bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying differentially expressed subnetworks with MMG
Authors: Noirel Josselin , Sanguinetti Guido , Wright Phillip C. 
Published: September 2008

Abstract
Background: Mixture model on graphs (MMG) is a probabilistic model that integrates network topology with (gene, protein) expression data to predict the regulation state of genes and proteins. It is remarkably robust to missing data, a feature particularly important for its use in quantitative proteomics. A new implementation in C and interfaced with R makes MMG extremely fast and easy to use and to extend.
Availability: The original implementation (Matlab) is still available from http://www.dcs.shef.ac.uk/~guido/; the new implementation is available from http://wrightlab.group.shef.ac.uk/people_noirel.htm, from CRAN, and has been submitted to BioConductor, http://www.bioconductor.org/.
Contact: j.noirel@sheffield.ac.uk
Physiological and Transcriptomic Evidence for a Close Coupling between Chloroplast Ontogeny and Cell Cycle Progression in the Pennate DiatomSeminavis robusta
Authors: Gillard Jeroen , Devos Valerie , Huysman Marie J.J. , De Veylder Lieven , D'Hondt Sofie , Martens Cindy , Vanormelingen Pieter , Vannerum Katrijn , Sabbe Koen , Chepurnov Victor A. , Inzé Dirk , Vuylsteke Marnik , Vyverman Wim 
Published: September 2008

AbstractDespite the growing interest in diatom genomics, detailed time series of gene expression in relation to key cellular processes are still lacking. Here, we investigated the relationships between the cell cycle and chloroplast development in the pennate diatom Seminavis robusta. This diatom possesses two chloroplasts with a well-orchestrated developmental cycle, common to many pennate diatoms. By assessing the effects of induced cell cycle arrest with microscopy and flow cytometry, we found that division and reorganization of the chloroplasts are initiated only after S-phase progression. Next, we quantified the expression of the S. robusta FtsZ homolog to address the division status of chloroplasts during synchronized growth and monitored microscopically their dynamics in relation to nuclear division and silicon deposition. We show that chloroplasts divide and relocate during the S/G2 phase, after which a girdle band is deposited to accommodate cell growth. Synchronized cultures of two genotypes were subsequently used for a cDNA-amplified fragment length polymorphism-based genome-wide transcript profiling, in which 917 reproducibly modulated transcripts were identified. We observed that genes involved in pigment biosynthesis and coding for light-harvesting proteins were up-regulated during G2/M phase and cell separation. Light and cell cycle progression were both found to affect fucoxanthin-chlorophyll a/c-binding protein expression and accumulation of fucoxanthin cell content. Because chloroplasts elongate at the stage of cytokinesis, cell cycle-modulated photosynthetic gene expression and synthesis of pigments in concert with cell division might balance chloroplast growth, which confirms that chloroplast biogenesis in S. robusta is tightly regulated.
Unique and Overlapping Expression Patterns among Members of Photosynthesis-Associated Nuclear Gene Families in Arabidopsis
Authors: Sawchuk Megan G. , Donner Tyler J. , Head Philip , Scarpella Enrico 
Published: September 2008

AbstractLight provides crucial positional information in plant development, and the morphogenetic processes that are orchestrated by light signals are triggered by changes of gene expression in response to variations in light parameters. Control of expression of members of the RbcS and Lhc families of photosynthesis-associated nuclear genes by light cues is a paradigm for light-regulated gene transcription, but high-resolution expression profiles for these gene families are lacking. In this study, we have investigated expression patterns of members of the RbcS and Lhc gene families in Arabidopsis (Arabidopsis thaliana) at the cellular level during undisturbed development and upon controlled interference of the light environment. Members of the RbcS and Lhc gene families are expressed in specialized territories, including root tip, leaf adaxial, abaxial, and epidermal domains, and with distinct chronologies, identifying successive stages of leaf mesophyll ontogeny. Defined spatial and temporal overlap of gene expression fields suggest that the light-harvesting and photosynthetic apparatus may have a different polypeptide composition in different cells and that such composition could change over time even within the same cell.
Root-Secreted Malic Acid Recruits Beneficial Soil Bacteria
Authors: Rudrappa Thimmaraju , Czymmek Kirk J. , Paré Paul W. , Bais Harsh P. 
Published: September 2008

AbstractBeneficial soil bacteria confer immunity against a wide range of foliar diseases by activating plant defenses, thereby reducing a plant's susceptibility to pathogen attack. Although bacterial signals have been identified that activate these plant defenses, plant metabolites that elicit rhizobacterial responses have not been demonstrated. Here, we provide biochemical evidence that the tricarboxylic acid cycle intermediate l-malic acid (MA) secreted from roots of Arabidopsis (Arabidopsis thaliana) selectively signals and recruits the beneficial rhizobacterium Bacillus subtilis FB17 in a dose-dependent manner. Root secretions of l-MA are induced by the foliar pathogen Pseudomonas syringae pv tomato (Pst DC3000) and elevated levels of l-MA promote binding and biofilm formation of FB17 on Arabidopsis roots. The demonstration that roots selectively secrete l-MA and effectively signal beneficial rhizobacteria establishes a regulatory role of root metabolites in recruitment of beneficial microbes, as well as underscores the breadth and sophistication of plant-microbial interactions.
Current research information systems, open access repositories and libraries
Authors: Joint Nicholas 
Published: September 2008

PurposeThe purpose of this paper is to give an overview of larger developments in the international research information environment, and to outline their impact on the open access movement within libraries.Design/methodology/approachA narrative account of recent historical developments such as national current research information systems (CRIS), and their local campus equivalents, together with an analysis of the relationship of these systems with national research policies, and particularly their relationship with research evaluation policy.FindingsDevelopments in the research landscape have important effects on grass‐roots LIS practice, and have given a great boost to open access repositories while preserving the traditional role of commercial journal publications. This complementary relationship was completely unexpected at the outset of the open access movement, which was specifically intended to reduce the importance of commercial journal publications.Research limitations/implicationsThis is an exploration of the relationship between open access and current research information environments. This relationship is of enormous significance and will need to be analysed and better understood in future. The analysis in this paper is thus an initial attempt to increase this understanding, and further, extended investigation is recommended.Practical implicationsPractitioner librarians must come to grips with the role of repositories within the CRIS environment, as well as the relationship of repositories to the local campus research information system.Originality/valueThis paper investigates trends in the broader research information environment which will be unfamiliar to many LIS practitioners, and puts them in the context of everyday professional practice.
The public library, exclusion and empathy: a literature review
Authors: Birdi Briony , Wilson Kerry , Cocker Joanne 
Published: September 2008

PurposeThe purpose of this paper is to present a review of the literature within the fields of public librarianship, social exclusion and empathy.Design/methodology/approachThe cross‐disciplinary review involved the consultation of material from disciplines including library and information management, politics, social policy and social sciences, cultural studies, psychology, management and organizational theory. It was structured according to the following themes: exclusion, inclusion and social policy, social inclusion in public services and the cultural sector, the role of public libraries in social inclusion and professional empathy and the public library service.Findings–The concept of social inclusion remains at the core of public library policy and strategy, and is embedded in contemporary social theory. Conflicting views have emerged as to the perceived and actual role of the public library in combating social exclusion, with a need expressed for research to be conducted that bridges the gap between the “philosophical” interpretations of community librarianship and the more practical, “real world” studies, in order to fully understand the concept of community librarianship. A critical link is made between social inclusion and public librarianship to professional empathy.Research limitations/implicationsThe paper provides an edited version of the overall literature review, yet it is felt that it would be of theoretical and practical relevance and value to the professional and academic communities.Originality/valueEmpathy is a relatively new concept in librarianship research, and prior to the study of which this review forms a part only limited findings have been available.
Students' attitudes towards e‐books in a Scottish higher education institute: part 1
Authors: Abdullah Noorhidawati , Gibb Forbes 
Published: September 2008

PurposeThe purpose of this paper is to present the first part of three inter‐related studies investigating the use and usability of e‐books in higher education based on experiments conducted at the University of Strathclyde.Design/methodology/approachA self‐selected sampling method was employed from undergraduate and postgraduate instructional students registered with the University of Strathclyde for academic year 2005/2006. An announcement email was posted to the student web portal for a period of three weeks inviting them to participate in the survey.FindingsThis survey found that e‐book awareness and the level of e‐book usage amongst students was lower than anticipated: 57 per cent of students were not aware of the availability of e‐books from the library and 60 per cent of them had not used an e‐book. Non‐users commented that e‐books were not widely advertised or promoted. Despite the low levels of e‐book awareness and usage non‐e‐book users indicated their desire to learn more about e‐books.Research limitations/implicationsThis survey was dependent on self‐selection and, therefore, there was no central control over the sample profile (e.g. gender, level of studies, academic discipline); hence, generalisation of the results should be treated with caution.Practical implicationsThis survey is beneficial in terms of obtaining a better understanding of e‐book usage among students and the reasons why students do, and do not, use e‐books. The findings should be of value to academic libraries in terms of emphasising the need to increase e‐book awareness and usage amongst students.Originality/valueThe findings should be of value to academic libraries in terms of emphasising the need to increase e‐book awareness and usage amongst students.
Role of library anxiety on cooperative group performance
Authors: Jiao Qun G. , Collins Kathleen M.T. , Onwuegbuzie Anthony J. 
Published: September 2008

PurposeThe purpose of this paper is to examine the extent that cooperative group members' levels of library anxiety, operationalized as barriers with staff, affective barriers, comfort with the library, knowledge of the library and mechanical barriers, predict: group performance, namely, the quality of an article critique assignment and research proposal assignment; and the degree that heterogeneity (namely, variability of the five library anxiety dimensions) is related to this outcome variable.Design/methodology/approachParticipants were 107 postgraduate students enrolled in a research methodology course at a mid‐southern university in the USA. Groups (n = 1) formed the unit of analysis. An all possible subsets multiple regression analysis was used to identify an optimal combination of library anxiety variables that predicted the group performance score.FindingsIt was found that cooperative learning groups attaining the lowest scores on the article critique and research proposal assignments combined tended to report the least variation with respect to barriers with staff and knowledge of the library, and the greatest variation with respect to affective barriers. These variables explained 41.8 per cent of the variance in performance, suggesting that library anxiety plays a role in the cooperative learning group process.Research limitations/implicationsThis study is based on a relatively small sample of postgraduate students from one university. Replications of this study with larger samples from different universities are needed to help validate the findings.Practical implicationsThe findings may help academic librarians and educators who work with postgraduate or adult students better understand the debilitating effects of library anxiety on these students' academic performance.Originality/valueTo date, no research has investigated levels of library anxiety on the performance of cooperative learning groups.
You will be …: a study of job advertisements to determine employers' requirements for LIS professionals in the UK in 2007
Authors: Orme Verity 
Published: September 2008

PurposeThe purpose of this paper is to investigate what employers seek when recruiting library and information professionals in the UK and whether professional skills, generic skills or personal qualities are most in demand.Design/methodology/approachA content analysis of a sample of 180 advertisements requiring a professional library or information qualification from Chartered Institute of Library and Information Professional's Library + Information Gazette over the period May 2006‐2007.FindingsThe findings reveal that a multitude of skills and qualities are required in the profession. When the results were compared with Information National Training Organisation and Library and Information Management Employability Skills research, customer service, interpersonal and communication skills, and general computing skills emerged as the requirements most frequently sought by employers. Overall, requirements from the generic skills area were most important to employers, but the research also demonstrates that professional skills are still valued. An unanticipated demand for profession related experience was found: this was the single most frequently sought requirement in the advertisements analysed.Research limitations/implicationsAlthough the Gazette is the largest source of library and information jobs, it does not provide a complete picture of the employment market.Originality/valueThe paper contributes to debates about the skillsbase of the profession, and raises awareness of the abilities professionals need to cultivate in order to progress through their careers.
Role for food‐specific IgG‐based elimination diets
Authors: Hicks Kate , Hart Gillian 
Published: September 2008

PurposeEvidence has suggested that elimination diets based on food‐specific IgG measurement can lead to improvements in chronic ill health symptoms. This paper aims to review the evidence from studies on food‐specific IgG measurement and dietary change.Design/methodology/approachA literature review of studies on the putative role for food‐specific IgG‐based elimination diets was undertaken.FindingsThe use of fully standardised clinically evaluated food‐specific IgG tests as a basis for elimination diet could lead to a considerable improvement in many patients' quality of life.Originality/valueThis unique review captures evidence for a viable alternative to the time consuming and expensive elimination diet/food challenge approach.
Raising food allergy awareness of caterers in Wales
Authors: Worsfold Denise 
Published: September 2008

PurposeThe purpose of this paper is to review the progress of the Allergen Strategy for Wales intended to raise food allergen awareness of caterers in the principality.Design/methodology/approachThe Allergen Action Plan survey programme was examined to determine the progress made to date. Data were collected by means of a literature search and questionnaire surveys of officers and trainers.FindingsThe surveys suggest that food enforcement officers are well informed about some allergen management issues but other aspects such as cross contamination and staff training are less likely to be included on routine inspections. Hygiene trainers appear to be adequately informed to cover key messages on elementary hygiene courses for caterers. Allergen training for officers and materials for use by businesses have been produced which will help advance the Allergen Strategy.Research limitations/implicationsThe surveys that are reported involved limited numbers of respondents.Practical implicationsAlthough food enforcement officers are identified in the Allergen Strategy as those charged with raising the profile of allergens and allergy awareness, there is limited time for them to cover food allergen management issues during routine inspections. Hygiene trainers and the use of training materials from the Food Standards Agency are valuable resources that can help to advance the Allergen Strategy.Originality/valueAlthough the Allergen Strategy is in the public domain there is limited published work on its progress to date and the preparedness of those charged with raising allergen management issues with a broad range of caterers.
Effects of konjac glucomannan hydrolysates on the gut microflora of mice
Authors: Elamir Abdulmnem A. , Tester Richard F. , Al‐Ghazzewi Farage H. , Kaal Hakim Y. , Ghalbon Amna A. , Elmegrahai Najat A. , Piggott John R. 
Published: September 2008

PurposeThe aim of this study is to determine the effects of depolymerised mannans and specifically konjac glucomannan hydrolysates (GMH) on the colonic microflora of mice. Blood glucose and cholesterol were also measured.Design/methodology/approachTwo groups (n = 20) of 12‐week old Wister mice were used for a period of 14 weeks. One group (treatment group) were fed diets containing 5 per cent konjac GMH dissolved in drinking water in addition to the control (group) standard diet. Faecal microflora, feed consumption, body weight, blood glucose and cholesterol were determined.FindingsThe GMH promoted the growth of anaerobes and lactobacilli in the treatment group where this was statistically, highly significant (P < 0.001). Also, the hydrolysate was able to reduce highly significantly (P < 0.001) faecal Clostridium perfringens and Escherichia coli counts. A significant increase in average daily feed consumption (P < 0.05) and weekly body weight (P < 0.001) was found for the treatment group. The mean ± SD (mmol/l) of blood glucose and cholesterol was lower in the treatment group.Originality/valueIn addition to modulating the gut microflora, GMH seems to lower the blood glucose and cholesterol in mice. Although this needs to be verified by further studies, GMH could also be a candidate for possible treatment of subjects with high cholesterol and for diabetics.
Special humanized milk as a supplementary food for infants
Authors: Sarkar S. 
Published: September 2008

PurposeIn absence of breast milk, humanized mammalian milk may not be adequate as it could not confer considerable protection to the infants as those extended by breast milk. With the objective of enhancing the nutritional and therapeutic attributes of humanized mammalian milk considerable efforts have been exercised to mimic infant formulae to the health‐promoting benefits of breast milk with the inclusion of probiotics, oligosaccharides and proteins. The purpose of this paper is to address this issue.Design/methodology/approachIn the present article an endeavour has been made to enlighten innovations in supplementary foods for infants in absence of human milk. Suitability of special humanized milk such as hypoallergenic formulae, neural formulae and gastrointestinal integrity formulae as a supplementary food for infants in absence of human milk is also justified.FindingsCharacterization of components of human milk and identification of nutritional needs of infants have resulted in formulation of special humanized milk such as hypoallergenic formulae for allergenic infants, neural formulae for normal physiological functions of infants and gastrointestinal integrity formulae for maintaining microbial balance in the intestine. Supplementation of infant formulae with sialic acid, long chain poly unsaturated fatty acids such as decosahexaenoic acid and arachidonic acid, probiotic cultures such as Bifidobacterium bifidum, Lactobacillus acidophilus, Lactobacillus GG and Lactobacillus casei and prebiotic such as galacto‐OS and fructo‐OS are recommended.Originality/valueThe paper emphasises that, with the characterization of components of human milk and identification of nutritional needs of infants, modification of infant formulae should be constantly carried.
Balancing food allergy in schools and achieving the school food standards
Authors: Higgs Jennette 
Published: September 2008

PurposeThe 2006 UK Government's school food standards has created an opportunity for schools to consider introducing highly nutritious, convenience snack alternatives, such as dried fruit, nuts and seeds. This has created anxiety among those who fear a consequent increase in incidence of allergic reactions in schools. The purpose of this paper is to present a controlled approach to secondary school vending, designed to minimise the risks of allergic reaction.Design/methodology/approachA consultation process with key organisations, together with an analysis of the vending process in schools has underpinned this work. The Health Education Trust, with experience of developing food and medicines policies in schools, has explored a practical solution to the common assumption that a nut ban in schools is the only way to offer protection to those students at risk.FindingsA best practice guidance tool for “allergy‐aware” vending has been developed. It provides a framework for a common sense approach to tackling two potentially conflicting issues, identifying vending as a practical solution.Practical implicationsThe toolkit is a free download, ready for pilot testing in secondary schools. This mutually beneficial approach to minimising risk is presented as a working draft. Revisions will be made following feedback from schools. This toolkit is not suitable for use in primary schools.Originality/valueAchieving healthy eating goals for the teenage school population and safeguarding those pupils who have serious food allergies are important issues that merit mutual consideration. This paper explores the issues and proposes, for the first time a best practice guidance to both minimise risks and maximise health benefit.