bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable isotopes and gut content show diet overlap among native and introduced piscivores in a large oligotrophic lake
Authors: Clarke L. R. , Vidergar D. T. , Bennett D. H.
Published: August 2005

Abstract –  In past dietary studies kokanee Oncorhynchus nerka were prominent in the diet of Pend Oreille Lake's large piscivores: native bull trout Salvelinus confluentus, cutthroat trout O. clarki and northern pikeminnow Ptychocheilus oregonensis, and introduced lake trout S. namaycush and Kamloops rainbow trout O. mykiss gairdneri. However, kokanee have declined to 10–20% of their former abundance. We therefore initiated this study to understand current predation demands on kokanee and diet overlap among piscivores, using gut content samples and analysis of stable nitrogen (δ15N) and carbon (δ13C) isotopes from the lake's fish and invertebrate community. In gut content samples, kokanee were the main prey item of large [i.e., ≥400 mm total length (TL)] bull and lake trout; a conclusion that was affirmed by stable isotope analysis. Rainbow trout >500 mm TL consumed mostly kokanee, thus there was a high degree of diet overlap among large bull, lake and rainbow trout. Small (i.e., <400 mm TL) rainbow and cutthroat trout diets overlapped, and were composed mostly of littoral benthic invertebrates. However, gut content and stable isotope analysis did not accord for 400–500 mm TL rainbow trout, small lake trout, and large cutthroat trout. In these instances, a linear mixing model using stable isotope results predicted kokanee consumption for each species, but no kokanee were identified in rainbow or lake trout gut content. Gut content and stable isotope analysis of native northern pikeminnow indicated a diet of mostly littoral benthic invertebrates at smaller (100–150 mm TL) lengths, with kokanee becoming more prominent in the diet of individuals >300 mm TL. Percent of kokanee in the diet of northern pikeminnow has declined from a prior study; otherwise piscivore diets have apparently remained unchanged. In this study, judgments as to the feeding of some piscvores, based on gut content alone, would be tenuous because of small sample sizes, but stable isotope analysis provided an efficient means for confirming diets.
Clinical pharmacological profile of etoposide in elderly patients with lung cancer
Authors: MIYAZAKI Mitsuru , FUJIWARA Yasushiro , OGURI Tetsuya , TAKAHASHI Toshiaki , OHUNE Terumasa , SUMIYOSHI Hidetaka , KOHNO Nobuoki , EGORIN Merrill J
Published: August 2005

To clarify the clinical pharmacological profile of etoposide in the elderly, we carried out prospective therapeutic drug monitoring in 14 patients with advanced lung cancer aged 75 or more years. The patients received 50 mg etoposide as oral capsules for 21 consecutive days during the first course, and intravenous etoposide for 3 days during the second course of palliative treatment. Plasma and urine samples were collected on days 1 and 21 of the first course and day 1 of the second course, and etoposide concentrations were measured using high‐performance liquid chromatography. We compared these data with those obtained from 17 adult patients under 75 years old who participated in our previous study of combined oral etoposide/carboplatin chemotherapy. Within the elderly group, no significant differences in the area under the concentration‐versus‐time curve, elimination half‐life, plasma clearance, urinary excretion or bioavailability of oral etoposide were observed between day 1 and day 21. However, the mean (±SD) elimination half‐lives for elderly and adult patients were 10.3 ± 1.9 h and 5.8 ± 2.5 h, respectively, while the mean (±SD) bioavailabilities were 62.8 ± 27.5% and 37.4 ± 15.4%; both were significantly increased in the elderly patients. Our previously proposed limited sampling model was validated using the elderly data set and proved to be unbiased and precise. In conclusion, although no accumulation of oral etoposide was observed in elderly patients, there were age‐dependent changes in its pharmacokinetics, especially in bioavailability.
Biochemotherapy for the treatment of metastatic melanoma: the experience of a tertiary oncology center
Authors: JOHN Thomas , CEBON Jonathan S , DAVIS Ian D
Published: August 2005

Background:  Malignant melanoma is generally resistant to cytotoxic chemotherapy. The addition of cytokines such as interleukin‐2 (IL‐2) and Interferon‐α (IFNα) to cytotoxic chemotherapy has been reported to result in significant improvement in response rates and time to treatment progression. There have also been reports of long‐term survival in a subset of patients who achieved a complete remission. While this treatment has promised significant improvement in tumor response, to date this has not translated into an increase in median overall survival in adequately powered randomized phase III studies. The Joint Ludwig Austin Oncology unit operates a clinic for patients with advanced malignant melanoma. On the basis of early encouraging reports, we have treated selected patients, over a 5‐year period, using a combination biochemotherapy regimen. Here, we report our experience with the treatment regimen.

Methods:  Records from patients treated with biochemotherapy were examined for baseline characteristics, prior treatments and sites of disease. Outcomes measured included response, toxicity, hospitalization and survival.

Results:  Between 1999 and 2003, 14 patients were treated at the Austin Hospital. There were four partial responses (PR) and two disease stabilizations lasting 7 months (SD). The overall clinical benefit (PR + SD) was 42.8% (6/14). The regimen was toxic with significant hematological and constitutional toxicity, although no treatment related deaths occurred. Patient survival with Stage 4 disease ranged from 2 to 60 months.

Conclusions:  These results are consistent with published data from other institutions. Because this is palliative treatment, results in significant toxicity and has failed to result in a survival benefit when tested in randomized studies we do not feel that off‐study treatment with this regimen is justified. Further studies are needed into mechanisms of resistance and response prediction to determine whether any subgroups of patients with metastatic melanoma might benefit from this treatment.
The Design of a Mechanical Damage Inspection Tool Using Dual Field Magnetic Flux Leakage Technology
Authors: Nestleroth J. Bruce , Davis Richard J.
Published: August 2005

This paper describes the design of a new magnetic flux leakage (MFL) inspection tool that performs an inline inspection to detect and characterize both metal loss and mechanical damage defects. An inspection tool that couples mechanical damage assessment as part of a routine corrosion inspection is expected to have considerably better prospects for application in the pipeline industry than a tool that complicates existing procedures. The design is based on study results that show it is feasible to detect and assess mechanical damage by applying a low magnetic field level in addition to the high magnetic field employed by most inspection tools. Nearly all commercially available MFL tools use high magnetic fields to detect and size metal loss such as corrosion. A lower field than is commonly applied for detecting metal loss is appropriate for detecting mechanical damage, such as the metallurgical changes caused by impacts from excavation equipment. The lower field is needed to counter the saturation effect of the high magnetic field, which masks and diminishes important components of the signal associated with mechanical damage. Finite element modeling was used in the design effort and the results have shown that a single magnetizer with three poles is the most effective design. Furthermore, it was found that for the three-pole system the high magnetization pole must be in the center, which was an unexpected result. The three-pole design has mechanical advantages, including a magnetic null in the backing bar, which enables installation of a pivot point for articulation of the tool through bends and restrictions. This design was prototyped and tested at Battelle’s Pipeline Simulation Facility (West Jefferson, OH). The signals were nearly identical to results acquired with a single magnetizer reconfigured between tests to attain the appropriate high and low field levels.
A Natural Focusing Low Frequency Guided Wave Experiment for the Detection of Defects Beyond Elbows
Authors: Rose Joseph L. , Zhang Li , Avioli Michael J. , Mudge Peter J.
Published: August 2005

Long range ultrasonic guided wave inspection is advancing rapidly and is quite commonplace today. Benefits of using longitudinal or torsional modes are being established in special circumstances of improved sensitivity, resolution, or penetration power. The possibility of inspection under insulation, coatings, or with water filled pipes or around elbows is possible. Detection of defects beyond a pipe elbow is difficult for axisymmetric wave impingement onto the elbow. For nonaxisymmetric input to the elbow region, however, via partial loading around the circumference, natural focusing occurs because of angular profile variation around the circumference of the pipe. Sample computations of possible angular profiles are illustrated. An experiment is also reported here to demonstrate this inspection process.
A Guided Wave Plate Experiment for a Pipe
Authors: Luo Wei , Zhao Xiaoliang , Rose Joseph L.
Published: August 2005

The plate approximation of a pipe is a topic discussed for decades. Rules have been established to make the comparisons. Presented here is a related topic, but one to answer the question of whether an easy-to-conduct plate experiment can be used to predict what happens in a pipe for ultrasonic guided wave. For longitudinal guided waves in a pipe, the approximation is valid clearly only over a very short distance or inordinate closeness to a defect for wave scattering analysis; but for circumferential guided waves, the validity is unclear and therefore it is worthwhile to study criteria on the approximation and simplification of a pipe experiment as a plate experiment by means of wave mechanics analysis and modeling computation. Circumferential shear horizontal (SH) waves in pipes and SH waves in plates were studied in this paper toward this goal and it was found that the wave frequency and wall thickness to radius ratio were the two key parameters with respect to the similarity. Dispersion curves and wave structures of the SH waves in plates and in pipes were compared to find the origin of the similarity. Experimental simulations and modeling with boundary element methods were also carried out for the reflection and transmission coefficients of the SH waves impinging into a defect, from which some criteria have been established for the plate model approximation. Although a pipe model is more accurate for pipe experiments, a plate model often gives a quick and reasonable solution especially when it is difficult to establish a pipe model.
Estimation of Corrosion Damage in Steel Reinforced Mortar Using Guided Waves
Authors: Reis Henrique , Ervin Benjamin L. , Kuchma Daniel A. , Bernhard Jennifer T.
Published: August 2005

Corrosion of reinforced concrete is a chronic infrastructure problem, particularly in areas with deicing salt and marine exposure. To maintain structural integrity, a testing method is needed to identify areas of corroding reinforcement. For purposes of rehabilitation, the method must also be able to evaluate the degree, rate, and location of damage. Toward the development of a wireless embedded sensor system to monitor and assess corrosion damage in reinforced concrete, reinforced mortar specimens were manufactured with seeded defects to simulate corrosion damage. Taking advantage of waveguide effects of the reinforcing bars, these specimens were then tested using an ultrasonic approach. Using the same ultrasonic approach, specimens without seeded defects were also monitored during accelerated corrosion tests. Both the ultrasonic sending and the receiving transducers were mounted on the steel rebar. Advantage was taken of the lower frequency (<250kHz) fundamental flexural propagation mode because of its relatively large displacements at the interface between the reinforcing steel and the surrounding mortar. Waveform energy (indicative of attenuation) is presented and discussed in terms of corrosion damage. Current results indicate that the loss of bond strength between the reinforcing steel and the surrounding concrete can be detected and evaluated.
Sonic Pressure Vessel Sensor
Authors: Tittmann B. R.
Published: August 2005

A sensor method and apparatus are described for measuring the pressure of a gas within a sealed commercial pressure vessel mounted into an assembly. A sonic transducer is used to apply an oscillating force to the surface of a vessel. The frequency of the sonic wave is swept through a range which caused resonant vibrations of the gas in the vessel. A receiving transducer measures the amplitude of the resultant vibration at the vessel surface and reveals the resonant frequency of the gas at peaks in the amplitude of the sweep. The resonant frequency obtained depends upon the composition of the gas, its pressure and temperature and the shape of the confining vessels. These relationships can be predetermined empirically so that the pressure inside the vessel can be calculated when the composition of the gas, its temperature and shape of the confining vessel are known. The output of the receiver is fed into a computer which is programmed to calculate the pressure based upon these predetermined relationships which are stored in the computer.
Acoustic Microscopy Applied to Ceramic Pressure Vessels and Associated Components
Authors: Miyasaka Chiaki , Tittmann Bernhard R.
Published: August 2005

Alumina ceramic is being used extensively for external pressure vessels in naval applications. The material is also used in valves and other components, where reliability, immunity from corrosion, and high temperatures are required. This report presents a technique for the nondestructive evaluation of alumina ceramic components. The cracks were produced by CO2 laser radiation. Since there is a need for the detection of very fine cracks, scanning acoustic microscopy was found to be superior to optical methods for imaging surface and subsurface cracks. We address the issue of crack initiation with the use of postirradiation analysis. This article reports our results on the evaluation of the surface and interior cracks with optical, scanning laser, scanning electron, and scanning acoustic microscopy. We present images of surface and subsurface microcracks generated at different power levels of a high power CO2 laser system. The spatial variation of the Rayleigh wave velocity is measured by the V(z) curve technique. These preliminary data suggest that, with some improvement, the V(z) technique may detect residual stress with high spatial resolution.
Stress and Temperature Effects on Ultrasonic Properties in Cross-Linked and High Density Polyethylene
Authors: Bray Don E. , Vela John , Al-Zubi Raed S.
Published: August 2005

Cross-linked polyethylene is widely used in the manufacturing of rotationally molded tanks for the agriculture, petroleum, and chemical industries. These tanks are exposed to a number of environmental effects, which can lead to material degradation. Measuring ultrasonic wave speed change in the outer wall of the tank is a method that shows promise for evaluating the ultraviolet (UV) degradation effects. In order to evaluate the UV effects in the field, however, the effect of stress and temperature on the wave speed first must be established. A series of tests was performed to establish the ultrasonic properties in cross-linked as well as linear polyethylene at a range of temperatures from −6°Cto44°C (22°Fto112°F). The change is linear, as expected. For the stress tests, the velocity decreased with tension, also as expected. Tests were performed from approximately 689kPato9.6MPa(100to1400psi). Results from these tests were incorporated into the overall algorithm used for evaluating tank degradation.
Condition Monitoring of a Nuclear Power Plant Check Valve Based on Acoustic Emission and a Neural Network
Authors: Lee Min-Rae , Lee Joon-Hyun , Kim Jung-Teak
Published: August 2005

The analysis of acoustic emission (AE) signals produced during object leakage is promising for condition monitoring of the components. In this study, an advanced condition monitoring technique based on acoustic emission detection and artificial neural networks was applied to a check valve, one of the components being used extensively in a safety system of a nuclear power plant. AE testing for a check valve under controlled flow loop conditions was performed to detect and evaluate disk movement for valve degradation such as wear and leakage due to foreign object interference in a check valve. It is clearly demonstrated that the evaluation of different types of failure modes such as disk wear and check valve leakage were successful by systematically analyzing the characteristics of various AE parameters. It is also shown that the leak size can be determined with an artificial neural network.
Review of Ultrasonic Phased Arrays for Pressure Vessel and Pipeline Weld Inspections
Authors: Moles Michael , Dubé Noël , Labbé Simon , Ginzel Ed
Published: August 2005

Major improvements in weld inspection are obtained using Phased Array technology with capability for beam steering, electronic scanning, focusing, and sweeping the ultrasonic beams. Electronic scanning is much faster than raster scanning, and can optimize angles and focusing to maximize defect detection. Pressure vessel (PV) inspections typically use “top, side, end” or “top, side, TOFD” views, though other imaging is possible. Special inspections can be performed, e.g., for specific defects, or increased coverage. Defects can be sized by pulse-echo as per code, by time-of-flight Diffraction or by back diffraction. New PV inspection codes, particularly ASME Code Case 2235, permit the use of advanced ultrasonic inspection techniques. Pipeline girth weld inspections use a unique inspection approach called “zone discrimination,” and have their own series of codes. While similar equipment is used in pipeline as in PV inspections, the pipeline philosophy is to tailor the inspection to the weld profile and predicted lack of fusion defects. Pipeline displays are specifically designed for near real-time data analysis. Both ASME CC 2235 and the pipeline codes permit the use of Fitness-For-Purpose, which reduces construction costs. Overall, phased array systems meet or exceed all PV and pipeline codes.
Molecular markers for seed colour inBrassica juncea
Authors: Mahmood T , Rahman M H , Stringam G R , Raney J P , Good A G
Published: August 2005

A detailed RFLP map was used to map QTLs associated with seed colour in Brassica juncea using a doubled-haploid population derived from a cross between a black/brown-seeded cultivar and a yellow-seeded breeding line. Segregation analysis suggested that seed colour was under control of 2 unlinked loci with duplicate gene action. However, QTL analysis revealed 3 QTLs, SC-B4, SC-A10 and SC-A6, affecting seed colour. The QTLs were consistent across environments, and individually explained 43%, 31%, and 16%, respectively, and collectively 62% of the phenotypic variation in the population. Digenic interaction analysis showed that closest flanking locus of QTL SC-B4, wg7b6cNM, had strong epistasis with the locus wg5a1a, which is tightly linked to QTL SC-A6. The interaction of these 2 loci explained 27% of the phenotypic variation in the population, while the whole model explained 84%. In a multiple regression model, the effects of QTL SC-A10, as well as its interaction with other loci, were non-significant, whereas the effects of loci wg7b6cNM and wg5a1a and their interaction were significant. Ninety-eight percent of the DH lines carried the expected alleles of loci wg7b6cNM and wg5a1a for seed colour, confirming that only these 2 loci were linked to seed colour in B. juncea. Four additional digenic interactions significantly affected seed colour, and all 5 digenic interactions were consistent across environments.Key words: epistasis, Brassica juncea, seed colour, quantitative trait loci, molecular mapping.
Tarsus determination inDrosophila melanogaster
Authors: Percival-Smith Anthony , Teft Wendy A , Barta Jodi Lynn
Published: August 2005

Arista versus tarsus determination is well investigated in Drosophila, yet it remains unresolved whether Antennapedia (ANTP) cell autonomously or noncell autonomously determines tarsus identity and whether Sex combs reduced (SCR) is the HOX protein required for normal tarsus determination. Three observations rule out a cell autonomous role for ANTP in tarsus determination. (i) Clonal ectopic overexpression of ANTP did not repress the expression of the arista determining protein Homothorax (HTH) in early 3rd stadium antennal imaginal discs. (ii) Clonal ectopic expression of ANTP did not transform the arista to a tarsus. (iii) Ectopic overexpression of ANTP, Labial (LAB), Deformed (DFD), SCR, Ultrabithorax (UBX), Abdominal-A (ABD-A), or Abdominal-B (ABD-B), using the dppGAL4 driver, resulted in arista-to-tarsus transformations, and repressed HTH/Extradenticle (EXD) activity noncell autonomously in early 3rd stadium antennal imaginal discs. SCR may not be the HOX protein required for normal tarsus determination, because co-ectopic expression of Proboscipedia (PB) inhibited the arista-to-tarsus transformations induced by ectopic expression of DFD, SCR, ANTP, UBX, ABD-A, and ABD-B. The proposal that SCR is the HOX protein required for normal tarsus determination is dependent on SCR being the sole target of PB suppression, which is not the case. Therefore, the possibility exists that normal tarsus determination is HOX independent.Key words: appendage development, Antennapedia, proboscipedia, sex combs reduced, homothorax.
Evidence of diversity within theSnRK1bgene family ofHordeumspecies
Authors: Clark Jeremy S.C , Dani Maria , Halford Nigel G , Karp Angela
Published: August 2005

Adaptor-specific polymerase chain reaction (PCR) was used to amplify 3 different products, termed variant A, B, and C, from the seed-specific class (SnRK1b) of the sucrose nonfermenting-1-related protein kinase gene family (SnRK1) of different Hordeum species and cultivars of barley (Hordeum vulgare). Standard PCR or reverse transcription-PCR (RT-PCR) at a high temperature, using primers that differed by 1 or 2 nucleotides, was then used to amplify and clone 3 specific variants. One primer pair amplified a variant from I genome species suggesting that this could be a useful I-genome specific marker. The corresponding genes of the 3 variants (A, B, and C) were termed SnRK1b.1, 2, and 3, respectively. SnRK1b.1 and 2, showed 98% – 100% nucleotide sequence identity in the coding region, and 89% – 90% identity in the promoter region (up to 200 bp upstream of the translation start site, ATG). However, they differed in having insertions, deletions, and base pair changes at potentially important sites in the polymerase binding regions. SnRK1b.3 showed 90% nucleotide sequence identity with SnRK1b.1 in the coding region and 86% in the promoter region. This gene predominates in H-genome species within the genus Hordeum and could be a useful marker for this group.Key words: Hordeum, sucrose nonfermenting-1, SNF1-related protein kinase, genetic diversity, metabolic signalling.
A novel approach for assessing the interaction of masonry walls under vertical loads
Authors: Corrêa Márcio R.S , Page Adrian W
Published: August 2005

This paper investigates the behaviour of masonry load-bearing walls subjected to differential vertical load. A new approach for evaluating the interaction of intersecting walls is used, focusing on the mechanism of load transfer and the resulting shear stresses. The study is carried out using finite element modelling. Previous full-scale tests are used to verify the features of the numerical model. Once confirmed, the model is then used to study the phenomenon, varying parameters such as the number of floors and the dimensions of the walls. It is shown that the distance down the wall at which homogenization of the applied loads occurs can be predicted by application of the Saint Venant's Principle. The distribution of shear stresses along the interface can be simulated by a simple parabolic distribution. A simple design procedure is proposed, allowing more realistic, cost-effective designs of load-bearing masonry structures.Key words: masonry, walls, vertical loads, finite elements, interaction of walls.
Establishing design guidelines for compound horizontal curves on three-dimensional alignments
Authors: Easa Said , Dabbour Essam
Published: August 2005

In current design guides, the minimum radii of compound horizontal curves are based on the design requirements of simple horizontal curves for each arc on flat terrain. Such a design ignores the effects of compound curvature and vertical alignment. This paper uses computer simulation software to establish the minimum radius requirements for compound curves, considering these effects. The actual lateral acceleration experienced by a vehicle negotiating a two-dimensional (2-D) simple curve is recorded as a base scenario to facilitate the analysis of a compound curve on a flat terrain or combined with vertical alignment (three-dimensional (3-D) compound curves). The vertical alignments examined include upgrades, downgrades, crest curves, and sag curves. Mathematical models for minimum radius requirements were developed for flat and 3-D compound curves. Three types of design vehicles were used. The results show that an increase in the minimum radius ranging from 5% to 26% is required to compensate for the effects of both compound curvature and vertical alignment.Key words: highway geometric design, compound horizontal alignments, side friction, vehicle simulation, 3-D alignments.
A structured model for evaluating countermeasures at highwayrailway grade crossings
Authors: Park Young-Jin , Saccomanno Frank F
Published: August 2005

Various countermeasures can be introduced to reduce collisions at highwayrailway grade crossings. These countermeasures may take different forms, such as passive and (or) active driver warning devices, supplementary traffic controls (four quadrant barriers, wayside horn, closed circuit television (CCTV) monitoring, etc.), illumination, signage and highway speed limit, etc. In this research, we present a structured model that makes use of data mining techniques to estimate the effect of changes in countermeasures on the expected number of collisions at a given crossing. This model serves as a decision-support tool for the evaluation and development of cost-effective and practicable safety program at highwayrailway grade crossings. The use of data mining techniques helps to resolve many of the problems associated with conventional statistical models used to predict the expected number of collisions for a given type of crossing. Statistical models introduce biases that limit their ability to fully represent the relationship between selected countermeasures and resultant collisions for a mix of crossing attributes. This paper makes use of Canadian inventory and collision data to illustrate the potential merits of the proposed model to provide decision support.Key words: highwayrailway grade crossing, collision prediction model, countermeasures, Poisson regression.
Field measurements of ice-jam-release surges
Authors: Beltaos Spyros , Burrell Brian C
Published: August 2005

Surges are the most violent and spectacular events that occur during the ice breakup. Upon the release of an ice jam, water and ice held by the jam are suddenly free to move. The resulting surge generates increased water stages and higher flow velocities, such that the water wave and ice run pose a risk to downstream structures, people, and aquatic life. Climate-induced changes to river ice processes, such as enhanced mid-winter jamming or increased spring flows, could result in more frequent occurrence of major and damaging surges. To address a dearth of related quantitative data, a remote water-level reporting method has been developed and used to obtain field measurements on ice-jam generated surges. The results are consistent with the few available data but only partly conform to existing theories.Key words: breakup, celerity, ice jam, release, river, surge, wave.
Stochastic control for risk under deregulated electricity market — a case study using a new formulation
Authors: Zhang Joyce Li , Ponnambalam K
Published: August 2005

This paper describes the implementation of a new solution approach — Fletcher-Ponnambalam model (FP) — for risk management in hydropower system under deregulated electricity market. The FP model is an explicit method developed for the first and second moments of the storage state distributions in terms of moments of the inflow distributions. This method provides statistical information on the nature of random behaviour of the system state variables without any discretization and hence suitable for multi-reservoir problems. Also avoiding a scenario-based optimization makes it computationally inexpensive, as there is little growth to the size of the original problem. In this paper, the price uncertainty was introduced into the FP model in addition to the inflow uncertainty. Lake Nipigon reservoir system is chosen as the case study and FP results are compared with the stochastic dual dynamic programming (SDDP). Our studies indicate that the method could achieve optimum operations, considering risk minimization as one of the objectives in optimization.Key words: reservoir operations, explicit method, uncertainty, stochastic programming, risk.
Nuclear receptor coactivators: the key to unlock chromatin
Authors: Xu Wei
Published: August 2005

The biological effects of hormones, ranging from organogenesis, metabolism, and proliferation, are transduced through nuclear receptors (NRs). Over the last decade, NRs have been used as a model to study transcriptional control. The conformation of activated NRs is favorable for the recruitment of coactivators, which promote transcriptional activation by directly communicating with chromatin. This review will focus on the function of different classes of coactivators and associated complexes, and on progress in our understanding of gene activation by NRs through chromatin remodeling.Key words: nuclear hormone receptor, p160 family of coactivators, histone modification, chromatin remodeling complex.
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases
Authors: Burton Zachary F , Feig Michael , Gong Xue Q , Zhang Chunfen , Nedialkov Yuri A , Xiong Yalin
Published: August 2005

Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMPNTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle to substrate loading and translocation for the next. We present a detailed model of the RNA polymerase II elongation complex based on 2 low-affinity NTP binding sites located in the main-enzyme channel. This model posits that NTP substrates, elongation factors, and the conserved Rpb2 subunit fork loop 2 cooperate to regulate opening of the downstream transcription bubble.Key words: RNA polymerase, NTP-driven translocation, transcriptional fidelity, transcriptional efficiency, α-amanitin.
Chromatin potentiation of the hsp70 promoter is linked to GAGA-factor recruitment
Authors: Georgel Philippe T
Published: August 2005

The events leading to transcription initiation of the Drosophila melanogaster heat-shock protein (hsp)70 gene have been demonstrated to be directly connected with nucleosome remodeling factor and GAGA-dependent chromatin remodeling on its promoter region. To investigate the relative importance of the multiple GAGA-factor binding sites in the process of chromatin remodeling and their effect on DNA conformation, the position of nucleosomes over the proximal region of the promoter was mapped. No real-positioned nucleosome was detected. By matching the relative position of the GAGA-factor binding sites with the distribution of nucleosomes over the hsp70 promoter, the GAGA site 2 appeared to be the most accessible, i.e., located close to a nucleosomal edge or within the linker DNA. This result, combined with previous observations, suggest a link between increased GAGA-factor accessibility and efficiency of transcription initiation. The effect of GAGA-binding-site mutations, both individually and in combination, on DNA structure and nucleosome remodeling was assessed using free DNA and fly embryo extract chromatin templates assembled in vitro. Results indicated that both the number of functional sites and their positions within the chromatin were important determinants for nucleosome-remodeling efficiency. Ultimately, the degree of accessibility of the GAGA factor to its cognate binding site(s) appears to be proportional to chromatin-remodeling competency of the hsp70 promoter.Key words: chromatin, remodeling, nucleosome, hsp70, GAGA, Drosophila.
Functional dissection of the catalytic mechanism of mammalian RNA polymerase II
Authors: Coulombe Benoit , Langelier Marie-France
Published: August 2005

High resolution X-ray crystal structures of multisubunit RNA polymerases (RNAP) have contributed to our understanding of transcriptional mechanisms. They also provided a powerful guide for the design of experiments aimed at further characterizing the molecular stages of the transcription reaction. Our laboratory used tandem-affinity peptide purification in native conditions to isolate human RNAP II variants that had site-specific mutations in structural elements located strategically within the enzyme's catalytic center. Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme.Key words: RNA polymerase II, transcriptional mechanisms, mutational analysis, mRNA synthesis.
H2AX: tailoring histone H2A for chromatin-dependent genomic integrity
Authors: Li Andra , Eirín-López José M , Ausió Juan
Published: August 2005

During the last decade, chromatin research has been focusing on the role of histone variability as a modulator of chromatin structure and function. Histone variability can be the result of either post-translational modifications or intrinsic variation at the primary structure level: histone variants. In this review, we center our attention on one of the most extensively characterized of such histone variants in recent years, histone H2AX. The molecular phylogeny of this variant seems to have run in parallel with that of the major canonical somatic H2A1 in eukaryotes. Functionally, H2AX appears to be mainly associated with maintaining the genome integrity by participating in the repair of the double-stranded DNA breaks exogenously introduced by environmental damage (ionizing radiation, chemicals) or in the process of homologous recombination during meiosis. At the structural level, these processes involve the phosphorylation of serine at the SQE motif, which is present at the very end of the C-terminal domain of H2AX, and possibly other PTMs, some of which have recently started to be defined. We discuss a model to account for how these H2AX PTMs in conjunction with chromatin remodeling complexes (such as INO80 and SWRI) can modify chromatin structure (remodeling) to support the DNA unraveling ultimately required for DNA repair.Key words: H2AX, DNA repair, double-stranded DNA breaks, phosphorylation.
Psoralen photocrosslinking, a tool to study the chromatin structure of RNA polymerase I - transcribed ribosomal genes
Authors: Toussaint Martin , Levasseur Geneviève , Tremblay Maxime , Paquette Michel , Conconi Antonio
Published: August 2005

The chromatin structure of RNA polymerase I - transcribed ribosomal DNA (rDNA) is well characterized. In most organisms, i.e., lower eukaryotes, plants, and animals, only a fraction of ribosomal genes are transcriptionally active. At the chromatin level inactive rDNA is assembled into arrays of nucleosomes, whereas transcriptionally active rDNA does not contain canonical nucleosomes. To separate inactive (nucleosomal) and active (non-nucleosomal) rDNA, the technique of psoralen photocrosslinking has been used successfully both in vitro and in vivo. In Saccharomyces cerevisiae, the structure of rDNA chromatin has been particularly well studied during transcription and during DNA replication. Thus, the yeast rDNA locus has become a good model system to study the interplay of all nuclear DNA processes and chromatin. In this review we focused on the studies of chromatin in ribosomal genes and how these results have helped to address the fundamental question: What is the structure of chromatin in the coding regions of genes?Key words: active chromatin, FACT, lexosome, psoralen, photo-crosslinking, rDNA, RNA polymerase I.
BRANEWORLD BLACK HOLES IN COSMOLOGY AND ASTROPHYSICS
Authors: MAJUMDAR A. S. , MUKHERJEE N.
Published: August 2005

The braneworld description of our universe entails a large extra dimension and a fundamental scale of gravity that might be lower by several orders of magnitude compared to the Planck scale. An interesting consequence of the braneworld scenario is in the nature of spherically symmetric vacuum solutions to the brane gravitational field equations which could represent black holes with properties quite distinct compared to ordinary black holes in 4-dimensions. We discuss certain key features of some braneworld black hole geometries. Such black holes are likely to have diverse cosmological and astrophysical ramifications. The cosmological evolution of primordial braneworld black holes is described highlighting their longevity due to modified evaporation and effective accretion of radiation during the early braneworld high energy era. Observational abundance of various evaporation products of the black holes at different eras impose constraints on their initial mass fraction. Surviving primordial black holes could be candidates of dark matter present in galactic haloes. We discuss gravitational lensing by braneworld black holes. Observables related to the relativistic images of strong field gravitational lensing could in principle be used to distinguish between different braneworld black hole metrics in future observations.
Modulation of intracellular Ca2+ release and capacitative Ca2+ entry by CaMKII inhibitors in bovine vascular endothelial cells
Authors: Aromolaran Ademuyiwa A. S. , Blatter Lothar A.
Published: August 2005

The effects of inhibitors of CaMKII on intracellular Ca2+ signaling were examined in single calf pulmonary artery endothelial (CPAE) cells using indo-1 microfluorometry to measure cytoplasmic Ca2+ concentration ([Ca2+]i). The three CaMKII inhibitors, KN-93, KN-62, and autocamtide-2-related inhibitory peptide (AIP), all reduced the plateau phase of the [Ca2+]i transient evoked by stimulation with extracellular ATP. Exposure to KN-93 or AIP alone in the presence of 2 mM extracellular Ca2+ resulted in a dose-dependent increase of [Ca2+]i consisting of a rapid and transient Ca2+ spike followed by a small sustained plateau phase of elevated [Ca2+]i. Exposure to KN-93 in the absence of extracellular Ca2+ caused a transient rise of [Ca2+]i, suggesting that exposure to CaMKII inhibitors directly triggered release of Ca2+ from intracellular endoplasmic reticulum (ER) Ca2+ stores. Repetitive stimulation with KN-93 and ATP, respectively, revealed that both components released Ca2+ largely from the same store. Pretreatment of CPAE cells with the membrane-permeable inositol 1,4,5-trisphosphate (IP3) receptor blocker 2-aminoethoxydiphenyl borate caused a significant inhibition of the KN-93-induced Ca2+ response, suggesting that exposure to KN-93 affects Ca2+ release from an IP3-sensitive store. Depletion of Ca2+ stores by exposure to ATP or to the ER Ca2+ pump inhibitor thapsigargin triggered robust capacitative Ca2+ entry (CCE) signals in CPAE cells that could be blocked effectively with KN-93. The data suggest that in CPAE cells, CaMKII modulates Ca2+ handling at different levels. The use of CaMKII inhibitors revealed that in CPAE cells, the most profound effects of CaMKII are inhibition of release of Ca2+ from intracellular stores and activation of CCE.
Differential Processing of Noxious Colonic Input by Thoracolumbar and Lumbosacral Dorsal Horn Neurons in the Rat
Authors: Wang Gexin , Tang Bin , Traub Richard J.
Published: August 2005

Previous studies suggest the lumbosacral (LS) spinal cord processes acute colorectal stimuli whereas the thoracolumbar (TL) and LS spinal segments process inflammatory stimuli. In this study, the effects of colorectal distention (CRD) on TL and LS dorsal horn neuronal activity were recorded in Nembutal-anesthetized male rats both with and without colonic inflammation. Both single cells (before and after inflammation) and populations (multiple cells from noninflamed or inflamed rats) were studied. CRD-responsive neurons had excitatory Abrupt (on–off with stimulus) or Sustained (prolonged after discharge) responses or were Inhibited by CRD. In noninflamed rats, a significantly greater percentage of LS neurons (63% Abrupt, 27% Sustained) were excited by CRD than TL neurons (61% Abrupt, 3% Sustained). The remaining cells were Inhibited (10% LS, 36% TL). LS Abrupt neurons had lower thresholds and greater response magnitudes to CRD compared with TL Abrupt neurons. After colonic inflammation, TL neurons became more excitable: the percentage of Inhibited neurons decreased, the response magnitude of Abrupt neurons increased, and the threshold decreased. In contrast, in single-cell recordings, the response of LS Sustained neurons increased, whereas LS Abrupt neurons decreased. These data suggest that in noninflamed rats, the net response to CRD of TL visceroceptive spinal sensory neurons is less than that of LS neurons. Colonic inflammation increases the net response of TL neurons and differentially modulates the response of LS neurons. These differences may contribute to the functional dichotomy between the TL and LS spinal segments in processing acute and inflammatory colorectal pain.
High Gamma Activity in Response to Deviant Auditory Stimuli Recorded Directly From Human Cortex
Authors: Edwards Erik , Soltani Maryam , Deouell Leon Y. , Berger Mitchel S. , Knight Robert T.
Published: August 2005

We recorded electrophysiological responses from the left frontal and temporal cortex of awake neurosurgical patients to both repetitive background and rare deviant auditory stimuli. Prominent sensory event-related potentials (ERPs) were recorded from auditory association cortex of the temporal lobe and adjacent regions surrounding the posterior Sylvian fissure. Deviant stimuli generated an additional longer latency mismatch response, maximal at more anterior temporal lobe sites. We found low gamma (30–60 Hz) in auditory association cortex, and we also show the existence of high-frequency oscillations above the traditional gamma range (high gamma, 60–250 Hz). Sensory and mismatch potentials were not reliably observed at frontal recording sites. We suggest that the high gamma oscillations are sensory-induced neocortical ripples, similar in physiological origin to the well-studied ripples of the hippocampus.
Responses of Ventral Cochlear Nucleus Neurons to Contralateral Sound After Conductive Hearing Loss
Authors: Sumner Christian J. , Tucci Debara L. , Shore Susan E.
Published: August 2005

Conductive hearing loss (CHL) is an attenuation of signals stimulating the cochlea, without damage to the auditory end organ. It can cause central auditory processing deficits that outlast the CHL itself. Measures of oxidative metabolism show a decrease in activity of nuclei receiving input originating at the affected ear but, surprisingly, an increase in the activity of second-order neurons of the opposite ear. In normal hearing animals, contralateral sound produces an inhibitory response to broadband noise in approximately one third of ventral cochlear nucleus (VCN) neurons. Excitatory responses also occur but are very rare. We looked for changes in the binaural properties of neurons in the VCN of guinea pigs at intervals immediately, 1 day, 1 wk, and 2 wk after the induction of a unilateral CHL by ossicular disruption. CHL was always induced in the ear ipsilateral to the VCN from which recordings were made. The main observations were as follows: 1) ipsilateral excitatory thresholds were raised by at least 40 dB; 2) contralateral inhibitory responses showed a small but statistically significant immediate decrease followed by an increase, returning to normal by 14 days; and 3) there was a large increase in the proportion of units with excitatory responses to contralateral BBN. The increase was immediate and lasting. The latencies of the excitatory responses were at least 6 ms, consistent with activation by a path involving several synapses and inconsistent with cross talk. The latencies and rate-level functions of contralateral excitation were similar to those seen occasionally in normal hearing animals, suggesting an upregulation of an existing pathway. In conclusion, contralateral excitatory inputs to the VCN exist, which are not normally effective, and can compensate rapidly for large changes in afferent input.
Optical Recording of Fast Neuronal Membrane Potential Transients in Acute Mammalian Brain Slices by Second-Harmonic Generation Microscopy
Authors: Dombeck Daniel A. , Sacconi Leonardo , Blanchard-Desce Mireille , Webb Watt W.
Published: August 2005

Although nonlinear microscopy and fast (∼1 ms) membrane potential ( Vm) recording have proven valuable for neuroscience applications, their potentially powerful combination has not yet been shown for studies of Vmactivity deep in intact tissue. We show that laser illumination of neurons in acute rat brain slices intracellularly filled with FM4-64 dye generates an intense second-harmonic generation (SHG) signal from somatic and dendritic plasma membranes with high contrast >125 μm below the slice surface. The SHG signal provides a linear response to Δ Vmof ∼7.5%/100 mV. By averaging repeated line scans (∼50), we show the ability to record action potentials (APs) optically with a signal-to-noise ratio (S/N) of ∼7–8. We also show recording of fast Vmsteps from the dendritic arbor at depths inaccessible with previous methods. The high membrane contrast and linear response of SHG to Δ Vmprovides the advantage that signal changes are not degraded by background and can be directly quantified in terms of Δ Vm. Experimental comparison of SHG and two-photon fluorescence Vmrecording with the best known probes for each showed that the SHG technique is superior for Vmrecording in brain slice applications, with FM4-64 as the best tested SHG Vmprobe.