bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic suffix array: efficient modeling and prediction of protein families
Authors: Lin Jie , Adjeroh Donald , Jiang Bing-Hua 
Published: April 2012

Abstract
Motivation: Markov models are very popular for analyzing complex sequences such as protein sequences, whose sources are unknown, or whose underlying statistical characteristics are not well understood. A major problem is the computational complexity involved with using Markov models, especially the exponential growth of their size with the order of the model. The probabilistic suffix tree (PST) and its improved variant sparse probabilistic suffix tree (SPST) have been proposed to address some of the key problems with Markov models. The use of the suffix tree, however, implies that the space requirement for the PST/SPST could still be high.
Results: We present the probabilistic suffix array (PSA), a data structure for representing information in variable length Markov chains. The PSA essentially encodes information in a Markov model by providing a time and space-efficient alternative to the PST/SPST. Given a sequence of length N, construction and learning in the PSA is done in O(N) time and space, independent of the Markov order. Prediction using the PSA is performed in O(mlog N|Σ|) time, where m is the pattern length, and Σ is the symbol alphabet. In terms of modeling and prediction accuracy, using protein families from Pfam 25.0, SPST and PSA produced similar results (SPST 89.82%, PSA 89.56%), but slightly lower than HMMER3 (92.55%). A modified algorithm for PSA prediction improved the performance to 91.7%, or just 0.79% from HMMER3 results. The average (maximum) practical construction space for the protein families tested was 21.58±6.32N (41.11N) bytes using the PSA, 27.55±13.16N (63.01N) bytes using SPST and 47±24.95N (140.3N) bytes for HMMER3. The PSA was 255 times faster to construct than the SPST, and 11 times faster than HMMER3.
Availability: http://www.csee.wvu.edu/~adjeroh/projects/PSA
Contact: don@csee.wvu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty
Authors: Yang Haixuan , Nepusz Tamás , Paccanaro Alberto 
Published: April 2012

Abstract
Motivation: Several measures have been recently proposed for quantifying the functional similarity between gene products according to well-structured controlled vocabularies where biological terms are organized in a tree or in a directed acyclic graph (DAG) structure. However, existing semantic similarity measures ignore two important facts. First, when calculating the similarity between two terms, they disregard the descendants of these terms. While this makes no difference when the ontology is a tree, we shall show that it has important consequences when the ontology is a DAG—this is the case, for example, with the Gene Ontology (GO). Second, existing similarity measures do not model the inherent uncertainty which comes from the fact that our current knowledge of the gene annotation and of the ontology structure is incomplete. Here, we propose a novel approach based on downward random walks that can be used to improve any of the existing similarity measures to exhibit these two properties. The approach is computationally efficient—random walks do not need to be simulated as we provide formulas to calculate their stationary distributions.
Results: To show that our approach can potentially improve any semantic similarity measure, we test it on six different semantic similarity measures: three commonly used measures by Resnik (1999), Lin (1998), and Jiang and Conrath (1997); and three recently proposed measures: simUI, simGIC by Pesquita et al. (2008); GraSM by Couto et al. (2007); and Couto and Silva (2011). We applied these improved measures to the GO annotations of the yeast Saccharomyces cerevisiae, and tested how they correlate with sequence similarity, mRNA co-expression and protein–protein interaction data. Our results consistently show that the use of downward random walks leads to more reliable similarity measures.
Availability: We have developed a suite of tools that implement existing semantic similarity measures and our improved measures based on random walks. The tools are implemented in Matlab and are freely available from: http://www.paccanarolab.org/papers/GOsim/
Contact: alberto@cs.rhul.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations
Authors: Stanhope Stephen A. , Abney Mark 
Published: April 2012

Abstract
Summary: Mixed model-based approaches to genome-wide association studies (GWAS) of binary traits in related individuals can account for non-genetic risk factors in an integrated manner. However, they are technically challenging. GLOGS (Genome-wide LOGistic mixed model/Score test) addresses such challenges with efficient statistical procedures and a parallel implementation. GLOGS has high power relative to alternative approaches as risk covariate effects increase, and can complete a GWAS in minutes.
Availability: Source code and documentation are provided at http://www.bioinformatics.org/~stanhope/GLOGS.
Contact: sstanhop@bsd.uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Plastid Genome-Encoded Ycf4 Protein Functions as a Nonessential Assembly Factor for Photosystem I in Higher Plants
Authors: Krech Katharina , Ruf Stephanie , Masduki Fifi F. , Thiele Wolfram , Bednarczyk Dominika , Albus Christin A. , Tiller Nadine , Hasse Claudia , Schöttler Mark A. , Bock Ralph 
Published: April 2012

Abstract
Photosystem biogenesis in the thylakoid membrane is a highly complicated process that requires the coordinated assembly of nucleus-encoded and chloroplast-encoded protein subunits as well as the insertion of hundreds of cofactors, such as chromophores (chlorophylls, carotenoids) and iron-sulfur clusters. The molecular details of the assembly process and the identity and functions of the auxiliary factors involved in it are only poorly understood. In this work, we have characterized the chloroplast genome-encoded ycf4 (for hypothetical chloroplast reading frame no. 4) gene, previously shown to encode a protein involved in photosystem I (PSI) biogenesis in the unicellular green alga Chlamydomonas reinhardtii. Using stable transformation of the chloroplast genome, we have generated ycf4 knockout plants in the higher plant tobacco (Nicotiana tabacum). Although these mutants are severely affected in their photosynthetic performance, they are capable of photoautotrophic growth, demonstrating that, different from Chlamydomonas, the ycf4 gene product is not essential for photosynthesis. We further show that ycf4 knockout plants are specifically deficient in PSI accumulation. Unaltered expression of plastid-encoded PSI genes and biochemical analyses suggest a posttranslational action of the Ycf4 protein in the PSI assembly process. With increasing leaf age, the contents of Ycf4 and Y3IP1, another auxiliary factor involved in PSI assembly, decrease strongly, whereas PSI contents remain constant, suggesting that PSI is highly stable and that its biogenesis is restricted to young leaves.
Atypical Thioredoxins in Poplar: The Glutathione-Dependent Thioredoxin-Like 2.1 Supports the Activity of Target Enzymes Possessing a Single Redox Active Cysteine
Authors: Chibani Kamel , Tarrago Lionel , Gualberto José Manuel , Wingsle Gunnar , Rey Pascal , Jacquot Jean-Pierre , Rouhier Nicolas 
Published: April 2012

Abstract
Plant thioredoxins (Trxs) constitute a complex family of thiol oxidoreductases generally sharing a WCGPC active site sequence. Some recently identified plant Trxs (Clot, Trx-like1 and -2, Trx-lilium1, -2, and -3) display atypical active site sequences with altered residues between the two conserved cysteines. The transcript expression patterns, subcellular localizations, and biochemical properties of some representative poplar (Populus spp.) isoforms were investigated. Measurements of transcript levels for the 10 members in poplar organs indicate that most genes are constitutively expressed. Using transient expression of green fluorescent protein fusions, Clot and Trx-like1 were found to be mainly cytosolic, whereas Trx-like2.1 was located in plastids. All soluble recombinant proteins, except Clot, exhibited insulin reductase activity, although with variable efficiencies. Whereas Trx-like2.1 and Trx-lilium2.2 were efficiently regenerated both by NADPH-Trx reductase and glutathione, none of the proteins were reduced by the ferredoxin-Trx reductase. Only Trx-like2.1 supports the activity of plastidial thiol peroxidases and methionine sulfoxide reductases employing a single cysteine residue for catalysis and using a glutathione recycling system. The second active site cysteine of Trx-like2.1 is dispensable for this reaction, indicating that the protein possesses a glutaredoxin-like activity. Interestingly, the Trx-like2.1 active site replacement, from WCRKC to WCGPC, suppresses its capacity to use glutathione as a reductant but is sufficient to allow the regeneration of target proteins employing two cysteines for catalysis, indicating that the nature of the residues composing the active site sequence is crucial for substrate selectivity/recognition. This study provides another example of the cross talk existing between the glutathione/glutaredoxin and Trx-dependent pathways.
Non‐agricultural databases and thesauri
Authors: Bartol Tomaz 
Published: April 2012

PurposeThe paper aims to assess the utility of non‐agriculture‐specific information systems, databases, and respective controlled vocabularies (thesauri) in organising and retrieving agricultural information. The purpose is to identify thesaurus‐linked tree structures, controlled subject headings/terms (heading words, descriptors), and principal database‐dependent characteristics and assess how controlled terms improve retrieval results (recall) in relation to free‐text/uncontrolled terms in abstracts and document titles.Design/methodology/approachSeveral different hosts (interfaces, platforms, portals) and databases were used: CSA Illumina (ERIC, LISA), Ebscohost (Academic Search Complete, Medline, Political Science Complete), Ei‐Engineering Village (Compendex, Inspec), OVID (PsycINFO), ProQuest (ABI/Inform Global). The search‐terms agriculture and agricultural and truncated word‐stem agricultur‐ were employed. Permuted (rotated index) search fields were used to retrieve terms from thesauri. Subject‐heading search was assessed in relation to free‐text search, based on abstracts and document titles.FindingsAll thesauri contain agriculture‐based headings; however, associative, hierarchical and synonymous relationships show important inter‐database differences. Using subject headings along with abstracts and titles in search syntax (query) sometimes improves retrieval by up to 60 per cent. Retrieval depends on search fields and database‐specifics, such as autostemming (lemmatization), explode function, word‐indexing, or phrase‐indexing.Research limitations/implicationsInter‐database and host comparison, on consistent principles, can be limited because of some particular host‐ and database‐specifics.Practical implicationsEnd‐users may exploit databases more competently and thus achieve better retrieval results in searching for agriculture‐related information.Originality/valueThe function of as many as ten databases in different disciplines in providing information relevant to subject matter that is not a topical focus of databases is assessed.
The role of agent conscientiousness and reciprocity norm in employee layoff decisions
Authors: Li Jin , Hung Kuo‐Ting , Tangpong Chanchai 
Published: April 2012

PurposeThe purpose of this paper is to better understand the main effects of agent conscientiousness and reciprocity norm and the interaction effect of these two factors on layoff decisions in firm‐employee relationships.Design/methodology/approachA scenario‐based experiment with 331 business professionals was conducted and three regression models were run to test three hypotheses proposed in the paper.FindingsThe norm of reciprocity reduces decision‐making agents' tendency to lay off employees in the face of an environmental change. In addition, the norm of reciprocity interacts with decision‐making agents' conscientiousness in influencing their layoff decision.Research limitations/implicationsThe limitations of this study are the use of single‐agent decision scenario and the specific focus on one aspect of agent personality – conscientiousness and its collective influence on layoff decisions. In a broader picture, the results of this study support the cross‐level analytical approach to investigating organizational phenomena, in which individual‐level and organizational‐level factors interact and determine organizational outcomes.Practical implicationsRecruiting and promoting managers who exhibit high levels of conscientiousness, coupled with proactively cultivating the norm of reciprocity with employees, are critical to a firm's thrust in attaining and sustaining stakeholder management practices with the emphasis on employees' well‐being.Originality/valueWhile the extant literature focuses largely on the effects of layoff and the individual perceptions of downsizing and layoff, this paper examines what actually influences decision‐making agents' layoff decisions. The paper expands the literature by investigating the impacts of agent conscientiousness and reciprocity norm on layoff decisions.
The effect of Hispanic accents on employment decisions
Authors: Hosoda Megumi , Nguyen Lam T. , Stone‐Romero Eugene F. 
Published: April 2012

PurposeDespite the fact that Hispanics are the largest and fastest growing segment of the population and that 44 percent of Hispanics of 18 years of age and older speak English less than very well, research examining the impact of Spanish‐accented English on employment‐related decisions has been scarce. Therefore, the present study aimed to examine the effects of the accent (standard American English and Mexican Spanish) of a hypothetical job applicant on employment‐related judgments and hiring decisions.Design/methodology/approachParticipants made employment‐related decisions (i.e. job suitability ratings, likelihood of a promotion, and hiring decision) and judgments of personal attributes (i.e. perceived competence and warmth) of a hypothetical applicant for an entry‐level software engineering job. The accent of the applicant was manipulated using the matched‐guise technique.FindingsResults showed that compared to an applicant with a standard American‐English accent, one with a Mexican‐Spanish accent was at a disadvantage when applying for the software engineering job. The Mexican‐Spanish‐accented applicant was rated as less suitable for the job and viewed as less likely to be promoted to a managerial position. In addition, fewer participants decided to hire the Mexican‐Spanish‐accented applicant than the standard American English‐accented applicant.Practical implicationsGiven the negative evaluations of the Mexican‐Spanish‐accented applicant, recruiters and interviewers should be selected who do not view foreign accents negatively. Furthermore, organizations should make a conscious effort to regard foreign accents as assets to their businesses.Originality/valueThis research contributes to our understanding of how foreign accents influence decisions that have important economic consequences for individuals.
Benefits of mentoring African‐American men
Authors: Robinson Davis M. , Reio Thomas G. 
Published: April 2012

PurposeThe aim of this study was to investigate the relationship between mentoring, job satisfaction and organizational commitment among African‐American males.Design/methodology/approachAn online questionnaire was completed by 359 African‐American males in a business setting.FindingsJob satisfaction and organizational commitment were higher for those who were being mentored versus those who were not. The multiple regression results suggested mentoring was a statistically significant predictor of job satisfaction and organizational commitment. Further, the relation between mentoring and organizational commitment was mediated by job satisfaction.Research limitations/implicationsCurrent organizational research is limited, in that it tends to focus on majority culture where findings can be inappropriately generalized to minority groups. Future mentoring research should include more minorities that can provide a new window for interpreting the contributions of minorities to organizational competitiveness.Practical implicationsMentoring programs should be continued and/or expanded upon to reduce the likelihood of poor job satisfaction and organizational commitment for African‐American males.Social implicationsOrganizations through their human resource efforts can contribute to the learning and development of African‐American males and other minorities by designing and implementing quality mentoring programs. Such programs could lessen the likelihood of costly under‐performance and turnover.Originality/valueThis is one of the relatively few organizational studies designed specifically for a minority group. The results have implications for how human resource professionals and managers might improve mentoring experiences for minorities.
Family purchase decision making at the bottom of the pyramid
Authors: Chikweche Tendai , Stanton John , Fletcher Richard 
Published: April 2012

PurposeThis paper seeks to argue that family purchase decision making at the bottom of the pyramid (BOP) is dynamic, heterogeneous and an evolving process that can be influenced by contextual macro‐environmental constraints. Because established perceptions of family purchase decision making are primarily drawn from western markets, this Zimbabwean study aims to provide a contrasting perspective.Design/methodology/approachQualitative data collection methods comprising in‐depth, one‐to‐one consumer interviews, focus groups, ethnographic observations and cases studies were used to conduct the research.FindingsKey findings include the identification of changing and multiple family buying models, which are influenced by the constraints consumers face at the BOP, as well as the distinct roles of children, which differ from those common in developed western countries.Research limitations/implicationsThe sample used for consumer interviews is small and confining the focus to the food and personal hygiene sector may limit generalization of findings to a broader population.Practical implicationsThe study provides managers with insights on the importance of understanding family purchase decision making at the BOP and the importance of adapting the marketing mix elements such as promotion strategies to suit the challenges faced by these consumers.Social implicationsThe study provides insights into how firms can improve livelihoods at the BOP by provision of employment and business opportunities through their partnerships with social networks.Originality/valueResearch into the BOP is a relatively new area of study in international business. The majority of studies have focused on Latin America and Asia, ignoring the 800 million BOP consumers in Africa. Hence this research expands knowledge in the area by employing empirical mixed research methods to study consumers in their real world setting thereby providing new insights on marketing to the BOP.
Decomposition of cross‐country differences in consumer attitudes toward marketing
Authors: Cui Geng , Lui Hon‐Kwong , Chan Tsang‐Sing , Joy Annamma 
Published: April 2012

PurposePrevious studies have found significant differences in consumer attitudes toward marketing between countries and attributed such variations to differences in the stage of consumerism development and cultural values. This study aims to test these competing hypotheses using econometric decomposition to identify the source of such cross‐country variations.Design/methodology/approachUsing survey data of consumer attitudes toward marketing from China and Canada, this study adopts econometric decomposition to examine the cross‐country difference in consumer attitudes toward marketing.FindingsThe results show that Chinese consumers have more positive attitudes toward marketing than Canadians and the two countries differ significantly across all predictor variables. However, the results of decomposition suggest that consumerism, individualism and relativism do not have any significant effect on the country gap in consumer attitudes toward marketing, while idealism has a significant coefficient effect.Research limitations/implicationsThe study finds different effects of cultural values on consumer attitudes across countries and has meaningful implications for international marketing strategies.Originality/valueThe study investigates the sources of cross‐national differences in consumer attitudes toward marketing using rigorous analyses to improve the accuracy of cultural attribution for international marketing and cross‐cultural consumer research.
Waiting for service at the checkout
Authors: van Riel Allard C.R. , Semeijn Janjaap , Ribbink Dina , Bomert‐Peters Yvette 
Published: April 2012

PurposeIn retail settings, customer satisfaction is generally associated with a global evaluation of the store, i.e. the store image. Waiting for service is not part of the store image dimensions, but it does play an increasingly important role in the retail experience where waits are often inevitable. The present study seeeks to investigate how waiting for service at the checkout counter influences overall satisfaction, along with the store image.Design/methodology/approachThe study combines services marketing and waiting literature. Data were collected in various supermarkets in The Netherlands. A partial least squares regression technique is used to analyze the data.FindingsThe paper demonstrates an important and complementary role of the behavioural construct “negative response to the wait” in explaining overall customer satisfaction in a retail environment. The effect of customers' negative emotional response to the wait on satisfaction is partially mediated by store image, and explained variance in the dependent variable increases by 24 percent when the effect of the wait at the checkout is included.Research limitations/implicationsMeasuring customer satisfaction without taking into account the effects of various waits during the retail experience will produce incomplete results.Practical implicationsMoreover, a range of controllable factors influences the customer's wait. Intelligently managing these factors can mitigate negative effects on customer satisfaction, or even increase the overall evaluation of the service. Specific recommendations for service managers and a research agenda are provided.Originality/valueThe study combines service marketing and waiting literature to address the issue of waiting in line and tests the theory with real‐world data from a field study.