bluuebunny/crossref_metadata_2025 huggingface dataset:
Far‐Field R Wave Sensing Causing Prolongation of the Atrial Escape Interval of DDD Pacemakers with Atrial‐Based Lower Rate Timing
Authors: BAROLD S. SERGE
Published: November 2003

This report describes the occurrence of prolonged atrial escape intervals (AEI) initiated by sensing of ventricular premature complexes (VPC) without a preceding atrial depolarization or an AV delay in two patients with DDD pacemakers with an atrial‐based lower rate response. The prolonged AEIs were due to ventriculoatrial cross‐talk so that atrial sensing of the far‐field R wave of the VPCs occurred before detection of the R wave by the ventricular channel as a near‐field signal. Early atrial sensing of the far‐field R wave was promoted by a high atrial sensitivity and/or low ventricular sensitivity and was eliminated by reducing atrial sensitivity and/or increasing ventricular sensitivity. This manifestation of far‐field sensing should not be interpreted as malfunction of dual chamber pacemakers with atrial‐based lower rate timing. (PACE 2003; 26:2188–2191)
A new research framework for family resource management applied to financial preparedness of mid‐life working couplesa
Authors: McGregor Sue , Ellison Margaret Bateman
Published: November 2003

In order to continue to move forward, the field of family resource management needs rich research programmes based on holistic, synergetic approaches. To this end, this paper presents a multi‐perspective research framework for designing family resource management research programmes using insights from five existing perspectives to understand families: life cycle stages, life spiral across generations, unplanned life transitions, the historical context of the course of one's life, and the different levels of influence on daily life ranging from the cosmos to the unknown (spheres of influence perspective). A modernization of the life cycle perspective is proposed as well to accommodate the gap between the full nest and the empty nest. We then use this new research framework to shape the development of a programme targeting retirement preparedness of mid‐life working couples with dependents (children and aged or infirm adults). We anticipate that deeper, more holistic insights into family resource management strategies can be gained from using this new research framework.
Effect of cooking method and variety on the sensory quality of rice
Authors: Crowhurst Daniel G. , Creed Philip G.
Published: November 2003

This study aimed to determine the effects of different cooking methods on white, milled rice. Two methods were evaluated (the Excess, or American method, and the Pilaf method, also known as the Oriental, or calculated‐water method), which are commonly used, both domestically and in the catering industry. The effects of the two cooking methods were assessed on four varieties of rice, American Long Grain, American Long Grain Easy Cook, Basmati, and Thai Jasmine rice. The study used sensory evaluation techniques and terminology previously used in the field of rice research. The aim of the study was to assess potential differences in sensory attributes and overall acceptability. Affective testing techniques (hedonic and relative‐to‐ideal scales) were used to measure consumer preference. A consumer questionnaire also investigated the effects of rice eating, buying and cooking behaviour on the preferred cooking method. The subjects taking part in the study were taken from a typical student population at Bournemouth University. In general, the Pilaf method resulted in rice products that were stickier, firmer and drier in texture, with a more acceptable flavour. Overall acceptability and preference for the Pilaf method was higher, except in the case of Basmati rice. Models of acceptability accounted for up to half the variation so sensory attributes could not be used to predict the acceptability of rice products reliably.
Rapid, inexpensive, actionable concept generation and optimization: the use and promise of self‐authoring conjoint analysis for the food service industry
Authors: Moskowitz Howard R. , Gofman Alex , Itty Barbara , Katz Rachel , Manchaiah Mahdu , Ma Zhenyu
Published: November 2003

This paper presents the background thinking, needs identification, technology, and user issues that have led to the creation of a self‐authoring system for conjoint measurement appropriate to the food service industry. Self‐authoring systems allow the user to create the study, deploy it on the Internet, and collect the data, without the help of a professional researcher or programming expert. The technology uses conjoint measurement, and is embodied in an Internet ASP system (application service provider) called IdeaMap®.Net. The technology empowers the user to do conjoint analysis studies rapidly and cost‐effectively, and to solicit new ideas from the same respondents who participate. This paper demonstrates IdeaMap®.Net for food service issues, but the applications transcend particular issues and problems, finding applicability in a broad range of topics.
Inactivation of refrigerator biofilm bacteria for application in the food service environment
Authors: Michaels Barry , Ayers Troy , Celis Marlene , Gangar Vidhya
Published: November 2003

Refrigerator biofilm formation in food environments can result in spoilage and food safety problems. Biofouling of food contact surfaces are difficult to combat, and while there are significant risks involved with tolerating their presence, methods for their removal are not commonly available. In this study, biofilms were grown on plastic refrigerator trays. Cultures of mixed wild strains were started using kitchen scraps suspended in nutrient broth. Biofilms were allowed to mature with approximately 109 CFU per tray test area. Spoilage species identified included Pseudomonas putida, Sphingobacterium multivorum, Citrobacter freundii and Proteus vulgaris. A series of 39 different treatment interventions were trialed during three different biofilm test runs. Results obtained from treatments ranged from a less than 1 log10 reduction for light duty cleaning operations to over a 5 log10 reduction involving more complex treatment methods. The latter included combinations of hot soapy water (75 °C), scrubbing, treatment with high pH (12.0) cleaners followed by acetic acid (vinegar) exposure and included pre‐ and post‐treatment wiping with paper towels.
The potential for baker’s yeast (Saccharomyces cerevisiae) in the production of wine from banana, cooking banana and plantain
Authors: Onwuka U. N. , Awam F. N.
Published: November 2003

Musa species (banana, cooking banana and plantain) were bought from a market in Umuahia Abia State, Nigeria. Samples were chemically analysed and subsequently used in wine production by conventional methods of must preparation, filtration, primary and secondary fermentation (with baker’s yeast as inoculum), pasteurization and bottling. Physical–chemical properties and microbial content were monitored during the process. Sensory characteristics of the Musa wines were evaluated. The Musa species were found to have a fermentable sugar level of 18.81–23.57%. The wines produced showed an alcohol content of 9.96–11.25, brix (scale of densities used in the sugar industry) level 8.00–8.15, ash 0.32–0.45, and titratable acidity 1.00–1.108. Sensory evaluation indicated a significant difference in taste, colour and general acceptability at P < 0.05 among the wines. Potential opportunities exist to develop and produce local fruit wines for consumption by both the domestic market and tourists.
Pressure–temperature conditions and retrograde paths of eclogites, garnet–glaucophane rocks and schists from South Sulawesi, Indonesia
Authors: MIYAZAKI K. , ZULKARNAIN I. , SOPAHELUWAKAN J. , WAKITA K.
Published: November 2003

High‐pressure metamorphic rocks exposed in the Bantimala area, c. 40 km north‐east of Ujung Pandang, were formed as a Cretaceous subduction complex with fault‐bounded slices of melange, chert, basalt, turbidite, shallow‐marine sedimentary rocks and ultrabasic rocks. Eclogites, garnet–glaucophane rocks and schists of the Bantimala complex have estimated peak temperatures of T =580–630 °C at 18 kbar and T =590–640 °C at 24 kbar, using the garnet–clinopyroxene geothermometer. The garnet–omphacite–phengite equilibrium is used to estimate pressures. The distribution coefficient KD1=[(Xpyr)3(Xgrs)6/(Xdi)6]/[(Al/Mg)M2,wm (Al/Si)T2,wm]3 among omphacite, garnet and phengite is a good index for metamorphic pressures. The KD1values of the Bantimala eclogites were compared with those of eclogites with reliable P–T  estimates. This comparison suggests that peak pressures of the Bantimala eclogites were P=18–24 kbar at T =580–640 °C. These results are consistent with the P–T  range calculated using garnet–rutile–epidote–quartz and lawsonite–omphacite–glaucophane–epidote equilibria.
Tectonometamorphic evolution of the Himalayan metamorphic core between the Annapurna and Dhaulagiri, central Nepal
Authors: VANNAY J.‐C. , HODGES K. V.
Published: November 2003

The metamorphic core of the Himalaya in the Kali Gandaki valley of central Nepal corresponds to a 5‐km‐thick sequence of upper amphibolite facies metasedimentary rocks. This Greater Himalayan Sequence (GHS) thrusts over the greenschist to lower amphibolite facies Lesser Himalayan Sequence (LHS) along the Lower Miocene Main Central Thrust (MCT), and it is separated from the overlying low‐grade Tethyan Zone (TZ) by the Annapurna Detachment. Structural, petrographic, geothermobarometric and thermochronological data demonstrate that two major tectonometamorphic events characterize the evolution of the GHS. The first (Eohimalayan) episode included prograde, kyanite‐grade metamorphism, during which the GHS was buried at depths greater than c. 35 km. A nappe structure in the lowermost TZ suggests that the Eohimalayan phase was associated with underthrusting of the GHS below the TZ. A c. 37 Ma 40Ar/39Ar hornblende date indicates a Late Eocene age for this phase. The second (Neohimalayan) event corresponded to a retrograde phase of kyanite‐grade recrystallization, related to thrust emplacement of the GHS on the LHS. Prograde mineral assemblages in the MCT zone equilibrated at average T =880 K (610 °C) and P =940 MPa (=35 km), probably close to peak of metamorphic conditions. Slightly higher in the GHS, final equilibration of retrograde assemblages occurred at average T =810 K (540 °C) and P=650 MPa (=24 km), indicating re‐equilibration during exhumation controlled by thrusting along the MCT and extension along the Annapurna Detachment. These results suggest an earlier equilibration in the MCT zone compared with higher levels, as a consequence of a higher cooling rate in the basal part of the GHS during its thrusting on the colder LHS. The Annapurna Detachment is considered to be a Neohimalayan, synmetamorphic structure, representing extensional reactivation of the Eohimalayan thrust along which the GHS initially underthrust the TZ. Within the upper GHS, a metamorphic discontinuity across a mylonitic shear zone testifies to significant, late‐ to post‐metamorphic, out‐of‐sequence thrusting. The entire GHS cooled homogeneously below 600–700 K (330–430 °C) between 15 and 13 Ma (Middle Miocene), suggesting a rapid tectonic exhumation by movement on late extensional structures at higher structural levels.
Progressive metamorphism of pelitic rocks from protolith to granulite facies, Dutchess County, New York, USA: constraints on the timing of fluid infiltration during regional metamorphism
Authors: WHITNEY D. L. , MECHUM T. A. , KUEHNER S. M. , DILEK Y. R.
Published: November 2003

A complete Barrovian sequence ranging from unmetamorphosed shales to sillimanite–K‐feldspar zone metapelitic gneisses crops out in a region extending from the Hudson River in south‐eastern New York state, USA, to the high‐grade core of the Taconic range in western Connecticut. NNE‐trending subparallel biotite, garnet, staurolite, kyanite, sillimanite and sillimanite–K‐feldspar isograds have been identified, although the assignment of Barrovian zones in the high‐grade rocks is complicated by the appearance of fibrolitic sillimanite at the kyanite isograd.

Thermobarometric results and reaction textures are used to characterize the metamorphic history of the sequence. Pressure–temperature estimates indicate maximum metamorphic conditions of 475 °C, c. 3–4 kbar in the garnet zone to >720 °C, c. 5–6 kbar in the highest grade rocks exposed. Some samples in the kyanite zone record anomalous (low) peak conditions because garnet composition has been modified by fluid‐assisted reactions.

There is abundant petrographic and mineral chemical information indicating that the sequence (with the possible exception of the granulite facies zone) was infiltrated by a water‐rich fluid after garnet growth was nearly completed. The truncation of fluid inclusion trails in garnet by rim growth or recrystallization, however, indicates that metamorphic reactions involving garnet continued subsequent to initial infiltration.

The presence of these textures in some zones of a well‐constrained Barrovian sequence allows determination of the timing of fluid infiltration relative to the P–T  paths. Thermobarometric results obtained using garnet compositions at the boundary between fluid–inclusion‐rich and inclusion‐free regions of the garnet are interpreted to represent peak metamorphic conditions, whereas rim compositions record slightly lower pressures and temperatures. Assuming that garnet grew during a single metamorphic event, infiltration must have occurred at or slightly after the peak of metamorphism, i.e. 4–5 kbar and a temperature of c. 525–550 °C for staurolite and kyanite zone rocks.
Carbon isotope exchange during polymetamorphism in the Panamint Mountains, California, USA
Authors: BERGFELD D. , NABELEK P. I. , LABOTKA T. C.
Published: November 2003

Carbon isotope fractionations between calcite and graphite in the Panamint Mountains, California, USA, demonstrate the importance of mass balance on carbon isotope values in metamorphosed carbon‐bearing minerals while recording the thermal conditions during peak regional metamorphism. Interbedded graphitic marbles and graphitic calcareous schists in the Kingston Peak Formation define distinct populations on a δ13C(gr)–δ13C(cc) diagram. The δ13C values of both graphite and calcite in the marbles are higher than the values of the respective minerals in the schists. δ13C values in both rock types were controlled by the relative proportions of the carbon‐bearing minerals: calcite, the dominant carbon reservoir in the marble, largely controlled the δ13C values in this lithology, whereas the δ13C values in the schists were largely controlled by the dominant graphite. This is in contrast to graphite‐poor calcsilicate systems where carbon isotope shifts in carbonate minerals are controlled by decarbonation reactions.

The marbles record a peak temperature of 531±30 °C of a Jurassic low‐pressure regional metamorphic event above the tremolite isograd. In the schists there is a much wider range of recorded temperatures. However, there is a mode of temperatures at c. 435 °C, which approximately corresponds to the temperatures of the principal decarbonation metamorphic reactions in the schists, suggesting that the carbon exchange was set by loss of calcite and armouring of graphite by newly formed silicate minerals. The armouring may explain the relatively large spread of apparent temperatures. Although the modal temperature also corresponds to the approximate temperature of the Cretaceous retrograde event, retrograde exchange is thought less likely due to very slow exchange rates involving well‐crystallized graphite, armouring of graphite by silicates during the earlier event, and because of other barriers to retrograde carbon exchange. Thus, only the calcite–graphite carbon isotope fractionations recorded by the marbles demonstrate the high‐temperature conditions of the low‐pressure Jurassic metamorphic event that was associated with the emplacement of granitic plutons to the west of the Panamint Mountains.
High‐pressure metamorphism caused by magma loading in Fiordland, New Zealand
Authors: BROWN E. H.
Published: November 2003

Cretaceous granulite facies metamorphism in the Fiordland area of New Zealand has distinctive mineralogical, textural and structural features that set it apart from most other regional metamorphic belts. The metamorphism, developed over a 30×150‐km area and the consequence of a 20‐km‐thick increment to crustal thickness, is closely associated in space and time with a large plutonic complex, the Western Fiordland Orthogneiss (WFO). Although temperatures and pressures as high as 700 °C and 12 kbar were attained, the metamorphic overprint on earlier low‐pressure assemblages is weak and incomplete. Little strain accompanied the metamorphism. The temperature threshold at which metamorphic recrystallization is recorded is over 500 °C. Zoned garnets are preserved at unusually high temperatures, indicating duration of metamorphism on the order of 10 times shorter than in most other regional terranes. This pattern of features bears close similarity to metamorphism in the Coast Plutonic Complex in North America, where a mechanism of ‘magma loading’ has been invoked. In Fiordland, the high‐pressure metamorphism can be explained by depression of country rock under a crustal zone that is inflated by intrusion of the WFO. Regional structure of the WFO as a horizontally sheeted complex suggests that the pluton was emplaced by vertical displacement of country rock, and supports the magma loading model.
Development of Silicone Rubber Hollow Fiber Membrane Oxygenator for ECMO
Authors: Motomura Tadashi , Maeda Tomohiro , Kawahito Shiniji , Matsui Takahiro , Ichikawa Seiji , Ishitoya Hiroshi , Kawamura Masaki , Shinohara Toshiyuki , Sato Koshiro , Kawaguchi Yoichiro , Taylor Deborah , Oestmann Daniel , Glueck Julie , Nosé Yukihiko
Published: November 2003

Abstract:  Silicone rubber hollow fiber membrane produces an ideal gas exchange for long‐term ECMO due to nonporous characteristics. The extracapillary type silicone rubber ECMO oxygenator having an ultrathin hollow fiber membrane was developed for pediatric application. The test modules were compared to conventional silicone coil‐type ECMO modules. In vitro experiments demonstrated a higher O2 and CO2 transfer rate, lower blood flow resistance, and less hemolysis than the conventional silicone coil‐type modules. This oxygenator was combined with the Gyro C1E3 centrifugal pump, and three ex vivo experiments were conducted to simulate pediatric V‐A ECMO condition. Four day and 6 day experiments were conducted in cases 1 and 2, respectively. Case 3 was a long‐term experiment up to 2 weeks. No plasma leakage and stable gas performances were achieved. The plasma free hemoglobin was maintained within a normal range. This compact pump‐oxygenator system in conjunction with the Gyro C1E3 centrifugal pump has potential for a hybrid total ECMO system.
Intraportal Transplantation of Allogenic Pancreatic Islets Encapsulated in Barium Alginate Beads in Diabetic Rats
Authors: Schneider Stephan , Von Mach Marc‐Alexander , Kraus Oliver , Kann Peter , Feilen; Peter Johannes
Published: November 2003

Abstract:  The survival of microencapsulated islets transplanted into the unmodified peritoneal cavity is limited, even if capsular overgrowth is restricted to a minimum, due to an insufficient oxygen supply to the islets. Therefore, research efforts should focus on finding or creating a transplantation site, which permits a closer contact between the encapsulated islets and the blood. For this reason, the liver could be an interesting candidate. The aim of the present study was to test the hypothesis that the intraportal transplantation of allogenic islets encapsulated in small‐sized barium alginate beads is safe and succeeds to induce normoglycemia in diabetic rats. The intraportal transplantation of 1,500 islets encapsulated in barium alginate beads leads within 10 h and up to 24 h to blood sugar concentrations below 40 mg/dL, most likely due to an acute cell lysis of the graft. Afterwards, the reappearance of the diabetic state could be detected in these animals. Most likely these findings are induced by a sudden hypoxia to the islets. We believe that the occlusion of small‐ and medium‐sized portal venules by the alginate beads is responsible for this effect. Therefore, in forthcoming studies, barium alginate beads, with a diameter below 350 µm, stabilized with medical approved additives should be used.
Apoptosis of Mesothelial Cells Caused by Unphysiological Characteristics of Peritoneal Dialysis Fluids
Authors: Alscher Dominik M. , Biegger Dagmar , Mettang Thomas , Van Der Kuip Heiko , Kuhlmann Ulrich , Fritz Peter
Published: November 2003

Abstract:  There is an ongoing debate as to which peritoneal dialysis fluids (PDFs) provide the best preservation of peritoneal cells. To investigate this topic further, we measured apoptosis and necrosis of cultured mesothelial cells (MCs) after exposure to different single unphysiological features of PDFs and PDFs for whole. MCs were incubated in buffers containing plasticizers, high osmolarity by sodium chloride, low pH, and high glucose for 0.5, 4, and 24 h. The same procedure was repeated with different PDFs. Apoptosis and necrosis were measured by FACS‐analysis (annexin‐FITC and propidium iodide). We found that plasticizers were clearly able to induce apoptosis after 24 h (18 ± 4%). The same result was observed with high osmolarity by sodium chloride (17 ± 5%), but not for high glucose (9 ± 8%). All fluids with low pH (5.2) caused severe and almost complete necrosis (after 4 and 24 h). Incubation in neutral, two‐compartment PDFs (glucose 4.25%) without plasticizers for 4 h showed no significant necrosis (3%), but after 24 h apoptosis was detectable in 10 ± 9% and necrosis in 29 ± 8% of MCs. In conclusion, after improving PDFs and introducing neutral fluids, further attention should be drawn to inducers of apoptosis. Apoptosis can be detected quite early (24 h) and is caused by plasticizers and  high  osmolarity.
Electronic Visual Prosthesis
Authors: Liu Wentai , Sivaprakasam Mohanasankar , Singh Praveen R. , Bashirullah Rizwan , Wang Guoxing
Published: November 2003

Abstract: Retinitis pigmentosa (RP) and age‐related macular degeneration (AMD) are incurable diseases that result in profound vision loss due to degeneration of the light sensing photoreceptors. However, the discovery that direct electrical stimulation of the retinal neurons creates visual sensation has inspired prosthetic devices aimed to restore useful vision in RP/AMD patients. The approach to one such electronic visual prosthesis is described in this article. The prosthesis consists of an external unit and an internal unit. The communication link has three components—power and data transfer from the external to the internal unit, and data transfer from the internal to the external unit. A novel method of integrating power transfer and back telemetry is described here. The goal is to design a stimulator chip with a small area with low power consumption. This chip, capable of stimulating 60 dedicated electrodes, is fabricated using AMI 1.2 µm process technology and the results are presented. Improvements in the design to increase the number of outputs to 1,000 have been discussed. The new circuit is aimed at increasing the circuit density, reducing power per stimulus, and meeting the requirements more closely than the previous designs. The results of the designed  chip  are presented.
The Artificial Synapse Chip: A Flexible Retinal Interface Based on Directed Retinal Cell Growth and Neurotransmitter Stimulation
Authors: Peterman Mark C. , Mehenti Neville Z. , Bilbao Kalayaan V. , Lee Christina J. , Leng Theodore , Noolandi Jaan , Bent Stacey F. , Blumenkranz Mark S. , Fishman Harvey A.
Published: November 2003

Abstract:  The Artificial Synapse Chip is an evolving design for a flexible retinal interface that aims to improve visual resolution of an electronic retinal prosthesis by addressing cells individually and mimicking the physiological stimulation achieved in synaptic transmission. We describe three novel approaches employed in the development of the Artificial Synapse Chip: (i) micropatterned substrates to direct retinal cell neurite growth to individual stimulation sites; (ii) a prototype retinal interface based on localized neurotransmitter delivery; and (iii) the use of soft materials to fabricate these devices. By patterning the growth of cells to individual stimulation sites, we can improve the selectivity of stimulation and decrease the associated power requirements. Moreover, we have microfabricated a neurotransmitter  delivery system based on a 5‐µm aperture in a 500‐nm‐thick silicon nitride membrane overlying a microfluidic channel. This device can release neurotransmitter volumes as small as 2 pL, demonstrating the possibility of chemical‐based prostheses. Finally, we have fabricated and implanted an equivalent device using soft flexible materials that conform to the retinal tissue more effectively. As many of the current retinal prosthesis devices use hard materials and electrical excitation at a lower resolution, our approach may provide more physiologic retinal stimulation.
A Model for Intracortical Visual Prosthesis Research
Authors: Troyk Philip , Bak Martin , Berg Joshua , Bradley David , Cogan Stuart , Erickson Robert , Kufta Conrad , McCreery Douglas , Schmidt Edward , Towle Vernon
Published: November 2003

Abstract:  In the field of visual prosthesis research, it has generally been held that animal models are limited to testing the safety of implantable hardware due to the inability of the animal to provide a linguistic report of perceptions. In contrast, vision scientists make extensive use of trained animal models to investigate the links between visual stimuli, neural activities, and perception. We describe an animal model for cortical visual prosthesis research in which novel animal psychophysical testing has been employed to compensate for the lack of a linguistic report. One hundred and fifty‐two intracortical microelectrodes were chronically implanted in area V1 of a male macaque. Receptive field mapping was combined with eye‐tracking to develop a reward‐based training procedure. The animal was trained to use electrically induced point‐flash percepts, called phosphenes, in performing a memory saccade task. It is our long‐term goal to use this animal model to investigate stimulation strategies in developing a multichannel sensory cortical interface.
Codon adaptation index as a measure of dominating codon bias
Authors: Carbone A. , Zinovyev A. , Képès F.
Published: November 2003

We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a ‘universal’ measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a sole source of biological information, the algorithm provides a reference set of genes which is highly representative of the bias. This set can be used to compute the CAI of genes of prokaryotic and eukaryotic organisms, including those whose functional annotation is not yet available. An important application concerns the detection of a reference set characterizing translational bias which is known to correlate to expression levels; in this case, the algorithm becomes a key tool to predict gene expression levels, to guide regulatory circuit reconstruction, and to compare species. The algorithm detects also leading–lagging strands bias, GC-content bias, GC3 bias, and horizontal gene transfer. The approach is validated on 12 slow-growing and fast-growing bacteria, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster.

Availability:  http://www.ihes.fr/~materials.
Applying signal theory to the analysis of biomolecules
Authors: Kauer Gerhard , Blöcker Helmut
Published: November 2003

Motivation: The accumulation of sequence-related and other biological data for basic research and application purposes invites disaster. It appears very likely that neither traditional thinking nor current technologies (including their foreseeable evolutionary developments) will be able to cope with this ever intensifying situation.

Results: We present the detailed theoretical background for applying signal theory, as known from speech recognition and image analysis, to the analysis of biomolecules. The general scheme is as follows: biochemical and biophysical properties of biomolecules are used to model an n-dimensional signal which represents the entire information-bearing biomolecule. Such signals are used to search for biological principles, analogies or similarities between biomolecules. In a series of simple experiments (bacterial DNA, generation of real signals using melting enthalpies, detection filtering by convolution of signals) we have shown that the novel system for comparative analysis of the properties of information-bearing biomolecules works as in theory.

Supplementary information:  http://genome.gbf.de/wavepaper
Development of an integrated laboratory information management system for the maize mapping project
Authors: Sanchez-Villeda H. , Schroeder S. , Polacco M. , McMullen M. , Havermann S. , Davis G. , Vroh-Bi I. , Cone K. , Sharopova N. , Yim Y. , Schultz L. , Duru N. , Musket T. , Houchins K. , Fang Z. , Gardiner J. , Coe E.
Published: November 2003

Motivation: The development of an integrated genetic and physical map for the maize genome involves the generation of an enormous amount of data. Managing this data requires a system to aid in genotype scoring for different types of markers coming from both local and remote users. In addition, researchers need an efficient way to interact with genetic mapping software and with data files from automated DNA sequencing. They also need ways to manage primer data for mapping and sequencing and provide views of the integrated physical and genetic map and views of genetic map comparisons.

Results: The MMP-LIMS system has been used successfully in a high-throughput mapping environment. The genotypes from 957 SSR, 1023 RFLP, 189 SNP, and 177 InDel markers have been entered and verified via MMP-LIMS. The system is flexible, and can be easily modified to manage data for other species. The software is freely available.

Availability: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.
A novel strategy for microarray quality control using Bayesian networks
Authors: Hautaniemi Sampsa , Edgren Henrik , Vesanen Petri , Wolf Maija , Järvinen Anna-Kaarina , Yli-Harja Olli , Astola Jaakko , Kallioniemi Olli , Monni Outi
Published: November 2003

Motivation: High-throughput microarray technologies enable measurements of the expression levels of thousands of genes in parallel. However, microarray printing, hybridization and washing may create substantial variability in the quality of the data. As erroneous measurements may have a drastic impact on the results by disturbing the normalization schemes and by introducing expression patterns that lead to incorrect conclusions, it is crucial to discard low quality observations in the early phases of a microarray experiment. A typical microarray experiment consists of tens of thousands of spots on a microarray, making manual extraction of poor quality spots impossible. Thus, there is a need for a reliable and general microarray spot quality control strategy.

Results: We suggest a novel strategy for spot quality control by using Bayesian networks, which contain many appealing properties in the spot quality control context. We illustrate how a non-linear least squares based Gaussian fitting procedure can be used in order to extract features for a spot on a microarray. The features we used in this study are: spot intensity, size of the spot, roundness of the spot, alignment error, background intensity, background noise, and bleeding. We conclude that Bayesian networks are a reliable and useful model for microarray spot quality assessment.

Supplementary information:  http://sigwww.cs.tut.fi/TICSP/SpotQuality/
Extraction of protein interaction information from unstructured text using a context-free grammar
Authors: Temkin Joshua M. , Gilder Mark R.
Published: November 2003

Motivation: As research into disease pathology and cellular function continues to generate vast amounts of data pertaining to protein, gene and small molecule (PGSM) interactions, there exists a critical need to capture these results in structured formats allowing for computational analysis. Although many efforts have been made to create databases that store this information in computer readable form, populating these sources largely requires a manual process of interpreting and extracting interaction relationships from the biological research literature. Being able to efficiently and accurately automate the extraction of interactions from unstructured text, would greatly improve the content of these databases and provide a method for managing the continued growth of new literature being published.

Results: In this paper, we describe a system for extracting PGSM interactions from unstructured text. By utilizing a lexical analyzer and context free grammar (CFG), we demonstrate that efficient parsers can be constructed for extracting these relationships from natural language with high rates of recall and precision. Our results show that this technique achieved a recall rate of 83.5% and a precision rate of 93.1% for recognizing PGSM names and a recall rate of 63.9% and a precision rate of 70.2% for extracting interactions between these entities. In contrast to other published techniques, the use of a CFG significantly reduces the complexities of natural language processing by focusing on domain specific structure as opposed to analyzing the semantics of a given language. Additionally, our approach provides a level of abstraction for adding new rules for extracting other types of biological relationships beyond PGSM relationships.

Availability: The program and corpus are available by request from the authors.
Protein structural class identification directly from NMR spectra using averaged chemical shifts
Authors: Mielke S.P. , Krishnan V.V.
Published: November 2003

Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic resonance (NMR) and X-ray crystallography. The full characterization of individual structures, using either of these techniques, is extremely time intensive. The demands of high throughput proteomics necessitate the development of new, faster experimental methods for providing structural information. As a first step toward such a method, we explore the possibility of determining the structural classes of proteins directly from their NMR spectra, prior to resonance assignment, using averaged chemical shifts. This is achieved by correlating NMR-based information with empirical structure-based information available in widely used electronic databases. The results are analyzed statistically for their significance. The robustness of the method as a structure predictor is probed by applying it to a set of proteins of unknown structure. Our results show that this NMR-based method can be used as a low-resolution tool for protein structural class identification.
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events
Authors: Farahi Kamyar , Whitman William B. , Kraemer Eileen T.
Published: November 2003

Summary: RED-T is a Java application for phylogenetic analysis based on a unique method, RED, that utilizes the ratios of evolutionary distances Ed to distinguish between alternative evolutionary histories. RED-T allows the user to examine if any given experimental gene shares the same evolutionary history as the designated control gene(s). Moreover, the tool detects any differences in evolutionary history and allows the user to examine comparisons of Ed for a likely explanation. Lateral gene transfer, which may have a significant influence in organismal evolution is one mechanism that could explain the findings of these RED-T analyses.

Availability: The application is available online at http://www.arches.uga.edu/~whitman/RED.
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize
Authors: Fang Z. , Cone K. , Sanchez-Villeda H. , Polacco M. , McMullen M. , Schroeder S. , Gardiner J. , Davis G. , Havermann S. , Yim Y. , Bi I. Vroh , Coe E.
Published: November 2003

Motivation: Because of the unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize is required for storing, integrating, accessing and visualizing the underlying data.

Results: The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig can be viewed via pop-up windows that feature links to external data resources. Searches can be conducted for genetic locus, probe or sequence accession number; search results include relevant map positions, anchored BAC contigs and links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org

Availability: The iMap utility package is available for non-commercial use upon request from the authors.
Personality Development: An Introduction Toward Process Approaches to Long‐Term Stability and Change in Persons
Authors: Graziano William G.
Published: November 2003

This special issue is concerned with the systematic transformation of persons and personalities as they move through their lives. The focus is on developmental processes early in the life course that influence both long‐term stability and change. Contributors represent diverse topics and viewpoints, but offer new data on classical issues of personality, including trait structure, self‐regulation and internalization, self‐evaluation, and self‐efficacy. In addition, the issue includes empirical contributions on newer approaches to bullying, developmental processes in psychopathology, the influence of racial and ethnic discrimination on subsequent adjustment, and cultural influences on personality development. The issue also includes a special contribution addressing methodological and statistical advances in dealing with prospective longitudinal data assessing personality over time.
The Contribution of Self‐Efficacy Beliefs to Dispositional Shyness: On Social‐Cognitive Systems and the Development of Personality Dispositions
Authors: Caprara Gian Vittorio , Steca Patrizia , Cervone Daniel , Artistico Danielle
Published: November 2003

AbstractThis longitudinal research explored the impact of self‐efficacy beliefs on self‐reported tendencies to experience shyness in interpersonal encounters among a population of adolescents studied over a two‐year period. Self‐efficacy measures, taken at the initial measurement period, included indices of perceived self‐efficacy for forming and maintaining social relationships, dealing effectively with parents, managing negative emotions, and expressing positive emotions towards others. Levels of self‐reported shyness as well as emotional stability were assessed also at time 1, with shyness measured again at the follow‐up assessment two years later. Structural equation modeling indicated that two of the four self‐efficacy measures uniquely contributed to levels of shyness reported at time 1, and that perceptions of social self‐efficacy uniquely contributed to shyness at time 2 even when considering the effects of time 1 shyness levels. Emotional stability did not uniquely contributed to time 2 shyness after considering the relation between shyness at the first and second measurement points. The broad implications of social‐cognitive analyses for the study of personality development are discussed.
Self‐Esteem, Personality and Achievement in High School: A Prospective Longitudinal Study in Texas
Authors: Hair Elizabeth C. , Graziano William G.
Published: November 2003

Abstract
This research explored four empirical questions: (1) Is self‐esteem a better predictor of academic success and adjustment than other aspects of personality? (2) How is self‐esteem related to Big‐Five dimensions of personality during the transition from middle school to high school? (3) Do dispositions like Agreeableness or Openness relate to an adolescent's adaptation and affect reactions to the self? and (4) Do sources of information about adolescents (e.g., self‐rating, other rating, objective “life history”) converge? We also explored the general hypothesis that personality, self‐esteem, and teachers' ratings of adjustment during the middle school years predict later life outcomes during high school. Overall, results indicate Big‐Five personality characteristics were more stable than self‐esteem across this transition period. Agreeableness and Openness assessed in middle school are related to later scholastic competence and behavioral conduct, academic success, and adjustment in high school. Results were discussed in terms of personality development and self‐evaluation.
Personality Structure as Derived From Parental Ratings of Free Descriptions of Children: The Inventory of Child Individual Differences
Authors: Halverson Charles F. , Havill Valerie L. , Deal James , Baker Spencer R. , Victor James B. , Pavlopoulos Vassilis , Besevegis Elias , Wen Liu
Published: November 2003

Based on over 50,000 parental descriptors of children gathered in eight different countries, we used a combination of focus group sorting of descriptors in each country and factor analyses of instruments developed in four of the countries (United States, China, Greece, and the Netherlands) to describe children ages 3 to 12 years to select items for an instrument that would work well across countries to access personality. Through many factor analyses of indigenous items in each country, a core set of 141 items was used in three of the countries, with over 3000 parents responding to our instruments in China, Greece, and the United States. Much cross‐comparative research analysis has resulted in 15 robust midlevel scales that describe the structures of parental descriptors that are common to the three countries. The data on the English (U.S.) sample are presented in detail. Links to temperament and behavior problems are presented and discussed.
Interpersonal Conflict, Agreeableness, and Personality Development
Authors: Jensen‐Campbell Lauri A. , Gleason Katie A. , Adams Ryan , Malcolm Kenya T.
Published: November 2003

Abstract This multimethod research linked the Big‐Five personality dimensions to interpersonal conflict in childhood. Agreeableness was the personality dimension of focus because this dimension has been associated with maintaining positive interpersonal relations in adolescents and adults. In two studies, elementary school children were assessed on the Big‐Five domains of personality. Study 1 (n=276) showed that agreeableness was uniquely associated with endorsements of conflict resolution tactics in children as well as parent and teacher reports of coping and adjustment. Study 2 (n=234) revealed that children's perceptions of themselves and others during conflict was influenced by their agreeableness regardless of their partner's agreeableness. Observers also reported that pairs higher in agreeableness had more harmonious, constructive conflicts. Overall findings suggest that of the Big‐Five dimensions, agreeableness is most closely associated with processes and outcomes related to interpersonal conflict and adjustment in children.
Developing Mechanisms of Temperamental Effortful Control
Authors: Rothbart Mary K. , Ellis Lesa K. , Rosario Rueda M. , Posner Michael I.
Published: November 2003

Abstract
Studies of temperament from early childhood to adulthood have demonstrated inverse relationships between negative affectivity and effortful control. Effortful control is also positively related to the development of conscience and appears as a protective factor in the development of behavior disorders. In this study, the development of attentional mechanisms underlying effortful control was investigated in 2‐ to 3‐year‐old children, as indexed by their performance in a) making anticipatory eye movements to ambiguous locations and b) resolving conflict between location and identity in a spatial conflict task. The ability to make anticipatory eye movements to ambiguous locations within a sequence was clearly present at 24 months. By 30 months, children could also successfully perform a spatial conflict task that introduced conflict between identity and location, and at that age, children's success on ambiguous anticipatory eye movements was related to lower interference from conflict in the spatial conflict task. Children's performance on the eye‐movement task was correlated with performance and reaction time on spatial tasks, and both were related to aspects of effortful control and negative affect as measured in children's parent‐reported temperament.
The Influence of Ethnic Discrimination and Ethnic Identification on African American adolescents' School and Socioemotional Adjustment
Authors: Wong Carol A. , Eccles Jacquelynne S. , Sameroff Arnold
Published: November 2003

Abstract Do experiences with racial discrimination at school predict changes in African American adolescents' academic and psy‐chological functioning? Does African American ethnic identity buffer these relations? This paper addresses these two questions using two waves of data from a longitudinal study of an economically diverse sample of African American adolescents living in and near a major East Coast metropolis. The data were collected at the beginning of the 7th grade and after the completion of the 8th grade. As expected, experiences of racial discrimination at school from one's teachers and peers predicts declines in grades, academic ability self‐concepts, academic task values, mental health (increases in depression and anger, decreases in self‐esteem and psychological resiliency), and increases in the proportion of one's friends who are not interested in school and who have problem behaviors. A strong, positive connection to one's ethnic group (our measure of ethnic identity) reduced the magnitude of the association of racial discrimination experiences with declines in academic self‐concepts, school achievement, and perception of friends' positive characteristics, as well as the association of the racial discrimination experiences with increases in problem behaviors.