bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated discovery of 3D motifs for protein function annotation
Authors: Polacco Benjamin J. , Babbitt Patricia C. 
Published: January 2006

Abstract
Motivation: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that correlate with function. As an alternative to often limited expert knowledge, we use machine-learning techniques to identify patterns of 3–10 residues that maximize function prediction. This approach allows us to test the assumption that residues that provide function are the most informative for predicting function.
Results: We apply our method, GASPS, to the haloacid dehalogenase, enolase, amidohydrolase and crotonase superfamilies and to the serine proteases. The motifs found by GASPS are as good at function prediction as 3D motifs based on expert knowledge. The GASPS motifs with the greatest ability to predict protein function consist mainly of known functional residues. However, several residues with no known functional role are equally predictive. For four groups, we show that the predictive power of our 3D motifs is comparable with or better than approaches that use the entire fold (Combinatorial-Extension) or sequence profiles (PSI-BLAST).
Availability: Source code is freely available for academic use by contacting the authors.
Contact: babbitt@cgl.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
Authors: Chiu Joanna C. , Lee Ernest K. , Egan Mary G. , Sarkar Indra Neil , Coruzzi Gloria M. , DeSalle Rob 
Published: January 2006

Abstract
Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.
Results: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
Availability:
Contact: gloria.coruzzi@nyu.edu
Tools for the SBML Community
Authors: Gillespie Colin S. , Wilkinson Darren J. , Proctor Carole J. , Shanley Daryl P. , Boys Richard J. , Kirkwood Thomas B. L. 
Published: January 2006

Abstract
Motivation: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be incorporated into SBML aware applications. The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user.
Availability: All tools described are available from and are licensed under GNU General Public License.
Contact: c.gillespie@ncl.ac.uk
LSAT: learning about alternative transcripts in MEDLINE
Authors: Shah Parantu K. , Bork Peer 
Published: January 2006

Abstract
Motivation: Generation of alternative transcripts from the same gene is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose the task of extracting information around this complex topic using a two-step procedure involving machine learning and information extraction.
Results: In the first step, we trained a classifier that inductively learns to identify sentences about physiological transcript diversity from the MEDLINE abstracts. Using a large hand-built corpus, we compared the sentence classification performance of various text categorization methods. Support vector machines (SVMs) followed by the maximum entropy classifier outperformed other methods for the sentence classification task. The SVM with the radial basis function kernel and optimized parameters achieved Fβ-measure of 91% during the 4-fold cross validation and of 74% when applied to all sentences in more than 12 million abstracts of MEDLINE. In the second step, we identified eight frequently present semantic categories in the sentences and performed a limited amount of semantic role labeling. The role labeling step also achieved very high Fβ-measure for all eight categories.
Availability: The results of our two-step procedure are summarized in the LSAT database of alternative transcripts. LSAT is available at
Contact: shah@embl.de
Supplementary information: Supplementary data are available at Bioinformatics online
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
Authors: Xirasagar Sandhya , Gustafson Scott F. , Huang Cheng-Cheng , Pan Qinyan , Fostel Jennifer , Boyer Paul , Merrick B. Alex , Tomer Kenneth B. , Chan Denny D. , Yost Kenneth J. , Choi Danielle , Xiao Nianqing , Stasiewicz Stanley , Bushel Pierre , Waters Michael D. 
Published: January 2006

Abstract
Motivation: The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein–protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner.
Results: An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data () which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium () that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here.
Availability: A universal modeling language (UML) depiction of the entire SysTox-OM is available at and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at . Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at
Contact: xirasagars@saic.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparison of Affymetrix GeneChip expression measures
Authors: Irizarry Rafael A. , Wu Zhijin , Jaffee Harris A. 
Published: January 2006

Abstract
Motivation: In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted.
Results: We benchmarked 31 probe set algorithms using a U95A dataset of spike in controls. Using this dataset, we found that background correction, one of the main steps in preprocessing, has the largest effect on performance. In particular, background correction appears to improve accuracy but, in general, worsen precision. The benchmark results put this balance in perspective. Furthermore, we have improved some of the original benchmark metrics to provide more detailed information regarding precision and accuracy. A handful of methods stand out as providing the best balance using spike-in data with the older U95A array, although different experiments on more current arrays may benchmark differently.
Availability: The affycomp package, now version 1.5.2, continues to be available as part of the Bioconductor project (). The webtool continues to be available at
Contact: rafa@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Hierarchical multi-label prediction of gene function
Authors: Barutcuoglu Zafer , Schapire Robert E. , Troyanskaya Olga G. 
Published: January 2006

Abstract
Motivation: Assigning functions for unknown genes based on diverse large-scale data is a key task in functional genomics. Previous work on gene function prediction has addressed this problem using independent classifiers for each function. However, such an approach ignores the structure of functional class taxonomies, such as the Gene Ontology (GO). Over a hierarchy of functional classes, a group of independent classifiers where each one predicts gene membership to a particular class can produce a hierarchically inconsistent set of predictions, where for a given gene a specific class may be predicted positive while its inclusive parent class is predicted negative. Taking the hierarchical structure into account resolves such inconsistencies and provides an opportunity for leveraging all classifiers in the hierarchy to achieve higher specificity of predictions.
Results: We developed a Bayesian framework for combining multiple classifiers based on the functional taxonomy constraints. Using a hierarchy of support vector machine (SVM) classifiers trained on multiple data types, we combined predictions in our Bayesian framework to obtain the most probable consistent set of predictions. Experiments show that over a 105-node subhierarchy of the GO, our Bayesian framework improves predictions for 93 nodes. As an additional benefit, our method also provides implicit calibration of SVM margin outputs to probabilities. Using this method, we make function predictions for multiple proteins, and experimentally confirm predictions for proteins involved in mitosis.
Supplementary information: Results for the 105 selected GO classes and predictions for 1059 unknown genes are available at:
Contact: ogt@cs.princeton.edu
Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting
Authors: Thomas Alun , Camp Nicola J. 
Published: January 2006

AbstractSummary: Graphical modeling is used to extend the gene counting method to compute maximum likelihood estimates of allele frequencies for samples of individuals related in extended pedigrees. Genotypes may be missing or partially observed, and error rates can be simultaneously estimated.Availability: The Java classes and Javadocs pages for GeneCountAllelescan be obtained from , which also has more information on its use and file formats.Contact: alun@genepi.med.utah.edu
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Authors: Kuhner Mary K. 
Published: January 2006

Abstract
Summary: We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters from genetic data. LAMARC can co-estimate subpopulation Θ = 4Neμ, immigration rates, subpopulation exponential growth rates and overall recombination rate, or a user-specified subset of these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP, microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and executables for all three major platforms.
Availability: LAMARC 2.0 is freely available at
Contact: lamarc@gs.washington.edu
Standard and new treatments in cutaneous B‐cell lymphomas
Authors: Dreno Brigitte 
Published: January 2006

Background:  Primary cutaneous B‐cell lymphomas (PCBCL) are cutaneous non‐Hodgkin lymphomas and can be classified clinically and by prognosis. The aim of this paper is to perform a review of standard and new treatments.Method:  This paper provides a literature review of the different treatments of PCBCL.Results:  Surgery and radiotherapy remain the standard therapies in isolated cutaneous lesions. Systemic or intralesional interferon (IFN)‐α may be an alternative in PCBCL with diffuse cutaneous lesions. In aggressive forms with poor prognosis, polychemotherapy is the first line of treatment although rituximab and radioimmunotherapy are evolving therapeutic options.Conclusion:  In the majority of cases, the treatment of CBCL is straightforward. In aggressive forms, new therapies and biologic therapies may be of real interest.
Patterns of frugivory of the Budongo Forest chimpanzees, Uganda
Authors: Tweheyo Mnason , Lye Kåre A. 
Published: January 2006

AbstractFrugivory patterns of the chimpanzees in the Budongo Forest Reserve, Uganda were studied between June 2000 and August 2001. Chimpanzee feeding habitats, movement, group size and food eaten were assessed using focal and scan sampling. It was found that fruits were scarce during the dry season, when chimpanzees appeared and moved in large groups over long distances and raided farms at the forest edge. Chimpanzee movement out of the forest to forage was influenced by seasonal fluctuations in availability of preferred foods as some cultivated crops are perennial. Presence of chimpanzees in a specific feeding habitat was related to the availability of edible fruits both within and between months, suggesting that the presence of food may influence chimpanzee movement patterns. Therefore, a good understanding of patterns of frugivory is essential for making informed decisions about conservation of chimpanzees and other frugivores like birds and monkeys in Budongo as different forest habitats are under varying human pressure because of logging and other forms of utilization.
Stand structure, species diversity and regeneration of an endemic palm forest on the Seychelles
Authors: Fleischmann Karl , Edwards Peter J. , Ramseier Dieter , Kollmann Johannes 
Published: January 2006

AbstractThe ‘Vallée de Mai’ on the island of Praslin in the Seychelles group is a World Heritage Site because of its unique forest vegetation dominated by the palmLodoicea maldivica. However, despite its great conservation importance, the stand structure, species diversity and regeneration of this forest have not previously been studied. Moreover, the conservation value of the reserve is currently threatened by invading alien plants and limited regeneration of some native species. The species composition of the forest was studied in six permanent plots (1985 and 1998) and along seven trail transects (1997). To explain potential variation in tree regeneration, the light climate within all plots was investigated using hemispherical photographs. The results reveal little change in forest structure, species diversity and regeneration in the permanent plots over the 13‐year period, but some regeneration of most woody species, presence of some alien species and a relatively high species turnover. We found no significant influence of local light climate upon forest structure, species diversity or regeneration. Although the stand characteristics seem to be relatively stable, the permanent plots and transects should be monitored in order to detect future changes in stand structure and to optimize the protection of this unique forest reserve.
Shifts in native ungulate communities on a former cattle ranch in Tanzania
Authors: Treydte Anna C. , Edwards Peter J. , Suter Werner 
Published: January 2006

AbstractWhen an area is brought under protection, current animal populations and their habitat preferences need to be assessed to predict population trends and future habitat availability. Using data from walking transects, we estimated the size of native ungulate populations on an abandoned cattle ranch in a coastal savannah in Tanzania, now included in the new Saadani National Park. Data were analysed withdistancesampling and conventional strip transect techniques and were compared with results of previous wildlife counts. Few individuals of mainly browsing species were present in former cattle grazing areas exhibiting high bush‐encroachment while a ten times higher biomass of browsers and grazers was found in the cattle‐unmodified savannah. Population sizes of some species increased twofold between 1991 and 2001 within the entire area but neither population size nor species richness increased in the abandoned rangeland during our 3‐year study period from 2001 to 2003. We conclude that the former ranch has potential for future recolonization by wild ungulates. Resettlement will take place gradually with ‘pioneer‐species’ facilitating the entry of more demanding species. Habitat restoration through wildlife can be observed and quantified on Mkwaja Ranch which will be of importance for future management of native ungulates reclaiming abandoned rangeland.
Estimating elephant densities from wells and droppings in dried out riverbeds
Authors: Rasmussen Henrik Barner , Kahindi Onesmas , Vollrath Fritz , Douglas‐Hamilton Iain 
Published: January 2006

AbstractIn this paper, we present a new method for estimating elephant densities by counting elephant wells and dung boli within dry seasonal flooding rivers. A combination of aerial and ground counts of elephant wells and dung boli in the Ewaso Ngiro River were related to elephant numbers, obtained from an on‐going monitoring program of individually identified elephants in Samburu and Buffalo Spring National Reserves, Kenya. The total number of elephant observations was highly correlated with both densities of wells and dung boli at a spatial resolution of 4‐km river‐section. This indicates that both wells and droppings can be used for estimating relative densities at such spatial resolution. The method can be used as a quick and reliable way of estimating relative elephant densities in semiarid regions but is sensitive to differences in the time when different parts of the river dry out and will be unreliable in areas with secondary un‐censused water sources. A short 4‐week period between the river dry out and the count is recommended, because of an error induced by a level of well reuse and the difficulties in counting areas of high well densities from the air.
Estimating larger carnivore numbers from track counts and measurements
Authors: Gusset Markus , Burgener Nicole 
Published: January 2006

AbstractKnowing the abundance of larger carnivores is critical for their conservation management. However, direct assessment of carnivore numbers is often difficult, expensive and time‐consuming, leaving indirect sampling as a valid and feasible alternative. Indirect census techniques have proved to be cost‐effective, repeatable and objective. We therefore estimated the numbers of six larger carnivore species in a relatively small area in northern South Africa, comparing three indirect sampling methods based on track counts and measurements: (i) a qualitative approach, whereby individuals were subjectively identified by comparing differences in track measurements; (ii) a quantitative approach using the strong linear correlation of track density with carnivore density found in other studies; and (iii) a quantitative approach applying repeated measures analysis of variance and post‐tests to the track measurement data, in order to test statistically for differences in track sets. All three methods provided similar results that appear to be reasonable and which might be an indication of the real number of larger carnivores that occur in the study area. These results support the reliability of indirect estimates of larger carnivore numbers based on tracking data, which is promising for future research and conservation efforts involving these animals.
Status of succulent shrubs in the southern Namib Desert, Succulent Karoo Biome
Authors: Burke Antje 
Published: January 2006

AbstractThe ratio of dead to alive succulent shrubs as an indicator of turnover was investigated to test whether the accepted notion of rapid turnover rates and cyclic succession in the Succulent Karoo Biome are applicable in the southern Namib. Based on counts of dead and alive plants, twelve species in two habitat types were investigated. These short‐term data which could not incorporate recruitment rates or changes over time, generated, however, some hypotheses. (i) Rapid turnover rates are likely not supported by all succulent plants at the Succulent Karoo Biome's northern boundary. With the exception of one species, mortality rates in succulent shrubs across a range of plant functional types were lower than reported in other parts of the biome. (ii) Sand plains appeared to support some transient species, indicating that there may be differences in vegetation dynamics between habitats. (iii) Species of different plant functional types showed no differences in ratio of dead to alive plants related to habitat. These species may have broad ecological tolerance limits and are perhaps less affected by changes in their environment. (iv) Shrubby Mesembryanthemaceae have high turnover rates and hence a short live span in the investigated area, but are longer lived than elsewhere in the Succulent Karoo Biome. As these hypotheses have implications for management and conservation of succulent species in this global biodiversity hotspot, a detailed evaluation of vegetation turnover, balancing mortality versus recruitment, should be investigated over a longer time span.