bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic retrieval and visualization of biologically relevant microarray experiments
Authors: Caldas José , Gehlenborg Nils , Faisal Ali , Brazma Alvis , Kaski Samuel 
Published: May 2009

Abstract
Motivation: As ArrayExpress and other repositories of genome-wide experiments are reaching a mature size, it is becoming more meaningful to search for related experiments, given a particular study. We introduce methods that allow for the search to be based upon measurement data, instead of the more customary annotation data. The goal is to retrieve experiments in which the same biological processes are activated. This can be due either to experiments targeting the same biological question, or to as yet unknown relationships.
Results: We use a combination of existing and new probabilistic machine learning techniques to extract information about the biological processes differentially activated in each experiment, to retrieve earlier experiments where the same processes are activated and to visualize and interpret the retrieval results. Case studies on a subset of ArrayExpress show that, with a sufficient amount of data, our method indeed finds experiments relevant to particular biological questions. Results can be interpreted in terms of biological processes using the visualization techniques.
Availability: The code is available from http://www.cis.hut.fi/projects/mi/software/ismb09.
Contact: jose.caldas@tkk.fi
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
Authors: Lubliner Shai , Segal Eran 
Published: May 2009

Abstract
Motivation: Understanding the mechanisms that govern nucleosome positioning over genomes in vivo is essential for unraveling the role of chromatin organization in transcriptional regulation. Until now, models for predicting genome-wide nucleosome occupancy have assumed that the DNA associations of neighboring nucleosomes on the genome are independent. We present a new model that relaxes this independence assumption by modeling interactions between adjacent nucleosomes.
Results: We show that modeling interactions between adjacent nucleosomes improves genome-wide nucleosome occupancy predictions in an in vitro system that includes only nucleosomes and purified DNA, where the resulting model has a preference for short spacings (linkers) of less than 20 bp in length between neighboring nucleosomes. Since nucleosome occupancy in vitro depends only on properties intrinsic to nucleosomes, these results suggest that the interactions we find are intrinsic to nucleosomes and do not depend on other factors, such as transcription factors and chromatin remodelers. We also show that modeling these intrinsic interactions significantly improves genome-wide predictions of nucleosome occupancy in vivo.
Contact: eran.segal@weizmann.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
PICKY: a novel SVD-based NMR spectra peak picking method
Authors: Alipanahi Babak , Gao Xin , Karakoc Emre , Donaldson Logan , Li Ming 
Published: May 2009

Abstract
Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear overhauser enhancement (NOE) distance restraint assignment, and structure calculation tasks. Manual or semi-automatic peak picking, which is currently the prominent way used in NMR labs, is tedious, time consuming and costly.
Results: We introduce new ideas, including noise-level estimation, component forming and sub-division, singular value decomposition (SVD)-based peak picking and peak pruning and refinement. PICKY is developed as an automated peak picking method. Different from the previous research on peak picking, we provide a systematic study of the proposed method. PICKY is tested on 32 real 2D and 3D spectra of eight target proteins, and achieves an average of 88% recall and 74% precision. PICKY is efficient. It takes PICKY on average 15.7 s to process an NMR spectrum. More important than these numbers, PICKY actually works in practice. We feed peak lists generated by PICKY to IPASS for resonance assignment, feed IPASS assignment to SPARTA for fragments generation, and feed SPARTA fragments to FALCON for structure calculation. This results in high-resolution structures of several proteins, for example, TM1112, at 1.25 Å.
Availability: PICKY is available upon request. The peak lists of PICKY can be easily loaded by SPARKY to enable a better interactive strategy for rapid peak picking.
Contact: mli@uwaterloo.ca
A Classifier-based approach to identify genetic similarities between diseases
Authors: Schaub Marc A. , Kaplow Irene M. , Sirota Marina , Do Chuong B. , Butte Atul J. , Batzoglou Serafim 
Published: May 2009

Abstract
Motivation: Genome-wide association studies are commonly used to identify possible associations between genetic variations and diseases. These studies mainly focus on identifying individual single nucleotide polymorphisms (SNPs) potentially linked with one disease of interest. In this work, we introduce a novel methodology that identifies similarities between diseases using information from a large number of SNPs. We separate the diseases for which we have individual genotype data into one reference disease and several query diseases. We train a classifier that distinguishes between individuals that have the reference disease and a set of control individuals. This classifier is then used to classify the individuals that have the query diseases. We can then rank query diseases according to the average classification of the individuals in each disease set, and identify which of the query diseases are more similar to the reference disease. We repeat these classification and comparison steps so that each disease is used once as reference disease.
Results: We apply this approach using a decision tree classifier to the genotype data of seven common diseases and two shared control sets provided by the Wellcome Trust Case Control Consortium. We show that this approach identifies the known genetic similarity between type 1 diabetes and rheumatoid arthritis, and identifies a new putative similarity between bipolar disease and hypertension.
Contact: serafim@cs.stanford.edu
Predictions of RNA secondary structure by combining homologous sequence information
Authors: Hamada Michiaki , Sato Kengo , Kiryu Hisanori , Mituyama Toutai , Asai Kiyoshi 
Published: May 2009

Abstract
Motivation: Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction from an RNA sequence is still limited. In many cases, however, homologous RNA sequences are available with the target RNA sequence whose secondary structure is to be predicted.
Results: In this article, we propose a new method for secondary structure predictions of individual RNA sequences by taking the information of their homologous sequences into account without assuming the common secondary structure of the entire sequences. The proposed method is based on posterior decoding techniques, which consider all the suboptimal secondary structures of the target and homologous sequences and all the suboptimal alignments between the target sequence and each of the homologous sequences. In our computational experiments, the proposed method provides better predictions than those performed only on the basis of the formation of individual RNA sequences and those performed by using methods for predicting the common secondary structure of the homologous sequences. Remarkably, we found that the common secondary predictions sometimes give worse predictions for the secondary structure of a target sequence than the predictions from the individual target sequence, while the proposed method always gives good predictions for the secondary structure of target sequences in all tested cases.
Availability: Supporting information and software are available online at: http://www.ncrna.org/software/centroidfold/ismb2009/.
Contact: hamada-michiaki@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
DISCOVER: a feature-based discriminative method for motif search in complex genomes
Authors: Fu Wenjie , Ray Pradipta , Xing Eric P. 
Published: May 2009

Abstract
Motivation: Identifying transcription factor binding sites (TFBSs) encoding complex regulatory signals in metazoan genomes remains a challenging problem in computational genomics. Due to degeneracy of nucleotide content among binding site instances or motifs, and intricate ‘grammatical organization’ of motifs within cis-regulatory modules (CRMs), extant pattern matching-based in silico motif search methods often suffer from impractically high false positive rates, especially in the context of analyzing large genomic datasets, and noisy position weight matrices which characterize binding sites. Here, we try to address this problem by using a framework to maximally utilize the information content of the genomic DNA in the region of query, taking cues from values of various biologically meaningful genetic and epigenetic factors in the query region such as clade-specific evolutionary parameters, presence/absence of nearby coding regions, etc. We present a new method for TFBS prediction in metazoan genomes that utilizes both the CRM architecture of sequences and a variety of features of individual motifs. Our proposed approach is based on a discriminative probabilistic model known as conditional random fields that explicitly optimizes the predictive probability of motif presence in large sequences, based on the joint effect of all such features.
Results: This model overcomes weaknesses in earlier methods based on less effective statistical formalisms that are sensitive to spurious signals in the data. We evaluate our method on both simulated CRMs and real Drosophila sequences in comparison with a wide spectrum of existing models, and outperform the state of the art by 22% in F1 score.
Availability and Implementation: The code is publicly available at http://www.sailing.cs.cmu.edu/discover.html.
Contact: epxing@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Proteome coverage prediction with infinite Markov models
Authors: Claassen Manfred , Aebersold Ruedi , Buhmann Joachim M. 
Published: May 2009

AbstractMotivation: Liquid chromatography tandem mass spectrometry (LC-MS/MS) is the predominant method to comprehensively characterize complex protein mixtures such as samples from prefractionated or complete proteomes. In order to maximize proteome coverage for the studied sample, i.e. identify as many traceable proteins as possible, LC-MS/MS experiments are typically repeated extensively and the results combined. Proteome coverage prediction is the task of estimating the number of peptide discoveries of future LC-MS/MS experiments. Proteome coverage prediction is important to enhance the design of efficient proteomics studies. To date, there does not exist any method to reliably estimate the increase of proteome coverage at an early stage.Results: We propose an extended infinite Markov model DiriSim to extrapolate the progression of proteome coverage based on a small number of already performed LC-MS/MS experiments. The method explicitly accounts for the uncertainty of peptide identifications. We tested DiriSim on a set of 37 LC-MS/MS experiments of a complete proteome sample and demonstrated that DiriSim correctly predicts the coverage progression already from a small subset of experiments. The predicted progression enabled us to specify maximal coverage for the test sample. We demonstrated that quality requirements on the final proteome map impose an upper bound on the number of useful experiment repetitions and limit the achievable proteome coverage.Contact: manfredc@inf.ethz.ch; jbuhmann@inf.ethz.ch
Developing an architecture model for enterprise knowledge
Authors: Jafari Mostafa , Akhavan Peyman , Nouranipour Elham 
Published: May 2009

PurposeThe main objective of this paper is to explore the role of knowledge architecture in an enterprise and to provide a model to architect enterprise knowledge based on the Zachman framework.Design/methodology/approachThis is a conceptual article providing a knowledge architecture model for an organization based on the Zachman framework that discussed several perspectives from the knowledge management point of view and information technology. To confirm the validity of the model a questionnaire was designed, applied and then analyzed by some statistical methods.FindingsThe paper provides a conceptual knowledge architecture model that can be applied to Iranian organizations practically. The validity of this model is confirmed by polling the opinion of knowledge architecture experts.Research limitations/implicationsThe lack of resources directly related to the subject of the research, the novelty of this kind of research in Iran and the lack of organizations which perform a knowledge architecture model in reality are the restrictions of this research. The authors' suggestion for further research studies is to execute the model and survey from foreigner experts.Practical implicationsThe paper may be beneficial for enterprise architects in the knowledge area.Originality/valueThe paper may be of high value to researchers in the knowledge management field and to practitioners involved with KM adoption in the organizations. It gives valuable information and guidelines that hopefully will help the leaders and the senior knowledge management managers to accomplish KM through their organization successfully.
Cloon Keen Atelier: scent for a premium position
Authors: Torres Ann M. 
Published: May 2009

PurposeCloon Keen Atelier develops candle and skin care products. The challenge for this small operator is to develop a strategy, which reinforces its chosen position as it develops new products and expands into other markets. Cloon Keen is known for its premium scented candles, but it is seeking to expand into the personal care market by creating their own line of skin care products and complementary accessories. Cloon Keen believes their handcrafted candles could provide a platform for developing a lifestyle brand. This paper aims to address these issues.Design/methodology/approachIn‐depth interviews and secondary sources are used to collate the information from which the case study is developed.FindingsAchieving the status of a lifestyle brand means the products embody the values and aspirations of particular group(s) or culture; it speaks powerfully to the core identity of its consumers. Typically, lifestyle brands are accompanied by a powerful promotional campaign to communicate the lifestyle brand values to audiences. To date, Cloon Keen's promotional efforts have been limited. The question is whether it can develop sufficient market presence to one day make the claim of being a lifestyle brand. The challenge for Cloon Keen is to find the optimum market position that provides a strategic advantage in a climate of robust competition.Originality/valueThe case study provides the opportunity to examine how an small‐ to medium‐sized enterprises may build its brand presence within a highly competitive market.
Home delivery at the Orange County Library System: an exemplar from the USA
Authors: Myers Jim 
Published: May 2009

PurposeThe purpose of this paper is to provide a case study of Florida's Orange County Library System (OCLS) home delivery program, including the history, processes and cost‐effectiveness of the service.Design/methodology/approachThe approach takes a descriptive form.FindingsIt was found that the service continues to grow from 9,000 books delivered in 1975 to 840,000 in 2008. It is cost‐effective and the most popular service with patrons.Originality/valueThe paper is one of the few that describes a successful home delivery service run by a public library. It should be useful for all librarians who are keen to introduce such a service in their own library.
The relationship between the uniform approximation rates and the shapes of fuzzy sets in fuzzy systems
Authors: Luo Qiang , Yi Dongyun , Yang Wenqiang 
Published: May 2009

PurposeThe purpose of this paper is to answer the question that what the best shape of fuzzy sets is in fuzzy systems for function approximation which is essential in many applications of fuzzy systems.Design/methodology/approachThe uniform approximation rates indicate the approximating capabilities of fuzzy systems for function approximation. By Fourier analysis, the uniform approximation rates are estimated for the fuzzy systems with various shapes of if‐part fuzzy sets in the case of single‐input and single‐output. Based on the approximation rates, the relationships between the approximating capabilities and the shapes of fuzzy sets are developed and compared.FindingsThe since functions as the input membership functions in fuzzy systems are proved to have the almost best approximation property in a particular class of membership functions.Research limitations/implicationsFrom the viewpoint of function approximation, the input membership functions are not necessarily positive in fuzzy systems.Practical implicationsFor engineers, the sinc‐shaped membership function is a good choice to improve their fuzzy systems in real applications.Originality/valueThe uniform approximation rates of fuzzy systems for function approximation are estimated. Mathematically, the relationships between the approximating capabilities and the shapes of fuzzy sets are analyzed for fuzzy systems.
Free object in the category of L‐fuzzy left R‐modules determined by L‐fuzzy set
Authors: Tang Jian‐Gang , Luo Mao‐Kang , Liu Miao 
Published: May 2009

PurposeThe purpose of this paper is to study free L‐fuzzy left R‐module, using the language of categories and functors for the general description of L‐fuzzy left R‐modules generated by L‐fuzzy set. In the language of categories and functors, an L‐fuzzy left R‐modules generated by L‐fuzzy set is called a free object in the category of L‐fuzzy left R‐modules determined by L‐fuzzy set.Design/methodology/approachCategory theory is used to study the existent quality, unique quality and material structure of L‐fuzzy left R‐modules generated by L‐fuzzy set.FindingsThe paper gives the uniqueness, structure and existence theorems of free object in the category of L‐fuzzy left R‐modules determined by L‐fuzzy set, and the authors prove that the fuzzy free functor is left adjoint to the fuzzy underlying functor.Research limitations/implicationsSome property of free L‐fuzzy left R‐modules will need to be further researched.Originality/valueThe paper defines a new class of L‐fuzzy left R‐modules, i.e. free L‐fuzzy left R‐modules, research and explore free L‐fuzzy left R‐modules in theory.
Marcuse on Senge: personal mastery, the child's mind, and individual transformation
Authors: Bokeno R. Michael 
Published: May 2009

PurposeThe purpose of this paper is to continue discussion of the merits of organizational learning as an emancipatory project, by articulating Peter Senge's concept of “personal mastery” (PM) against the radical subjectivity of Herbert Marcuse.Design/methodology/approachConceptual comparison of extant works by both authors.FindingsIt is argued in the paper that while Senge and Marcuse share several affinities for the nature of individual, organizational and social transformation, Senge's concept of PM leaves several questions unaddressed, questions which concern the extent to which “the child's mind” may be usefully employed as a metaphor for the recovery of individuality and liberatory work. Marcuse's Marxian appropriation of Freudian psychoanalysis retains the possibility of the creative impulse, and suggests that “play” may enter work relations as the new sensibility for transformed work practices.Originality/valueThe paper puts forward the view that adult play, as the memory of a more unencumbered past, may be the radical subjectivity necessary for PM and individual transformation, and thus for more emancipated workplaces.
Have budgetary controls in the US club industry changed from the mid‐1980s to the twenty‐first century?
Authors: Oak Seonghee , Schmidgall Raymond S. 
Published: May 2009

PurposeThe purpose of this paper is to understand whether budgetary controls at clubs have changed from the mid‐1980s to the first decade of the twenty‐first century.Design/methodology/approachThe survey instrument is mailed to the members of the Club Managers Association of America. The questionnaire includes demographic data as well as information on budgetary controls.FindingsFor control purposes, comparisons to the original budget and actual numbers during the current decade have increased significantly from comparisons in the prior decade. The median variance tolerance for food and labor costs has declined from the mid‐1980s to the mid‐1990s and now to the first decade of the twenty‐first century. Median variance tolerances for beverage costs are slightly higher in this study than in the mid‐1990s study.Research limitations/implicationsThe authors are unable to determine any statistical differences between current and prior studies due to a lack of prior data. Further research on tolerable control variances can be studied for other costs, such as supplies, energy, and fixed charges.Practical implicationsThis paper provides findings that can help managers as they compare their budgetary control practices with US club industry practices. Educators can provide selected cost control information to their hospitality students focusing on club management and researchers can use this information as a base for further research in cost control areas.Originality/valueThis paper is the first paper on budgetary controls in the US club industry in the twenty‐first century.
Open access indicators and information society: the Latin American case
Authors: Gómez Nancy , Bustos‐Gonzalez Atilio , Santillan‐Aldana Julio , Arias Olga 
Published: May 2009

PurposeThe purpose of this paper is to estimate open access penetration ratios through cross‐analysis of existing social context and open access indicators in Latin America.Design/methodology/approachThe following parameters were used to characterize the chosen countries. On one hand, it takes social context indicators like digital opportunity index (DOI), GDP 2007 (Organization for Economic Co‐operation and Development) (www.oecd.org/home/0,3305,en_2649_201185_1_1_1_1_1,00.html), scientific output 2005, and investment in science and technology vs GDP 2004. On the other hand, it analyses open access indicators considering the two main open access strategies – the green and gold routes – and the existing legal framework.FindingsThis paper discusses the evolution of DOI and compares with open access parameters (numbers of repositories, number of registries in repositories, DOAJ journals and number of creative commons licences) in the context of scientific information in developing countries in Latin America.Research limitations/implicationsThis paper is not an exhaustive survey and limits the comparison to the Latin American Countries, focalized in Brazil, Chile and Argentina.Originality/valueThis paper gives an overview of the situation of three particular countries: Brazil, Chile and Argentina, and explains the position of these countries in the open access movement in Latin America.