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

Subplate subpopulations in the hypoxic-ischemic neonatal rat brain

Subplate neurons are among the earliest born cells of the neocortex and play a fundamental role in cortical development, in particular in the formation of thalamocortical connections. Subplate abnormalities have been described in several neuropathological disorders including schizophrenia, autism and periventricular eukomalacia (Eastwood and Harrison, Schizophr Res, 79, 2005; McQuillen and Ferriero, Brain Pathol, 15, 2005). We have identified and confirmed a range of specific markers for murine subplate using a microarray based approach and found that different subplate subpopulations are characterized by distinct expression patterns of these genes (Hoerder-Suabedissen et al., Cereb Cortex, 19, 2009). In this current study, we are making use of these markers to investigate neuropathological changes of the subplate after cerebral hypoxia-ischemia (HI) in the neonatal rat. First, we characterized the expression of a number of murine subplate markers in the postnatal rat using immunohistochemistry and in situ hybridization. While several genes (Nurr1, Cplx3, Ctgf and Tmem163) presented very similar expression patterns as in the mouse, others (Ddc, MoxD1 and TRH) were completely absent in the rat cortex. This finding suggests important differences in the subplate populations of these two rodent species. In a neonatal rat model of HI, selective vulnerability of subplate has been suggested using BrdU birthdating methods (McQuillen et al., J Neurosci, 15, 2003). We hypothesized that certain subplate subpopulations could be more susceptible than others and analyzed the above subplate markers in a similar yet slightly milder HI model. Two-day old male rat pups underwent permanent occlusion of the right common carotid artery followed by a period of hypoxia (6% O2, 1.5h or 2h) and were analyzed six days later. Preliminary counts on three subplate subpopulations (Nurr1+, Cplx3+ and Ctgf+ cells, respectively) showed similar reductions in cell numbers for all three groups. In addition, we found that the majority of cases which show changes in the subplate also exhibit lesions in the deep cortical layers VI (identified by FoxP2 expression) and sometimes even layer V (revealed by Er81 immunoreactivity), which questions the selective susceptibility of subplate over other cortical layers under the conditions we used in our model. Supported by MRC, FMO holds a Berrow Scholarship, Lincoln College, Oxford.

Information sharing and social network dynamics : a coevolutionary approach

The capacity to interact socially and share information underlies the success of many animal species, humans included. Researchers of many fields have emphasized the evo¬lutionary significance of how patterns of connections between individuals, or the social networks, and learning abilities affect the information obtained by animal societies. To date, studies have focused on the dynamics either of social networks, or of the spread of information. The present work aims to study them together. We make use of mathematical and computational models to study the dynamics of networks, where social learning and information sharing affect the structure of the population the individuals belong to. The number and strength of the relationships between individuals, in turn, impact the accessibility and the diffusion of the shared information. Moreover, we inves¬tigate how different strategies in the evaluation and choice of interacting partners impact the processes of knowledge acquisition and social structure rearrangement. First, we look at how different evaluations of social interactions affect the availability of the information and the network topology. We compare a first case, where individuals evaluate social exchanges by the amount of information that can be shared by the partner, with a second case, where they evaluate interactions by considering their partners' social status. We show that, even if both strategies take into account the knowledge endowments of the partners, they have very different effects on the system. In particular, we find that the first case generally enables individuals to accumulate higher amounts of information, thanks to the more efficient patterns of social connections they are able to build. Then, we study the effects that homophily, or the tendency to interact with similar partners, has on knowledge accumulation and social structure. We compare the case where individuals who know the same information are more likely to learn socially from each other, to the opposite case, where individuals who know different information are instead more likely to learn socially from each other. We find that it is not trivial to claim which strategy is better than the other. Depending on the possibility of forgetting information, the way new social partners can be chosen, and the population size, we delineate the conditions for which each strategy allows accumulating more information, or in a faster way For these conditions, we also discuss the topological characteristics of the resulting social structure, relating them to the information dynamics outcome. In conclusion, this work paves the road for modeling the joint dynamics of the spread of information among individuals and their social interactions. It also provides a formal framework to study jointly the effects of different strategies in the choice of partners on social structure, and how they favor the accumulation of knowledge in the population. - La capacité d'interagir socialement et de partager des informations est à la base de la réussite de nombreuses espèces animales, y compris les humains. Les chercheurs de nombreux domaines ont souligné l'importance évolutive de la façon dont les modes de connexions entre individus, ou réseaux sociaux et les capacités d'apprentissage affectent les informations obtenues par les sociétés animales. À ce jour, les études se sont concentrées sur la dynamique soit des réseaux sociaux, soit de la diffusion de l'information. Le présent travail a pour but de les étudier ensemble. Nous utilisons des modèles mathématiques et informatiques pour étudier la dynamique des réseaux, où l'apprentissage social et le partage d'information affectent la structure de la population à laquelle les individus appartiennent. Le nombre et la solidité des relations entre les individus ont à leurs tours un impact sur l'accessibilité et la diffusion de l'informa¬tion partagée. Par ailleurs, nous étudions comment les différentes stratégies d'évaluation et de choix des partenaires d'interaction ont une incidence sur les processus d'acquisition des connaissances ainsi que le réarrangement de la structure sociale. Tout d'abord, nous examinons comment des évaluations différentes des interactions sociales influent sur la disponibilité de l'information ainsi que sur la topologie du réseau. Nous comparons un premier cas, où les individus évaluent les échanges sociaux par la quantité d'information qui peut être partagée par le partenaire, avec un second cas, où ils évaluent les interactions en tenant compte du statut social de leurs partenaires. Nous montrons que, même si les deux stratégies prennent en compte le montant de connaissances des partenaires, elles ont des effets très différents sur le système. En particulier, nous constatons que le premier cas permet généralement aux individus d'accumuler de plus grandes quantités d'information, grâce à des modèles de connexions sociales plus efficaces qu'ils sont capables de construire. Ensuite, nous étudions les effets que l'homophilie, ou la tendance à interagir avec des partenaires similaires, a sur l'accumulation des connaissances et la structure sociale. Nous comparons le cas où des personnes qui connaissent les mêmes informations sont plus sus¬ceptibles d'apprendre socialement l'une de l'autre, au cas où les individus qui connaissent des informations différentes sont au contraire plus susceptibles d'apprendre socialement l'un de l'autre. Nous constatons qu'il n'est pas trivial de déterminer quelle stratégie est meilleure que l'autre. En fonction de la possibilité d'oublier l'information, la façon dont les nouveaux partenaires sociaux peuvent être choisis, et la taille de la population, nous déterminons les conditions pour lesquelles chaque stratégie permet d'accumuler plus d'in¬formations, ou d'une manière plus rapide. Pour ces conditions, nous discutons également les caractéristiques topologiques de la structure sociale qui en résulte, les reliant au résultat de la dynamique de l'information. En conclusion, ce travail ouvre la route pour la modélisation de la dynamique conjointe de la diffusion de l'information entre les individus et leurs interactions sociales. Il fournit également un cadre formel pour étudier conjointement les effets de différentes stratégies de choix des partenaires sur la structure sociale et comment elles favorisent l'accumulation de connaissances dans la population.

Tamanho de parcela para produtividade de grãos de sorgo granífero em diferentes densidades de plantas

O objetivo deste trabalho foi verificar a influência do arranjo de plantas na estimativa do tamanho ótimo de parcela da cultura de sorgo granífero, para a variável produtividade de grãos. O delineamento estatístico utilizado foi o de blocos ao acaso, num esquema fatorial com dois espaçamentos entre linhas (0,50 m e 0,80 m), três densidades de semeadura (100 mil, 160 mil e 220 mil plantas ha-1) e quatro repetições. Cada repetição foi composta, na área útil, por 12 unidades básicas de 0,50 m da linha de cultivo. Foram ajustados modelos, na estimativa do tamanho ótimo de parcela, que relacionam a variância ou o coeficiente de variação com quatro tamanhos simulados das parcelas. O tamanho estimado de parcelas, na cultura de sorgo granífero, é de 3,2 m² para a variável produtividade de grãos. O aumento do número de plantas, na linha, não proporciona incrementos na produtividade de grãos, porém resulta em melhorias da qualidade de experimentos com sorgo. A estimativa do tamanho ótimo de parcela depende do número de plantas utilizadas na unidade básica. O espaçamento entre linhas não influencia na estimativa do tamanho ótimo de parcela.

Do protein–protein interaction databases identify moonlighting proteins?

One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However, a less-known way to increase the number of protein functions is the existence of multifunctional, multitask, or ‘‘moonlighting’’, proteins. By and large, moonlighting proteins are experimentally disclosed by serendipity. Proteomics is becoming one of the very active areas of biomedical research, which permits researchers to identify previously unseen connections among proteins and pathways. In principle, protein–protein interaction (PPI) databases should contain information on moonlighting proteins and could provide suggestions to further analysis in order to prove the multifunctionality. As far as we know, nobody has verified whether PPI databases actually disclose moonlighting proteins. In the present work we check whether well-established moonlighting proteins present in PPI databases connect with their known partners and, therefore, a careful inspection of these databases could help to suggest their different functions. The results of our research suggest that PPI databases could be a valuable tool to suggest multifunctionality.

Norbert Elias : una proposta d’intellectual portrait vint anys després de la seva mort

L’estiu de 1990 moria a Amsterdam un dels sociòlegs més preeminents del segle XX, l’alemany Norbert Elias. La seva vida i la seva obra, profundament imbricades, són un reflex de la complexitat, de les llums i les ombres del segle passat. Amb aquesta proposta de retrat intel·lectual pretenem per una banda commemorar l’efemèride dels 20 anys de la mort d’un sociòleg poc reconegut i poc emprat. I d’altra banda, oferir una introducció a un personatge i una obra que, per la seva magnitud i originalitat, mereixen estar entre les més rellevants de la sociologia. Com a fil conductor de l’article proposem una combinació de llocs físics i simbòlics que van marcar la seva trajectòria.

Increased alpha activity and modulations of fronto-parietal balance during motor transitions in the elderly

A hallmark of aging is the sensorimotor deficit, characterized by an increased reaction time and a reduction of motor abilities. Some mechanisms such as motor inhibition deteriorate with aging because of neuronal density alterations and modifications of connections between brain regions. These deficits may be compensated throughout a recruitment of additional areas. Studies have shown that old adults have increased difficulty in performing bimanual coordination tasks compared with young adults. In contrast, motor switching is poorly documented and is expected to engage increasing resources in the elderly. The present study examines performances and electro-cortical correlates of motor switching in young and elderly adults.

MyTopRoom : Aplicación para Android: Buscador de ofertas de hoteles

El objetivo de este proyecto es el desarrollo de una aplicación móvil para dispositivos con sistema operativo Android que permita la búsqueda de ofertas de hotel de una forma diferente a las actuales. Para ello se ha empleado el modelo del ciclo de vida en cascada, con las fases de análisis, diseño, construcción y pruebas del sistema desarrollado. El software final sigue una arquitectura de tipo cliente/servidor y ha sido realizado con Java como lenguaje base de programación, haciendo uso de algunas librerías como Apache HTTP Request para las conexiones con el servidor remoto como las propias de Android, que facilitan la creación de interfaces gráficas y la gestión de los recursos de los dispositivos en el desarrollo de aplicaciones móviles.

The jasmonate biochemical pathway.

Plants possess an interrelated and interacting family of potent fatty acid-derived regulators--the jasmonates. These compounds, which play roles in both defense and development, are derived from tri-unsaturated fatty acids [alpha-linolenic acid (18:3) or 7Z,10Z,13Z-hexadecatrienoic acid (16:3)]. The lipoxygenase-catalyzed addition of molecular oxygen to alpha-linolenic acid initiates jasmonate synthesis by providing a 13-hydroperoxide substrate for the formation of an unstable allene oxide that is then subject to enzyme-guided cyclization to produce 12-oxo-phytodienoic acid (OPDA). OPDA, a key regulatory lipid in the plant immune system, has several fates, including esterification into plastid lipids or transformation into the 12-carbon co-regulator jasmonic acid (JA). JA, the best-characterized member of the family, regulates both male and female fertility (depending on the plant species), and is an important mediator of defense gene expresssion. JA is itself a substrate for further diverse modifications. Genetic dissection of the pathway is revealing how the different jasmonates modulate different physiological processes. Each new family member that is discovered provides another key to understanding the fine control of gene expression in immune responses, in the initiation and maintenance of long-distance signal transfer in response to wounding, and in the regulation of fertility, among other processes. The Jasmonate Biochemical Pathway provides an overview of the growing jasmonate family, and new members will be included in future versions of the Connections Map. Science Viewpoint R. Liechti, E. E. Farmer, The jasmonate pathway. Science 296, 1649-1650 (2002). [Abstract] [Full Text]

Demonstration Project using Railroad Flatcars for Low-Volume Road Bridges, TR-444, 2003

The use of Railroad Flatcars (RRFCs) as the superstructure on low-volume county bridges has been investigated in a research project conducted by the Bridge Engineering Center at Iowa State University. These bridges enable county engineers to replace old, inadequate county bridge superstructures for less than half the cost and in a shorter construction time than required for a conventional bridge. To illustrate their constructability, adequacy, and economy, two RRFC demonstration bridges were designed, constructed, and tested: one in Buchanan County and the other in Winnebago County. The Buchanan County Bridge was constructed as a single span with 56-ft-long flatcars supported at their ends by new, concrete abutments. The use of concrete in the substructure allowed for an integral abutment at one end of the bridge with an expansion joint at the other end. Reinforced concrete beams (serving as longitudinal connections between the three adjacent flatcars) were installed to distribute live loads among the RRFCs. Guardrails and an asphalt milling driving surface completed the bridge. The Winnebago County Bridge was constructed using 89-ft-long flatcars. Preliminary calculations determined that they were not adequate to span 89 ft as a simple span. Therefore, the flatcars were supported by new, steel-capped piers and abutments at the RRFCs' bolsters and ends, resulting in a 66-ft main span and two 10-ft end spans. Due to the RRFC geometry, the longitudinal connections between adjacent RRFCs were inadequate to support significant loads; therefore, transverse, recycled timber planks were utilized to effectively distribute live loads to all three RRFCs. A gravel driving surface was placed on top of the timber planks, and a guardrail system was installed to complete the bridge. Bridge behavior predicted by grillage models for each bridge was validated by strain and deflection data from field tests; it was found that the engineered RRFC bridges have live load stresses significantly below the AASHTO Bridge Design Specification limits. To assist in future RRFC bridge projects, RRFC selection criteria were established for visual inspection and selection of structurally adequate RRFCs. In addition, design recommendations have been developed to simplify live load distribution calculations for the design of the bridges. Based on the results of this research, it has been determined that through proper RRFC selection, construction, and engineering, RRFC bridges are a viable, economic replacement system for low-volume road bridges.

Statistical mechanics of multi-edge networks

Statistical properties of binary complex networks are well understood and recently many attempts have been made to extend this knowledge to weighted ones. There are, however, subtle yet important considerations to be made regarding the nature of the weights used in this generalization. Weights can be either continuous or discrete magnitudes, and in the latter case, they can additionally have undistinguishable or distinguishable nature. This fact has not been addressed in the literature insofar and has deep implications on the network statistics. In this work we face this problem introducing multiedge networks as graphs where multiple (distinguishable) connections between nodes are considered. We develop a statistical mechanics framework where it is possible to get information about the most relevant observables given a large spectrum of linear and nonlinear constraints including those depending both on the number of multiedges per link and their binary projection. The latter case is particularly interesting as we show that binary projections can be understood from multiedge processes. The implications of these results are important as many real-agent-based problems mapped onto graphs require this treatment for a proper characterization of their collective behavior.

Feasibility Investigation of Segmentally Precast Bridge Piers for Accelerated Construction, TR-556, 2009

An innovative structural system for pier columns was investigated through a series of laboratory experiments. The columns and connections examined were comprised of precast concrete segments to accelerate construction. In addition some of the columns employed unbonded post-tensioning to self-center the columns when subjected to lateral loads and structural fuses to control large lateral deflections, dissipate energy, and expedite repair in the event of a catastrophic loading event. Six cantilever columns with varying component materials and connection details were subjected to a regimen of vertical dead loads and cyclic, quasi-static lateral loads. One column was designed as a control column to represent the behavior of a conventional reinforced concrete column and provide a basis for comparison with the remaining five jointed columns designed with the proposed structural system. After sustaining significant damage, the self-centering, jointed columns were repaired by replacing the structural fuses and retested to failure to investigate the effectiveness of the repair. The experiments identified both effective and unsatisfactory details for the jointed system. Two of the jointed columns demonstrated equivalent lateral strength, greater lateral stiffness, and greater lateral deformation capacity than the control column. The self-centering capability of the jointed columns was clearly demonstrated as well, and the repair technique proved effective as demonstrated by nearly identical pre and post repair behavior. The authors believe the proposed system to be a feasible alternative to conventional pier systems and recommend further development of details.

Correlational study: illness representations and coping styles in caregivers for individuals with schizophrenia.

BACKGROUND: Caring for individuals with schizophrenia can create distress for caregivers which can, in turn, have a harmful impact on patient progress. There could be a better understanding of the connections between caregivers' representations of schizophrenia and coping styles. This study aims at exploring those connections. METHODS: This correlational descriptive study was conducted with 92 caregivers of individuals suffering from schizophrenia. The participants completed three questionnaires translated and validated in French: (a) a socio-demographic questionnaire, (b) the Illness Perception Questionnaire for Schizophrenia and (c) the Family Coping Questionnaire. RESULTS: Our results show that illness representations are slightly correlated with coping styles. More specifically, emotional representations are correlated to an emotion-focused coping style centred on coercion, avoidance and resignation. CONCLUSION: Our results are coherent with the Commonsense Model of Self-Regulation of Health and Illness and should enable to develop new interventions for caregivers.

Wind Loads on Dynamic Message Cabinets and Behavior of Supporting Trusses, TR-612, 2013

Large Dynamic Message Signs (DMSs) have been increasingly used on freeways, expressways and major arterials to better manage the traffic flow by providing accurate and timely information to drivers. Overhead truss structures are typically employed to support those DMSs allowing them to provide wider display to more lanes. In recent years, there is increasing evidence that the truss structures supporting these large and heavy signs are subjected to much more complex loadings than are typically accounted for in the codified design procedures. Consequently, some of these structures have required frequent inspections, retrofitting, and even premature replacement. Two manufacturing processes are primarily utilized on truss structures - welding and bolting. Recently, cracks at welding toes were reported for the structures employed in some states. Extremely large loads (e.g., due to high winds) could cause brittle fractures, and cyclic vibration (e.g., due to diurnal variation in temperature or due to oscillations in the wind force induced by vortex shedding behind the DMS) may lead to fatigue damage, as these are two major failures for the metallic material. Wind and strain resulting from temperature changes are the main loads that affect the structures during their lifetime. The American Association of State Highway and Transportation Officials (AASHTO) Specification defines the limit loads in dead load, wind load, ice load, and fatigue design for natural wind gust and truck-induced gust. The objectives of this study are to investigate wind and thermal effects in the bridge type overhead DMS truss structures and improve the current design specifications (e.g., for thermal design). In order to accomplish the objective, it is necessary to study structural behavior and detailed strain-stress of the truss structures caused by wind load on the DMS cabinet and thermal load on the truss supporting the DMS cabinet. The study is divided into two parts. The Computational Fluid Dynamics (CFD) component and part of the structural analysis component of the study were conducted at the University of Iowa while the field study and related structural analysis computations were conducted at the Iowa State University. The CFD simulations were used to determine the air-induced forces (wind loads) on the DMS cabinets and the finite element analysis was used to determine the response of the supporting trusses to these pressure forces. The field observation portion consisted of short-term monitoring of several DMS Cabinet/Trusses and long-term monitoring of one DMS Cabinet/Truss. The short-term monitoring was a single (or two) day event in which several message sign panel/trusses were tested. The long-term monitoring field study extended over several months. Analysis of the data focused on trying to identify important behaviors under both ambient and truck induced winds and the effect of daily temperature changes. Results of the CFD investigation, field experiments and structural analysis of the wind induced forces on the DMS cabinets and their effect on the supporting trusses showed that the passage of trucks cannot be responsible for the problems observed to develop at trusses supporting DMS cabinets. Rather the data pointed toward the important effect of the thermal load induced by cyclic (diurnal) variations of the temperature. Thermal influence is not discussed in the specification, either in limit load or fatigue design. Although the frequency of the thermal load is low, results showed that when temperature range is large the restress range would be significant to the structure, especially near welding areas where stress concentrations may occur. Moreover stress amplitude and range are the primary parameters for brittle fracture and fatigue life estimation. Long-term field monitoring of one of the overhead truss structures in Iowa was used as the research baseline to estimate the effects of diurnal temperature changes to fatigue damage. The evaluation of the collected data is an important approach for understanding the structural behavior and for the advancement of future code provisions. Finite element modeling was developed to estimate the strain and stress magnitudes, which were compared with the field monitoring data. Fatigue life of the truss structures was also estimated based on AASHTO specifications and the numerical modeling. The main conclusion of the study is that thermal induced fatigue damage of the truss structures supporting DMS cabinets is likely a significant contributing cause for the cracks observed to develop at such structures. Other probable causes for fatigue damage not investigated in this study are the cyclic oscillations of the total wind load associated with the vortex shedding behind the DMS cabinet at high wind conditions and fabrication tolerances and induced stresses due to fitting of tube to tube connections.