bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB
Authors: Xu Qifang , Dunbrack Roland L. 
Published: September 2012

AbstractMotivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed.Results: We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM–HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains &gt;50 residues.Availability: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.Contact: Roland.Dunbracks@fccc.edu
CSB: a Python framework for structural bioinformatics
Authors: Kalev Ivan , Mechelke Martin , Kopec Klaus O. , Holder Thomas , Carstens Simeon , Habeck Michael 
Published: September 2012

Abstract
Summary: Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice.
Availability: Stable release packages are available for download from the Python Package Index (PyPI) as well as from the project’s website http://csb.codeplex.com.
Contacts: ivan.kalev@gmail.com or michael.habeck@tuebingen.mpg.de
Rosette Tracker: An Open Source Image Analysis Tool for Automatic Quantification of Genotype Effects
Authors: De Vylder Jonas , Vandenbussche Filip , Hu Yuming , Philips Wilfried , Van Der Straeten Dominique 
Published: September 2012

Abstract
Image analysis of Arabidopsis (Arabidopsis thaliana) rosettes is an important nondestructive method for studying plant growth. Some work on automatic rosette measurement using image analysis has been proposed in the past but is generally restricted to be used only in combination with specific high-throughput monitoring systems. We introduce Rosette Tracker, a new open source image analysis tool for evaluation of plant-shoot phenotypes. This tool is not constrained by one specific monitoring system, can be adapted to different low-budget imaging setups, and requires minimal user input. In contrast with previously described monitoring tools, Rosette Tracker allows us to simultaneously quantify plant growth, photosynthesis, and leaf temperature-related parameters through the analysis of visual, chlorophyll fluorescence, and/or thermal infrared time-lapse sequences. Freely available, Rosette Tracker facilitates the rapid understanding of Arabidopsis genotype effects.
Characterization of the procera Tomato Mutant Shows Novel Functions of the SlDELLA Protein in the Control of Flower Morphology, Cell Division and Expansion, and the Auxin-Signaling Pathway during Fruit-Set and Development
Authors: Carrera Esther , Ruiz-Rivero Omar , Peres Lazaro Eustaquio Pereira , Atares Alejandro , Garcia-Martinez Jose Luis 
Published: September 2012

Abstract
procera (pro) is a tall tomato (Solanum lycopersicum) mutant carrying a point mutation in the GRAS region of the gene encoding SlDELLA, a repressor in the gibberellin (GA) signaling pathway. Consistent with the SlDELLA loss of function, pro plants display a GA-constitutive response phenotype, mimicking wild-type plants treated with GA3. The ovaries from both nonemasculated and emasculated pro flowers had very strong parthenocarpic capacity, associated with enhanced growth of preanthesis ovaries due to more and larger cells. pro parthenocarpy is facultative because seeded fruits were obtained by manual pollination. Most pro pistils had exserted stigmas, thus preventing self-pollination, similar to wild-type pistils treated with GA3 or auxins. However, Style2.1, a gene responsible for long styles in noncultivated tomato, may not control the enhanced style elongation of pro pistils, because its expression was not higher in pro styles and did not increase upon GA3 application. Interestingly, a high percentage of pro flowers had meristic alterations, with one additional petal, sepal, stamen, and carpel at each of the four whorls, respectively, thus unveiling a role of SlDELLA in flower organ development. Microarray analysis showed significant changes in the transcriptome of preanthesis pro ovaries compared with the wild type, indicating that the molecular mechanism underlying the parthenocarpic capacity of pro is complex and that it is mainly associated with changes in the expression of genes involved in GA and auxin pathways. Interestingly, it was found that GA activity modulates the expression of cell division and expansion genes and an auxin signaling gene (tomato AUXIN RESPONSE FACTOR7) during fruit-set.
Altered Starch Turnover in the Maternal Plant Has Major Effects on Arabidopsis Fruit Growth and Seed Composition
Authors: Andriotis Vasilios M.E. , Pike Marilyn J. , Schwarz Sabine L. , Rawsthorne Stephen , Wang Trevor L. , Smith Alison M. 
Published: September 2012

Abstract
Mature seeds of both the high-starch starch-excess1 (sex1) mutant and the almost starchless phosphoglucomutase1 mutant of Arabidopsis (Arabidopsis thaliana) have 30% to 40% less lipid than seeds of wild-type plants. We show that this is a maternal effect and is not attributable to the defects in starch metabolism in the embryo itself. Low lipid contents and consequent slow postgerminative growth are seen only in mutant embryos that develop on maternal plants with mutant phenotypes. Mutant embryos that develop on plants with wild-type starch metabolism have wild-type lipid contents and postgerminative growth. The maternal effect on seed lipid content is attributable to carbohydrate starvation in the mutant fruit at night. Fruits on sex1 plants grow more slowly than those on wild-type plants, particularly at night, and have low sugars and elevated expression of starvation genes at night. Transcript levels of the transcription factor WRINKLED1, implicated in lipid synthesis, are reduced at night in sex1 but not in wild-type seeds, and so are transcript levels of key enzymes of glycolysis and fatty acid synthesis. sex1 embryos develop more slowly than wild-type embryos. We conclude that the reduced capacity of mutant plants to convert starch to sugars in leaves at night results in low nighttime carbohydrate availability in the developing fruit. This in turn reduces the rate of development and expression of genes encoding enzymes of storage product accumulation in the embryo. Thus, the supply of carbohydrate from the maternal plant to the developing fruit at night can have an important influence on oilseed composition and on postgerminative growth.
Instantaneous impedance evaluation of dissolution of AISI 304 stainless steel during intergranular corrosion
Authors: Arutunow Anna 
Published: September 2012

PurposeThe purpose of this paper is to focus on diversification between electrical parameters determined on the basis of instantaneous impedance measurements within the activation and reactivation scan of dissolution of sensitized AISI 304 stainless steel during a proceeding intergranular corrosion process.Design/methodology/approachThe investigations were carried out by means of dynamic electrochemical impedance spectroscopy (DEIS). DEIS measurements were conducted “on‐line” while the samples were polarized in agreement with a measurement procedure presented in the ASTM G108‐94 standard, in order to guarantee conditions equivalent with the DL‐EPR tests performed on AISI 304 stainless steel.FindingsPerformed researches revealed the advantages of the DEIS technique over standard double‐loop electrochemical potentiokinetic reactivation (DL‐EPR) tests in the field of intergranular corrosion investigations. Application of the DEIS technique made it possible to trace instantaneous changes in the examined system's impedance versus potential during the intergranular corrosion process. The form of recorded DEIS spectra and obtained distribution of measurement frequencies within the reactivation potential range were equivalent to those obtained for pure iron dissolution in sulfuric acid medium. As a result, instantaneous changes of electrical double layer capacitance and charge transfer resistance as a function of potential have been obtained in the range of activation and reactivation scans.Originality/valueThe paper provides information regarding diversification between the electrical double layer capacitance and the charge transfer resistance determined for sensitized AISI 304 stainless steel with respect to polarization conditions during the standard DL‐EPR test, which were obtained in order to evaluate the susceptibility to intergranular corrosion.
Formation process and properties of phytic acid conversion coatings on magnesium
Authors: Liu Jian‐Rui , Guo Yi‐Na , Huang Wei‐Dong 
Published: September 2012

PurposeThe purpose of this paper is to investigate a chromium‐free conversion coating treatment for magnesium with phytic acid solution.Design/methodology/approachPure magnesium was selected for the tests. Phytic acid solution was used as the conversion solution of surface treatment. The samples of magnesium were immersed in the solution under certain conditions to form a conversion coating on the surface of magnesium. The formation process of phytic acid conversion coating was studied by detecting the open circuit potential (OCP) and weight change of the pure magnesium for different conversion treatment times. Scanning electron microscopy (SEM) and electron energy spectrum (EDS) were used to examine the morphologies and compositions of the coatings, respectively.FindingsThe experimental results showed that the conversion coating had a multideck structure with netlike morphology, which is similar in nature to chromate conversion coatings, and was composed mainly of Mg, P, O and C. The contents of C and P and the size of the cracks in different conversion layers decreased from the external layer to the inner layer. The thickness of the conversion coating varied from 1.0μm to 15μm according to the processing parameters. The hydroxyl groups and phosphate carboxyl groups in the coating, which have similar properties to an organic paint coat, are beneficial to the combination of substrate and organic paint coating. The formation mechanism and thickness variation of the conversion coatings also are discussed.Originality/valueThe paper shows that phytic acid conversion coating could improve the electrochemical properties of magnesium and provide effective protection, which can improve the corrosion resistance of magnesium.
FeB and FeB/h‐BN based anti‐corrosive composite coatings for aluminium alloys
Authors: Dikici B. , Ozdemir I. 
Published: September 2012

PurposeThe purpose of this paper is to investigate the corrosion behaviour of ferroboron (FeB) and FeB/h‐BN (hexagonal boron nitride) coatings deposited onto A383 substrates by atmospheric plasma spraying.Design/methodology/approachPotentiodynamic scanning (PDS) and electrochemical impedance spectroscopy (EIS) were used to evaluate the corrosion susceptibilities of the composite coatings. Microstructural characterizations were carried out by using scanning electron microscopy (SEM) and energy dispersion spectroscopy (EDS).FindingsIt was observed that the coatings resisted localized corrosion in NaCl solutions and protective oxide films on the coatings repaired themselves over the corrosion potential. Hexagonal‐BN is not only a limiting factor in the corrosion of the FeB based coatings. The corrosion morphologies of the coatings are strictly dependent on pores and micro‐cracks in the coating.Practical implicationsThe iron‐based borides act as solid lubricants and have a positive influence on tribological properties such as hardness, friction and corrosion of the coating.Originality/valueKnowledge of the effects of FeB on the corrosion behaviour of thermal spray coatings is still incomplete and this is the most important obstacle to the widespread use of the coatings in engineering applications. The paper reports electrochemical test results of the coatings and discusses the morphologic effects of h‐BN on the corrosion behaviour.
Corporate social responsibility: a study of savings banks
Authors: Jesús Barroso María , Galera Clementina , Valero Víctor , Mercedes Galán María 
Published: September 2012

PurposeSociety's concern about issues related to development aid to underdeveloped countries has grown significantly in recent years. The gross inequalities between North and South, constant conflicts, political crises, and natural disasters have sensitized society to the urgent need to help these depressed areas. The objective of the present study is to examine the role Spain's savings banks play in international cooperation and development as a field that society and the general public see as ever more crucial.Design/methodology/approachThe paper describes an exploratory analysis of the interventions carried out by all Spain's savings banks during 2009.FindingsThe results of this exploratory study reflect an increasingly relevant role of these savings banks in cooperation for development, mainly due to pressure from their customers and from society in general. They also show the importance of so‐called “Works in collaboration”, mainly with non‐governmental organizations/non‐governmental development organizations, in designing and implementing corporate social responsibility programs.Originality/valueMuch of the value of the present work is because of the lack of previous studies focused specifically on analyzing the role of Spanish savings banks in the field of cooperation for development. Its originality also lies in its proposing new courses of action in this area to improve that role.
A purchase intention model for foreign banks within Indonesia
Authors: Muchtar Fatimah , Kingshott Russel P.J. , Wong David , Laksamana Patria 
Published: September 2012

PurposeThis paper aims to present a conceptual model that highlights the complexities associated with foreign banks wishing to operate with the Indonesian marketplace.Design/methodology/approachThe paper is conceptual in nature and draws upon the marketing literature and theory to present a number of propositions.FindingsThe paper melds key international marketing constructs by positing that Indonesian consumers using foreign banks yield utilitarian, hedonistic and symbolic benefits. These underlying consumer outcomes are modeled into variables likely to impact purchase intentions.Research limitations/implicationsThis paper represents the first attempt to conceptualize the many challenges facing foreign banks operating within an Indonesian setting. As Indonesia has a diverse range of cultures and values systems the model highlights the considerations associated with operating in such a diverse country.Practical implicationsA number of important implications are presented for bank decision makers operating within Indonesia.Originality/valueA conceptual model is presented and the paper suggests a future research agenda applicable to both the Indonesian and wider banking context.
Market‐creating service innovation: verification and its associations with new service development and customer involvement
Authors: Cheng Colin C. , Chen Ja‐Shen , Tai Tsou Hun 
Published: September 2012

PurposeThe present study aims to develop a measure of the market‐creating service innovation (MCSI) proposed by Berry et al., verify the typology, identify the relationship between MCSI and each new service development (NSD) stage, and assess the degree to which the role of customers involved in each NSD stage contributes to each type of MCSI.Design/methodology/approachA mail survey was sent to service companies in Taiwan, the target respondents being senior managers with experience in developing successful new services in the past three years. A total of 179 usable questionnaires were collected, resulting in a respondent rate of 21.2 per cent. The responses covered a wide range of service industries.FindingsThe present study confirms that the four MCSIs proposed by Berry et al. do indeed exist in practice. The degree of association between each NSD stage and each type of MCSI varies according to MCSI type. The statistical weights for customers involved in each type of MCSI are also different.Research limitations/implicationsThis study extends a theoretical mechanism of NSD that customers indeed contribute to service innovation, but their involvement varies depending on the characteristics of the service innovation.Practical implicationsUtilizing a new scale of MCSI, service providers can evaluate what types of MCSI are a better fit for their business.Originality/valueThis study provides a better understanding of MCSI, which helps service providers to properly allocate their limited resources. In addition, this study clarifies the degree to which the values of customer involvement in NSD contribute to MCSI.
The impact of unprofitable customer abandonment on current customers' exit, voice, and loyalty intentions: an empirical analysis
Authors: Haenlein Michael , Kaplan Andreas M. 
Published: September 2012

PurposeThe management of unprofitable customer relationships and particularly their abandonment is a topic that has received increasing interest among practitioners and researchers over recent years. Within this manuscript, the authors aim to analyze the impact of unprofitable customer abandonment on the abandoning firm's current customers, specifically their exit, voice, and loyalty intentions toward the abandoning firm.Design/methodology/approachThe study is based on an online experiment conducted among 385 US customers. Respondents were allocated randomly to one of ten conditions (five levels of tie strength x two types of abandonment strategy) and exposed to a scenario describing a customer abandonment decision implemented by a mobile phone provider. The resulting data were analyzed using a combination of analysis of variance (ANOVA) and structural equation modeling.FindingsThe study shows that current customers are significantly more likely to respond actively to unprofitable customer abandonment (exit/voice) than passively through silence and loyalty. Additionally, it shows that increasing satisfaction or switching cost among current customers are unlikely to limit the potential negative consequences of unprofitable customer abandonment. The only variable that drives the choice between exit, voice, and loyalty is the perceived attractiveness of the best alternative relationship.Originality/valueThis work analyzes for the first time how existing customers that the firm would like to retain react toward the news that the company proactively terminates unprofitable customer relationships. Therefore, insight is provided into the likely cost associated with unprofitable customer abandonment – a question that has not been the subject of any empirical study as of today.
Voluntary corporate governance disclosures by post‐Apartheid South African corporations
Authors: Ntim Collins G. , Opong Kwaku K. , Danbolt Jo , Thomas Dennis A. 
Published: September 2012

PurposeThe purpose of this paper is to investigate as to whether post‐Apartheid South African (SA) listed corporations voluntarily comply with and disclose recommended good corporate governance (CG) practices and, if so, the major factors that influence such voluntary CG disclosure behaviour.Design/methodology/approachThe paper constructs a broad voluntary CG disclosure index containing 50 CG provisions from the 2002 King Report using a sample of 169 SA listed corporations from 2002 to 2006. The authors also conduct regression analysis to identify the main drivers of voluntary CG disclosure.FindingsThe results suggest that while compliance with, and disclosure of, good CG practices varies substantially among the sampled companies, CG standards have generally improved over the five‐year period examined. The authors also find that block ownership is negatively associated with voluntary CG disclosure, while board size, audit firm size, cross‐listing, the presence of a CG committee, government ownership and institutional ownership are positively related to voluntary CG disclosure.Practical implicationsThese findings have important implications for policy‐makers and regulators. Evidence of improving CG standards implies that efforts by various stakeholders at improving CG standards in SA companies have had some positive impact on CG practices of SA firms. However, the substantial variation in the levels of compliance implies that enforcement may need to be strengthened further.Originality/valueThere is a dearth of evidence on the level of compliance with the King Report. This study fills this gap by providing evidence for the first time on the level of compliance achieved, as well as contributing generally to the literature on compliance with codes of good governance and voluntary disclosure.
The determinants of board meetings: evidence from categorical analysis
Authors: Al‐Najjar Basil 
Published: September 2012

PurposeThe purpose of this paper is to investigate the determinants of the frequency of board meetings as an index for board activity including their monitoring role.Design/methodology/approachThe research sample is composed of 120 UK firms based on their market capitalization for the period from 2003 to 2008. The study applies multinomial logistic modelling and conditional logistic modelling to investigate the frequency of board meetings.FindingsThe study finds that board size and structure are positively related to the frequency of board meetings. In addition, a negative impact of audit committee diligence on the frequency board meetings is reported. The study finds no evidence that the frequency of board meetings are reduced when there is a CEO duality. Finally, the results show that firm size, leverage, free cash flows, and Tobin's Q have an impact on the frequency of board meetings.Practical implicationsThis study shows the factors that affect the board effectiveness in the UK, namely that board meetings, board composition, and board size, are key indicators for good internal governance practices and, in turn, enhance board monitoring activities.Originality/valueThe research offers the first major study to examine the determinants of the frequency of board meetings in UK non‐financial firms. The paucity of the UK literature regarding board effectiveness in the UK reinforces the empirical importance of the results for researchers, managers, and UK policy makers.