CiteULike: Author Kloos

TRANSFAC: transcriptional regulation, from patterns to profiles.

V Matys — 2005-07-18T07:56:57-00:00

Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 374-378.

The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.

Reprogramming of the human atrial transcriptome in permanent atrial fibrillation: expression of a ventricular-like genomic signature.

AS Barth — 2008-07-24T13:10:45-00:00

Circulation research, Vol. 96, No. 9. (13 May 2005), pp. 1022-1029.

Atrial fibrillation is associated with increased expression of ventricular myosin isoforms in atrial myocardium, regarded as part of a dedifferentiation process. Whether reexpression of ventricular isoforms in atrial fibrillation is restricted to transcripts encoding for contractile proteins is unknown. Therefore, this study compares atrial mRNA expression in patients with permanent atrial fibrillation to atrial mRNA expression in patients with sinus rhythm and to ventricular gene expression using Affymetrix U133 arrays. In atrial myocardium, we identified 1434 genes deregulated in atrial fibrillation, the majority of which, including key elements of calcium-dependent signaling pathways, displayed downregulation. Functional classification based on Gene Ontology provided the specific gene sets of the interdependent processes of structural, contractile, and electrophysiological remodeling. In addition, we demonstrate for the first time a prominent upregulation of transcripts involved in metabolic activities, suggesting an adaptive response to increased metabolic demand in fibrillating atrial myocardium. Ventricular-predominant genes were 5 times more likely to be upregulated in atrial fibrillation (174 genes upregulated, 35 genes downregulated), whereas atrial-specific transcripts were predominantly downregulated (56 genes upregulated, 564 genes downregulated). Overall, in fibrillating atrial myocardium, functional classes of genes characteristic of ventricular myocardium were found to be upregulated (eg, metabolic processes), whereas functional classes predominantly expressed in atrial myocardium were downregulated (eg, signal transduction and cell communication). Therefore, dedifferentiation with adoption of a ventricular-like signature is a general feature of the fibrillating atrium.

A Modular Architecture for Intelligent Web Resource Based Tutoring Systems

Sergio Gutiérrez — 2007-07-09T13:19:25-00:00

Intelligent Tutoring Systems (2006), pp. 753-755.

In this document a platform for the development of ITSs is presented. The objective of this architecture is to provide a tutoring platform with a modular structure suitable to accommodate different sequencing paradigms through a common functional interface. The platform has been tested with positive results.

Some Ideas for a Collaborative Search of the Optimal Learning Path

Gutiérrez — 2007-05-16T22:08:15-00:00

Adaptive Hypermedia and Adaptive Web-Based Systems (2006), pp. 430-434.

One of the challenges of adaptive hypermedia educational (AHE) systems is that of adapting the sequencing of learning units presented to the student. One approach is to model the set of possible sequencings with a graph, but the process of designing and maintaining the graph may be tedious and error-prone. This paper presents some ideas to overcome this, inpired by swarm intelligence techniques. Problems that may arise, as well as possible solutions, are presented.

An Adaptive Tutoring System Based on Hierarchical Graphs

Sergio Gutiérrez — 2007-07-09T12:26:00-00:00

Adaptive Hypermedia and Adaptive Web-Based Systems (2004), pp. 401-404.

An adaptive tutoring system is presented based on hierarchical graphs that capture the sequencing of a set of learning objects depending on how students interact with them. The use of hierarchy allows the definition of complex transition structures over arbitrarily large sets of objects. Using this approach a tutoring tool has been designed and tested in the context of an introductory course in Computer Architecture. Experimental results clearly show the positive impact of the proposed content adaptation over how students learn concepts.

Approach to the Patient with a Positive Serum Thyroglobulin and a Negative Radioiodine Scan after Initial Therapy for Differentiated Thyroid Cancer

Richard Kloos — 2008-05-09T19:55:08-00:00

J Clin Endocrinol Metab, Vol. 93, No. 5. (1 May 2008), pp. 1519-1525.

The 10-yr survival of differentiated thyroid cancer is about 76-93%, and at least 10% of patients manifest tumor persistence or recurrence, depending on their disease stage, after initial therapy, which typically includes total thyroidectomy and 131I ablation. Previously the realization of their residual/recurrent cancer often presented simultaneously with the additional surprise that they lacked pathological uptake on their diagnostic whole-body radioiodine image despite their elevated stimulated serum thyroglobulin (Tg) level, a scenario referred to as the scan-negative, Tg-positive patient. Now that serum Tg and neck ultrasonography have supplanted the diagnostic whole-body scan because of its inferior sensitivity, patients are often recognized to harbor residual disease without radioiodine imaging, and a new challenging scenario has emerged: the ultrasonography-negative, Tg-positive patient. Similarities and differences of these two patient populations aside, these Tg-positive patients are frequently encountered, and some are considered for additional 131I therapy, although now typically after negative anatomic +/- 18F-fluorodeoxyglucose positron emission tomography imaging or in the setting of known or suspected distant metastases already localized by anatomic imaging. Thus, the scan-negative, Tg-positive patient of today differs from those of the past, but the term still has relevance to current practice. The optimal evaluation and treatment of these patients remain controversial, partly because many of these patients will not die from thyroid cancer, and there are no randomized trials to demonstrate that intervention could have prevented the deaths that do occur. Here a case is presented that adds the complexity of advanced age, and one approach to these challenging patients is offered. 10.1210/jc.2007-2357

Creating and Deploying Effective eLearning Experiences Using .LRN

R Hernandez — 2008-03-17T22:49:28-00:00

Education, IEEE Transactions on, Vol. 50, No. 4. (2007), pp. 345-351.

The significant quality increase in open-source e-learning platforms allows for large-scale e-learning courses with significantly reduced costs. This document describes a pedagogical model enhanced for effectively providing courses to a large number of students and producing media-rich content suitable to be managed by the open-source e-learning platform .LRN. Two case studies are presented: 1) a course for high school students to increase the popularity of engineering degrees; and 2) a regular engineering course with a blended learning approach. In both cases the proposed paradigm allowed the creation of successful learning experiences impossible with conventional teaching methodologies and tools.

On photoelasticity and the quadratic electrostrictive effect

G Kloos — 2007-12-01T18:29:42-00:00

(1997), pp. 1536-1539.

The contribution of the photoelastic effect to quadratic electrostriction is studied from a macroscopic point of view. The predicted values are found to be an order of magnitude or more smaller than the total quadratic electrostrictive effect of typical alkali halides.

Service providers' views of psychiatric mutual support groups

Matthew Chinman — 2007-09-02T01:08:07-00:00

Journal of Community Psychology, Vol. 30, No. 4. (2002), pp. 349-366.

Despite evidence that mutual support groups can be beneficial for those with serious mental illnesses, professionals have been reluctant to utilize this resource. We surveyed over 400 providers across several disciplines and settings within the state of Connecticut's public mental health system to assess their attitudes and practices regarding the use of mutual support groups for their patients. We found that being a rehabilitation worker and possessing more advanced training, greater numbers of years in their setting and discipline, and personal experience with psychiatric disorders or mutual support were associated with more favorable attitudes and behaviors toward mutual support. In addition, traditional 12-step groups (e.g., Alcoholics Anonymous) were viewed more favorably than psychiatric mutual support groups. Implications for educational efforts about the benefits of mutual support for those with serious mental illnesses are discussed. © 2002 Wiley Periodicals, Inc.

Interlinking physical beliefs: Children's bias towards logical congruence

Heidi Kloos — 2007-03-20T11:32:06-00:00

Cognition, Vol. 103, No. 2. (May 2007), pp. 227-252.

Young children's naive beliefs about physics are commonly studied as isolated pieces of knowledge. The current paper takes a different approach. It asks whether preschoolers interlink individual beliefs into larger configurations or Gestalts. Such Gestalts bring together knowledge such as how an object's mass relates to its sinking speed, how an object's volume relates to its sinking speed, and how mass and volume are correlated. The particular form of organization explored here is referred to as logical congruence, the logical correspondence in directions among three physical relations. Are children's guesses about one physical relation congruent with their beliefs about the other two relations? And can they learn a congruent set of relations more readily than an incongruent set? Two different physical domains were explored, one in which children commonly hold pre-existing beliefs, and one in which they are likely to lack such beliefs. The results in both domains show a strong bias towards congruent knowledge configurations in young children. These findings may explain children's difficulties learning inherently incongruous concepts such as density.

Finding a learning path: toward a swarm intelligence approach

Sergio Guti&\#233;rrez — 2007-02-04T11:16:28-00:00

(2006), pp. 94-99.

Adaptive Peer Review Based on Student Profiles

Raquel García — 2007-07-09T13:19:52-00:00

Intelligent Tutoring Systems (2006), pp. 781-783.

Intelligent tutoring systems cover a wide range of educational processes. However, in the context of peer review methodology, there is no previous work about adaptation of the process according to the student’s profile. In this paper, a methodology for adaptive peer review is introduced. Experimental application of adaptive peer review through two courses allows to confirm pedagogical benefits with actual students’ results.

Sequencing Parametric Exercises for an Operating System Course

Pilar Linillos — 2007-07-09T12:27:59-00:00

Artificial Intelligence Applications and Innovations (2006), pp. 450-458.

An adaptive tutoring system for an Operating System course is presented. The architecture, based on sequencing graphs, that supports an adaptive sequencing of the learning units is described. The content structure is presented as well. The system is now in use in regular university courses and results of this experience will be published in the future.

When Looks Are Everything: Appearance Similarity Versus Kind Information in Early Induction

Sloutsky — 2007-03-26T06:51:35-00:00

Psychological Science, Vol. 18, No. 2. (February 2007), pp. 179-185.

Management guidelines for patients with thyroid nodules and differentiated thyroid cancer.

DS Cooper — 2007-04-13T21:23:43-00:00

Thyroid, Vol. 16, No. 2. (February 2006), pp. 109-142.

A kinesin heavy chain (KIF5A) mutation in hereditary spastic paraplegia (SPG10).

E Reid — 2007-03-05T14:30:34-00:00

Am J Hum Genet, Vol. 71, No. 5. (November 2002), pp. 1189-1194.

We have identified a missense mutation in the motor domain of the neuronal kinesin heavy chain gene KIF5A, in a family with hereditary spastic paraplegia. The mutation occurs in the family in which the SPG10 locus was originally identified, at an invariant asparagine residue that, when mutated in orthologous kinesin heavy chain motor proteins, prevents stimulation of the motor ATPase by microtubule-binding. Mutation of kinesin orthologues in various species leads to phenotypes resembling hereditary spastic paraplegia. The conventional kinesin motor powers intracellular movement of membranous organelles and other macromolecular cargo from the neuronal cell body to the distal tip of the axon. This finding suggests that the underlying pathology of SPG10 and possibly of other forms of hereditary spastic paraplegia may involve perturbation of neuronal anterograde (or retrograde) axoplasmic flow, leading to axonal degeneration, especially in the longest axons of the central nervous system.

Peer Support Among Individuals With Severe Mental Illness: A Review of the Evidence

Larry Davidson — 2007-01-07T02:07:29-00:00

Clinical Psychology: Science and Practice, Vol. 6, No. 2. (1999), pp. 165-187.

This article reviews the history and potential effectiveness of peer support among persons with severe mental illness. Following a historical overview, we describe the three primary forms of peer support that have been developed to date by and for this population, and examine the existing empirical evidence of the feasibility, effectiveness, and utilization of each of these approaches in contributing to the recovery of individuals with psychiatric disabilities. These three forms are (1) naturally occurring mutual support groups, (2) consumer-run services, and (3) the employment of consumers as providers within clinical and rehabilitative settings. Existing studies of mutual support groups suggest that they may improve symptoms, promote larger social networks, and enhance quality of life. This research is largely from uncontrolled studies, however, and will need to be evaluated further using prospective, controlled designs. Consumer-run services and the use of consumers as providers promise to broaden the access of individuals with psychiatric disabilities to peer support, but research on these more recent developments is only preliminary and largely limited to demonstrations of their feasibility. We discuss issues entailed in participating in peer support for this population, and then close with a discussion of the implications for future policy, research, and practice.

The role of microRNA genes in papillary thyroid carcinoma.

H He — 2006-01-25T14:02:30-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 52. (27 December 2005), pp. 19075-19080.

Apart from alterations in the RET/PTC-RAS-BRAF pathway, comparatively little is known about the genetics of papillary thyroid carcinoma (PTC). We show that numerous microRNAs (miRNAs) are transcriptionally up-regulated in PTC tumors compared with unaffected thyroid tissue. A set of five miRNAs, including the three most up-regulated ones (miR-221, -222, and -146), distinguished unequivocally between PTC and normal thyroid. Additionally, miR-221 was up-regulated in unaffected thyroid tissue in several PTC patients, presumably an early event in carcinogenesis. Tumors in which the up-regulation (11- to 19-fold) of miR-221, -222, and -146 was strongest showed dramatic loss of KIT transcript and Kit protein. In 5 of 10 such cases, this down expression was associated with germline single-nucleotide changes in the two recognition sequences in KIT for these miRNAs. We conclude that up-regulation of several miRs and regulation of KIT are involved in PTC pathogenesis, and that sequence changes in genes targeted by miRNAs can contribute to their regulation.

An ontology-based mechanism for assembling learning objects

LP Santacruz-Valencia — 2006-10-06T08:31:43-00:00

Telecommunications, 2005. Advanced Industrial Conference on Telecommunications/Service Assurance with Partial and Intermittent Resources Conference/ E-Learning on Telecommunications Workshop. AICT/SAPIR/ELETE 2005. Proceedings (2005), pp. 472-477.

The paper presents OntoGlue, an ontology-based mechanism for assembling learning objects. This mechanism introduces the concept of associated knowledge, which represents the set of requirements that a learning object needs in order to be used and a set of competencies that the learning object provides after its comprehension. According OntoGlue, in order to assemble two learning objects, the requirements of one learning object must be covered by the competencies of the other. In addition, to facilitate interoperability between different domains (vocabularies), the concepts that conforms the associated knowledge are selected among the classes of educational ontologies.

Applying model checking to BPEL4WS business collaborations

Jes&\#250;s Fisteus — 2006-09-21T17:03:33-00:00

(2005), pp. 826-830.

Providing impetus for conceptual change: The effect of organizing the input

Heidi Kloos — 2006-02-28T16:35:06-00:00

Cognitive Development, Vol. 16, No. 2. ( 2001), pp. 737-759.

This study was designed to test whether calling to mind an initial belief and presenting information that challenges that belief affects the extent to which preschoolers will modify it. The belief that was challenged in a controlled demonstration concerns the effect of the size of an object on its sinking speed (holding weight constant). In addition, children's belief about the effect of weight on sinking speed (holding size constant) was examined, a belief that was confirmed in a demonstration. The final belief about size for those who received nothing but empirical demonstrations was less likely to be compatible with the demonstration than the final belief of those in two other conditions. Children in the other conditions were given the opportunity in the context of interviews to form expectations about how size and weight separately relate to sinking speed, in addition to receiving the demonstrations. An interview either directly preceded the demonstration for the variable concerned (coordinated sequence) or did not (uncoordinated sequence). The tendency for the final belief about size to be compatible with the demonstration was related more strongly to age in the condition with an uncoordinated sequence than in either of the other conditions. Some children among those whose final belief about the effect of size on sinking speed was compatible with the demonstration also refined their belief about the effect of weight, suggesting that these two beliefs may cohere as a system. These findings show that a relatively short experimental procedure can be an effective means of bringing about some refinement of a young child's beliefs.

Gene expression phenotypic models that predict the activity of oncogenic pathways.

E Huang — 2006-01-17T17:38:33-00:00

Nat Genet, Vol. 34, No. 2. (June 2003), pp. 226-230.

High-density DNA microarrays measure expression of large numbers of genes in one assay. The ability to find underlying structure in complex gene expression data sets and rigorously test association of that structure with biological conditions is essential to developing multi-faceted views of the gene activity that defines cellular phenotype. We sought to connect features of gene expression data with biological hypotheses by integrating 'metagene' patterns from DNA microarray experiments in the characterization and prediction of oncogenic phenotypes. We applied these techniques to the analysis of regulatory pathways controlled by the genes HRAS (Harvey rat sarcoma viral oncogene homolog), MYC (myelocytomatosis viral oncogene homolog) and E2F1, E2F2 and E2F3 (encoding E2F transcription factors 1, 2 and 3, respectively). The phenotypic models accurately predict the activity of these pathways in the context of normal cell proliferation. Moreover, the metagene models trained with gene expression patterns evoked by ectopic production of Myc or Ras proteins in primary tissue culture cells properly predict the activity of in vivo tumor models that result from deregulation of the MYC or HRAS pathways. We conclude that these gene expression phenotypes have the potential to characterize the complex genetic alterations that typify the neoplastic state, whether in vitro or in vivo, in a way that truly reflects the complexity of the regulatory pathways that are affected.