Automatic filtering and substantiation of drug safety signals

Drug safety issues pose serious health threats to the population and constitute a major cause of mortality worldwide. Due to the prominent implications to both public health and the pharmaceutical industry, it is of great importance to unravel the molecular mechanisms by which an adverse drug reaction can be potentially elicited. These mechanisms can be investigated by placing the pharmaco-epidemiologically detected adverse drug reaction in an information-rich context and by exploiting all currently available biomedical knowledge to substantiate it. We present a computational framework for the biological annotation of potential adverse drug reactions. First, the proposed framework investigates previous evidences on the drug-event association in the context of biomedical literature (signal filtering). Then, it seeks to provide a biological explanation (signal substantiation) by exploring mechanistic connections that might explain why a drug produces a specific adverse reaction. The mechanistic connections include the activity of the drug, related compounds and drug metabolites on protein targets, the association of protein targets to clinical events, and the annotation of proteins (both protein targets and proteins associated with clinical events) to biological pathways. Hence, the workflows for signal filtering and substantiation integrate modules for literature and database mining, in silico drug-target profiling, and analyses based on gene-disease networks and biological pathways. Application examples of these workflows carried out on selected cases of drug safety signals are discussed. The methodology and workflows presented offer a novel approach to explore the molecular mechanisms underlying adverse drug reactions

Lomborg, Vanhanen ja Intelligent Design - kommentti Matti Kamppiselle

Kommentti Matti Kamppisen kirjoitukseen TT -lehdessä 1/2005

Development of Preliminary Load and Resistance Factor Design of Drilled Shafts in Iowa, RB03-012, 2014

The Federal Highway Administration (FHWA) mandated utilizing the Load and Resistance Factor Design (LRFD) approach for all new bridges initiated in the United States after October 1, 2007. To achieve part of this goal, a database for Drilled Shaft Foundation Testing (DSHAFT) was developed and reported on by Garder, Ng, Sritharan, and Roling in 2012. DSHAFT is aimed at assimilating high-quality drilled shaft test data from Iowa and the surrounding regions. DSHAFT is currently housed on a project website (http://srg.cce.iastate.edu/dshaft) and contains data for 41 drilled shaft tests. The objective of this research was to utilize the DSHAFT database and develop a regional LRFD procedure for drilled shafts in Iowa with preliminary resistance factors using a probability-based reliability theory. This was done by examining current design and construction practices used by the Iowa Department of Transportation (DOT) as well as recommendations given in the American Association of State Highway and Transportation Officials (AASHTO) LRFD Bridge Design Specifications and the FHWA drilled shaft guidelines. Various analytical methods were used to estimate side resistance and end bearing of drilled shafts in clay, sand, intermediate geomaterial (IGM), and rock. Since most of the load test results obtained from O-cell do not pass the 1-in. top displacement criterion used by the Iowa DOT and the 5% of shaft diameter for top displacement criterion recommended by AASHTO, three improved procedures are proposed to generate and extend equivalent top load-displacement curves that enable the quantification of measured resistances corresponding to the displacement criteria. Using the estimated and measured resistances, regional resistance factors were calibrated following the AASHTO LRFD framework and adjusted to resolve any anomalies observed among the factors. To illustrate the potential and successful use of drilled shafts in Iowa, the design procedures of drilled shaft foundations were demonstrated and the advantages of drilled shafts over driven piles were addressed in two case studies.

Referral from primary care to a physical activity programme: establishing long-term adherence? A randomized controlled trial. Rationale and study design

Background: Declining physical activity is associated with a rising burden of global disease. There is little evidence about effective ways to increase adherence to physical activity. Therefore, interventions are needed that produce sustained increases in adherence to physical activity and are cost-effective. The purpose is to assess the effectiveness of a primary care physical activity intervention in increasing adherence to physical activity in the general population seen in primary care. Method and design: Randomized controlled trial with systematic random sampling. A total of 424 subjects of both sexes will participate; all will be over the age of 18 with a low level of physical activity (according to the International Physical Activity Questionnaire, IPAQ), self-employed and from 9 Primary Healthcare Centres (PHC). They will volunteer to participate in a physical activity programme during 3 months (24 sessions; 2 sessions a week, 60 minutes per session). Participants from each PHC will be randomly allocated to an intervention (IG) and control group (CG). The following parameters will be assessed pre and post intervention in both groups: (1) health-related quality of life (SF-12), (2) physical activity stage of change (Prochaska's stages of change), (3) level of physical activity (IPAQ-short version), (4) change in perception of health (vignettes from the Cooperative World Organization of National Colleges, Academies, and Academic Associations of Family Physicians, COOP/WONCA), (5) level of social support for the physical activity practice (Social Support for Physical Activity Scale, SSPAS), and (6) control based on analysis (HDL, LDL and glycated haemoglobin).Participants' frequency of visits to the PHC will be registered over the six months before and after the programme. There will be a follow up in a face to face interview three, six and twelve months after the programme, with the reduced version of IPAQ, SF-12, SSPAS, and Prochaska's stages. Discussion: The pilot study showed the effectiveness of an enhanced low-cost, evidence-based intervention in increased physical activity and improved social support. If successful in demonstrating long-term improvements, this randomised controlled trial will be the first sustainable physical activity intervention based in primary care in our country to demonstrate longterm adherence to physical activity. Trial Registration: A service of the U.S. National Institutes of Health. Developed by the National Library of Medicine. ClinicalTrials.gov ID: NCT00714831.

El principio del Universal Design. Concepto y desarrollos en la enseñanza superior

Los principios, las prácticas y la investigación sobre diseño universal han sidoimplantados progresivamente en diferentes ámbitos, respecto al diseño y la preparación de entornos para la atención a las necesidades de las personas con discapacidad. En el contexto internacional, este desarrollo ha estado vinculado al avance en derechos sobre igualdad de oportunidades. En el contexto legislativo español, en la Ley 51/2003 se introducen definiciones sobre «accesibilidad universal» y «diseño para todos», con lo que se genera un marco que posibilita el análisis de fuentes conceptuales y de aplicación en nuestro contexto, de las aportaciones del diseño universal, así como su consideración para la fundamentación de prácticas de innovación e investigación en nuestros ámbitos universitarios. En este trabajo, a partir de una amplia revisión de fuentes y aportaciones de gran trayectoria en este campo, se presentan y analizan distintos enfoques, a través de los cuales se están desarrollando y aplicando prácticas de diseño universal en el ámbito de la enseñanza universitaria, y se plantean sus implicaciones educativas. Este análisis permite concluir que las aplicaciones del diseño universal parecen más prometedoras para el progreso hacia metas de inclusión en el entorno universitario que una perspectiva de «adaptación curricular»; aunque se pone de manifiesto la necesidad de que la investigación que se desarrolle en nuestros contextos aporte pruebas y elementos que favorezcan su implementa- ción. Aplicar prácticas docentes y de planificación en la enseñanza universitaria con bases en el diseño universal podría contribuir a superar, eliminar o evitar en un futuro barreras en el aprendizaje, no solo limitadoras del progreso de las personas con discapacidad, sino también del conjunto del alumnado. Asimismo, las conclusiones de este trabajo plantean aplicaciones y estimaciones de nuevas muestras empíricas como puntos de partida para futuras y posibles determinaciones de enfoques conceptuales.

Concrete Pavement Mixture Design and Analysis (MDA): Development and Evaluation of Vibrating Kelly Ball Test (VKelly Test) for the Workability of Concrete, 2015

Due to the low workability of slipform concrete mixtures, the science of rheology is not strictly applicable for such concrete. However, the concept of rheological behavior may still be considered useful. A novel workability test method (Vibrating Kelly Ball or VKelly test) that would quantitatively assess the responsiveness of a dry concrete mixture to vibration, as is desired of a mixture suitable for slipform paving, was developed and evaluated. The objectives of this test method are for it to be cost-effective, portable, and repeatable while reporting the suitability of a mixture for use in slipform paving. The work to evaluate and refine the test was conducted in three phases: 1. Assess whether the VKelly test can signal variations in laboratory mixtures with a range of materials and proportions 2. Run the VKelly test in the field at a number of construction sites 3. Validate the VKelly test results using the Box Test developed at Oklahoma State University for slipform paving concrete The data collected to date indicate that the VKelly test appears to be suitable for assessing a mixture’s response to vibration (workability) with a low multiple operator variability. A unique parameter, VKelly Index, is introduced and defined that seems to indicate that a mixture is suitable for slipform paving when it falls in the range of 0.8 to 1.2 in./√s.

Concrete Pavement Mixture Design and Analysis (MDA): An Innovative Approach To Proportioning Concrete Mixtures, TPF-5(205), 2015

Mixture proportioning is routinely a matter of using a recipe based on a previously produced concrete, rather than adjusting the proportions based on the needs of the mixture and the locally available materials. As budgets grow tighter and increasing attention is being paid to sustainability metrics, greater attention is beginning to be focused on making mixtures that are more efficient in their usage of materials yet do not compromise engineering performance. Therefore, a performance-based mixture proportioning method is needed to provide the desired concrete properties for a given project specification. The proposed method should be user friendly, easy to apply in practice, and flexible in terms of allowing a wide range of material selection. The objective of this study is to further develop an innovative performance-based mixture proportioning method by analyzing the relationships between the selected mix characteristics and their corresponding effects on tested properties. The proposed method will provide step-by-step instructions to guide the selection of required aggregate and paste systems based on the performance requirements. Although the provided guidance in this report is primarily for concrete pavements, the same approach can be applied to other concrete applications as well.

Lake dwellers occupation gap in Lake Geneva (France-Switzerland) possibly explained by an earthquake-mass movement-tsunami event during Early Bronze Age

High-resolution seismic and sediment core data from the 'Grand Lac' basin of Lake Geneva reveal traces of repeated slope instabilities with one main slide-evolved mass-flow (minimum volume 0.13 km3) that originated from the northern lateral slope of the lake near the city of Lausanne. Radiocarbon dating of organic remains sampled from the top of the main deposit gives an age interval of 1865-1608 BC. This date coincides with the age interval for a mass movement event described in the 'Petit Lac' basin of Lake Geneva (1872-1622 BC). Because multiple mass movements took place at the same time in different parts of the lake, we consider the most likely trigger mechanism to be a strong earthquake (Mw 6) that occurred in the period between 1872 and 1608 BC. Based on numerical simulations, we show the major deposit near Lausanne would have generated a tsunami with local wave heights of up to 6 m. The combined effects of the earthquake and the following tsunami provide a possible explanation for a gap in lake dwellers occupation along the shores of Lake Geneva revealed by dendrochronological dating of two palafitte archaeological sites.

Respiratory viruses in HIV-infected patients with suspected respiratory opportunistic infection.

OBJECTIVE: To assess the incidence and epidemiological pattern of respiratory viruses in HIV-infected patients and to evaluate their potential clinical impact. DESIGN AND METHODS: A prospective population-based cohort study was conducted at three Swiss university hospitals. Study participants were HIV-infected patients who underwent a bronchoalveolar lavage to rule out an opportunistic event. All bronchoalveolar lavage specimens were screened using a set of real-time reverse transcriptase-polymerase chain reaction assays targeting 17 different respiratory viruses. RESULTS: Between November 2003 and November 2006, 59 bronchoalveolar episodes from 55 HIV-infected patients were analysed. Eleven of 59 episodes (18.6%) were positive for at least one respiratory virus. Coronavirus OC43 was identified in three cases (27.3%) followed by influenza A in two (18.2%). Parainfluenza virus (PIV) 2, PIV 3, PIV 4, bocavirus, human rhinovirus A and human metapneumovirus were each identified in one case (9%). In the majority of these cases (63.6%) no other concomitant microorganism was isolated. CONCLUSIONS: Clinical investigation of respiratory viral infections in HIV-infected patients should not be restricted to prototype viruses and also need to target all the different family of viruses as it seems likely that these viruses contribute to pulmonary complications and morbidity in this population.

Rethinking study and management of agricultural systems for policy design

There is a concern that agriculture will no longer be able to meet, on a global scale, the growing demand for food. Facing such a challenge requires new patterns of thinking in the context of complexity and sustainability sciences. This paper, focused on the social dimension of the study and management of agricultural systems, suggests that rethinking the study of agricultural systems entails analyzing them as complex socio-ecological systems, as well as considering the differing thinking patterns of diverse stakeholders. The intersubjective nature of knowledge, as studied by different philosophical schools, needs to be better integrated into the study and management of agricultural systems than it is done so far, forcing us to accept that there are no simplistic solutions, and to seek a better understanding of the social dimension of agriculture. Different agriculture related problems require different policy and institutional approaches. Finally, the intersubjective nature of knowledge asks for the visualization of different framings and the power relations taking place in the decision-making process. Rethinking management of agricultural systems implies that policy making should be shaped by different principles: learning, flexibility, adaptation, scale-matching, participation, diversity enhancement and precaution hold the promise to significantly improve current standard management procedures.

Remote collaborative multi-user informal learning experiences: design and evaluation

This paper presents a customizable system used to develop a collaborative multi-user problem solving game. It addresses the increasing demand for appealing informal learning experiences in museum-like settings. The system facilitates remote collaboration by allowing groups of learners tocommunicate through a videoconferencing system and by allowing them to simultaneously interact through a shared multi-touch interactive surface. A user study with 20 user groups indicates that the game facilitates collaboration between local and remote groups of learners. The videoconference and multitouch surface acted as communication channels, attracted students’ interest, facilitated engagement, and promoted inter- and intra-group collaboration—favoring intra-group collaboration. Our findings suggest that augmentingvideoconferencing systems with a shared multitouch space offers newpossibilities and scenarios for remote collaborative environments and collaborative learning.

Concrete Pavement Mixture Design and Analysis (MDA): Evaluation of Foam Drainage Test to Measure Air Void Stability in Concrete

The stability of air bubbles in fresh concrete can have a profound influence of the potential durability of the system, because excessive losses during placement and consolidation can compromise the ability of the mixture to resist freezing and thawing. The stability of air void systems developed by some air entraining admixtures (AEAs) could be affected by the presence of some polycarboxylate-based water reducing admixtures (WRAs). The foam drainage test provides a means of measuring the potential stability of air bubbles in a paste. A barrier to acceptance of the test was that there was little investigation of the correlation with field performance. The work reported here was a limited exercise seeking to observe the stability of a range of currently available AEA/WRA combinations in the foam drainage test; then, to take the best and the worst and observe their stabilities on concrete mixtures in the lab. Based on the data collected, the foam drainage test appears to identify stable combinations of AEA and WRA.