bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vitro Rat Hepatic Metabolism of n-Alkanes: Nonane, Decane, and Tetradecane
Authors: Anand Sathanandam S. , Campbell Jerry L. , Fisher Jeffrey W.
Published: July 2007

Jet propellant 8 (JP-8) jet fuel is a complex mixture of aromatic and aliphatic hydrocarbons. The aim of this study was to determine in vitro metabolic rate constants for semivolatile n-alkanes, nonane (C9), decane (C10), and tetradecane (C14), by rat liver microsomal oxidation. The metabolism was assessed by measuring the disappearance of parent compound by gas chromatography. Various concentrations of n-alkanes were incubated with liver microsomes from adult male F-344 rats. Nonlinear kinetic constants for nonane and decane were Vmax (nmol/mg protein/min) = 7.26 ± 0.20 and 2.80 ± 0.35, respectively, and KM ( μM) = 294.83 ± 68.67 and 398.70 ± 42.70, respectively. Metabolic capacity as assessed by intrinsic clearance ( Vmax/ KM) was ~four-fold higher for nonane (0.03 ± 0.005) than for decane (0.007 ± 0.001). There was no appreciable metabolism of tetradecane even with higher microsomal protein concentration and longer incubation time. These results show a negative correlation between metabolic clearance and chain length of n-alkanes. These metabolic rate constants will be used to update existing physiologically based pharmacokinetic (PBPK) models for nonane and decane as part of developing a PBPK model for JP-8.
Tobacco Smoke–Induced Lung Cancer in Animals—A Challenge to Toxicology (?)
Authors: Witschi Hanspeter
Published: July 2007

Tobacco smoke is a known human carcinogen that primarily produces malignant lesions in the respiratory tract, although it also affects multiple other sites. A reliable and practical animal model of tobacco smoke–induced lung cancer would be helpful for in studies of product modification and chemoprevention. Over the years, many attempts to reproduce lung cancer in experimental animals exposed to tobacco smoke have been made, most often with negative or only marginally positive results. In hamsters, malignant lesions have been produced in the larynx, but not in the deeper lung. Female rats and female B6C3F1 mice, when exposed over lifetime to tobacco smoke, develop tumors in the nasal passages and also in the lung. Contrary to what is seen in human lung cancers, most rodent tumors are located peripherally and only about half of them show frank malignant features. Distant metastases are extremely rare. Male and female strain A mice exposed to 5 months to tobacco smoke and then kept for another 4 months in air respond to tobacco smoke with increased lung tumor multiplicities. However, the increase over background levels is comparatively small, making it difficult to detect significant differences when the effects of chemopreventive agents are evaluated. On the other hand, biomarkers of exposure and of effect as well as evaluation of putative carcinogenic mechanisms in rats and mice exposed to tobacco smoke allow detection of early events and their modification by different smoke types or chemopreventive agents. The challenge will be to make such data broadly acceptable and accepted in lieu of having to do more and more long term studies involving larger and larger number of animals.
The Role of Skin Painting in Predicting Lung Cancer
Authors: Walaszek Z. , Hanausek M. , Slaga T. J.
Published: July 2007

The mouse skin cancer model provides an important system for studying mechanisms involved in the various stages of carcinogenesis and for bioassaying tobacco smoke constituents and additives for carcinogenic/cocarcinogenic and tumor-promoting properties as well as for identifying compounds that may inhibit tumor formation and malignant conversion. In addition, it is an excellent model for studying the formation of precancerous lesions as well as squamous cell carcinomas. It relates very well to other squamous cell carcinoma models and contributes to better understanding of the human epithelial cancers including lung cancer. The SENCAR mouse is an established model system demonstrated to be more sensitive than the B6C3F1 or Swiss CD-1 strains in the initiation/promotion skin-painting test method. Although the relationship between mouse skin tumors and any manifestation of the toxicity of tobacco smoke and other complex environmental mixtures in humans is unknown, the skin-painting model is the only assay that provides a practical method of obtaining a tumorigenic end point with cigarette smoke condensates and other complex mixtures. This assay provides a rapid response with relative ease of quantification of various parameters of tumorigenic response including tumor incidence, latency, multiplicity, and malignancy.
Smoking and Lung Cancer: Future Research Directions
Authors: Haussmann Hans-Juergen
Published: July 2007

The aim of future research in this area is to provide the mechanistic understanding and the tools for effective prevention, early diagnosis, and therapy of lung cancer. With the established causal link between cigarette smoking and the risk of developing lung cancer, the most effective prevention is certainly not to smoke. A much better mechanistic understanding of lung cancer and its variability will support the development and evaluation of potentially reduced risk products for those who maintain smoking as well as for the development of early diagnostic tools and targeted therapies. Because of the complexity of lung cancer and the long duration for its development, nonclinical and clinical research efforts need to complement each other. Recent promising advances in this research area are the understanding of the interaction between genotoxic and epigenetic effects of smoking, the development of laboratory animal models for lung tumorigenesis by smoke inhalation, the unraveling of molecular pathways and signatures in clinical lung cancer research useful for developing diagnostic tools and therapeutic approaches, and the first successful therapy for lung cancer—although less suitable for smokers. The above—in combination with emerging data sets from explorative non-clinical and clinical studies as well as improved modeling approaches—are setting the stage for accelerated progress towards developing successful early diagnostic tools and therapies as well as for the assessment of new consumer products with potentially reduced risk.
Epidemic Preparedness in New Hampshire: Assessment of Increased Airborne Infection Isolation Capacity 1 Year After Distribution of Portable Isolation Units
Authors: Plotinsky Rachel N. , Talbot Elizabeth A. , Yeager Deborah , Montero Jose T.
Published: August 2007

We surveyed hospital personnel regarding their preparedness to use and their actual use of portable isolation units that were distributed to increase facilities' capacity to place patients under airborne infection isolation precautions. Although personnel reported feeling prepared to use portable isolation units, the effectiveness of the unit deployment program would be enhanced by retrofitted rooms and an improved ability to monitor negative air pressure.
Robust smooth segmentation approach for array CGH data analysis
Authors: Huang Jian , Gusnanto Arief , O'Sullivan Kathleen , Staaf Johan , Borg Åke , Pawitan Yudi
Published: July 2007

Motivation: Array comparative genomic hybridization (aCGH) provides a genome-wide technique to screen for copy number alteration. The existing segmentation approaches for analyzing aCGH data are based on modeling data as a series of discrete segments with unknown boundaries and unknown heights. Although the biological process of copy number alteration is discrete, in reality a variety of biological and experimental factors can cause the signal to deviate from a stepwise function. To take this into account, we propose a smooth segmentation (smoothseg) approach.

Methods: To achieve a robust segmentation, we use a doubly heavy-tailed random-effect model. The first heavy-tailed structure on the errors deals with outliers in the observations, and the second deals with possible jumps in the underlying pattern associated with different segments. We develop a fast and reliable computational procedure based on the iterative weighted least-squares algorithm with band-limited matrix inversion.

Results: Using simulated and real data sets, we demonstrate how smoothseg can aid in identification of regions with genomic alteration and in classification of samples. For the real data sets, smoothseg leads to smaller false discovery rate and classification error rate than the circular binary segmentation (CBS) algorithm. In a realistic simulation setting, smoothseg is better than wavelet smoothing and CBS in identification of regions with genomic alterations and better than CBS in classification of samples. For comparative analyses, we demonstrate that segmenting the t-statistics performs better than segmenting the data.

Availability: The R package smoothseg to perform smooth segmentation is available from http://www.meb.ki.se/~yudpaw

Contact:  yudi.pawitan@ki.se
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
Authors: Liu Hongfang , Zeeberg Barry R. , Qu Gang , Koru A. Gunes , Ferrucci Alessandro , Kahn Ari , Ryan Michael C. , Nuhanovic Antej , Munson Peter J. , Reinhold William C. , Kane David W. , Weinstein John N.
Published: July 2007

Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error.

Results: AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are ‘transcript-consistent’ in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6 % of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface.

Availability: The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer.

Contact:  hl224@georgetown.edu or barry@discover.nci.nih.gov
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
Authors: Ingsriswang Supawadee , Pacharawongsakda Eakasit
Published: July 2007

Summary: sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create personal databases by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools from Weka and R packages to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data and (4) building the classification model of biological activity.

Availability: sMOL Explorer is an Open Source project and is freely available to all interested users at http://www.biotec.or.th/ISL/SMOL/

Contact:  supawadee@biotec.or.th
BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences
Authors: Meng Hailong , Banerjee Arunava , Zhou Lei
Published: July 2007

Summary: BLISS 2.0 is a web-based application for identifying conserved regulatory modules in distantly related orthologous sequences. Unlike existing approaches, it performs the cross-genome comparison at the binding site level. Experimental results on simulated and real world data indicate that BLISS 2.0 can identify conserved regulatory modules from sequences with little overall similarity at the DNA sequence level.

Availability:  http://www.blisstool.org/

Contact:  leizhou@ufl.edu
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection
Authors: Yoon Jeongah , Si Yaguang , Nolan Ryan , Lee Kyongbum
Published: July 2007

Motivation: The rational decomposition of biochemical networks into sub-structures has emerged as a useful approach to study the design of these complex systems. A biochemical network is characterized by an inhomogeneous connectivity distribution, which gives rise to several organizational features, including modularity. To what extent the connectivity-based modules reflect the functional organization of the network remains to be further explored. In this work, we examine the influence of physiological perturbations on the modular organization of cellular metabolism.

Results: Modules were characterized for two model systems, liver and adipocyte primary metabolism, by applying an algorithm for top–down partition of directed graphs with non-uniform edge weights. The weights were set by the engagement of the corresponding reactions as expressed by the flux distribution. For the base case of the fasted rat liver, three modules were found, carrying out the following biochemical transformations: ketone body production, glucose synthesis and transamination. This basic organization was further modified when different flux distributions were applied that describe the liver's metabolic response to whole body inflammation. For the fully mature adipocyte, only a single module was observed, integrating all of the major pathways needed for lipid storage. Weaker levels of integration between the pathways were found for the early stages of adipocyte differentiation. Our results underscore the inhomogeneous distribution of both connectivity and connection strengths, and suggest that global activity data such as the flux distribution can be used to study the organizational flexibility of cellular metabolism.

Contact:  kyongbum.lee@tufts.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
AssociationDB: web-based exploration of genomic association
Authors: Seelow Dominik , Hoffmann Katrin , Lindner Tom H.
Published: July 2007

Summary: Genome-wide association studies use hundreds of thousands of markers making it challenging to present and finally interpret the results. We developed a graphical, web-based solution for an interactive exploration of the results of case-control studies, with a tight integration of related gene information and tissue-specific expression data. Association results are presented as physical position-based vertical bars with known genes included as horizontal bars at their respective physical positions. The interface allows the specification of filtering criteria for the association data and highlights potentially interesting genes with user-specified terms occurring in their reports or with relevant expression patterns. Pop-up windows and hyperlinks provide drill-down capabilities and quick access to relevant data AssociationDB can either be used as a stand-alone solution or as a front-end joining association results obtained by other software with genomic information.

Availability:  http://genetik.charite.de/AssociationDB

Contact:  dominik.seelow@charite.de

Supplementary information: The source code, a web-based demo, a step-by-step manual, and an installation guide are available at http://genetik.charite.de/AssociationDB.
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)
Authors: Cheng Haitao , Sen Taner Z. , Jernigan Robert L. , Kloczkowski Andrzej
Published: July 2007

Summary: One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database Mining (FDM) and GOR V. FDM harnesses the availability of the known protein structures in the Protein Data Bank and provides highly accurate secondary structure predictions when sequentially similar structural fragments are identified. In contrast, the GOR V algorithm is based on information theory, Bayesian statistics, and PSI-BLAST multiple sequence alignments to predict the secondary structure of residues inside a sliding window along a protein chain. A combination of these two different methods benefits from the large number of structures in the PDB and significantly improves the secondary structure prediction accuracy, resulting in Q3 ranging from 67.5 to 93.2%, depending on the availability of highly similar fragments in the Protein Data Bank.

Availability: The CDM server is freely accessible by public users and private institutions at http://gor.bb.iastate.edu/cdm

Contact:  taner@iastate.edu
Experimental method for quantifying resistance to the opening of netting panels
Authors: Sala A. , O'Neill F. G. , Buglioni G. , Lucchetti A. , Palumbo V. , Fryer R. J.
Published: July 2007

Sala, A., O'Neill, F. G., Buglioni, G., Lucchetti, A., Palumbo, V., and Fryer, R. J. 2007. Experimental method for quantifying resistance to the opening of netting panels. – ICES Journal of Marine Science, 64: 1573–1578. In recent years, the tendency in some sectors of the fishing industry has been to use thicker and stiffer twines in the manufacture of netting material. This increases the mesh's resistance to opening and, consequently, reduces the selective performance of fishing gears. The main characteristic of netting twine contributing to mesh resistance to opening is flexural rigidity (EI). We present a methodology for quantifying mesh resistance to opening through the use of a prototype called the resistance to opening and deflection meter (ROD-m). It incorporates four tension load cells and four stepping motors that are driven by four ministep bipolar chopper drives. Small panels of netting (3 × 3 meshes) can be mounted on ROD-m, which can measure the forces acting on the netting and the position of the knots. Estimates of the flexural rigidity of the netting twine can be made from these data. We present the results of the analysis of Mediterranean polyamide netting, and standard and Brezline polyethylene (PE) netting from the North Sea. In all netting, regardless of the material used, EI increases with increasing linear density. Furthermore, Brezline is much stiffer than standard green PE, although they are equally thick.
Ageism: Does it Exist Among Children?
Authors: Davidovic Mladen , Djordjevic Zorana , Erceg Predrag , Despotovic Nebojsa , Milosevic Dragoslav P.
Published: July 2007

Ageism is stereotyping and prejudice against individuals or groups because of their age. Robert Butler first used it in 1969, to express a systematic stereotyping and discrimination against elderly people. Available data appears to confirm that attitudes of children to the old age differ from that of adults. The study population consisted of 162 subjects (56 school children, 48 nurses and 58 elderly patients). Each subject in the survey was asked to respond to the following three questions: Question #1: “Is the old age unattractive ?”; Question #2: “How old is an old man? Question #3: “What should you do to have a long life (what is good for longevity)? The majority of polled children (33) gave positive statements about ageing in their responses to the first item, while most of the nurses gave condition answers, like: “It is not unattractive if you are healthy”. Elderly subjects made up a group with the majority of negative responses (in percentage), as only 33% of them answered that old age is not unattractive. All three groups of subjects demonstrated a good knowledge of what is considered good for longevity, and had a generally positive health attitude. Our results indicate that majority of children have positive perception and attitude about old age, which leads us to conclusion that ageism is adopted later in life.
Correlation of Serum Androgens and Pituitary Hormone Levels with Serum PSA Less Than 2.5 NG/ML
Authors: Sofikerim Mustafa , Oruç Özgür , Eskicorapci Sadettin , Guliyev Fuad , Özen Haluk
Published: July 2007

The aim of this clinical study was to determine whether there is a relationship between total serum testosterone, free testosterone, FSH (Follicle-Stimulating Hormone), LH (Luteinizing Hormone) and serum prostate specific antigen (PSA) levels. We postulated that such a correlation existed then the use of hormone specific reference ranges might enhance the usefullness of PSA concentrations <2.5 ng/mL as a marker for prostate cancer.

Prior to digital rectal examination, serum was obtained from all patients between 8.30-10:00 AM for hormone and PSA concentrations. The study was performed on 210 male patients >40 years of age visiting our urology outpatient clinics. PSA was correlated to age (r = 0.23, p = 0.019), but there none between serum testosterone and age. No significant correlation was noted between testosterone or free testosterone and serum PSA levels, and none between serum FSH or LH and PSA. In age specific reference groups (41-49; 50-59; 60-69 years), we found no significant correlation between PSA and hormone concentrations.

In this population of eugonadal men with serum PSA values less than 2.5 ng/ml, serum androgens and pituitary hormones do not appear to correlate with serum PSA.
Novel Tonoplast Transporters Identified Using a Proteomic Approach with Vacuoles Isolated from Cauliflower Buds
Authors: Schmidt Ulrike G. , Endler Anne , Schelbert Silvia , Brunner Arco , Schnell Magali , Neuhaus H. Ekkehard , Marty-Mazars Daniéle , Marty Francis , Baginsky Sacha , Martinoia Enrico
Published: July 2007

Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.
Gibberellin Regulation of Fruit Set and Growth in Tomato
Authors: Serrani Juan Carlos , Sanjuán Rafael , Ruiz-Rivero Omar , Fos Mariano , García-Martínez José Luis
Published: July 2007

The role of gibberellins (GAs) in tomato (Solanum lycopersicum) fruit development was investigated. Two different inhibitors of GA biosynthesis (LAB 198999 and paclobutrazol) decreased fruit growth and fruit set, an effect reversed by GA3 application. LAB 198999 reduced GA1 and GA8 content, but increased that of their precursors GA53, GA44, GA19, and GA20 in pollinated fruits. This supports the hypothesis that GA1 is the active GA for tomato fruit growth. Unpollinated ovaries developed parthenocarpically in response to GA3 > GA1 = GA4 > GA20, but not to GA19, suggesting that GA 20-oxidase activity was limiting in unpollinated ovaries. This was confirmed by analyzing the effect of pollination on transcript levels of SlCPS, SlGA20ox1, -2, and -3, and SlGA3ox1 and -2, encoding enzymes of GA biosynthesis. Pollination increased transcript content of SlGA20ox1, -2, and -3, and SlCPS, but not of SlGA3ox1 and -2. To investigate whether pollination also altered GA inactivation, full-length cDNA clones of genes encoding enzymes catalyzing GA 2-oxidases (SlGA2ox1, -2, -3, -4, and -5) were isolated and characterized. Transcript levels of these genes did not decrease early after pollination (5-d-old fruits), but transcript content reduction of all of them, mainly of SlGA2ox2, was found later (from 10 d after anthesis). We conclude that pollination mediates fruit set by activating GA biosynthesis mainly through up-regulation of GA20ox. Finally, the phylogenetic reconstruction of the GA2ox family clearly showed the existence of three gene subfamilies, and the phylogenetic position of SlGA2ox1, -2, -3, -4, and -5 was established.
AtNUDT7, a Negative Regulator of Basal Immunity in Arabidopsis, Modulates Two Distinct Defense Response Pathways and Is Involved in Maintaining Redox Homeostasis
Authors: Ge Xiaochun , Li Guo-Jing , Wang Sheng-Bing , Zhu Huifen , Zhu Tong , Wang Xun , Xia Yiji
Published: July 2007

Plants have evolved complicated regulatory systems to control immune responses. Both positive and negative signaling pathways interplay to coordinate development of a resistance response with the appropriate amplitude and duration. AtNUDT7, a Nudix domain-containing protein in Arabidopsis (Arabidopsis thaliana) that hydrolyzes nucleotide derivatives, was found to be a negative regulator of the basal defense response, and its loss-of-function mutation results in enhanced resistance to infection by Pseudomonas syringae. The nudt7 mutation does not cause a strong constitutive disease resistance phenotype, but it leads to a heightened defense response, including accelerated activation of defense-related genes that can be triggered by pathogenic and nonpathogenic microorganisms. The nudt7 mutation enhances two distinct defense response pathways: one independent of and the other dependent on NPR1 and salicylic acid accumulation. In vitro enzymatic assays revealed that ADP-ribose and NADH are preferred substrates of NUDT7, and the hydrolysis activity of NUDT7 is essential for its biological function and is sensitive to inhibition by Ca2+. Further analyses indicate that ADP-ribose is not likely the physiological substrate of NUDT7. However, the nudt7 mutation leads to perturbation of cellular redox homeostasis and a higher level of NADH in pathogen-challenged leaves. The study suggests that the alteration in cellular antioxidant status caused by the nudt7 mutation primes the cells for the amplified defense response and NUDT7 functions to modulate the defense response to prevent excessive stimulation.
Light-Independent Phytochrome Signaling Mediated by Dominant GAF Domain Tyrosine Mutants ofArabidopsisPhytochromes in Transgenic Plants
Authors: Su Yi-shin , Lagarias J. Clark
Published: July 2007

The photoreversibility of plant phytochromes enables continuous surveillance of the ambient light environment. Through expression of profluorescent, photoinsensitive Tyr-to-His mutant alleles of Arabidopsis thaliana phytochrome B (PHYBY276H) and Arabidopsis phytochrome A (PHYAY242H) in transgenic Arabidopsis plants, we demonstrate that photoconversion is not a prerequisite for phytochrome signaling. PHYBY276H-expressing plants exhibit chromophore-dependent constitutive photomorphogenesis, light-independent phyBY276H nuclear localization, constitutive activation of genes normally repressed in darkness, and light-insensitive seed germination. Fluence rate analyses of transgenic plants expressing PHYBY276H, PHYAY242H, and other YGAF mutant alleles of PHYB demonstrate that a range of altered light-signaling activities are associated with mutation of this residue. We conclude that the universally conserved GAF domain Tyr residue, with which the bilin chromophore is intimately associated, performs a critical role in coupling light perception to signal transduction by plant phytochromes.
Managerialism: a threat to professional librarianship?
Authors: McMenemy David
Published: July 2007

Purpose

The paper seeks to discuss the potential impact of managerialism on public libraries in the UK, and to suggest a potential methodology to investigate the reality of the situation based on previous works in the field.

Design/methodology/approach

The article provides a reflective viewpoint.

Findings

The paper proposes that managerialism in libraries and professional librarians are potentially bad fits, and that a broader understanding of the incompatibilities through proper research is necessary if a healthy future for the profession is to be ensured.

Research limitations/implications

The paper proposes a methodology for investigating a potentially crucial impactor on professional librarianship.

Originality/value

The paper discusses a topic that is much discussed in relation to other professional groupings, but is little discussed in terms of librarianship.
Consumer advice in the library
Authors: Wainwright Gordon
Published: July 2007

Purpose

The paper is presented as part of the 80th birthday commemorations of Library Review. It seeks to discuss taking a more interventionist line in helping library users develop their reading habit.

Design/methodology/approach

The paper provides a reflective viewpoint.

Findings

The paper finds that public librarians should be more proactive in helping users develop their reading skills by using the wide literature in the field.

Originality/value

The paper is of interest as a historical paper related to libraries and reading.
Making choices: research paradigms and information management
Authors: Burke M.E.
Published: July 2007

Purpose

The purpose of this paper is to examine a variety of research approaches which information managers may find useful to meet the needs of working in the networked, digitized age.

Design/methodology/approach

This is achieved by a discussion of the research paradigms inherent within both information theory and social theory.

Findings

The findings work towards a final justification for an interpretist approach as the most appropriate context in which to work, in order to meet the emerging trends and current challenges of information technology management.

Practical implications

The central theme of this paper is that research which deals primarily with people and information in a world of change, competition, and fluid communications technology should take into account and allow for an understanding of human behaviour. This understanding helps to highlight different contexts, backgrounds, and cultures and therefore provides assistance in making appropriate choices concerning research paradigms and information management, which in turn will ensure thoughtful methodology and justifiable research results.

Originality/value

This paper examined questions regarding the choices of research paradigms and the practical application of philosophy to the life of professional information managers.
On reading: consumer advice in the library
Authors: Poulter Alan
Published: July 2007

Purpose

This paper seeks to reflect on an earlier paper “Consumer advice in the library”, by Gordon Wainwright, Library Review, Winter 1966.

Design/methodology/approach

The paper pursues a reflective viewpoint.

Findings

The original paper was possibly ahead of its time in some ways in its thoughts about public libraries.

Practical implications

The paper discusses viewpoints from 40 years ago and compares them with contemporary practice.

Originality/value

The paper compares past with contemporary thinking about the role of public libraries.
Managing e‐books at the University of Derby: a case study
Authors: Wilkins Valerie
Published: July 2007

Purpose

The purpose of the paper is to describe the practical experience of managing e‐books in an academic library.

Design/methodology/approach

An overview of the three main e‐book collections used (netLibrary, Taylor & Francis, and Ebook Library via Dawson) is provided, along with details such as the acquisition, cataloguing and maintenance of e‐books; funding, licensing and authentication; varying interfaces; publicity, promotion and user education; subject coverage, statistics and usage.

Findings

Variations in approach and services by the suppliers of e‐books can provide challenges for those managing e‐books.

Originality/value

The paper provides practical details of managing e‐books in an academic library that might be of relevance to others.
The online reading list project using Talis List at the University of Glamorgan
Authors: Morgan Rachael
Published: July 2007

Purpose

The purpose of this paper is to demonstrate the issues surrounding the implementation of an online reading list system at the University of Glamorgan.

Design/methodology/approach

The paper reports on an implementation project, using Talis List, which took place between November 2005 and March 2006.

Findings

The project itself was a success, with the target number of reading lists made available being exceeded. As with any new system, the development of the processes involved in its day‐to‐day running can be unpredictable. Workflows did not develop as anticipated; the ways in which reading lists were collected from academics varied, as did the styles of the lists themselves. Some issues were encountered around linking to electronic resources and embedding the system into the university's virtual learning environment (VLE).

Originality/value

This paper will be of value to those interested in the development and use of online reading lists.
Desa Informasi: a virtual village of “new” information resources and services in Indonesia
Authors: Toong Tjiek Liauw
Published: July 2007

Purpose

The purpose of this paper is to introduce Desa Informasi (Information Village), an institutional repository project carried out by Petra Christian University Library in Surabaya, Indonesia, and discuss its potential for enabling academic libraries to remain relevant in the digital era.

Design/methodology/approach

Definitions of an institutional repository are discussed and a short description of Desa Informasi and its digital contents are given. The potential of the digital contents in the repository as a “new species” of resource, as well as for a base for offering new services by academic libraries, is discussed. Lastly, the possibility of an institutional repository project being used by academic libraries to reach out to society is described, with relevant examples from the Desa Informasi project.

Findings

An institutional repository project can result in “new” resources and services for academic libraries, and has the potential to reach out to communities outside their traditional user base.

Originality/value

This paper identifies opportunities for academic libraries to remain relevant in the digital era.
Library and IT mergers: how successful are they?
Authors: McKinzie Steve
Published: July 2007

Purpose

The purpose of this paper is to provide an introduction to four articles from Reference Services Review focusing on the theme of library/IT mergers. It aims to place the articles that follow in their larger historical context and draw conclusions about the success or lack of success of such mergers in general.

Design/methodology/approach

The paper frames the four articles that follow, explaining their approach to library/IT mergers and their place in the ongoing discussion of the service effectiveness of such converged organizations.

Findings

The paper suggests that library/IT service mergers may be analogous to management's or labor's decision to unionize.

Practical implications

The success of academic libraries and IT services has more to do with the quality of leadership and professional commitment to service than it does with the question of whether these two academic units should merge.

Originality/value

The paper provides an introduction to the special issue on library and IT mergers.
The perception of effectiveness of merged information services organizations
Authors: Stemmer John K.
Published: July 2007

Purpose

The purpose of this paper is to assess the perceptions of chief information officers and academic deans with respect to the effectiveness of merged information services organizations (MISOs) at liberal arts colleges.

Design/methodology/approach

This study is descriptive exploratory survey research. A survey of chief information officers (CIOs) and academic deans of liberal arts colleges with merged information services organizations was undertaken. In addition to a general assessment of the MISO, a taxonomy of expected benefits was developed from the literature. Respondents provided information on both the general effectiveness of the MISO and its delivery of the expected benefits. Both quantitative and qualitative data were collected.

Findings

The paper finds that both CIOs and academic deans had a favorable impression of the MISO and believed it was effective in providing support and delivering expected benefits. Concerns were raised that the MISO organization requires staff development time and can contribute to a loss of focus among constituent units.

Research limitations/implications

The study is limited to Carnegie bachelor's level institutions with a MISO.

Practical implications

MISOs are effective in providing support and the expected benefits. Institutions implementing or considering the MISO model should be aware of possible problem areas (staff development and loss of unit focus) and plan to address them appropriately.

Originality/value

The study identified areas of concern among both CIOs and deans with the implementation of a MISO. Information services units' leadership as well as institutional administration should consider these findings when considering or implementing a MISO.
Get it in writing: MOUs and library/IT partnerships
Authors: Mary Walters Carolyn , Van Gordon Elizabeth Ann
Published: July 2007

Purpose

Increasingly academic libraries are partnering with other campus units to improve efficiency and to better serve students and faculty. This paper aims to focus on the importance of developing a memorandum of understanding (MOU) to foster a relationship between an academic library and IT unit. It seeks to identify what the MOU should include, pitfalls to be avoided, and lessons learned. It also proposes demonstrating how the MOU has been used as a model for other alliances and how, because of the MOU, a partnership has flourished.

Design/methodology/approach

This paper will outline the steps taken that led to the successful MOU created by the Indiana University Bloomington (IUB) Libraries and University Information Technology Services (UITS.)

Findings

The paper finds that a well‐crafted MOU that allows for flexibility in ongoing decision making by service stakeholders permits partnerships to evolve and mature and creates the avenue for continued success and innovation.

Practical implications

This paper describes the execution and ongoing evolution of a successful partnership based on a MOU and commitment by the IUB Libraries and the central technology organization, UITS.

Originality/value

Libraries interested in entering into or strengthening partnerships with IT or other campus organizations can use the Indiana University experience and MOU as a model.
Creating collaborative technology‐rich workspaces in an academic library
Authors: Barton Emily , Weismantel Arlene
Published: July 2007

Purpose

The purpose of this paper is to describe the process of the planning, implementation, promotion, management and assessment of the Collaborative Technology Laboratories (CTLs) at the Michigan State University Libraries. It aims to emphasize the need to move quickly due to funding considerations and how to make the most out of a truncated timetable.

Design/methodology/approach

The paper describes the information gathering, decision‐making, promotion, and assessment processes in the construction of the CTLs.

Findings

The paper finds that the process by which new CTLs are created, and existing ones maintained, evolves as experience begins to inform the decision‐making process.

Practical implications

Creating technology‐rich group space is attainable, practical, appreciated by the students and faculty, and assists in advancing the educational mission of the University.

Originality/value

Other libraries can use this information to inform their own decision making when creating technology‐rich collaborative workspaces in academic libraries.
Do academic enquiry services scare students?
Authors: Robinson Catherine M. , Reid Peter
Published: July 2007

Purpose

The purpose of this paper is to clarify the ways in which students seek help in libraries, and their feelings about using library enquiry services. In this way, it should bring practical benefits to academic libraries seeking to design and introduce new forms of reference service. The paper also aims to touch on the issue of whether anonymity offered by digital reference services is likely to make more students ask for help. A major aim of this study is to find ways to encourage those students who need help, to seek it.

Design/methodology/approach

This paper uses the results taken from 12 qualitative interviews with undergraduate students to examine these students' help‐seeking methods and their use of academic library reference services.

Findings

The study finds that the reasons for not using enquiry services were various and complex and included a lack of awareness of services, embarrassment or shyness, anxiety caused by mechanical barriers and affective barriers. The interviews revealed that shyness is more widespread than libraries might imagine and seemingly confident students can find asking for help embarrassing in some circumstances.

Originality/value

This paper focuses on students' thoughts and opinions, and it is this student‐centred approach which gives particular insight into the reasons students do not seek help. This adds to the body of qualitative research examining undergraduates' help seeking methods and provides practical advice for encouraging students to ask for help.
From paper to electronic, the evolution of pathfinders: a review of the literature
Authors: Vileno Luigina
Published: July 2007

Purpose

The purpose of this paper is to provide a review of the literature on pathfinders, from the 1970s to the present.

Design/methodology/approach

The paper reviews a range of publications which describe the methodology of pathfinders, provide practical advice and information, present research results, to aid librarians and library administrators in how to best manage the production and marketing of pathfinders.

Findings

It was found that not much has been written on pathfinders. A few articles on traditional pathfinders were published between 1972 and 1995. In 1996, the electronic format took over. Most of the articles are of a practical nature although some describe empirical research. One void in the literature that has been found is librarians' lack of knowledge of users' needs and preferences. This results in much time and effort being dedicated to the production of pathfinders but without any consideration of users, thus discouraging them from using the available resources.

Practical implications

This paper will be a useful source of information for librarians. It provides an overview of guidelines and best practices currently reported in the literature as well as the latest technical and educational trends.

Originality/value

Such an extensive review of the literature on pathfinders has not been done before. It provides practical information for librarians wanting to embark on the production of pathfinders. It also identifies possible areas of future study.
Viewing information needs through a Johari Window
Authors: Shenton Andrew K.
Published: July 2007

Purpose

The purpose of this paper is to apply to the study of information needs the Johari Window framework that has long been accepted as a useful model for understanding interpersonal communication.

Design/methodology/approach

The work presents a newly‐constructed version of the Window to delineate a typology of information needs and to identify implications that emerge for information professionals.

Findings

The paper finds that information needs can be seen to fall into five broad categories: needs that are known to the individual but not to the information professional; needs that are known to both parties; needs that are known to the information professional but not the individual; needs that are misunderstood by the individual; and needs that are not known to either the individual or the information professional.

Practical implications

Conceptualising information needs in terms of the revised Johari Window highlights how information professionals are of crucial importance in helping clients satisfy their information needs, even in an era in which much information searching is done by end‐users themselves.

Originality/value

No previous paper has applied the Johari Window to the investigation of information needs and few authors have made an attempt to use the framework in any area of library and information science (LIS) whatsoever. The fact that the work deals with both theoretical and practical dimensions will interest LIS academics and library professionals who work regularly with information users.