bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple testing on the directed acyclic graph of gene ontology
Authors: Goeman Jelle J. , Mansmann Ulrich 
Published: January 2008

AbstractMotivation: Current methods for multiplicity adjustment do not make use of the graph structure of Gene Ontology (GO) when testing for association of expression profiles of GO terms with a response variable.Results: We propose a multiple testing method, called the focus level procedure, that preserves the graph structure of Gene Ontology (GO). The procedure is constructed as a combination of a Closed Testing procedure with Holm's method. It requires a user to choose a ‘focus level’ in the GO graph, which reflects the level of specificity of terms in which the user is most interested. This choice also determines the level in the GO graph at which the procedure has most power. We prove that the procedure strongly controls the family-wise error rate without any additional assumptions on the joint distribution of the test statistics used. We also present an algorithm to calculate multiplicity-adjusted P-values. Because the focus level procedure preserves the structure of the GO graph, it does not generally preserve the ordering of the raw P-values in the adjusted P-values.Availability: The focus level procedure has been implemented in the globaltest and GlobalAncova packages, both of which are available on www.bioconductor.org.Contact: j.j.goeman@lumc.nlSupplementary information: Supplementary data are available at Bioinformatics online.
Predicting disulfide bond connectivity in proteins by correlated mutations analysis
Authors: Rubinstein Rotem , Fiser Andras 
Published: January 2008

Abstract
Motivation: Prediction of disulfide bond connectivity facilitates structural and functional annotation of proteins. Previous studies suggest that cysteines of a disulfide bond mutate in a correlated manner.
Results: We developed a method that analyzes correlated mutation patterns in multiple sequence alignments in order to predict disulfide bond connectivity. Proteins with known experimental structures and varying numbers of disulfide bonds, and that spanned various evolutionary distances, were aligned. We observed frequent variation of disulfide bond connectivity within members of the same protein families, and it was also observed that in 99% of the cases, cysteine pairs forming non-conserved disulfide bonds mutated in concert. Our data support the notion that substitution of a cysteine in a disulfide bond prompts the substitution of its cysteine partner and that oxidized cysteines appear in pairs. The method we developed predicts disulfide bond connectivity patterns with accuracies of 73, 69 and 61% for proteins with two, three and four disulfide bonds, respectively.
Contact: rrubinst@aecom.yu.edu, andras@fiserlab.org
BEN: a novel domain in chromatin factors and DNA viral proteins
Authors: Abhiman Saraswathi , Iyer Lakshminarayan M. , Aravind L. 
Published: January 2008

Abstract
We report a previously uncharacterized α-helical module, the BEN domain, in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Contextual analysis suggests that the BEN domain mediates protein–DNA and protein–protein interactions during chromatin organization and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role for them in organization of viral DNA during replication or transcription.
Contact: aravind@ncbi.nlm.nih.gov
Supplementary information: Supplementary data for this study can also be accessed at http://www.ncbi.nlm.nih.gov/CBBresearch/Lakshmin/BEN/
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion
Authors: Birin Hadas , Gal-Or Zohar , Elias Isaac , Tuller Tamir 
Published: January 2008

Abstract
Motivation: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input.
Results: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets.
Availability: The code is available from the authors upon request.
Contact: tamirtul@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Minimum landing size for Northeast Atlantic stocks of deep-water red crab, Chaceon affinis (Milne Edwards and Bouvier, 1894)
Authors: Robinson Martin 
Published: January 2008

Abstract
Robinson, M. 2008. Minimum landing size for Northeast Atlantic stocks of deep-water red crab, Chaceon affinis (Milne Edwards and Bouvier, 1894). – ICES Journal of Marine Science, 65: 148–154. Annual landings of the deep-water red crab (Chaceon affinis) in the NE Atlantic have fluctuated around 1000 t for much of the past decade, but they dropped significantly in 2006. No EU or National Member State legislation governs the harvest of the species, and because of the on-board processing, it is difficult to set a single minimum landing size (MLS) based on carapace width (CW) alone. As the claws are detached during processing and represent the most valuable component of the catch, a supplementary MLS based on claw length (CL) for onshore inspection and enforcement would seem appropriate. Physiological size-at-maturity and morphometric claw data were used to derive primary (CW) and secondary (CL) MLS. All males and females are mature at 110 and 125 mm CW, respectively, and 50% of females are mature at 109 mm CW. Because of a lack of information relating to the biology, distribution, and fishing mortality of the species, and a doubt as to real landing statistics, a conservative MLS of 120 mm CW and 72 mm CL is suggested, representing the first use of commercial fisheries data to suggest MLS for this otherwise unregulated fishery.
AnAGAMOUS-Related MADS-Box Gene,XAL1(AGL12), Regulates Root Meristem Cell Proliferation and Flowering Transition in Arabidopsis
Authors: Tapia-López Rosalinda , García-Ponce Berenice , Dubrovsky Joseph G. , Garay-Arroyo Adriana , Pérez-Ruíz Rigoberto V. , Kim Sun-Hyung , Acevedo Francisca , Pelaz Soraya , Alvarez-Buylla Elena R. 
Published: January 2008

AbstractMADS-box genes are key components of the networks that control the transition to flowering and flower development, but their role in vegetative development is poorly understood. This article shows that the sister gene of the AGAMOUS (AG) clade, AGL12, has an important role in root development as well as in flowering transition. We isolated three mutant alleles for AGL12, which is renamed here as XAANTAL1 (XAL1): Two alleles, xal1-1 and xal1-2, are in Columbia ecotype and xal1-3 is in Landsberg erecta ecotype. All alleles have a short-root phenotype with a smaller meristem, lower rate of cell production, and abnormal root apical meristem organization. Interestingly, we also encountered a significantly longer cell cycle in the strongest xal1 alleles with respect to wild-type plants. Expression analyses confirmed the presence of XAL1 transcripts in roots, particularly in the phloem. Moreover, XAL1∷β-glucuronidase expression was specifically up-regulated by auxins in this tissue. In addition, mRNA in situ hybridization showed that XAL1 transcripts were also found in leaves and floral meristems of wild-type plants. This expression correlates with the late-flowering phenotypes of the xal1 mutants grown under long days. Transcript expression analysis suggests that XAL1 is an upstream regulator of SOC, FLOWERING LOCUS T, and LFY. We propose that XAL1 may have similar roles in both root and aerial meristems that could explain the xal1 late-flowering phenotype.
Electropolymerization and corrosion protection of polyaniline and its copolymer on carbon steel
Authors: Srikanth A.P. , Raman V. , Tamilselvi S. , Nanjundan S. , Rajendran N. 
Published: January 2008

PurposeThis paper aims to investigate the protection efficiency of a thin film of electrochemically synthesized conducting polymers, such as poly m‐toluidine, poly N‐methyl aniline, and its copolymer, poly (aniline‐co‐N‐methyl aniline) (PANINMA), on plain carbon steel in 0.1 M HCl. It also attempts to compare the protection efficiency of these compounds with polyaniline (PANI)‐coated carbon steel.Design/methodology/approachThe green coloured and adherent coatings were obtained by cyclic voltammetry during sequential scanning of the potential region between −0.6 and 1.6 V at a scan rate of 10 mVs−1. Potentiodynamic polarization measurement (DC) was used to obtain an estimate of the corrosion rate and protection efficiency for these electrodeposited polymers on the carbon steel. Scanning electron micrographs (SEM) also were obtained to characterize the deposited coatings.FindingsIt was observed that these polymer coatings showed better protection efficiency than the PANI coating. Of the compounds studied, the copolymer PANINMA coating showed higher protection efficiency than other coatings. The SEM observations revealed that the compact continuous dense morphology of PANINMA provided better protection than other coatings.Originality/valueThis paper explains the protection efficiency of the substituted and copolymer coatings of PANI on carbon steel.
Failure investigation of stainless steel piping in a sulphur recovery unit of a gas‐processing plant
Authors: Cherian V. , Srivastava S.K. , Katarki M.V. 
Published: January 2008

PurposeThis paper seeks to determine the causes and mechanism of failure of stainless steel piping in a sulphur recovery unit of a gas‐processing plant and to recommend suitable measures to avoid recurrences.Design/methodology/approachThe integrity of the material of construction was verified using various laboratory and analytical techniques. Standard metallographic techniques were used to prepare representative samples obtained from failed stainless steel piping for metallurgical evaluation. Microstructural characterization was carried out in an inverted metallurgical microscope equipped with an imaging facility. Elemental analysis and hardness were used to confirm the identification of the material. Corrosion product/deposits were analyzed using wet chemistry supported by X‐ray diffraction analysis. Microbes were enumerated through standard methods.FindingsThe piping failed due to severe pitting corrosion, which resulted in the formation of holes. Microbial‐induced corrosion (MIC) and under‐deposit corrosion were chief contributing factors that caused the failure in stainless steel piping. In addition, the HAZ near welds at some places was found to be sensitized causing accelerated pitting corrosion at these sites.Practical implicationsThe expected service life of stainless steel piping could not be realized as the piping failed due to the combined effect of MIC and under‐deposit corrosion. Periodic monitoring of sulphate‐reducing bacteria and sulphur‐oxidizing bacteria coupled with implementation of an effective biocide treatment programme in process fluid was recommended, together with the introduction of a procedure for frequent cleaning of the pipe walls to minimize under‐deposit attack.Originality/valueThe paper – a technical case study of process industry – provides an account of failure investigation. It identifies the causes and mechanism of failure and suggests suitable preventive and corrective measures. This is useful industrial experience that provides valuable information for process and plant corrosion engineers involved in the operation of this type of equipment.
A study of the influence of chloride ion concentration on the corrosion behavior of carbon steel in phosphate high‐temperature boiler water chemistries
Authors: Shun'an Cao , Qing Zhu , Zhixin Zhang 
Published: January 2008

PurposeThis paper sets out to study the corrosion of No. 20 carbon steel without film and with films of different qualities in high‐temperature boiler water with different Cl− concentrations.Design/methodology/approachThe static simulated experiment in high‐pressure autoclave and the surface analysis methods of EPMA and XRD were carried out to study the corrosion effect.FindingsUnder the following conditions: T=360±3°C, pH = 9.40±0.10, cO2<0.020 mg/l, the density of pitting corrosion on specimens without a protective film increased with the increase of CCl− content, while CCl− was > 0.2 mg/l. The film on specimens with integral films would not dissolve observably even until the CCl− concentration was as high as 0.8 mg/l. Films with corrosion pits would begin dissolving when the Cl− concentration reached 0.4 mg/l. The main constituents of the oxidative films in the gas and liquid phases both were Fe3O4.Practical implicationsIn order to prevent carbon steel from corroding in boiler water containing Cl− under conditions of low‐phosphate and low‐sodium hydroxide treatment, the concentration of Cl− should be strictly controlled.Originality/valueIt was found that the presence of excessive Cl− in boiler water accelerated the corrosion of No. 20 carbon steel and the maximum permissible concentration of Cl− under the conditions (temperature and pressure) of sub‐critical drum boilers was 0.2 mg/l. The research results can provide theoretical guidelines for preventing the facilities of power plants from corroding.
Safari books online: currency, usage and book release policies of an e‐book database
Authors: Stephens Jane , Melgoza Pauline , Wan Gang (Gary) 
Published: January 2008

PurposeThe purpose of this paper is to determine the overall currency of electronic books in the Safari database; to determine currency and release policies of the individual publishers who contribute books to the Safari database; to compare the usage patterns of Safari books to their print counterparts at Texas A&M University; and to discuss the impact of the Safari e‐book collection and chosen purchase model upon collection management at the university.Design/methodology/approachTo determine currency of titles in Safari, the availability of the most recent edition of a title in the Safari database was checked against the availability of the print edition on the publisher's website. To determine the publishers' release policies, a questionnaire was developed and e‐mailed to them.FindingsOf the titles in the Safari database 98.4 percent were the most current edition available. Release policies of the major Safari publishers (O'Reilly and Pearson) indicate that the electronic version of a title is released when the print version is sent to press. No Starch Press, a minor Safari publisher releases its books in Safari 90 days after the print goes on sale. Thomson would not make this information public and the remainder did not respond to the questionnaire.Practical implicationsSubscription to the Safari database (current file) makes available to multiple users the most current computer science and information technology books released by popular publishers. It eliminates the need to expend funds for multiple and replacement copies of this highly requested material.Originality/valueThe current file purchase model assumes that the most recent editions of these popular books are available in Safari. The study indicates that librarians and patrons can be assured that they are accessing the most current editions available.
A survey of manufacturing engineering databases
Authors: Osorio Nestor L. , Otieno Andrew W. 
Published: January 2008

PurposeThe purpose of this paper is to examine current databases available for manufacturing engineering and summarizes their relevance.Design/methodology/approachTo promote research in manufacturing engineering, comprehensive literature should be made accessible through relevant databases. Databases not only provide information on global research but aid in assessing the impacts of research and identify promising research directions. The databases are presented in eight sections according to the type of document being sought.FindingsThe manufacturing engineering literature is robust; there are excellent products available to support this highly technical field. The databases found are from many different sources: commercial publishers, professional organizations, national and international agencies, and collaborative endeavors.Research limitations/implicationsSources found originate mainly from the USA and Europe.Originality/valueThis paper demonstrates the importance of literature mining in manufacturing engineering which is ingrained in the processes to designing, developing and producing goods and services. It is also a teaching tool for students, a guide to professional engineers, and a valuable resource for librarians.
Project portfolio management for product innovation
Authors: Killen Catherine P. , Hunt Robert A. , Kleinschmidt Elko J. 
Published: January 2008

PurposeThe purpose of this paper is to create a benchmark and identify best practices for Project Portfolio Management (PPM) for both tangible product‐based and service product‐based development project portfolios.Design/methodology/approachA questionnaire was developed to gather data to compare the PPM methods used, PPM performance, PPM challenges, and resulting new product success measures in 60 Australian organisations in a diverse range of service and manufacturing industries.FindingsThe paper finds that PPM practices are shown to be very similar for service product development project portfolios and tangible product development project portfolios. New product success rates show strong correlation with measures of PPM performance and the use of some PPM methods is correlated with specific PPM performance outcomes.Research limitations/implicationsThe findings in this paper are based on a survey of a diverse sample of 60 Australian organisations. The results are strengthened by comparisons with similar North American research; however, they may not be representative of all environments. Research in other regions would further qualify the findings. As each organisation's PPM process is unique, case study methods are recommended for future studies to capture more of the complexity in the environment.Practical implicationsThe paper shows that PPM practitioners and executives who make decisions about the development of tangible products and/or service products will benefit from the findings.Originality/valueThis paper extends the existing understanding of PPM practices to include service development project portfolios as well as tangible product development project portfolios and strengthens the links between PPM practices and outcomes.
Risk management in a multi‐project environment
Authors: Olsson Rolf 
Published: January 2008

PurposeThe purpose of this paper is to identify differences in managing a single project compared with that of a project portfolio, where focus and requirements are expanded, and where clear links to organizational objectives exist. Further, the aim is to propose a methodology for the management of risk within the context of a project portfolio.Design/methodology/approachThe concepts and framework described in this paper have emerged primarily from an in‐depth action research study in a major provider of transport solutions. The work has been conducted within one division, with presence in most of mainland Europe, Scandinavia, and the UK.FindingsThe paper finds that the proposed methodology would manage portfolio risk in two ways. First, it provides a means for single projects to gain experiences from other projects within the portfolio. Second, portfolio common risks and trends of issues can be identified. Such risks can become risks for succeeding projects, or require action from outside the single project.Research limitations/implicationsThe paper shows that the pilot study consisted of 16 projects within one project portfolio. Other project portfolios, with other prerequisites, might result in different findings, since some factors not included in this research such as cultural aspects or organizational factors could affect the findings.Practical implicationsIn this paper the identification and analysis of commonalities and risk trends between projects provide the possibility to manage risks from a portfolio perspective.Originality/valueThe paper sees that existing risk management processes do not support projects in managing risk within a project portfolio. Instead, the proposed methodology provides the project portfolio manager with a consolidated view of the total risk exposure within the portfolio. Additionally, this methodology finds risks and trends not otherwise possible to identify.
Modelling resource allocation of R&D project portfolios using a multi‐criteria decision‐making methodology
Authors: Morcos Maged S. 
Published: January 2008

PurposeThe purpose of this paper is to outline a structured Multi‐Criteria Decision Making (MCDM) methodology to help organisations efficiently allocate limited resources (investments in this case) to different R&D projects within attainable project portfolio strategy packages and select the efficient portfolios that align R&D investments to the corporate long‐term objectives.Design/methodology/approachIn this paper a case study is used to present a proposed multi‐criteria methodology approach for project resource allocation. The method provides the decision maker with an ability to easily assess the impact of trading off R&D project portfolios tangible benefits (short‐term profits) and intangible benefits (reliability and risk) against constrained budget resources (investment costs), without the requirement for sophisticated and time‐consuming mathematical formulations.FindingsSuperior findings are achieved when decisions are assisted by computer‐based MCDM methodology.Practical implicationsThe paper shows that the concept embodied in this multi‐criteria approach is applied in a case study to identify and select the efficient R&D project portfolios of a multi‐national manufacturing company.Originality/valueThe novelty of this paper lies in applying a multi‐criteria methodology that offers an integrated framework that allows efficient modelling of resource allocation of project portfolios. The ultimate benefit of this work can be seen in its dual effect of specifying efficient R&D projects within different attainable portfolio packages and in defining appropriate R&D investment strategies based on trading off benefits against organisationally constrained budget resources.