bluuebunny/crossref_metadata_2025 huggingface dataset:
Nursing Advocacy: an Ethic of Practice
Authors: Gaylord Nan , Grace Pamela
Published: November 2007

Advocacy is an important concept in nursing practice; it is frequently used to describe th nurse-client relationship. The term advocacy, however, is subject to ambiguity of interpretation. Such ambiguity was evidenced recently in criticisms levelled at the nursing profession by hospital ethicist Ellen Bernal. She reproached nursing for using 'patient rights advocate' as a viable role for nurses. We maintain that, for nursing, patient advocacy may encompass, but is not limited to, patient rights advocacy. Patient advocacy is not merely the defence of infringements of patient rights. Advocacy for nursing stems from a philosophy of nursing in which nursing practice is the support of an individual to promote his or her own well-being, as understood by that individual. It is an ethic of practice.

La défense des malades joue un grand rôle dans la pratique des infirmiers/ères. Le terme est souvent utilisé pour définir les rapports entre malades et soignants. Le mot 'defénse' pourtant, peut être mal compris. Une ambiguïté était évidente récemment dans la critique de la profession infirmière faite par la philosophe éthique Ellen Bernal. Elle reproche à la profession d'utiliser le terme 'avocat des droits des malades' pour désigner le rôle primordial des infirmiers/ères. Nous croyons que pour les soignants, la défense des malades peut comprendre le rôle 'd'avocat des droits des malades' mais elle ne s'y borne pas. La défense n'est pas limitée à la défense des infractions des droits des malades. La défense dans la profession infirmière est basée sur une philosophie où la pratique infirmière est le soutien des malades dans leur quête de promouvoir leur propre bien-être.

Die Fürsprache spielt eine wichtige Rolle in der Krankenpflege. Sie wird oft als kennzeichnend für die Beziehung zwischen Patient und Pflegepersonal beschrieben. Der Ausdruck 'Fürsprache' kann aber auch mehrdeutig interpretiert werden. Das wurde letzthin in der Kritik der Ethikerin Ellen Bernal an der Krankenpflege sichtbar. Sie machte den Pflegenden den Vorwurf, dass sie sich die Rolle des 'Rechts-Advokat des Patienten' aneignen. Wir sind der Meinung, dass es die Aufgabe des Pflegepersonals ist, auch die Rechte der Patienten zu vertreten, aber dass das nur ein Teil der Fürsprache ist. Sie ist nicht nur Verteidignung von verletzten Patientenrechten. Die Fürsprache in der Krankenpflege stammt von einer Philosophie, deren Ausübung die Unterstützung der Patienten für ihr Wohlergehen zum Ziel hat, so wie die Patienten selbst ihr Wohlergehen verstehen. Sie ist eine Ethik der Tat.
Suicide and Voluntary Active Euthanasia: Why the Difference in Attitude?
Authors: Beech Ian
Published: November 2007

It appears that the attitudes of health professionals differ towards suicide and voluntary active euthanasia. An acceptance of, if not an agreement with, voluntary active eutha nasia exists, while there is a general consensus that suicide should be prevented.

This paper searches for a working definition of suicide, to discover ethical reasons for the negative value that suicide assumes, and also to provide a term of reference when comparing suicide with euthanasia.

On arriving at a working definition of suicide, it is compared with voluntary active euthanasia. An analysis of utilitarian and deontological considerations is provided and proves to be inconclusive with respect to the ethical principles informing the attitudes of professionals. Therefore, a search for other influences is attempted; this indicates that psychological influences inform attitudes to a greater degree than ethical principles.
Culture and Ethics: a Tool for Analysing the Effects of Biases on the Nurse-Patient Relationship
Authors: Greipp Mary Elizabeth
Published: November 2007

For most nurses world-wide, activities are centred around working directly with patients and so the nurse-patient relationship is of the greatest importance. Ethnocentrism on the part of the health care community has led to misdiagnosis, mistreatment and undertreatment of culturally diverse individuals world-wide. This author discusses a tool, Greipp's Model of Ethical Decision-Making, which can be used to assist nurses in analysing the effects of culture, beliefs and diversity upon the caregiver and care recipient within an ethical framework.
Gossip, Stories and Friendship: Confidentiality in Midwifery Practice
Authors: James Susan
Published: November 2007

Women often seek midwifery care as an alternative to the maternity services that are readily available within the insured health care system in Alberta. Some aspects of community-based, primary care midwifery in Alberta that characterize this alternative are the use of story-telling as a form of knowledge, the development of social con nections among women seeking midwifery care, and nonauthoritarian relationships between midwives and women. In this paper, the concept of confidentiality, as it relates to these aspects of midwifery practice, is explored, using traditional, caring and feminist models of ethics.
Measuring Nurses' Moral Reasoning
Authors: Oberle Kathleen
Published: November 2007

The purpose of this exploratory study was to examine the possibility of designing a satisfactory method, using written responses to hypotheical scenarios, for evaluating the quality of moral reasoning in student nurses. Scenarios were developed from interviews with practising nurses. Nurses and student nurses provided written responses to the scenarios, and nursing faculty members from six institutions sorted the responses according to their perceptions of quality (i.e. 'best', 'next best', 'worst' etc.). There was very little agreement among faculty members on the quality of the responses. Consequently, it was impossible to develop a 'best' response on which the faculty members could agree. Analysis revealed a framework used by the participants for ethical decision-making. The results of this study have important implications for the way in which we think about the teaching and the evaluation of nursing ethics.
Euphemisms for Euthanasia
Authors: Sellman Derek
Published: November 2007

Many patients are subject to 'do not resuscitate' orders or are 'allowed to die'. The predominant moral position within health care seems to be that this is permissible, while voluntary euthanasia is not. This paper attempts to consider the logic of that position. It is not intended as a case for or against voluntary euthanasia; those cases are made elsewhere. Instead, this is an attempt to challenge implicit assumptions. It is the experience of many nurses that issues relating to matters at the end of life are far from being resolved. This paper does not try to offer any practical solutions but aims at some clarification of the language used. This, it is hoped, will enable nurses to contribute to the debate.
Electroconvulsive Therapy, Children and Adolescents: the Power to Stop
Authors: Oxlad Melissa , Baldwin Steve
Published: November 2007

The administration of electroconvulsive therapy (ECT) to children and adolescents remains an unresolved area of clinical debate for nurses. Thus, some nurses have refused to participate in the treatment of minors with ECT, invoking codes of conduct to justify their actions. Other nurses have supported the use of ECT with children and adolescents, via provision of technical assistance to medical colleagues. A cross-national comparison of ethical codes of conduct has confirmed that nurses should take decisive action in the clinical arena when the needs or rights of vulnerable minors are compromised. The provision of clinical guidelines is suggested as one method to enshrine the rights of at-risk children and adolescents.
Values and Canadian Health Care: an Alberta Exploration
Authors: Wilson Donna M. , Kieser Doris M.
Published: November 2007

In March 1994, a health care conference was held in Edmonton, Alberta, at which the values of conference participants towards health care were systematically recorded and analysed. This exploration is significant because the values that underpin the structure of the current publicly-funded and administered Canadian health care system rarely enter current discussions regarding health care system reform. Rather, economic and other sociopolitical forces now seem to be having a major impact on plans and actual changes within the health care system. Thus, the underlying attitudes and beliefs of Canadians towards health care have not been articulated or given due credence. The conference par ticipants identified three dominant values: (1) the dignity of the human person as an indi vidual and social being; (2) respect for pluralism and difference; and (3) accountability These values were found to be robust, in that they sustain a focus on the 'common good'. The common good is the core of the Canadian health care system, and is enshrined in the 1984 Canada Health Act. Conceptually, these values could also lead to significant changes in health care, in keeping with the common good, particularly those changes focusing on the current deficiencies of the Canadian health care system.
Ethics Education and Nursing Practice
Authors: Scott P. Anne
Published: November 2007

This paper suggests that a consideration of health care practice is a necessary step in gaining insight into the appropriate composition of an ethics course for students in the health care professional. Health care practice, if it responds to the needs of society, is dynamic in nature. In the current climate of change in the health service, the author sug gests that the nursing profession needs to become more proactive in analysing and attempting to determine the future shape of nursing. To protect patient care the nursing profession needs to have its eyes open to the ethical dimensions of changes in role and practice.

The author argues that, in attempting to ensure that the education to which nursing students are exposed is of relevance, it is necessary to introduce an element of the ideal into the ethics component of their professional education. From early on in their profes sional development students should be aware of the scope and standards of practice, and the type of role enactment to which the profession requires them to aspire.
Nursing Ethics: What Lies Ahead? The Case of Bulgaria
Authors: Popova Sashka
Published: November 2007

In Bulgaria, we are sharing a transition to a civic society and a market economy, which means transferring to new parameters of our culture. Many old customs based on coer cion, obedience and unacceptable interference are gradually dying out, and new princi ples tend to shape the way we live our collective lives. These include the ethics of partnership, which tend to create an assertion of individual rights and an affirmation of free will and autonomy, and within which the individual is protected in the pursuit of personal judgements. It is remarkable, however, that we have so much difficulty in talk ing about and identifying the most beneficial approaches for the achievement of the new design of our society.

In this paper, I propose to illustrate the current crisis in nursing ethics with informa tion mainly from Bulgaria. However, I think that the problems and trends in the other Eastern European countries are similar.
Respect for Autonomy: Is It Always Paramount?
Authors: Morgan Diane
Published: November 2007

Following the argument proposed by Tschudin in 1986 that many nurses do not have the skills for ethical decision-making, this article identifies and discusses one ethical prob lem from practice.

The problem concerns an extremely obese patient who refuses to be moved by a hoist. The nurses acquiesce to the patient's wishes and she is moved manually by four mem bers of staff. The issues identified for discussion are: the paramountcy of the principle of respect for the patient's autonomy; the rights and obligations of the nurses; and the jus tification for influencing patient choice. The approach used by the ward nurses is analysed and the value of using an ethical decision-making model is considered.
Ethics of Assisted Autonomy in the Nursing Home: Types of Assisting Among Long-Term Care Nurses
Authors: Whitler June M.
Published: November 2007

Twenty-five long-term care nurses in eight nursing homes in central Kentucky were inter viewed concerning ways in which they might assist elderly residents to preserve and enhance their personal autonomy. Data from the interviews were analysed using grounded theory methodology. Seven specific categories of assisting were discovered and described: personalizing, informing, persuading, shaping instrumental circumstances, considering, mentioning opportunities, and assessing causes of an impaired capacity for decision-making. The ethical implications of these categories of assisting for clinical prac tice are examined. Although nurses recognized the importance of resident autonomy, the majority of them failed consistently to employ the categories of assistance to foster resi dent self-determination and most of them held an inadequate understanding of the con cepts of consent and decisional capacity. To assure confidentiality, pseudonyms are used in the following cases and discussions for all names of nurses, residents and facilities.
Resolving the Ethical Dilemma of Nurse Managers Over Chemically-Dependent Colleagues
Authors: Chiu Wilfred , Wilson Donna
Published: November 2007

This paper addresses the nurse manager's role regarding chemically-dependent nurses in the workplace. The manager may intervene by: terminating the contract of the impaired colleague; notifying a disciplinary committee; consulting with a counselling committee; or referring the impaired nurse to an employee assistance programme. A dilemma may arise about which of these interventions is ethically the best. The ethical theories relevant to nursing involve ethical relativism, utilitarianism, Kantian ethics, Kohlberg's justice, and Gilligan's ethic of care. Nurse managers first need to understand these theories in order to clarify their own perceptions and attitudes towards chemical dependency, and then satisfactorily resolve this ethical dilemma. Education and social learning are routes to a better understanding of chemical dependency and to broadening the ethical dimensions of nurse managers.
Policy Options for a Regulatory Body for Nursing in South Africa
Authors: Uys Leana
Published: November 2007

This article describes the use of a Policy Delphi to explore the options for restructuring the regulatory body for nursing in South Africa. Two rounds using postal questionnaires were used, the second of which also included group interviews. Aspects such as the statutory home of the body, its structure, who should appoint or elect members, and its composition, were explored. To a large extent, there was agreement on many issues. It would seem that this approach to consulting the profession is a profitable one, which informs while it consults.
Climate and Crisis in Eighteenth Century Mexico
Authors: Endfield Georgina H.
Published: November 2007

Signals of social and economic growth and prosperity in late colonial Mexico, and especially in the eighteenth century, masked a number of deeper, longer-standing structural problems. Drives towards market integration and the development of international trade associated with the Bourbon reforms stimulated a phase of remarkably rapid economic and administrative change, but also exacerbated a growing social inequality. Some groups benefitted from the economic developments of the 1700s, others suffered serious economic deprivation. This article suggests that repeated periods of anomalous weather and subsistence crisis between the 1690s through to the early 1800s might have served to at once reveal and compound these inequalities and may have also contributed to local and collective social unrest at different points throughout this period.
Natural Disasters? Droughts and Epidemics in Pre-colonial Sudanic Africa
Authors: Meier Astrid
Published: November 2007

Droughts and epidemics are recurrent phenomena in the history of Sudanic Africa. Only in the aftermath of the famines of 1973–74 and 1984–85 in the Sahel zone did historians begin to question their easy classification as ‘natural disasters’ and to look more closely at the interplay of climatic and societal stress factors in the causation process. Research into the history of disasters in pre-colonial Sudanic Africa has to face the problem of a distinctive lack of available source material. This article will address the problems surrounding the identification of droughts and epidemics, before getting to the question of how they turned into disasters, mostly in the form of famines. It argues that before the colonial period the regional food systems seem to have been better adapted to deal with climatic stress than with the specific forms of violence that were an intrinsic part of the fabric of Sudanic Africa since the political reorganisation of the sixteenth century. Thus, both vulnerability and resilience, but also the ways to explain disasters have to be understood in the context of the political, economic and social history of these African societies.
Methods for Modal Model Quality Improvement — Parameter Estimation Process (part II)
Authors: Iwaniec Joanna , Uhl Tadeusz
Published: November 2007

This paper concerns quality improvement of modal models estimated by the use of “standard” modal analysis methods. The authors proposed application of the Least Squares Frequency Domain method making use of the Gauss—Newton algorithm to the quality improvement of stabilization diagrams as well as application of the Balanced Realization method to identify and remove spurious poles from stabilization diagrams. Formulated algorithms were implemented in the Matlab environment and verified for data measured on real structures. Created software supports critical stages of modal analysis, which results in quality improvement of estimated modal models and higher credibility of drawn conclusions.
Straight and White
Authors: Myers W. Benjamin
Published: November 2007

By using straight and white teeth as a metaphor for a straight and White identity, the author reflects on how this identity is performed, maintained, and often problematic. Using literature about identity performance, three different voices speak to and from straight and White identity. Using irony by blending arrogance and ignorance in the voice of the straight and White author, these voices illustrate the cracks in straight and White performance by taking the extreme positions that these performances often rest on. These voices illustrate how education, religion, and hygiene make and maintain (often) arrogant and ignorant straight and White identities. These three voices speak to each other to demonstrate how a methodology that foregrounds our bodies provides space to understand the visibility of identity performances and the politics of writing about with that visibility.
Grounded Theory
Authors: O'Connor Mary Katherine , Netting F. Ellen , Thomas M. Lori
Published: November 2007

The authors examine one of the earliest systematic forms of qualitative inquiry to identify some of the boundaries needed in grounded theory designs to provide a small corner of clarity in the discourse about what is acceptable science from the Institutional Review Board (IRB) perspective. Beginning with an overview of grounded theory research as it was originally conceived and extended, the challenges for establishment of a uniform standard are put forth. Within this background and context, the authors report the results of a content analysis of a sampling of dissertation abstracts claiming to use grounded theory. Results reveal the need to clarify standards for different types of grounded theory research to help those facing IRB oversight. The authors assert that there are two useful sets of standards that should be applied to the assessment of the quality of a grounded theory design and researchers should not confuse the two.
Research Ethics Boards as Spaces of Marginalization
Authors: patterson donna
Published: November 2007

This article complicates how Canadian universities are pressured to capitalize on research and how these same pressures affect both the collaborative and community-based research within the academy by privileging one type of research and relationships within community over others. Through examining historical influences on Research Ethics Boards in Canada, ways these pressures shape qualitative research and disturb how and what we know, as well as what can be known about who and how we work move in and out of focus. Questions are raised about living ethically as qualitative researchers within an institutional context.
Celebrity culture and public connection: Bridge or chasm?
Authors: Couldry Nick , Markham Tim
Published: November 2007

Media and cultural research has an important contribution to make to recent debates about declines in democratic engagement: for example, is celebrity culture a route into democratic engagement for those otherwise disengaged? This article contributes to this debate by reviewing qualitative and quantitative findings from a UK project on `public connection'. Using self-produced diaries (with in-depth multiple interviews) and a nationwide survey, the authors argue that while celebrity culture is an important point of social connection sustained by media use, it is not linked in citizens' own accounts to issues of public concern. Survey data suggest that those who particularly follow celebrity culture are the least engaged in politics and least likely to use their social networks to involve themselves in action or discussion about public-type issues. This does not mean that `celebrity culture' is `bad', but it challenges suggestions of how popular culture might contribute to effective democracy. •
Early Damage Detection in Composite Wingbox Structures using Hilbert-Huang Transform and Genetic Algorithm
Authors: Chen H.G. , Yan Y.J. , Chen W.H. , Jiang J.S. , Yu L. , Wu Z.Y.
Published: November 2007

A vibration-based approach to detect crack damage for large structural systems by using the Hilbert—Huang transform (HHT) has been proposed. The proposed method has been numerically implemented on a composite wingbox. In the implementation process, the following steps have been identified as being important: (a) An optimization procedure is developed by genetic algorithm (GA) in order to determine the location of piezoelectric sensor for damage detection in a composite wingbox; (b) To solve the end effect problem of empirical mode decomposition (EMD), axis-symmetry signal extension method is introduced; (c) Finally, a damage detection method by using HHT is developed. Furthermore, the effect of noise is considered. Examination of the results confirms that the identification method is very robust.
Saint Petersburg 300
Authors: Hutchings Stephen C.
Published: November 2007

Focusing on the televising of Saint Petersburg's 300th anniversary, this article elucidates, and ultimately complicates, the notion of Russian media complicity in a state-led national identity mission in which the city's mythology is used to (re)integrate prerevolutionary imperial tradition with Soviet ritual and Western ideology. It draws on Dayan and Katz's notion of media event and on Bakhtin's concepts of chronotope and carnival that facilitate this particular media event's cultural contextualization. The analysis reveals how television articulates a distinctive Saint Petersburg space-time accommodating an ideologically sanitized national carnival of popular participation, but also a local identity project that, precisely by offsetting the latter, authenticates it. It further identifies the rudiments of a generic model for televising national celebrations. Through the metatextuality characterizing that model, the medium inscribes itself into the participatory process it describes, confirming that, far from suppressing democratic rhetoric, Russian television internalizes it, recasting it for nation-building purposes.
Finding family for prospective consent in emergency research
Authors: Robertson Claudia S. , McCullough Laurence B. , Brody Baruch
Published: November 2007

Background Innovative approaches are needed to allow for research in the emergency setting while not compromising either the rights or the interests of the subjects enrolled in such research. The emergency consent exception was developed to meet this need.

Purpose The goal was to describe the timing of initial contact with relatives and the timing of obtaining informed consent for a research study in patients with severe traumatic brain injury.

Methods The study was designed as a prospective, observational study of 129 patients enrolled in an emergency study of traumatic brain injury conducted under the emergency consent exception. Detailed descriptive information was collected both about the availability of relatives of patients enrolled in a study of traumatic brain injury to give prospective consent within the time period required for entering the study and about the extent to which they did give prospective consent during that time period.

Results The number of patients with relatives who could be contacted by research staff increased with time after injury, with 3% (95% CI=0 to 6%), 25% (95% CI=18 to 32%), and 43% (95% CI=35 to 52%) having family at 1, 3, and 6 h, respectively postinjury. An additional 15% were available within the next 6 h. The median time after injury to the initial family contact by the research staff was 2.0 h for patients who had relatives already present at the hospital and 5.7 h for patients whose family had already been contacted by the hospital. The percentage of family members actually giving prospective research consent was much smaller; only 18% actually gave prospective consent within 6 h postinjury. The proportion of critically ill patients with family available to give prospective consent for enrollment in emergency research studies depends primarily on the time period allowed for enrollment in the individual study and the length of the transition from initial contact to completed prospective consent.

Limitations The study was performed in a specific patient population and may not be generalizable to other settings.

Conclusions Careful attention should be paid by investigators and IRBs as to whether the emergency consent exception is really required for a particular study, or whether the study could proceed using only prospective consent with a longer recruitment period, more research sites, and a higher yield of available family members giving prospective consent. Measures that could shorten the time between initial contact and obtaining informed consent (for example, allowing consent over the phone rather than requiring written consent) might decrease the need for the emergency consent exception. Clinical Trials 2007; 4: 631—637. http://ctj.sagepub.com
Using causal models to show the effect of untestable assumptions on effect estimates in randomized controlled trials
Authors: Allard Robert , Boivin Jean-François
Published: November 2007

Background The methods by which randomized controlled trials (RCTs) are analyzed rest on several assumptions, most of which are untestable.

Purpose To show how estimates of the net effect of treatment on survival can be obtained requiring only the assumption that randomization produced equivalent groups.

Methods The assumptions underlying ratio measures of effect, based on disease occurrence times (DOT) obtained from survival curves, are identified and cumulatively removed.

Results The four assumptions usually made are that (1) the ratio of disease incidence rates under treatment and under reference exposure is constant over time, (2) the groups being compared are exchangeable (equivalent), (3) a subject's DOT under treatment is independent of what his DOT would have been under the reference exposure, and (4) the treatment effect, if any, is in the same direction in all subjects. Removing Assumption 4 leads to an estimator of effect resembling the etiologic fraction, but able to accommodate both causative and preventive effects. Removing all assumptions but that of exchangeability still permits the estimation, directly from the survival curves, of a range of effect magnitudes, causative or preventive, compatible with the observed DOTs. The exchangeability assumption is the easiest to meet, by randomizing enough subjects.

Limitations The statistical uncertainty that affects the estimates of survival probabilities has been ignored. Taking uncertainty into account further widens the range of effects compatible with the observations.

Conclusions Retaining only the exchangeability assumption allows for a range of possible treatment effects to be estimated, although it may be wide. Readers of RCT reports should understand that the determination of a point estimate of effect within this range is entirely a function of unverifiable analytic assumptions. Clinical Trials 2007; 4: 611—620. http://ctj.sagepub.com
IL-7 promotes Glut1 trafficking and glucose uptake via STAT5-mediated activation of Akt to support T-cell survival
Authors: Wofford Jessica A. , Wieman Heather L. , Jacobs Sarah R. , Zhao Yuxing , Rathmell Jeffrey C.
Published: November 2007

Lymphocyte homeostasis requires coordination of metabolic processes with cellular energetic and biosynthetic demands but mechanisms that regulate T-cell metabolism are uncertain. We show that interleukin-7 (IL-7) is a key regulator of glucose uptake in T lymphocytes. To determine how IL-7 affects glucose uptake, we analyzed IL-7 signaling mechanisms and regulation of the glucose transporter, Glut1. The IL-7 receptor (IL-7R) stimulated glucose uptake and cell-surface localization of Glut1 in a manner that required IL-7R Y449, which promoted rapid signal transducer and activator of transcription 5 (STAT5) activation and a delayed yet sustained activation of Akt. Each pathway was necessary for IL-7 to promote glucose uptake, as Akt1−/− T cells or PI3-kinase inhibition and RNAi of STAT5 led to defective glucose uptake in response to IL-7. STAT5 and Akt acted in a linear pathway, with STAT5-mediated transcription leading to Akt activation, which was necessary for STAT5 and IL-7 to promote glucose uptake and prevent cell death. Importantly, IL-7 required glucose uptake to promote cell survival. These data demonstrate that IL-7 promotes glucose uptake via a novel signaling mechanism in which STAT5 transcriptional activity promotes Akt activation to regulate Glut1 trafficking and glucose uptake that is critical for IL-7 to prevent T-cell death and maintain homeostasis.
Identification of DNA-binding proteins using support vector machines and evolutionary profiles
Authors: Kumar Manish , Gromiha Michael M , Raghava Gajendra PS
Published: November 2007

Background

Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation, as these proteins play a crucial role in gene-regulation. In this paper, we developed various SVM modules for predicting DNA-binding domains and proteins. All models were trained and tested on multiple datasets of non-redundant proteins.

Results

SVM models have been developed on DNAaset, which consists of 1153 DNA-binding and equal number of non DNA-binding proteins, and achieved the maximum accuracy of 72.42% and 71.59% using amino acid and dipeptide compositions, respectively. The performance of SVM model improved from 72.42% to 74.22%, when evolutionary information in form of PSSM profiles was used as input instead of amino acid composition. In addition, SVM models have been developed on DNAset, which consists of 146 DNA-binding and 250 non-binding chains/domains, and achieved the maximum accuracy of 79.80% and 86.62% using amino acid composition and PSSM profiles. The SVM models developed in this study perform better than existing methods on a blind dataset.

Conclusion

A highly accurate method has been developed for predicting DNA-binding proteins using SVM and PSSM profiles. This is the first study in which evolutionary information in form of PSSM profiles has been used successfully for predicting DNA-binding proteins. A web-server DNAbinder has been developed for identifying DNA-binding proteins and domains from query amino acid sequences http://www.imtech.res.in/raghava/dnabinder/.
Detection of inflammatory bowel disease by proton magnetic resonance spectroscopy (1H MRS) using an animal model
Authors: Varma Sonal , Bird Ranjana , Eskin Michael , Dolenko Brion , Raju Jayadev , Bezabeh Tedros
Published: November 2007

Background

The aim of this study was to analyze the potential of proton magnetic resonance spectroscopy (1H MRS) in diagnosing early inflammatory bowel disease (IBD).

Methods

Thirty male Sprague Dawley rats were fed 2% carrageenan in their diet for either 1 or 2 weeks. 1H MRS was performed ex-vivo on colonic mucosal samples (n = 123) and the spectra were analyzed by a multivariate method of analysis. The results of the multivariate analysis were correlated with histological analysis performed using H & E stain for the presence of inflammation in the samples from each group.

Results

Multivariate analysis classified the samples in their respective groups with an accuracy of 82%. Our region selection algorithm identified four regions in the spectra as being discriminatory. The metabolites assigned to these regions include creatine, phosphatidylcholine, the -CH
2HC= group in fatty acyl chain, and the glycerol backbone of lipids. The differences in concentration of these metabolites in each group offer insight into the biochemical changes occurring during IBD and confer diagnostic potential to 1H MRS as a tool to study colonic inflammation in conjunction with biopsy.

Conclusion

1H MRS is a sensitive tool to detect early colonic inflammation in an animal model of IBD.
Antibody microarray analysis of cell surface antigens on CD4+ and CD8+ T cells from HIV+ individuals correlates with disease stages
Authors: Wu Jing Qin , Wang Bin , Belov Larissa , Chrisp Jeremy , Learmont Jenny , Dyer Wayne B , Zaunders John , Cunningham Anthony L , Dwyer Dominic E , Saksena Nitin K
Published: November 2007

Background

Expression levels of cell surface antigens such as CD38 and HLA-DR are related to HIV disease stages. To date, the immunophenotyping of cell surface antigens relies on flow cytometry, allowing estimation of 3–6 markers at a time. The recently described DotScan antibody microarray technology enables the simultaneous analysis of a large number of cell surface antigens. This new technology provides new opportunities to identify novel differential markers expressed or co-expressed on CD4+ and CD8+ T cells, which could aid in defining the stage of evolution of HIV infection and the immune status of the patient.

Results

Using this new technology, we compared cell surface antigen expression on purified CD4+ and CD8+ T cells between 3 HIV disease groups (long-term non-progressors controlling viremia naturally; HIV+ patients on highly active antiretroviral therapy (HAART) with HIV plasma viral loads <50 copies/ml; and HIV+ patients with viremia during HAART) and uninfected controls. Pairwise comparisons identified 17 statistically differential cell surface antigens including 5 novel ones (CD212b1, CD218a, CD183, CD3 epsilon and CD9), not previously reported. Notably, changes in activation marker expression were more pronounced in CD8+ T cells, whereas changes in the expression of cell membrane receptors for cytokines and chemokines were more pronounced in CD4+ T cells.

Conclusion

Our study not only confirmed cell surface antigens previously reported to be related to HIV disease stages, but also identified 5 novel ones. Of these five, three markers point to major changes in responsiveness to certain cytokines, which are involved in Th1 responses. For the first time our study shows how density of cell surface antigens could be efficiently exploited in an array manner in relation to HIV disease stages. This new platform of identifying disease markers can be further extended to study other diseases.
Semiquantitative RT-PCR measurement of gene expression in rat tissues including a correction for varying cell size and number
Authors: Romero Maria del Mar , Grasa Maria del Mar , Esteve Montserrat , Fernández-López José Antonio , Alemany Marià
Published: November 2007

Background

Current methodology of gene expression analysis limits the possibilities of comparison between cells/tissues of organs in which cell size and/or number changes as a consequence of the study (e.g. starvation). A method relating the abundance of specific mRNA copies per cell may allow direct comparison or different organs and/or changing physiological conditions.

Methods

With a number of selected genes, we analysed the relationship of the number of bases and the fluorescence recorded at a present level using cDNA standards. A lineal relationship was found between the final number of bases and the length of the transcript. The constants of this equation and those of the relationship between fluorescence and number of bases in cDNA were determined and a general equation linking the length of the transcript and the initial number of copies of mRNA was deduced for a given pre-established fluorescence setting. This allowed the calculation of the concentration of the corresponding mRNAs per g of tissue. The inclusion of tissue RNA and the DNA content per cell, allowed the calculation of the mRNA copies per cell.

Results

The application of this procedure to six genes: Arbp, cyclophilin, ChREBP, T4 deiodinase 2, acetyl-CoA carboxylase 1 and IRS-1, in liver and retroperitoneal adipose tissue of food-restricted rats allowed precise measures of their changes irrespective of the shrinking of the tissue, the loss of cells or changes in cell size, factors that deeply complicate the comparison between changing tissue conditions. The percentage results obtained with the present methods were essentially the same obtained with the delta-delta procedure and with individual cDNA standard curve quantitative RT-PCR estimation.

Conclusion

The method presented allows the comparison (i.e. as copies of mRNA per cell) between different genes and tissues, establishing the degree of abundance of the different molecular species tested.
Evaluating the protein coding potential of exonized transposable element sequences
Authors: Piriyapongsa Jittima , Rutledge Mark T , Patel Sanil , Borodovsky Mark , Jordan I King
Published: November 2007

Background

Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons.

Results

We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences.

Conclusion

The exaptation of the numerous TE sequences found in exons asbona fideprotein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence.

Reviewers:

This article was reviewed by Itai Yanai, Kateryna D. Makova, Melissa Wilson (nominated by Kateryna D. Makova) and Cedric Feschotte (nominated by John M. Logsdon Jr.).
The Concept of a Central – Local Government Partnership: Issues obscured by ideas
Authors: Thrasher Michael
Published: November 2007

Controversy currently surrounds the relationship between central and local government as policies designed to control and curb public expenditure are viewed by local authorities as yet another attempt to erode their capacity for autonomous action. In recent years the whole issue of central–local relations has been typified by a mood of despondency and frustration as efforts to improve the situation have failed, unable to move beyond the most basic of accusations and recriminations. Perhaps research currently being undertaken will enable the various contestants in this debate to substantiate their often wild assertions but there is a danger that the differences between the two sides have become so great that restoring trust and respect will require a great deal of time.

Discussion between central and local government cannot be aided, we suspect, by the fact that there appears so little agreement about the nature and purpose of local government. This surely has important implications for the way in which central government formulates policies regarding local government since the role of ideas, values and attitudes in public policy-making is crucial. The aim of this article, therefore, is to explore the historical origins and development of some ideas about central–local government relations.
Epigenetic alteration of the donor cells does not recapitulate the reprogramming of DNA methylation in cloned embryos
Authors: Wee Gabbine , Shim Jung-Jae , Koo Deog-Bon , Chae Jung-Il , Lee Kyung-Kwang , Han Yong-Mahn
Published: November 2007

Epigenetic reprogramming is a prerequisite process during mammalian development that is aberrant in cloned embryos. However, mechanisms that evolve abnormal epigenetic reprogramming during preimplantation development are unclear. To trace the molecular event of an epigenetic mark such as DNA methylation, bovine fibroblasts were epigeneticallyaltered by treatment with trichostatin A (TSA) and then individually transferred into enucleated bovine oocytes. In the TSA-treated cells, expression levels of histone deacetylases and DNA methyltransferases were reduced, but the expression level of histone acetyltransferases such as Tip60 and histone acetyltransferase 1 (HAT1) did not change compared with normal cells. DNA methylation levels of non-treated (normal) and TSA-treated cells were 64.0 and 48.9% in the satellite I sequence (P < 0.05) respectively, and 71.6 and 61.9% in the α-satellite sequence respectively. DNA methylation levels of nuclear transfer (NT) and TSA-NT blastocysts in the satellite I sequence were 67.2 and 42.2% (P < 0.05) respectively, which was approximately similar to those of normal and TSA-treated cells. In the α-satellite sequence, NT and TSA-NT embryos were substantially demethylated at the blastocyst stage as IVF-derived embryos were demethylated. The in vitro developmental rate (46.6%) of TSA-NT embryos that were individually transferred with TSA-treated cells was higher than that (31.7%) of NT embryos with non-treated cells (P < 0.05). Our findings suggest that the chromatin of a donor cell is unyielding to the reprogramming of DNA methylation during preimplantation development, and that alteration of the epigenetic state of donor cells may improve in vitro developmental competence of cloned embryos.
Impact of Previous Statin and Angiotensin II Receptor Blocker Use on Mortality in Patients Hospitalized with Sepsis
Authors: Mortensen Eric M. , Restrepo Marcos I. , Copeland Laurel A. , Pugh Jacqueline A. , Anzueto Antonio , Cornell John E. , Pugh Mary Jo V.
Published: November 2007

Study Objective. To examine the effect of previous outpatient use of 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors (statins) and/or angiotensin II receptor blockers (ARBs) on 30‐day mortality in patients hospitalized with sepsis.

Design. Retrospective national cohort study.

Data Source. Department of Veterans Affairs (VA) national patient care and pharmacy databases.

Patients. A total of 3018 patients who were hospitalized with sepsis in fiscal year 2000, had at least 1 year of previous VA outpatient care, and had at least one active and filled VA prescription within 90 days of admission.

Measurements and Main Results. The primary outcome was 30‐day mortality. The primary analysis was a multilevel model with hospital as a random effect and control variables that included comorbid conditions, demographics, and other drugs. Among the 3018 patients hospitalized with sepsis, mean age was 74.4 years, 2975 (98.6%) were male, and 811 (26.9%) died within 30 days of admission. Regarding prescription drug use, 480 patients (15.9%) were taking statins and 107 (3.5%) were taking ARBs. After adjusting for potential confounders, statin use (odds ratio [OR] 0.48, 95% confidence interval [CI] 0.36‐0.64) and ARB use (OR 0.42, 95% CI 0.24‐0.76) were significantly associated with decreased 30‐day mortality.

Conclusions. Use of statins and/or ARBs before admission was associated with decreased mortality in patients hospitalized with sepsis. Further research is needed to determine if these drugs might be started on admission for those with sepsis.
Self-adjoint differential equations and generalized Karamata functions
Authors: Jaros Jaroslav , Kusano Takasi
Published: November 2007

Howard and Maric have recently developed nice nonoscillation theorems for the differential equation U" + q(t)y = 0 (*) by means of regularly varying functions in the sense of Karamata. The purpose of this paper is to show that their results can be fully generalized to differential equations of the form, (p(t)y?)? + q(t)y = o (**) by using the notion of generalized Karamata functions, which is needed to comprehend how delicately the asymptotic behavior of solutions of (**) is affected by the function p(t).