 2 from one family. The age of onset of these cases was between 16 and 37 years. The presenting symptom was cervical dystonia and/or dystonic head tremor in 3 patients and hand or lower limb tremor in 2. In 2 cases, cervical dystonia and/or dystonic head tremor developed approximately 6 to 10 years before cerebellar dysfunction, and in three they developed at the same time. Apart from cervical dystonia, there was mild dystonic limb involvement in 2 cases, but generalized dystonia was not seen. Cerebellar ataxia was slowly progressive. A literature search showed 10 cases of cervical dystonia associated with genetically undetermined (n = 5) or genetically proven (n = 5) spinocerebellar ataxia (SCA). When the genotype was known, these patients had either SCA3, 6, 7, or 12. However, our 5 cases (or their first‐degree relatives) tested negative for SCA1, 2, 3, 6, and 7, and in the 4 cases (or their first‐degree relatives) tested for SCA12, the result was negative. We propose that this rare phenotype manifesting as a combination of cerebellar ataxia and cervical dystonia may represent one or more new, as yet uncharacterized, genotypes of inherited young‐onset spinocerebellar ataxia. © Movement Disorder Society
Long‐term efficacy of thalamic deep brain stimulation for tremor: Double‐blind assessments
Authors: Rehncrona Stig , Johnels Bo , Widner Håkan , Törnqvist Anna‐Lena , Hariz Marwan , Sydow Olof 
Published: January 2003

AbstractThalamic deep brain stimulation (DBS) is proven to suppress tremor in Parkinson's disease (PD) and essential tremor (ET). However, there are few reports on its long‐term efficacy. We studied the efficacy of DBS at 2 years and 6–7 years after electrode implantations in the ventrointermediate nucleus of the thalamus in 39 patients (20 PD, 19 ET) with severe tremor. Twenty‐five of the patients completed the study. Evaluations were done in a double‐blind manner with the Unified Parkinson's Disease Rating Scale (UPDRS) and Essential Tremor Rating Scale (ETRS). DBS decreased tremor sum scores in PD (P < 0.025) compared to the preoperative baseline (median, 7; Q25–75, 6–9) both at 2 years (median, 2; Q25–75, 2–3.5; n = 16) and at 6 to 7 years (median, 2.5; Q25–75, 0.5–3; n = 12). Stimulation on improved tremor sum as well as sub scores (P < 0.025) compared to stimulation off conditions. In ET, thalamic stimulation improved (P < 0.025) kinetic and positional tremor at both follow‐up periods (n = 18 and n = 13, respectively) with significant improvements (P < 0.025) in hand‐function tests. PD but not ET patients showed a general disease progression. Stimulation parameters were remarkably stable over time. We conclude that high‐frequency electric thalamic stimulation can efficiently suppress severe tremor in PD and ET more than 6 years after permanent implantation of brain electrodes. © 2002 Movement Disorder Society
Primary orthostatic tremor is an exaggeration of a physiological response to instability
Authors: Sharott Andrew , Marsden Jon , Brown Peter 
Published: January 2003

AbstractPrimary orthostatic tremor (POT) is a rare disorder characterised by an intense sense of unsteadiness upon standing and a 16‐Hz tremor in which the timing between tremor bursts in different muscles (unilateral and bilateral) remains constant. Hitherto, similar EMG activity has not been described in healthy subjects and it has been postulated that the oscillations seen in POT are primarily pathological. In this study, EMG was recorded from tibialis anterior in healthy subjects who were made unsteady through vestibular galvanic stimulation or leaning backwards. Under these conditions, a peak at approximately 16 Hz was seen in the coherence between the left and right tibialis anterior. This bilateral coherence was absent when the subjects activated the same muscles when not unsteady. These data indicate the existence of a physiological system involved in organising postural responses under circumstances of imbalance and characterised by a highly synchronised output at approximately 16 Hz. In addition, the results suggest that the core abnormality in POT may be an exaggerated sense of unsteadiness when standing still, which then elicits activity from a 16‐Hz oscillator normally engaged in postural responses. © 2002 Movement Disorder Society
A polarization‐independent athermal electro‐optic bulk modulator using a unique sandwich configuration
Authors: Yin Shizhuo , Purwosumarto Purwadi , Guo Zhuanyun , Luo Fang 
Published: January 2003

AbstractIn this paper, a unique polarization‐independent athermal electro‐optic modulator using lithium niobate (LiNbO3) and/or lithium tantalite (LiTaO3) crystals is presented. The modulator uses a unique sandwich configuration, in which a pair of lithium niobate crystals are bonded together and an embedded electrode is sandwiched in between them. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 157–160, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10707
Periodic‐loaded sinusoidal patterned electromagnetic bandgap coplanar waveguides
Authors: Martín Ferran , Falcone Francisco , Bonache Jordi , Lopetegi Txema , Laso Miguel A. G. , Coderch M. , Sorolla Mario 
Published: January 2003

AbstractIn this paper, coplanar waveguides (CPWs) periodically loaded with shunt‐connected capacitances and periodically perturbed by varying the slot width are studied. Both square‐ and sinusoidal‐shaped structures are considered. It is demonstrated that by a proper choice of the perturbation period, the spurious passbands—inherent with the presence of reactive elements—can be completely rejected, even in the case of singly tuned (sinusoidal) structures. Rejection levels near and above 30 dB (depending on the spurious band), inferred from electromagnetic based simulations, are experimentally verified. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 181–184, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10714
Application of online FDTD on microstrip cross and T‐junction structures
Authors: Zhong Xiaolong , Mei Kenneth K. , Liu Yaowu 
Published: January 2003

AbstractThe online FDTD method derived from general transmission line equations [1] has been introduced in [2, 3]. Following the research on non‐uniform transmission lines, we further explore the application of online FDTD in the microstrip cross and T‐junction structures. As the theoretic difficulties of modeling the connection of multi‐transmission lines have been solved, many microstrip structures that have cross or stub substructures can be easily simulated by online FDTD. Three examples are presented to test the validity of this application. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 184–187, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10715
A unit cell waveguide model of a reflectarray formed by microstrip patches and slots
Authors: Bialkowski Marek E. , Tsai Feng‐Chi E. 
Published: January 2003

AbstractAn equivalent unit cell waveguide approach (WGA) is described to obtain reflection coefficient phase curves for designing a microstrip patch reflectarray supported by a ground plane with periodic apertures or slots. Based on the presented theory, a computer algorithm for determining the reflection coefficient of a plane wave normally incident on a multi‐layer structure of patches and apertures is developed. The validity of the developed algorithm is verified by comparing the obtained results with those published in the literature and the ones generated by Agilent High Frequency Structure Simulator (HFSS). A good agreement in all the presented examples is obtained, proving that the developed theory and computer algorithm can be an effective tool for designing multi‐layer microstrip reflectarrays with a periodically perforated ground plane. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 206–210, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10721
Natural hierarchical refinement for finite element methods
Authors: Krysl Petr , Grinspun Eitan , Schröder Peter 
Published: January 2003

AbstractCurrent formulations of adaptive finite element mesh refinement seem simple enough, but their implementations prove to be a formidable task. We offer an alternative point of departure which yields equivalent adapted approximation spaces wherever the traditional mesh refinement is applicable, but our method proves to be significantly simpler to implement. At the same time it is much more powerful in that it is general (no special tricks are required for different types of finite elements), and applicable for some newer approximations where traditional mesh refinement concepts are not of much help, for instance on subdivision surfaces. Copyright © 2003 John Wiley & Sons, Ltd.
Safety and patient tolerance of standard and slow‐release formulations of NSAIDs
Authors: Langman Michael , Kong Sheldon X. , Zhang Qiaoyi , Kahler Kristijan H. , Finch Elizabeth 
Published: January 2003

AbstractObjectiveTo examine the rates of co‐prescribing of gastro‐protective drugs (GPDs) and the frequency of gastrointestinal (GI) investigations associated with standard and slow‐release (SR) formulations of nonsteroidal antiinflammatory drugs (NSAIDs).MethodsPatients were identified from the MediPlus database, which contains the medical records of some 2 million patients throughout the United Kingdom. We selected all new NSAID users who received at least one prescription between 1 July 1997 and 31 December 1997. Patients were classified as starting SR or standard formulations by their first prescription and followed for 12 months. Events specified as of interest included GPDs prescribed and GI investigations. GPDs included prescriptions for all proton pump inhibitors, H2‐antagonists and misoprostol. GI investigations included endoscopies and barium contrast studies.ResultsTaken overall, patients prescribed SR formulations of NSAIDs were significantly more likely to receive GPDs than those prescribed standard formulations, odds ratio (OR) 1.34, 95% confidence intervals (CI) 1.21–1.47. They also tended to be more likely to need GI investigations (OR 1.25, CI 0.91–1.71). Differences were not explained by prior predisposition to GI damage as judged by the previous need for GPDs, and were evident whether the NSAID prescription was the first, the second, or the third or later in the series (OR 1.40, CI 1.21–1.62; 1.33, 1.08–1.62; and 1.17, 1.00–1.38 respectively).ConclusionThis study found that patients prescribed SR formulations of NSAIDs were significantly more likely to receive GPDs, and may be more likely to need GI investigations than those receiving standard formulations. In addition, switching away from SR formulations was far more common than switching to them. Copyright © 2002 John Wiley & Sons, Ltd.
Selenomethionine does not affect PSA secretion independent of its effect on LNCaP cell growth
Authors: Bhamre Suvarna , Whitin John C. , Cohen Harvey J. 
Published: January 2003

AbstractBACKGROUNDIndividuals supplemented with selenium have reduced incidence of prostate cancer. This study determines whether selenomethionine specifically affects the secretion of prostate specific antigen (PSA) in vitro.METHODSLNCaP cells were supplemented with selenomethionine for 7 days. PSA secretion was determined by ELISA. Cell proliferation was assessed by enumeration of trypan blue excluding cells. Colony formation was determined in soft agar. Cell cycle distribution was determined by FACS analysis of propidium iodide stained cells.RESULTSSelenomethionine at ≥ 70 μM inhibited LNCaP cell growth and colony formation. 0–100 μM selenomethionine did not affect the secretion of PSA by LNCaP cells in cell culture supernatants when normalized to the number of cells in culture. At supra‐nutritional concentrations of selenomethionine, LNCaP cells had longer G0/G1 phase in agreement with the inhibitory effects on cell growth.CONCLUSIONSPSA secretion is not specifically inhibited by concentrations of selenomethionine corresponding to plasma selenium concentrations found in individuals supplemented with chemopreventive concentrations of selenized yeast. These data suggest that changes in serum PSA levels in individual patients during selenium supplementation is not an effect specific for PSA secretion, but rather may be a useful indicator for changes in disease progression in individual patients. Prostate 54: 315–321, 2003. © 2003 Wiley‐Liss, Inc.
Tracking control of second‐order chained form systems by cascaded backstepping
Authors: Aneke N. P. I. , Nijmeijer H. , de Jager A. G. 
Published: January 2003

AbstractA design methodology is presented for tracking control of second‐order chained form systems. The methodology separates the tracking‐error dynamics, which are in cascade form, into two parts: a linear subsystem and a linear time‐varying subsystem. The linear time‐varying subsystem, after the first subsystem has converged, can be treated as a chain of integrators for the purposes of a backstepping controller. The two controllers are designed separately and the proof of stability is given by using a result for cascade systems. The method consists of three steps. In the first step we apply a stabilizing linear state feedback to the linear subsystem. In the second step the second subsystem is exponentially stabilized by applying a backstepping procedure. In the final step it is shown that the closed‐loop tracking dynamics of the second‐order chained form system are globally exponentially stable under a persistence of excitation condition on the reference trajectory. The control design methodology is illustrated by application to a second‐order non‐holonomic system. This planar manipulator with two translational and one rotational joint (PPR) is a special case of a second‐order non‐holonomic system. The simulation results show the effectiveness of our approach. Copyright © 2002 John Wiley & Sons, Ltd.
Firms' knowledge‐sharing strategies in the global innovation system: empirical evidence from the flat panel display industry
Authors: Spencer Jennifer W. 
Published: January 2003

AbstractThis paper explores the relationship between firms' strategies to share knowledge with their innovation system and innovative performance. The empirical analysis showed that many firms designed strategies to share technological knowledge with competitors, and those firms that shared knowledge with their innovation system earned higher innovative performance than firms that did not share knowledge. In addition, firms that interacted with their global innovation system earned higher innovative performance than firms that interacted with only their national innovation system. These results should help managers and researchers understand how to devise technology strategies in globally integrated industries. Copyright © 2003 John Wiley & Sons, Ltd.
Same as it ever was: the search for evidence of increasing hypercompetition
Authors: McNamara Gerry , Vaaler Paul M. , Devers Cynthia 
Published: January 2003

AbstractSome strategy scholars and practitioners contend that markets have become increasingly hypercompetitive in recent years. We examine this contention by analyzing industry and business performance patterns in a broad sample of firms drawn from the Compustat Industry Segment database for the 1978–97 period. We find little support for the argument that markets have become more hypercompetitive. From the late 1970s to the late‐1980s we observe decreased performance and market stability, consistent with increasing hypercompetition contentions. From the late 1980s to the mid‐1990s, however, trends reverse and performance and market stability increase. For strategy research, our results suggest that hypercompetitive perspectives are important but no more so now than they were in recent years. For practice, our results suggest that managers today face markets no more dynamic and opportunities to gain and sustain competitive advantage no more challenging than in the past. Accordingly, they should continue developing a portfolio of skills to manage businesses whether conditions are increasingly stable or unstable. Copyright © 2002 John Wiley & Sons, Ltd.
Subject‐regulated dosing alters morphine self‐administration behavior and morphine‐stimulated [35S]GTPγS binding
Authors: Kruzich P.J. , Chen A.C.H. , Unterwald E.M. , Kreek M.J. 
Published: January 2003

AbstractRepeated intake of opioids is associated with dose escalation and alterations in signal transduction at the G‐protein‐coupled receptor level. The current study utilized two experiments to identify factors in rats that influence consumption rates such as daily intake of self‐administered morphine and receptor desensitization. In Experiment 1, rats self‐administered either 0.30, 1.00, or 3.00 mg/kg/infusion morphine sulfate (morphine) during 7 daily 4‐h sessions. For Experiment 2, rats were assigned to groups that self‐administered either 1) self‐regulated escalating doses of morphine, 2) a fixed dose of morphine, or 3) saline during 18‐h sessions for 7 days to determine if dose control would increase consumption without significantly decreasing response rate. We then assessed morphine‐stimulated [35S]GTPγS binding in the amygdala and thalamus from these three groups in Experiment 2. Results from Experiment 1 demonstrated that 0.30 mg/kg/morphine did not support stable self‐administration. For Experiment 2, the self‐escalation group self‐administered more morphine than the fixed‐dose group, yet maintained similar response rates. Additionally, self‐escalation rats demonstrated decreased morphine‐stimulated [35S]GTPγS binding in membranes prepared from amygdalar and thalamic nuclei compared to the fixed‐dose and control groups. Our results suggest that session length inversely affects consumption rates for fixed doses of morphine. Self‐regulated dosing of morphine is also associated with rapid escalation of daily consumption and no significant alterations in consumption rates. These results suggest subject‐regulated dosing is a useful approach for modeling dose escalation associated with opioid dependence. Synapse 47:243–249, 2003. © 2003 Wiley‐Liss, Inc.