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Analysis of common k-mers for whole genome sequences using SSB-tree.

As sequenced genomes become larger and sequencing process becomes faster, there is a need to develop a tool to analyze sequences in the whole genomic scale. However, on-memory algorithms such as suffix tree and suffix array are not applicable to the analysis of whole genome sequence set, since the size of individual whole genome ranges from several million base pairs to hundreds billion base pairs. In order to effectively manipulate the huge sequence data, it is necessary to use the indexed data structure for external memory. In this paper, we introduce a workbench called SequeX for the analysis and visualization of whole genome sequences using SSB-tree (Static SB-tree). It consists of two parts: the analysis query subsystem and the visualization subsystem. The query subsystem supports various transactions such as pattern matching, k-occurrence, and k-mer analysis. The visualization subsystem helps biologists to easily understand whole genome structure and feature by sequence viewer, annotation viewer, CGR (Chaos Game Representation) viewer, and k-mer viewer. The system also supports a user-friendly programming interface based on Java script for batch processing and the extension for a specific purpose of a user. SequeX can be used to identify conserved genes or sequences by the analysis of the common k-mers and annotation. We analyze the common k-mer for 72 microbial genomes announced by Entrez, and find an interesting biological fact that the longest common k-mer for 72 sequences is 11-mer, and only 11 such sequences exist. Finally we note that many common k-mers occur in conserved region such as CDS, rRNA, and tRNA.

Archaea↗

Nature vs nurture: are leaders born or made? A behavior genetic investigation of leadership style.

With the recent resurgence in popularity of trait theories of leadership, it is timely to consider the genetic determination of the multiple factors comprising the leadership construct. Individual differences in personality traits have been found to be moderately to highly heritable, and so it follows that if there are reliable personality trait differences between leaders and non-leaders, then there may be a heritable component to these individual differences. Despite this connection between leadership and personality traits, however, there are no studies of the genetic basis of leadership using modern behavior genetic methodology. The present study proposes to address the lack of research in this area by examining the heritability of leadership style, as measured by self-report psychometric inventories. The Multifactor Leadership Questionnaire (MLQ), the Leadership Ability Evaluation, and the Adjective Checklist were completed by 247 adult twin pairs (183 monozygotic and 64 same-sex dizygotic). Results indicated that most of the leadership dimensions examined in this study are heritable, as are two higher level factors (resembling transactional and transformational leadership) derived from an obliquely rotated principal components factors analysis of the MLQ. Univariate analyses suggested that 48% of the variance in transactional leadership may be explained by additive heritability, and 59% of the variance in transformational leadership may be explained by non-additive (dominance) heritability. Multivariate analyses indicated that most of the variables studied shared substantial genetic covariance, suggesting a large overlap in the underlying genes responsible for the leadership dimensions.

Adult↗

An efficient learning algorithm for improving generalization performance of radial basis function neural networks.

This paper presents an efficient recursive learning algorithm for improving generalization performance of radial basis function (RBF) neural networks. The approach combines the rival penalized competitive learning (PRCL) [Xu, L., Kizyzak, A. & Oja, E. (1993). Rival penalized competitive learning for clustering analysis, RBF net and curve detection, IEEE Transactions on Neural Networks, 4, 636-649] and the regularized least squares (RLS) to provide an efficient and powerful procedure for constructing a minimal RBF network that generalizes very well. The RPCL selects the number of hidden units of network and adjusts centers, while the RLS constructs the parsimonious network and estimates the connection weights. In the RLS we derived a simple recursive algorithm, which needs no matrix calculation, and so largely reduces the computational cost. This combined algorithm significantly enhances the generalization performance and the real-time capability of the RBF networks. Simulation results of three different problems demonstrate much better generalization performance of the present algorithm over other existing similar algorithms.

Algorithms↗

[Humanistic care--a vital dialog with myself as a nurse].

The author documents the use of "humanistic care" as described by Paterson & Zderad (1988) and presents two case studies. Humanistic care is a transactional process, the carer entering into a relationship with the person for whom he/she cares. At the same time the carer embarks on a conscious dialogue with him/her self. To be "present" means being conscious of ones own thoughts, feelings, impressions and reactions. During a course of graduate study in Canada, the author enrolled in a "self-directed learning programme". She set herself the task of self-analysis. She conducted interviews with two patients suffering from cancer and with their relatives. She hoped that she would be able to reexamine, in this new situation, feelings and emotions which she had repressed earlier in her hospital nursing experience. The goal of the learning experience was to develop personal "authenticity" by becoming aware of existential experiences (her own and others').

Education, Nursing, Continuing↗

[The effect of supportive nursing care on depression, mood and satisfaction in military patients with low back pain].

Support has always been considered an important nursing concept. However, there is no agreement among nurse researchers as to a conceptual definition of supportive nursing or meaningful supportive behaviors. Clarification of the concept, support in nursing, is necessary to promote communication among nurses on nursing behaviors that are effective in providing support and on understanding the relevant properties and characteristics of the concept, supportive nursing care. The objectives of the study were: 1. to analyze the concept, support in nursing, in order to provide a definition of supportive nursing care, and 2. to operationalize the definition of supportive nursing care and use it as an experimental nursing intervention for patients with low back pain. The first part of the study used the concept analysis approach developed by Walker and Avant (1983) to define the concept of supportive nursing care. The properties of supportive nursing care, defined by this analysis, included perception of supportive need, reciprocal interaction (Transaction), listening, providing empathy and information related to health, and confirmation of the patient's verbal and non-verbal response. The second part, the experimental part of the study, was done using King's(1970) Interpersonal Theory for Nursing. The concept, supportive nursing care, as defined in the concept analysis was operationalized and used as the experimental intervention. The experiment tested the effectiveness of the independent variable, supportive nursing care on the dependent variables, depression, mood and patient satisfaction, in the patients with low back pain in army hospitals. The instruments used to measure the dependent variables were Zung's(1965) Self-Rating Depression Scale, Ryman and Colleagues' (1974) Mood Questionnaire and LaMonica and Colleagues' (1986) Patient Satisfaction Scale. The experimental design used for this study was a Solomon 4 group experimental design. This design has the strength of allowing for observation of the main effects of supportive nursing care and pretesting, and for observation of the interaction effects of pretesting and supportive nursing care. The design includes one experimental group and three control groups. The Subjects of this study were 150 young male patients with low back pain on Neuro-Surgical Wards in three general army hospitals. There were 35 in the experimental group, 39 in the pre-posttest control group, 36 in the treatment-posttest control group and 40 in the posttest only control group. Supportive nursing care, as operationalized by the researcher according to the concept analysis, was given to the patients in the experimental group and the treatment-posttest control group, individually for 30 minute sessions, every other day for 5 days.(ABSTRACT TRUNCATED AT 400 WORDS)

Affect↗

Communication between older women and physicians: preliminary implications for satisfaction and intention to have mammography.

OBJECTIVE: To explore the associations between physician communication styles and their older patients' intentions to get mammography and satisfaction with physician communication. METHODS: This cross-sectional mixed methods study was conducted in a teaching hospital outpatient clinic with faculty general internists (n=7) and their female patients aged 65 years and older (n=56). Audiotaped communication was coded by researchers using the multidimensional interactional analysis and assisted doctor-elderly patient transactions coding systems. Demographic data was collected prior to the visit. Data on intention to have mammography and satisfaction with communication were collected immediately post-visit. RESULTS: The majority of encounters had some degree of joint decision-making. Communication styles tended to be associated with women's intentions to have screening mammography. Patients who described communication as "deep", "trusting" and "bonding" were more satisfied with communication than women who rated physician communication as less trusting (p=0.03, 0.02 and 0.02, respectively). CONCLUSION: Physicians' communication styles affect their older female patients' satisfaction. In this preliminary study, older women who rated communication as being deep, trusting and bonding tended to have a greater intention to have mammography. PRACTICE IMPLICATIONS: Improving physicians' communication styles may increase satisfaction with physician communication and result in higher mammography adherence among older female patients.

Aged↗

Establishing and maintaining healthy environments. Toward a social ecology of health promotion.

Earlier research on health promotion has emphasized behavior change strategies rather than environmentally focused interventions. The advantages of integrating lifestyle modification, injury control, and environmental enhancement strategies of health promotion are substantial. The author offers a social ecological analysis of health promotive environments, emphasizing the transactions between individual or collective behavior and the health resources and constraints that exist in specific environmental settings. Directions for future research on the creation and maintenance of health promotive environments also are examined.

Adaptation, Psychological↗

Trends in total hospital financial performance under the prospective payment system.

In this article, the author examines trends in determinants of total hospital facility revenues, expenses, and net profits during the period 1977-89. Measures of change in transaction prices are developed, which enable an analysis of trends in real hospital outputs and total factor productivity. The main source of hospital spending growth in excess of the gross national product is identified as growth in hospital employee compensation.

Capital Expenditures↗

A novel psychophysiological treatment for vasovagal syncope.

The objective of this study was to evaluate the efficacy of transactional psychophysiological therapy (TPT) in a patient with recurrent vasovagal syncope (VVS) and to quantify the capacity of human dialogue to effect significant and consistent measurable therapeutic cardiovascular (CV) changes. A 31-year-old nurse with recurrent VVS and a reproducibly abnormal tilt-table test was refractory to pharmacological and conventional psychiatric treatments. She was treated with TPT. Her CV responses during psychotherapy were incorporated into the dialogue as an important source of communicative information, and she was taught psychophysiological techniques to correct exaggerated CV responses. These responses, during 16 weekly and 12 subsequent monthly sessions, were analysed using a one-way multiple analysis of variance. As TPT progressed, the magnitude and lability of CV responses as well as frequency of VVS were reduced. She has been relatively asymptomatic for 14 years posttherapy. In conclusion, (1) TPT may be an effective primary/adjunctive treatment for patients with VVS; (2) TPT may reduce syncopal episodes, perhaps by normalizing limbic input to the brainstem baroreflex system.

Adrenergic alpha-Agonists↗

Analysis of the upstream regulatory region of a chicken skeletal myosin heavy chain gene.

The organization of the cis-acting regulatory elements of a chick myosin heavy chain gene has been investigated. The data show that a gene which is transcribed in vivo in the fast white embryonic musculature is also the major transcript expressed during myotube differentiation of primary myoblasts derived from 12-day embryonic chick leg muscles. The upstream region of this gene consists of 7500 base pairs, and we have tested the ability of these sequences to drive expression of the chloramphenicol acetyltransferase gene in developing primary muscle cultures. Deletion analyses of the upstream region show that negative regulatory elements are present within 2000 base pairs of the basal promoter elements, the CCAAT and TAATA boxes. Removal of these elements reveals the presence of a strong positive element located near the start site of transcription. Sequence analysis showed that the region also contains a sequence characteristic of an enhancer found in the immunoglobulin heavy chain gene, ATGCAAAT, the "octa" element. Gel band-shift assays show that this octa sequence binds a transacting factor present in muscle nuclear extracts, although footprint analysis indicates a limited interaction. Transient assays carried out with a fragment in which the octa sequence has been mutated, with the subsequent abolition of protein binding, shows that the particular interaction probably plays a role in negatively modulating the action of the strong positive promoter element.

Animals↗

The concept of dependence as developed by Birtchnell: a critical evaluation.

Birtchnell (1988) appeals for an accurate definition of dependence. Such accuracy would help with measurement, prevention and treatment of depression. He describes dependence as a developmental deficiency. In so doing, he presupposes a psychodynamic trait-based, and gender-related development model, but does not acknowledge its influence on his thinking. Birtchnell's analysis has three types of problem. The reasoning may be questioned because of faulty inferential leaps, undue reliance on the concept of 'maturity', the use of a tautology, ('The dependent person is...dependent'), internal contradictions, and a questionable analogy between children's and adults' behaviour. Secondly, he appears to suggest that there is empirical evidence to support his theoretical approach, but he does not provide explicit evidence. He draws conclusions about causal links and neglects alternative interpretations, especially the transactional interpersonal element in social relationships. Finally, the analysis is potentially weakened by what may be described as an androcentric bias and relies upon a 'medical model' of psychological disorder, which fails to consider the impact of social influences on the expression of emotion. The author argues that it is at present premature and inappropriate to define dependence, but appeals for methods of research which would be more helpful in understanding it.

Dependency, Psychological↗

Selection and analysis of a mutant cell line defective in the hypoxia-inducible factor-1 alpha-subunit (HIF-1alpha). Characterization of hif-1alpha-dependent and -independent hypoxia-inducible gene expression.

Hypoxia-inducible expression has been demonstrated for many groups of mammalian genes, and studies of transcriptional control have revealed the existence of hypoxia-responsive elements (HREs) in the cis-acting sequences of several of these genes. These sequences generally contain one or more binding sites for a heterodimeric DNA binding complex termed hypoxia-inducible factor-1 (HIF-1). To analyze this response further, Chinese hamster ovary cells were stably transfected with plasmids bearing HREs linked to genes encoding immunoselectable cell surface markers, and clones that showed reduced or absent hypoxia-inducible marker expression were selected from a mutagenized culture of cells. Analysis of these cells revealed several clones with transacting defects in HRE activation, and in one the defect was identified as a failure to express the alpha-subunit of HIF-1. Comparison of hypoxia-inducible gene expression in wild type, HIF-1alpha-defective, and HIF-1alpha-complemented cells revealed two types of response. For some genes (e.g. glucose transporter-1), hypoxia-inducible expression was critically dependent on HIF-1alpha, whereas for other genes (e.g. heme oxygenase-1) hypoxia-inducible expression appeared largely independent of the expression of HIF-1alpha. These experiments show the utility of mutagenesis and selection of mutant cells in the analysis of mammalian transcriptional responses to hypoxia and demonstrate the operation of HIF-1alpha-dependent and HIF-1alpha-independent pathways of hypoxia-inducible gene expression in Chinese hamster ovary cells.

Animals↗

Outsourcing and benchmarking in a rural public hospital: does economic theory provide the complete answer?

INTRODUCTION: The ideology and pronouncements of the Australian Government in introducing 'competitive neutrality' to the public sector has improved efficiency and resource usage. In the health sector, the Human Services Department directed that non-clinical and clinical areas be market tested through benchmarking services against the private sector, with the possibility of outsourcing. These services included car parking, computing, laundry, engineering, cleaning, catering, medical imaging (radiology), pathology, pharmacy, allied health and general practice. Managers, when they choose between outsourcing, and internal servicing and production, would thus ideally base their decision on economic principles. Williamson's transaction cost theory studies the governance mechanisms that can be used to achieve economic efficiency and proposes that the optimal organisation structure is that which minimises transaction costs or the costs of exchange. Williamson proposes that four variables will affect such costs, namely: (i) frequency of exchange; (ii) asset specificity; (iii) environmental uncertainty; and (iv) threat of opportunism. This paper provides evidence from a rural public hospital and examines whether Williamson's transaction cost theory is applicable. METHOD: Case study research operates within the interpretivism paradigm and is used in this research to uncover why the outsourcing decision was made. Such research aims to study real-life experiences by examining the way people think and act and, in contrast to positivism, allows the interviewer to participate to better understand the details and features of the experiences. In the present research, individual interviews were conducted with managers of the hospital and owners and staff of the vendor organisations using semi- and unstructured questions to ascertain the extent of, and processes used in, outsourcing specific functional areas, and areas that were not outsourced. RESULTS: Pathology, radiology, dental technician services and lawn mowing were outsourced while food services was retained internally. The outsourcing of radiology was due to the hospital being unable (or unwilling) to finance new equipment and the problematical relationship between the existing radiologists, and hospital management and staff. Outsourcing resulted in increased staff morale, upgraded capital equipment and improved services. The outsourcing of pathology and dental technical services aimed to increase labour flexibility, thereby decreasing costs. Additional drivers in pathology were the changing nature of the funding arrangements rendering it profitable for the private sector to move into the provision of pathology and the increasing power of the medical scientists' union. The outsourcing of lawn mowing was simply to reduce costs. Food services was not outsourced because there was a lack of evidence that costs could be reduced. In addition, the existing relationships with food services staff were regarded as important because they had previously made immense changes to work practices, reduced staff numbers and decreased costs. CONCLUSION: Transaction costs are important when analysing how managers make the outsourcing decision, but the evidence from this case is that not all transaction costs are included in the decision, and that such costs are more complex than can be included in the type of analysis often undertaken by decision-makers. Taking into account Williamson's variables, the research shows that the outsourcing of services did not comply solely with the levels of transaction frequency or the requirement of asset specificity. In addition, opportunistic behaviour was evident on the part of all parties and was used in some cases as a reason for outsourcing, and in others to sway the decision to the manager's predisposed choice. A variety of arrangements were used to reduce environmental uncertainty, such as the transfer of staff to the contractor and the use of long-term contracts. Indeed the case shows that relationships between the hospital, its staff and the vendor are an important consideration that may not always be factored into an analysis that relies solely on transaction costs.

Journal Article↗

Nurse executive transformational leadership and organizational commitment.

OBJECTIVE: To investigate the relationship between nurse executive leadership and organizational commitment among nurses in acute care hospitals. BACKGROUND: A key challenge for organizations is to maximize the contributions of all workers by cultivating their commitment. Nurse leaders are in a position to influence organizational commitment among nurses. METHODS: The theoretical constructs underlying this study are the transformational leadership theory and the Etzioni's organizational theory. A cross-sectional, field survey of nurse executives, nurse managers, and staff nurses was conducted to assess nurse executive transformational and transactional leadership and their relationship to organizational commitment. Hypotheses were tested using correlational analysis, and univariate statistics were used to describe the sample. RESULTS: An inverse relationship between nurse executive transformational and transactional leadership and alienative (highly negative) organizational commitment was statistically significant. A positive association was demonstrated between nurse executive leadership and nurse manager leadership. CONCLUSIONS: This study supports the effect of nurse executive leadership on nurse manager leadership and on organizational commitment among nurses despite role distance. To the extent that transformational leadership is present, alienative organizational commitment is reduced. This relationship shows the importance of nurse executive leadership in organizational involvement among nurses in the dynamic context of contemporary hospital settings.

Adult↗

Conjugative mobilization of the cloned M6 protein gene from Streptococcus pneumoniae to Streptococcus pyogenes.

The host-vector system omega 6001-pDP36 was used to transfer the M6 protein gene (emm-6.1) of Streptococcus pyogenes to other S. pyogenes strains, isogenic and nonisogenic to D471, the strain from which emm-6.1 was originally cloned. The first step was to subclone emm-6.1 into the insertion vector pDP36. The resulting plasmid, pRMB20, was used as donor in transformation to insert emm-6.1 into the conjugative transposon omega 6001. Streptococcus pneumoniae DP1322, carrying omega 6001 integrated into the chromosome, was the recipient in the transformation experiment. omega 6001 containing emm-6.1 was then transferred by conjugation from S. pneumoniae to the chromosomes of M+ and M- S. pyogenes strains. S. pyogenes transconjugants contained one intact copy of emm-6.1 integrated into the chromosome, but no expression of M6 protein could be detected by Western blot analysis. We found no evidence of the positive transacting regulation of emm gene expression postulated by other authors. In fact, the cloned emm-6.1 was not expressed in three strains expressing their own M proteins (M5, M17 and a shorter M6). In these partial diploids M protein genes were expressed only when present in the original chromosomal locus.

Antigens, Bacterial↗

Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture.

A system called MAGPIE (Multipurpose Automated Genome Project Investigation Environment) has been designed and implemented to meet the challenges of automated whole genome analysis. The system initiates large numbers of remote and local transactions, each depending on evolving criteria and on changing remote and local conditions. Transactions are requested from different types of remote and local resources. The remote request load is fairly balanced with other community demands on server resources. Local decision modules monitor and obey user preferences and combine evidence from multiple sources to formulate credible hypotheses about sequence function. Consistency checks from multiple types of data are integrated into the ongoing local analysis. The system performs reliably on local UNIX workstations and communicates with remote resources through standard networking protocols.

Automation↗

Switching portfolios.

A constant rebalanced portfolio is an asset allocation algorithm which keeps the same distribution of wealth among a set of assets along a period of time. Recently, there has been work on on-line portfolio selection algorithms which are competitive with the best constant rebalanced portfolio determined in hindsight (Cover, 1991; Helmbold et al., 1996; Cover and Ordentlich, 1996). By their nature, these algorithms employ the assumption that high returns can be achieved using a fixed asset allocation strategy. However, stock markets are far from being stationary and in many cases the wealth achieved by a constant rebalanced portfolio is much smaller than the wealth achieved by an ad hoc investment strategy that adapts to changes in the market. In this paper we present an efficient portfolio selection algorithm that is able to track a changing market. We also describe a simple extension of the algorithm for the case of a general transaction cost, including the transactions cost models recently investigated in (Blum and Kalai, 1997). We provide a simple analysis of the competitiveness of the algorithm and check its performance on real stock data from the New York Stock Exchange accumulated during a 22-year period. On this data, our algorithm outperforms all the algorithms referenced above, with and without transaction costs.

Algorithms↗