bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of zinc-binding sites in proteins from sequence
Authors: Shu Nanjiang , Zhou Tuping , Hovmöller Sven 
Published: February 2008

AbstractMotivation: Motivated by the abundance, importance and unique functionality of zinc, both biologically and physiologically, we have developed an improved method for the prediction of zinc-binding sites in proteins from their amino acid sequences.Results: By combining support vector machine (SVM) and homology-based predictions, our method predicts zinc-binding Cys, His, Asp and Glu with 75% precision (86% for Cys and His only) at 50% recall according to a 5-fold cross-validation on a non-redundant set of protein chains from the Protein Data Bank (PDB) (2727 chains, 235 of which bind zinc). Consequently, our method predicts zinc-binding Cys and His with 10% higher precision at different recall levels compared to a recently published method when tested on the same dataset.Availability: The program is available for download at www.fos.su.se/~nanjiang/zincpred/download/Contact: svenh@struc.su.seSupplementary information: All Supplementary Data can be accessed at www.fos.su.se/~nanjiang/zincpred/suppliment
Model-based Bayesian clustering (MBBC)
Authors: Joo Yongsung , Booth James G. , Namkoong Younghwan , Casella George 
Published: February 2008

Abstract
Motivation: The program MBBC 2.0 clusters time–course microarray data using a Bayesian product partition model.
Results: The Bayesian product partition model in Booth et al. (2007) simultaneously searches for the optimal number of clusters, and assigns cluster memberships based on temporal changes of gene expressions. MBBC 2.0 to makes this method easily available for statisticians and scientists, and is built with three free computer language software packages: Ox, R and C++, taking advantage of the strengths of each language. Within MBBC, the search algorithm is implemented with Ox and resulting graphs are drawn with R. A user-friendly graphical interface is built with C++ to run the Ox and R programs internally. Thus, MBBC users are not required to know how to use Ox, R or C++, but they must be pre-installed.
Availability: A self-extractable zip file, MBBC20zip.exe, is available at the MBBC webpage www.stat.ufl.edu/~casella/mbbc/, which contains MBBC.exe, source files, and all other related files. The current version works only in the Windows operating system. A free installation program and overview for Ox is available at www.doornik.com. A detailed installation guide for Ox is provided by MBBC, and is accessible without installing Ox. R is available at www.r-project.org/.
Contact: casella@stat.ufl.edu
De novo identification of highly diverged protein repeats by probabilistic consistency
Authors: Biegert A. , Söding J. 
Published: February 2008

Abstract
Motivation: An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments.
Results: We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane β-barrels. HHrepID uses HMM–HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance.
Availability: Server: http://toolkit.tuebingen.mpg.de/hhrepid; Executables: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHrepID
Contact: soeding@lmb.uni-muenchen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian models based on test statistics for multiple hypothesis testing problems
Authors: Ji Yuan , Lu Yiling , Mills Gordon B. 
Published: February 2008

AbstractMotivation: We propose a Bayesian method for the problem of multiple hypothesis testing that is routinely encountered in bioinformatics research, such as the differential gene expression analysis. Our algorithm is based on modeling the distributions of test statistics under both null and alternative hypotheses. We substantially reduce the complexity of the process of defining posterior model probabilities by modeling the test statistics directly instead of modeling the full data. Computationally, we apply a Bayesian FDR approach to control the number of rejections of null hypotheses. To check if our model assumptions for the test statistics are valid for various bioinformatics experiments, we also propose a simple graphical model-assessment tool.Results: Using extensive simulations, we demonstrate the performance of our models and the utility of the model-assessment tool. In the end, we apply the proposed methodology to an siRNA screening and a gene expression experiment.Contact: yuanji@mdanderson.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Effects of climate and overfishing on zooplankton dynamics and ecosystem structure: regime shifts, trophic cascade, and feedback loops in a simple ecosystem
Authors: Möllmann Christian , Müller-Karulis Bärbel , Kornilovs Georgs , St John Michael A. 
Published: February 2008

Abstract
Möllmann, C., Müller-Karulis, B., Kornilovs, G., and St John, M. A. 2008. Effects of climate and overfishing on zooplankton dynamics and ecosystem structure: regime shifts, trophic cascade, and feeback loops in a simple ecosystem. – ICES Journal of Marine Science, 65: 302–310. The Central Baltic Sea is the largest brackish waterbody in the world ocean, containing a highly productive but low-diversity ecosystem. Climate-induced changes in hydrography recently caused an ecosystem regime shift with changes at all trophic levels. The most pronounced changes in the ecosystem occurred at the zooplankton and fish trophic levels. In the zooplankton, dominance changed between the copepods Pseudocalanus acuspes and Acartia spp., a result of reduced salinities and increased temperatures. The change in hydrography also affected the reproductive success of the major fish species, resulting in a change in dominance from the piscivorous cod (Gadus morhua) to the planktivorous sprat (Sprattus sprattus). First, we investigate statistically the occurrence of regime shifts in time-series of key hydrographic variables and the biomass time-series of key species. Second, we demonstrate a three-level trophic cascade involving zooplankton. Finally, we model the ecosystem effects of the abiotic and biotic changes on copepod biomass and recruitment of fish stocks. Our results demonstrate the linkage between climate-induced zooplankton and fish regime changes, and how overfishing amplified the climate-induced changes at both trophic levels. Hence, our study demonstrates (i) the multiple pathways along which climatic and anthropogenic pressures can propagate through the foodweb; (ii) how both effects act synergistically to cause and stabilize regime changes; and (iii) the crucial role of zooplankton in mediating these ecosystem changes.
An analysis of phase change material as thermal mass
Authors: Richardson M.J , Woods A.W 
Published: February 2008

Temperature fluctuations within a building can be attenuated by thermal mass. Adding phase change material (PCM) to thermal mass increases the effective heat capacity during the phase transition. This can anchor the temperature of the mass in a narrow band around the melting point of the PCM, further reducing the temperature swings perceived by occupants of the room. A simple dimensionless model for thermal mass forced by a sinusoidally varying air temperature is developed to calculate the performance of the PCM. The mass temperature satisfies the heat equation, with a temperature-dependent thermal diffusivity, and is solved numerically.
For a given PCM, the energy stored and returned to the room, the surface temperature amplitude and the penetration depth of heat pulses into a hypothetical semi-infinite mass can all be calculated as a function of a single dimensionless parameter. For optimal performance, the latent heat of the PCM should be as large as possible, the melting temperature range should be narrow and the thickness of the mass should exceed the penetration depth. The PCM wallboard is shown to be potentially as effective as conventional concrete, so lightweight buildings could enjoy the benefits of thermal inertia commonly associated with heavyweight structures.
Preparation and Hydrolysis of Digoxygenin-Labeled Probes for In Situ Hybridization of Plant Tissues
Authors: Ferrandiz Cristina , Sessions Allen 
Published: February 2008

INTRODUCTIONAntisense RNA is typically labeled using digoxygenin (DIG), which is subsequently detected with an anti-DIG antibody coupled to alkaline phosphatase. This protocol describes the synthesis and hydrolysis of a DIG-labeled probe to be used for in situ hybridization.
Immunohistochemistry on Sections of Plant Tissues Using Alkaline-Phosphatase-Coupled Secondary Antibody
Authors: Sessions Allen 
Published: February 2008

INTRODUCTIONLike RNA, proteins can be localized in situ on tissue sections. In situ localization or immunohistochemistry provides information on the cellular and subcellular distribution of proteins in different tissues. This protocol describes an alternative to the use of ABC (a preformed Avidin:Biotinylated enzyme Complex used in conjunction with a biotinylated secondary antibody) for non-fluorescent detection in immunohistochemistry. Here, an alkaline-phosphatase-coupled secondary antibody is used with colorimetric substrates for antigen detection.
Herbivore-Induced Callose Deposition on the Sieve Plates of Rice: An Important Mechanism for Host Resistance
Authors: Hao Peiying , Liu Caixiang , Wang Yuanyuan , Chen Rongzhi , Tang Ming , Du Bo , Zhu Lili , He Guangcun 
Published: February 2008

Abstract
The brown planthopper (Nilaparvata lugens Stål; BPH) is a specialist herbivore on rice (Oryza sativa) that ingests phloem sap from the plant through its stylet mouthparts. Electronic penetration graphs revealed that BPH insects spent more time wandering over plants carrying the resistance genes Bph14 and Bph15, but less time ingesting phloem than they did on susceptible plants. They also showed that their feeding was frequently interrupted. Tests with [14C]sucrose showed that insects ingested much less phloem sap from the resistant than the susceptible plants. BPH feeding up-regulated callose synthase genes and induced callose deposition in the sieve tubes at the point where the stylet was inserted. The compact callose remained intact in the resistant plants, but genes encoding β-1,3-glucanases were activated, causing unplugging of the sieve tube occlusions in susceptible plants. Continuing ingestion led to a remarkable reduction in the susceptible plants' sucrose content and activation of the RAmy3D gene, leading to starch hydrolysis and ultimately carbohydrate deprivation in the plants. Our results demonstrate that BPH feeding induces the deposition of callose on sieve plates in rice and that this is an important defense mechanism that prevents insects from ingesting phloem sap. In response, however, the BPH can unplug sieve tube occlusions by activating β-1,3-glucanase genes in rice plants.
Robust stabilization of input‐delayed systems with design example for rocket motor control
Authors: Jafarov Elbrous M. 
Published: February 2008

PurposeThis paper aims to use a new design approach based on a Lagrange mean value theorem for the stabilization of multivariable input‐delayed system by linear controller.Design/methodology/approachThe delay‐dependent asymptotical stability conditions are derived by using augmented Lyapunov‐Krasovskii functionals and formulated in terms of conventional Lyapunov matrix equations and some simple matrix inequalities. Proposed design approach is extended to robust stabilization of multi‐variable input‐delayed systems with unmatched parameter uncertainties. The maximum upper bound of delay size is computed by using a simple optimization algorithm.FindingsA liquid monopropellant rocket motor with a pressure feeding system is considered as a numerical design example. Design example shows the effectiveness of the proposed design approach.Research limitations/implicationsThe proposed approach can be used in the analysis and design of the uncertain multivariable time‐delay systems.Originality/valueThe paper has a great potential in the stability analysis of time‐delay systems and design of time‐delay controllers and may openup a new direction in this area.
Food processing: barriers to, or opportunities for, organic foods in the catering sector?
Authors: Post Anna , Shanahan Helena , Jonsson Lena 
Published: February 2008

PurposeThe aim of this article is to examine whether food processing is a limitation when using organic potatoes and tubers and to suggest which catering category is most likely to purchase processed organic products.Design/methodology/approachA nationwide questionnaire was distributed by post to 808 Swedish catering managers in five categories: commercial restaurants, fast food restaurants, school canteens, day care centres, and homes for the elderly. The results were analysed on the basis of size and category.FindingsThe demand for processed organic potatoes and tubers differs between sizes and categories, and various catering units require different types of processing. Catering units in the public food sector also face a dilemma in terms of rationalised production systems and the ideological concerns about organic foods.Research limitations/implicationsFurther studies on ideological concerns and rationalised production systems are required.Originality/valueThe paper shows that product development should take place in cooperation between all actors in the food supply system and be adjusted to fit each specific catering category.
Wine origin and organic elaboration, differentiating strategies in traditional producing countries
Authors: Bernabéu Rodolfo , Brugarolas Margarita , Martínez‐Carrasco Laura , Díaz Mónica 
Published: February 2008

PurposeThis article aims to analyse various wine differentiation strategies (price, origin, type and production system) to counteract the commercial success of new wine producers compared to traditional ones.Design/methodology/approachThe methodology consisted of a survey of 400 Castilla‐La Mancha wine consumers during the month of March 2004, whose preferences were determined through several multivariate techniques.FindingsThree consumer segments were identified: the first shops for wine mainly by price, the second, by origin and the third, by a combination of price and type of wine. In this sense, except for the first segment, where competition by a cheaper wine from other places could endanger the local market, possible strategies would be to continue emphasising origin in a traditional approach and to search for a new wine differentiation based on organic production. Both strategies, which can be carried out jointly, would require government backing in addition to support from the business sector.Originality/valueThis paper contributes to a greater knowledge of Spanish consumer habits by analysing the degree of influence that various factors have on attitudes towards the purchasing of wine.
Grocery lists: connecting family, household and grocery store
Authors: Bassett Raewyn , Beagan Brenda , Chapman Gwen E. 
Published: February 2008

PurposeThis paper aims to investigate grocery list use in the lives of participant families in a study on decision making about food choices and eating practices.Design/methodology/approachA total of 46 families from three ethno‐cultural groups living in two regions in Canada participated in the study: in British Columbia, 12 Punjabi Canadian and 11 European Canadian families; in Nova Scotia, 13 African Canadian and ten European Canadian families. In each family, at least three individuals over the age of 13 years, one of whom was a woman between the ages of 25 and 55 years, were interviewed. Researchers participated in a meal and accompanied each family on a grocery trip.FindingsMost family members contributed to a grocery list. The shopper(s) in the family may take the written list with them, have the list in memory, use a combination of both memory and written list, or shop without a list. Finds the articulation of taken‐for‐granted, intersecting knowledge about family, household and grocery store, necessary to the compilation of a list, were largely unseen, unrecognised, and undervalued.Originality/valueStudies on grocery lists have focused on who uses lists, how they are used, and what their use says about consumers. In the literature, non‐list use is conflated with the absence of a tangible grocery list. Shows that lack of a tangible list does not mean absence of a list in all cases. Further, extends and contextualises existing literature, showing that grocery list compilation relies upon interrelated knowledge of family, household and store.
Dietary fibre in human nutrition: the problem of providing nutrition advice
Authors: Sibbel Anne 
Published: February 2008

PurposeThe aim of this paper to explain the difficulties associated with applying the science of nutrition in formulating advice to protect public health, using the example of dietary fibre.Design/methodology/approachBased on this review of relevant literature published between 1953 and 2006, the first section traces the history of attempts at constructing useful definitions of dietary fibre. Then the problems of measurement of the fibre content of foods, measurement of fibre intake in individuals and with testing for correlations with disease, are outlined.FindingsThe equivocal nature of current definitions of dietary fibre, and the lack of accuracy, validity or reliability of methods of determination, have been major limitations to developing an understanding its role in protecting human health. Perhaps more than for any other dietary constituent, the elucidation of the science describing the role of dietary fibre in human nutrition has been confounded by both known and unidentified variables.Practical implicationsThis paper reflects an increasing scientific awareness that developments in nutrition are subject to the limitations of methods of analysis and research design. It explains why the processes of scientific investigation are often slow to reveal important relationships between dietary factors and health. This presents some difficulties for authorities charged with promoting health protective eating behaviours.Originality/valueAlthough it has not been possible to unequivocally quantify dietary fibre or its effects on human metabolism, the research provides strong support for choosing a wide range of fresh or minimally intact plant food sources to protect health, as recommended in the FBDG's promoted in many countries around the world. The health protective effects may be achieved with moderation of the information disseminated about dietary fibre, particularly via the marketing of manufactured foods supplemented with fibre isolates.
Different roles, different perspectives: perceptions about the purpose of training needs analysis
Authors: Bowman Jill , Wilson John P. 
Published: February 2008

PurposeThis paper aims to investigate the experiences of managers who underwent a training needs analysis (TNA) within a large bus transport company. It compares their perceptions of the TNA process with two external groups of training managers and training consultants. Recommendations are made to address and reconcile the differing interpretations and misunderstandings which occur between the different groups about TNA.Design/methodology/approachThe approach uses qualitative grounded theory to identify the main perspectives about the purpose of training needs analysis.FindingsThe findings are that business needs are the main focus of the TNA. The various actors in the TNA process should be aware of their part in the process. Line managers should receive instruction in TNA.Originality/valueThe article addresses the similarities and differences which are found among training managers, training consultants, and managers who were recipients of training needs analysis.
Information science: an interdisciplinary effort?
Authors: Adam Holland George 
Published: February 2008

PurposeThe purpose of this paper is to investigate the nature of collaboration within information science, to argue for distinct meanings for interdisciplinary and multidisciplinary research and to answer two questions: What philosophic distinction can be made between inter‐ and multi‐disciplinary efforts? Is one more valuable than the other to information science research?Design/methodology/approachThe semantic inconsistency for describing collaboration is identified in information science. Philosophic analysis of the terms interdisciplinary and multidisciplinary is conducted, arguing for distinct meanings. A case study through cognitive science exploring the philosophic meanings is developed.FindingsInterdisciplinarity and multidisciplinarity are very distinct in terms of methods and frameworks. Interdisciplinary research has longer‐term benefits for information science, but multidisciplinary research can also fulfil valid collaborative roles in information science.Research limitations/implicationsA brief technical discussion of cognitive science theory lends itself to those interested in cognitive science. The paper is philosophic in nature.Practical implicationsThe inconsistencies surrounding the terms interdisciplinary and multidisciplinary have impact on professional practice. The argument for more consistent terminology will introduce more semantic integrity and reduce miscommunication. There is a challenge to engage in more interdisciplinary research and practice within information science.Originality/valueCollaboration is a common term used, but little research into what it precisely means within information science has been conducted. The paper argues for a clear distinction between various types of collaboration, and provides a case study with cognitive science.