bluuebunny/crossref_metadata_2025 huggingface dataset:
Distributions of larval mosquitoes among bamboo‐stump pools which vary in persistence and resource input
Authors: Sunahara Toshihiko , Mogi Motoyoshi
Published: December 2007

We studied the seasonal occurrence and the distribution patterns of larval mosquitoes in a bamboo grove in northern Kyushu, Japan. The number of pools was large from June to August and was small in winter. Deep stumps and semi‐closed‐type stumps held water more persistently than shallow and open‐type stumps, respectively. Open‐type stumps trapped more leaves than semi‐closed‐type stumps and the number of leaves trapped in the open‐type stump was positively correlated with the area of the pool. The incidences of Tripteroides bambusa and Aedes albopictus were low early in their breeding season and gradually increased thereafter. In August, the density of T. bambusa larvae per pool was higher in the old (>2 months) pools than in the new pools and was positively correlated with the depth of the stumps. In contrast, the density of A. albopictus did not differ significantly between the new‐and old pools and was not significantly correlated with the depth of the stump. The density of A. albopictus was positively correlated with the number of leaves that had been trapped in the stump, whereas the density of T. bambusa was not. In addition to the seasonal fluctuation in habitat‐patch availability, the variations in habitat persistence and resource input among bamboo stumps may facilitate the coexistence of the two mosquitoes that were differentially limited by these factors.
Effects of spatio‐temporal intervals between newly‐hatched larvae on larval survival and development in Monochamus alternatus (Coleoptera: Cerambycidae)
Authors: Anbutsu Hisashi , Togashi Katsumi
Published: December 2007

The effects of distance between hatching larvae on survival and development were investigated in Monochamus alternatus. Two newly‐hatched larvae were inoculated into Pinus densiflora bolts at a distance of 2.5 cm or 10 cm, simultaneously or at an interval of 2 weeks. Some larvae were inoculated singly as a control. When larvae were inoculated simultaneously, mortality of the closely‐inoculated larvae was significantly higher than that of distantly‐inoculated larvae. Such high mortality was identified as due to conspecific bites. When the two larvae were inoculated asynchronously, the first‐inoculated larvae killed some second‐inoculated larvae but were never killed by them. Consequently, mortality was higher in second‐inoculated larvae than in first‐inoculated larvae. In particular, there was a significant difference in mortality between them when the larvae had been inoculated closely. The mortality of second‐inoculated larvae was higher in the closely‐inoculated group than in the distantly‐inoculated group although there was no significant difference between them. In the case of two simultaneously‐inoculated larvae, the initial distance between them had no significant effect on the development and growth in the early larval stage. When the larvae were inoculated asynchronously, the first‐inoculated larvae grew more quickly than singly‐inoculated control larvae.
Speciation and evolutionary dynamics of asymmetric mating preference
Authors: Yoshimura Jin , Starmer William T.
Published: December 2007

Asymmetric mating preferences occur in two closely related species, if females of one species are highly selective against males of the second, while females of the second show less selection against males of the first species. It has been suggested that such asymmetry is an indicator of common ancestry between the two species, but actual observations are contradictory and inconclusive. We developed a scenario of speciation history and asymmetric mating preference, incorporating invasion dynamics via frequency‐dependent interspecific sexual competition. A newly isolated (derived) species may form at the periphery of the ancestral species’ distribution by invading a new range. Only a few closely related species would be expected in the new area, while many related species are expected to coexist with the ancestral species. In a peripherally derived species, female mating preferences should be relaxed through sexual character release, owing to a lack of sympatric species and a scarcity of intraspecific mating opportunities. Secondary contacts may then happen as: 1. repeated invasions, i.e. subsequent invasion by the ancestral species into the new range or, 2. backward invasions, i.e. derived species incursions into the ancestral range. Repeated invasions could lead to the coexistence of both the derived species and the newly invading ancestor. Backward invasions by the derived species can succeed only when the derived females develop a strict mating discrimination against the ancestral males. We then expect strong character displacement in the derived species. Thus, peripheral isolation and repeated invasions lead to the relaxed female mating preferences in the derived species and backward invasions lead to stronger female mating preferences in the derived species. This agrees with Drosophila data from Hawaii and the continents. Experimental data of the Drosophila arizonaemojavensis species cluster also support the hypothesis.
Changes in searching responses with temperature of Cyrtorhinus lividipennis reuter (Hemiptera: Miridae) on the eggs of the brown planthopper, Nilaparvata lugens (Stål.) (Homoptera: Delphacidae)
Authors: Song Y. H. , Heong K. L.
Published: December 2007

The functional response of Cyrtorhinus lividipennis Reuter attacking the brown planthopper (Nilaparvata lugens (Stål.), BPH) eggs on rice was determined at six constant temperatures of 20°C, 23°C, 26°C, 29°C, 32°C and 35°C. Rogers’ (1972) random predator equations were fitted to the data for each temperature separately. The equation model adequately described a Holling's Type II functional response for C. lividipennis and produced biologically realistic estimates of attack rates and handling times at five experimental temperatures between 20°C and 32°C. However, at 35°C, a negative handling time (Th = ‐ 0.0029) was produced. The effect of temperature was incorporated in to Rogers’ equation by making the attack rate (a) and handling time (Th) functions of temperature within the range 20°C to 32°C. The attack rate and handling time were fitted as hyperbola and reciprocal hyperbola functions of temperature respectively. The temperature incorporating fourparameter composite model fitted the combined data as well as did separate Rogers’ equations based on the parameter estimates.
The effect of vegetation patterns on oviposition habitat preference: A driving mechanism in terrestrial chironomid (Diptera: Chironomidae) succession?
Authors: Frouz Jan
Published: December 2007

Relationships between changes of two species of terrestrial chironomids(Smittia cf. aterrimaandBryophaenocladius cf. virgo)and changes of vegetation cover during succession were studied with respect to plant — chironomid interaction in particular stages of chironomid life cycle. Several vegetation types forming vegetation mosaics in suburban fallow were distinguished according to their spatial architecture (height; density etc.). Abundance of chironomid larvae in particular type of vegetation and an area covered by these vegetation types were studied for three years. During one year the effect of vegetation types on density of aerial drift, oviposition habitat preference and adult emergence was studied in detail. Aerial drift was studied using pan traps, oviposition using soil sampling and adult emergence using emergence trap. Main results were similar for both species. Chironomid larvae were abundant in soil in initial years of succession. They were concentrated in patches with open and low height vegetation. Later their abundance decreased corresponding to a reduction of open and low vegetation areas. Greater density of aerial drift and oviposition preference was observed in areas of open and low vegetation. The success of larval development agreed with oviposition preference for winter larval generation only. The less preferred habitats seemed to be more suitable for summer generation. The results indicated that successional changes of terrestrial chironomids can be explained by the effect of vegetation cover on oviposition habitat preference.
An individual‐based model for competing Drosophila populations
Authors: Jansen Vincent A. A. , Sevenster Jan G.
Published: December 2007

An individual‐based model for Drosophila is formulated, based on competition amongst larvae consuming the same batch of food. The predictions of the model are supported by data for single species Drosophila populations reared in the laboratory. The model is used to build a simple discrete model for the dynamics of Drosophila populations that are kept over a number of generations. The dynamics of a single species is shown to give either a stable equilibrium or fluctuations which can be periodic or chaotic. When the dynamics of a species in the absence of the other is periodic or chaotic, we found coexistence or two alternative states, on neither of which the species can coexist.
Loss of genetic variability in a fragmented continuously distributed population
Authors: Kawata Masakado
Published: December 2007

An individual‐based simulation model was used to examine the effect of population subdivision, dispersal distance of offspring, and migration rates between subpopulations on genetic variability (H1HS and HT) in a continuously distributed population. Some difficulties with mathematical models of a continuously distributed population have been pointed out. The individual‐based model can avoid these difficulties and can be used to examine genetic variability in a population within which individuals are distributed continuously and in which the dispersal of individuals is disturbed by geographical or artificial barriers. The present simulation showed that the pattern of decrease in H1 had three stages. During the first stage, H1 decreased at the rates predicted by Wright's neighborhood size. During the second stage, H1 decreased more rapidly when the migration rate decreased, while during the third stage, it decreased less rapidly when the migration rate decreased. Increasing the number of subdivisions increased the rate of decrease after the 200th generation. The pattern of decrease in HT was classified into 2 stages. During the first stage, the rates of decrease corresponded with those of a randomly mating population. During the second stage, a decrease in the migration rates of the subpopulations slowed the rate of decrease in HT. A uniform spatial distribution and a reduced total dispersal distance of offspring caused H1HS, and HT to decrease more rapidly. Habitat fragmentation in a continuously distributed population usually was detrimental to the genetic variability in the early generations. Other implications of the results for conservation are discussed.
A population size estimate of the finless porpoise, Neophocaena phocaenoides, from aerial sighting surveys in Ariake Sound and Tachibana Bay, Japan
Authors: Yoshida Hideyoshi , Shirakihara Kunio , Kishino Hirohisa , Shirakihara Miki
Published: December 2007

We estimated the population size of the finless porpoise (Neophocaena phocaenoides) in Ariake Sound and Tachibana Bay of western Kyushu, southwestern Japan, from aerial sighting surveys using line transect methods. All 12 surveys were conducted from May 1993 to May 1994 (8 in Ariake Sound and 4 in Tachibana Bay). In addition to these, 14 surveys were also carried out to obtain information on porpoise occurrence in Tachibana Bay (5 surveys) and in neighboring Sumo Nada (5) and Yatsushiro Sound (4). In Ariake Sound, 225 porpoise groups (369 animals) were detected during all flights totalling 1,694.4 km. In Tachibana Bay, a total of 997.8 km was surveyed and 55 groups (290 animals) were sighted. However, no sightings were recorded in Sumo Nada (distance searched = 148.7 km) and Yatsushiro Sound (208.4 km). In Ariake Sound, few sightings were recorded from waters shallower than 5 m in depth. In Tachibana Bay all animals were detected from waters of less than 50 m depth. The population size was estimated as 1,983 animals in Ariake Sound (95% CI = 1,382‐2,847), 1,110 in Tachibana Bay (95% CI = 642‐1,920), and 3,093 in the 2 waters (1.3 individuals/km2, 95% CI = 2,278‐4,201).
The effects of spatial and temporal environmental heterogeneities on persistence in a laboratory experimental community
Authors: Mitsunaga Takayuki , Fujii Koichi
Published: December 2007

Abstracts

Among many stabilizing factors for community dynamics, spatial and temporal heterogeneities have been widely considered in recent years as two of the most important properties. However, the difference between the two types of heterogeneities have not been studied, except for Clark and Yoshimura (1993). We evaluated experimentally the effect of temporal and spatial heterogeneities on the persistence of a biological community. The experimental communities consisted of one parasitic wasp species, one bean weevil species, and two kinds of bean. Temporal and spatial heterogeneities of experimental communities were generated by kinds and timing of bean supply. Of all the experimental communities, the most persistent community was a temporally and spatially homogeneous community with Red Kidney bean as primary resource. Compared to spatially heterogeneous communities, temporally heterogeneous communities were more persistent. These results were easily explained by considering the attack rate of parasitic wasps and the difference between arithmetic and geometric means. In order to discuss the relative importance of environmental heterogeneity and the mode of biological interaction on community persistence, we have to measure the degree of environmental heterogeneity as the rate of change of the strength of interspecific interactions.
VR to OR: A Review of the Evidence that Virtual Reality Simulation Improves Operating Room Performance
Authors: Seymour Neal E.
Published: December 2007

The use of virtual reality (VR) simulation to train surgeons has been supported by a body of experimental data derived from randomized trials of VR simulation training versus no such training. These investigations have focused on the use of VR devices to train surgeons in laparoscopic and flexible endoscopic skills, and the studies have generally demonstrated that skills acquired through courses of training in VR transfer to the clinical or animal laboratory setting, where assessments of various types have been used to measure performance. These studies, as well as the study model that describes them, and the future of randomized trials of this type are reviewed.
Excellent Field Emission Properties of Short Conical Carbon Nanotubes Prepared by Microwave Plasma Enhanced CVD Process
Authors: Srivastava SanjayKumar , Vankar Vasant D , Kumar Vikram
Published: December 2007

Randomly oriented short and low density conical carbon nanotubes (CNTs) were prepared on Si substrates by tubular microwave plasma enhanced chemical vapor deposition process at relatively low temperature (350–550 °C) by judiciously controlling the microwave power and growth time in C2H2 + NH3gas composition and Fe catalyst. Both length as well as density of the CNTs increased with increasing microwave power. CNTs consisted of regular conical compartments stacked in such a way that their outer diameter remained constant. Majority of the nanotubes had a sharp conical tip (5–20 nm) while its other side was either open or had a cone/pear-shaped catalyst particle. The CNTs were highly crystalline and had many open edges on the outer surface, particularly near the joints of the two compartments. These films showed excellent field emission characteristics. The best emission was observed for a medium density film with the lowest turn-on and threshold fields of 1.0 and 2.10 V/μm, respectively. It is suggested that not only CNT tip but open edges on the body also act as active emission sites in the randomly oriented geometry of such periodic structures.
In vitronematicidal effects of medicinal plants from the Sierra de Huautla, Biosphere Reserve, Morelos, Mexico againstHaemonchus contortusinfective larvae
Authors: López-Aroche U. , Salinas-Sánchez D.O. , Mendoza de Gives P. , López-Arellano M.E. , Liébano-Hernández E. , Valladares-Cisneros G. , Arias-Ataide D.M. , Hernández-Velázquez V.
Published: December 2007

Twenty extracts from plants from Sierra de Huautla Biosphere Reserve, Morelos, Mexico were evaluated againstHaemonchus contortusinfective larvae in anin vitroassay. The plant species evaluated wereBursera copallifera,B. grandifolia,Lippia graveolens,Passiflora mexicana,Prosopis laevigata,Randia echinocarpaandUrtica dioica. The plants were separated into their parts and macerated with different solvents (n-hexane, acetone, ethanol and methanol). Anin vitroassay was used to evaluate the anthelmintic activity against unsheathed third stageH. contortusinfective larvae. The experiment was carried out in 24-well cell culture plates at room temperature with three replicates per treatment and using a concentration of 20 mg ml− 1. Ten 5 μl aliquots were taken from the corresponding wells and deposited on a slide for microscopical observation at 24, 48, 72 and 96 h post-exposure. The evaluation criteria were based on the average numbers of live and/or dead larvae in the different treatments. Alive and dead larval numbers were statistically analysed through the ANOVA test (P>0.01). The Tukey test was used as a complementary tool to determine which treatment was different from the other treatments (P>0.05). The highest mortality was observed withP. laevigatahexanic extract from stem and leaves combined, which produced 51%, 81% and 86% larval mortality at 24, 48 and 72 h post-exposure, respectively. On the other hand,B. copalliferastem acetonic extract exhibited 18%, 59% and 66% nematicidal activity after 24, 48 and 72 h of exposure, respectively.
Can quality be managed and assured in architecture? Issues of qualification and quantification
Authors: Kite Stephen
Published: December 2007

‘Quality’ has become ubiquitous in the management vocabulary of Western societies. In consequence, the word's familiar usage has grown slippery. Formerly grounded in ethical values or skilled craftsmanship, ‘quality’ is now commonly associated with the management of administrative or technical processes. Whereas the appreciation of quality was founded in the exercise of individual judgement and taste – of connoisseurship – organisations now seek to ground its assessment in supposedly objective systems of evaluation. Practitioners are under pressure to quantify quality, but it remains questionable whether it is possible or even desirable to do so. Several papers in this issue of arq derive from a conference exploring such themes around the idea of Quality, an event held at the Welsh School of Architecture in July 2007 and reviewed here.
Consequences of natural variation in maternal investment and larval nutrition on larval growth of a marine polychaete
Authors: Smith Benjamin L. , Bolton Toby F.
Published: December 2007

Growth rates and planktonic development periods of marine invertebrate larvae have important consequences for the ecology of marine invertebrates. The growth and development of the larvae of a common southern Australian polychaete was examined to determine whether it was limited by natural concentrations of planktonic food, and whether naturally occurring variation in maternal investment in offspring influenced larval growth and development. Larvae that were provided concentrated diets of natural planktonic food were larger than larvae that were provided with food at ambient concentrations, but both experimental groups of larvae reached developmental stages immediately preceding settlement at the same time. Thus, larval growth was limited at natural concentrations of planktonic food but larval development rates were unaffected. These trends were also apparent in larvae fed with different concentrations of laboratory cultured food. Maternal investment in offspring (eggs) was higher on average for larger females than for smaller females. Larvae developing from smaller eggs were also smaller before settlement than larvae developing from larger eggs. Both maternal investment in offspring and the extent to which larval growth is food limited may vary spatially and seasonally along the southern coastline of Australia owing to the yearly occurrence of nutrient-rich oceanographic upwellings.
Transport-determined early growth and development of jack mackerel Trachurus japonicus juveniles immigrating into Sagami Bay, Japan
Authors: Xie Songguang , Watanabe Yoshiro
Published: December 2007

Oceanographic conditions and transport processes are often critical factors that affect the early growth, survival and recruitment of marine fishes. Sagittal otoliths were analysed to determine age and early growth for 381 jack mackerel (Trachurus japonicus) juveniles from Sagami Bay on the Pacific coast of Japan. Two separate hatching periods (December and February–March) were identified. They originated from the spawning grounds in the East China Sea. Early growth and developmental rates of December-hatching fish were lower than those for February–March-hatching fish. It is likely that these differences were determined in the Kuroshio Current during transport from the spawning grounds to Sagami Bay, and the lower December water temperatures in the bay. Origin and hatch dates of juveniles in Sagami Bay were in contrast to previous research on Fukawa Bay, where April-or-later-hatching fish from spawning grounds in the coastal waters of southern Japan constituted about half of the juvenile population. Management of these two jack mackerel stocks needs to consider these differences in hatch date composition and spawning origins, as these differences could affect early growth and subsequent mortality.
Tag retention, survival and growth of marron Cherax tenuimanus (Crustacea:Decapoda) marked with coded micro wire tags
Authors: de Graaf Martin
Published: December 2007

Detailed information on the growth and survival of small, juvenile crustaceans during the earliest part of their benthic life is rare. Tagging crustaceans is difficult; external tags can be lost during moulting, negatively effect growth, and owing to their size can only be used in larger (>50 mm carapace length) (sub)adult individuals. To evaluate the suitability of small internal, coded micro wire tags (<1 mm) to mark marron, Cherax tenuimanus, a laboratory trial was conducted to compare growth and survival of juvenile (<20 mm orbital-carapace length) marked and unmarked marron. After 394 days no significant differences in growth or survival were observed between tagged and control groups. Mortality was high (~80%) but similar between both treatments. Tag loss, ~12% between Day 1 and Day 54, appeared to be confined to the first post-tag moult. No further tag loss was observed during the remaining 340 days of the experiment. Mark–recapture programs could provide the first detailed estimates of growth and survival of C. tenuimanus under natural conditions, enhancing the sustainable management of the declining recreational marron fishery. The present study illustrates the potential usefulness of coded micro wire tags as a tool in crustacean biology and fisheries management.
45. TABOO TOPICS IN THE SEXY SIXTIES “THROWING THE BABY (BOOMERS) OUT WITH THE BATHWATER”
Authors: Weerakoon P.
Published: December 2007

"A woman's sex life ends with the menopause; Sex is for the young, I'm too old to bother with all that; older people are asexual."
"Later life sexuality in women is about words, images, ritual and fantasy as it is about the body"

Sexuality in older adults especially the sexual behavior of older women has been shrouded in discreet silence distaste and ignorance (Oppenheimer 2002).1 Recent literature however has demythologised sexuality and revealed that men and women continue to be sexually active well into old age. A recent study from US reported in the New England Journal of Medicine (Lindau et al. 2007)2 reports that 73% of those 57-64 age, 53% of those 65-74 years of age and 26% of those 74-85 years of age reported to being sexually active (defined as any mutually voluntary activity with another person that involves sexual contact, whether or not intercourse or orgasm occurs). In all groups, sexual activity for men was higher. It is interesting that 35% of all women and 13% of all men interviewed said "sex was not at all important".
It is recognized that leading an active and fulfilling sexual life is related to physical health, ability to function sexually, availability of a partner and perceptions of self esteem and body image (Lindau 2007; Clarke 2006).2,3 Overlying all of these is the personal knowledge, attitude and perceptions of the role of sexuality and sexual behaviors in wellbeing.
With the 'Baby Boomer' generation coming of age as 'Older Adults', this presentation will explore whether the discourses of positive ageing have created the sexy ageless consumer as a personally and socially responsible citizen. Is the availability and apparent popularity of adult on-line dating for relationships; gyms and health fads for the healthy body; drugs and devices (sex toys such as the Eros clitoral device, and ben-wa balls); cosmetic treatments (Clarke 2006)3 and now surgical procedures for the body beautiful (Goodman et al. 2007)4 indicative of a need for assistance in sexuality? Or a use of the 'Baby Boomer' demographic bulge in the population as a marketing target?
52. THE AUSTRALIAN WOMEN'S HEALTH SURVEY: ASSESSING THE PSYCHOSOCIAL BURDEN OF HPV RELATED ILLNESS AND PREVENTIVE INTERVENTIONS
Authors: Ung L. , Conway E. L. , Pirotta M. , Mast C. , Stein A. N. , Palmer D. , Tan J. , Fairley C. K. , Quinn M. , Carter R. , Garland S.
Published: December 2007

There is increasing recognition of the psychosocial impact of cervical cytology screening programs as well as of the treatment of screening-detected human papillomavirus (HPV) - related disease. The HPV Impact Profile (HIP) includes 29 items with standard response categories representing nine psychosocial impact domains: 'worries and concerns, emotional impact, sexual impact, self image, health perception, cognition, partner and social relations, interaction with doctors and sleep'. Higher scores (0-100) are associated with higher disease burden. The HIP and other generic quality of life instruments such as the Sheehan Disability Scale were administered to women who had experienced and were aware of an HPV related diagnosis in the past 3 months (total n�=�333): 103 women with normal Pap test results (N. Pap), 111 with abnormal Pap tests (58 low grade squamous intraepithelial lesions (LSIL) and 53 high grade SIL (HSIL)), 80 women with biopsy confirmed cervical intraepithelial neoplasia (CIN) (36 CIN1 and 44 CIN 2/3) and 39 women with external genital warts (EGW). In univariate analysis, estimated HIP scores (95% CI) were lower for N.Pap than for all other groups (p�<�0.0001), N. Pap: 25.8 (22.6-29.0); LSIL: 38.8 (34.6-43.1); HSIL: 41.7 (37.2-46.2); CIN1: 41.7 (36.3-47.1); CIN 2/3: 46.6 (41.6-51.5) (p�=�0.013 vs LSIL); EGW: 44.6 (39.4-49.8). The effect was maintained after adjusting for age, race and occupation. On the Sheehan scale, CIN 2/3 and EGW demonstrated increased interference with work and social activities. Results demonstrate: a) HPV infection and disease are associated with significantly increased psychosocial burden, beyond that of the Pap test experience; b) The HIP instrument can adequately distinguish between different HPV conditions; c) Despite their non life threatening nature, the psychosocial impact of genital warts is similar to that of potentially life threatening high grade cervical lesions.
Déjà vu—A study of duplicate citations in Medline
Authors: Errami Mounir , Hicks Justin M. , Fisher Wayne , Trusty David , Wren Jonathan D. , Long Tara C. , Garner Harold R.
Published: December 2007

Motivation: Duplicate publication impacts the quality of the scientific corpus, has been difficult to detect, and studies this far have been limited in scope and size. Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts.

Results: A sample of 62 213 Medline citations was examined and a database of manually verified duplicate citations was created to study author publication behavior. We found that 0.04% of the citations with no shared authors were highly similar and are thus potential cases of plagiarism. 1.35% with shared authors were sufficiently similar to be considered a duplicate. Extrapolating, this would correspond to 3500 and 117 500 duplicate citations in total, respectively.

Availability: eTBLAST, an automated citation matching tool, and Déjà vu, the duplicate citation database, are freely available at http://invention.swmed.edu/ and http://spore.swmed.edu/dejavu

Contact:  harold.garner@utsouthwestern.edu
Automated manipulation of systems biology models using libSBML within Taverna workflows
Authors: Li Peter , Oinn Tom , Soiland Stian , Kell Douglas B.
Published: December 2007

Summary: Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model.

Availability: Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net

Contact:  peter.li@manchester.ac.uk

Supplementary information: Supplementary data and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html
KEGGanim: pathway animations for high-throughput data
Authors: Adler Priit , Reimand Jüri , Jänes Jürgen , Kolde Raivo , Peterson Hedi , Vilo Jaak
Published: December 2007

Motivation: Gene expression analysis with microarrays has become one of the most widely used high-throughput methods for gathering genome-wide functional data. Emerging -omics fields such as proteomics and interactomics introduce new information sources. With the rise of systems biology, researchers need to concentrate on entire complex pathways that guide individual genes and related processes. Bioinformatics methods are needed to link the existing knowledge about pathways with the growing amounts of experimental data.

Results: We present KEGGanim, a novel web-based tool for visualizing experimental data in biological pathways. KEGGanim produces animations and images of KEGG pathways using public or user uploaded high-throughput data. Pathway members are coloured according to experimental measurements, and animated over experimental conditions. KEGGanim visualization highlights dynamic changes over conditions and allows the user to observe important modules and key genes that influence the pathway. The simple user interface of KEGGanim provides options for filtering genes and experimental conditions. KEGGanim may be used with public or private data for 14 organisms with a large collection of public microarray data readily available. Most common gene and protein identifiers and microarray probesets are accepted for visualization input.

Availability:  http://biit.cs.ut.ee/KEGGanim/

Contact:  vilo@ut.ee
An integrated system for studying residue coevolution in proteins
Authors: Yip Kevin Y. , Patel Prianka , Kim Philip M. , Engelman Donald M. , McDermott Drew , Gerstein Mark
Published: December 2007

Residue coevolution has recently emerged as an important concept, especially in the context of protein structures. While a multitude of different functions for quantifying it have been proposed, not much is known about their relative strengths and weaknesses. Also, subtle algorithmic details have discouraged implementing and comparing them. We addressed this issue by developing an integrated online system that enables comparative analyses with a comprehensive set of commonly used scoring functions, including Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Variation (ELSC), mutual information and correlation-based methods. A set of data preprocessing options are provided for improving the sensitivity and specificity of coevolution signal detection, including sequence weighting, residue grouping and the filtering of sequences, sites and site pairs. A total of more than 100 scoring variations are available. The system also provides facilities for studying the relationship between coevolution scores and inter-residue distances from a crystal structure if provided, which may help in understanding protein structures.

Availability: The system is available at http://coevolution.gersteinlab.org. The source code and JavaDoc API can also be downloaded from the web site.

Contact:  mark.gerstein@yale.edu

Supplementary information: Additional materials can be found at http://coevolution.gersteinlab.org/coevolution/supp.jsp
Model-based deconvolution of genome-wide DNA binding
Authors: Reiss David J. , Facciotti Marc T. , Baliga Nitin S.
Published: December 2007

Motivation: Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray (ChIP-chip) is a routinely used protocol for localizing the genomic targets of DNA-binding proteins. The resolution to which binding sites in this assay can be identified is commonly considered to be limited by two factors: (1) the resolution at which the genomic targets are tiled in the microarray and (2) the large and variable lengths of the immunoprecipitated DNA fragments.

Results: We have developed a generative model of binding sites in ChIP-chip data and an approach, MeDiChI, for efficiently and robustly learning that model from diverse data sets. We have evaluated MeDiChI's performance using simulated data, as well as on several diverse ChIP-chip data sets collected on widely different tiling array platforms for two different organisms (Saccharomyces cerevisiae and Halobacterium salinarium NRC-1). We find that MeDiChI accurately predicts binding locations to a resolution greater than that of the probe spacing, even for overlapping peaks, and can increase the effective resolution of tiling array data by a factor of 5× or better. Moreover, the method's performance on simulated data provides insights into effectively optimizing the experimental design for increased binding site localization accuracy and efficacy.

Availability:  MeDiChI is available as an open-source R package, including all data, from http://baliga.systemsbiology.net/medichi.

Contact:  dreiss@systemsbiology.org

Supplementary information: Supplementary data are available at Bioinformatics online.
OBO Explorer: an editor for open biomedical ontologies in OWL
Authors: Aitken Stuart , Chen Yin , Bard Jonathan
Published: December 2007

Motivation: To clarify the semantics, and take advantage of tools and algorithms developed for the Semantic Web, a mapping from the Open Biomedical Ontologies (OBO) format to the Web Ontology Language (OWL) has been established. We present an ontology editor that allows end users to work directly with this OWL representation of OBO format ontologies.

Availability:  http://www.aiai.ed.ac.uk/project/cobra-ct

Contact:  stuart@aiai.ed.ac.uk
COMPARE, a multi-organism system for cross-species data comparison and transfer of information
Authors: Salgado David , Gimenez Gregory , Coulier François , Marcelle Christophe
Published: December 2007

Motivation: COMPARE is a multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species. The COMPARE interface provides access to a wide array of information including genomic structure, expression data, annotations, pathways and literature links for human and three widely studied animal models (zebrafish, Drosophila and mouse). A consensus ortholog-finding pipeline combining several ortholog prediction methods allows accurate comparisons of data across species and has been utilized to transfer information from well studied organisms to more poorly annotated ones.

Availability:  http://compare.ibdml.univ-mrs.fr

Contact:  marcelle@ibdm.univ-mrs.fr
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence
Authors: Oberto Jacques
Published: December 2007

Summary: BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction, by molecular geneticists and phylogeneticists, of specific gene and protein sequences from completely determined prokaryotic genomes. Upon selection of a particular prokaryotic organism and gene, two levels of visual gene context information are provided on a single dynamic page: (i) a graphical representation of a user defined portion of the chromosome centered on the gene of interest and (ii) the DNA sequence of the query gene, of the immediate neighboring genes and the intergenic regions each identified by a consistent color code. The aminoacid sequence is provided for protein-coding query genes. Query results can be exported as a rich text format (RTF) word processor file for printing, archival or further analysis.

Availability:  http://archaea.u-psud.fr/bin/baget.dll

Contact:  jacques.oberto@igmors.u-psud.fr
Estimation of the carbon dioxide (CO2) fertilization effect using growth rate anomalies of CO2 and crop yields since 1961
Authors: LOBELL DAVID B. , FIELD CHRISTOPHER B.
Published: December 2007

The effect of elevated carbon dioxide (CO2) on crop yields is one of the most uncertain and influential parameters in models used to assess climate change impacts and adaptations. A primary reason for this uncertainty is the limited availability of experimental data on CO2 responses for crops grown under typical field conditions. However, because of historical variations in CO2, each year farmers throughout the world perform uncontrolled yield ‘experiments’ under different levels of CO2. In this study, measurements of atmospheric CO2 growth rates and crop yields for individual countries since 1961 were compared to empirically determine the average effect of a 1 ppm increase of CO2 on yields of rice, wheat, and maize. Because the gradual increase in CO2 is highly correlated with major changes in technology, management, and other yield controlling factors, we focused on first differences of CO2 and yield time series. Estimates of CO2 responses obtained from this approach were highly uncertain, reflecting the relatively small importance of year‐to‐year CO2 changes for yield variability. Combining estimates from the top 20 countries for each crop resulted in estimates with substantially less uncertainty than from any individual country. The results indicate that while current datasets cannot reliably constrain estimates beyond previous experimental studies, an empirical approach supported by large amounts of data may provide a potentially valuable and independent assessment of this critical model parameter. For example, analysis of reliable yield records from hundreds of individual, independent locations (as opposed to national scale yield records with poorly defined errors) may result in empirical estimates with useful levels of uncertainty to complement estimates from experimental studies.
Genotypic differences in leaf biochemical, physiological and growth responses to ozone in 20 winter wheat cultivars released over the past 60 years
Authors: BISWAS D. K. , XU H. , LI Y. G. , SUN J. Z. , WANG X. Z. , HAN X. G. , JIANG G. M.
Published: December 2007

Ozone (O3) concentrations in periurban areas in East Asia are sufficiently high to decrease crop yield. However, little is known about the genotypic differences in O3 sensitivity in winter wheat in relation to year of cultivar release. This paper reports genotypic variations in O3 sensitivity in 20 winter wheat cultivars released over the past 60 years in China highlighting O3‐induced mechanisms. Wheat plants were exposed to elevated O3 (82 ppb O3, 7 h day−1) or charcoal‐filtered air (<5 ppb O3) for 21 days in open top chambers. Responses to O3 were assessed by the levels of antioxidative activities, protein alteration, membrane lipid peroxidation, gas exchange, leaf chlorophyll, dark respiration and growth. We found that O3 significantly reduced foliar ascorbate (−14%) and soluble protein (−22%), but increased peroxidase activity (+46%) and malondialdehyde (+38%). Elevated O3 depressed light saturated net photosynthetic rate (−24%), stomatal conductance (−8%) and total chlorophyll (−11%), while stimulated dark respiration (+28%) and intercellular CO2 concentration (+39%). O3 also reduced overall plant growth, but to a greater extent in root (−32%) than in shoot (−17%) biomass. There was significant genotypic variation in potential sensitivity to O3 that did not correlate to observed O3 tolerance. Sensitivity to O3 in cultivars of winter wheat progressed with year of release and correlated with stomatal conductance and dark respiration in O3‐exposed plants. O3‐induced loss in photosynthetic rate was attributed primarily to impaired activity of mesophyll cells and loss of integrity of cellular membrane as evidenced by increased intercellular CO2 concentration and lipid peroxidation. Our findings demonstrated that higher sensitivity to O3 in the more recently released cultivars was induced by higher stomatal conductance, larger reduction in antioxidative capacity and lower levels of dark respiration leading to higher oxidative damage to proteins and integrity of cellular membranes.
KIT and PDGFRα mutational analyses of mixed cell‐type gastrointestinal stromal tumours
Authors: Wong N A C S , Mangwana S
Published: December 2007

Aims:  To determine whether the epithelioid and spindle components of a mixed cell‐type gastrointestinal stromal tumour (GIST) show the same receptor tyrosine kinase mutation and, by inference, the same sensitivity to imatinib.

Methods and results:  Six mixed cell‐type GISTs were identified from 108 gastric GISTs. Clinicopathological and immunohistochemical data of the six neoplasms were collated. For each neoplasm, DNA was extracted separately from the laser‐microdissected epithelioid and spindle components and non‐neoplastic tissue and sequenced for KIT and platelet‐derived growth factor receptor (PDGFR)α mutations. The epithelioid component often showed less CD117 and/or CD34 immunoreactivity than the spindle component of the same mixed cell‐type GIST. Four mixed cell‐type GISTs showed somatic KIT mutations (deletions in exon 11 in three tumours and an insertion in exon 9 in one tumour) and one showed a somatic PDGFRα mutation (point mutation in exon 18); in each of the five cases, both epithelioid and spindle components showed identical mutations.

Conclusions:  The presence of the same receptor tyrosine kinase mutation in both components of a mixed cell‐type GIST suggests that both components should be equally responsive to imatinib treatment, and that such mutation is an early key event in the pathogenesis of these neoplasms.
Clear‐cell dermal duct tumour: another distinctive, previously underrecognized cutaneous adnexal neoplasm
Authors: Rütten A , Hantschke M , Angulo J , Requena L
Published: December 2007

Aims:  To describe 13 examples of clear cell dermal duct tumour, a neoplasm previously underrecognized in the literature.

Methods and results:  Thirteen examples of a neoplasm that we have named clear‐cell dermal duct tumour were studied histopathologically and immunohistochemically. Histopathologically, all lesions consisted of mostly dermal neoplasms mainly composed of multiple solid aggregations of clear cells involving the dermis. Although the neoplasms were mostly solid, ductal structures were identified in all cases. Immunohistochemically, neoplastic cells were immunoreactive for MNF116 and AE1/AE3 cytokeratins, but not for CAM5.2 or cytokeratin 7. Epithelial membrane antigen, carcinoembryonic antigen and glial cystic disease fibrillary protein 15 decorated the ductal structures, but neoplastic cells were negative. In contrast to some other clear cell neoplasms of the skin, which may be associated with diabetes mellitus, none of our cases of clear cell dermal duct tumour developed in a diabetic patient.

Conclusions:  We consider these neoplasms to be clear cell dermal duct tumours for the following reasons: (i) the neoplasms were mostly composed of multiple solid aggregations of epithelial clear cells; (ii) neoplastic aggregations mostly involved the dermis; (iii) in some cases, neoplastic aggregations of conventional poroid cells were intermingled with the aggregations of clear cells; (iv) ductal structures were identified within some neoplastic aggregations; (iv) small areas of necrosis en masse were seen in some neoplastic aggregations; and (v) the stroma of the neoplasm was scant.
Expression of c‐FLIP is primarily detected in diffuse large B‐cell lymphoma and Hodgkin’s lymphoma and correlates with lack of caspase 8 activation
Authors: Van Houdt I S , Muris J J , Hesselink A T , Kramer D , Cillessen S A G M , Moesbergen L M , Vos W , Hooijberg E , Meijer C J L M , Kummer J A , Oudejans J J
Published: December 2007

Aims:  Inhibition of apoptosis is important in the pathogenesis of lymphomas. c‐FLIP, a regulator of caspase 8‐mediated apoptosis, plays an important role in protecting normal B and T cells from apoptosis and possibly also in lymphomas. Because of contradictory reports about immunohistochemical detection of c‐FLIP expression, the aim was to test the specificity of four antibodies in c‐FLIP‐transfected cells and subsequently to investigate expression of c‐FLIP in different types of lymphoma.

Methods and results:  Two of four antibodies were specific. In primary lymphomas c‐FLIP expression was restricted to Hodgkin’s lymphomas (> 90%) and diffuse large B‐cell lymphomas (44%). Burkitt lymphomas and indolent B‐cell lymphomas were negative in all cases. No expression was detected in primary T‐cell lymphomas, although expression was observed in one relapsed ALK+ anaplastic large cell lymphoma. Expression of c‐FLIP was inversely correlated with caspase 8 activation.

Conclusions:  c‐FLIP is important in escape of B cells from apoptosis during normal follicle centre cell reaction and may thus be an important early event in the development of B‐cell‐derived lymphomas. Moreover, non‐specific staining of frequently used antibodies might explain discrepancies in different reports of c‐FLIP expression.