bluuebunny/crossref_metadata_2025 huggingface dataset:
Cogeneration System Simulation and Control to Meet Simultaneous Power, Heating, and Cooling Demands
Authors: Sancho-Bastos Francisco , Perez-Blanco Horacio
Published: April 2005

Gas turbines are projected to meet increasing power demand throughout the world. Cogeneration plants hold the promise of increased efficiency at acceptable cost. In a general case, a cogen plant could be able to meet power, heating and cooling demands. Yet those demands are normally uncoupled. Control and storage strategies need to be explored to ensure that each independent demand will be met continuously. A dynamic model of a mid-capacity system is developed, including gas and steam turbines, two heat recovery steam generators (HRSG) and an absorption-cooling machine. Controllers are designed using linear quadratic regulators (LQR) to control two turbines and a HRSG with some novelty. It is found that the power required could be generated exclusively with exhaust gases, without a duct burner in the high-pressure HRSG. The strategy calls for fuel and steam flow rate modulation for each turbine. The stability of the controlled system and its performance are studied and simulations for different demand cases are performed.
Detailed Investigation of Heat Flux Measurements Made in a Standard Propane-Air Fire-Certification Burner Compared to Levels Derived From a Low-Temperature Analog Burner
Authors: Abu Talib Abd. Rahim , Neely Andrew J. , Ireland Peter T. , Mullender Andrew J.
Published: April 2005

This paper presents detailed heat flux measurements on a flat plate subjected to the ISO2685 [The International Organization for Standardization (ISO), 1992, “Aircraft—Environmental Conditions and Test Procedures for Airborne Equipment—Resistance to Fire in Designated Fire Zones,” ISO2685:1992(E)] standard, propane fueled burner used throughout the industry in aero-engine fire-certification. The authors have developed a custom-built heat transfer gauge to measure the heat flux from the burner under isothermal wall conditions. The heat flux from the standard burner is normally calibrated using either a water-cooled copper tube or a Gardon gauge, each sited at a single position in the flame. There are no reports in the literature of a detailed survey of heat flux distribution for the burner and the results are of considerable interest to engineers involved in fire-certification. The reported measurements constitute the first, detailed distribution of heat flux from the actual burner flame during a fire test. These measurements provided benchmark data which allowed the heat flux distribution from the ISO burner to be compared to levels derived from the low-temperature analog burner developed by the authors. The analog burner uses liquid crystals to measure heat transfer coefficient and adiabatic wall temperature on scale models of engine components and provides key data to facilitate the successful design of components used in fire zones. The objective of this paper is to further validate the low-temperature analog burner technique developed by the authors which simulates the standard large propane-air burner for fire-certification in aero engine.
Flow and Thermal Field Measurements in a Combustor Simulator Relevant to a Gas Turbine Aeroengine
Authors: Vakil S. S. , Thole K. A.
Published: April 2005

The current demands for high performance gas turbine engines can be reached by raising combustion temperatures to increase power output. Predicting the performance of a combustor is quite challenging, particularly the turbulence levels that are generated as a result of injection from high momentum dilution jets. Prior to predicting reactions in a combustor, it is imperative that these turbulence levels can be accurately predicted. The measurements presented in this paper are of flow and thermal fields produced in a large-scale combustor simulator, which is representative of an aeroengine. Three-component laser Doppler velocimeter measurements were made to quantify the velocity field while a rake of thermocouples was used to quantify the thermal field. The results indicate large penetration depths for the high momentum dilution jets, which result in a highly turbulent flow field. As these dilution jets interact with the mainstream flow, kidney-shaped thermal fields result due to counter-rotating vortices that develop.
Parametric Study on Economic Feasibility of Microturbine Cogeneration Systems by an Optimization Approach
Authors: Gamou Satoshi , Yokoyama Ryohei , Ito Koichi
Published: April 2005

Economic feasibility of microturbine cogeneration systems is investigated by analyzing relationships between the optimal number of microturbine units and the maximum energy demands under various conditions. For this purpose, a method to obtain the maximum energy demand at which the optimal number changes is proposed by combining a nonlinear equation problem and an optimal unit sizing problem hierarchically. Based on the proposed method, a map expressing the aforementioned relationships can be illustrated. Through numerical studies carried out on systems installed in hotels by changing the electrical generating efficiency and the capital unit cost of the microturbine cogeneration unit as parameters, the influence of the parameters on the economic feasibility of the microturbine cogeneration system is clarified.
Dr. Max Bentele—Pioneer of the Jet Age
Authors: Meher-Homji Cyrus B. , Prisell Erik
Published: April 2005

This paper documents the pioneering work of Dr. Max Bentele during his long and distinguished career in Germany, the UK, and the United States. His early work on turbojets at the Heinkel-Hirth Corporation in conjunction with his life-long friend, Dr. Hans von Ohain, culminated in the development of the advanced HeS 011 turbojet. Dr. Bentele’s pioneering work in the area of blade vibration is documented along with details of his spectacular solution of the turbine blade vibration problem of the Junkers 004B engine which propelled the world’s first operational jet fighter—the Me-262. Also covered are his pioneering contributions to turbine blade cooling and blade manufacturing and his important work at Curtiss—Wright and Avco Lycoming prior to his retirement.
Application of CFD Analysis for Rotating Machinery—Part I: Hydrodynamic, Hydrostatic Bearings and Squeeze Film Damper
Authors: Guo Zenglin , Hirano Toshio , Kirk R. Gordon
Published: April 2005

The traditional method for bearing and damper analysis usually involves a development of rather complicated numerical calculation programs that may just focus on a simplified and specific physical model. The application of the general CFD codes may make this analysis available and effective where complex flow geometries are involved or when more detailed solutions are needed. In this study, CFX-TASCflow is employed to simulate various fixed geometry fluid-film bearing and damper designs. Some of the capabilities in CFX-TASCflow are applied to simulate the pressure field and calculate the static and dynamic characteristics of hydrodynamic, hydrostatic, and hybrid bearings as well as squeeze film dampers. The comparison between the CFD analysis and current computer programs used in industry has been made. The results show reasonable agreement in general. Some of the possible reasons for the differences are discussed. It leaves room for further investigation and improvement on the methods of computation.
Transient Analysis of and Control System for Advanced Cycles Based on Micro Gas Turbine Technology
Authors: Traverso Alberto , Calzolari Federico , Massardo Aristide
Published: April 2005

Microturbines have a less complex mechanical design than large-size gas turbines that should make it possible to fit them with a more straightforward control system. However, these systems have very low shaft mechanical inertia and a fast response to external disturbances, such as load trip, that make this very difficult to do. Furthermore, the presence of the recuperator requires smooth variations to the Turbine Outlet Temperature (TOT), when possible, to ensure reduced thermal stresses to the metallic matrix. This paper, after a brief overview of microturbine control systems and typical transients, presents the expected transient behavior of two advanced cycles: the Externally Fired micro Gas Turbine (EFmGT) cycle, where the aim is to develop a proper control system set-up to manage safe part-load operations at constant rotational speed, and a solar Closed Brayton Cycle (CBC), whose control system has to ensure the maximum efficiency at constant rotational speed and constant Turbine Inlet Temperature (TIT).
Surface-Stabilized Fuel Injectors With Sub-Three PPM NOx Emissions for a 5.5 MW Gas Turbine Engine
Authors: Greenberg Steven J. , McDougald Neil K. , Weakley Christopher K. , Kendall Robert M. , Arellano Leonel O.
Published: April 2005

ALZETA Corporation has developed surface-stabilized fuel injectors for use with lean premixed combustors which provide extended turndown and ultralow NOx emission performance. These injectors use a patented technique to form interacting radiant and blue-flame zones immediately above a selectively perforated porous metal surface. This allows stable operation at low reaction temperatures. A previous ASME paper (IJPGC2002-26088) described the development of this technology from the proof-of-concept stage to prototype testing. In 2002 development of these fuel injectors for the 5.5 MW turbine accelerated. Additional single-injector rig tests were performed which also demonstrated ultralow emissions of NOx and CO at pressures up to 1.68 MPa (16.6 atm) and inlet temperatures up to 670°K (750°F). A pressurized multi-injector “sector rig” test was conducted in which two injectors were operated simultaneously in the same geometric configuration as that expected in the engine combustor liner. The multi-injector package was operated with various combinations of fired and unfired injectors, which resulted in low emissions performance and no adverse affects due to injector proximity. To date sub-3 ppm NOx emissions with sub-10 ppm CO emissions have been obtained over an operating range of 0.18–1.68 MPa (1.8–16.6 atm), inlet temperatures from 340 to 670K (186–750°F), and adiabatic flame temperatures from 1740 to 1840K (2670–2850°F). A full scale multi-injector engine simulation is scheduled for the beginning of 2003, with engine tests beginning later that year.
Economic and Performance Evaluation of Heat Sink Options in Combined Cycle Applications
Authors: Tawney Rattan , Khan Zahid , Zachary Justin
Published: April 2005

This paper is a guideline to selecting the most appropriate technology for the power plant heat sink based on water availability, site location, and wastewater disposal requirements. The paper discusses wet as well as dry cooling systems and evaluates the impact of the heat sink technology on the performance and cost of combined cycle power plants. Cogeneration applications and cycling plant operations are also considered. For each proposed option, the performance, relative costs, and noise issues will be presented.
Application of “H Gas Turbine” Design Technology to Increase Thermal Efficiency and Output Capability of the Mitsubishi M701G2 Gas Turbine
Authors: Fukuizumi Y. , Masada J. , Kallianpur V. , Iwasaki Y.
Published: April 2005

Mitsubishi completed design development and verification load testing of a steam-cooled M501H gas turbine at a combined cycle power plant at Takasago, Japan in 2001. Several advanced technologies were specifically developed in addition to the steam-cooled components consisting of the combustor, turbine blades, vanes, and the rotor. Some of the other key technologies consisted of an advanced compressor with a pressure ratio of 25:1, active clearance control, and advanced seal technology. Prior to the M501H, Mitsubishi introduced cooling-steam in “G series” gas turbines in 1997 to cool combustor liners. Recently, some of the advanced design technologies from the M501H gas turbine were applied to the G series gas turbine resulting in significant improvement in output and thermal efficiency. A noteworthy aspect of the technology transfer is that the upgraded G series M701G2 gas turbine has an almost equivalent output and thermal efficiency as H class gas turbines while continuing to rely on conventional air cooling of turbine blades and vanes, and time-proven materials from industrial gas turbine experience. In this paper we describe the key design features of the M701G2 gas turbine that make this possible such as the advanced 21:1 compressor with 14 stages, an advanced premix DLN combustor, etc., as well as shop load test results that were completed in 2002 at Mitsubishi’s in-house facility.
Endosomal Proteolysis of the Ebola Virus Glycoprotein Is Necessary for Infection
Authors: Chandran Kartik , Sullivan Nancy J. , Felbor Ute , Whelan Sean P. , Cunningham James M.
Published: April 2005

Ebola virus (EboV) causes rapidly fatal hemorrhagic fever in humans and there is currently no effective treatment. We found that the infection of African green monkey kidney (Vero) cells by vesicular stomatitis viruses bearing the EboV glycoprotein (GP) requires the activity of endosomal cysteine proteases. Using selective protease inhibitors and protease-deficient cell lines, we identified an essential role for cathepsin B (CatB) and an accessory role for cathepsin L (CatL) in EboV GP-dependent entry. Biochemical studies demonstrate that CatB and CatL mediate entry by carrying out proteolysis of the EboV GP subunit GP1 and support a multistep mechanism that explains the relative contributions of these enzymes to infection. CatB and CatB/CatL inhibitors diminish the multiplication of infectious EboV-Zaire in cultured cells and may merit investigation as anti-EboV drugs.
Taxonomy, phylogeny, and paleoecology ofEoseira wilsoniigen. et sp. nov., a Middle Eocene diatom (Bacillariophyceae: Aulacoseiraceae) from lake sediments at Horsefly, British Columbia, Canada
Authors: Wolfe Alexander P , Edlund Mark B
Published: April 2005

A new centric diatom genus is described from laminated freshwater sediments of Middle Eocene age near Horsefly, British Columbia, Canada. This diatom, Eoseira wilsonii gen. et sp. nov., grew in filaments that constitute dense monospecific sub-horizons within the white couplets that represent summer deposition in the varved sequence. Although Eoseira clearly belongs within the Family Aulacoseiraceae, several features distinguish its valve structure from Aulacoseira. Gigantism of spines and the lack of geometric relationships between spine position and mantle areolae are the most conspicuous features of the genus. Eoseira is among the oldest freshwater diatoms known and one of relatively few extinct freshwater genera. In addition to serving as a potential biostratigraphic marker, Eoseira is a cornerstone to undertanding the evolutionary trajectory of the Aulacoseiraceae, likely the oldest family of freshwater diatoms. As such, it refines our understanding of early radiations from the marine realm in western North America. Furthermore, paleoecological inferences based on Eoseira life strategy pertain directly to limnological conditions during early Cenozoic hot-house conditions.
Systematics and phytogeography of selected Eocene Okanagan Highlands plants
Authors: DeVore Melanie L , Pigg Kathleen B , Wehr Wesley C
Published: April 2005

The diverse Early to Middle Eocene Okanagan Highlands floras of south central British Columbia and northeastern Washington reflect a time of rapid evolution and the early radiation of many dicot families that are currently significant elements of temperate floras. Recent studies of the Republic, Washington flora (Klondike Mountain Formation) and related Okanagan floras in British Columbia have documented both the earliest, and sometimes the only, known fossil occurrences of genera. Today many once more widespread taxa are restricted, particularly to Asian and (or) eastern North American refugia. Examples include members of the families Betulaceae (birch, hazelnut), Rosaceae (rose), Hamamelidaceae (witch hazel), and the endemic Asian family Trochodendraceae. Earliest occurrences are noted for Neviusia (Rosaceae), Trochodendron (Trochodendraceae), Corylus and Carpinus (both Betulaceae). The first unequivocal leaf records of Corylopsis and Fothergilla (both Hamamelidaceae), and two new Eocene species of the extinct fruit Palaeocarpinus (Betulaceae) are also recognized. Today, Trochodendron and Corylopsis are restricted to Asia, whereas Neviusia and Fothergilla, genera with close Asian relatives, occur only in North America. Corylus johnsonii from Republic is most similar to the extant Asian species C. heterophylla, C. wangii, and C. ferox. Neviusia leaves from One Mile Creek near Princeton, British Columbia are more similar to N. cliftonii, an endemic from Mount Shasta, California, than to N. alabamensis of southeastern North America. A better documentation of the Okanagan Highlands floras is essential to our understanding of the evolution of North American temperate floras and the nature of Asian  North American disjunct taxa.
The Okanagan Highlands: Eocene biota, environments, and geological setting, southern British Columbia, Canada and northeastern Washington, USA
Authors: Archibald S Bruce , Greenwood David R
Published: April 2005

Climate change is a matter of concern to society, decision makers, and scientists. As part of the debate about the science of climate change, and in particular the extent to which current climate change is due to human activity or part of the natural variability of the global climate system, earth scientists try to understand how climates have changed in the past, and how past warming and cooling episodes affected the landscape and the plants and animals that occupied that landscape. It is also clear from the fossil record that past climate change has played a role in the evolution of animal and plant lineages, as well as plant and animal communities. Preserved in a series of lake deposits across northeastern Washington State, USA., to Smithers in north-central British Columbia, Canada, the Okanagan Highlands fossil deposits preserve a record of a time when the world was much warmer than now because of a naturally enhanced greenhouse effect, and the poles were ice-free and supported great forests. These sites are well known to fossil collectors for their beautifully preserved insects, fish, and plants. The Okanagan Highlands were an upland 50 million years ago, during the Early Eocene, and supported diverse forests swarming with insects and other animals that today are found in both temperate and tropical areas. The trees, shrubs, and herbs of these Eocene forests echo this pattern, including palms and bald cypress, together with spruce and birches. This special issue presents a series of papers that resulted from a symposium held in 2003 on the Okanagan Highlands that details the warm Eocene world of the interior uplands of northeastern Washington and British Columbia. Topics include reconstructing the landscape, biogeography, palaeoclimates, and fossil plants, insects, diatoms, and fish.
Wes Wehr dedication
Authors: Archibald S Bruce , Pigg Kathleen B , Greenwood David R , Manchester Steven R , Barksdale Lisa , Johnson Kirk R , Sternberg Michael , Stockey Ruth A , DeVore Melanie L , Rothwell Gar W
Published: April 2005

We dedicate this issue to the memory of Wesley C. Wehr, former Affiliate Curator of Paleobotany, Burke Museum of Natural History and Culture, Seattle, Washington. Wes' contributions to paleontology, particularly in the Okanagan Highlands of Washington State and British Columbia; his influence on a generation of paleontologists (particularly paleobotanists) working in and coming from this region; and his warm friendship that brought together members of the scientific and arts communities were deeply influential, and will be fondly remembered.
Calculating penalties for reforestation failures: an Alberta case study
Authors: Perry Marilea Pattison , Beck James A , Luckert Martin K , White William A
Published: April 2005

Provincial governments across Canada rely on regeneration requirements and penalties to promote reforestation following harvesting. However, little has been written on how to determine optimal levels of penalties for noncompliance such that tenure holders have incentives to further social reforestation objectives. This paper shows how reforestation penalties may be calculated in the case of Alberta. The calculation of the penalty is shown to be dependent on (i) changes in the values of future annual allowable cuts caused by failure to promptly regenerate, (ii) the portion of stumpage values collected with stumpage fees, (iii) nontimber values influenced by reforestation, (iv) differences in private and social discount rates, (v) costs of detecting noncompliance, and (vi) the probability of detecting infractions. In the case of Alberta, (v) and (vi) are minor considerations, as detection costs are low and probability of detection is high. However, values of (i) through (iv) have large potential impacts on the optimal penalties. For example, if (i) annual allowable cuts drop by 99 m3 for a 3-year reforestation delay (vs. an acceptable 2-year delay) on a 783-ha forest, (ii) stumpage fees are $10 below stumpage value, (iii) nontimber values are zero, and (iv) the private discount is 9%, while the social rate is 6%, then the optimal penalty is $49.17CAN·ha1. However, if we change (ii) and (iv) such that stumpage fees are $30CAN below stumpage value and the private discount is 9%, while the social rate is 3%, then the optimal penalty is $168.58CAN·ha1. With zero nontimber values, zero monitoring costs, no divergence between public and private interest rates at 9%, and a probability of detection of 1.00, the current penalty of $30CAN·ha1·year1 would approximate the optimal amount if stumpage fees were $20CAN·m3. The variability in values of (i) through (iv) across forests and over time suggests that problems will arise in establishing a constant penalty for all provincial forests and that penalties should be revised as values change over time.
Landscape-level variability in the age underestimation of understory black spruce in the northern boreal forest of Quebec
Authors: Parisien Marc-André , Sirois Luc , Parent Sylvain
Published: April 2005

This study examines the variability of the potential aging error for saplings (height ≤1.5 m) of black spruce (Picea mariana (Mill.) B.S.P.) in mature fire-dominated stands (n = 14 stands) of the northern boreal forest of northwestern Quebec. Age underestimation was determined by counting the number of underground bud scars of saplings. The magnitude and variability of age underestimation was compared within and among stands. The relationship between corrected ages (the sum of age underestimation and the number of growth rings at ground level) and ground-level ages was strongly linear and was therefore described with simple linear regression models. To evaluate landscape-level variability in this relationship, the regressions were compared among stands using mixed models. Despite high variability in age underestimation at the stand level, the relationship between corrected and ground-level age was highly significant (p < 0.0001) for all stands except one. However, there were many significant statistical differences between these regressions, indicating high landscape-level variability. The magnitude of age underestimation was found to be highly site specific (means of 726 years), the phenomenon being more marked and variable in older stands. Given high landscape-level variability, age underestimation of understory black spruce saplings in northern boreal stands must be documented for every sampled stand to apply a valid age correction in studies that involve multiple stands.
Spatial relationships and tree species associations across a 236-year boreal mixedwood chronosequence
Authors: Park Andrew , Kneeshaw Daniel , Bergeron Yves , Leduc Alain
Published: April 2005

We studied community development and mortality among tree species at multiple spatial scales in a 236-year mixedwood chronosequence at Lake Duparquet, Quebec. Spatial relationships, species associations, and understoryoverstory replacement patterns were studied using spatial statistics, patch indices, G tests, and transition matrices. Results of these analyses showed that shade-intolerant and shade-tolerant tree communities formed increasingly fine-grained patches in midsuccession. These fine-grained associations appear to be partly due to suppressed stems being released into a slowly thinning canopy and partly due to new recruitment of shade-tolerant conifers. In 1-ha plots, tree species richness and evenness peaked in 25-, 100-, and 400-m2subplots during midsuccession. Forest cover type diversity also peaked in midsuccessional landscapes assessed using aerial photographs. The oldest 1-ha plot was dominated by monospecific patches of eastern white cedar (Thuja occidentalis L.), which was the most likely replacement for live and dead trees and the most abundant species in the numerous subplots that were occupied by trees smaller than 8 cm DBH. In spite of this dominance, long-lived paper birch (Betula papyrifera Marsh.) and residual fir (Abies balsamea (L.) Mill.) seedlings may maintain the mixedwood character of this stand into the future. The implications of our findings for stand management and conservation are discussed.
Stream habitat and rainbow trout (Oncorhynchus mykiss) physiological stress responses to streamside clear-cut logging in British Columbia
Authors: Mellina Eric , Hinch Scott G , Donaldson Edward M , Pearson Greg
Published: April 2005

The impacts associated with streamside clear-cut logging (e.g., increased temperatures and sedimentation, loss of habitat complexity) are potentially stressful to stream-dwelling fish. We examined stream habitat and rainbow trout physiological stress responses to clear-cut logging in north-central British Columbia using 15 streams divided into three categories: old growth (reference), recently logged (clear-cut to both banks 19 years prior to the study), and second growth (clear-cut 2528 years prior to the study). We used plasma cortisol and chloride concentrations as indicators of acute stress, and interrenal nuclear diameters, impairment of the plasma cortisol response, and trout condition and length-at-age estimates as indicators of chronic stress. No statistically significant acute or chronic stress responses to streamside logging were found, despite increases in summertime stream temperatures (daily maxima and diurnal fluctuations) and a reduction in the average overall availability of pool habitat. Our observed stress responses were approximately an order of magnitude lower than what has previously been reported in the literature for a variety of different stressors, and trout interrenal nuclear diameters responses to the onset of winter were approximately five times greater than those to logging. The overall consistency of our results suggests that the impacts of streamside clear-cut logging are not acutely or chronically stressful to rainbow trout in our study area.
Factors affecting interannual variation in growth of western Canadian aspen forests during 1951-2000
Authors: Hogg EH (Ted) , Brandt James P , Kochtubajda B
Published: April 2005

Trembling aspen (Populus tremuloides Michx.) is the most important deciduous tree in the North American boreal forest and is also the dominant tree in the aspen parkland zone along the northern edge of the Canadian prairies. Since the 1990s, observations of dieback and reduced growth of aspen forests have led to concerns about the potential impacts of climate change. To address these concerns, a regional-scale study (CIPHA) was established in 2000 that includes annual monitoring of forest health and productivity of 72 aspen stands across the western Canadian interior. Tree-ring analysis was conducted to determine the magnitude and cause of temporal variation in stand growth of aspen at the scale (1800 km × 500 km area) encompassed by this study. The results showed that during 19512000 the region's aspen forests underwent several cycles of reduced growth, notably between 1976 and 1981, when mean stand basal area increment decreased by about 50%. Most of the growth variation was explained by interannual variation in a climate moisture index in combination with insect defoliation. The results of the analysis indicate that a major collapse in aspen productivity likely occurred during the severe drought that affected much of the region during 20012003.
Estimating forest canopy bulk density using six indirect methods
Authors: Keane Robert E , Reinhardt Elizabeth D , Scott Joe , Gray Kathy , Reardon James
Published: April 2005

Canopy bulk density (CBD) is an important crown characteristic needed to predict crown fire spread, yet it is difficult to measure in the field. Presented here is a comprehensive research effort to evaluate six indirect sampling techniques for estimating CBD. As reference data, detailed crown fuel biomass measurements were taken on each tree within fixed-area plots located in five important conifers types in the western United States, using destructive sampling following a series of four sampling stages to measure the vertical and horizontal distribution of canopy biomass. The six ground-based indirect measurement techniques used these instruments: LI-COR LAI-2000, AccuPAR ceptometer, CID digital plant canopy imager, hemispherical photography, spherical densiometer, and point sampling. These techniques were compared with four aggregations of crown biomass to compute CBD: foliage only, foliage and small branchwood, foliage and all branchwood (no stems), and all canopy biomass components. Most techniques had the best performance when all canopy biomass components except stems were used. Performance dropped only slightly when the foliage and small branchwood canopy biomass aggregation (best approximates fuels available for crown fires) was employed. The LAI-2000, hemispherical photography, and CID plant canopy imager performed best. Regression equations that predict CBD from gap fraction are presented for all six techniques.
Two-year response of American chestnut (Castanea dentata) seedlings to shelterwood harvesting and fire in a mixed-oak forest ecosystem
Authors: McCament Corinne L , McCarthy Brian C
Published: April 2005

The American chestnut (Castanea dentata (Marsh.) Borkh.) was once an important tree species in the eastern United States prior to its devastation by the chestnut blight. The American Chestnut Foundation will soon release seeds that are blight resistant. However, the necessary site requirements for restoration efforts have not yet been explored. The goal of this study was to evaluate the survival and growth of chestnut seedlings within a diverse forest management regime. Seedlings were experimentally grown for 2 years in three mixed-oak forests subjected to thinning, burning, thinning followed by burning, and an untreated control. Seedling biomass parameters were most influenced by treatments that increased light availability. Soil chemistry and texture parameters were also correlated (p < 0.05) with chestnut biomass. Thus, site fertility should also be considered in reintroduction efforts. While site quality may influence growth, light conditions appear to be overwhelmingly important. Therefore, we recommend that American chestnut seeds be planted in areas with moderate to high light conditions (recently disturbed), with low surrounding competing vegetation (possibly after a burn) for optimal growth benefits.
A new parameterization of Johnson's SB distribution with application to fitting forest tree diameter data
Authors: Rennolls Keith , Wang Mingliang
Published: April 2005

The SB distributional model of Johnson's 1949 paper was introduced by a transformation to normality, that is, z ~ N(0, 1), consisting of a linear scaling to the range (0, 1), a logit transformation, and an affine transformation, z = γ + δu. The model, in its original parameterization, has often been used in forest diameter distribution modelling. In this paper, we define the SB distribution in terms of the inverse transformation from normality, including an initial linear scaling transformation, u = γ′ + δ′z (δ′ = 1/δ and γ′ = γ/δ). The SB model in terms of the new parameterization is derived, and maximum likelihood estimation schema are presented for both model parameterizations. The statistical properties of the two alternative parameterizations are compared empirically on 20 data sets of diameter distributions of Changbai larch (Larix olgensis Henry). The new parameterization is shown to be statistically better than Johnson's original parameterization for the data sets considered here.
Photosynthesis of birch (Betula pendula) is sensitive to springtime frost and ozone
Authors: Oksanen Elina , Freiwald Vera , Prozherina Nadezhda , Rousi Matti
Published: April 2005

Impacts of springtime frost and ozone enrichment, alone and in combination, on six birch (Betula pendula Roth) genotypes regenerated from a naturally occurring birch stand in southeastern Finland were studied. The seedlings were exposed to 65 ppb ozone (AOT40 (accumulated over a threshold of 40 ppb) exposure of 10.7 ppm·h) over 62 d in climate chambers, simulating spring conditions, and to 2 °C over two consecutive nights 33 d after the start of the experiment. The plants were measured for net photosynthesis, stomatal conductance, and concentrations of photosynthetic pigments, Rubisco, soluble proteins, carbohydrates, and macronutrients. Frost treatment caused a rapid 60%77% decline in net photosynthesis and stomatal conductance rates. Recovery of net photosynthesis from frost was not complete during the subsequent 14 d, mainly because of impaired light capture through significant pigment loss and structural injuries. Concomitant ozone enrichment exacerbated the negative effect of frost on pigments and stomatal conductance. Both frost and ozone caused nutrient imbalance and increase in soluble proteins in leaves, whereas metabolism of carbohydrates was disturbed only when ozone was present. Responses to ozone and frost varied greatly among the genotypes, suggesting that there is a high capacity within the birch population to adapt to climate change through "preadapted" individuals.
GENERALIZED CSP-(C1, C2) SAMPLING PLAN FOR CONTINUOUS PRODUCTION PROCESSES
Authors: BALAMURALI S. , KALYANASUNDARAM M. , JUN CHI-HYUCK
Published: April 2005

In this paper, a new continuous sampling plan is introduced whose sampling inspection phase is characterized by the maximum allowable number of nonconforming units c1 and c2 and the sampling rates f1 and f2 and is designated as CSP-(C1, C2). A Markov chain model for the proposed plan is formulated and certain common measures of performance are derived. The continuous sampling plan of type CSP-C developed by Govindaraju and Kandasamy12 is a special case of this new sampling plan. Moreover, Dodge's continuous sampling plan (CSP-1) also becomes a special case of proposed plan. The advantage of the proposed plan is to achieve a reduction in the average fraction inspected at good quality levels compared with the CSP-1 and other continuous sampling plans.
ESTIMATION OF THE CHANGE POINT OF THE PROCESS FRACTION NONCONFORMING IN SPC APPLICATIONS
Authors: PERRY MARCUS B. , PIGNATIELLO JOSEPH J.
Published: April 2005

Knowing when a process has changed would simplify the search for and identification of the special cause. In this paper, we compare the maximum likelihood estimator (MLE) of the process change point (that is, when the process changed) to built-in change point estimators from binomial CUSUM and EWMA control charts. We conclude that it is better to use the maximum likelihood change point estimator when a CUSUM or EWMA control chart signals a change in the process fraction nonconforming. The results show that the MLE provides process engineers with an accurate and useful estimate of the last subgroup from the unchanged process.
A HIERARCHICAL MODEL OF RELIABILITY BY IMPRECISE PARAMETERS OF LIFETIME DISTRIBUTIONS
Authors: UTKIN LEV V.
Published: April 2005

A hierarchical uncertainty model of reliability is studied when a type of probability distributions of the component times to failure is known, but their parameters or some of parameters are defined by experts with corresponding degrees of belief. Two methods for computing the reliability measures are developed and analyzed from their practical application point of view. A procedure of updating the beliefs after observing a failure is investigated. Numerical examples illustrating the proposed model are given.
MULTIPLE SEQUENCE ALIGNMENT USING AN EXHAUSTIVE AND GREEDY ALGORITHM
Authors: WANG YI , LI KUO-BIN
Published: April 2005

We describe an exhaustive and greedy algorithm for improving the accuracy of multiple sequence alignment. A simple progressive alignment approach is employed to provide initial alignments. The initial alignment is then iteratively optimized against an objective function. For any working alignment, the optimization involves three operations: insertions, deletions and shuffles of gaps. The optimization is exhaustive since the algorithm applies the above operations to all eligible positions of an alignment. It is also greedy since only the operation that gives the best improving objective score will be accepted. The algorithms have been implemented in the EGMA (Exhaustive and Greedy Multiple Alignment) package using Java programming language, and have been evaluated using the BAliBASE benchmark alignment database. Although EGMA is not guaranteed to produce globally optimized alignment, the tests indicate that EGMA is able to build alignments with high quality consistently, compared with other commonly used iterative and non-iterative alignment programs. It is also useful for refining multiple alignments obtained by other methods.
CLUSTERING AND RE-CLUSTERING FOR PATTERN DISCOVERY IN GENE EXPRESSION DATA
Authors: MA PATRICK C. H. , CHAN KEITH C. C. , CHIU DAVID K. Y.
Published: April 2005

The combined interpretation of gene expression data and gene sequences is important for the investigation of the intricate relationships of gene expression at the transcription level. The expression data produced by microarray hybridization experiments can lead to the identification of clusters of co-expressed genes that are likely co-regulated by the same regulatory mechanisms. By analyzing the promoter regions of co-expressed genes, the common regulatory patterns characterized by transcription factor binding sites can be revealed. Many clustering algorithms have been used to uncover inherent clusters in gene expression data. In this paper, based on experiments using simulated and real data, we show that the performance of these algorithms could be further improved. For the clustering of expression data typically characterized by a lot of noise, we propose to use a two-phase clustering algorithm consisting of an initial clustering phase and a second re-clustering phase. The proposed algorithm has several desirable features: (i) it utilizes both local and global information by computing both a "local" pairwise distance between two gene expression profiles in Phase 1 and a "global" probabilistic measure of interestingness of cluster patterns in Phase 2, (ii) it distinguishes between relevant and irrelevant expression values when performing re-clustering, and (iii) it makes explicit the patterns discovered in each cluster for possible interpretations. Experimental results show that the proposed algorithm can be an effective algorithm for discovering clusters in the presence of very noisy data. The patterns that are discovered in each cluster are found to be meaningful and statistically significant, and cannot otherwise be easily discovered. Based on these discovered patterns, genes co-expressed under the same experimental conditions and range of expression levels have been identified and evaluated. When identifying regulatory patterns at the promoter regions of the co-expressed genes, we also discovered well-known transcription factor binding sites in them. These binding sites can provide explanations for the co-expressed patterns.
HIDDEN MARKOV MODELS, GRAMMARS, AND BIOLOGY: A TUTORIAL
Authors: MUKHERJEE SHIBAJI , MITRA SUSHMITA
Published: April 2005

Biological sequences and structures have been modelled using various machine learning techniques and abstract mathematical concepts. This article surveys methods using Hidden Markov Model and functional grammars for this purpose. We provide a formal introduction to Hidden Markov Model and grammars, stressing on a comprehensive mathematical description of the methods and their natural continuity. The basic algorithms and their application to analyzing biological sequences and modelling structures of bio-molecules like proteins and nucleic acids are discussed. A comparison of the different approaches is discussed, and possible areas of work and problems are highlighted. Related databases and softwares, available on the internet, are also mentioned.
SUPPORT VECTOR MACHINES FOR PREDICTION AND ANALYSIS OF BETA AND GAMMA-TURNS IN PROTEINS
Authors: PHAM THO HOAN , SATOU KENJI , HO TU BAO
Published: April 2005

Tight turns have long been recognized as one of the three important features of proteins, together with α-helix and β-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are β-turns and most of the rest are γ-turns. Analysis and prediction of β-turns and γ-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of β-turns and γ-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict β-turns and γ-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of β-turns and γ-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.
THE INCOMPLETE PERFECT PHYLOGENY HAPLOTYPE PROBLEM
Authors: KIMMEL GAD , SHAMIR RON
Published: April 2005

The problem of resolving genotypes into haplotypes, under the perfect phylogeny model, has been under intensive study recently. All studies so far handled missing data entries in a heuristic manner. We prove that the perfect phylogeny haplotype problem is NP-complete when some of the data entries are missing, even when the phylogeny is rooted. We define a biologically motivated probabilistic model for genotype generation and for the way missing data occur. Under this model, we provide an algorithm, which takes an expected polynomial time. In tests on simulated data, our algorithm quickly resolves the genotypes under high rates of missing entries.
EXPLORING PROTEIN'S OPTIMAL HP CONFIGURATIONS BY SELF-ORGANIZING MAPPING
Authors: ZHANG XIANG-SUN , WANG YONG , ZHAN ZHONG-WEI , WU LING-YUN , CHEN LUONAN
Published: April 2005

Self-organizing map (SOM) has been used in protein folding prediction when the HP model is employed. The existing work uses a square-like shape lattice with l = m×n points to represent the optimal compact structure of a sequence of l amino acids. In this paper, a general l′-size sequence of amino acids is self-organized in a two dimensional lattice with l (> l′) points. The obtained minimum configuration then has a flexible shape, in contrast to the compact structure limited in the lattice. To fulfil this extension, a new self-organizing map (SOM) technique is proposed to deal with the difficulty of the unsymmetric input and output spaces. New competition rules in the training phase are introduced and a local search method is applied to overcome the multi-mapping phenomena. Several HP benchmark examples with up to 36 amino acids are tested to verify the effectiveness of the proposed approach in this paper.
THE PROBABILITY DISTRIBUTION FOR A RANDOM MATCH BETWEEN AN EXPERIMENTAL-THEORETICAL SPECTRAL PAIR IN TANDEM MASS SPECTROMETRY
Authors: FRIDMAN TEMA , RAZUMOVSKAYA JANE , VERBERKMOES NATHAN , HURST GREG , PROTOPOPESCU VLADIMIR , XU YING
Published: April 2005

Proteomic techniques are fast becoming the main method for qualitative and quantitative determination of the protein content in biological systems. Despite notable advances, efficient and accurate analysis of high throughput proteomic data generated by mass spectrometers remains one of the major stumbling blocks in the protein identification problem. We present a model for the number of random matches between an experimental MS-MS spectrum and a theoretical spectrum of a peptide. The shape of the probability distribution is a function of the experimental accuracy, the number of peaks in the experimental spectrum, the length of the interval over which the peaks are distributed, and the number of theoretical spectral peaks in this interval. Based on this probability distribution, a goodness-of-fit tool can be used to yield fast and accurate scoring schemes for peptide identification through database search. In this paper, we describe one possible implementation of such a method and compare the performance of the resulting scoring function with that of SEQUEST. In terms of speed, our algorithm is roughly two orders of magnitude faster than the SEQUEST program, and its accuracy of peptide identification compares favorably to that of SEQUEST. Moreover, our algorithm does not use information related to the intensities of the peaks.
DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS
Authors: RAMSEY STEPHEN , ORRELL DAVID , BOLOURI HAMID
Published: April 2005

We describe Dizzy, a software tool for stochastically and deterministically modeling the spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling networks. Notable features include a modular simulation framework, reusable modeling elements, complex kinetic rate laws, multi-step reaction processes, steady-state noise estimation, and spatial compartmentalization.
Stratigraphic development of synkinematic deposits in a large growth-fault system, onshore Brunei Darussalam
Authors: Back S. , Tioe H.J. , Thang T.X. , Morley C.K.
Published: April 2005

Kilometre-scale synsedimentary faults associated with well-preserved sedimentary successions on both hanging-wall and footwall sides are rarely seen in outcrop. However, one such example is found in a Middle Miocene deltaic sand–shale sequence exposed along the Jerudong Anticline in onshore Brunei Darussalam. Integration of detailed outcrop information with regional geophysical subsurface data documents that: (1) initiation of the Jalan Tutong growth fault was related to delta-front instability and failure; (2) sediment loading under shallow-marine conditions maintained syndepositional faulting; (3) growth-fault abandonment coincided with a significant basinward shift of deposition and subaerial exposure. High-resolution analysis of facies characteristics, stratal expansion and throw development within the studied growth sequence indicates that differential fault movement strongly influenced facies composition, sedimentary geometry and bedding characteristics: sandstone-poor shelf to lower-shoreface successions developed during periods of rapidly increasing fault movement, whereas sandstone-rich, amalgamated upper-shoreface deposits preferentially formed during intervals of constant or decreasing throw development. The data and interpretations presented may help to focus attention on the complex interplay between tectonics and sedimentation associated with the growth and decay of deltaic faults by providing for the first time an outcrop-based view on a feature documented in similar scale only by geophysical subsurface data.