bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractWe 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

AbstractsAmong 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

AbstractThe 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

Abstract
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

AbstractTwenty 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.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractThe 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

AbstractOzone (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.