bluuebunny/crossref_metadata_2025_split huggingface dataset:
An effective statistical evaluation of ChIPseq dataset similarity
Authors: D. Chikina Maria , G. Troyanskaya Olga 
Published: January 2012

Abstract
Motivation: ChIPseq is rapidly becoming a common technique for investigating protein–DNA interactions. However, results from individual experiments provide a limited understanding of chromatin structure, as various chromatin factors cooperate in complex ways to orchestrate transcription. In order to quantify chromtain interactions, it is thus necessary to devise a robust similarity metric applicable to ChIPseq data. Unfortunately, moving past simple overlap calculations to give statistically rigorous comparisons of ChIPseq datasets often involves arbitrary choices of distance metrics, with significance being estimated by computationally intensive permutation tests whose statistical power may be sensitive to non-biological experimental and post-processing variation.
Results: We show that it is in fact possible to compare ChIPseq datasets through the efficient computation of exact P-values for proximity. Our method is insensitive to non-biological variation in datasets such as peak width, and can rigorously model peak location biases by evaluating similarity conditioned on a restricted set of genomic regions (such as mappable genome or promoter regions).
Applying our method to the well-studied dataset of Chen et al. (2008), we elucidate novel interactions which conform well with our biological understanding. By comparing ChIPseq data in an asymmetric way, we are able to observe clear interaction differences between cofactors such as p300 and factors that bind DNA directly.
Availability: Source code is available for download at http://sonorus.princeton.edu/IntervalStats/IntervalStats.tar.gz
Contact: ogt@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
Authors: Göke Jonathan , Schulz Marcel H. , Lasserre Julia , Vingron Martin 
Published: January 2012

Abstract
Motivation: The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets.
Results: We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2.
Conclusion: N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences.
Availability: The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html
Contact: goeke@molgen.mpg.de; vingron@molgen.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Factors Associated With Peptide‐based Formula Prescription in a Pediatric Intensive Care Unit
Authors: Vidigal Maria V.M. , Leite Heitor P. , Nogueira Paulo C.K. 
Published: January 2012

ABSTRACTObjectives:There is no evidence‐based consensus on the use of peptide‐based formulas for critically ill children. The present study aimed to identify the factors associated with the choice of peptide‐based formulas in the first enteral nutrition prescription for critically ill children and to compare the direct costs of the enteral formulas used in a pediatric intensive care unit.Methods:In a prospective study, children admitted to the intensive care unit and receiving tube feeding for ≥48 hours were evaluated. The potential exposure variables for the use of peptide‐based formulas as the first nutrition prescription were age, sex, malnutrition, sepsis/septic shock, fasting period >2 days, use of α‐adrenergic drugs before initiating first diet, and the revised Pediatric Index of Mortality score. A direct cost comparison of prescribed formulas was performed.Results:Of 291 patients included, 85 (29.2%) were given peptide‐based formulas in the first nutrition prescription. This choice was independently associated with malnutrition (odds ratio [OR] 2.94; 95% confidence interval [CI] 1.60%–5.39%; P < 0.01), fasting period >2 days (OR 3.46; 95% CI 1.93%–6.20%; P < 0.01), and use of α‐adrenergic drugs (OR 2.32; 95% CI 1.24%–4.31%; P < 0.01). Peptide‐based formula costs were up to 10 times higher than standard polymeric formula costs.Conclusions:The choice of peptide‐based formula as the first enteral nutrition prescription is associated with the greater severity of patients' clinical status—patients receiving α‐adrenergic drugs, those who are malnourished, and those with longer fasting periods. These prescriptions engender costs higher than those associated with standard polymeric formula.
Assessing the market potential for a local food product
Authors: Akaichi Faical , Gil José M. , Nayga Rodolfo M. 
Published: January 2012

PurposeThe purpose of this paper is to analyze the market potential of a locally produced and high quality food product (i.e. white bean “Mongeta Ganxet” (MG)) from Catalonia, Spain. Consumers' willingness to pay (WTP) for the product is elicited using a non‐hypothetical economic experiment and then the sensitivity of WTP values is analyzed with regard to additional information provided to participants that includes reference prices, leaflets and tasting. Finally, a sample‐selection model is estimated to assess the factors that significantly affect consumers' WTP for the product.Design/methodology/approachTo elicit the willingness to pay a premium for the local food product, 90 subjects were invited to participate in a random nth price experimental auction. Before auctioning the product, participants were asked to complete a questionnaire about consumer attitudes and purchase habits.FindingsOnly 7 percent of participants are willing to pay a price higher than the minimum price from which the MG product may be purchased directly from a producer or the local producing market. Also, it was found that providing reference prices of substitute products (both conventional and alternative high quality white beans) positively affects WTP for the MG. Interestingly, however, provision of information on organoleptic, nutritional and cooking characteristics of the MG and product tasting do not significantly influence WTP. Finally, the level of consumption, the degree of knowledge about the product and the participants' previous experience increase the purchasing intention for the MG.Originality/valueIn contrast to traditional market research studies that use hypothetical methods, the authors use non‐hypothetical elicitation mechanism to elicit consumers' valuation for an important local food product in Catalonia, Spain. Since actual products and cash were used in the experiments, the authors provided the respondents with an incentive to reveal their true preferences and valuation for the product of interest. The authors also tested the effect of provision of certain types of information on WTP and analyzed the factors that significantly influence consumers' WTP for the product.
A dictionary‐based approach to normalizing gene names in one domain of knowledge from the biomedical literature
Authors: Galvez Carmen , de Moya‐Anegón Félix 
Published: January 2012

PurposeGene term variation is a shortcoming in text‐mining applications based on biomedical literature‐based knowledge discovery. The purpose of this paper is to propose a technique for normalizing gene names in biomedical literature.Design/methodology/approachUnder this proposal, the normalized forms can be characterized as a unique gene symbol, defined as the official symbol or normalized name. The unification method involves five stages: collection of the gene term, using the resources provided by the Entrez Gene database; encoding of gene‐naming terms in a table or binary matrix; design of a parametrized finite‐state graph (P‐FSG); automatic generation of a dictionary; and matching based on dictionary look‐up to transform the gene mentions into the corresponding unified form.FindingsThe findings show that the approach yields a high percentage of recall. Precision is only moderately high, basically due to ambiguity problems between gene‐naming terms and words and abbreviations in general English.Research limitations/implicationsThe major limitation of this study is that biomedical abstracts were analyzed instead of full‐text documents. The number of under‐normalization and over‐normalization errors is reduced considerably by limiting the realm of application to biomedical abstracts in a well‐defined domain.Practical implicationsThe system can be used for practical tasks in biomedical literature mining. Normalized gene terms can be used as input to literature‐based gene clustering algorithms, for identifying hidden gene‐to‐disease, gene‐to‐gene and gene‐to‐literature relationships.Originality/valueFew systems for gene term variation handling have been developed to date. The technique described performs gene name normalization by dictionary look‐up.
Diffusionism and open access
Authors: Xia Jingfeng 
Published: January 2012

PurposeThis article aims to explore the geographic distribution of open access practices in the world from a diffusionist perspective.Design/methodology/approachThe article applies a tempo‐spatial analysis to examine the diffusion movement of open access practices from the West to the entire world during the past several decades. Both maps and tables are used to support the analysis. The diffusionist theory is reviewed and applied to the understanding of open access.FindingsThe paper discovers that technology is not the only factor determining the diffusion pattern of information systems as discussed in the literature. Cultural dissimilarities across countries have played a significant role in open access development. Open access can only be effectively established after it meets local standards.Practical implicationsThe findings help understanding of why open access has a disproportionate growth among developing countries, and even among developed countries, where the ICT infrastructure has been in place.Originality/valueFew studies have taken a transnational view to analyze open access geography at the global level, and few have been able to synthesize models to interpret diverse discoveries. Furthermore, a chronological evaluation tracing the history of open access spatial expansion is absent in the literature.
Document theory for the design of socio‐technical systems
Authors: Ivar Olsen Bernt , Windfeld Lund Niels , Ellingsen Gunnar , Hartvigsen Gunnar 
Published: January 2012

PurposeThis conceptual article aims to discuss how the concept of a document and documentation along with a general document model could inform us in the design and engineering of information or rather documentation systems.Design/methodology/approachThis paper presents a broad and complementary document model, derived from the last couple of decades' discussion on what is a document and what is documentation. This model is used as a basis for a method, a conceptual tool or a template for analysis of socio‐technical systems.FindingsThe authors contend that the document systems analysis is a holistic approach compared to the traditional systems design and engineering reductionist approach, and also in the context of sociotechnical systems design. The document model is a taxonomy of the constituents of the document and, the authors argue, a potential communication tool in systems design.Research limitations/implicationsThe document model presented in this article is discussed more or less solely in the context of information systems design, specifically sociotechnical systems. Moreover, the authors have tried to fit the theory and model within this context here, even though the concepts and thoughts can have much more general implications.Practical implicationsThis presentation of a novel document model and framework is presented as a potential tool for systems analysis and design. The authors regard this as a realistic vision for the framework, but at the current stage of development for the model it is probably more useful as draft for such a tool or framework; a point of departure for the discussion of practical – and theoretical – implications of a broad and holistic document model.Originality/valueA novel, unpublished document model, derived from theoretical discourses of document ontology in the “neo‐documentalist” movement spawned from a particular research community in Tromsø, Norway, is presented and discussed in the light of information systems design.
The social role of the Raffles Library, Singapore, in the inter‐war years
Authors: Luyt Brendan 
Published: January 2012

PurposeThe purpose of this article is to examine the inter‐war history of the Raffles Library in Singapore with the aim of understanding what the management of the library believed its role should be as well as the role others in that society considered that it should fulfill.Design/methodology/approachThe article is based on historical research using archival sources.FindingsTo a great extent the management of the library narrowly construed the institution's mission in terms of appealing to that class of persons likely to become paying members – that is, the European elite and its high‐level local collaborators. Financial constraints, relations between the library and museum as well as prevalent negative attitudes regarding class and race in colonial society are likely reasons for the lack of sustained attention to non‐European populations.Originality/valueThe library history of much of Asia remains relatively unexplored, especially from a viewpoint that stresses the importance of social context to library structure and operation.
Corporate sustainability: historical development and reporting practices
Authors: Christofi Andreas , Christofi Petros , Sisaye Seleshi 
Published: January 2012

PurposeThe purpose of this paper is to compare the sustainability disclosure methods‐instruments practiced by the two most widely employed indexes/instruments (DJSI World and GRI‐G3 Guidelines). The paper suggests that the newly created triple bottom line (TBL) reporting practices need to undergo further standardization and enforcement to avoid, or give early warnings about, future corporate mismanagement that leads to socio‐economic consequences detrimental to investors and consumers in general.Design/methodology/approachThis paper utilizes sample firms from the DJSI World Index and the GRI‐G3 Sustainability Guidelines membership list to draw inferences on sustainability indicators of performance. The authors compare the GRI reporting guidelines with the disclosure indicators of the DJSI World.FindingsThe authors' findings suggest that TBL reporting has made enormous progress over the last two decades. However, the two widely used sustainability reporting instruments/indexes (DJSI World and GRI‐G3 Guidelines) differ in disclosure practice‐methods and the authors recommend that further standardization and enforcement is necessary. The authors' view is that the Securities and Exchange Commission (SEC) and Financial Accounting Standards Board (FASB) should become actively involved with the issue of standardization and enforcement of corporate socio‐environmental disclosures. The paper presents evidence that investors have neither rewarded nor penalized firms for adhering to or violating sustainability matters in their corporate decisions.Practical implicationsThe authors argue for further standardization and enforcement with regard to the disclosure methods of the two widely used (GRI and DJSI) sustainability indicators in order to avoid future corporate mismanagement that leads to (systemic) economic and socio‐environmental consequences detrimental to citizen investors and consumers in general.Originality/valueThe research is of interest to academicians and practitioners who are interested in the theory and practice of sustainability reporting or TBL reporting. The findings suggest that this newly created disclosure instrument needs to undergo further standardization and enforcement for meaningful and accurate disclosure of economic‐social and environmental performance. The authors' view is that the SEC and FASB should become actively involved with the issue of standardization and enforcement of socio‐environmental disclosure of corporate sustainability.
Design and implementation of a fully autonomous humanoid soccer robot
Authors: Mohades Kasaei Seyed H. , Kasaei Mohammadreza , Alireza Kasaei S. 
Published: January 2012

PurposeThe purpose of this paper is to design and implement a team of kid size humanoid soccer robots conforming to RoboCup Humanoid league.Design/methodology/approachThe project is described in two main parts: hardware and software. The hardware section consists of the mechanical structure and the driver circuit board enabling each robot to walk, fast walk, autonomously get up, kick and dribble when it catches the ball. The software is developed as a robot application which consists of motion controller, autonomous motion robot, self localization based on vision system, AI, trajectory planning and network.FindingsThis year, the authors' developments for the humanoid robot include: the design and construction of our new humanoid robots structure and implementation of a new recurrent hybrid neural network for walking control. The control system consists of two neural network controllers, two standard PD controllers and a robot walking planar. The proposed neural network controller has three layers, which are input, hidden, and output layers.Originality/valueThis paper presents results of research work in the field of autonomous robot‐middle size soccer robot, supported by IAU‐ Isfahan Branch (Khorasgan).
Assessment of the positioning performance of an industrial robot
Authors: Slamani Mohamed , Nubiola Albert , Bonev Ilian 
Published: January 2012

PurposeThe purpose of this paper is to investigate the use of a laser tracker, a laser interferometer system and a telescopic ballbar for assessing the positioning performance of a six‐axis industrial serial robot. The paper also aims to illustrate the limitations of these three metrology instruments for the assessment of robot positioning performance and to demonstrate the inadequacy of simplistic performance tests.Design/methodology/approachSpecific test methods in the case of the laser interferometer system and the telescopic ballbar are proposed. Measurements are analyzed in accordance to the ISO 9283 norm.FindingsIt is found that, in static conditions and after a relatively short warm‐up, the unidirectional position repeatability of the non‐calibrated industrial robot under study (an ABB IRB 1600) is better than 37 μm, the unidirectional orientation repeatability is at worst 87 μrad, the linear position accuracy is better than 650 μm, and the rotation accuracy is at worst 2.8 mrad (mainly because of the sixth robot axis). It was also found that the dynamic (radial) errors due to vibrations can be up to approximately ±250 μm along a small circular path at TCP speed of 700 mm/s.Practical implicationsIt is pointed out that the use of a laser tracker (or any other large range portable 3D measurement system) is questionable for assessing – let alone analyzing in depth – the unidirectional position repeatability of some of today's industrial robots. It is also demonstrated that the laser interferometer system can be used for measuring linear errors along a linear path of motion as well as angular errors about axes orthogonal to the path of motion. Finally, it is shown that the telescopic ballbar is an excellent, comparably low‐cost, high‐precision tool for assessing the static and dynamic positioning performance of industrial robots and its use in robotics should be further developed.Originality/valueThis work is the first to detail the use of three metrology equipments for assessing the positioning performance of an industrial robot. Experimental results are presented and discussed. Some guidelines for optimizing the positioning performance of an industrial robot are provided.
Research, design and experiment of end effector for wafer transfer robot
Authors: Liu Yanjie , Xu Meng , Cao Yumei 
Published: January 2012

PurposeWafer transfer robots play a significant role in IC manufacturing industry and the end effector is an important component of the robots. The purpose of this paper is to improve transfer efficiency of a wafer transfer robot through study of its end effector, and at the same time to reduce wafer deformation.Design/methodology/approachFinite element method is adopted to analyze wafer deformation. For wafer transfer robot working in vacuum, for the first time, the authors apply the research of microfiber arrays inspired by gecko to the design of robot's end effector, and present equations between robot's transit acceleration and parameters of microfiber arrays. Based on these studies, a kind of micro‐array bump is designed and fixed to a structure optimized end effector. For wafer transfer robot working in atmospheric environment, the authors have analyzed the effects of different factors on wafer deformation. The pressure distributions in absorption area and calculation formula of maximal transfer acceleration are put forward. Finally, a new kind of end effector for atmospheric robot is designed according to these studies.FindingsThe experiments results show that transfer efficiency of wafer transfer robot has been significantly improved through application of the research in this paper. Also wafer deformation under absorption force has been controlled.Practical implicationsThrough experiments it can be seen that the research in this paper can be used to improve robot transfer ability and decrease wafer deformation in the production environment. Also the studies of end effector lay a solid foundation for further improvement.Originality/valueThis is the first application of the research of gecko‐inspired microfiber arrays to vacuum wafer transfer robot. This paper also carefully analyzes effects of different factors on wafer deformation through finite element method.