bluuebunny/crossref_metadata_2025_split huggingface dataset:
Priority conservation areas for birds in El Salvador
Authors: Komar Oliver 
Published: September 2002

AbstractEl Salvador has the smallest protected areas system in Central America. High levels of habitat destruction and disturbance throughout the country make the reserve system especially important for conservation of biodiversity. I used complementarity approaches to assess the relative conservation importance of ten reserves in El Salvador. The principal criterion was presence of nationally threatened and endangered bird species. Additional criteria included residency status (resident species were more important than migratory non‐breeding species) and regionally endemic species. Montecristo National Park was the most important area, with 42% of all nationally threatened birds present. El Imposible National Park, El Salvador's largest park (5000 ha), scored second, followed by Laguna El Jocotal wildlife refuge and Barra de Santiago wildlife refuge. In all, these four areas provide refuge for 83% of El Salvador's 268 nationally threatened bird species in less than 7600 ha of natural habitat. Because of small reserve sizes, all of El Salvador's threatened birds may need additional protection.
Measuring genetic diversity in translocation programmes: principles and application to a chimpanzee release project
Authors: Goossens Benoît , Funk Stephan M. , Vidal Carmen , Latour Stéphanie , Jamart Aliette , Ancrenaz Marc , Wickings Elisabeth J. , Tutin Caroline E. G. , Bruford Michael W. 
Published: September 2002

AbstractLogging and poaching have dramatically reduced chimpanzee density and distribution in the Republic of Congo. Most chimpanzee translocations attempted in the past failed because a number of biological and non‐biological factors can influence success. Biological considerations include knowledge of behaviour, disease, habitat requirements and genetics. We critically review genetic considerations in pre‐ and post‐release phases of translocations and apply them to a welfare‐based chimpanzee release project in the Republic of Congo which aimed to re‐establish orphan chimpanzees in the wild with a native chimpanzee population. We analyze genetic diversity and relatedness in released animals and devise a genotyping strategy for monitoring of released individuals and their future offspring. Fifty‐nine confiscated chimpanzees from different areas of the Republic of Congo were typed for 20 microsatellites using plucked hair as the DNA source. Genetic diversity was high, with an average expected heterozygosity of 81%, and three to 18 alleles per locus. Between 1996 and 1998, 19 individuals were released, and genetic analysis showed that these are unrelated (mean r± jack‐knifed SD =−0.014 ± 0.001). Using FST and population admixture analysis, we identified population structure in wild chimpanzees. For long‐term genetic monitoring of released and native chimpanzees, we identified a set of six informative markers, which are easy to score using basic techniques.
Declines in the numbers of amateur and professional taxonomists: implications for conservation
Authors: Hopkins G. W. , Freckleton R. P. 
Published: September 2002

AbstractTo ensure the effective conservation of biodiversity the distribution of species needs to be accurately characterized and areas of high species richness located. For many taxa this can be achieved only by experienced taxonomists. Taxonomic research has a large input from non‐professional or amateur researchers, in addition to professionals working at museums or universities. The decline of taxonomy and the number of taxonomists within the professional community has been widely publicized, but the trends in the activities of amateur taxonomists are unclear. Because amateurs contribute many valuable records of species occurrence this may have a disproportionate impact upon the information available for conservation planning and represents an underappreciated threat to conservation planning. We use taxonomic research by UK entomologists in order to evaluate the changing role of both amateur and professional taxonomists. We reviewed contributions by British‐based authors to Entomologist's Monthly Magazine over the past century. Our results show that both amateur and professional taxonomy have undergone a long and persistent decline since the 1950s, in terms of both the number of contributors and the number of papers contributed. It is argued that the conservation community needs to help try and reverse the decline of taxonomy.
The Cardiac Output and Blood Volume of the Anaesthetized Cat
Authors: A C Groom  , S Rowlands  
Published: September 2002

1. The cardiac output and blood volume have been measured in thirty-two cats by an indicator dilution2. In six experiments both32P-labelled red cells and131I-labelled human serum albumin were used as indicators. In the rest one or other indicator was used.3. Cardiac output of the cat anaesthetized with chloralose is 113±30 ml/min/kg (32 animals).4. Repeated determinations show random variations of cardiac output to be about 5%.5. The blood volume of the cat anaesthetized with chloralose is 49·0±10 ml/kg (25 animals) and the ` central ' blood volume, as defined, 16·9±1·2 ml/kg.6. The ratio of the value of the whole body haematocrit to that of the arterial haematocrit is 0·93±0·09. The causes of the large variation are considered.7. The accuracy of the technique and its advantages are discussed.
The Sensitivity of Blood Cells to Light of Different Wavelengths
Authors: K W Keohane  , W K Metcalf  
Published: September 2002

1. Lymphocytes and polymorphonuclear leucocytes are very sensitive to radiation of 265 mμ and 254 mμ. This corresponds to a region of the spectrum in which the nucleic acids and nucleoproteins have a strong absorption. Whilst polymorphs are also sensitive to 404 mμ, lymphocytes are not appreciably affected by visible light.2. Haemolysis of mammalian red cells occurred following irradiation with monochromatic ultra-violet light of 265 mμ.3. Irradiation with visible light caused the conversion of haemoglobin to methaemoglobin.4. The time for haemolysis to commence was dependent on the intensity of the light falling on the cell.5. The duration of the process of haemolysis was independent of the light intensity.6. The products of haemolysis did not precipitate further haemolysis nor did they affect the white cells.7. Red cells in hypertonic saline failed to haemolyze even after 12 hours' irradiation.8. Irradiation causes disc-sphere transformation followed by haemolysis of both mammalian and non-mammalian cells.
A Biochemical Change in the Blood in Pregnancy and Malignant Disease
Authors: W K Metcalf  
Published: September 2002

1. An increased sensitivity of intact red cells to nitrites has been demonstrated in children, pregnant women and patients with carcinomata.2. The cause of this phenomenon is as yet unexplained.3. Further work is needed before the reliability of this technique as a test for carcinoma or pregnancy can be assessed.
A critical survey of ionospheric temperatures
Authors: N C Gerson  
Published: September 2002

The relative order of importance of the various methods available for the evaluation of temperature from an ionospheric parameter is (a) temperature and collisional frequency, (b) temperature and auroral scale heights, (c) temperature and electron concentration, (d) temperature and the influx function, and (e) temperature and the recombination coefficient. Method (e), still in its infancy, does not yet permit accurate temperature evaluations in the ionosphere. Some indication of a diurnal temperature variation may be obtained from method (d).The probable temperature-altitude relationship in the atmospheric regions 100-400 km., as determined by several techniques, is tabulated below:Upper Atmospheric Temperatures (°K.)Altitude (km.)Method of DeterminationCollisional frequenciesAuroral scale heightsElectron concentration100300219-150825531-20013501580-25021752073-30024002455-330--1530-268035032252704-4003450--500--2200-3910These values are considered to represent mean annual temperatures at middle latitudes.The electron and gas temperatures are essentially identical. If the free electrons have an excess of energy (as may result during an ionization process) this energy is quickly distributed among the gas and other particles.Thermal equilibrium and therefore a Maxwellian velocity distribution of the atmospheric particles exists among the gaseous constituents in the range 100-400 km. The kinetic temperature is therefore equivalent to the gas temperature. Fluctuation phenomena and deviations of the particles from a Maxwellian velocity distribution probably do not occur in the terrestrial atmosphere until much higher altitudes.A totally ionized atmosphere below 400 km. does not agree with the experimental evidence inasmuch as the temperature deduced on such a basis will not support the observed number density.Tentatively it has been shown that no large diurnal temperature variations are found in the altitude range 100-400 km. Preliminary estimates of a probable rate of heating based upon the dissipation of excess energy absorbed during an ionization process appear to confirm the preceding statement. However, the rate of heating attributable to non-detectable absorption processes, to large electrical currents in the ionosphere or to the bombardment by large numbers of high energy electrons is unknown.The existence of temperatures much higher than those given in the above Table would be difficult to explain in the terrestrial atmosphere. Indeed, it may be qualitatively concluded that the maximum atmospheric temperatures occur in the ionospheric regions at an altitude near or somewhat above 400 km. Above this temperature maximum, a general decrease probably occurs to meet the atmospheric boundary temperature with interstellar space. A temperature maximum near the ionospheric regions probably arises from the various absorption or heating processes together with a sufficient number density of particles.
The evolution of the solar system
Authors: M M Woolfson  
Published: September 2002

A brief description of the solar system is given which highlights those features that a plausible theory should explain. A review of theories up to 1960 sets the scene for the description of more modern work and also points out the major features for which explanations are difficult to find. The major obstacle, on which all the older theories founder, is the explanation of the distribution of angular momentum in the system whereby the planets with 0·14% of the mass possess 98% of the angular momentum. The other problem, which has been more recently emphasized by Hoyle, is the slow rotation of the Sun, which is difficult to explain in terms of it having condensed from material possessing the basic galactic rotation.The modern theories described are:Hoyle's nebula theory, which invokes the transfer of angular momentum by magnetic forces;the accretion theory, which proposes that planetary material was captured by the Sun from an interstellar cloud;McCrea's floccule theory, which describes the solar system as having formed from initial condensations of planetary mass;the capture theory, which proposes that the Sun captured planets from a tidal filament drawn out of a light star;a nebula theory proposed by Urey based on chemical evidence derived primarily from meteorites.
DIANA-EST: a statistical analysis
Authors: Hatzigeorgiou Artemis G. , Fiziev Petko , Reczko Martin 
Published: September 2002

Abstract
Motivation: Expressed Sequence Tags (ESTs) are next to cDNA sequences as the most direct way to locate in silico the genes of the genome and determine their structure. Currently ESTs make up more than 60% of all the database entries. The goal of this work is the development of a new program called DNA Intelligent Analysis for ESTs (DIANA-EST) based on a combination of Artificial Neural Networks (ANN) and statistics for the characterization of the coding regions within ESTs and the reconstruction of the encoded protein.
Results: 89.7% of the nucleotides from an independent test set with 127 ESTs were predicted correctly as to whether they are coding or non coding.
Availability: The program is available upon request from the author.
Contact: Present address: Department of Genetics, University of Pennsylvania, School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6145, USA. artemis@pcbi.upenn.edu.
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
Authors: Kretschmann Ernst , Fleischmann Wolfgang , Apweiler Rolf 
Published: September 2002

Abstract
Motivation: The gap between the amount of newly submitted protein data and reliable functional annotation in public databases is growing. Traditional manual annotation by literature curation and sequence analysis tools without the use of automated annotation systems is not able to keep up with the ever increasing quantity of data that is submitted. Automated supplements to manually curated databases such as TrEMBL or GenPept cover raw data but provide only limited annotation. To improve this situation automatic tools are needed that support manual annotation, automatically increase the amount of reliable information and help to detect inconsistencies in manually generated annotations.
Results: A standard data mining algorithm was successfully applied to gain knowledge about the Keyword annotation in SWISS-PROT. 11 306 rules were generated, which are provided in a database and can be applied to yet unannotated protein sequences and viewed using a web browser. They rely on the taxonomy of the organism, in which the protein was found and on signature matches of its sequence. The statistical evaluation of the generated rules by cross-validation suggests that by applying them on arbitrary proteins 33% of their keyword annotation can be generated with an error rate of 1.5%. The coverage rate of the keyword annotation can be increased to 60% by tolerating a higher error rate of 5%.
Availability: The results of the automatic data mining process can be browsed on http://golgi.ebi.ac.uk:8080/Spearmint/ Source code is available upon request.
Contact: kretsch@ebi.ac.uk
Sequence and structural aspects of functional diversification

in class I α-mannosidase evolution
Authors: Jordan I. King , Bishop G. Reid , Gonzalez Daniel S. 
Published: September 2002

Abstract
Motivation: Class I α-mannosidases comprise a homologous and functionally diverse family of glycoside hydrolases. Phylogenetic analysis based on an amino acid sequence alignment of the catalytic domain of class I α-mannosidases reveals four well-supported phylogenetic groups within this family. These groups include a number of paralogous members generated by gene duplications that occurred as far back as the initial divergence of the crown-group of eukaryotes. Three of the four phylogenetic groups consist of enzymes that have group-specific biochemical specificity and/or sites of activity. An attempt has been made to uncover the role that natural selection played in the sequence and structural divergence between the phylogenetically and functionally distinct Endoplasmic Reticulum (ER) and Golgi apparatus groups.
Results: Comparison of site-specific amino acid variability profiles for the ER and Golgi groups revealed statistically significant evidence for functional diversification at the sequence level and indicated a number of residues that are most likely to have played a role in the functional divergence between the two groups. The majority of these sites appear to contain residues that have been fixed within one organelle-specific group by positive selection. Somewhat surprisingly these selected residues map to the periphery of the α-mannosidase catalytic domain tertiary structure. Changes in these peripherally located residues would not seem to have a gross effect on protein function. Thus diversifying selection between the two groups may have acted in a gradual manner consistent with the Darwinian model of natural selection.
Contact: bishogr@millsaps.edu
* To whom correspondence should be addressed.
Principal component analysis for clustering gene expression
data
Authors: Yeung K. Y. , Ruzzo W. L. 
Published: September 2002

Abstract
Motivation: There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expression data. Other classical techniques, such as principal component analysis (PCA), have also been applied to analyze gene expression data. Using different data analysis techniques and different clustering algorithms to analyze the same data set can lead to very different conclusions. Our goal is to study the effectiveness of principal components (PCs) in capturing cluster structure. Specifically, using both real and synthetic gene expression data sets, we compared the quality of clusters obtained from the original data to the quality of clusters obtained after projecting onto subsets of the principal component axes.
Results: Our empirical study showed that clustering with the PCs instead of the original variables does not necessarily improve, and often degrades, cluster quality. In particular, the first few PCs (which contain most of the variation in the data) do not necessarily capture most of the cluster structure. We also showed that clustering with PCs has different impact on different algorithms and different similarity metrics. Overall, we would not recommend PCA before clustering except in special circumstances.
Contact: kayee@cs.washington.edu
Supplementary information: http://www.cs.washington.edu/homes/kayee/pca
* To whom correspondence should be addressed.
Detecting the impact of sequencing errors on SAGE data
Authors: Colinge Jacques , Feger Georg 
Published: September 2002

Abstract
Summary: SAGE data are obtained by sequencing short DNA tags. Due to the mistakes in DNA sequencing, SAGE data contain errors. We propose a new approach to identify tags whose abundance is biased by sequencing errors. This approach is based on a concept of neighbourhood: abundant tags can contaminate tags whose sequence is very close. The application of our approach reveals that moderately abundant tags can be generated by sequencing errors uniquely. It also allows for detecting correct rare tags.
Availability: Software is available only to non-profit entities and for non-commercial purposes upon request.
Contact: Georg.Feger@serono.com
* To whom all correspondence should be addressed.
2 Present address: GeneProt Inc., Pré-de-la-Fontaine 2, CH-1217 Meyrin, Switzerland.
CHROMA: consensus-based colouring of multiple alignments for
publication
Authors: Goodstadt Leo , Ponting Chris P. 
Published: September 2002

Abstract
CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.
* To whom correspondence should be addressed.
BioWAP, mobile Internet service for bioinformatics
Authors: Riikonen Pentti , Boberg Jorma , Salakoski Tapio , Vihinen Mauno 
Published: September 2002

Abstract
Summary: We have developed a new Internet service, which provides mobile access to bioinformatics databases and software tools. The BioWAP service facilitates access to basic bioinformatics databases and analysis tools from everywhere without a PC or a laptop computer. Both open source bioinformatics program suites and Internet services, which are not designed for mobile Internet access, were utilized in the BioWAP service.
Availability: The BioWAP service starting page can be browsed with any WAP terminal from http://bioinf.uta.fi/wml/welcome.wml.
Contact: Mauno.Vihinen@uta.fi
* To whom correspondence should be addressed.
Analysis of expression profile using fuzzy adaptive
resonance theory
Authors: Tomida Shuta , Hanai Taizo , Honda Hiroyuki , Kobayashi Takeshi 
Published: September 2002

Abstract
Motivation: It is well understood that the successful clustering of expression profiles give beneficial ideas to understand the functions of uncharacterized genes. In order to realize such a successful clustering, we investigate a clustering method based on adaptive resonance theory (ART) in this report.
Results: We apply Fuzzy ART as a clustering method for analyzing the time series expression data during sporulation of Saccharomyces cerevisiae. The clustering result by Fuzzy ART was compared with those by other clustering methods such as hierarchical clustering, k-means algorithm and self-organizing maps (SOMs). In terms of the mathematical validations, Fuzzy ART achieved the most reasonable clustering. We also verified the robustness of Fuzzy ART using noised data. Furthermore, we defined the correctness ratio of clustering, which is based on genes whose temporal expressions are characterized biologically. Using this definition, it was proved that the clustering ability of Fuzzy ART was superior to other clustering methods such as hierarchical clustering, k-means algorithm and SOMs. Finally, we validate the clustering results by Fuzzy ART in terms of biological functions and evidence.
Availability: The software is available at http//www.nubio.nagoya-u.ac.jp/proc/index.html
Contact: taizo@brs.kyushu-u.ac.jp
* To whom correspondence should be addressed. Present address: Laboratory for Applied Biological Regulation Technology, School of Bioresource and Bioenvironmental Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
A branch-and-bound algorithm for the inference of ancestral amino-acid
sequences when the replacement rate varies among sites: Application to the
evolution of five gene families
Authors: Pupko Tal , Pe'er Itsik , Hasegawa Masami , Graur Dan , Friedman Nir 
Published: September 2002

Abstract
Motivation: We developed an algorithm to reconstruct ancestral sequences, taking into account the rate variation among sites of the protein sequences. Our algorithm maximizes the joint probability of the ancestral sequences, assuming that the rate is gamma distributed among sites. Our algorithm provably finds the global maximum. The use of ‘joint’ reconstruction is motivated by studies that use the sequences at all the internal nodes in a phylogenetic tree, such as, for instance, the inference of patterns of amino-acid replacement, or tracing the biochemical changes that occurred during the evolution of a given protein family.
Results: We give an algorithm that guarantees finding the global maximum. The efficient search method makes our method applicable to datasets with large number sequences. We analyze ancestral sequences of five gene families, exploring the effect of the amount of among-site-rate-variation, and the degree of sequence divergence on the resulting ancestral states.
Availability and supplementary information: http://evolu3.ism.ac.jp/~tal/
Contact: tal@ism.ac.jp
* To whom correspondence should be addressed.