bluuebunny/crossref_metadata_2025 huggingface dataset:
An approach to the measurement of software evolution
Authors: Nikora Allen P. , Munson John C.
Published: January 2005

Our current work involves developing methods of measuring changes to evolving software systems. We study a system's change characteristics over a large number of builds using the distinct sources of variation in the software metrics used to measure the system.

We have been collaborating with a flight software technology development effort at the Jet Propulsion Laboratory (JPL) and have progressed in resolving the limitations of our earlier work in two distinct steps. First, we have developed a repeatable and consistent fault enumeration methodology, allowing them to be precisely and accurately measured. Second, we have developed a practical framework for automating fault measurement, which we applied to the JPL software system during its development. Every change to the system was measured and every identified fault was tracked to a specific code module.

Our analysis indicates that measures of the evolving system's structure are strongly related to the number of faults inserted during its development, and that some types of change are more likely to result in the insertion of faults than others. The fault enumeration methodology ensures that the resulting fault model has greater predictive validity; it also provides a higher quality model than other popular definitions of a fault. Copyright © 2005 John Wiley & Sons, Ltd.
Automating regression testing for evolving GUI software
Authors: Memon Atif , Nagarajan Adithya , Xie Qing
Published: January 2005

With the widespread deployment of broadband connections worldwide, software development and maintenance are increasingly being performed by multiple engineers, often working around‐the‐clock to maximize code churn rates. To ensure rapid quality assurance of such software, techniques such as ‘nightly/daily building and smoke testing’ have become widespread since they often reveal bugs early in the software development process. During these builds, a development version of the software is checked out from the source code repository tree, compiled, linked, and (re)tested with the goal of (re)validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically re‐run for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (Daily Automated Regression Tester) that addresses the needs of frequent and automated re‐testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis, smoke‐test‐case generation, test‐oracle creation, to code instrumentation, test execution, coverage evaluation, regeneration of test cases, and their re‐execution. Together with the operating system's task scheduler, DART can execute frequently with little input from the developer/tester to re‐test the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We empirically compare the relative costs of employing different levels of detail in the GUI test oracle. We also show the events and statements covered by the smoke test cases. Copyright © 2005 John Wiley & Sons, Ltd.
An analysis of some ‘core studies’ of software process improvement
Authors: Rainer Austen , Hall Tracy
Published: January 2005

In this paper we analyse 39 publications that have reported issues relating to software process improvement. Together, the 39 publications refer to 14 sites in 11 organizations. The 11 organizations include all five of the organizations that have been awarded the IEEE Computer Society Award for Process Achievement. Twelve of the 14 sites have been assessed at CMM level 3 or higher. Two main issues, and a number of more specific issues, emerge from our analysis. The two main issues are organizational stability and process expertise. We further distinguish between inter‐ and intra‐organizational stability. Several other specific issues are identified and discussed. We direct attention at how the specific issues relate to each other, how the two main issues relate to each other, and how all these issues relate to software process improvement. We speculate that organizational stability provides a stable environment within which to perform the process and to develop expertise. In addition to the 39 publications, the paper provides cross‐references to survey studies and other case studies on process improvement, and studies into process understanding. Copyright © 2001 John Wiley & Sons, Ltd.
Managing instructional software acquisition
Authors: Demirors Onur , Demirors Elif , Tarhan Ayca
Published: January 2005

Managing acquisition and development efforts of contracted software is hard work for many organisations which require high‐quality products to be produced. Mature supplier processes best work with mature acquisition processes which are able to appropriately plan, track and evaluate the work of the supplier. However, acquirer organisations might not always be that mature, so selecting and managing the best‐fit suppliers becomes rather difficult. This paper introduces a study performed to overcome this difficulty for the Ministry of National Education (MONE) of Turkey. The first phase of the study includes defining the evaluation criteria for pre‐qualification of software development companies, and the second phase includes defining the basic instructional software development process as well as the standards for the deliverables of the process. The paper also identifies the effort required by the Ministry for evaluating and managing the pre‐qualification and development work in practice. Copyright © 2001 John Wiley & Sons, Ltd.
Serotonin modulation of cerebral blood flow measured with positron emission tomography (PET) in humans
Authors: Geday Jacob , Hermansen Flemming , Rosenberg Raben , Smith Donald F.
Published: January 2005

To develop a method to measure the dynamic response of the serotonin system in vivo, the effects of intravenously administered citalopram (the most selective of the serotonin reuptake inhibitors) or clomipramine on cerebral blood flow (CBF) were evaluated. CBF was measured with positron emission tomography (PET) in 27 normal subjects scanned under baseline conditions and, on the same day, after an intravenous (IV) infusion of placebo, citalopram, or clomipramine using a randomized, double‐blind design. The main effects of the drugs on blood flow occurred in the thalamus, hypothalamus, and cingulate cortex. Compared to placebo, clomipramine reduced blood flow in the mediodorsal and ventral lateral nuclei of the thalamus, whereas citalopram reduced blood flow in the pulvinar nucleus and the hypothalamus. Compared to clomipramine, citalopram decreased blood flow in the cingulate cortex. The findings support previous reports showing acute central effects of citalopram and clomipramine on regional serotonergic functions measured by PET. Acute side effects may, however, require that care is taken in the selection of experimental designs for future PET studies using IV administration of these antidepressants. Synapse 55:224–229, 2005. © 2005 Wiley‐Liss, Inc.
Optimization of experimental conditions of thin‐window EPMA for light‐element analysis of individual environmental particles
Authors: Szalóki I. , Osán J. , Worobiec A. , de Hoog J. , Van Grieken R.
Published: January 2005

Different metallic substrates such as beryllium, aluminium, silicon and silver were rigorously tested in all aspects of energy‐dispersive electron probe x‐ray microanalysis of single particles, including the semi‐quantitative determination of low‐Z elements. The effect of the collecting substrate on the capability to locate, to analyse and to classify particles automatically was extensively studied by the analysis of particulate standards and aerosol particles collected at the Belgian coast. Beam‐sensitive particles such as ammonium sulphate and ammonium nitrate were analysed using a liquid nitrogen‐cooled sample stage. The dependence of the beam‐damage effect on the type of collecting substrate was also studied using standard aerosol particles. The results obtained show that the use of beryllium as a collecting surface offers some advantages: (i) detailed spectral information can be obtained in a broad elemental range (6 ≤ Z ≤ 92) without overlap with x‐ray lines of the substrate and (ii) complete chemical classification can be done with one set of analyses. Copyright © 2001 John Wiley & Sons, Ltd.
Rapid method for EDXRF analysis of clayey and sandy soil
Authors: Laursen Jens , Vestergaard Brian Tang , Pind Niels , Karlsen Kresten , Bruun Hansen Hans Christian
Published: January 2005

The success of quantitative full soil EDXRF analysis is strongly related to the ability establish a homogeneous and representative sample. When practicing thin‐film deposition techniques the soil particle size will furthermore have an influence on the quantification capability, especially when analyzing the light elements. Finally, the deposition of material on a substrate is coupled with the sedimentation mechanism, which again is influenced by the material grain size and uniformity. In the present investigation, an effective and simple micro‐milling technique for soil and sediment materials was tested. By light scattering it is demonstrated that a grain size of about 600 nm within a milling period of 15 min is obtained. The deposition of the crushed material on a polypropylene thin‐film support is carried out by adding a cationic detergent, thereby obtaining a homogeneous and geometrically well defined droplet. The detergent quality and strength together with its correlation with the soil cation‐exchange capacity are discussed. Clayey and sandy soil samples from different soil profiles containing a wide range of organic materials were investigated. Samples of 0.5–1 mg cm−2 were analyzed by use of a monochromatic Mo Kα irradiation technique. The utility of the data fitting and quantification software X‐Spec32 is discussed. A brief comment is made on the environmental aspects of soil analysis, especially in relation to metal and mineral transport and distribution through the different types of soil and soil profiles. Copyright © 2001 John Wiley & Sons, Ltd.
Human teeth elemental profiles measured by synchrotron x‐ray fluorescence: dietary habits and environmental influence
Authors: Carvalho M. L. , Casaca C. , Marques J. P. , Pinheiro T. , Cunha A. S.
Published: January 2005

This paper reports on the measurements of elemental profiles in teeth collected from two different populations, both living in isolated Portuguese islands of the Azores: S. Miguel and Terceira. Both populations are good producers of cattle, in spite of the proximity of the sea. The purpose of this work was to establish the influence of basic diet, based on meat, fish and dairy products, on teeth elemental content. Moreover, for a few elements, the differences between concentrations in corresponding regions of teeth was correlated with the proximity of the sea for the subjects of one of the islands. An x‐ray fluorescence set‐up with microprobe capabilities, installed at the LURE synchrotron (France), was used for elemental determination. The resolution of the synchrotron microprobe was 100 µm and the energy of the incident photons was 18 keV. Concentration profiles of Fe, Cu, Zn, Br, Sr and Pb in different parts of a tooth are discussed and correlated for both populations. The teeth collected for both populations show a similar behaviour with respect to the elemental distribution. Mn and Cu occur at low concentrations and they are almost constant in all the studied parts of teeth. The content of Sr is higher in the external enamel while the concentrations of Fe, Zn, Br and Pb increase in the inner part of the teeth. However, the contents of Br and Pb are different in the two populations. Higher levels of both elements were found in Terceira subjects. Moreover, the Sr concentration levels indicate that the diet of the studied individuals is richer in meat than in fish. Copyright © 2001 John Wiley & Sons, Ltd.
Overexpression of HUT1 gene stimulates in vivo galactosylation by enhancing UDP–galactose transport activity in Saccharomyces cerevisiae
Authors: Kainuma Mami , Chiba Yasunori , Takeuchi Makoto , Jigami Yoshifumi
Published: January 2005

Transfer of activated sugar‐nucleotides from the cytoplasm to the lumen of the Golgi is an essential requirement for glycosylation of glycoproteins, proteoglycans and glycosphingolipids. Although mannosylation is the major modification in the yeast Saccharomyces cerevisiae, several reports suggest the presence of galactose residues on yeast proteins and sphingolipids. We have detected α‐galactosylated O‐linked chitinase by lectin blotting from cells that functionally express the gma12+ gene, encoding α1,2‐galactosyltransferase from Schizosaccharomyces pombe. This result implies the presence of a UDP–galactose transporter in S. cerevisiae. A conserved gene, HUT1, which encodes a putative multi‐transmembrane protein, was cloned and characterized for its possible involvement in galactosylation. The HUT1 gene is not essential and is expressed at a relatively low level under the physiological conditions we examined. The disruption of this gene did not show any apparent impairments in glycosylation. However, a temperature‐ and concentration‐dependent increase in UDP–galactose transport activity was detected from cells overexpressing HUT1 in the presence of gma12+. The surface of these cells was confirmed to carry galactose residues by staining with FITC‐conjugated α‐galactose‐specific lectin. These results suggest a role for Hut1p in the transport of UDP–galactose from the cytosol into the Golgi lumen in S. cerevisiae. Copyright © 2001 John Wiley & Sons, Ltd.
Co‐consumption of sugars or ethanol and glucose in a Saccharomyces cerevisiae strain deleted in the HXK2 gene
Authors: Raamsdonk Léonie M. , Diderich Jasper A. , Kuiper Arthur , van Gaalen Monique , Kruckberg Arthur L. , Berden Jan A. , Van Dam Karel
Published: January 2005

An Erratum has been published for this article in Yeast 19(2) 2002, 183.

In previous studies it was shown that deletion of the HXK2 gene in Saccharomyces cerevisiae yields a strain that hardly produces ethanol and grows almost exclusively oxidatively in the presence of abundant glucose. This paper reports on physiological studies on the hxk2 deletion strain on mixtures of glucose/sucrose, glucose/galactose, glucose/maltose and glucose/ethanol in aerobic batch cultures. The hxk2 deletion strain co‐consumed galactose and sucrose, together with glucose. In addition, co‐consumption of glucose and ethanol was observed during the early exponential growth phase. In S.cerevisiae, co‐consumption of ethanol and glucose (in the presence of abundant glucose) has never been reported before. The specific respiration rate of the hxk2 deletion strain growing on the glucose/ethanol mixture was 900 µmol·min−1·(g protein)−1, which is four to five times higher than that of the hxk2 deletion strain growing oxidatively on glucose, three times higher than its parent growing on ethanol (when respiration is fully derepressed) and is almost 10 times higher than its parent growing on glucose (when respiration is repressed). This indicates that the hxk2 deletion strain has a strongly enhanced oxidative capacity when grown on a mixture of glucose and ethanol. Copyright © 2001 John Wiley & Sons, Ltd.
Extensive chromosome translocation in a clinical isolate showing the distinctive carbohydrate assimilation profile from a candidiasis patient
Authors: Iwaguchi Shin‐Ichi , Sato Mihoko , Magee Beatrice B. , Magee Paul T. , Makimura Koichi , Suzuki Takahito
Published: January 2005

Variation of the electrophoretic karyotype is common among clinical strains of Candida albicans and chromosome translocation is considered one of the causes of karyotypic variation. Such chromosome translocations may be a mechanism to confer phenotypic diversity on the imperfect fungus C. albicans. A clinical strain, TCH23, from a vaginal candidiasis patient shows distinct carbohydrate assimilation profile, serotype B, no chlamydospore formation and an atypical karyotype (Asakura et al., 1991). To examine the taxonomic relationship among C. albicans, Candida dubliniensis and this strain, we sequenced the internal transcribed spacer 1 (ITS1) of nuclear ribosomal DNA. The ITS1 sequence of TCH23 was identical with that of C. albicans but not of C. dubliniensis. Thus, strain TCH23 was classified as a variant of C. albicans with an atypical phenotype. The chromosomal DNAs of this strain were resolved into 13 bands on pulse‐field gel electrophoresis (PFGE). Using DNA probes located at or near both ends of each chromosome of C. albicans, we investigated the chromosome organization of this strain. Referring to the SfiI map of C. albicans 1006 (Chu et al., 1993), we found that seven chromosomal DNA bands in strain TCH23 were reciprocal chromosome translocations. One homologue from chromosomes 1, 2 and 6 and both homologues from chromosomes 4 and 7 participated in these events. One translocation product was composed of three SfiI fragments, one each from chromosomes 2, 4 and 7. We deduced the breakpoints of chromosome translocation from the physical map of this strain; between 1J and 1J1, between 2A and 2U, both ends of 4F2, between 6C and 6O and both ends of 7F. Copyright © 2001 John Wiley & Sons, Ltd.
High efficiency transformation of Schizosaccharomyces pombe pretreated with thiol compounds by electroporation
Authors: Suga Minoru , Hatakeyama Toyomasa
Published: January 2005

A highly efficient method for transformation of the fission yeast Schizosaccharomyces pombe by electroporation has been developed. Significantly higher transformation efficiency was obtained when intact cells grown in SD medium (0.67% Bacto yeast nitrogen base without amino acids, 2% glucose) were pretreated with thiol compounds before an electric pulse was applied to the cells. Among the thiol compounds tested, dithiothreitol (DTT) was the most effective for pretreatment. A high transformation efficiency was obtained when the cells were pretreated with 25 mM DTT at 30°C for 15 min in an osmotically adjusted buffer, since the cells were sensitive to osmotic pressure. It was important to exclude glucose from the DTT pretreatment buffer, as it caused a drastic decrease in efficiency. The optimal cell concentration and amount of DNA during the electric pulse were 1×109 cells/ml and 10 ng, respectively. The maximum transformation efficiency, 1.2×107 transformants/µg plasmid DNA, was obtained when an electric pulse of 11.0 kV/cm was applied for 5 ms. Furthermore, the high competency of cells pretreated with DTT was maintained by freezing them in a non‐permeating cryoprotectant such as sorbitol. Copyright © 2001 John Wiley & Sons, Ltd.
The yeast Rvs161 and Rvs167 proteins are involved in secretory vesicles targeting the plasma membrane and in cell integrity
Authors: Breton Annick M. , Schaeffer Jacques , Aigle Michel
Published: January 2005

The Rvs161 and Rvs167 proteins are known to play a role in actin cytokeleton organization and endocytosis. Moreover, Rvs167p functionally interacts with the myosin Myo2p. Therefore, we explored the involvement of the Rvs proteins in vesicle traffic and in cell integrity. The rvs mutants accumulate late secretory vesicles at sites of membrane and cell wall construction. They are synthetic‐lethal with the slt2/mpk1 mutation, which affects the MAP kinase cascade controlled by Pkc1p and is required for cell integrity. The phenotype of the double mutants is close to that described for the pkc1 mutant. Synthetic defects for growth are also observed with mutation in KRE6, a gene coding for a glucan synthase, required for cell wall construction. These data support the idea that the Rvs proteins are involved in the late targeting of vesicles whose cargoes are required for cell wall construction. Copyright © 2001 John Wiley & Sons, Ltd.
The centromere‐binding factor Cbf1p from Candida albicans complements the methionine auxotrophic phenotype of Saccharomyces cerevisiae
Authors: Eck Raimund , Stoyan Tanja , Künkel Waldemar
Published: January 2005

A gene encoding the centromere binding factor 1 (Cbf1p) of the human pathogenic yeast Candida albicans was cloned and characterized. An open reading‐frame was detected which encoded a 223 amino acid protein with a calculated molecular weight of 25.8 kDa and a relative isoelectric point of 5.55. It shares 39% overall amino acid sequence identity with Saccharomyces cerevisiae Cbf1p. We localized the CaCBF1 gene on chromosome 4. Southern analysis indicated that CaCBF1 is probably present as a single copy gene per haploid genome. The CaCBF1 gene under the control of its own promoter was able to complement the methionine auxotrophic growth, the increased mitotic instability of CEN plasmids and the slow growth of a Saccharomyces cerevisiae cbf1Δ mutant strain. The GenBank Accession No. for this gene is AJ303083. Copyright © 2001 John Wiley & Sons, Ltd.
Mutational study of the role of tyrosine‐49 in the Saccharomyces cerevisiae xylose reductase
Authors: Ye Jeong Eun , Sopher Coralie , Seon Kim In , Lee Hung
Published: January 2005

The xyl1 gene encoding xylose reductase was cloned from Saccharomyces cerevisiae and expressed in Escherichia coli. The purified enzyme readily carried out xylose reduction in vitro. It prefers NADPH as the co‐enzyme by about 80‐fold over NADH. Compared to the native enzyme purified from S. cerevisiae (Kuhn et al., 1995), the recombinant xylose reductase displayed slightly higher (about two‐fold) affinities (Km) for the substrate (xylose) and co‐factor (NADPH), as well as a 3.9‐fold faster turnover number (Kcat) and 7.4‐fold greater catalytic efficiency (Kcat/Km). The reason for the apparent discrepancies in kinetic constants between the recombinant and native S. cerevisiae xylose reductases is not known. Replacement of Tyr49 by Phe in the recombinant enzyme led to greater than 98% loss of activity, suggesting that this residue plays a critical role in catalysis. Intrinsic enzyme fluorescence spectroscopic analysis showed that the wild‐type and the Y49F variant both bound the co‐enzyme NADPH with similar affinity. This supports the view that Tyr49 is involved in interaction with the substrate and not the co‐factor during catalysis. Copyright © 2001 John Wiley & Sons, Ltd.
Effect of snowmelt timing on the genetic structure of an Erythronium grandiflorum population in an alpine environment
Authors: Yamagishi Hiroki , Allison Taber D. , Ohara Masashi
Published: January 2005

In alpine environments, flowering phenology can differ within local populations even at the same elevation. We assessed the effects of differences in flowering phenology due to snowmelt timing caused by local geographic heterogeneity on the genetic structure of a population of an alpine plant, Erythronium grandiflorum Pursh. We established a study plot of 250×70 m at 3,340 m above sea level in the Front Range of the Rocky Mountains, CO, USA. The flowering phenology was considerably influenced by snowmelt timing due to local geographic heterogeneity. Twenty‐two patches of E. grandiflorum were recognized in the study plot and were classified into three phenological groups: early, middle, and late. To express the differentiation of flowering phenology among the patches, we defined phenological distance and analyzed the relationship between genetic and phenological distances. Additionally, since genetic distance is expected to co‐vary with geographic distance, we also analyzed the relationship between genetic distance and geographic distance among patches. The results revealed not only that isolation by distance was present among patches, but also that the differences in snowmelt timing gave rise to phenologically distant patches of E. grandiflorum, which in turn determine the genetic structure caused by the limited pollen flow between patches.
Chromatin structure and the state of human organism
Authors: Shckorbatov Yuriy G. , Zhuravlyova Lyubov A. , Navrotskaya Valeria V. , Miroshnichenko Elena V. , Montvid Pavel Y. , Shakhbazov Valery G. , Sutushev Takhir A.
Published: January 2005

The state of chromatin in human buccal epithelium cell nuclei upon the influence of sport trainings was investigated. Chromatin state was evaluated in interphase buccal cell nuclei after orcein staining. The heterochromatin granule quantity (HGQ) was estimated in 30 nuclei per sample, and for every donor the mean HGQ value per 30 cells was determined. Donors of masculine sex, aged from 18 to 48 years performed training walks and samples of buccal epithelium were collected. Sportive charges induced the process of chromatin condensation in cell nuclei. After the period of repose (24–48 h) the HGQ decreased to control level therefore the process of chromatin decondensation was observed. The state of chromatin changes in connection with circadian rhythm. Chromatin became more condensed at nighttime and less condensed in the morning. Hormones such as adrenaline, noradrenaline, and hydrocortisone in vitro induced the increase of HGQ.
Sexual dysfunction and chronic pain: the role of psychological variables and impact on quality of life
Authors: Kwan Kellie S.H. , Roberts Lindy J. , Swalm Delphin M.
Published: January 2005

We report two studies examining the prevalence of sexual dysfunction, and the role of psychological variables, including quality of life, on sexual activity in patients at the commencement of an outpatient cognitive‐behavioural pain management programme. In Study 1, 151 patients with non‐cancer pain, predominantly of musculoskeletal origin, completed a range of standardised measures, including the Pain Disability Index, Beck Depression Inventory and Coping Strategies Questionnaire. Sexual dysfunction was common, and using stepwise multiple regression analysis was found to be more frequently reported by those with greater disability and depression, shorter pain duration, and infrequent use of coping self‐statements. Study 2 was a pilot investigation of the impact of sexual dysfunction on quality of life (as measured by the WHOQOL‐100) in a similar sample (n = 41). Although sexual dysfunction was again commonly reported, subjects perceived it had less importance in quality of life than did other factors. The combined results support the previously proposed notion of adaptation to the impact of chronic illness on sexual function. In conclusion, sexual dysfunction is common in this population and is predicted by psychological factors and pain duration. However, other issues impact more significantly on quality of life. Therapeutic approaches to sexual dysfunction in these patients might best be focused on improving psychological factors, particularly depression and coping skills.
Microarray analysis of fiber cell maturation in the lens
Authors: Ivanov Dmitry , Dvoriantchikova Galina , Pestova Anna , Nathanson Lubov , Shestopalov Valery I.
Published: January 2005

The mammalian lens consists of an aged core of quiescent cells enveloped by layers of mature fully elongated cells and younger, continuously elongating transcriptionally active cells. The fiber cell maturation is initiated when fiber cells cease to elongate. The process of maturation represents a radical switch from active elongation to a life‐long quiescence and has not been studied previously. It may also include critical stages of preparation for the organelle removal and denucleation. In the present study, we used laser capture microdisection (LCM) microdissection and RNA amplification to compare global gene expression profiles of young elongating and mature, non‐elongating fiber cells. Analysis of microarray data from three independent dye‐swap experiments identified 65 differentially expressed genes (FDR < 0.1) with greater than 2‐fold change in expression levels. Microarray array results for a group of randomly selected genes were confirmed by quantitative RT‐PCR. These microarray results provide clues to understanding the molecular pathways underlying lens development. The identified changes in the profile of gene expression reflected a shift in cell physiology characterizing the lens fiber maturation.
The teratology of autism
Authors: Arndt Tara L. , Stodgell Christopher J. , Rodier Patricia M.
Published: January 2005

Autism spectrum disorders affect behaviors that emerge at ages when typically developing children become increasingly social and communicative, but many lines of evidence suggest that the underlying alterations in the brain occur long before the period when symptoms become obvious. Studies of the behavior of children in the first year of life demonstrate that symptoms are often detectable in the first 6 months. The environmental factors known to increase the risk of autism have critical periods of action during embryogenesis. Minor malformations that occur frequently in people with autism are known to arise in the same stages of development. Anomalies reported from histological studies of the brain are consistent with an early alteration of development. Congenital syndromes with high rates of autism include somatic that originate early in the first trimester. In addition, it is possible to duplicate a number of anatomic and behavioral features characteristic of human cases by exposing rat embryos to a teratogenic dose of valproic acid at the time of neural tube closure.
Tubal patency after clinical treatment of unruptured ectopic pregnancy
Authors: Elito J. , Han K.K. , Camano L.
Published: January 2005

Objective

To evaluate tubal patency using hysterosalpingography after clinical treatment of tubal pregnancy.

Method

Of 80 patients who underwent hysterosalpingography after clinical treatment of tubal pregnancy from April 1994 to February 2002, 30 were treated with a single 50 mg/m2 dose of methotrexate intramuscularly (n=30) and 50 were followed up expectantly.

Results

Patency of the ipsilateral tube was 84% after methotrexate treatment and 78% after expectant management. In addition, contralateral tubal patency was 97% after methotrexate treatment and 92% after expectant management. There were no statistically significant differences between the groups.

Conclusion

Findings from this study suggest similar tubal patency rates after methotrexate treatment and expectant management.
Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers
Authors: CURTIS J. , SORENSEN R. E. , MINCHELLA D. J.
Published: January 2005

Blood flukes in the genusSchistosomaare important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found inSchistosoma mansoniand some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers forS. mansoniprovided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.
Shakespeare, the Natyasastra, and Discovering Rasa for Performance
Authors: Brown John Russell
Published: January 2005

Recognizing analogies between the assumptions about theatricality found in the classic Sanskrit treatise on acting, the Natyasastra, and those of the Elizabethan theatre, John Russell Brown suggests that the concept of rasa as the determining emotion of a performance is similar to that of the Elizabethan ‘humour’, or prevailing passion, as defined by Ben Jonson. Here he describes his work exploring what happens when actors draw on their own life experiences to imagine and assume the basic rasa of the character they are going to present, based on experiments in London with New Fortune Theatre; in Bremen with actors of the Bremer Shakespeare Company; and in New Delhi with actors of the National School of Drama. Using actors both young and experienced, familiar and unfamiliar with ensemble playing, and well or poorly acquainted with the concepts involved, he suggests that the results merit further exploration of a technique which could empower actors to bring Shakespeare's plays to new kinds of life. John Russell Brown founded the Department of Drama and Theatre Arts at Birmingham University, and for fifteen years was an Associate Director of the Royal National Theatre. His New Sites for Shakespeare: Theatre, the Audience, and Asia was published by Routledge in 1999, and his Shakespeare Dancing: a Theatrical Study of the Plays by Palgrave Macmillan in 2004. He edited and contributed to The Oxford Illustrated History of Theatre (1995), and for Routledge has been General Editor of the ‘Theatre Production Studies’, ‘Theatre Concepts’, and forthcoming ‘Theatres of the World’ series.
‘A Whole New World Still to Make’: a Valedictory for Peter Barnes
Authors: Woolland Brian
Published: January 2005

Brian Woolland is the author of a major study of Peter Barnes's work, Dark Attractions: the Theatre of Peter Barnes, published by Methuen in the autumn of 2004 – too late to take more than brief note of the playwright's death in July. The following critical retrospective serves, then, both as a valedictory postscript to the author's full-length study and as a critical afterword to the personal tributes paid to Peter Barnes by Alan Rickman, Charles Marowitz, and Elaine Turner in NTQ80. Brian Woolland is Senior Lecturer in Drama and Theatre at the University of Reading. His research interests are in Renaissance theatre in performance, modern European theatre, and theatre in education. He also works as a playwright and as a theatre director.
Extracellular phospholipids of isolated bacterial communities
Authors: Tetz V. V. , Korobov V. P. , Artemenko N. K. , Lemkina L. M. , Panjkova N. V. , Tetz G. V.
Published: January 2005

We have made a comparative analysis of the extracellular phospholipid composition of biofilms of Gram-negative and Gram-positive bacteria. The surface film of a growing bacterial community contains small membrane vesicles and a bilipid layer covering the entire surface of that community. These supracommunity films containing the bilipid layer can cover the entire surface of a Petri dish and form a boundary between bacterial communities and the environment. A mixed bacterial lawn, formed by unrelated bacteria, also becomes covered with a single film containing a lipid bilayer. The phospholipid compositions of the bacterial cell and surface film bilipid layer reflect the nature of the bacterial strains forming the community, but have some specific differences.
An FTIR study of Pseudomonas aeruginosa PAO1 biofilm growth and dispersion. An improved ATR method for studying biofilms: the C–H stretch spectral region
Authors: Pink J. , Smith-Palmer T. , Beveridge T. J. , Pink D. A.
Published: January 2005

Pseudomonas aeruginosa PAO1 was grown on 40° ZnSe and 40° AMTIR® (Amorphous Material Transmitting Infrared Radiation, Ge33As12Se55) internal reflection elements in a thermostatted flow cell. Information about the chemistry of the biofilm development was obtained using Fourier transform infrared spectroscopy. The weakly absorbing C–H stretching region of the infrared spectrum was measured for the first time and revealed qualitative and quantitative changes not evident in the amide region studied by previous investigators. There is a chemical difference between the early growth period and subsequent development of the biofilm.
Ultrastructural preservation of biofilms formed by non-typeable Hemophilus influenzae
Authors: Webster P. , Wu S. , Webster S. , Rich K. A. , McDonald K.
Published: January 2005

There is growing evidence to suggest that non-typeable Hemophilus influenzae (NTHi), an important cause of otitis media in children, is able to grow as a biofilm in the middle ear. This observation may help to explain bacterial persistence in chronic infections. We evaluate the usefulness of rapid freezing and freeze substitution as a means of preparing biofilms for ultrastructural examination by comparing the morphology of cryofixed specimens with the morphology produced using more conventional chemical fixation and dehydration methods. Chemical fixation and dehydration methods produced substantial ultrastructural damage to individual NTHi in the biofilm and loss of extracellular matrix, even in the presence of ruthenium red. In comparison, cryofixed and freeze-substituted NTHi biofilms showed significantly improved preservation of bacterial ultrastructure and biofilm organization. The intracellular contents of NTHi prepared using the cryomethods showed little evidence of aggregation, and bacteria within the biofilm were closely packed and surrounded by an abundant extracellular matrix. Although high-pressure freezing of NTHi biofilms followed by freeze substitution was highly effective for preserving ultrastructure when examined by transmission electron microscopy, immersion in liquid propane offered an alternative, “less technical”, freezing method. Immersion in liquid propane followed by freeze substitution and critical point drying was most effective for preserving ultrastructural details in specimens examined by scanning electron microscopy.
Mode of extension and rifting history of upper Tiburón and upper Delfín basins, northern Gulf of California
Authors: González‐Fernández A. , Dañobeitia J. J. , Delgado‐Argote L. A. , Michaud F. , Córdoba D. , Bartolomé R.
Published: January 2005

The crustal structure of the northern Gulf of California transtensional margin has been investigated by a 280‐km‐long NW‐SE profile, including deep multichannel seismic reflection and densely sampled refraction/wide‐angle reflection seismic information combined with gravity modeling. The seismic and gravity modeling constrains two thinned crustal areas, corresponding to the upper Delfín and the upper Tiburón basins. On both sides of the profile, toward the Baja California Peninsula and the Mexico mainland, a progressive thickening of the continental crust is observed. Our results indicate that the crustal thickness is 19 km below the coastline, and it decreases to 14 and 17 km below the upper Delfín and upper Tiburón basins, respectively. In the area between both basins, the crust thickens to 19.5 km. There are significant lateral thickness variations for the different levels of the crust. The interpreted structure is consistent with the existence of an aborted rift below the upper Tiburón basin. Prominent dipping reflections in the multichannel data under upper Tiburón basin and the ridge between upper Tiburón and upper Delfín basins can be explained as a mylonite like zone related to a detachment fault. This interpretation suggests that the structural evolution of upper Tiburón basin could be controlled by a major fault that cuts through the upper crust and merges into a zone of subhorizontal reflections in the lower crust. The mode and locus of extension have evolved from a core complex in upper Tiburón to a narrow rift mode in upper Delfín basin.
Pliocene transpressional modification of depositional basins by convergent thrusting adjacent to the “Big Bend” of the San Andreas fault: An example from Lockwood Valley, southern California
Authors: Kellogg Karl S. , Minor Scott A.
Published: January 2005

The “Big Bend” of the San Andreas fault in the western Transverse Ranges of southern California is a left stepping flexure in the dextral fault system and has long been recognized as a zone of relatively high transpression compared to adjacent regions. The Lockwood Valley region, just south of the Big Bend, underwent a profound change in early Pliocene time (∼5 Ma) from basin deposition to contraction, accompanied by widespread folding and thrusting. This change followed the recently determined initiation of opening of the northern Gulf of California and movement along the southern San Andreas fault at about 6.1 Ma, with the concomitant formation of the Big Bend. Lockwood Valley occupies a 6‐km‐wide, fault‐bounded structural basin in which converging blocks of Paleoproterozoic and Cretaceous crystalline basement and upper Oligocene and lower Miocene sedimentary rocks (Plush Ranch Formation) were thrust over Miocene and Pliocene basin‐fill sedimentary rocks (in ascending order, Caliente Formation, Lockwood Clay, and Quatal Formation). All the pre‐Quatal sedimentary rocks and most of the Pliocene Quatal Formation were deposited during a mid‐Tertiary period of regional transtension in a crustal block that underwent little clockwise vertical‐axis rotation as compared to crustal blocks to the south. Ensuing Pliocene and Quaternary transpression in the Big Bend region began during deposition of the poorly dated Quatal Formation and was marked by four converging thrust systems, which decreased the areal extent of the sedimentary basin and formed the present Lockwood Valley structural basin. None of the thrusts appears presently active. Estimated shortening across the center of the basin was about 30 percent. The formerly defined eastern Big Pine fault, now interpreted to be two separate, oppositely directed, contractional reverse or thrust faults, marks the northwestern structural boundary of Lockwood Valley. The complex geometry of the Lockwood Valley basin is similar to other Tertiary structural basins in southern California, such those that underlie Cuyama Valley, the Ridge basin, and the east Ventura basin.
Poroelastic damage rheology: Dilation, compaction, and failure of rocks
Authors: Hamiel Yariv , Lyakhovsky Vladimir , Agnon Amotz
Published: January 2005

We present three‐dimensional numerical simulations for the behavior of porous rocks under loading based on the theoretical formulation recently developed by Y. Hamiel et al. This theoretical formulation combines the classic Biot poroelastic theory with a damage rheology model. The numerical simulations of triaxial compression tests reproduce the gradual transition from localized brittle failure to distributed cataclastic flow with increasing pressure at high‐porosity rocks. Under relatively low confining pressures (approximately lower than 100 MPa for Berea sandstone samples), porous rocks fail in a brittle mode with sharp localization of damage in a narrow deformation zone and dilatancy preceding the total failure. At these pressures the yield stress increases with confining pressure (positive slope for yield curve). In simulations with higher confining pressures, instead of dilatancy, the deformation zone has a reduced porosity due to compaction. The porosity reduction plays an essential role in strengthening the deformation zone, and therefore continuous loading of the sample leads to the progressive development of a wide deformation zone. Under relatively high confining pressures (approximately higher than 300 MPa for Berea sandstone samples), damage is nonlocalized, and the macroscopic deformation of the model corresponds to experimentally observed cataclastic flow. At these pressures the yield stress decreases with confining pressure (negative slope for yield curve). We found good agreement between the measured and calculated yield curve for Berea sandstone.
Mixed particle acceleration at CME‐driven shocks and flares
Authors: Li G. , Zank G. P.
Published: January 2005

A recent study of Cane et al. [2003] showed that in some intense SEP events, the time‐intensity profiles exhibit two peaks, with an earlier one having a high Fe/O and a later one with a low Fe/O ratio. They suggested that these two‐component events are due to CMEs and their accompanying flares occurring together, with the first peak being flare‐related and the second peak being CME‐driven shock related. In this paper, we develop a model which examines particle acceleration and transport when both flares and CME‐driven shocks are present. We study time‐intensity profiles for three different scenarios: a pure shock case, a pure flare case and a shock‐flare‐mixed case. Using reasonable estimates of the relative timing between CMEs and associated flares, we find that a large portion of the flare accelerated material is subject to absorption and re‐acceleration by the CME‐driven shock. Consequently, the time intensity profile for the shock‐flare‐mixed case shows an initial rapid increase, owing to particles accelerated at the flare and followed by a plateau similar to that of a pure shock case.
Estimation of monthly mean air‐sea temperature difference from satellite observations using genetic algorithm
Authors: Singh Randhir , Kishtawal C. M. , Joshi P. C.
Published: January 2005

We present a new method to determine the monthly mean air sea temperature difference (ΔT = SST − Ta) from satellite observations. The satellite observed parameters viz., vertically integrated water vapour (W), sea surface temperature (SST) and wind speed (U) are used to derive ΔT. Genetic Algorithm (GA) is used to find the optimum relations between the input (W, SST, U) and output (ΔT) parameters. The input data consist of 6 years (January 1988–December 1993) of monthly averages of water vapour and wind speed from SSM/I (Special Sensor Microwave Imager), and sea surface temperature data from AVHRR (Advanced Very High Resolution Radiometer). Surface Marine Data (based on COADS observations) of SST and Ta (air temperature) are used to develop and evaluate the non‐linear empirical relationship. Largest seasonal dependent differences between ΔT derived from the new method and in‐situ data are found over the western boundary currents (such as the Kuroshio and Gulf Stream). After removal of the systematic biases, ΔT can be determined with accuracy of 0.40 ± 0.11°C.
Can near‐inertial internal waves in the East Sea be observed by synthetic aperture radar?
Authors: Kim Duk‐jin , Nam SungHyun , Kim Hyoung Rok , Moon Wooil M. , Kim Kuh
Published: January 2005

Near‐inertial (∼18 hours) internal waves were observed in the mid‐western part of the East Sea on May 18 and 19, 2004 using C‐band Synthetic Aperture Radar (SAR) images. Current and temperature measurements obtained during the field experiment from 10 May to 9 June 2004 (IWXES2004, Internal Wave eXperiment in the East Sea), were analyzed to investigate the processes by which near‐inertial internal waves can be seen in SAR images and how they progress. The spatial distributions of horizontal wavelength and phase speed estimated from two successively acquired SAR images are consistent with those inferred from water temperature and current measurements carried out during the field experiment. Based on these two independent observations (SAR and IWXES2004), we report a strong possibility that the observed wave patterns in the SAR images during IWXES2004 are near‐inertial internal waves propagating westward off the east coast of the Korean peninsula with a phase speed of about 0.3 m/s.