bluuebunny/crossref_metadata_2025_split huggingface dataset:
ERK1/2 is a negative regulator of homeodomain protein Arix/Phox2a
Authors: Hsieh Marlene M. , Lupas George , Rychlik Jennifer , Dziennis Suzan , Habecker Beth A. , Lewis Elaine J. 
Published: August 2005

SummaryThe homeodomain protein Arix/Phox2a plays a role in the development and maintenance of the noradrenergic cell type by regulating the transcription of genes involved in the biosynthesis and metabolism of noradrenaline. Previous work has shown that Arix/Phox2a is a phosphoprotein, and the phosphorylated form of Arix/Phox2a exhibits poorer DNA‐binding activity than does the dephosphorylated form. Here, we demonstrate that Arix/Phox2a is phosphorylated by extracellular signal‐related kinase (ERK)1/2 at two sites within the N‐terminal transactivation domain. The phosphorylation level of Arix in cultured SH‐SY5Y neuroblastoma cells is reduced when cells are treated with the mitogen activated protein kinase kinase 1 (MEK1) inhibitor UO126. Treatment of sympathetic neurons with the MEK1 inhibitor, PD98059, results in an elevation of mRNAs encoding noradrenergic proteins, dopamine ß‐hydroxylase (DBH) and norepinephrine transporter (NET), but not tyrosine hydroyxlase (TH). Treatment of neuroblastoma cultures with PD98059 increases the interaction of Arix with DBH and NET genes, but not the TH gene. Together, these results suggest that phosphorylation of Arix by ERK1/2 inhibits its ability to interact with target genes, and that both specificity of expression and modulation by external stimuli are monitored through the same transcription factor.
Evidence for low GluR2 AMPA receptor subunit expression at synapses in the rat basolateral amygdala
Authors: Gryder Divina S. , Castaneda Dora C. , Rogawski Michael A. 
Published: August 2005

AbstractFast excitatory synaptic responses in basolateral amygdala (BLA) neurons are mainly mediated by ionotropic glutamate receptors of the α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate (AMPA) subtype. AMPA receptors containing an edited GluR2 subunit are calcium impermeable, whereas those that lack this subunit are calcium permeable and also inwardly rectifying. Here, we sought to determine the extent to which synapses in the rat BLA have AMPA receptors with GluR2 subunits. We assessed GluR2 protein expression in the BLA by immunocytochemistry with a GluR2 subunit‐specific antiserum at the light and electron microscopic level; for comparison, a parallel examination was carried out in the hippocampus. We also recorded from amygdala brain slices to examine the voltage‐dependent properties of AMPA receptor‐ mediated evoked synaptic currents in BLA principal neurons. At the light microscopic level, GluR2 immunoreactivity was localized to the perikarya and proximal dendrites of BLA neurons; dense labeling was also present over the pyramidal cell layer of hippocampal subfields CA1 and CA3. In electron micrographs from the BLA, most of the synapses were asymmetrical with pronounced postsynaptic densities (PSD). They contained clear, spherical vesicles apposed to the PSD and were predominantly onto spines (86%), indicating that they are mainly with BLA principal neurons. Only 11% of morphological synapses in the BLA were onto postsynaptic elements that showed GluR2 immunoreactivity, in contrast to hippocampal subfields CA1 and CA3 in which 76% and 71% of postsynaptic elements were labeled (p < 0.001). Synaptic staining in the BLA and hippocampus, when it occurred, was exclusively postsynaptic, and particularly heavy over the PSD. In whole‐cell voltage clamp recordings, 72% of BLA principal neurons exhibited AMPA receptor‐mediated synaptic currents evoked by external capsule stimulation that were inwardly rectifying. Although BLA principal neurons express perikaryal and proximal dendritic GluR2 immunoreactivity, few synapses onto these neurons express GluR2, and a preponderance of principal neurons have inwardly rectifying AMPA‐mediated synaptic currents, suggesting that targeting of GluR2 to synapses is restricted. Many BLA synaptic AMPA receptors are likely to be calcium permeable and could play roles in synaptic plasticity, epileptogenesis and excitoxicity.
Ten polymorphic microsatellite markers in the wandering albatross Diomedea exulans
Authors: DUBOIS MARIE‐PIERRE , JARNE PHILIPPE , JOUVENTIN PIERRE 
Published: August 2005

AbstractWe describe 10 new variable dinucleotide microsatellites in the wandering albatross Diomedea exulans, as well as conditions for multiplexing and simultaneous genotyping sets of loci. Their variability was assessed in two and one populations from the Crozet and Kerguelen archipelagos (southern Indian Ocean), respectively. Two to 13 alleles were detected per population, and the mean gene diversity was around 0.4. The low genetic differentiation suggests that these populations constitute a single panmictic unit. Cross‐species amplification provided some variability at three and five loci in two other marine birds (Bulweria bulwerii and Pagodroma nivea), but none in Calonectris diomedea.
Isolation and characterization of 27 polymorphic microsatellite loci for the common snook, Centropomus undecimalis
Authors: SEYOUM SEIFU , TRINGALI MICHAEL D. , SULLIVAN JAMIE G. 
Published: August 2005

AbstractHere we describe 32 di‐, tri‐ and tetranucleotide microsatellite loci isolated by PIMA, a polymerase chain reaction (PCR)‐based procedure, for the common snook (Centropomus undecimalis). Five loci were monomorphic, and the remaining loci averaged 6.7 alleles per locus in a sample of 45 common snook. For polymorphic loci, expected heterozygosities ranged from 0.02 to 0.91 (mean = 0.538). Significant departures from Hardy–Weinberg equilibrium expectations occurred in two loci. Exact tests for genotype disequilibrium gave evidence for linkage at one pair of loci. Many cross‐species primer assays yielded PCR fragments of the expected size for 11 species of Centropomus and two species of the confamilial genus Lates.
Development and characterization of ten new microsatellite markers in a mangrove tree species Bruguiera gymnorrhiza (L.)
Authors: ISLAM M. S. , LIAN C. L. , KAMEYAMA N. , WU B. , HOGETSU T. 
Published: August 2005

Abstract Bruguiera gymnorrhiza is an ecologically and somewhat economically important mangrove tree species. We isolated 10 polymorphic microsatellite loci from B. gymnorrhiza using a dual‐suppression polymerase chain reaction (PCR) technique. These loci provided microsatellite markers with polymorphism of two to five alleles per locus within 216 individuals from nine natural populations of B. gymnorrhiza on Iriomote Island, the Sakishima Islands, Japan. The expected and observed heterozygosities ranged from 0.220 to 0.720 and from 0.104 to 0.447, respectively.
FINANCIAL LIBERALIZATION AND EFFICIENCY IN TUNISIAN BANKING INDUSTRY: DEA TEST
Authors: COOK WADE D. , HABABOU MOEZ , LIANG LIANG 
Published: August 2005

IMF policies have been widely criticized in the aftermath of the Asian crisis. Key critics questioned the appropriateness and the sequencing of financial liberalization programs which, along with insufficient monitoring and inadequate prudential regulations, left the financial sectors of the affected countries highly leveraged and exposed. This paper examines the impacts of similar reforms on the efficiency of the banking system in Tunisia, a country whose economy has been reshaped by the IMF/World Bank prescribed economic adjustment plans since 1987. Using various DEA models and panel data covering the period 1992–1997, we evaluate the individual effects of each component of the reforms on the banking industry overall. Meanwhile, we compare the effects on banks because of the different ownership structures over time. We also pay particular attention to specific factors that have kept the financial sector in Tunisia relatively stable in the midst of the global market turmoil caused by the Asian crisis.
A Method for Measuring the Efficiency Gap between Average and Best Practice Energy Use: The ENERGY STAR Industrial Energy Performance Indicator
Authors: Boyd Gale A. 
Published: August 2005

SummaryA common feature distinguishing between parametric/statistical models and engineering economics models is that engineering models explicitly represent best practice technologies, whereas parametric/statistical models are typically based on average practice. Measures of energy intensity based on average practice are of little use in corporate management of energy use or for public policy goal setting. In the context of companyor plant‐level indicators, it is more useful to have a measure of energy intensity that is capable of indicating where a company or plant lies within a distribution of performance. In other words, is the performance close to (or far from) the industry best practice? This article presents a parametric/statistical approach that can be used to measure best practice, thereby providing a measure of the difference, or “efficiency gap,” at a plant, company, or overall industry level. The approach requires plant‐level data and applies a stochastic frontier regression analysis used by the ENERGY STARTM industrial energy performance indicator (EPI) to energy intensity. Stochastic frontier regression analysis separates energy intensity into three components: systematic effects, inefficiency, and statistical (random) error. The article outlines the method and gives examples of EPI analysis conducted for two industries, breweries and motor vehicle assembly. In the EPI developed with the stochastic frontier regression for the auto industry, the industry median “efficiency gap” was around 27%.
Pulp Nonfiction: Regionalized Dynamic Model of the U.S. Pulp and Paper Industry
Authors: Davidsdottir Brynhildur , Ruth Matthias 
Published: August 2005

SummaryThis article presents a modeling framework that enhances our ability to analyze the implications of policy for future sustainability of industrial systems. The framework quantifies the relationship between physical input and waste flows, capital vintage, and investment behavior in the U.S. pulp and paper industry. A regional vintage model is developed that simultaneously incorporates investment decisions, vintage structure of the capital stock, and physical material and energy flows, in addition to paper demand. Each capital vintage is specified by size, output structure, and age‐specific retirement rates, as well as fiber use and energy intensities. Both embodied and disembodied technological change are incorporated, as well as greenhouse gas emissions from fuel use, and decomposition and incineration of waste. Estimated equations are used to simulate industrial futures until 2020, from a system of nonlinear differential equations.Our results demonstrate the economic and physical inter‐dependence between material and energy flows and the central role energy prices have in decision‐making. For instance, an increase in average energy prices, ceteris paribus, will on average discourage paper recycling, which has implications for greenhouse gas emissions as well as for changes in energy intensity. The analysis of the data reveals diminishing rates of energy self‐generation, and the immense longevity of capital, which hampers rapid change in input and carbon intensity. This stresses the importance of investment‐led strategies in facilitating faster capital turnover to enhance future sustainability of the system.
Internet‐Based Integrated Environmental Assessment Using Ontologies to Share Computational Models
Authors: Kraines Steven , Batres Rafael , Koyama Michihisa , Wallace David , Komiyama Hiroshi 
Published: August 2005

SummaryNew advances in Internet technologies and computer modeling provide opportunities for collaborative systems to support research and development in the field of industrial ecology. In particular, new information technologies such as semantic search engines based on ontologies could help researchers to link fragments of knowledge generated at research centers from around the world. Using a storyline of four imaginary researchers who hope to find collaborators in order to develop their research findings, we illustrate two levels of a four‐level architecture for an Internet‐based knowledge integration and collaboration environment for integrated environmental assessment. The foundation of the proposed architecture is a belief that computational models are an effective medium for conveying expert knowledge of various phenomena. Drawing from this premise, the first level of the architecture stands on a base of computational models that in some way represent the expert knowledge of the model builder. At the second level, we provide markup and interface definition tools to describe the type of knowledge contained in each model, together with the types of information services that can be provided.The results of research at these two levels of an Internet‐based knowledge integration environment for integrated environmental assessment in industrial ecology are presented in this article. Our work on the third level of model searching and matching and the fourth level of parametric model integration and solving will be presented in subsequent articles.
Mixtures of UK Wheat as an Efficient and Environmentally Friendly Source for Bioethanol
Authors: Swanston J. Stuart , Newton Adrian C. 
Published: August 2005

SummaryConcerns about access to oil supplies have encouraged the exploration of renewable fuel and energy sources. Industrial ecology offers tools to compare the energy implications and benefits of differing strategies, but using botanical sources of raw materials to replace nonrenewable ones also requires appreciation of plant science, especially the variation in genetic potential within species. Whereas cultivation methods determine whether genetic potential is realized, different methods impact the environment to varying degrees. Experience with barley variety mixtures, aimed at reducing chemical input, has shown them to improve yield and reduce disease, while maintaining or even enhancing quality. Yield improvements still occurred in the absence of disease and increased in proportion to the number of component varieties. Because other research showed mixtures to be similarly effective in wheat, a protocol to grow and exploit a complex mixture of soft wheat is proposed, offering a cost‐effective and energy efficient feedstock for a possible bioethanol industry in the United Kingdom. Ethanol would be produced initially from grain, with the straw used for heating or electricity generation. Fertilizer production and use and vehicle fuels have been shown as the main forms of energy consumption in growing a crop, and targets for enhancing the energy balance, by growing mixtures under an integrated farming system, are postulated. A close but negative association between grain protein and alcohol yield is demonstrated and a mixture giving comparable grain yield, but superior alcohol yield, to its best component is identified. Mixing varieties differing in plant morphology may also increase total biomass yield and, therefore, the energy generated from the crop. Pesticide reduction has another positive, though small, effect on the energy balance, from using mixtures. Eliminating prophylactic spraying also reduces vehicle fuel consumption, and may provide the low‐toxicity benefits of organic agriculture without the yield penalty. A range of alternative uses for straw and other by‐products is also discussed.
Novel Isothermal, Linear Nucleic Acid Amplification Systems for Highly Multiplexed Applications
Authors: Kurn Nurith , Chen Pengchin , Heath Joe Don , Kopf-Sill Anne , Stephens Kathryn M , Wang Shenglong 
Published: August 2005

Abstract
Background: Global analysis of the genome, transcriptome, and proteome is facilitated by the recent development of tools for large-scale, highly parallel analysis. We describe a novel nucleic acid amplification system that generates products by several methods. 3′-Ribo-SPIA™ primes cDNA synthesis at the 3′ polyA tail, and whole transcript (WT)-Ribo-SPIA primes cDNA synthesis across the full length of the transcripts and thus provides whole-transcriptome amplification, independent of the 3′ polyA tail.
Methods: We developed isothermal linear nucleic acid amplification systems, which use a single chimeric primer, for amplification of DNA (SPIA) and RNA (Ribo-SPIA). The latter allows mRNA amplification from as little as 1 ng of total RNA. Amplification efficiency was calculated based on the delta threshold cycle between nonamplified cDNA targets and amplified cDNA. The amounts and quality of total RNA and amplification products were determined after purification of the amplification products. GeneChip® array gene expression profiling and real-time PCR were used to test the accuracy and reproducibility of the method. Quantification of cDNA products (before and after amplification) at the 2 loci along the transcripts was used to assess product length (for evaluation of the 3′-initiated Ribo-SPIA) and equal representation throughout the length of the transcript (for evaluation of the whole transcript amplification system, WT-Ribo-SPIA™).
Results: Ribo-SPIA–based global RNA amplification exhibited linearity over 6 orders of magnitude of transcript abundance and generated microgram amounts of amplified cDNA from as little as 1 ng of total RNA.
Conclusions: The described methods enable comprehensive gene expression profiling and analysis from limiting biological samples. The WT-Ribo-SPIA procedure, which enables amplification of non–polyA-tailed RNA, is suitable for amplification and gene expression analysis of both eukaryotic and prokaryotic biological samples.
Sound propagation in the time-domain by the Split-Operator technique
Authors: Bosquetti Diogenes , Sánchez-Dehesa José 
Published: August 2005

Abstract
This work presents a finite-difference scheme to study the scattering of sound in the time-domain. It can be applied to heterogeneous fluids in any dimensionality. The scheme is based on the split-operator technique introduced in quantum mechanics to solve the time-dependent Schrödinger equation. This scheme presents advantages in comparison with the usual finite-difference time-domain algorithms. Its main characteristics are: a) its precision is of the order (Δt)3; b) it can work with non-homogeneous space-discretizations; and c) it satisfies the energy conservation law. Here, the scheme is also applied to solve four simple tests cases in one-dimensional space.
Assessment of Exposures To Pneumoconiosis‐Producing Mineral Dusts
Authors: Ayer Howard E. , Rice Carol H. 
Published: August 2005

AbstractPneumoconiosis is produced by significant long‐term exposure to certain mineral dusts of particle sizes that can penetrate to the gas exchange region of the lungs. Thus, assessment of exposure may include size separation as well as measurement of concentration and composition of the dusts. When the dust is fibrous, as the various forms of asbestos, the assessment is by collection of air samples, light microscopic fiber counts of the samples, and possibly electron microscopic identification of the fiber types. For all other minerals with particles of regular shapes, current methods of assessment use air sampling devices that discriminate against particles too large to penetrate to the sensitive regions of the lung. The dust collected is then identified as the “respirable” fraction, using an international definition of the fraction. Chemical or physical analysis of the samples may then be required.Assessment also includes the length and pattern of exposure. For estimation of pneumoconiosis hazard the cumulative exposure over a period of days, weeks, months and years is considered. Air sampling for hazard estimation is typically done over full working shifts. For design of efficient control measures those tasks or operations that produce the major portions of the exposures must be identified. To accomplish this identification, the minute by minute exposure pattern may be required.The principal pneumoconiosis‐producing dusts as they are now recognized in the United States areThose containing free crystalline silica (quartz or cristobalite).Coal dust (both bituminous and anthracite).Asbestos (chrysotile, amosite, crocidolite, anthophyllite and tremolite).Other minerals may also produce lung fibrosis, but usually only at very much higher concentrations.As with other physical and chemical hazards, it is impossible to predict with certainty the precise hazard to a particular individual. The degree of pneumoconiosis hazard from respirable coal dust depends not only on the cumulative exposure, but in a not well understood manner to the chemical and mineralogical composition of the seam being mined. To these differences in collective hazard is added the differences in individual susceptibility of the people exposed. For this reason, the concentration limits and measurement methods are intended to protect the more susceptible individuals against the agents with greater potential to cause disease. Further changes in the limits and measurement methods may be expected, but if experience is a guide, they will be decade by decade rather than year by year.This chapter describes the methods in use at the beginning of the twenty‐first century, and the development of these methods over a major part of the twentieth century.
Analytical Methods
Authors: Lieckfield Robert G. 
Published: August 2005

Abstract
The laboratory analysis of occupational health samples is an important aspect of determining occupational health exposures. The accurate determination of workplace exposures begins with the selection of an appropriate sampling device and continues through the analysis of the collected samples in the industrial hygiene laboratory. The focus of this chapter is on the methods used in the analysis of industrial hygiene samples.
Industrial hygiene chemistry covers a wide diversity of chemical substances found in modern industry with hundreds more being added yearly. The complexity of this field is compounded by the need to identify and quantify trace quantities of organic and inorganic substances in the presence of numerous potential interferences.

The industrial hygiene analytical laboratory incorporates a substantial number and wide‐array of chemical and instrumental methods. The majority of industrial hygiene analyses are performed using one of the following techniques:

Atomic Absorption Spectrophotometry (AAS)

Electron Microscopy (Transmission and scanning microscopes)

Gas Chromatography (GC)

High‐Pressure Liquid Chromatography (HPLC)

Inductively Coupled Argon Plasma Spectrophotometry (ICAP)

Ion Chromatography (IC)

Optical Microscopy (Phase‐contrast and polarized‐light microscopes)

Ultraviolet/Visible Spectrophotometry

X‐ray Diffraction

Gravimetric

Additional methods used, although not as common, include titration, ion‐selective electrode, inductively coupled argon plasma/mass spectrometry (ICP/MS), and gas chromatography/mass spectrometry (GC/MS). A basic understanding of the analytical methods and techniques is essential to the industrial hygienist, allowing for the proper interpretation of the reported laboratory results.
The technology of laboratory instrumentation evolved through the development of both operating design and microprocessing advancements. These technology gains provided for the commercialization and the significantly lower cost of sophisticated instrumentation to the industrial hygiene community.