CiteULike: Tag self

A Feminist Approach to Working With Homeless Women

Kaaren Brown — 2008-03-31T21:12:57-00:00

Affilia, Vol. 5, No. 1. (1 April 1990), pp. 6-20.

This article describes the application of a developmental model in work with groups of homeless women in two shelters and delineates the types of homeless women and the stages through which the women go as they develop. The women's development occurs in the context of affiliation, attachment, and relationship and moves from an emphasis on self to a reconnection to the community. 10.1177/088610999000500101

The plant immune system

Jonathan Jones — 2006-11-16T03:45:43-00:00

Nature, Vol. 444, No. 7117., pp. 323-329.

Cluster analysis of Wisconsin Breast Cancer dataset using self-organizing maps.

S Pantazi — 2005-11-22T02:49:34-00:00

Stud Health Technol Inform, Vol. 90 (2002), pp. 431-436.

This work deals with multidimensional data analysis, precisely cluster analysis applied to a very well known dataset, the Wisconsin Breast Cancer dataset. After the introduction of the topics of the paper the cluster analysis concept is shortly explained and different methods of cluster analysis are compared. Further, the Kohonen model of self-organizing maps is briefly described together with an example and with explanations of how the cluster analysis can be performed using the maps. After describing the data set and the methodology used for the analysis we present the findings using textual as well as visual descriptions and conclude that the approach is a useful complement for assessing multidimensional data and that this dataset has been overused for automated decision benchmarking purposes, without a thorough analysis of the data it contains.

Calculation of the persistence length of a flexible polymer chain with short-range self-repulsion

L Schã¤fer — 2006-10-18T23:58:31-00:00

The European Physical Journal E - Soft Matter, Vol. V13, No. 3. (1 March 2004), pp. 225-237.

Performance Scaling of Multi-objective Evolutionary Algorithms

V Khare — 2005-09-14T13:41:49-00:00

MOEAs axe getting immense populaxity in the recent past, mainly because of their ability to find a wide spread of Paxeto-optimal solutions in a single simulation run. Vaxious evolutionary approaches to multi-objective optimization have been proposed since 1985. Some of fairly recent ones axe NSGA-II [9], SPEA2 [19], PESA [1] (which axe included in this study) and others. They all have been mainly applied to two to three objectives. In order to establish their superiority over classical...

Small-time scaling behaviors of Internet backbone traffic: an empirical study Small-time scaling behaviors of Internet backbone traffic: an empirical study

ZL Zhang — 2007-12-19T04:07:37-00:00

INFOCOM 2003. Twenty-Second Annual Joint Conference of the IEEE Computer and Communications Societies. IEEE, Vol. 3 (2003), pp. 1826-1836 vol.3.

The small-time (sub-seconds) scaling behaviors of Internet backbone traffic, based on traces collected from OC3/12/48 links in a tier-1 ISP is studied. We observe that for a majority of these traces, the (second-order) scaling exponents at small time scales (1 ms - 100 ms) are fairly close to 0.5, indicating that traffic fluctuations at these time scales are (nearly) uncorrelated. In addition, the traces manifest mostly monofractal behaviors at small time scales. The objective of the paper is to understand the potential causes or factors that influence the small-time scalings of Internet backbone traffic via empirical data analysis. We analyze the traffic composition of the traces along two dimensions - flow size and flow density. Our study uncovers dense flows (i.e., flows with bursts of densely clustered packets) as the correlation-causing factor in small time scales, and reveals that the traffic composition in terms of proportions of dense vs. sparse flows plays a major role in influencing the small-time scalings of aggregate traffic.

Self-theories: Their Role in Motivation, Personality, and Development (Essays in Social Psychology)

Carol Dweck — 2006-07-17T23:48:49-00:00

(01 January 2000)

(Psychology Press) <Essays in Social Psychology> Columbia Univ., NY. Shed light on how people work: why they sometimes function well, and at other times, behave in ways that are self-defeating or destructive. Presents research on adaptive and maladaptive cognitive-motivational patterns. For researchers and students. Softcover.

The Drama of the Gifted Child: The Search for the True Self

Alice Miller — 2006-07-08T05:07:18-00:00

(02 January 1997)

As charming performers who skillfully reflect their parents expectations, far too many children grow into adults driven to greater and greater achievements by an underlying sense of worthlessness. Never allowed to express their true feelings, and having lost touch with their true selves, they act out their repressed feelings with episodes of depression and compulsive behavior. They in turn inflict the same legacy of repression on their own children. This poignant and thought-provoking book shows how narcissistic parents form and deform the lives of their children. The Drama of the Gifted Child is the first step toward helping readers reclaim their lives by discovering their own needs and their own truth.

Christianity, Cargo and Ideas of Self: Patterns of Literacy in a Papua New Guinean Village

Don Kulick — 2007-10-18T15:02:49-00:00

Literacy in a small, rural, newly literate Papua New Guinean village is analysed by placing it in the context of local notions of Christianity, the self and language. Villagers' interpretations of the relationship between Catholicism and the written word are based on their Cargo-oriented world-view and on their pre-Christian beliefs about language as a powerful means by which individuals could bring about transformations in their world. Local ideas of the self and others are articulated and reinforced through an emphasis on particular dimensions of oral language use. This emphasis has consequences for the uses to which literacy is put, the structure of the writing the villagers produce, and the ways in which they attribute meaning to written texts.

Recursive self-organizing maps

T Voegtlin — 2005-11-02T14:42:00-00:00

(2002)

A temporal extension of the Self-Organizing Map (SOM) is presented. The learning algorithm is based on self-reference, and is called Recursive SOM. This network learns local representations of the temporal context associated with a time series, and extends classical properties of SOM to time.

Self-organizing linear search

JH Hester — 2005-04-03T11:11:54-00:00

ACM Comput. Surv., Vol. 17, No. 3. (September 1985), pp. 295-311.

Self-Organizing Maps

Teuvo Kohonen — 2005-05-10T06:12:32-00:00

(28 December 2000)

Improved power in multinomial goodness-of-fit tests

Ayanendranath Basu — 2008-05-12T21:51:02-00:00

Journal of the Royal Statistical Society: Series D (The Statistician), Vol. 51, No. 3. (2002), pp. 381-393.

Summary. Pearson's chi2- and the log-likelihood ratio chi2-statistics are fundamental tools in goodness-of-fit testing. Cressie and Read constructed a general family of divergences which includes both statistics as special cases. This family is indexed by a single parameter, and divergences at either end of the scale are more powerful against alternatives of one type while being rather poor against the opposite type. Here we present several new goodness-of-fit testing procedures which have reasonably high powers for both kinds of alternative. Graphical studies illustrate the advantages of the new methods.

Signaling local non-credibility in an automatic segmentation pipeline

JH Levy — 2008-05-12T21:47:03-00:00

Vol. 6512 (March 2007)

The advancing technology for automatic segmentation of medical images should be accompanied by techniques to inform the user of the local credibility of results. To the extent that this technology produces clinically acceptable segmentations for a significant fraction of cases, there is a risk that the clinician will assume every result is acceptable. In the less frequent case where segmentation fails, we are concerned that unless the user is alerted by the computer, she would still put the result to clinical use. By alerting the user to the location of a likely segmentation failure, we allow her to apply limited validation and editing resources where they are most needed. We propose an automated method to signal suspected non-credible regions of the segmentation, triggered by statistical outliers of the local image match function. We apply this test to m-rep segmentations of the bladder and prostate in CT images using a local image match computed by PCA on regional intensity quantile functions. We validate these results by correlating the non-credible regions with regions that have surface distance greater than 5.5mm to a reference segmentation for the bladder. A 6mm surface distance was used to validate the prostate results. Varying the outlier threshold level produced a receiver operating characteristic with area under the curve of 0.89 for the bladder and 0.92 for the prostate. Based on this preliminary result, our method has been able to predict local segmentation failures and shows potential for validation in an automatic segmentation pipeline.

The topography of multivariate normal mixtures

Surajit Ray — 2008-05-12T21:42:35-00:00

(11 Feb 2006)

Multivariate normal mixtures provide a flexible method of fitting high-dimensional data. It is shown that their topography, in the sense of their key features as a density, can be analyzed rigorously in lower dimensions by use of a ridgeline manifold that contains all critical points, as well as the ridges of the density. A plot of the elevations on the ridgeline shows the key features of the mixed density. In addition, by use of the ridgeline, we uncover a function that determines the number of modes of the mixed density when there are two components being mixed. A followup analysis then gives a curvature function that can be used to prove a set of modality theorems.

A Nonparametric Statistical Approach to Clustering via Mode Identification

Jia Li — 2008-05-12T21:38:34-00:00

Journal of Machine Learning Research, Vol. 8 (August 2007), pp. 1687-1723.

A new clustering approach based on mode identification is developed by applying new optimization techniques to a nonparametric density estimator. A cluster is formed by those sample points that ascend to the same local maximum (mode) of the density function. The path from a point to its associated mode is efficiently solved by an EM-style algorithm, namely, the Modal EM (MEM). This method is then extended for hierarchical clustering by recursively locating modes of kernel density estimators with increasing bandwidths. Without model fitting, the mode-based clustering yields a density description for every cluster, a major advantage of mixture-model-based clustering. Moreover, it ensures that every cluster corresponds to a bump of the density. The issue of diagnosing clustering results is also investigated. Specifically, a pairwise separability measure for clusters is defined using the ridgeline between the density bumps of two clusters. The ridgeline is solved for by the Ridgeline EM (REM) algorithm, an extension of MEM. Based upon this new measure, a cluster merging procedure is created to enforce strong separation. Experiments on simulated and real data demonstrate that the mode-based clustering approach tends to combine the strengths of linkage and mixture-model-based clustering. In addition, the approach is robust in high dimensions and when clusters deviate substantially from Gaussian distributions. Both of these cases pose difficulty for parametric mixture modeling. A C package on the new algorithms is developed for public access at http://www.stat.psu.edu/∼jiali/hmac.

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding

Surajit Ray — 2007-10-29T20:33:22-00:00

Immunome Research, Vol. 3 (29 October 2007), 9.

Model selection in high dimensions: a quadratic-risk-based approach

Ray — 2008-01-09T03:04:30-00:00

Journal of the Royal Statistical Society: Series B (Statistical Methodology), Vol. 70, No. 1. (February 2008), pp. 95-118.

Why Comply? Social Learning and European Identity Change

Jeffrey Checkel — 2006-08-28T23:54:08-00:00

International Organization, Vol. 55, No. 3. (2001), pp. 553-588.

Why do agents comply with the norms embedded in regimes and international institutions? Scholars have proposed two competing answers to this compliance puzzle, one rationalist, the other constructivist. Rationalists emphasize coercion, cost/benefit calculations, and material incentives; constructivists stress social learning, socialization, and social norms. Both schools, however, explain important aspects of compliance. To build a bridge between them, I examine the role of argumentative persuasion and social learning. This makes explicit the theory of social choice and interaction implicit in many constructivist compliance studies, and it broadens rationalist arguments about the instrumental and noninstrumental processes through which actors comply. I argue that domestic politics-in particular, institutional and historical contexts-delimit the causal role of persuasion/social learning, thus helping both rationalists and constructivists to refine the scope of their compliance claims. To assess the plausibility of these arguments, I examine why states comply with new citizenship/membership norms promoted by European regional organizations.

The Context of Social Identity: Domination, Resistance, and Change

Stephen Reicher — 2004-12-28T16:06:45-00:00

Political Psychology, Vol. 25, No. 6., 921.

Identity and Search in Social Networks

DJ Watts — 2005-02-27T09:16:28-00:00

(17 May 2002)

Social networks have the surprising property of being "searchable": Ordinary people are capable of directing messages through their network of acquaintances to reach a specific but distant target person in only a few steps. We present a model that offers an explanation of social network searchability in terms of recognizable personal identities: sets of characteristics measured along a number of social dimensions. Our model defines a class of searchable networks and a method for searching them that may be applicable to many network search problems, including the location of data files in peer-to-peer networks, pages on the World Wide Web, and information in distributed databases.

The Immune System as a Self-Identification Process: a Survey and a Proposal

I Yoshiteru — 2007-06-24T07:22:02-00:00

(1996)

We first compare the paradigm of the immunity-based system with other biological paradigm such as neural networks and genetic algorithm. We review studies of the immunity-based system dividing them into three classes: recognition/learning based on Jerne's network, adaptation based on Edelman's selection principle, and search/optimization based on Holland's genetic algorithm. We also propose that the self-identification process is yet another important aspect of the immune system, which has not ...

The Therapist's Self in Dialogical Family Therapy: Some Ideas About Not-Knowing and the Therapist's Inner Conversation

Peter Rober — 2005-11-12T13:19:28-00:00

Family Process, Vol. 44, No. 4. (December 2005), pp. 477-495.

Selfless Self-Love

Bransen — 2006-05-10T12:21:36-00:00

Ethical Theory and Moral Practice, Vol. 9, No. 1. (February 2006), pp. 3-25.

Key educational experiences and self-discovery in higher education

Gad Yair — 2007-06-08T03:58:30-00:00

Teaching and Teacher Education, Vol. In Press, Corrected Proof

This study investigates key educational experiences in higher education. Key experiences are short and intense instructional episodes that students remember to have had a decisive effect on their lives. Data comes from a sample of 3045 key educational experiences, focusing on the 11.6% that relate to higher education. The paper uses a qualitative analysis to describe different features of key experiences in higher education. The results suggest that key experiences involve a process of self-discovery where students find features about themselves they knew nothing of previously. They also help to characterize three main contexts for self-discovery in higher education. First, key experiences take place in academically challenging circumstances that get students to embark on identity adventures. Second, challenging circumstances also provided ripe ground for sage advice that professors provided their students with. These words of wisdom became leitmotifs for students' lives henceforth. Finally, the results indicate the importance of second chance opportunities for self-discovery and identity rehabilitation in higher education.

Where in the brain is the self?

Todd Feinberg — 2006-02-20T05:18:28-00:00

Consciousness and Cognition, Vol. 14, No. 4. (December 2005), pp. 661-678.

Localizing the self in the brain has been the goal of consciousness research for centuries. Recently, there has been an increase in attention to the localization of the self. Here we present data from patients suffering from a loss of self in an attempt to understand the neural correlates of consciousness. Focusing on delusional misidentification syndrome (DMS), we find that frontal regions, as well as the right hemisphere appear to play a significant role in DMS and DMS related disorders. These data are placed in the context of neuroimaging findings.

Productive power and the practices of the self in contraceptive counselling

Mark Hayter — 2006-02-25T19:51:57-00:00

Nursing Inquiry, Vol. 13, No. 1. (March 2006), pp. 33-43.

Teaching Counselors Self-Care Through Mindfulness Practices

Sandy Newsome — 2006-08-18T05:52:51-00:00

The Teachers College Record, Vol. 108, No. 9. (September 2006), pp. 1881-1900.

Fordham, feeling, and countertransference: reflections on defences of the self

Astor — 2007-04-05T15:53:27-00:00

Journal of Analytical Psychology, Vol. 52, No. 2. (April 2007), pp. 185-205.

Developing creativity, motivation, and self-actualization with learning systems

Winslow Burleson — 2005-09-08T15:31:44-00:00

International Journal of Human-Computer Studies, Vol. 63, No. 4-5. (October 2005), pp. 436-451.

Developing learning experiences that facilitate self-actualization and creativity is among the most important goals of our society in preparation for the future. To facilitate deep understanding of a new concept, to facilitate learning, learners must have the opportunity to develop multiple and flexible perspectives. The process of becoming an expert involves failure, as well as the ability to understand failure and the motivation to move onward. Meta-cognitive awareness and personal strategies can play a role in developing an individual's ability to persevere through failure, and combat other diluting influences. Awareness and reflective technologies can be instrumental in developing a meta-cognitive ability to make conscious and unconscious decisions about engagement that will ultimately enhance learning, expertise, creativity, and self-actualization. This paper will review diverse perspectives from psychology, engineering, education, and computer science to present opportunities to enhance creativity, motivation, and self-actualization in learning systems.

Private Materialism, Personal Self-Fulfillment, Family Life, and Public Interest: The Nature, Effects, and Causes of Recent Changes in the Values of American Youth

Richard Easterlin — 2006-10-01T00:27:09-00:00

The Public Opinion Quarterly, Vol. 55, No. 4. (1991), pp. 499-533.

From the early seventies through 1986-87, private materialism as a life goal increased greatly in importance among American youth, goals relating to family life increased somewhat, public interest concerns diminished modestly, and the goal of personal self-fulfillment decline sharply. Accompanying this shift in values was a change in young people's college majors and career plans toward those leading to higher paying jobs and a marked increase in the attractiveness of working in large corporations. Jobs offering money and status became more preferred relative to those with opportunities for self-fulfillment or public service. Support grew for capitalist institutions such as profit making and advertising. At the same time, there was a retreat from political involvement, and a conservative shift in political beliefs. Explanations of the shift in values in terms of the impact on the young of major political and social events or the emergence of a feeling of economic insecurity among the young are not supported by the evidence. Nor are a number of hypotheses relating to changes in young people's family structure or socialization experience. The shift in values of the young does, however, apparently correspond to a similar change in the values of adults generally and, thus, may reflected changes in the values transmitted to young people as they were growing up. We speculate that the shift in values among adults was, in turn, caused by a growing feeling of economic deprivation in the post-1973 period as real wage rates declined and material aspirations continued to rise. In the last few years, the shift in the life goals of the young appears to have ended and may even have started to reverse, but young people today are still much different from those 15 years ago.

Social identity and the recognition of creativity in groups

Adarves-Yorno — 2006-09-14T06:12:05-00:00

British Journal of Social Psychology, Vol. 45, No. 3. (September 2006), pp. 479-497.

Which is the `self' in `self-interest'?

Paul Dugay — 2005-07-30T21:48:44-00:00

The Sociological Review, Vol. 53, No. 3. (August 2005), pp. 391-411.

'Self-knowledge is the prerequisite of humanity': personal development and self-awareness for aid workers

Jane Gilbert — 2005-02-18T05:25:32-00:00

Development in Practice, Vol. 15, No. 1. (February 2005), pp. 64-69.

The "self digest": self-knowledge serving self-regulatory functions.

ET Higgins — 2007-02-13T03:19:35-00:00

J Pers Soc Psychol, Vol. 71, No. 6. (December 1996), pp. 1062-1083.

Self-knowledge is conceptualized as a self digest that summarizes one's relations to the world and the personal consequences of these relations. It is a handy sourcebook that serves self-regulatory functions. It is distinguished from the classic notion that self-knowledge contains one descriptive actual self. The self digest contains information about three kinds of actual selves that differ in self-regulatory function: (a) an instrumental self, (b) an expectant self, and (c) a monitored self. It represents not only the actual self but desired (and undesired) selves that reflect different kinds of self-regulatory focus (i.e., promotion or prevention). It represents not only one's own standpoint but also the standpoint of others whose beliefs one is motivated to take into account. This self-regulatory perspective is used to reconsider self-esteem, self-enhancement, self-consistency, self-presentation, and cross-cultural differences in the self.

Whats So Special about Self-Knowledge?

Medina — 2006-07-07T00:53:25-00:00

Philosophical Studies, Vol. 129, No. 3. (June 2006), pp. 575-603.

Random organization in periodically driven systems

Laurent Corte — 2008-05-02T18:54:40-00:00

Nat Phys, Vol. 4, No. 5. (May 2008), pp. 420-424.

On self-referencing differences in judgment and choice

Sanjay Sood — 2005-10-27T13:53:16-00:00

Organizational Behavior and Human Decision Processes, Vol. 98, No. 2. (November 2005), pp. 144-154.

Compared to judgment, choice is argued to elicit more self-referent processing and thereby produce greater subsequent recall of evaluated information. This response mode effect is shown to be dependent upon sufficient visualization to overcome the use of heuristic processing during choice. When visualizing prior to the task, choice leads to increased thinking about personal consumption occasions relative to judgment, leading to enhanced recall of vivid (vs. non-vivid) attributes. This proposed interaction of task and visualization was found in two experiments that assessed incidental recall following a choice or judgment task. In experiment 1, participants recalled more vivid product attribute information after choosing between options than after rating each option separately, but only when instructed to visualize during evaluation. To eliminate a comparison-based explanation of this effect, a second experiment was conducted that presented only one option in each category. Participants who evaluated their intention to purchase the option (a judgment equivalent of choice) demonstrated greater recall of vivid product attribute information than did participants who rated their liking for the option, and this recall difference was again moderated by instructions to visualize.

Memory and the self

Martin Conway — 2005-11-10T11:04:00-00:00

Journal of Memory and Language, Vol. 53, No. 4. (October 2005), pp. 594-628.

The Self-Memory System (SMS) is a conceptual framework that emphasizes the interconnectedness of self and memory. Within this framework memory is viewed as the data base of the self. The self is conceived as a complex set of active goals and associated self-images, collectively referred to as the working self. The relationship between the working self and long-term memory is a reciprocal one in which autobiographical knowledge constrains what the self is, has been, and can be, whereas the working self-modulates access to long-term knowledge. Specific proposals concerning the role of episodic memories and autobiographical knowledge in the SMS, their function in defining the self, the neuroanatomical basis of the system, its development, relation to consciousness, and possible evolutionary history are considered with reference to current and new findings as well as to findings from the study of impaired autobiographical remembering.

Initiation of dust explosions by electric spark discharges triggered by the explosive dust cloud itself

Erlend Randeberg — 2006-04-24T20:58:47-00:00

Journal of Loss Prevention in the Process Industries, Vol. 19, No. 2-3. ( 2006), pp. 154-160.

An investigation of ignition of dust clouds by the use of electric spark discharges triggered by the explosive dust cloud itself has been conducted. This method of triggering capacitive sparks probably represents a realistic mechanism for initiating accidental dust explosions in industrial practice. Unlike the conventional method for determining the minimum ignition energy (MIE) in the laboratory, the delay between dust dispersion and spark discharge is not a degree of freedom. In stead, the transient dust cloud itself is used to initiate spark breakdown between electrodes set at a high voltage lower than breakdown in pure air. In the present study, different kinds of dusts were tested as 'spark triggers', and they exhibited quite different abilities to trigger breakdown. Large particles were found to initiate breakdown at lower voltages than smaller ones. In general, conductive particles were not found to initiate breakdown at lower voltages than dielectric ones when using the same dust concentration.Minimum ignition energies (MIE) of three dusts (Lycopodium clavatum, sulphur and maize starch) were determined using the authors' method of study. The MIEs were somewhat higher than those obtained using conventional methods, but relatively close to the values obtained through conventional methods.

Independent origins of self-compatibility in Arabidopsis thaliana

Kentaro Shimizu — 2008-01-18T00:04:54-00:00

Molecular Ecology, Vol. 17, No. 2. (January 2008), pp. 704-714.

Policies Designed for Self-Interested Citizens May Undermine "The Moral Sentiments": Evidence from Economic Experiments

Samuel Bowles — 2008-06-20T08:07:59-00:00

Science, Vol. 320, No. 5883. (20 June 2008), pp. 1605-1609.

High-performance organizations and economies work on the basis not only of material interests but also of Adam Smith's "moral sentiments." Well-designed laws and public policies can harness self-interest for the common good. However, incentives that appeal to self-interest may fail when they undermine the moral values that lead people to act altruistically or in other public-spirited ways. Behavioral experiments reviewed here suggest that economic incentives may be counterproductive when they signal that selfishness is an appropriate response; constitute a learning environment through which over time people come to adopt more self-interested motivations; compromise the individual's sense of self-determination and thereby degrade intrinsic motivations; or convey a message of distrust, disrespect, and unfair intent. Many of these unintended effects of incentives occur because people act not only to acquire economic goods and services but also to constitute themselves as dignified, autonomous, and moral individuals. Good organizational and institutional design can channel the material interests for the achievement of social goals while also enhancing the contribution of the moral sentiments to the same ends. 10.1126/science.1152110

The Question of Happiness: On Finding Meaning, Pleasure, and the Ultimate Currency

Tal Ben-Shahar — 2007-09-12T18:53:12-00:00

(01 January 2001)

Why are our levels of emotional wealth decreasing despite an overall increase in material wealth? Is it possible to be successful and happy? How can we become happier? The Question of Happiness is a philosophical and psychological investigation into the nature of happiness: providing a new way of thinking about what happiness actually is, and exploring how we can be happier in relationships, at work, and in school. Tal Ben-Shahar's ideas are both rigorous and accessible, building on academic work while remaining practical and clear.

“How can we know the dancer from the dance?”: Discourses of the self-body

Leslie Bloom — 2008-03-09T21:32:13-00:00

Human Studies, Vol. 15, No. 4. (1 October 1992), pp. 313-334.

Critical Configurations for Projective Reconstruction from Multiple Views

Hartley — 2006-09-23T01:46:52-00:00

International Journal of Computer Vision, Vol. 71, No. 1. (January 2007), pp. 5-47.

Genetic analysis of Israel acute paralysis virus: distinct clusters are circulating in the United States.

G Palacios — 2008-07-03T18:46:04-00:00

Journal of virology, Vol. 82, No. 13. (July 2008), pp. 6209-6217.

Israel acute paralysis virus (IAPV) is associated with colony collapse disorder of honey bees. Nonetheless, its role in the pathogenesis of the disorder and its geographic distribution are unclear. Here, we report phylogenetic analysis of IAPV obtained from bees in the United States, Canada, Australia, and Israel and the establishment of diagnostic real-time PCR assays for IAPV detection. Our data indicate the existence of at least three distinct IAPV lineages, two of them circulating in the United States. Analysis of representatives from each proposed lineage suggested the possibility of recombination events and revealed differences in coding sequences that may have implications for virulence.

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

Gustavo Palacios — 2008-05-04T23:51:48-00:00

N Engl J Med, Vol. 358, No. 10. (6 March 2008), pp. 991-998.

Background Three patients who received visceral-organ transplants from a single donor on the same day died of a febrile illness 4 to 6 weeks after transplantation. Culture, polymerase-chain-reaction (PCR) and serologic assays, and oligonucleotide microarray analysis for a wide range of infectious agents were not informative. Methods We evaluated RNA obtained from the liver and kidney transplant recipients. Unbiased high-throughput sequencing was used to identify microbial sequences not found by means of other methods. The specificity of sequences for a new candidate pathogen was confirmed by means of culture and by means of PCR, immunohistochemical, and serologic analyses. Results High-throughput sequencing yielded 103,632 sequences, of which 14 represented an Old World arenavirus. Additional sequence analysis showed that this new arenavirus was related to lymphocytic choriomeningitis viruses. Specific PCR assays based on a unique sequence confirmed the presence of the virus in the kidneys, liver, blood, and cerebrospinal fluid of the recipients. Immunohistochemical analysis revealed arenavirus antigen in the liver and kidney transplants in the recipients. IgM and IgG antiviral antibodies were detected in the serum of the donor. Seroconversion was evident in serum specimens obtained from one recipient at two time points. Conclusions Unbiased high-throughput sequencing is a powerful tool for the discovery of pathogens. The use of this method during an outbreak of disease facilitated the identification of a new arenavirus transmitted through solid-organ transplantation. 10.1056/NEJMoa073785

Comprehensive viral oligonucleotide probe design using conserved protein regions.

OJ Jabado — 2008-07-03T19:01:58-00:00

Nucleic acids research, Vol. 36, No. 1. (January 2008)

Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.

Using the Gibbs Motif Sampler for phylogenetic footprinting.

W Thompson — 2008-07-03T18:52:17-00:00

Methods in molecular biology (Clifton, N.J.), Vol. 395 (2007), pp. 403-424.

The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promoters upstream of gene sequences. We will describe approaches that use Gibbs to locate TFBSs in a collection of orthologous nucleotide sequences, i.e., phylogenetic footprinting. To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions.

A Metagenomic Survey of Microbes in Honey Bee Colony Collapse Disorder.

Diana L Cox-Foster — 2007-09-09T13:26:15-00:00

Science (6 September 2007)

In colony collapse disorder (CCD), honey bee colonies inexplicably lose their workers. CCD has resulted in a loss of 50 to 90% of colonies in beekeeping operations across the United States. The observation that irradiated combs from affected colonies can be repopulated with naive bees suggests that infection may contribute to CCD. We used an unbiased metagenomic approach to survey microflora in CCD hives, normal hives, and imported royal jelly. Candidate pathogens were screened for significance of association with CCD by examination of samples collected from several sites over a period of 3 years. One organism, Israeli acute paralysis virus of bees (IAPV), was strongly correlated with CCD.