bluuebunny/crossref_metadata_2025 huggingface dataset:
Out of Time
Authors: Parkins Wendy
Published: September 2004

Slow living involves the conscious negotiation of the different temporalities which make up our everyday lives, deriving from a commitment to occupy time more attentively. This article considers the significance of time in practices of slow living and the imbrication of time and speed in notions of ‘slowness’ where slowness is constructed as a deliberate subversion of the dominance of speed. By purposely adopting slowness, subjects seek to generate alternative practices of work and leisure, family and sociality. I will focus on the Slow Food movement as a significant manifestation of both the desire for and the implementation of slow living through a reconceptualization of time in everyday life.
Uncertain Times
Authors: Reith Gerda
Published: September 2004

This article examines the ways in which understandings of uncertainty have evolved during the development of modernity, and in particular, how they are expressed in the notion of ‘risk’. It demonstrates how this concept is embedded in socio-economic contexts and grounded in particular temporal orientations, specifically as expressed in notions of determinism and indeterminism. It suggests that, although the concept of risk initially embodied an orientation to the future as something that was predictable and open to human intervention, transformations in the structure of capitalism mean that its utility is now to be found in its role as a guide for action in late modern societies, in which the future has ‘collapsed’ into an indeterminate present.
Two-Dimensional Static Fields in Magnetoelectroelastic Laminates
Authors: Heyliger Paul R. , Ramirez Fernando , Pan Ernian
Published: September 2004

The two-dimensional behavior of laminated magnetoelectroelastic plates is investigated for two specific geometries: laminates under conditions of cylindrical bending and homogeneous plates under traction-free conditions. These plates are composed of a collection of elastic, piezoelectric, and magnetostrictive layers with perfect bonding between each interface. We investigate the through-thickness behavior of the five primary unknowns (the three displacements and the electric and magnetic potentials) under a variety of boundary conditions and aspect ratios using a discrete-layer theory. Results are compared with exact solutions for the case of cylindrical bending and finite element models for traction-free deformation. Excellent agreement is found between the approaches, and generalizations regarding global plate behavior are summarized.
On the Application of Shunted Piezoelectric Material to Enhance Structural Damping of a Plate
Authors: Fein Oliver M. , Gaul Lothar
Published: September 2004

In this work the application of resistively shunted piezoelectric material for reducing vibration amplitudes of a plate is studied. The ability to tailor the frequency-dependent loss factor is a consequence of the applied passive electrical network. To predict the damping performance of resistively shunted piezoelectrics, an approach based on the effective strain energy fraction is proposed. A finite element model may be used to accurately determine the effective modal strain energy fraction. However, for placing purposes of the piezoelectric elements, an analytical model, which does not account for local stiffening due to the piezoceramics, can be used. Design considerations include the frequency dependence of piezoceramic properties as well as the effect of stiff piezoceramic material on mode shapes. Experimental results are presented for a rectangular plate with eight pairs of resistively shunted piezoelectric elements.
Smart Layer for Damage Diagnostics
Authors: Hurlebaus Stefan , Gaul Lothar
Published: September 2004

In this research damage diagnostics is carried out by a novel design of a smart layer that consists of piezoelectric films. This thin layer is attached to the structure being monitored. First, some fundamental investigations are carried out in order to examine the influence of the thickness of the film, the influence of different adhesives, and the influence of the couplant. The wave field generated by the smart layer propagates into a solid. The directional dependency is investigated. Moreover, an improved type of polyvinylidene fluoride (PVDF) copolymer is presented and investigated for the potential application in the field of structural health monitoring. The use of this PVDF copolymer makes the manufacturing process of a self-sensing actuating layer in ultrasonics much easier than conventional PVDF films since the piezoelectric film is directly sputtered onto the surface of a metallic specimen or onto a metallic layer. This smart layer technique is a valuable tool for identifying the location and size of cracks and delaminations in composites as well as for determining local material thicknesses which might occur due to corrosion. It can be applied in order to monitor the so-called ‘hot spots’ on new structures as well as on already existing structures. The application of the smart layer is demonstrated on a plate-like structure containing a damage. The identified damage corresponds well with the actual damage.
Adaptive Structural Control Experiment Using Recursive System Identification
Authors: Kim Youdan , Hyung Seungyong , Suk Jinyoung
Published: September 2004

This paper presents a real time adaptive active control system for vibration suppression of flexible structural systems with piezoelectric actuators–sensors. The system considered in this paper is a plate model with segmented piezoelectric actuators. An input–output model is developed for the identification of the systems, and on-line recursive identification scheme that is adequate to the proposed input–output model is used. An adaptive control method combined with model following control scheme is proposed for vibration suppression. An estimator is considered to exclude the effect of noise from the output signals. The proposed control strategy is successful in improving the dynamic characteristics of the structural systems. The experiments demonstrated the benefit of the proposed algorithm.
The “Fish-Mouth” Actuator: Design Issues and Test Results
Authors: Campanile L. F. , Keimer R. , Breitbach E. J.
Published: September 2004

The so-called “fish-mouth actuator”, developed at DLR in the framework of the Adaptive Wing project (ADIF), is a compact hybrid actuator based on the interaction of a shape memory material and a composite flexible mechanism. The actuator offers a high effective strain (ratio between actuator’s stroke and mounting dimension in the activation direction) and is therefore particularly interesting for the shape control of thin surfaces.

In the ADIF project, the actuator development was focused on the realization of a wind-tunnel model for an adaptive wing with transonic bump. The actuator is designed and tested for a maximum stroke of 2 mm and a maximum force of 200 N. Its thickness (in activation direction) amounts to about 8 mm. If used with a feedback control system, it can reach a displacement precision of less than 1 mm. More than 400 single actuators were built and tested; 84 of them were integrated in the final system.

In this paper, several design issues are discussed that are typical for such fully coupled hybrid systems. The design analysis and procedure used for the actuator development is described and a choice of experimental results is shown and discussed.

The reported design philosophy and the related discussion include many concepts and solutions of general relevance which can be adopted for the development of similar hybrid actuators in the future.
Doctors, “Dirty Work” Patients, and “Revolving Doors”
Authors: Shaw Ian
Published: September 2004

Using information from research into the phenomenon of “revolving-door” psychiatric patients, the author explores general practitioners’ perceptions of difficult patients and the consequences for patient management. He first considers the concept of “good and bad” as a possible subtype of dirty work. He then presents the evidence of medical irritation with patients from interview data and explores the rationalizations for the way in which patients are subsequently managed. In line with previous studies, the author argues that the construction of patients as difficult and the subsequent dynamics of exclusion lie in the breakdown of the “normal” doctor-patient relationship coupled with the doctor’s need to get on with the day’s workload. Moral judgments formed a part of the exclusion process.
At the Margins? Discourse Analysis and Qualitative Research
Authors: Cheek Julianne
Published: September 2004

Discourse analysis is a qualitative research approach that offers the potential to challenge our thinking about aspects of the reality of health and health care practice. In this article, the author explores one approach to discourse analysis and examines how it offers possibilities for different ways of viewing health and health care practices. She concludes by raising questions as to whether discourse analysis is at the margins of qualitative research, whether that matters, and where discourse analysis might take those margins.
The Role of Humor for Men with Testicular Cancer
Authors: Chapple Alison , Ziebland Sue
Published: September 2004

In this article, the authors examine how 45 men talked about “pure” and “applied” humor in qualitative interviews about their experience of testicular cancer. Most described using applied humor in work and social settings to challenge assumptions about the disease, and in health settings to manage feelings, hide embarrassment, reduce tension, share a sense of solidarity with others, or encourage others to examine themselves. Men also described their usually positive reaction to jokes made by others; jokes helped to dispel tension and reassured men that they were being treated as normal. In a few accounts, men revealed how humor was hurtful. They were sometimes upset about jokes made by others, or by the idea of jokes being made, fearing humiliation and stigma. Humor might ease difficult interactions, but our results suggest that clinicians and others should be careful not to initiate humor without a clear lead from the patient.
Philosophical Inquiry in Nursing: An Argument for Radical Empiricism as a Philosophical Framework for the Phenomenology of Addiction
Authors: Gray Mary Tod
Published: September 2004

Philosophical inquiry involves examination of the meaning of a phenomenon within the larger framework of the human condition and a particular view of reality. Argumentation is the method. In this study, the author argues that the metaphysics of radical empiricism enhances the understanding of the immediate subjective experience or phenomenology of addiction. When applied to subjective narratives of the addiction experience from literature, this metaphysics confers meaning to the changes in consciousness that occur in the immediate subjective experience of addiction. Conclusions revealed from the application of this perspective highlight novel feelings, the will and changing sense of self, and the human values of belonging and freedom. This study also revealed the value of the philosophical method of inquiry: to temporize our moral judgments and enrich our perspective of the human values within the addiction phenomenon. These values support and clarify the belief system of nursing.
Being Present in a Distant Room: Aspects of Teleconsultations with Older People in a Nursing Home
Authors: Sävenstedt Stefan , Zingmark Karin , Sandman P. -O.
Published: September 2004

In a telecare project in Northern Sweden, videophones have been used to facilitate teleconsultations between nurses and elders at a nursing home. The authors designed this study to elucidate qualities in the communication in the professional encounter between nurses and elders assisted by nursing staff in the teleconsultations. They interviewed 2 registered nurses and 5 nursing staff members with long experience of using videophones in the telecare project, out of 20 staff members, and analyzed them using a phenomenological-hermeneutic method. In a comprehensive interpretation, teleconsultations could be understood as glimpses of the experience of being in the other’s room with a feeling of providing nursing presence. This was attained when aspects such as familiarity, safety, transparency, and interest were promoted.
Poverty, Structural Barriers, and Health: A Santali Narrative of Health Communication
Authors: Dutta-Bergman Mohan J.
Published: September 2004

Recent years have witnessed a surge in scholarship that problematizes the linear, Eurocentric approach to international health communication and suggests the pressing need for a culture-centered approach. This author takes a culture-centered approach to exploring the Santali meanings of health in rural Bengal. The open-ended interviews conducted with the Santals bring to surface key issues and meaningful theories of health. Central to the Santali experience of health is food; for the Santal, it is his or her hunger that is the greatest cause of disease and illness. Poverty and the presence of structural barriers that cripple Santali existence emerge as the critical themes of Santali health meanings. The study also illuminates the complex process of meaning making engaged in by participants of marginalized sectors. The author draws policy-based implications from the findings of this research.
The Stress and Coping of Israeli Emergency Room Social Workers Following Terrorist Attacks
Authors: Somer Eli , Buchbinder Eli , Peled-Avram Maya , Ben-Yizhack Yael
Published: September 2004

The authors of this qualitative study analyze Israeli hospital social workers’ emotional responses to working with civilian casualties in the wake of an unprecedented surge of terrorist violence. Data are based on four focus groups conducted with 38 hospital social workers in relation to their experience with clients in the emergency room. Three themes were identified: (a) Restoring a lost sense of personal security as a necessary stepping-stone toward resuming professional performance, (b) Meeting the families’pain and responding to it, and (c) Disconnecting emotionally in the service of the professional self. The authors discuss the findings in light of the literature on peritraumatic dissociation among helpers.
The Collaborative Construction of a Management Report in a Municipal Community of Practice
Authors: Wegner Diana
Published: September 2004

Drawing on rhetorical genre studies and recent work in activity system theory, this study focuses on the collaborative development of a new written form, a municipal plan for protecting and managing natural areas. The author advances a twofold claim: (a) that the written plan is developed in the absence of a stable textual model and (b) that the text, as part of the context, functions, in turn, as a mediational tool for solving the rhetorical problem of audience resistance. Findings show that as participants reconfigure the project into successive cycles of activity, they create corresponding zones of proximal development. This study contributes to our understanding of the dynamics of the text-context relationship and to recent elaborations of genre as an activity system that help explain the relationship between genre and learning.
Technical Communication Instruction in Engineering Schools
Authors: Reave Laura
Published: September 2004

This survey of 73 top-ranked U.S. and Canadian engineering schools examines initiatives that engineering schools are taking to improve communication instruction for their students. The survey reveals that 50% of the U.S. schools and 80% of the Canadian schools require a course in technical communication. About 33% of the schools utilize some form of integrated communication instruction, and another 33% offer elective courses in communication. Just 10 schools have created engineering communication centers to provide additional individualized coaching and feedback for their students. The most comprehensive preparation that engineering schools provide is a communication-across-the-curriculum approach that combines these instructional methods to offer concentrated instruction, continual practice, situated learning, and individualized feedback.
Protecting the Voices of Our Research
Authors: Cross Geoffrey A.
Published: September 2004

Although discussion of composition research methods over the last 10 years has culminated in Conference on College Composition and Communication (CCCC) guidelines, these guidelines do not include procedures for verifying qualitative data. Such procedures would entail having a third party check to some degree that the researcher spent the time claimed at the site and that the subjects did what was described and said what was quoted in the published research. This commentary reviews federal policies on research misconduct and government and professional association responses to data faking, noting the additional danger of incompetent investigations of research misconduct. Arguing that the discipline should take appropriate measures to verify qualitative data, I recommend a two-tiered approach.
The Impact of Culture and Minority Status on Women’s Experience of Domestic Violence
Authors: Kasturirangan Aarati , Krishnan Sandhya , Riger Stephanie
Published: September 2004

The influence of culture and ethnic background on women’s experience of domestic violence has been explored in research only recently. Here the authors review research about the impact of culture and minority status in the United States on women’s experience of domestic violence, considering family structure,immigration, acculturation, oppression, and community response. The authors encourage researchers and service providers to acknowledge the effects on women of sociopolitical dynamics, including racism, and to identify specific aspects of culture that are relevant to intimate partner abuse.
Ethnic Differences in Intimate Partner Violence in the U.S. General Population
Authors: Field Craig A. , Caetano Raul
Published: September 2004

This article reviews cross-sectional and longitudinal research on ethnic differences related to intimate partner violence (IPV) in the U.S. general population and the role of alcohol use and socioeconomic characteristics. Evidence indicates that significant ethnic differences exist in the prevalence of IPV. Although ethnic minorities report higher rates of IPV, differences in crude rates are reduced after controlling for socioeconomic circumstances and alcohol use. However, Black couples appear to be at greater risk of IPV than their White or Hispanic counterparts even after controlling for such risk factors. Overall, socioeconomic characteristics,demographic characteristics, and alcohol use appear to play important roles in the occurrence of IPV. These findings suggests that IPV continues to be a significant public health problem and represents an area of health disparity for ethnic minorities.
Wound Outcomes: The Utility of Surface Measures
Authors: Gilman Thomas
Published: September 2004

The value of using quantitative measures to follow the progress of wound healing is well recognized. However, several methods are in use, and the best way to do this is not always clear from the literature. This article describes the advantages of the linear healing parameter and the disadvantages of the area- and volume-based parameters. The shapes and sizes of wounds influence area- and volume-based parameters, hence these will give biased comparisons. Healing rates based on the linear parameter are independent of initial wound size or shape, and they allow unbiased comparisons within and across studies. A formula for predicting healing time from measurements early in the healing course is presented and discussed. Less precise linear healing measurements that are easy to obtain, and that are as valid as the more precise measurements, are also described.
An Audit of Lower Extremity Complications in Octogenarian Patients with Diabetes Mellitus
Authors: Reed James F.
Published: September 2004

Podiatric pathology is common in the elderly patient population per se. Whether the presence of diabetes mellitus in the elderly imposes an additional risk for podiatric problems is questionable. The purpose of this study was to determine if the prevalence of podiatric problems in octogenarian diabetic patients differed from that found in a similarly aged group of nondiabetic patients. For this study, the prevalence of lower extremity complications in octogenarian patients (age 80) with diabetes and without diabetes was estimated using data from the 1996 through 2002 National Hospital Discharge Survey. The diabetic octogenarian patients had twice the risk for developing an ulcer; 3 times the risk of developing a foot abscess, and a 4-fold risk of developing osteomyelitis. Furthermore, the octogenarian diabetic patient is nearly twice as likely to undergo ulceration debridement and 3 to 5 times more likely to have a lower leg amputation, toe amputation, or any amputation. The incidence of amputations, ulcerations, and other serious conditions is significantly higher in the diabetic group compared to normal age-matched control patients. This study shows that in the octogenarian patient the presence of diabetes imposes an additive risk for complications.
An Audit of Foot Infections in Patients with Diabetes Mellitus Following Renal Transplantation
Authors: George Robbie K. , Verma Ashok K. , Agarwal Amit , Agarwal Gaurav , Mishra Saroj K.
Published: September 2004

Foot lesions in postrenal transplant diabetics are often overlooked and hence underestimated. An audit of patients attending the authors’ department was done. They reviewed the case notes to assess the presentation, clinical profiles, and outcomes of foot infections in patients with diabetes mellitus who received renal transplants at their center. Medical records of 192 diabetic foot patients were assessed, of which 8.8% (n = 17) had a history of previous renal transplantation for diabetic nephropathy. All 17 patients had noninsulin-dependent diabetes of mean duration of 16.2 years (range 7-27 years). Common complications and risk factors were studied. Mean duration to development of foot lesions in renal allograft recipients was 19.7 months (range 6-84 months). The big toe was the most commonsite of infection. Neuropathy and poor foot care appear to be important factors in the development of these foot lesions. Escherichia coli was the predominant organism on pus culture. Thirty-eight percent of patients needed major amputations; absence of an intact distal vascular tree was associated with a high major amputation rate. Two patients expired due to foot-related septicemia, and healing occurred in the remainder. Mean hospitalization time was 32.7 days. Most patients required more than one admission. The study emphasizes the need for greater attention to lower extremity complications in this patient group.
Buried Chip Skin Grafting in Neuropathic Diabetic Foot Ulcers Following Vacuum-Assisted Wound Bed Preparation: Enhancing a Classic Surgical Tool with Novel Technologies
Authors: Kopp Jürgen , Kneser Ulrich , Bach Alexander D. , Horch Raymund E.
Published: September 2004

In patients with diabetes mellitus, complications such as polyneuropathy and peripheral angiopathy inevitably lead to diabetic foot complications including foot ulcers, gangrene, and osteoarthropathy. These conditions necessitate minor or major amputation as part of treatment. In patients with Charcot’s arthropathy and predominant neuropathy, recurrent foot ulcers are common in areas of high pressure. Such high pressure is caused by the degrading of the architecture of the foot and inadequate footwear. These patients are a clinical challenge. A select group of such patients may benefit from free surgical tissue transfer, though free or local flap surgery is often difficult or even impossible owing to an impaired arterial circulation. In such wounds, surgical debridement followed by skin grafts often fail due to bacterial burden in the wounds. To circumvent these problems, the authors developed a therapeutic approach using buried chip skin grafting to close granulation wound beds in diabetic feet. Locally applied vacuum therapy (VAC®) for wound bed preparation of chronic, nonresponsive foot ulcers and subsequent grafting using the burying technique with a minute fraction of skin was used. Firm closure was achieved. The closed wound was resistant to mechanical irritation.
Sciatic Nerve Schwannoma
Authors: Rekha A. , Ravi A.
Published: September 2004

Schwannomas are benign tumors of the nerve sheath, commonly seen in the vestibular nerve. Although they are common in the head and neck areas, their occurrence in extra-cranial locations is rare. We report a case of a sciatic nerve schwannoma and review the literature.
Wound Healing Potential of Pterocarpus Santalinus Linn: A Pharmacological Evaluation
Authors: Biswas Tuhin Kanti , Maity Lakshmi Narayan , Mukherjee Biswapati
Published: September 2004

The need for new therapeutics for wound healing has encouraged the drive to examine the nature and value of plant products. Ayurveda, the Indian traditional system of medicine, mentions the values of medicinal plants for wound healing. One of these is Pterocarpus santalinus. This article describes a pharmacological study to evaluate its toxicity as well as wound-healing potential in animal studies. Powder made from the wood of the P. santalinus tree was used to make up an ointment in a petroleum jelly base. No toxic effects were observed in 72 hours. Studies were done on punch and burn wound models on normal and diabetic rats using the test ointment, untreated and vehicle controls, and standard therapy. Physical and biochemical measurements were made. The test ointment-treated wounds healed significantly faster. On healing, collagenesis and biochemical measurements yielded supportive data. These studies permit the conclusion that the P. santalinus ointment is safe and effective in treating acute wounds in animal models.
A Review of the Principles and Use of Lasers in Lower Limb Problems
Authors: Cotton A. M.
Published: September 2004

Lasers present a unique light source with many clinical uses including a number of applications relevant to the lower extremity. In this article, the basic principles of lasers and their interactions with tissue will be reviewed. The article examines laser applications in skin and vascular disease including wound healing. The principles of laser safety are discussed, and relevant future developments are considered.
Analysis of Skin Wound Images Using Digital Color Image Processing: A Preliminary Communication
Authors: Oduncu Hakan , Hoppe Andreas , Clark Michael , Williams Robert J. , Harding Keith G.
Published: September 2004

This article presents the use of digital image processing using hue, saturation, and intensity measurements as a technique for the color analysis of chronic wounds on the skin. An adaptive spline technique was used to segment the wound boundary in the images of venous leg ulcers. This technique was further used to approximate the position of venous leg ulcers. The amount of slough within the wound site was quantified using the software developed and was compared with a grading system based on visual inspection by an experienced clinician, and the results were compared by deriving Kappa (K) statistic. There was moderate agreement over all grades between the computer and clinician. At lower grades 1 and 2, there was excellent agreement. The results from this preliminary study suggest that this analytical technique has the potential to image process chronic skin wounds.
Toward an Integral Education for the Ecozoic Era
Authors: Gunnlaugson Olen
Published: September 2004

This article explores the 2002-2003 change in vision and educational philosophy of a grassroots international college in rural Sweden. The author proceeds with an integral assessment of the strengths and shortcomings of Holma College of Holistic Studies former modes of learning guided by a postmodern epistemology infected with narcissism, hypersubjectivity, and new age thought. Exploring new territory beyond the scope of the former holistic vision, the author articulates an integrally informed vision of education for young adults that offers a shared integral language, a functional life-world ethic, and comprehensive frameworks for transformative learning and development appropriate to our time. With the intent of proposing a model of praxis directly informed by the fields of transformative learning and integral studies, the author outlines and reflects on the first wave of integral education that emerged during the transition year to Holma College of Integral Studies.
Developing Authenticity as a Transformative Process
Authors: Cranton Patricia , Carusetta Ellen
Published: September 2004

The authors explored the meaning of authenticity in teaching by talking to a group of 22 educators over 3 years. Educators’ ways of being authentic in their teaching moved from concrete understandings of self, others, relationships, context, and reflection through to multifaceted and integrative perspectives. The authors used transformative learning theory and Jung’s concept of individuation to understand the development of authenticity.
Reinventing Your Life after 60
Authors: Bliss Tamara J.
Published: September 2004

This article provides a range of resources for individuals in the 55-to-75 age range who are seeking ways to regenerate and reinvent themselves for their Third Age bonus years. Descriptions and Web addresses are listed for national-, state-, and community-based organizations plus university-based research and policy centers and businesses that focus on the special interests and needs of individuals in the Third Age. Organizations such as Civic Ventures and the Massachusetts Coming of Age Coalition focus on tapping the talents and skills of older Americans by developing avenues for meaningful community service. The Elderhostel Institute Network is a resource for identifying Lifelong Learning Institutes, community-based organizations of retirement-age people dedicated to meeting the educational interests of its members. At the local level Discovering What’s Next: Re Vitalizing Retirement is a prototype of a community-based life options planning initiative.
Centering Spirituality in the Academy
Authors: Shahjahan Riyad Ahmed
Published: September 2004

In this article, the author’s foremost objective is to render the answer to the following question: How would centering spirituality transform our ways of teaching and learning? The author explores the terrain of the answer to this question by discussing some of his personal reflections and experiences as a teacher and a student of the academy, especially in the context of how spirituality can inform teaching about equity and social justice issues. Some of the issues raised are teaching to inspire, facilitating student spirituality, creating an inclusive curricula for the sacred, embodying the spirit of equity, and the perils of drawing on spirituality in the higher education classroom. Finally, the author discusses the relevance of centering spirituality in transformative education and concludes that this journey is endless and this article is just a stepping-stone to the discussion on centering spirituality within the academy.
Estimating mutual information using B-spline functions – an improved similarity measure for analysing gene expression data
Authors: Daub Carsten O , Steuer Ralf , Selbig Joachim , Kloska Sebastian
Published: September 2004

Background

The information theoretic concept of mutual information provides a general framework to evaluate dependencies between variables. In the context of the clustering of genes with similar patterns of expression it has been suggested as a general quantity of similarity to extend commonly used linear measures. Since mutual information is defined in terms of discrete variables, its application to continuous data requires the use of binning procedures, which can lead to significant numerical errors for datasets of small or moderate size.

Results

In this work, we propose a method for the numerical estimation of mutual information from continuous data. We investigate the characteristic properties arising from the application of our algorithm and show that our approach outperforms commonly used algorithms: The significance, as a measure of the power of distinction from random correlation, is significantly increased. This concept is subsequently illustrated on two large-scale gene expression datasets and the results are compared to those obtained using other similarity measures.

A C++ source code of our algorithm is available for non-commercial use from kloska@scienion.de upon request.

Conclusion

The utilisation of mutual information as similarity measure enables the detection of non-linear correlations in gene expression datasets. Frequently applied linear correlation measures, which are often used on an ad-hoc basis without further justification, are thereby extended.
Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)
Authors: Vêncio Ricardo ZN , Brentani Helena , Patrão Diogo FC , Pereira Carlos AB
Published: September 2004

Background

An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error.

Results

We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries") and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it.

Conclusion

Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site.
SED, a normalization free method for DNA microarray data analysis
Authors: Wang Huajun , Huang Hui
Published: September 2004

Background

Analysis of DNA microarray data usually begins with a normalization step where intensities of different arrays are adjusted to the same scale so that the intensity levels from different arrays can be compared with one other. Both simple total array intensity-based as well as more complex "local intensity level" dependent normalization methods have been developed, some of which are widely used. Much less developed methods for microarray data analysis include those that bypass the normalization step and therefore yield results that are not confounded by potential normalization errors.

Results

Instead of focusing on the raw intensity levels, we developed a new method for microarray data analysis that maps each gene's expression intensity level to a high dimensional space of SEDs (Signs of Expression Difference), the signs of the expression intensity difference between a given gene and every other gene on the array. Since SED are unchanged under any monotonic transformation of intensity levels, the SED based method is normalization free. When tested on a multi-class tumor classification problem, simple Naive Bayes and Nearest Neighbor methods using the SED approach gave results comparable with normalized intensity-based algorithms. Furthermore, a high percentage of classifiers based on a single gene's SED gave good classification results, suggesting that SED does capture essential information from the intensity levels.

Conclusion

The results of testing this new method on multi-class tumor classification problems suggests that the SED-based, normalization-free method of microarray data analysis is feasible and promising.
Automatic annotation of protein motif function with Gene Ontology terms
Authors: Lu Xinghua , Zhai Chengxiang , Gopalakrishnan Vanathi , Buchanan Bruce G
Published: September 2004

Background

Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base.

Results

This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria.

Conclusions

In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.
Systemic endopolyploidy in Spathoglottis plicata (Orchidaceae) development
Authors: Yang Maocheng , Loh Chiang Shiong
Published: September 2004

Background

Endopolyploidy is developmentally regulated. Presence of endopolyploidy as a result of endoreduplication has been characterized in insects, mammals and plants. The family Orchidaceae is the largest among the flowering plants. Many of the members of the orchid family are commercially micropropagated. Very little has been done to characterize the ploidy variation in different tissues of the orchid plants during development.

Results

The DNA contents and ploidy level of nuclei extracted from various tissues of a tropical terrestrial orchid Spathoglottis plicata were examined by flow cytometry. Sepals, petals and ovary tissues were found to have only a 2C (C, DNA content of the unreplicated haploid chromosome complement) peak. Columns, floral pedicels of newly open flowers and growing flower stems were observed to have an endopolyploid 8C peak in addition to 2C and 4C peaks. In developing floral pedicels, four peaks were observed for 2C, 4C, 8C and 16C. In root tips, there were 2C, 4C and 8C peaks. But in the root tissues at the region with root hairs, only a 2C peak was observed. Nuclei extracted from young leaves shown three peaks for 2C, 4C and 8C. A similar pattern was found in the vegetative tissues of both greenhouse-grown plants and tissue-cultured plantlets. In mature leaves, a different pattern of ploidy level was found at different parts of the leaves. In the leaf tips and middle parts, there were 2C and 4C peaks. Only at the basal part of the leaves, there were three peaks for 2C, 4C and 8C.

Conclusions

Systemic variation of cellular endopolyploidy in different tissues during growth and development of Spathoglottis plicata from field-grown plants and in vitro cultures was identified. The implication of the findings was discussed.
Molecular clock in neutral protein evolution
Authors: Wilke Claus O
Published: September 2004

Background

A frequent observation in molecular evolution is that amino-acid substitution rates show an index of dispersion (that is, ratio of variance to mean) substantially larger than one. This observation has been termed the overdispersed molecular clock. On the basis of in silico protein-evolution experiments, Bastolla and coworkers recently proposed an explanation for this observation: Proteins drift in neutral space, and can temporarily get trapped in regions of substantially reduced neutrality. In these regions, substitution rates are suppressed, which results in an overall substitution process that is not Poissonian. However, the simulation method of Bastolla et al. is representative only for cases in which the product of mutation rate μ and population size Ne is small. How the substitution process behaves when μNe is large is not known.

Results

Here, I study the behavior of the molecular clock in in silico protein evolution as a function of mutation rate and population size. I find that the index of dispersion decays with increasing μNe, and approaches 1 for large μNe . This observation can be explained with the selective pressure for mutational robustness, which is effective when μNe is large. This pressure keeps the population out of low-neutrality traps, and thus steadies the ticking of the molecular clock.

Conclusions

The molecular clock in neutral protein evolution can fall into two distinct regimes, a strongly overdispersed one for small μNe, and a mostly Poissonian one for large μNe. The former is relevant for the majority of organisms in the plant and animal kingdom, and the latter may be relevant for RNA viruses.
Hypoxia upregulates the expression of the NDRG1 gene leading to its overexpression in various human cancers
Authors: Cangul Hakan
Published: September 2004

Background

The expression of NDRG1 gene is induced by nickel, a transition metal sharing similar physical properties to cobalt. Nickel may create hypoxia-like conditions in cells and induce hypoxia-responsive genes, as does cobalt. Therefore NDRG1 is likely to be another gene induced by hypoxia. HIF-1 is a transcription factor which has a major role in the regulation of hypoxia-responsive genes, and thus it could be involved in the transcriptional regulation of NDRG1 gene. Hypoxia is such a common feature of solid tumours that it is of interest to investigate the expression of Ndrg1 protein in human cancers.

Results

Hypoxia and its mimetics induce in vitro expression of NDRG1 gene and cause the accumulation of Ndrg1 protein. Protein levels remain high even after cells revert to normoxia. Although HIF-1 is involved in the regulation of NDRG1, long term hypoxia induces the gene to some extent in HIF-1 knock-out cells. In the majority of human tissues studied, Ndrg1 protein is overexpressed in cancers compared to normal tissues and also reflects tumour hypoxia better than HIF-1 protein.

Conclusions

Hypoxia is an inducer of the NDRG1 gene, and nickel probably causes the induction of the gene by interacting with the oxygen sensory pathway. Hypoxic induction of NDRG1 is mostly dependent on the HIF-1 transcription factor, but HIF-1 independent pathways are also involved in the regulation of the gene during chronic hypoxia. The determination of Ndrg1 protein levels in cancers may aid the diagnosis of the disease.
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
Authors: Shippy Richard , Sendera Timothy J , Lockner Randall , Palaniappan Chockalingam , Kaysser-Kranich Tamma , Watts George , Alsobrook John
Published: September 2004

Background

Despite the widespread use of microarrays, much ambiguity regarding data analysis, interpretation and correlation of the different technologies exists. There is a considerable amount of interest in correlating results obtained between different microarray platforms. To date, only a few cross-platform evaluations have been published and unfortunately, no guidelines have been established on the best methods of making such correlations. To address this issue we conducted a thorough evaluation of two commercial microarray platforms to determine an appropriate methodology for making cross-platform correlations.

Results

In this study, expression measurements for 10,763 genes uniquely represented on Affymetrix U133A/B GeneChips® and Amersham CodeLink™ UniSet Human 20 K microarrays were compared. For each microarray platform, five technical replicates, derived from the same total RNA samples, were labeled, hybridized, and quantified according to each manufacturers' standard protocols. The correlation coefficient (r) of differential expression ratios for the entire set of 10,763 overlapping genes was 0.62 between platforms. However, the correlation improved significantly (r = 0.79) when genes within noise were excluded. In addition to levels of inter-platform correlation, we evaluated precision, statistical-significance profiles, power, and noise levels for each microarray platform. Accuracy of differential expression was measured against real-time PCR for 25 genes and both platforms correlated well with r values of 0.92 and 0.79 for CodeLink and GeneChip, respectively.

Conclusions

As a result of this study, we recommend using only genes called 'present' in cross-platform correlations. However, as in this study, a large number of genes may be lost from the correlation due to differing levels of noise between platforms. This is an important consideration given the apparent difference in sensitivity of the two platforms. Data from microarray analysis need to be interpreted cautiously and therefore, we provide guidelines for making cross-platform correlations. In all, this study represents the most comprehensive and specifically designed comparison of short-oligonucleotide microarray platforms to date using the largest set of overlapping genes.
A robust, low- to medium-throughput prnpgenotyping system in sheep
Authors: Buitkamp Johannes , Semmer Jördis
Published: September 2004

Background

In many countries breeding programs for resistance to scrapie in sheep are established. Therefore, the demand on genotyping capacities of the polymorphisms of the prion protein gene (prnp) relevant to presently known disease associations and EU regulations is steadily increasing. Most published typing methods are not well suited for routine typing of large sample numbers in smaller service laboratories for different reasons: they require partly manual data processing, sophisticated and sensitive protocols, high efforts regarding time and manpower, multiple step reactions or substantial hardware investments. To overcome these drawbacks, we developed a prnp typing method that is based on a `multiplex amplification refractory mutation system' (ARMS) reaction.

Methods

In this study we combined the amplification refractory mutation system (ARMS) with standard fluorescent based fragment length analyses method to develop a prnp genotyping method (PRNP ARMS).

Results

By optimised primer design it was possible to type the 4 relevant single nucleotide polymorphisms (SNPs) in the prnp simultaneously in one multiplex reaction. Automated fragment length analysis enabled automated allele designation. Suitability of the PRNP ARMS for routine application was proven by typing samples with known genotypes and larger sample numbers from half-sib families.

Conclusion

The ARMS PRNP typing method established in this study is universally suited for a broad range of typing projects with different requirements. It provides an efficient and inexpensive diagnostic mutation analysis that will improve the quality of prnp genotyping compared with other low-cost methods. It can be implemented by most molecular genetic laboratories using standard equipment.