bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting
Authors: Beveridge D. L. , Dixit Surjit B. , Barreiro Gabriela , Thayer Kelly M. 
Published: January 2004

AbstractRecent studies of DNA axis curvature and flexibility based on molecular dynamics (MD) simulations on DNA are reviewed. The MD simulations are on DNA sequences up to 25 base pairs in length, including explicit consideration of counterions and waters in the computational model. MD studies are described for ApA steps, A‐tracts, for sequences of A‐tracts with helix phasing. In MD modeling, ApA steps and A‐tracts in aqueous solution are essentially straight, relatively rigid, and exhibit the characteristic features associated with the B′‐form of DNA. The results of MD modeling of A‐tract oligonucleotides are validated by close accord with corresponding crystal structure results and nuclear magnetic resonance (NMR) nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC) structures of d(CGCGAATTCGCG) and d(GGCAAAAAACGG). MD simulation successfully accounts for enhanced axis curvature in a set of three sequences with phased A‐tracts studied to date. The primary origin of the axis curvature in the MD model is found at those pyrimidine/purine YpR “flexible hinge points” in a highroll, open hinge conformational substate. In the MD model of axis curvature in a DNA sequence with both phased A‐tracts and YpR steps, the A‐tracts appear to act aspositioning elementsthat make the helix phasing more precise, and key YpR steps in the open hinge state serve ascurvature elements. Our simulations on a phased A‐tract sequence as a function of temperature show that the MD simulations exhibit a premelting transition in close accord with experiment, and predict that the mechanism involves a B′‐to‐B transition within A‐tracts coupled with the prediction of a transition in key YpR steps from the high roll, open hinge, to a low roll, closed hinge substate. Diverse experimental observations on DNA curvature phenomena are examined in light of the MD model with no serious discrepancies. The collected MD results provide independent support for the “non‐A‐tract model” of DNA curvature. The “junction model” is indicated to be a special case of the non‐A‐tract model when there is a Y base at the 5′ end of an A‐tract. In accord with crystallography, the “ApA wedge model” is not supported by MD. © 2004 Wiley Periodicals, Inc. Biopolymers 73: 380–403, 2004
Effect of immobilization support, water activity, and enzyme ionization state on cutinase activity and enantioselectivity in organic media
Authors: Vidinha Pedro , Harper Neil , Micaelo Nuno M. , Lourenco Nuno M.T. , Gomes da Silva Marco D.R. , Cabral Joaquim M.S. , Afonso Carlos A.M. , Soares Claudio M. , Barreiros Susana 
Published: January 2004

AbstractWe studied the reaction between vinyl butyrate and 2‐phenyl‐1‐propanol in acetonitrile catalyzed by Fusarium solani pisi cutinase immobilized on zeolites NaA and NaY and on Accurel PA‐6. The choice of 2‐phenyl‐1‐propanol was based on modeling studies that suggested moderate cutinase enantioselectivity towards this substrate. With all the supports, initial rates of transesterification were higher at a water activity (aw) of 0.2 than at aw = 0.7, and the reverse was true for initial rates of hydrolysis. By providing acid–base control in the medium through the use of solid‐state buffers that control the parameter pH‐pNa, which we monitored using an organo‐soluble chromoionophoric indicator, we were able, in some cases, to completely eliminate dissolved butyric acid. However, none of the buffers used were able to improve the rates of transesterification relative to the blanks (no added buffer) when the enzyme was immobilized at an optimum pH of 8.5. When the enzyme was immobilized at pH 5 and exhibited only marginal activity, however, even a relatively acidic buffer with a pKa of 4.3 was able to restore catalytic activity to about 20% of that displayed for a pH of immobilization of 8.5, at otherwise identical conditions. As aw was increased from 0.2 to 0.7, rates of transesterification first increased slightly and then decreased. Rates of hydrolysis showed a steady increase in that aw range, and so did total initial reaction rates. The presence or absence of the buffers did not impact on the competition between transesterification and hydrolysis, regardless of whether the butyric acid formed remained as such in the reaction medium or was eliminated from the microenvironment of the enzyme through conversion into an insoluble salt. Cutinase enantioselectivity towards 2‐phenyl‐1‐propanol was indeed low and was not affected by differences in immobilization support, enzyme protonation state, or aw. © 2004 Wiley Periodicals, Inc.
Online detection of feed demand in high cell density cultures of Escherichia coli by measurement of changes in dissolved oxygen transients in complex media
Authors: Whiffin Victoria S. , Cooney Michael J. , Cord‐Ruwisch Ralf 
Published: January 2004

AbstractA starvation‐based dissolved oxygen (DO) transient controller was developed to supply growth‐limiting substrate to high cell density fed‐batch cultures of recombinant Escherichia coli. The algorithm adjusted a preexisting feed rate in proportion to the culture's oxygen demand, which was estimated from transients in the DO concentration after short periods of feed interruption. In this manner, the addition of glucose feed was precisely controlled at a rate that did not exceed the acetate production threshold, thus preventing acetate accumulation. In comparison to exponential feed algorithms commonly used in industry, the implementation of the new feeding strategy increased the final cell density from 32 to 44 g (dry cell weight).L−1, with less than 16 mM acetate accumulated, producing an ideal culture for subsequent induction. Despite a constant starvation level and relatively low levels of acetate, experimental cultivations still tended to produce acetate towards the end of the process. The use of a simple Monod model provided an explanation as to why this may occur in high cell density cultivations and suggests how it may be overcome. © 2004 Wiley Periodicals, Inc.
Analyzing and modeling of photobioreactors by combining first principles of physiology and hydrodynamics
Authors: Luo Hu‐Ping , Al‐Dahhan Muthanna H. 
Published: January 2004

AbstractMixing in photobioreactors is known to enhance biomass productivity considerably, and flow dynamics play a significant role in the reactor's performance, as they determine the mixing and the cells' movement. In this work we focus on analyzing the effects of mixing and flow dynamics on the photobioreactor performance. Based on hydrodynamic findings from the CARPT(Computer Automated Radioactive Particle Tracking) technique, a possible mechanism for the interaction between the mixing and the physiology of photosynthesis is presented, and the effects of flow dynamics on light availability and light intensity fluctuation are discussed and quantitatively characterized. Furthermore, a dynamic modeling approach is developed for photobioreactor performance evaluation, which integrates first principles of photosynthesis, hydrodynamics, and irradiance distribution within the reactor. The results demonstrate the reliability and the possible applicability of this approach to commercially interesting microalgae/cyanobacteria culture systems. © 2004 Wiley Periodicals, Inc.
Biocatalytic scrubbing of gaseous acrylonitrile using Rhodococcus ruber immobilized in synthetic silicone polymer (ImmobaSil™) rings
Authors: Roach P.C.J. , Ramsden D.K. , Hughes J. , Williams P. 
Published: January 2004

AbstractMicrobial detoxification of acrylonitrile vapor was performed using Rhodococcus ruber immobilized into rings of a synthetic silicone polymer (ImmobaSil™) sponge. The immobilization matrix was used as both the cell support material and also as the trickle‐bed column packing. The elimination capacity of the biocatalytic scrubber was determined for different influent concentrations of gaseous acrylonitrile. The working life of the nongrowing biocatalyst was also examined under test conditions and was found to be at least 70 days before biocatalyst replacement was required. An elimination capacity of 4.0 kg m−3 h−1 was achieved with a 95% removal efficiency, and an elimination capacity of over 7.2 kg m−3 h−1 acrylonitrile was achieved with a removal efficiency of 90%. This elimination capacity is 10 times that previously published in the literature. © 2003 Wiley Periodicals, Inc.
Salt‐activation of nonhydrolase enzymes for use in organic solvents
Authors: Morgan John A. , Clark Douglas S. 
Published: January 2004

AbstractEnzymatic reactions are important for the synthesis of chiral molecules. One factor limiting synthetic applications of enzymes is the poor aqueous solubility of numerous substrates. To overcome this limitation, enzymes can be used directly in organic solvents; however, in nonaqueous media enzymes usually exhibit only a fraction of their aqueous‐level activity. Salt‐activation, a technique previously demonstrated to substantially increase the transesterification activity of hydrolytic enzymes in organic solvents, was applied to horse liver alcohol dehydrogenase, soybean peroxidase, galactose oxidase, and xanthine oxidase, which are oxidoreductase and oxygenase enzymes. Assays of the lyophilized enzyme preparations demonstrated that the presence of salt protected enzymes from irreversible inactivation. In organic solvents, there were significant increases in activity for the salt‐activated enzymes compared to nonsalt‐activated controls for every enzyme tested. The increased enzymatic activity in organic solvents was shown to result from a combination of protection against inactivation during the freeze‐drying process and other as‐yet undetermined factors. © 2004 Wiley Periodicals, Inc.
Characterization of the cellular uptake and metabolic conversion of acetylated N‐acetylmannosamine (ManNAc) analogues to sialic acids
Authors: Jones Mark B. , Teng Howard , Rhee Jun Kyu , Lahar Nicholas , Baskaran Gautam , Yarema Kevin J. 
Published: January 2004

Abstract“Sialic acid engineering” refers to the strategy where cell surface carbohydrates are modified by the biosynthetic incorporation of metabolic intermediates, such as non‐natural N‐acetylmannosamine (ManNAc) analogues, into cellular glycoconjugates. While this technology has promising research, biomedical, and biotechnological applications due to its ability to endow the cell surface with novel physical and chemical properties, its adoption on a large scale is hindered by the inefficient metabolic utilization of ManNAc analogues. We address this limitation by proposing the use of acetylated ManNAc analogues for sialic acid engineering applications. In this paper, the metabolic flux of these “second‐generation” compounds into a cell, and, subsequently, into the target sialic acid biosynthetic pathway is characterized in detail. We show that acetylated ManNAc analogues are metabolized up to 900‐fold more efficiently than their natural counterparts. The acetylated compounds, however, decrease cell viability under certain culture conditions. To determine if these toxic side effects can be avoided, we developed an assay to measure the cellular uptake of acetylated ManNAc from the culture medium and its subsequent flux into sialic acid biosynthetic pathway. This assay shows that the majority ( > 80%) of acetylated ManNAc is stored in a cellular “reservoir” capable of safely sequestering this analogue. These results provide conditions that, from a practical perspective, enable the acetylated analogues to be used safely and efficaciously and therefore offer a general strategy to facilitate metabolic substrate‐based carbohydrate engineering efforts. In addition, these results provide fundamental new insights into the metabolic processing of non‐natural monosaccharides. © 2004 Wiley Periodicals, Inc.
Resonance energy transfer for assessing the molecular integrity of proteins for local delivery
Authors: Wu David , Edelman Elazer R. 
Published: January 2004

AbstractIt remains unclear whether the limitations to the therapeutic potential of angiogenic growth factors stem from pharmacokinetic concerns related to inadequate delivery or from a reduced sensitivity of target tissues. Here, we report a novel method using resonance energy transfer to assess the molecular integrity of proteins after local delivery. As an example, we labeled fibroblast growth factor‐2 with a fluorescent donor and nonfluorescent acceptor pair, tetramethylrhodamine and QSY‐7, and demonstrate in an ex vivo bovine carotid artery model that this growth factor is not limited by proteolytic constraints imposed by the tissue. Our data indicate that FGF‐2 is unlikely to be degraded within the arterial wall and suggest that pharmacokinetic limitations alone cannot fully explain the muted response seen thus far in therapeutic angiogenesis. In general, resonance energy transfer may serve as a novel approach to assess the molecular integrity of protein‐based therapies in local delivery. © 2004 Wiley Periodicals, Inc.
Effect of initial moisture content and chip size on the bioconversion efficiency of softwood lignocellulosics
Authors: Cullis Ian F. , Saddler John N. , Mansfield Shawn D. 
Published: January 2004

AbstractPrevious optimization strategies for the bioconversion of lignocellulosics by steam explosion technologies have focused on the effects of temperature, pH, and treatment time, but have not accounted for changes in severity brought about by properties inherent in the starting feedstock. Consequently, this study evaluated the effects of chip properties, feedstock size (40‐mesh, 1.5 × 1.5 cm, 5 × 5 cm), and moisture content (12% and 30%) on the overall bioconversion process, and more specifically on the efficacy of removal of recalcitrant lignin from the lignocellulosic substrates following steam explosion. Increasing chip size resulted in an improvement in the solids recovery, with concurrent increases in the water soluble, hemicellulose‐derived sugar recovery (7.5%). This increased recovery is a result of a decrease in the “relative severity” of the pretreatment as chip size increases. Additionally, the decreased relative severity minimized the condensation of the recalcitrant residual lignin and therefore increased the efficacy of peroxide fractionation, where a 60% improvement in lignin removal was possible with chips of larger initial size. Similarly, increased initial moisture content reduced the relative severity of the pretreatment, generating improved solids and hemicellulose‐derived carbohydrate recovery. Both increased chip size and higher initial moisture content results in a substrate that performs better during peroxide delignification, and consequently enzymatic hydrolysis. Furthermore, a post steam‐explosion refining step increased hemicellulose‐derived sugar recovery and was most effectively delignified (to as low as 6.5%). The refined substrate could be enzymatically hydrolyzed to very high levels (98%) and relatively fast rates (1.23 g/L/h). © 2004 Wiley Periodicals, Inc.
Managing distributed shared arrays in a bulk‐synchronous parallel programming environment
Authors: Kessler Christoph W. 
Published: January 2004

AbstractNestStep is a parallel programming language for the BSP (bulk‐hronous parallel) programming model. In this article we describe the concept of distributed shared arrays in NestStep and its implementation on top of MPI. In particular, we present a novel method for runtime scheduling of irregular, direct remote accesses to sections of distributed shared arrays. Our method, which is fully parallelized, uses conventional two‐sided message passing and thus avoids the overhead of a standard implementation of direct remote memory access based on one‐sided communication. The main prerequisite is that the given program is structured in a BSP‐compliant way. Copyright © 2004 John Wiley & Sons, Ltd.
Data partitioning‐based parallel irregular reductions
Authors: Gutiérrez Eladio , Plata Oscar , Zapata Emilio L. 
Published: January 2004

AbstractDifferent parallelization methods for irregular reductions on shared memory multiprocessors have been proposed in the literature in recent years. We have classified all these methods and analyzed them in terms of a set of properties: data locality, memory overhead, exploited parallelism, and workload balancing. In this paper we propose several techniques to increase the amount of exploited parallelism and to introduce load balancing into an important class of these methods. Regarding parallelism, the proposed solution is based on the partial expansion of the reduction array. Load balancing is discussed in terms of two techniques. The first technique is a generic one, as it deals with any kind of load imbalance present in the problem domain. The second technique handles a special case of load imbalance which occurs whenever a large number of write operations are concentrated on small regions of the reduction arrays. Efficient implementations of the proposed optimizing solutions for a particular method are presented, experimentally tested on static and dynamic kernel codes, and compared with other parallel reduction methods. Copyright © 2004 John Wiley & Sons, Ltd.
Group‐SPMD programming with orthogonal processor groups
Authors: Rauber Thomas , Reilein Robert , Rünger Gudula 
Published: January 2004

AbstractMany programs for message‐passing machines can benefit from an implementation in a group‐SPMD programming model due to the potential to reduce communication overhead and to increase scalability. In this paper, we consider group‐SPMD programs exploiting different orthogonal processor partitions in one program. For each program this is a fixed set of predefined processor partitions given by the parallel hyperplanes of a two‐ or multi‐dimensional virtual processor organization. We introduce a library built on top of MPI to support the programming with those orthogonal processor groups. The parallel programming model is appropriate for applications with a multi‐dimensional task grid and task dependencies mainly aligned in the dimensions of the task grid. The library can be used to specify the appropriate processor partitions, which are then created by the library, and to define the mapping of tasks to the processor hyperplanes. Examples from numerical analysis illustrate the programming style and show that the runtime on distributed memory machines can be considerably reduced by using the library. Copyright © 2004 John Wiley & Sons, Ltd.
The effect of cache models on iterative compilation for combined tiling and unrolling
Authors: Knijnenburg P. M. W. , Kisuki T. , Gallivan K. , O'Boyle M. F. P. 
Published: January 2004

AbstractIterative compilation, where we search for the best program transformation based on profile feedback information, has been highly successful in determining good program optimizations, typically outperforming all static approaches. However, this benefit has come at a price, namely, a large number of executions of the target program which in many cases is unacceptable. This paper is concerned with reducing the number of program executions needed by iterative compilation by incorporating static models. We examine how static models may be incorporated into a purely iterative approach by developing several characterized heuristics. We empirically explore the tradeoff between reducing the number of executions required and the ultimate performance achieved for differing parameters or slack factors. We focus on tiling and unrolling as transformations and cache models as a test case for the feasibility of this approach. We show that a highly accurate model, used as a filter to profiling and appropriately parameterized, can reduce the number of executions by 50%. We also show that using a simple model to rank transformations and profiling, only those with the highest ranking can reduce the number of executions even further up to 70%, in cases where there is only a limited number of profiles available. We conclude that a production compiler might perform best using the last approach, gaining the benefit of iterative compilation at a much reduced cost. Copyright © 2004 John Wiley & Sons, Ltd.
A fast and accurate method for determining a lower bound on execution time
Authors: Fursin G. , O'Boyle M. F. P. , Temam O. , Watts G. 
Published: January 2004

AbstractIn performance critical applications, memory latency is frequently the dominant overhead. In many cases, automatic compiler‐based optimizations to improve memory performance are limited and programmers frequently resort to manual optimization techniques. However, this process is tedious and time‐consuming. Furthermore, as the potential benefit from optimization is unknown there is no way to judge the amount of effort worth expending, nor when the process can stop, i.e. when optimal memory performance has been achieved or sufficiently approached. Architecture simulators can provide such information but designing an accurate model of an existing architecture is difficult and simulation times are excessively long. In this article, we propose and implement a technique that is both fast and reasonably accurate for estimating a lower bound on execution time for scientific applications. This technique has been tested on a wide range of programs from the SPEC benchmark suite and two commercial applications, where it has been used to guide a manual optimization process and iterative compilation. We compare our technique with that of a simulator with an ideal memory behaviour and demonstrate that our technique provides comparable information on memory performance and yet is over two orders of magnitude faster. We further show that our technique is considerably more accurate than hardware counters. Copyright © 2004 John Wiley & Sons, Ltd.
Seismic microzonation of the greater Bangkok area using microtremor observations
Authors: Tuladhar Rabin , Yamazaki Fumio , Warnitchai Pennung , Saita Jun 
Published: January 2004

AbstractBangkok, the capital city of Thailand, is located at a remote distance from seismic sources. However, it has a substantial risk from these distant earthquakes due to the ability of the underlying soft clay to amplify ground motions. It is therefore imperative to conduct a detailed seismic hazard assessment of the area. Seismic microzonation of big cities, like Bangkok, provides a basis for site‐specific hazard analysis, which can assist in systematic earthquake mitigation programs. In this study, a seismic microzonation map for the greater Bangkok area is constructed using microtremor observations. Microtremor observations were carried out at more than 150 sites in the greater Bangkok area. The predominant periods of the ground were determined from the horizontal‐to‐vertical (H/V) spectral ratio technique. A microzonation map was then developed for the greater Bangkok area based on the observations. Moreover, the transfer functions were calculated for the soil profile at eight sites, using the computer program SHAKE91, to validate the results from the microtremor analysis. The areas near the Gulf of Thailand, underlaid by a thick soft clay layer, were found to have long natural periods ranging from 0.8s to 1.2s. However, the areas outside the lower central plain have shorter predominant periods of less than 0.4s. The study shows that there is a great possibility of long‐period ground vibration in Bangkok, especially in the areas near the Gulf of Thailand. This may have severe effects on long‐period structures, such as high‐rise buildings and long‐span bridges. Copyright © 2003 John Wiley & Sons, Ltd.