bluuebunny/crossref_metadata_2025_split huggingface dataset:
800-yr-long records of annual air temperature and precipitation over southern Siberia inferred from Teletskoye Lake sediments
Authors: Kalugin Ivan , Daryin Andrei , Smolyaninova Lyubov , Andreev Andrei , Diekmann Bernhard , Khlystov Oleg 
Published: March 2007

AbstractA unique 800-yr-long record of annual temperatures and precipitation over the south of western Siberia has been reconstructed from the bottom sediments of Teletskoye Lake, Altai Mountains using an X-ray fluorescence scanner (XRF) providing 0.1-mm resolution timeseries of elemental composition and X-ray density (XRD). Br content appears to be broadly correlative with mean annual temperature variations because of changes in catchment vegetation productivity. Sr/Rb ratio reflects the proportion of the unweathered terrestrial fraction. XRD appears to reflect water yield regime and sediment flux. Sedimentation is rather continuous because annual clastic supply and deposited mass are the same. The artificial neural networks method was applied to convert annual sedimentary time-series of XRD, Br content, and Sr/Rb ratio to annual records of temperature and precipitation using a transfer function. Comparison of these reconstructed Siberian records with the annual record of air temperature for the Northern Hemisphere shows similar trends in climatic variability over the past 800 yr. Estimated harmonic oscillations of temperature and precipitation values for both historical and reconstructed periods reveal subdecadal cyclicity.
Stratigraphy and environmental reconstruction at the middle Wisconsinan Gilman Canyon formation type locality, Buzzard's Roost, southwestern Nebraska, USA
Authors: Johnson William C. , Willey Karen L. , Mason Joseph A. , May David W. 
Published: March 2007

AbstractThe middle Wisconsinan Gilman Canyon Formation at the Buzzard's Roost type locality in southwestern Nebraska was investigated to document the stratigraphy and to reconstruct the environmental and climate record. The Gilman Canyon Formation was subdivided into three loess units and three soils, with radiocarbon ages constraining it between about 40 ka and 25 ka. Stable carbon isotope ratios, magnetic susceptibility, and carbon content were used to define and characterize soils within both the Gilman Canyon Formation and underlying Illinoian Loveland Loess. At the height of soil development within the Gilman Canyon Formation, climate was supporting C4-dominated grassland, with July temperatures equal to or exceeding those of today. Soil-forming intervals within the Loveland Loess, including the Sangamon Soil, also exhibited relative increases in C4 biomass. Climate, as recorded in the Gilman Canyon Formation, is corroborated by regional proxy data. The formation accumulated during MIS 3, and concurrent soil formation coincided with a summer insolation maximum.
Climatic controls of Holocene fire patterns in southern South America
Authors: Whitlock Cathy , Moreno Patricio I. , Bartlein Patrick 
Published: March 2007

AbstractHolocene fire–climate–vegetation linkages are mostly understood at individual sites by comparing charcoal and pollen records with other paleoenvironmental proxy and model simulations. This scale of reconstruction often obscures detection of large-scale patterns in past fire activity that are related to changes in regional climate and vegetation. A network of 31 charcoal records from southern South America was examined to assess fire history along a transect from subtropic to subantarctic biomes. The charcoal data indicate that fire activity was greater than present at ca. 12,000 cal yr BP and increased further and was widespread at 9500 cal yr BP. Fire activity decreased and became more spatially variable by 6000 cal yr BP, and this trend continued to present. Atmospheric circulation anomalies during recent high-fire years show a southward shift in westerlies, and paleoclimate model simulations and data syntheses suggest that such conditions may have prevailed for millennia in the early Holocene when the pole-to-equator temperature gradients were weaker and annual temperatures were higher than present, in response to orbital-time-scale insolation changes.
Chemical Caspase Inhibitors Enhance Cell Culture Viabilities and Protein Titer
Authors: Arden Nilou , Ahn Shin‐hyung , Vaz Wayne , Rhodes Malcolm , Hancock Christina , Abitorabi M. Abi , Betenbaugh Michael J. 
Published: March 2007

AbstractMammalian cell cultures are integral to the production of therapeutic and diagnostic proteins. A common problem encountered in culturing these cell lines, however, is a loss in viability at later stages of the cell culture process. In this study the effects of three newly synthesized chemical caspase inhibitors were investigated for their capacity to inhibit cell death. Findings show that these protease inhibitors were successful in prolonging cellular viabilities among anchorage‐dependent CHO‐K1 and HEK‐293 cells lines. Cells treated with one inhibitor, 7312, performed as well or better when compared with the commercially known caspase inhibitor, zVAD.fmk. Suspension CHO cells producing an IgG were used to investigate the capacity of 7312 to improve protein production. Treatment of cells with 7312 increased integrated cell densities by 33% with treated cells having a higher maximum cell density and higher viability. As a result, monoclonal antibody titers increased by 20% and higher in spinner flask experiments. Increasing productivity in mammalian cell cultures has key implications for the pharmaceutical and biotechnology sectors, which are presently focused on developing methods to enhance cell performance in bioreactor environments.
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets
Authors: Davey Robert , Savva George , Dicks Jo , Roberts Ian N. 
Published: March 2007

AbstractMPP is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposon-based insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.Availability: MPP source code, executables and online help are available at http://cbr.jic.ac.uk/dicks/software/Contact: robert.davey@bbsrc.ac.uk
Improved centroids estimation for the nearest shrunken centroid classifier
Authors: Wang Sijian , Zhu Ji 
Published: March 2007

AbstractMotivation: The nearest shrunken centroid (NSC) method has been successfully applied in many DNA-microarray classification problems. The NSC uses ‘shrunken’ centroids as prototypes for each class and identifies subsets of genes that best characterize each class. Classification is then made to the nearest (shrunken) centroid. The NSC is very easy to implement and very easy to interpret, however, it has drawbacks.Results: We show that the NSC method can be interpreted in the framework of LASSO regression. Based on that, we consider two new methods, adaptive L∞-norm penalized NSC (ALP-NSC) and adaptive hierarchically penalized NSC (AHP-NSC), with two different penalty functions for microarray classification, which improve over the NSC. Unlike the L1-norm penalty used in LASSO, the penalty terms that we consider make use of the fact that parameters belonging to one gene should be treated as a natural group. Numerical results indicate that the two new methods tend to remove irrelevant genes more effectively and provide better classification results than the L1-norm approach.Availability: R code for the ALP-NSC and the AHP-NSC algorithms are available from authors upon request.Contact: jizhu@umich.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Semantic Web Service provision: a realistic framework for Bioinformatics programmers
Authors: Gordon Paul M.K. , Trinh Quang , Sensen Christoph W. 
Published: March 2007

AbstractSummary: Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework (‘MobyServlet’) that very simply allows an existing Java application to conform to the MOBY-S semantic Web Services protocol. Using an existing Java program for codon-pair bias determination as an example, we enumerate the steps required for MOBY-S compliance. With minimal programming effort, such a deployment has the advantages of: (1) wider exposure to the user community by automatic inclusion in all MOBY-S client programs and (2) automatic interoperability with other MOBY-S services for input and output. Complex on-line analysis will become easier for biologists as more developers adopt MOBY-S.Availability: The framework and documentation are freely available from the Java developer's section of http://www.biomoby.org/.Contact: gordonp@ucalgary.ca
POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
Authors: Tung Chun-Wei , Ho Shinn-Ying 
Published: March 2007

AbstractMotivation: Both modeling of antigen-processing pathway including major histocompatibility complex (MHC) binding and immunogenicity prediction of those MHC-binding peptides are essential to develop a computer-aided system of peptide-based vaccine design that is one goal of immunoinformatics. Numerous studies have dealt with modeling the immunogenic pathway but not the intractable problem of immunogenicity prediction due to complex effects of many intrinsic and extrinsic factors. Moderate affinity of the MHC–peptide complex is essential to induce immune responses, but the relationship between the affinity and peptide immunogenicity is too weak to use for predicting immunogenicity. This study focuses on mining informative physicochemical properties from known experimental immunogenicity data to understand immune responses and predict immunogenicity of MHC-binding peptides accurately.Results: This study proposes a computational method to mine a feature set of informative physicochemical properties from MHC class I binding peptides to design a support vector machine (SVM) based system (named POPI) for the prediction of peptide immunogenicity. High performance of POPI arises mainly from an inheritable bi-objective genetic algorithm, which aims to automatically determine the best number m out of 531 physicochemical properties, identify these m properties and tune SVM parameters simultaneously. The dataset consisting of 428 human MHC class I binding peptides belonging to four classes of immunogenicity was established from MHCPEP, a database of MHC-binding peptides (Brusic et al., 1998). POPI, utilizing the m = 23 selected properties, performs well with the accuracy of 64.72% using leave-one-out cross-validation, compared with two sequence alignment-based prediction methods ALIGN (54.91%) and PSI-BLAST (53.23%). POPI is the first computational system for prediction of peptide immunogenicity based on physicochemical properties.Availability: A web server for prediction of peptide immunogenicity (POPI) and the used dataset of MHC class I binding peptides (PEPMHCI) are available at http://iclab.life.nctu.edu.tw/POPIContact: syho@mail.nctu.edu.tw
GoSh: a web-based database for goat and sheep EST sequences
Authors: Caprera Andrea , Lazzari Barbara , Stella Alessandra , Merelli Ivan , Caetano Alexandre R. , Mariani Paola 
Published: March 2007

AbstractSummary: The GoSh database is a collection of 58 990 Capra hircus and Ovis aries expressed sequence tags. A perl pipeline was prepared to process sequences, and data were collected in a MySQL database. A PHP-based web interface allows browsing and querying the database. Putative single nucleotide polymorphism (SNP) detection, as well as search to repeats were performed, and links to external related resources were provided. Sequences were annotated against three different databases and an algorithm was implemented to create statistics of the distribution of retrieved homologous ontologies in the Gene Ontology categories. The GoSh database is a repository of data and links related to goat and sheep expressed genes.Availability: The GoSh database is available at http://www.itb.cnr.it/gosh/Contact: andrea.caprera@tecnoparco.org
Ngila: global pairwise alignments with logarithmic and affine gap costs
Authors: Cartwright Reed A. 
Published: March 2007

AbstractSummary: Ngila is an application that will find the best alignment of a pair of sequences using log-affine gap costs, which are the most biologically realistic gap costs.Availability: Portable source code for Ngila can be downloaded from its development website, http://scit.us/projects/ngila/. It compiles on most operating systems.Contact: racartwr@ncsu.edu or reed@scit.usSupplementary information: Appendices
Unsupervised segmentation of continuous genomic data
Authors: Day Nathan , Hemmaplardh Andrew , Thurman Robert E. , Stamatoyannopoulos John A. , Noble William S. 
Published: March 2007

AbstractSummary: The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line utility for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs). Scale specificity is achieved by an optional wavelet-based smoothing operation. HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data.Availability: http://noble.gs.washington.edu/proj/hmmsegContact: rthurman@u.washington.edu
IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform
Authors: Schultze Joachim L. , Eggle Daniela 
Published: March 2007

AbstractSummary: IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality control, normalization, inference and classification methods are provided in a ‘point and click’ approach. IlluminaGUI is implemented as a R package based on the R-Tcl/Tk interface and is available for platforms on which R runs including Windows, Mac and Unix-type machines.Availability: http://IlluminaGUI.dnsalias.orgContact: joachim.schultze@uk-koeln.de
Quantitating tissue specificity of human genes to facilitate biomarker discovery
Authors: Vasmatzis George , Klee Eric W. , Kube Dagmar M. , Therneau Terry M. , Kosari Farhad 
Published: March 2007

AbstractWe describe a method to identify candidate cancer biomarkers by analyzing numeric approximations of tissue specificity of human genes. These approximations were calculated by analyzing predicted tissue expression distributions of genes derived from mapping expressed sequence tags (ESTs) to the human genome sequence using a binary indexing algorithm. Tissue-specificity values facilitated high-throughput analysis of the human genes and enabled the identification of genes highly specific to different tissues. Tissue expression distributions for several genes were compared to estimates obtained from other public gene expression datasets and experimentally validated using quantitative RT-PCR on RNA isolated from several human tissues. Our results demonstrate that most human genes (∼98%) are expressed in many tissues (low specificity), and only a small number of genes possess very specific tissue expression profiles. These genes comprise a rich dataset from which novel therapeutic targets and novel diagnostic serum biomarkers may be selected.Contact: vasm@mayo.eduSupplementary information: Supplementary data are available at Bioinformatics online.
A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups
Authors: Lai Yinglei , Adam Bao-ling , Podolsky Robert , She Jin-Xiong 
Published: March 2007

AbstractMotivation: Due to advances in experimental technologies, such as microarray, mass spectrometry and nuclear magnetic resonance, it is feasible to obtain large-scale data sets, in which measurements for a large number of features can be simultaneously collected. However, the sample sizes of these data sets are usually small due to their relatively high costs, which leads to the issue of concordance among different data sets collected for the same study: features should have consistent behavior in different data sets. There is a lack of rigorous statistical methods for evaluating this concordance or discordance.Methods: Based on a three-component normal-mixture model, we propose two likelihood ratio tests for evaluating the concordance and discordance between two large-scale data sets with two sample groups. The parameter estimation is achieved through the expectation-maximization (E-M) algorithm. A normal-distribution-quantile-based method is used for data transformation.Results: To evaluate the proposed tests, we conducted some simulation studies, which suggested their satisfactory performances. As applications, the proposed tests were applied to three SELDI-MS data sets with replicates. One data set has replicates from different platforms and the other two have replicates from the same platform. We found that data generated by SELDI-MS showed satisfactory concordance between replicates from the same platform but unsatisfactory concordance between replicates from different platforms.Availability: The R codes are freely available at http://home.gwu.edu/~ylai/research/ConcordanceContact: ylai@gwu.edu
SBML export interface for the systems biology toolbox for MATLAB
Authors: Schmidt Hening , Drews Gunnar , Vera Julio , Wolkenhauer Olaf 
Published: March 2007

AbstractSummary: In this application note, we present an Systems biology markup language (SBML) export interface for the Systems Biology Toolbox for MATLAB. This interface allows modelers to automatically convert models, represented in the toolbox's own format (SBmodels) to SBML files. Since SBmodels do not explicitly contain all the information that is required to generate SBML, the necessary information is gathered by parsing SBmodels. The export can be done in two different ways. First, it is possible to call the export from the command line, thereby directly converting a model to an SBML file. The second option is to inspect and edit the conversion results with the help of a graphical user interface and to subsequently export the model to SBML.Availability: The SBML export interface has been integrated into the Systems Biology Toolbox for MATLAB, which is open source and freely available from http://www.sbtoolbox2.org. The website also contains a tutorial, extensive documentation and examples.Contact: henning@fcc.chalmers.se
Mediante: a web-based microarray data manager
Authors: Le Brigand Kevin , Barbry Pascal 
Published: March 2007

AbstractSummary: Mediante is a MIAME-compliant microarray data manager that links together annotations and experimental data. Developed as a J2EE three-tier application, Mediante integrates a management system for production of long oligonucleotide microarrays, an experimental data repository suitable for home made or commercial microarrays, and a user interface dedicated to the management of microarrays projects. Several tools allow quality control of hybridizations and submission of validated data to public repositories.Availability: http://www.microarray.frContact: barbry@ipmc.cnrs.fr or lebrigand@ipmc.cnrs.frSupplementary information: http://www.microarray.fr/SP/lebrigand2007/
GenABEL: an R library for genome-wide association analysis
Authors: Aulchenko Yurii S. , Ripke Stephan , Isaacs Aaron , van Duijn Cornelia M. 
Published: March 2007

AbstractHere we describe an R library for genome-wide association (GWA) analysis. It implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of single nucleotide polymorphisms with binary or quantitative traits, visualization of results and also provides easy interfaces to standard statistical and graphical procedures implemented in base R and special R libraries for genetic analysis. We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers.Availability: http://cran.r-project.orgContact: i.aoultchenko@erasmusmc.nl
Using DNA microarrays to study gene expression in closely related species
Authors: Oshlack Alicia , Chabot Adrien E. , Smyth Gordon K. , Gilad Yoav 
Published: March 2007

AbstractMotivation: Comparisons of gene expression levels within and between species have become a central tool in the study of the genetic basis for phenotypic variation, as well as in the study of the evolution of gene regulation. DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. Thus, in order to study gene expression levels in species for which microarrays are not available, researchers face three sets of choices: (i) use a microarray designed for another species, but only compare gene expression levels within species, (ii) construct a new microarray for every species whose gene expression profiles will be compared or (iii) build a multi-species microarray with probes from each species of interest. Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach.Results: We find that, for inter-species comparisons, estimates of expression differences based on multi-species microarrays are more accurate than those based on multiple species-specific arrays. We also demonstrate that within-species expression differences can be estimated using a microarray for a closely related species, without discernible loss of information.Contact: A.O. (oshlack@wehi.edu.au) or Y.G. (gilad@uchicago.edu)Supplementary information: Supplementary data are available at Bioinformatics online.