bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endophytic fungi alter relationships between diversity and ecosystem properties
Authors: Rudgers Jennifer A. , Koslow Jennifer M. , Clay Keith 
Published: December 2003

AbstractRecent studies have expanded research on biodiversity by investigating whether the effects of diversity on ecosystem functioning hinge on the presence of symbiotic microorganisms. Cool‐season grasses commonly harbour endophytic fungi that can enhance plant resistance to herbivory, drought and competition. We address whether these endosymbionts modify relationships between diversity and two ecosystem properties: productivity and invasibility. We develop a graphical model that predicts endophyte infection of a grass host will weaken correlations between diversity and ecosystem properties. We then use a long‐term field experiment to test this prediction by manipulating symbiosis in tall fescue grass (Festuca arundinacea), a common and invasive species in the US. As predicted, endophyte infection reduced the strength of correlations between diversity and both primary productivity and the invasiveness of tall fescue. By altering relationships between diversity and ecosystem functioning, endophytic fungi may contribute more to the dynamics of communities than previously supposed.
Combining DNA expression with positional information to detect functional silencing of chromosomal regions
Authors: Hüsing Johannes , Zeschnigk Michael , Boes Tanja , Jöckel Karl-Heinz 
Published: December 2003

Abstract
Motivation: Loss of chromosomal material is often observed in cancer cells. In this situation the expression of genes is related to their position on the genome. Epigenetic phenomena may also silence several genes in the same region of a chromosome. While cytogenetic or other molecular genetic methods spot changes of DNA copy number, they cannot detect other causes of silencing.
Results: We propose a method that utilizes the link from expression information gained from high-density DNA microarrays to the gene locus according to current databases. Statistical methods adequate to spot conspicuous runs of non-expressed genes are introduced and compared to one another by merit of their power and robustness against false positives.
Availability: Code for the formulae can be obtained (R code) via http://www.panix.com/~derwisch/hannes/longrun
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration
Authors: Huang Yihua , Ni Tianyun , Zhou Lei , Su Stanley 
Published: December 2003

Abstract
Motivation: In the post-genomic era, biologists interested in systems biology often need to import data from public databases and construct their own system-specific or subject-oriented databases to support their complex analysis and knowledge discovery. To facilitate the analysis and data processing, customized and centralized databases are often created by extracting and integrating heterogeneous data retrieved from public databases. A generalized methodology for accessing, extracting, transforming and integrating the heterogeneous data is needed.
Results: This paper presents a new data integration approach named JXP4BIGI (Java XML Page for Biological Information Gathering and Integration). The approach provides a system-independent framework, which generalizes and streamlines the steps of accessing, extracting, transforming and integrating the data retrieved from heterogeneous data sources to build a customized data warehouse. It allows the data integrator of a biological database to define the desired bio-entities in XML templates (or Java XML pages), and use embedded extended SQL statements to extract structured, semi-structured and unstructured data from public databases. By running the templates in the JXP4BIGI framework and using a number of generalized wrappers, the required data from public databases can be efficiently extracted and integrated to construct the bio-entities in the XML format without having to hard-code the extraction logics for different data sources. The constructed XML bio-entities can then be imported into either a relational database system or a native XML database system to build a biological data warehouse.
Availability: JXP4BIGI has been integrated and tested in conjunction with the IKBAR system (http://www.ikbar.org/) in two integration efforts to collect and integrate data for about 200 human genes related to cell death from HUGO, Ensembl, and SWISS-PROT (Bairoch and Apweiler, 2000), and about 700 Drosophila genes from FlyBase (FlyBase Consortium, 2002). The integrated data has been used in comparative genomic analysis of x-ray induced cell death. Also, as explained later, JXP4BIGI is a middleware and framework to be integrated with biological database applications, and cannot run as a stand-alone software for end users. For demonstration purposes, a demonstration version is accessible at (http://www.ikbar.org/jxp4bigi/demo.html).
Algorithms for large-scale genotyping microarrays
Authors: Liu Wei-min , Di Xiaojun , Yang Geoffrey , Matsuzaki Hajime , Huang Jing , Mei Rui , Ryder Thomas B. , Webster Teresa A. , Dong Shoulian , Liu Guoying , Jones Keith W. , Kennedy Giulia C. , Kulp David 
Published: December 2003

Abstract
Motivation: Analysis of many thousands of single nucleotide polymorphisms (SNPs) across whole genome is crucial to efficiently map disease genes and understanding susceptibility to diseases, drug efficacy and side effects for different populations and individuals. High density oligonucleotide microarrays provide the possibility for such analysis with reasonable cost. Such analysis requires accurate, reliable methods for feature extraction, classification, statistical modeling and filtering.
Results: We propose the modified partitioning around medoids as a classification method for relative allele signals. We use the average silhouette width, separation and other quantities as quality measures for genotyping classification. We form robust statistical models based on the classification results and use these models to make genotype calls and calculate quality measures of calls. We apply our algorithms to several different genotyping microarrays. We use reference types, informative Mendelian relationship in families, and leave-one-out cross validation to verify our results. The concordance rates with the single base extension reference types are 99.36% for the SNPs on autosomes and 99.64% for the SNPs on sex chromosomes. The concordance of the leave-one-out test is over 99.5% and is 99.9% higher for AA, AB and BB cells. We also provide a method to determine the gender of a sample based on the heterozygous call rate of SNPs on the X chromosome. See http://www.affymetrix.com for further information. The microarray data will also be available from the Affymetrix web site.
Availability: The algorithms will be available commercially in the Affymetrix software package.
LOX-DB—a database on lipoxygenases
Authors: Lütteke T. , Krieg P. , Fürstenberger G. , von der Lieth C.-W. 
Published: December 2003

Abstract
Summary: Lipoxygenases are a family of enzymes involved in a variety of human diseases like inflammation, asthma, artherosclerosis and cancer. The lipoxygenases database (LOX-DB) aims to be a web accessible compendium of information in particular on the mammalian members of this multigene family. This resource includes molecular structures, reference data, tools for structural and computational analysis as well as links to related information maintained by others. The data can be retrieved by the use of various search options and analyzed applying publicly available visualization tools.
Availability: LOX-DB is available at http://www.dkfz-heidelberg.de/spec/lox-db/
Global snapshot of a protein interaction network—a percolation based approach
Authors: Chin Chen-Shan , Samanta Manoj Pratim 
Published: December 2003

Abstract
Motivation: Biologically significant information can be revealed by modeling large-scale protein interaction data using graph theory based network analysis techniques. However, the methods that are currently being used draw conclusions about the global features of the network from local connectivity data. A more systematic approach would be to define global quantities that measure (1) how strongly a protein ties with the other parts of the network and (2) how significantly an interaction contributes to the integrity of the network, and connect them with phenotype data from other sources. In this paper, we introduce such global connectivity measures and develop a stochastic algorithm based upon percolation in random graphs to compute them.
Results: We show that, in terms of global connectivities, the distribution of essential proteins is distinct from the background. This observation highlights a fundamental difference between the essential and the non-essential proteins in the network. We also find that the interaction data obtained from different experimental methods such as immunoprecipitation and two-hybrid techniques contribute differently to network integrities. Such difference between different experimental methods can provide insight into the systematic bias present among these techniques.
Supplementary information: The full list of our results can be found in the supplemental web site http://www.nas.nasa.gov/Groups/SciTech/nano/msamanta/projects/percolation/index.php
Susceptibility of non-linear systems as an approach to metabolic responses
Authors: Torralba Antonio S. 
Published: December 2003

Abstract
Motivation: Recent developments of several analytical techniques and fast sampling procedures are making it possible to study non-linear dynamics on an automated basis. Approaches that suggest experimental setups and fully exploit the data are needed. To prevent unreliable fits of parameters to experimental data, model-independent methods would be advantageous. One such method consists in representing the response of a system by means of a transformation or functional, of an excitation, i.e. a flux of a metabolite.
Results: A functional of unknown form can be expanded in series if its functional derivatives are known. An algorithm for calculating such generalized derivatives from impulse-perturbation experiments was developed. The only assumption was that the implicit kinetics is time-independent, i.e. the system is time-invariant. The method is illustrated on a part of fructose catabolism. A reaction network that involves 14 metabolites and 11 enzymes and includes several branches and feedback loops is considered. It is shown that the method provides good approximations to the responses of this complex system.
Availability: FUNDER is available from http://bbm1.ucm.es/torralba/funder/down/
Supplementary information: http://bbm1.ucm.es/torralba/funder/
Assessing sequence comparison methods with the average precision criterion
Authors: Chen Zhuoran 
Published: December 2003

Abstract
Motivation: Comprehensive performance assessment is important for improving sequence database search methods. Sensitivity, selectivity and speed are three major yet usually conflicting evaluation criteria. The average precision (AP) measure aims to combine the sensitivity and selectivity features of a search algorithm. It can be easily visualized and extended to analyze results from a set of queries. Finally, the time–AP plot can clearly show the overall performance of different search methods.
Results: Experiments are performed based on the SCOP database. Popular sequence comparison algorithms, namely Smith–Waterman (SSEARCH), FASTA, BLAST and PSI-BLAST are evaluated. We find that (1) the low-complexity segment filtration procedure in BLAST actually harms its overall search quality; (2) AP scores of different search methods are approximately in proportion of the logarithm of search time; and (3) homologs in protein families with many members tend to be more obscure than those in small families. This measure may be helpful for developing new search algorithms and can guide researchers in selecting most suitable search methods.
Availability: Test sets and source code of this evaluation tool are available upon request.
Characterizing gene sets with FuncAssociate
Authors: Berriz Gabriel F. , King Oliver D. , Bryant Barbara , Sander Chris , Roth Frederick P. 
Published: December 2003

Abstract
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate include the ability to handle ranked input lists, and a Monte Carlo simulation approach that is more appropriate to determine significance than other methods, such as Bonferroni or S̆idák p-value correction. FuncAssociate currently supports 10 organisms (Vibrio cholerae, Shewanella oneidensis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhaebditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus and Homo sapiens).
Availability: FuncAssociate is freely accessible at http://llama.med.harvard.edu/Software.html. Source code (in Perl and C) is freely available to academic users ‘as is’.
International NGOs and the Role of Network Centrality in Humanitarian Aid Operations: A Case Study of Coordination During the 2000 Mozambique Floods
Authors: Moore Spencer , Eng Eugenia , Daniel Mark 
Published: December 2003

In February 2000, Mozambique suffered its worst flooding in almost 50 years: 699 people died and hundreds of thousands were displaced. Over 49 countries and 30 international non‐governmental organisations provided humanitarian assistance. Coordination of disaster assistance is critical for effective humanitarian aid operations, but limited attention has been directed toward evaluating the system‐wide structure of inter‐organisational coordination during humanitarian operations.Network analysis methods were used to examine the structure of inter‐organisational relations among 65 non‐governmental organisations (NGOs) involved in the flood operations in Mozambique. Centrality scores were used to estimate NGO‐specific potential for aid coordination and tested against NGO beneficiary numbers. The average number of relief‐ and recovery‐period beneficiaries was significantly greater for NGOs with high relative to low centrality scores (p<0.05). This report addresses the significance of these findings in the context of the Mozambican 2000 floods and the type of data required to evaluate system‐wide coordination.
Colonising aliens: caterpillars (Lepidoptera) feeding on Piper aduncum and P. umbellatum in rainforests of Papua New Guinea
Authors: Novotny Vojtech , Miller Scott. E. , Cizek Lukas , Leps Jan , Janda Milan , Basset Yves , Weiblen George D. , Darrow Karolyn 
Published: December 2003

Abstract.  1. Caterpillar assemblages feeding on two alien plants, Piper aduncum and P. umbellatum, were studied in lowland rainforest in Papua New Guinea and compared with assemblages from 69 species of native woody hosts, including congeneric P. macropiper.2. Species richness of caterpillars feeding on P. aduncum (29 species per 1500 m2 of foliage) and P. umbellatum (36 species) was higher than the median richness for the 69 native hosts (23 species).3. The probability that a caterpillar species colonised alien Piper increased with its host range from 3% for the species feeding on a single plant family to 92% for the species with host range >10 plant families.4. The assemblage on P. aduncum was dominated by a single species (Herpetogramma sp. near licarsisalis, Crambidae), which represented 48% of individuals, and also had a high proportion (34%) of rare species, collected as single individuals. This community structure was indistinguishable from that of a typical native host. In contrast, the P. umbellatum assemblage was unusual as no species represented >10% of individuals.5. The aggressive invasion by P. aduncum of early successional vegetation is not explained by a competitive advantage due to low herbivore load, as the abundance of caterpillars feeding on it was comparable to that of native pioneer plants.6. The caterpillar assemblage on P. aduncum demonstrated that an assemblage indistinguishable from native assemblages in density, species richness, and dominance structure (but not in host specificity) can originate from the existing species pool in lowland rainforests on a recently established tree species in <50 years.
Influence of habitat structure on the phonotactic strategy of a parasitoid fly Emblemasoma auditrix
Authors: Lakes‐Harlan Reinhard , Köhler Ulrike 
Published: December 2003

Abstract.  1. Females of the parasitoid fly Emblemasoma auditrix find their host cicadas (Okanagana rimosa) using the acoustic signals produced by the host. The phonotactic behaviour of the parasitoid was studied with regard to differently structured habitats.2. Habitats were modified experimentally within a distance of 2.5 m (approximately the natural range of phonotaxis) from a loudspeaker broadcasting a model of the host calling song.3. Video analysis showed that in an open habitat (no landmarks) more than 60% of the flies performed a direct flight towards the loudspeaker.4. In structured habitats (with one to three landmarks) more than 90% of the flies landed on their way to the acoustic target.5. In about 50% of the landings flies paused for several seconds indicating re‐orientation during that time. Several flies included sequences of walking in their approach behaviour, whereby most walking occurred close to the loudspeaker.6. In summary, the phonotactic approach and host finding depends on the habitat structure.
Laparoscopic‐assisted surgery and irradiation in an 87‐year‐old‐woman with a large ovarian cystic tumour and uterine cervical cancer
Authors: Yamada Takashi , Kasamatsu Hajime , Mori Hiroshi 
Published: December 2003

ABSTRACTObjective To report a case of useful treatment for a patient with a large ovarian cystic tumour and uterine cervical cancer.Results An 87‐year‐old woman was admitted to our hospital because of abdominal distension and genital bleeding. A large ovarian cystic tumour was removed by laparoscopic‐assisted oöphorosalpingectomy through a 2.5‐cm incision in the abdominal wall. Irradiation was carried out for cervical cancer of clinical stage IIb.Conclusions Laparoscopic‐assisted surgery and irradiation are useful, minimally invasive therapies in elderly patients with large ovarian cystic tumour and uterine cancer.
Delivery outcomes following laparoscopic ovarian cystectomy during pregnancy
Authors: Ishihara Yuki , Inoue Hiromi , Kohata Yutaka , Yamamoto Kenji , Nakamura Takumi , Utsugisawa Yukari , Ohgi Shirei , Suzuki Yukinari 
Published: December 2003

ABSTRACTObjective  The purpose of this study was to survey delivery outcomes following gasless laparoscopic ovarian cystectomy with minilaparotomy during pregnancy, and to discuss the safety and benefits of this approach for benign ovarian lesions presenting during pregnancy.Patients and methods  Asymptomatic patients underwent operation in the second trimester; symptomatic patients underwent operation when diagnosed. Written informed consent was obtained. Using the database of operation details, we retrospectively assessed the patients who had laparoscopic surgery during pregnancy, and the delivery outcomes for both mothers and babies.Results  A total of 44 pregnant patients with benign ovarian mass underwent laparoscopic operation in our hospital. After exclusion of eight patients who had delivered at other hospitals or with complications from pre‐existing diseases, details from 36 patients were analysed. The mean gestational week at the time of surgery was 15.5 weeks; the mean surgical time was 93.2 min. There were no intraoperative or postoperative complications. Pathological examination showed benign cystic teratoma in 24 patients, lutein cyst in six, endometrial cyst in five and a paraovarian cyst in one patient. The mean length of hospitalization was 2.2 days. Of the patients, 32 had a normal vaginal delivery at term, and four delivered by Caesarean section, because of breech presentation, pre‐eclampsia or failure to progress. All the babies were healthy. There was no delivery complication related to the laparoscopic surgery during pregnancy.Conclusions  The benefits of laparoscopic management in pregnancy for benign ovarian lesions have been discussed mainly from the point of view of safety and short hospitalization. The delivery outcomes at our hospital showed that gasless laparoscopic cystectomy with minilaparotomy during pregnancy has no effect with regard to subsequent normal delivery.
Adhesion formation after uterine horn resection in rabbit model: comparative study of laparoscopic procedure vs. laparotomy
Authors: Telles de Sousa Iuri Donati , Candido dos Reis Francisco José , Brito Garcia Sérgio , Alberto Nogueira Antonio 
Published: December 2003

ABSTRACTObjective  To determine whether laparoscopic surgery causes less adhesion formation than standard laparotomy for uterine horn resection in the rabbit model.Design  Experimental prospective animal study: 10 New Zealand female rabbits were randomly allocated to operation by laparoscopy and 10 to standard laparotomy for uterine horn resection.Setting  Tertiary referral centre for laparoscopic surgery.Interventions  Laparoscopy and laparotomy.Main outcome measures  Blauer's adhesions score, fibrous tissue layers and mesothelium layers at the site of the lesion.Results  The median Blauer score was 1.0 in the laparoscopy group and 2.5 in the laparotomy group (P = 0.0003). The median number of layers of the area of fibrous tissue was 20 in the animals submitted to laparoscopy, and 65 in those submitted to laparotomy (P < 0.0001). The median number of layers of mesothelium was 1 in the laparoscopy group and 4 in the laparotomy group (P < 0.0001).Conclusion  Laparoscopy caused less postoperative adhesion than laparotomy. Rabbits subjected to laparotomy presented a greater degree of mesothelial hyperplasia and more formation of fibrous tissue than the animals subjected to laparoscopy.
Laparoscopic appendectomy at 34 weeks of gestation
Authors: Aleywan Nadine , Nassar Anwar , Hussein Maher , Usta Ihab , Khalil Ali 
Published: December 2003

ABSTRACTObjective  To present a case of laproscopic appendectomy in a pregnant woman at 34 weeks of gestation. Using an open Hasson technique for the epigastric trocar, combined with low‐pressure pneumoperitoneum and two trocars in the right and left upper quadrants as the working channels, appendectomy was performed safely and effectively. The procedure was well tolerated with favourable maternal and perinatal outcomes.Conclusion  The open laparoscopy technique seems to be a safe option for accessing the abdominal cavity to perform an appendectomy late in pregnancy.
Effect of intraperitoneal bupivacaine on postoperative pain following laparoscopic pelvic surgery
Authors: Shalan Hesham , Badawy Ahmed , Yousef Hamed , Nazar Mohamed 
Published: December 2003

ABSTRACTBackground  There is much debate on the effectiveness of intraperitoneal local anaesthetic instillation, during laparoscopic surgical procedures, as a means of relieving postoperative pain and reducing analgesia use.Study design  Randomized, double‐blind, placebo‐controlled clinical trial.Setting  Department of Obstetrics and Gynaecology, Mansoura University Hospital.Material and methods  A group of 120 patients, admitted for elective laparoscopic pelvic surgery, were randomly allocated to two study arms: study group patients (n = 60) received instillation with 20 ml 0.5% bupivacaine intraperitoneally, before and at the end of the laparoscopic procedures, and placebo group patients (n = 60) patients received instillation with 20 ml 0.9% saline. Pain was evaluated by means of a visual analogue scale (VAS) at 0, 4, 8, 12 and 24 h postoperatively. The need for postoperative analgesia was also recorded.Results  Pain scores and analgesia use were lower in the bupivacaine (study) group than in the saline (placebo) group. This difference was statistically significant (P < 0.05).Conclusion  Topical instillation of 0.5% bupivacaine during laparoscopic gynaecological surgery reduces postoperative pain and analgesia use compared with that in a placebo group.