bluuebunny/crossref_metadata_2025 huggingface dataset:
Freshwater Fish Habitats in Amazonia: State of Knowledge, Management, and Protection
Authors: Junk Wolfgang J. , Soares Maria Gercilia M.
Published: November 2002

With an estimated 2,500 to 3,000 fish species, the Amazon basin is the largest biodiversity center of freshwater fishes. The large number is related to the size of the basin, a large habitat diversity, high speciation rates of different groups, and low extinction rates resulting from a rather stable tropical climate which has persisted over long geological periods. Amazonia is characterized by a very dense network of streams and rivers, connected to extended floodplains and wetland areas. There are only a few small permanently isolated deep lakes in the area. Rapids and waterfalls along the border of the Guyana shield, the Central Brazilian shield and the Andes separate the downstream and upstream fish faunas of major rivers. Estimates indicate that about half of the fish fauna colonizes the large river floodplain systems along the lower and middle reaches of the rivers and the other half the headwater streams. Knowledge about fish habitats is concentrated mostly on large river floodplains near large cities, which provide infrastructure for research, and habitat conditions in large areas are virtually unknown. Information is scattered in limnological, botanical, geographical, and aquarium literature. Ongoing research concentrates mostly on the inland fisheries.

Large parts of the Amazon River basin are still in pristine condition as are the fish habitats. However, human activities, including the transformation of large savanna and rain forest areas into agricultural land, the construction of large reservoirs for hydroelectric power generation, and mining profoundly modify fish habitats, and threaten species diversity mainly in small streams. Environmental legislation for the protection of streamside vegetation is sometimes contradictory and often not respected by the landowners. In the long run, specific fish communities and their habitats will only be fully protected in national parks and other protected areas. Even these areas suffer illegal human activities because of insufficient administration. There is an urgent need for the classification of fish habitats throughout the basin and the proposal of specific protection measures.
A Framework for the Advancement of Aquatic Science — Lake Habitat Experiments as an Example
Authors: Kelso J.R.M. , Steedman R.J. , Gunn J.M. , Smokorowski K.E. , Lester N.P. , Cole W.G. , Minns C.K. , Mills K.H.
Published: November 2002

Resource managers must often act to protect fisheries and fish habitat without the certainty that their actions are justified. Delivering the science needed to support and direct management decisions is a daunting exercise, likely beyond the capabilities of a single research group or management agency. This problem is exacerbated by the lack of a common framework to formulate and test important hypotheses about biotic response to aquatic habitat change. A partial solution may be provided by co-operative research networks to produce an integrated design and synthesis of quasi-independent studies within a common framework for hypothesis generation and testing. A well-designed framework should attract scientists and agencies who recognize the benefit of cooperative research. We demonstrate such an approach by using it to test hypotheses about lake fish community response to habitat change. Our framework includes a list of hypotheses, a list of treatments (i.e., habitat manipulations), an experimental design specifying the number of lakes per treatment, and advice for measuring habitat and fish parameters. Because our procedure uses ‘before-after’ comparisons to measure effects of habitat changes, lakes can be studied independently (and hypotheses can be tested independently) yet still contribute synergistically to the larger experiment. A ‘staircase’ design, ensuring that treatment effects are independent of environmental correlates such as climate variables, would be implemented, largely by default, because contributions to the design would accumulate over time. We believe this cooperative approach will improve the ability of researchers to meet the growing demands for useful, reliable aquatic science.
Toxicity Studies of Tobacco Wastewater
Authors: Sponza Delia Teresa
Published: November 2002

Investigations carried out on tobacco industry wastewater showed that important sources of toxic contaminants are flavoring agents containing glycogen and alcohol, absorbable organic halogens and pesticides from tobacco leaves. Shock loading of these contaminants inhibited bacterial activity during biological treatment. Input of wastewater containing such toxic substances caused decreases in bacterial number and reduced the efficiency of the treatment plant.

Viable numbers of floc-forming, total and faecal coliform bacteria within the biological treatment unit were monitored. Mortalities in bacterial populations and low chemical oxygen demand removal efficiencies were detected when absorbable organic halogens and pesticide concentrations were above 100 and 120 mg l-1, respectively. Short-term bioassays (using bacteria, protozoa or algae) and enrichment toxicity tests (including bacteria) performed to determine potential toxicity demonstrated that 90% mortalities in microbial populations were detected when absorbable organic halogens and pesticide concentrations were as high as 200 and 290 mg l-1, respectively. Enrichment toxicity tests indicated whether toxic, growth limiting or stimulation conditions were present. These tests showed that sufficient nutrients can stimulate bacterial growth, and high organic halogens and pesticide concentrations and chemical to biological oxygen demand ratios may inhibit microbial growth. Furthermore, results of chemical coagulation/flocculation test experiments showed that chemical treatment is effective at reducing toxicity.
Impact of environmental aberrations on fisheries of the Ganga (Ganges) River
Authors: Sinha M. , Khan M. A.
Published: November 2002

Ganga River basin, which was comparatively free from anthropocentric activities until the 1940s, became a disposal site for agricultural, industrial and sewerage wastes after independence of India in 1947. Discharge of wastes generated due to developmental activities including irrigation projects, river course modifications and demographic explosion in the basin, have ecologically impaired the river system, so that water quality is degraded, and fish yield as well as biodiversity has decreased. Amongst these, irrigation projects and flood control measures have almost destroyed flood plains, sloughs, inundation zones and oxbow lakes, all of which are the breeding and nursing grounds of the prized Indian major carp. This led to decline of the major carp population, while less economic fishes (minor carps and small catfishes) are increasing in relative abundance. The hydraulic structures have destroyed the anadromous fisheries (Tenualosa ilisha, Pangasius pangasius) of the riverine stretch of the Ganga. However, launching of the Ganga Action Plan phase-1 by the Central Government in the mid-1980s for cleansing the river has resulted in amelioration of some water quality parameters (increased DO and decreased BOD) to the level of the 1960's in the riverine stretch. However, some fisheries remain in decline. This is mainly due to reduction in water volume in the river due to siltation of the riverbed and increased water abstraction. However, improvement of fisheries in general and that of Tenualosa ilisha in particular in the estuarine zone, on account of release of water from the Farakka barrage in the estuary is also observed. The present paper discusses the impact of environmental aberrations on the fisheries of the Ganga River.
Photoelectron polarisation in the photoionisation of Hg (6s21S0e)
Authors: K Bartschat  , P Scott
Published: November 2002

The relativistic R-matrix method is used to study the spin polarisation of the photoelectron when Hg (6s21S0e) is photoionised leaving the Hg+ion in the 5d106s2S1/2state and the photoelectron in either the epsilon p1/2or epsilon p3/2continuum. The spin parameters xi , A and alpha are calculated along with the total cross section sigma and the asymmetry parameter beta for the angular distribution of the photoelectrons. The energy region considered is that between the ionisation threshold of Hg (10.43 eV) and the 5d96s22D5/2threshold of Hg+(14.83 eV) which is dominated by autoionising states of Hg.
Optically tooled bowl feeders
Authors: Connolly Christine
Published: November 2002

This paper reviews bowl feeders with optical sensors, used in industrial automation and assembly, describing their advantages over mechanically tooled bowl feeders, their underlying technology and development trends.
Sheet metal FMS gives more space to Airflow
Authors: Rooks Brian
Published: November 2002

Describes the use of a laser for profiling sheet metal and a sophisticated handling system that eliminates hard tooling and reduces stockholding.
Computer‐aided fixture design verification
Authors: Kang Y. , Rong Y. , Yang J. , Ma W.
Published: November 2002

Computer‐aided fixture design (CAFD) techniques have been advanced so rapidly that computers can now generate fixture configurations automatically, for both modular fixtures and dedicated fixtures. Computer‐aided fixture design verification (CAFDV) is the techniques for verifying and improving existing fixture designs. It verifies the followings: geometric constraining ability, achieved tolerance, fixturing stability, and fixturing accessibility. Two models – one geometric and one kinematic – are created for the verification.
Reduction of printed circuit board group assembly time through the consideration of efficiency loss of placement time
Authors: Chen Wei‐Shing , Chyu Chiuh‐Cheng
Published: November 2002

In a high‐mix middle‐volume production environment for printed circuit board (PCB) assembly, the production efficiency strongly depends not only on the tactical level of how to group PCBs but also on the operational level of how to assign feeders and determine placement sequences in the group setup strategy. The present study discusses the problem of clustering PCBs into groups in such a way that total placement and setup time can be minimized. This problem is motivated by a situation that the reduction of group setup‐time and efficiency loss of placement time should be balanced in a PCB group setup optimization. This research incorporates placement time into the PCB job grouping and presents a weighting similarity measure. To solve component‐feeder assignment and placement sequences for a family of PCBs, an efficient procedure based upon an ant colony optimization (ACO) algorithm is developed. Group setup performance is evaluated and compared under a variety of grouping algorithms. Experiments are conducted to discover situations where the consideration of efficiency loss of placement time can make a significant improvement in PCB group assembly.
Measuring the effect of higher education on university students
Authors: Tam Maureen
Published: November 2002

A study to measure the influence of higher education on students’ academic, social and personal growth was conducted at a local university in Hong Kong in 2000. The setting was Lingnan University in Hong Kong, a small government‐funded liberal arts university. The empirical investigation adopts an approach of assessing quality of university education using data collected from individual students about their subjective experiences during the university years and their perceptions of the value of the educational experience.
The E‐College and quality assurance: the irresistible and the immovable
Authors: Jones Norah , Morgan Arthur , Turner David
Published: November 2002

Existing quality assurance arrangements do not consider the variations in design and delivery opportunities offered through the utilisation of emerging technologies and its application in non‐traditional forms of educational arrangements. One particular form of delivery, aided by technology, is on‐line delivery, either to the workplace or the home. This mode offers considerable significance for developing the role and principles of work‐based learning in providing a much broader population the opportunity to participate in higher education. This article reviews the development of the online E‐College and its role in work‐based learning with particular focus on the arrangements for quality assurance.
The Internet as a new medium for the sciences? The effects of Internet use on traditional scientific communication media among social scientists in Germany
Authors: Eisend Martin
Published: November 2002

Scientific communication takes place within two main fields: research and publication. Whereas twentieth century audio‐visual media did not become established in the scientific communication system, the Internet, with its variety of communication options, is able to enter both fields of communication and has even revolutionised this communication system to some extent. The investigation of this relationship is based on data from a study of social scientists taken in Berlin in autumn 1999. The Internet substitutes written communication media and complements forms of spoken communication in the field of research. It also complements traditional publisher‐oriented forms of publication and is even a substitute for works that have previously avoided publication. Therefore, the Internet should not be regarded as a new alternative to traditional and institutionalised structures of communication of scientific publications, as it has already become institutionalised in the field of research as a medium of interpersonal communication.
Internet use in South Korea
Authors: John Yong J. , Gorman G.E.
Published: November 2002

This paper provides an insight into how South Koreans access the Internet and use Internet services such as banking and commerce. The paper shows overall Internet use in relation to users and their behaviour, and presents data on Internet services such in banking and e‐commerce. Data are taken from reports issued by the Korean Network Information Centre in 2002
Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles
Authors: Larson Stefan M. , England Jeremy L. , Desjarlais John R. , Pande Vijay S.
Published: November 2002

Modeling the inherent flexibility of the protein backbone as part of computational protein design is necessary to capture the behavior of real proteins and is a prerequisite for the accurate exploration of protein sequence space. We present the results of a broad exploration of sequence space, with backbone flexibility, through a novel approach: large‐scale protein design to structural ensembles. A distributed computing architecture has allowed us to generate hundreds of thousands of diverse sequences for a set of 253 naturally occurring proteins, allowing exciting insights into the nature of protein sequence space. Designing to a structural ensemble produces a much greater diversity of sequences than previous studies have reported, and homology searches using profiles derived from the designed sequences against the Protein Data Bank show that the relevance and quality of the sequences is not diminished. The designed sequences have greater overall diversity than corresponding natural sequence alignments, and no direct correlations are seen between the diversity of natural sequence alignments and the diversity of the corresponding designed sequences. For structures in the same fold, the sequence entropies of the designed sequences cluster together tightly. This tight clustering of sequence entropies within a fold and the separation of sequence entropy distributions for different folds suggest that the diversity of designed sequences is primarily determined by a structure's overall fold, and that the designability principle postulated from studies of simple models holds in real proteins. This has important implications for experimental protein design and engineering, as well as providing insight into protein evolution.
Sequence conserved for subcellular localization
Authors: Nair Rajesh , Rost Burkhard
Published: November 2002

The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large‐scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS‐PROT database and five entirely sequenced eukaryotes.
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
Authors: Marsden Russell L. , McGuffin Liam J. , Jones David T.
Published: November 2002

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed.
Regulatory implications of a novel mode of interaction of calmodulin with a double IQ‐motif target sequence from murine dilute myosin V
Authors: Martin Stephen R. , Bayley Peter M.
Published: November 2002

Apo‐Calmodulin acts as the light chain for unconventional myosin V, and treatment with Ca2+ can cause dissociation of calmodulin from the 6IQ region of the myosin heavy chain. The effects of Ca2+ on the stoichiometry and affinity of interactions of calmodulin and its two domains with two myosin‐V peptides (IQ3 and IQ4) have therefore been quantified in vitro, using fluorescence and near‐ and far‐UV CD. The results with separate domains show their differential affinity in interactions with the IQ motif, with the apo‐N domain interacting surprisingly weakly. Contrary to expectations, the effect of Ca2+ on the interactions of either peptide with either isolated domain is to increase affinity, reducing the Kd at physiological ionic strengths by >200‐fold to ∼75 nM for the N domain, and ∼10‐fold to ∼15 nM for the C domain. Under suitable conditions, intact (holo‐ or apo‐) calmodulin can bind up to two IQ‐target sequences. Interactions of apo‐ and holo‐calmodulin with the double‐length, concatenated sequence (IQ34) can result in complex stoichiometries. Strikingly, holo‐calmodulin forms a high‐affinity 1:1 complex with IQ34 in a novel mode of interaction, as a “bridged” structure wherein two calmodulin domains interact with adjacent IQ motifs. This apparently imposes a steric requirement for the α‐helical target sequence to be discontinuous, possibly in the central region, and a model structure is illustrated. Such a mode of interaction could account for the Ca2+‐dependent regulation of myosin V in vitro motility, by changing the structure of the regulatory complex, and paradoxically causing calmodulin dissociation through a change in stoichiometry, rather than a Ca2+‐dependent reduction in affinity.
Definition of the tempo of sequence diversity across an alignment and automatic identification of sequence motifs: Application to protein homologous families and superfamilies
Authors: May Alex C.W.
Published: November 2002

It is often possible to identify sequence motifs that characterize a protein family in terms of its fold and/or function from aligned protein sequences. Such motifs can be used to search for new family members. Partitioning of sequence alignments into regions of similar amino acid variability is usually done by hand. Here, I present a completely automatic method for this purpose: one that is guaranteed to produce globally optimal solutions at all levels of partition granularity. The method is used to compare the tempo of sequence diversity across reliable three‐dimensional (3D) structure‐based alignments of 209 protein families (HOMSTRAD) and that for 69 superfamilies (CAMPASS). (The mean alignment length for HOMSTRAD and CAMPASS are very similar.) Surprisingly, the optimal segmentation distributions for the closely related proteins and distantly related ones are found to be very similar. Also, optimal segmentation identifies an unusual protein superfamily. Finally, protein 3D structure clues from the tempo of sequence diversity across alignments are examined. The method is general, and could be applied to any area of comparative biological sequence and 3D structure analysis where the constraint of the inherent linear organization of the data imposes an ordering on the set of objects to be clustered.
Transmembrane helix predictions revisited
Authors: Chen Chien Peter , Kernytsky Andrew , Rost Burkhard
Published: November 2002

Methods that predict membrane helices have become increasingly useful in the context of analyzing entire proteomes, as well as in everyday sequence analysis. Here, we analyzed 27 advanced and simple methods in detail. To resolve contradictions in previous works and to reevaluate transmembrane helix prediction algorithms, we introduced an analysis that distinguished between performance on redundancy‐reduced high‐ and low‐resolution data sets, established thresholds for significant differences in performance, and implemented both per‐segment and per‐residue analysis of membrane helix predictions. Although some of the advanced methods performed better than others, we showed in a thorough bootstrapping experiment based on various measures of accuracy that no method performed consistently best. In contrast, most simple hydrophobicity scale‐based methods were significantly less accurate than any advanced method as they overpredicted membrane helices and confused membrane helices with hydrophobic regions outside of membranes. In contrast, the advanced methods usually distinguished correctly between membrane‐helical and other proteins. Nonetheless, few methods reliably distinguished between signal peptides and membrane helices. We could not verify a significant difference in performance between eukaryotic and prokaryotic proteins. Surprisingly, we found that proteins with more than five helices were predicted at a significantly lower accuracy than proteins with five or fewer. The important implication is that structurally unsolved multispanning membrane proteins, which are often important drug targets, will remain problematic for transmembrane helix prediction algorithms. Overall, by establishing a standardized methodology for transmembrane helix prediction evaluation, we have resolved differences among previous works and presented novel trends that may impact the analysis of entire proteomes.
Long membrane helices and short loops predicted less accurately
Authors: Chen Chien Peter , Rost Burkhard
Published: November 2002

Low‐resolution experiments suggest that most membrane helices span over 17–25 residues and that most loops between two helices are longer than 15 residues. Both constraints have been used explicitly in the development of prediction methods. Here, we compared the largest possible sequence—unique data sets from high‐ and low‐resolution experiments. For the high‐resolution data, we found that only half of the helices fall into the expected length interval and that half of the loops were shorter than 10 residues. We compared the accuracy of detecting short loops and long helices for 28 advanced and simple prediction methods: All methods predicted short loops less accurately than longer ones. In particular, loops shorter than 7 residues appeared to be very difficult to detect by current methods. Similarly, all methods tended to be more accurate for longer than for shorter helices. However, helices with more than 32 residues were predicted less accurately than all other helices. Our findings may suggest particular strategies for improving predictions of membrane helices.
Crystal structure of a major secreted protein of Mycobacterium tuberculosis—MPT63 at 1.5‐Å resolution
Authors: Goulding Celia W. , Parseghian Angineh , Sawaya Michael R. , Cascio Duilio , Apostol Marcin I. , Gennaro Maria Laura , Eisenberg David
Published: November 2002

MPT63 is a small, major secreted protein of unknown function from Mycobacterium tuberculosis that has been shown to have immunogenic properties and has been implicated in virulence. A BLAST search identified that MPT63 has homologs only in other mycobacteria, and is therefore mycobacteria specific. As MPT63 is a secreted protein, mycobacteria specific, and implicated in virulence, MPT63 is an attractive drug target against the deadliest infectious disease, tuberculosis (TB). As part of the TB Structural Genomics Consortium, the X‐ray crystal structure of MPT63 was determined to 1.5‐Ångstrom resolution with the hope of yielding functional information about MPT63. The structure of MPT63 is an antiparallel β‐sandwich immunoglobulin‐like fold, with the unusual feature of the first β‐strand of the protein forming a parallel addition to the small antiparallel β‐sheet. MPT63 has weak structural similarity to many proteins with immunoglobulin folds, in particular, Homo sapiens β2‐adaptin, bovine arrestin, and Yersinia pseudotuberculosis invasin. Although the structure of MPT63 gives no conclusive evidence to its function, structural similarity suggests that MPT63 could be involved in cell‐host interactions to facilitate endocytosis/phagocytosis.
Extension of a local backbone description using a structural alphabet: A new approach to the sequence‐structure relationship
Authors: de Brevern Alexandre G. , Valadié Hélène , Hazout Serge , Etchebest Catherine
Published: November 2002

Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 Cα long. They make it possible to approximate and correctly predict local protein three‐dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 Cα long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.
Redox‐dependent structural changes in archaeal and bacterial Rieske‐type [2Fe‐2S] clusters
Authors: Cosper Nathaniel J. , Eby D. Matthew , Kounosu Asako , Kurosawa Norio , Neidle Ellen L. , Kurtz Donald M. , Iwasaki Toshio , Scott Robert A.
Published: November 2002

Proteins containing Rieske‐type [2Fe‐2S] clusters play important roles in many biological electron transfer reactions. Typically, [2Fe‐2S] clusters are not directly involved in the catalytic transformation of substrate, but rather supply electrons to the active site. We report herein X‐ray absorption spectroscopic (XAS) data that directly demonstrate an average increase in the iron–histidine bond length of at least 0.1 Å upon reduction of two distantly related Rieske‐type clusters in archaeal Rieske ferredoxin from Sulfolobus solfataricus strain P‐1 and bacterial anthranilate dioxygenases from Acinetobacter sp. strain ADP1. This localized redox‐dependent structural change may fine tune the protein–protein interaction (in the case of ARF) or the interdomain interaction (in AntDO) to facilitate rapid electron transfer between a lower potential Rieske‐type cluster and its redox partners, thereby regulating overall oxygenase reactions in the cells.
Modifying specificity of antidigoxin antibodies using insertional mutagenesis
Authors: Krykbaev Rustem A. , Tsantili Panayota , Jeffrey Philip D. , Margolies Michael N.
Published: November 2002

Certain antibodies (Abs) elicited using the cardiac glycoside digoxin (digoxigenin tridigitoxoside) bind preferentially to analogs that differ from digoxin by substitutions on the cardenolide rings, the lactone, or by the presence or absence of attached sugars. Antibody 26–10 binds equally well to digoxin and digitoxin, which differ only by the presence in the former and the absence in the latter of an hydroxyl group at C12. Other antidigoxin Abs, however, can distinguish between these ligands by three orders of magnitude in binding. Inspection of the structure of Fab 26–10 complexed with digoxin shows a gap in complementarity in the region between the digoxin O12 and LCDR3. We proposed that insertions in LCDR3 might result in Abs that bind digitoxin preferentially. We produced libraries of mutants displayed on bacteriophage which were randomized at LCDR3 and contained LCDR3 insertions. Mutants were selected by panning against digoxin and analogs. The mutants bound digitoxin preferentially up to 47‐fold greater than digoxin. The mutants that bound well to digitoxin demonstrated a consensus sequence including the substitution of Trp at position L:94. Using site‐directed mutagenesis, the binding to digitoxin was shown to be maximized by the combination of an insertion and L:Trp94 mutation, moving the L 94 side chain closer to digoxin. We also selected mutants that bound preferentially to gitoxin, which, like digitoxin, lacks the 12‐hydroxyl, increasing relative binding to gitoxin up to 600‐fold compared to the unmutated Ab 26–10.
Cloning, overexpression, and characterization of a bacterial Ca2+‐dependent phospholipase D
Authors: Yang Hongying , Roberts Mary F.
Published: November 2002

Phospholipase D (PLD), an important enzyme involved in signal transduction in mammals, is also secreted by many microorganisms. A highly conserved HKD motif has been identified in most PLD homologs in the PLD superfamily. However, the Ca2+‐dependent PLD from Streptomyces chromofuscus exhibits little homology to other PLDs. We have cloned (using DNA isolated from the ATCC type strain), overexpressed in Escherichia coli (two expression systems, pET‐23a(+) and pTYB11), and purified the S. chromofuscus PLD. Based on attempts at sequence alignment with other known Ca2+‐independent PLD enzymes from Streptomyces species, we mutated five histidine residues (His72, His171, His187, His200, His226) that could be part of variants of an HKD motif. Only H187A and H200A showed dramatically reduced activity. However, mutation of these histidine residues to alanine also significantly altered the secondary structure of PLD. Asparagine replacements at these positions yielded enzymes with structure and activity similar to the recombinant wild‐type PLD. The extent of phosphatidic acid (PA) activation of PC hydrolysis by the recombinant PLD enzymes differed in magnitude from PLD purified from S. chromofuscus culture medium (a 2‐fold activation rather than 4–5‐fold). One of the His mutants, H226A, showed a 12‐fold enhancement by PA, suggesting this residue is involved in the kinetic activation. Another notable difference of this bacterial PLD from others is that it has a single cysteine (Cys123); other Streptomyces Ca2+‐independent PLDs have eight Cys involved in intramolecular disulfide bonds. Both C123A and C123S, with secondary structure and stability similar to recombinant wild‐type PLD, exhibited specific activity reduced by 10−5 and 10−4. The Cys mutants still bound Ca2+, so that it is likely that this residue is part of the active site of the Ca2+‐dependent PLD. This would suggest that S. chromofuscus PLD is a member of a new class of PLD enzymes.
Prediction of partial membrane protein topologies using a consensus approach
Authors: Nilsson Johan , Persson Bengt , von Heijne Gunnar
Published: November 2002

We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole‐genome analysis reveals that a reliable partial consensus topology can be predicted for ∼70% of all membrane proteins in a typical bacterial genome and for ∼55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.
Global Optimization of Gas Allocation to a Group of Wells in Artificial Lift Using Nonlinear Constrained Programming
Authors: Alarco´n Gabriel A. , Torres Carlos F. , Go´mez Luis E.
Published: November 2002

Continuous flow gas lift is one of the most common artificial lift methods widely used in the oil industry. A continuous volume of high-pressure gas is injected as deep as possible into the tubing, to gasify the oil column, and thus facilitate the production. If there is no restriction in the amount of injection gas available, sufficient gas can be injected into each oil well to reach maximum production. However, the injection gas available is generally insufficient. An inefficient gas allocation in a field with limited gas supply reduces the revenues, since excessive gas injection is expensive due to the high gas prices and compressing costs. Therefore, it is necessary to assign the injection gas into each well in optimal form to obtain the field maximum oil production rate. The gas allocation optimization can be considered as a maximization of a nonlinear function, which models the total oil production rate for a group of wells. The variables or unknowns for this function are the gas injection rates for each well, which are subject to physical restrictions. In this work a nonlinear optimization technique, based on an objective function with constraints, was implemented to find the optimal gas injection rates. A new mathematical fit to the gas-lift performance curve (GLPC) is presented and the numeric results of the optimization are given and compared with those of other methods published in the specialized literature. The GLPC can be either measured in the field, or alternatively generated by computer simulations, by mean of nodal analysis. The optimization technique proved fast convergence and broad application.
Numerical Simulation of Corrosion Inhibitor Transport in Pipelines Carrying Oil-Water Mixtures
Authors: Rojas-Figueroa Antonio , Fairuzov Yuri V.
Published: November 2002

The transport of corrosion inhibitors in a pipeline carrying crude oil-water mixture has been studied using a transient liquid-liquid two-phase flow model. The fluid flow model (the hydrodynamic model) is based on a two-fluid model of two-phase flow. The model allows simulating the transfer of inhibitor from one phase to another (inhibitor partitioning) under steady-state and transient oil-water flow conditions. Both stratified and dispersed flow patterns can be modeled. Numerical simulations are presented to demonstrate the effects of topography of the line, locations of the inhibitor injection point, flow pattern, and partitioning of the inhibitor between the phases on the distribution of inhibitor concentration along the pipeline. The modeling can be used to predict the inhibitor volume needed to be injected (the dose rate) in order to provide the required inhibitor concentration in critical sections of crude-oil pipelines.
Chemically Improved Filter Cakes for Drilling Wells
Authors: Nandurdikar Neeraj S. , Takach Nicholas E. , Miska Stefan Z.
Published: November 2002

Blast furnace slag (BFS) is a latent hydraulic material similar in composition to Portland cement. BFS was originally studied for mud to cement (MTC) purposes. This application called for large quantities of BFS (40–500 ppb (lb/bbl)) and ultimately proved to be ineffective. Subsequently, BFS has been investigated as an additive in drilling fluids. In a recent study, muds containing additive-level concentrations (5–30 lb/bbl) of BFS were shown to be effective in reducing formation damage. The present work extends the investigation of BFS as a drilling fluid additive. Specifically, we have explored the use of chemical reagents to activate the BFS in filter cakes to achieve cakes that are thin, impervious and firm. Filter cakes were formed from slag-laden drilling fluids in a high-pressure, high-temperature reverse filtration apparatus (permeability plugging apparatus). Studies were conducted with partially hydrolyzed polyacrlyamide (PHPA) muds and CaCO3-based fluids containing different loadings of BFS. Filter cakes of these fluids were treated with several different activators and the results were compared to cakes containing no BFS. Different activation techniques were investigated and a novel device was designed to measure the strength of the filter cakes. An environmental scanning electron microscope examined the relationship between the structural features of the activated cakes and their strengths. This study demonstrates that filter cakes containing BFS can be chemically activated to produce thin, firm cakes with improved filtration properties. These cakes should be able to form better bonds with cement subsequently used for completion.
Drillstring Vibration and Wellbore Instability
Authors: Pla´cido Joa˜o Carlos R. , Santos He´lio M. R. , Galeano Yadira Diaz
Published: November 2002

Wellbore instability can be attributed to several causes. The ones thought to be most important include: chemical interaction with the drilling fluid, high tectonic stresses, and insufficient mud weight. Drillstring vibration, although not traditionally addressed as a potential cause, might influence the stability of wellbores drilled in specific formations. Evidence of the strong correlation between severe vibration and wellbore instability has been reported in the literature. However, a more thorough understanding of the phenomenon is still lacking. This paper describes a study that has been developed by PETROBRAS focusing on how drillstring vibration impacts wellbore instability. Vibration has been monitored in some wells, and events related to borehole enlargement were observed. Four field cases are presented showing a strong correlation between high vibration level and wellbore enlargement in different lithologies. Other sources of wellbore enlargement have also been identified, and they can be clearly separated from vibration.
Analysis of Leak-off Tests in Shallow Marine Sediments
Authors: Zhou Desheng , Wojtanowicz Andrew K.
Published: November 2002

Typical analysis of the Leak-off testing (LOT) in wells assumes elastic wellbore and involves identification of diversion points from linear trends of the recorded plots. However, LOTs from wells in the shallow marine sediments (SMS) are inherently nonlinear and their analysis becomes a problem. The paper presents mathematical models of the pressure-volume behavior for two different possible failures around the casing shoe, annular crack (cement-rock parting) and formation fracture. The study submits that these two failure modes would control abnormal LOT patterns. A general pressure-volume model of LOT has been developed including volumetric effects of wellbore expansion, mud loss into the rock, and propagation of an annular crack or plastic fracture. A diagnostic method is proposed to identify LOT-control mechanisms (i.e., formation fracture, annular crack, or mud loss) by analyzing the shut-in section of the LOT’s plot.
A Simplified Semi-Analytical Model for Water-Coning Control in Oil Wells With Dual Completions System
Authors: Siemek Jakub , Stopa Jerzy
Published: November 2002

In this paper, a mathematical model and numerical investigations on dynamic water/oil contact (WOC) in a reservoir with active bottom waters are addressed. An original analytical solution describing the theoretical shape of the dynamic oil-water contact in the reservoir is presented and compared with some results of numerical simulations made by a commercial flow-simulator. It is shown that both water and oil may be produced simultaneously but selectively from their respective zones. This allows a theoretical control of the dynamic WOC by the water flow rate. Consequently, an increased amount of oil can be produced along with water, depending on the well completion interval in relation to the oil/water contact in the reservoir. This shows the possibility of an “in situ” separation concept. The advantage of such a separate production of water and oil is to prevent the mixing oil with water within the pump and tubing.
Studying collisions in the general physics laboratory with quadrature light emitting diode sensors
Authors: DeYoung P. A. , Mulder B.
Published: November 2002

We have developed the means to measure position rapidly and precisely as a function of time in the general physics laboratory. These measurements are of sufficient quality that velocities and accelerations can be calculated from the position data using numerical derivatives. The precision of the measurements is such that any disagreement between theoretical expectations and experimental measurements is less than a few percent. Measurements of the system under study can be made as rapidly as every 200 μs, which is faster than the typical time scales over which the system changes. Measuring rapidly also allows one to investigate additional phenomena not previously accessible and to see features of the physics previously unobserved. The measurement system is based on commercially available sensors, computer hardware, and computer software (LABVIEW™). Many general physics laboratories based on this system have been developed but only an investigation of Newton’s second law will be described here.
Tabletop thermoacoustic refrigerator for demonstrations
Authors: Russell Daniel A. , Weibull Pontus
Published: November 2002

An inexpensive (less than $25) tabletop thermoacoustic refrigerator for demonstration purposes was built from a boxed loudspeaker, acrylic tubing and sheet, a roll of 35 mm film, fishing line, an aluminum plug, and two homemade thermocouples. Temperature differences of more than 15 °C were achieved after running the cooler for several minutes. While nowhere near the efficiency of devices described in the literature, this demonstration model effectively illustrates the behavior of a thermoacoustic refrigerator.
A simple instrument for measuring time intervals with subnanosecond resolution
Authors: Fontanelli F. , Repetto L. , Chittofrati R.
Published: November 2002

We have built a simple and inexpensive instrument capable of measuring time intervals from 0 up to 100 ns with a 0.1-ns resolution. We use easy-to-find components, and the construction can be performed by an undergraduate student.
Thin lens ray tracing
Authors: Gatland Ian R.
Published: November 2002

A ray tracing approach to thin lens analysis, based on a vector form of Snell’s law for paraxial rays, is proposed as an alternative to the usual approach in introductory physics courses. The ray tracing approach accommodates skew rays and thus provides a complete analysis.
Energy balance problems in systems of induced and permanent electric and magnetic dipoles
Authors: Anderson Robert A. , Martin James E.
Published: November 2002

There are many problems where a detailed understanding of the interaction energy of systems of dipoles is needed, including electrorheological and magnetorheological fluids, ferrofluids, magnetic composites, and dielectrics. We have constructed soluble microscopic problems involving electric and magnetic dipoles to investigate energy balance, and have come to some understanding of the proper form of the dipolar free energy in aggregations of induced or permanent dipoles and mixtures thereof. The resulting equations clarify misconceptions sometimes found in the literature, and lead to greater intuition about the subtle aspects of the dipolar interactions. We discuss the application of these equations to dipole simulations to extract the dipole energy and material dielectric constant.
Transient behavior of simple RC circuits
Authors: Preyer Norris W.
Published: November 2002

I report on simulations of the evolution of surface charges, the retarded electric potential, and the electric field in a simple resistor–capacitor (RC) circuit and in an RC circuit with a switch. The circuits have high resistance, so radiation and inductive effects are not significant. The simulations illustrate nonquasistatic effects due to the finite speed of light, and should be useful in teaching students how circuits respond to changes.
Experimental study of the Neumann and Dirichlet boundary conditions in two-dimensional electrostatic problems
Authors: Gil Salvador , Saleta Martı́n Eduardo , Tobia Dina
Published: November 2002

We present the results of an experimental study of the implications of the Neumann and Dirichlet boundary conditions on the solution of two-dimensional electrostatic problems. The experimental setup is simple and low cost. The experimental results are compared with theoretical expectations using a spreadsheet program to solve Laplace’s equation with the appropriate boundary conditions. Excellent agreement is found between the experimental results and the calculations. The simplicity of the experiment and of the theoretical interpretation makes this experiment accessible to beginning students.
Harmonic? Anharmonic? Inharmonic?
Authors: Fletcher Neville H.
Published: November 2002

In molecular spectroscopy, an anharmonic oscillator has a nonparabolic potential which results in a nonharmonic absorption spectrum, but the same oscillator treated classically has a precisely harmonic vibrational spectrum. To avoid confusion, it is suggested that such an oscillator should simply be called nonlinear. The term “inharmonic” is suggested as an appropriate descriptor for classical oscillators, such as metal bars, that have nonharmonic vibrational spectra even in the linear limit of small vibrations.