Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets.

Background: Microarray data is frequently used to characterize the expression profile of a whole genome and to compare the characteristics of that genome under several conditions. Geneset analysis methods have been described previously to analyze the expression values of several genes related by known biological criteria (metabolic pathway, pathology signature, co-regulation by a common factor, etc.) at the same time and the cost of these methods allows for the use of more values to help discover the underlying biological mechanisms. Results: As several methods assume different null hypotheses, we propose to reformulate the main question that biologists seek to answer. To determine which genesets are associated with expression values that differ between two experiments, we focused on three ad hoc criteria: expression levels, the direction of individual gene expression changes (up or down regulation), and correlations between genes. We introduce the FAERI methodology, tailored from a two-way ANOVA to examine these criteria. The significance of the results was evaluated according to the self-contained null hypothesis, using label sampling or by inferring the null distribution from normally distributed random data. Evaluations performed on simulated data revealed that FAERI outperforms currently available methods for each type of set tested. We then applied the FAERI method to analyze three real-world datasets on hypoxia response. FAERI was able to detect more genesets than other methodologies, and the genesets selected were coherent with current knowledge of cellular response to hypoxia. Moreover, the genesets selected by FAERI were confirmed when the analysis was repeated on two additional related datasets. Conclusions: The expression values of genesets are associated with several biological effects. The underlying mathematical structure of the genesets allows for analysis of data from several genes at the same time. Focusing on expression levels, the direction of the expression changes, and correlations, we showed that two-step data reduction allowed us to significantly improve the performance of geneset analysis using a modified two-way ANOVA procedure, and to detect genesets that current methods fail to detect.

Development and validation of a self-report version of the Spinal Cord Independence Measure (SCIM III).

Study design:Cross-sectional validation study.Objectives:To develop and validate a self-report version of the Spinal Cord Independence Measure (SCIM III).Setting:Two SCI rehabilitation facilities in Switzerland.Methods:SCIM III comprises 19 questions on daily tasks with a total score between 0 and 100 and subscales for 'self-care', 'respiration & sphincter management' and 'mobility'. A self-report version (SCIM-SR) was developed by expert discussions and pretests in individuals with spinal cord injury (SCI) using a German translation. A convenience sample of 99 inpatients with SCI was recruited. SCIM-SR data were analyzed together with SCIM III data obtained from attending health professionals.Results:High correlations between SCIM III and SCIM-SR were observed. Pearson's r for the total score was 0.87 (95% confidence interval (CI) 0.82-0.91), for the subscales self-care 0.87 (0.81-0.91); respiration & sphincter management 0.81 (0.73-0.87); and mobility 0.87 (0.82-0.91). Intraclass correlations were: total score 0.90 (95% CI 0.85-0.93); self-care 0.86 (0.79-0.90); respiration & sphincter management 0.80 (0.71-0.86); and mobility 0.83 (0.76-0.89). Bland-Altman plots showed that patients rated their functioning higher than professionals, in particular for mobility. The mean difference between SCIM-SR and SCIM III for the total score was 5.14 (point estimate 95% CI 2.95-7.34), self-care 0.89 (0.19-1.59), respiration & sphincter management 1.05 (0.18-2.28 ) and mobility 3.49 (2.44-4.54). Particularly patients readmitted because of pressure sores rated their independence higher than attending professionals.Conclusion:Our results support the criterion validity of SCIM-SR. The self-report version may facilitate long-term evaluations of independence in persons with SCI in their home situation.

Adaptive integral assessment package for the A2UN@ project

This paper presents a first approach of Evaluation Engine Architecture (EEA) as proposal to support adaptive integral assessment, in the context of a virtual learning environment. The goal of our research is design an evaluation engine tool to assist in the whole assessment process within the A2UN@ project, linking that tool with the other key elements of a learning design (learning task, learning resources and learning support). The teachers would define the relation between knowledge, competencies, activities, resources and type of assessment. Providing this relation is possible obtain more accurate estimations of student's knowledge for adaptive evaluations and future recommendations. The process is supported by usage of educational standards and specifications and for an integral user modelling

Evaluation clinique d'une polyarthrite rhumatoïde en pratique quotidienne [Clinical evaluation of rheumatoid arthritis in practice]

Clinical evaluation is an integral part of medical practice. However, recent data have demonstrated that a systematic and standardized evaluation modifies the prognosis of our rheumatoid arthritis patients. The systematic use of activity indexes allows us to better appreciate the needs of our patients and the necessity to optimize and intensifie treatment. Likewise, auto-evaluations tools bring useful information to patient management.

Die epidurale Rückenmarkstimulation (SCS) zur Therapie peripherer arterieller Durchblutungsstörungen [Spinal cord stimulation (SCS) in the treatment of peripheral arterial occlusive disease]

Spinal cord stimulation (SCS) represents a well established procedure in the treatment of critical ischemia of the extremities. The knowledge and distribution of SCS in Austria are still poor despite satisfactory data. The evaluations and recommendations from the consensus group demonstrate that SCS might represent a suitable additional treatment option for selected patients with peripheral arterial disease (PAD) when performed in experienced centers under clear indications. The complication rate is low and mainly due to device-related problems. There are valid scientific criteria proving that SCS treatment can reduce the risk of amputation, decrease pain and improve wound healing in patients with non-reconstructable, non-unstable PAD in stages IV and V according to Rutherford (stages III and IV according to Fontaine).This effect is more evident when patient selection is based on tcPO(2) measurements. A careful selection of patients is essential for the success of this neuromodulatory treatment, in addition a certain degree of patient compliance in terms of perception and understanding of the therapy is mandatory.

Simulation methods with extended stability for stiff biochemical kinetics

Background: With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results: In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK) τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes.Conclusions: The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.

Effective Structural Concrete Repair, Volume 1 of 3, Repair of Impact Damaged Prestressed Concrete Beams with CFRP, March 2004

Structural concrete is one of the most commonly used construction materials in the United States. However, due to changes in design specifications, aging, vehicle impact, etc. – there is a need for new procedures for repairing concrete (reinforced or pretressed) superstructures and substructures. Thus, the overall objective of this investigation was to develop innovative cost effective repair methods for various concrete elements. In consultation with the project advisory committee, it was decided to evaluate the following three repair methods: • Carbon fiber reinforced polymers (CFRPs) for use in repairing damaged prestressed concrete bridges • Fiber reinforced polymers (FRPs) for preventing chloride penetration of bridge columns • Various patch materials The initial results of these evaluations are presented in this three volume final report. Each evaluation is briefly described in the following paragraphs. A more detailed abstract of each evaluation accompanies the volume on that particular investigation.

Development of a Method to Determine Pavement Damage Due to Detours, Project 02-105, Apirl 2005

The research presented in this report provides the basis for the development of a new procedure to be used by the Iowa DOT and cities and counties in the state to deal with detours. Even though the project initially focused on investigating new tools to determine condition and compensation, the focus was shifted to traffic and the gas tax method to set the basis for the new procedure. It was concluded that the condition-based approach, even though accurate and consistent condition evaluations can be achieved, is not feasible or cost effective because of the current practices of data collection (two-year cycle) and also the logistics of the procedure (before and after determination). The gas tax method provides for a simple, easy to implement, and consistent approach to dealing with compensation for use of detours. It removes the subjectivity out of the current procedures and provides for a more realistic (traffic based) approach to the compensation determination.

Effective Structural Concrete Repair, Volume 2 of 3, Use of FRP to Prevent Chloride Penetration in Bridge Columns, March 2004

Structural concrete is one of the most commonly used construction materials in the United States. However, due to changes in design specifications, aging, vehicle impact, etc. – there is a need for new procedures for repairing concrete (reinforced or pretressed) superstructures and substructures. Thus, the overall objective of this investigation was to develop innovative cost effective repair methods for various concrete elements. In consultation with the project advisory committee, it was decided to evaluate the following three repair methods: • Carbon fiber reinforced polymers (CFRPs) for use in repairing damaged prestressed concrete bridges • Fiber reinforced polymers (FRPs) for preventing chloride penetration of bridge columns • Various patch materials The initial results of these evaluations are presented in this three volume final report. Each evaluation is briefly described in the following paragraphs. A more detailed abstract of each evaluation accompanies the volume on that particular investigation.

Effective Structural Concrete Repair, Volume 3 of 3, Evaluation of Repair Materials for Use in Patching Damaged Concrete, March 2004

Structural concrete is one of the most commonly used construction materials in the United States. However, due to changes in design specifications, aging, vehicle impact, etc. – there is a need for new procedures for repairing concrete (reinforced or pretressed) superstructures and substructures. Thus, the overall objective of this investigation was to develop innovative cost effective repair methods for various concrete elements. In consultation with the project advisory committee, it was decided to evaluate the following three repair methods: • Carbon fiber reinforced polymers (CFRPs) for use in repairing damaged prestressed concrete bridges • Fiber reinforced polymers (FRPs) for preventing chloride penetration of bridge columns • Various patch materials The initial results of these evaluations are presented in this three volume final report. Each evaluation is briefly described in the following paragraphs. A more detailed abstract of each evaluation accompanies the volume on that particular investigation.

Synthesis of Nondestructive Testing Technologies for Geomaterial Applications, May 2005

Current monitoring techniques for determination of compaction of earthwork and asphalt generally involve destructive testing of the materials following placement. Advances in sensor technologies show significant promise for obtaining necessary information through nondestructive and remote techniques. To develop a better understanding of suitable and potential technologies, this study was undertaken to conduct a synthesis review of nondestructive testing technologies and perform preliminary evaluations of selected technologies to better understand their application to testing of geomaterials (soil fill, aggregate base, asphalt, etc.). This research resulted in a synthesis of potential technologies for compaction monitoring with a strong emphasis on moisture sensing. Techniques were reviewed and selectively evaluated for their potential to improve field quality control operations. Activities included an extensive review of commercially available moisture sensors, literature review, and evaluation of selected technologies. The technologies investigated in this study were dielectric, nuclear, near infrared spectroscopy, seismic, electromagnetic induction, and thermal. The primary disadvantage of all the methods is the small sample volume measured. In addition, all the methods possessed some sensitivity to non-moisture factors that affected the accuracy of the results. As the measurement volume increases, local variances are averaged out providing better accuracy. Most dielectric methods with the exception of ground penetrating radar have a very small measurement volume and are highly sensitive to variations in density, porosity, etc.

Chronic deep brain stimulation in mesial temporal lobe epilepsy.

The objective of this study was to evaluate the efficiency and the effects of changes in parameters of chronic amygdala-hippocampal deep brain stimulation (AH-DBS) in mesial temporal lobe epilepsy (TLE). Eight pharmacoresistant patients, not candidates for ablative surgery, received chronic AH-DBS (130 Hz, follow-up 12-24 months): two patients with hippocampal sclerosis (HS) and six patients with non-lesional mesial TLE (NLES). The effects of stepwise increases in intensity (0-Off to 2 V) and stimulation configuration (quadripolar and bipolar), on seizure frequency and neuropsychological performance were studied. The two HS patients obtained a significant decrease (65-75%) in seizure frequency with high voltage bipolar DBS (≥1 V) or with quadripolar stimulation. Two out of six NLES patients became seizure-free, one of them without stimulation, suggesting a microlesional effect. Two NLES patients experienced reductions of seizure frequency (65-70%), whereas the remaining two showed no significant seizure reduction. Neuropsychological evaluations showed reversible memory impairments in two patients under strong stimulation only. AH-DBS showed long-term efficiency in most of the TLE patients. It is a valuable treatment option for patients who suffer from drug resistant epilepsy and who are not candidates for resective surgery. The effects of changes in the stimulation parameters suggest that a large zone of stimulation would be required in HS patients, while a limited zone of stimulation or even a microlesional effect could be sufficient in NLES patients, for whom the importance of the proximity of the electrode to the epileptogenic zone remains to be studied. Further studies are required to ascertain these latter observations.

An Investigation of User Costs and Benefits of Winter Road Closures, June 2005

This project explores the user costs and benefits of winter road closures. Severe winter weather makes travel unsafe and dramatically increases crash rates. When conditions become unsafe due to winter weather, road closures should allow users to avoid crash costs and eliminate costs associated with rescuing stranded motorists. Therefore, the benefits of road closures are the avoided safety costs. The costs of road closures are the delays that are imposed on motorists and motor carriers who would have made the trip had the road not been closed. This project investigated the costs and benefits of road closures and found that evaluating the benefits and costs is not as simple as it appears. To better understand the costs and benefits of road closures, the project investigates the literature, conducts interviews with shippers and motor carriers, and conducts case studies of road closures to determine what actually occurred on roadways during closures. The project also estimates a statistical model that relates weather severity to crash rates. Although, the statistical model is intended to illustrate the possibility to quantitatively relate measurable and predictable weather conditions to the safety performance of a roadway. In the future, weather conditions such as snow fall intensity, visibility, etc., can be used to make objective measures of the safety performance of a roadway rather than relying on subjective evaluations of field staff. The review of the literature and the interviews clearly illustrate that not all delays (increased travel time) are valued the same. Expected delays (routine delays) are valued at the generalized costs (value of the driver’s time, fuel, insurance, wear and tear on the vehicle, etc.), but unexpected delays are valued much higher because they result in interruption of synchronous activities at the trip’s destination. To reduce the costs of delays resulting from road closures, public agencies should communicate as early as possible the likelihood of a road closure.

Developing an Effective Construction Training Program for Hispanic Supervisors and Craft Workers, January 2004

Hispanics make up a growing percentage of the craft workers entering the construction industry, and this has created several challenges for American construction companies. This study addresses the situation by investigating training needs for Hispanic construction craft workers and developing a training program for them within the industry. In order to evaluate current craft workers’ conditions within the construction industry, Iowa State University researchers conducted a survey, with 98 Hispanic craft workers as respondents from 10 construction companies, to determine current working conditions. The results confirm that the language barrier is an obstacle for both the Hispanic workers and the English-speaking employees involved in construction projects. As a part of this research, two training courses were designed to help both American construction companies and their Hispanic labor force to overcome the barriers that keep them from succeeding safely and productively. A training course titled English as a Second Language Survival Course was developed to facilitate basic communication between Hispanic workers and their American supervisors using construction-focused terminology. This course was delivered once as a trial run for a two-hour duration and twice for a full-length duration of eight hours. Important feedback was obtained from participants as part of the evaluations of the course. “How much of the course contents will be useful in your working environment” was asked; 40% of workers said “all of it” and 60% said “most of it.” Another question was “Was it worth taking the time to attend the course?” to which 94% answered “definitely” and 6% answered “yes.” A second training course titled Stepping Up to Supervisor Course for Hispanic Construction Workers was also developed to provide an effective tool to help companies promote those Hispanic craft workers whose willingness and skills meet the requirements to advance to a supervisory position in an American construction company. This course will be offered in the spring of 2004.

La evaluación como elemento clave de la formación basada en competencias: tres casos en el ámbito de la ingenierías

El Espacio Europeo de Educación Superior implica cambios organizativos y académicos referentes a la formación basada en competencias. El proyecto AlineaME, coordinado por la Unidad de Soporte a la Calidad y la Innovación Docente de la Escuela Superior Politécnica - Universidad Pompeu Fabra, propuso a docentes del área TIC y a pedagogos la reflexión conjunta en aras a diseñar recomendaciones centradas en la alineación entre los tres elementos clave del proyecto: competencias, metodología y evaluación (C*M*E). Este trabajo recoge tres casos de aplicación de recomendaciones, concretamente de Ingeniería Telemática (dos casos - Universidad de Valladolid y Pompeu Fabra) y de Ingeniería Técnica en Informática de Gestión (un caso - Universidad de Sevilla).Las recomendaciones aplicadas hacen referencia a la necesidad de explicitar la alineación C*M*E en los Planes Docentes de Asignaturas y de presentar esta alineación al estudiantado. También a la integración de la evaluación de la asignatura como tarea-proceso de aprendizaje. La metodología seguida para laaplicación de ambas es (salvo pequeñas diferencias) parecida en los tres casos. La primera recomendación consistió en recoger en el Plan Docente la Alineación y en verbalizar dicha alineación en la sesión de presentación de la asignatura. La segunda se incorporó incluyendo actividades formativas en las que se favorecía la evaluación entre iguales. Para evaluar la aplicación de recomendaciones se recogieron evidencias en clave de satisfacción por parte del estudiantado así como valoraciones de los propios docentes. Para ello se diseñaron instrumentos específicos.En cuanto a la presentación de la alineación C*M*E en los Planes Docentes de asignaturas, los resultados indican que los alumnos son más conscientes de qué, cómo y por qué van a trabajar y ser evaluados. Globalmente valoran positivamente su utilidad para la autorregulación. Asimismo, plantear la evaluación como tarea deaprendizaje resultó ser para los estudiantes un interesante elemento de reflexión.