7,637 research outputs found
TAPAs: A Tool for the Analysis of Process Algebras
Process algebras are formalisms for modelling concurrent systems that permit mathematical reasoning with respect to a set of desired properties. TAPAs is a tool that can be used to support the use of process algebras to specify and analyze concurrent systems. It does not aim at guaranteeing high performances, but has been developed as a support to teaching. Systems are described as process algebras terms that are then mapped to labelled transition systems (LTSs). Properties are verified either by checking equivalence of concrete and abstract systems descriptions, or by model checking temporal formulae over the obtained LTS. A key feature of TAPAs, that makes it particularly suitable for teaching, is that it maintains a consistent double representation of each system both as a term and as a graph. Another useful didactical feature is the exhibition of counterexamples in case equivalences are not verified or the proposed formulae are not satisfied
Exploiting limited valence patchy particles to understand autocatalytic kinetics
Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description
Scaling in soft spheres: fragility invariance on the repulsive potential softness
We address the question of the dependence of the fragility of glass forming
supercooled liquids on the softness of an interacting potential by performing
numerical simulation of a binary mixture of soft spheres with different power n
of the interparticle repulsive potential. We show that the temperature
dependence of the diffusion coefficients for various collapses onto a
universal curve, supporting the unexpected view that fragility is not related
to the hard core repulsion. We also find that the configurational entropy
correlates with the slowing down of the dynamics for all studied n.Comment: 4 pages, 4 figure
Self-assembly of bi-functional patchy particles with anisotropic shape into polymers chains: theory and simulations
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base
pairs, are known to order into the nematic liquid crystal phase. This
self-assembly is due to the stacking interactions between the duplex terminals
that promotes their aggregation into poly-disperse chains with a significant
persistence length. Experiments show that liquid crystals phases form above a
critical volume fraction depending on the duplex length. We introduce and
investigate via numerical simulations, a coarse-grained model of DNA
double-helical duplexes. Each duplex is represented as an hard quasi-cylinder
whose bases are decorated with two identical reactive sites. The stacking
interaction between terminal sites is modeled via a short-range square-well
potential. We compare the numerical results with predictions based on a free
energy functional and find satisfactory quantitative matching of the
isotropic-nematic phase boundary and of the system structure. Comparison of
numerical and theoretical results with experimental findings confirm that the
DNA duplexes self-assembly can be properly modeled via equilibrium
polymerization of cylindrical particles and enables us to estimate the stacking
energy
Report of a traineeship : audit of antidepressant prescribing in Primary and Mental Care: how to address appropriateness and keep a curb on costs. A tool suitable for all contexts?
RESUMO: Este é o relatório de um estágio realizado na Autoridade de Saúde Local de Bolonha com o objectivo de desenvolver capacidades e competências na área de projectos orientados para a avaliação com base epidemiológica.
As prescrições de anti-depressivos aumentaram consideravelmente em todo o mundo durante as últimas décadas. O uso cada vez maior dos agentes mais dispendiosos desempenha um papel na subida do custo dos tratamentos. A Autoridade de Saúde Local de Bolonha implementou um processo de auditoria com o objectivo de melhorar a adequação das prescrições de pacientes externos, centrando-se em dois anti-depressivos de marca ainda protegidos por patente, Escitalopram e Duloxetine.
Os Departamentos de Cuidados de Saúde Primários e de Cuidados de Saúde Mental, assim como o Departamento Farmacêutico e a Unidade de Gestão Clínica, estiveram envolvidos na fase de planeamento da auditoria. O grupo da auditoria, maioritariamente composto por médicos de clínica geral e psiquiatras, reuniu e analisou provas da eficácia e segurança dos anti-depressivos. Os dados sobre as prescrições das Unidades de Cuidados de Saúde Primários e dos Centros de Saúde Mental
Comunitários da Autoridade de Saúde Local (866.294 habitantes) foram comparados, em particular as taxas de consumo de Escitalopram e Duloxetine. O grupo da auditoria definiu os standards a
serem abordados, os indicadores a serem avaliados e as medidas a empreender para atingir os objectivos definidos. As directrizes do NICE sobre a depressão foram escolhidas como referência.
O objectivo da auditoria foi definido como evitar o Escitalopram e Duloxetine como medicamentos de primeira escolha num tratamento anti-depressivo. De modo a verificar a eficácia das medidas
empreendidas foi seleccionado um indicador, consistindo numa redução de 25% das prescrições de ambos os anti-depressivos na prática clínica de pacientes externos e numa redução de 20% da variabilidade nas Unidades de Cuidados de Saúde Primários.
O relatório retrospectivo pré-auditoria (Janeiro a Abril de 2012) revelou que os tratamentos com anti-depressivos para pacientes externos eram prescritos pelos médicos de clínica geral em mais de90% dos casos. As medidas da auditoria foram implementadas entre Novembro de 2012 e Maio de 2013. Algumas medidas relevantes foram integradas com a revisão da auditoria, tais como reuniões educacionais de pequena escala com os médicos de clínica geral e psiquiatras, visitas de apoio do
assessor de prescrições da Autoridade de Saúde Local aos médicos de clínica geral e Centros de Saúde Mental Comunitários, panfletos para profissionais com informação retirada das directrizes clínicas do NICE, implementação de um serviço de consulta na Web para médicos de clínica geral
sobre provas relativas a anti-depressivos.
O relatório de feedback é aguardado em Novembro de 2013 depois de se verificar nos standards atingidos a eficácia das medidas implementadas.
Foi realizada uma análise SWOT para comprovar as forças e fraquezas, as oportunidades e ameaças do processo. Como identificação de fraquezas poderá ser útil identificar estratégias relevantes para
melhoria interna, para que o conhecimento das ameaças possa amortizar factores que possam ter impactos adversos que fujam ao controlo do Departamento de Saúde Mental. Uma melhor compreensão das forças e das oportunidades facilita a consecução dos objectivos estabelecidos no projecto.
O primeiro, mas não o último, resultado deste processo consistiu numa maior integração entre os Cuidados de Saúde Primários e de Saúde Mental, permitindo assim que a Autoridade de Saúde
Local coloque as alterações em prática.------------ABSTRACT: This is the report of a traineeship held in the Local Health Authority of Bologna with the aim to develop skills and competencies in the field of epidemiogically based evaluation oriented
projects.
Antidepressants prescriptions have considerably increased all over the world in the last decades.
The increasing use of the most expensive agents plays a part in the rising cost of treatments. The Local Health Authority of Bologna has implemented an audit process aimed at improving the appropriateness of outpatient prescriptions focusing on the two branded antidepressants still protected by patent, Escitalopram and Duloxetine.
The Primary Care and the Mental Health Care Departments, as well as the Pharmaceutical
Department and the Clinical Governance Unit, were involved in the planning phase of the audit.
The audit group, mainly composed of general practitioners and psychiatrists, collected and analyzed scientific evidence on effectiveness and safety of antidepressants. Data on prescriptions of Primary Care Units and Community Mental Health Centers of the Local Health Authority (866.294 inhabitants) were compared, in particular consumption rates of Escitalopram and Duloxetine. The
audit group defined the standards to be addressed, the indicators to be evaluated and the actions aimed at reaching the defined goals. NICE guidelines on depression were chosen as reference. The aim of the audit was settled as avoiding Escitalopram and Duloxetine as first choice drugs starting
an AD treatment. In order to check the efficacy of the actions undertaken an indicator was selected, consisting in a reduction of 25% of prescriptions of both ADs in outpatient practice and in a 20%
reduction of To develop skills and competencies across Primary Care Units.
The pre-audit retrospective report (January-April 2012) showed that outpatient antidepressant treatments were prescribed by GPs in over 90% of cases. Audit actions were implemented between November 2012 and May 2013. Some relevant actions have been integrated with the audit review, such as small-scale educational meetings with GPs and psychiatrists, outreach visits of the LHA prescribing adviser to GPs and CMHCs,leaflets for professionals with information extracted from NICE clinical guidelines, implementation of a web consultation service for GPs about evidence on antidepressants.
The feedback report is expected in November 2013 after checking through the standards attained the effectiveness of actions implemented.
A SWOT Analysis was carried out to evidence the strengths and weaknesses, opportunities and threats of the process. As identification of weaknesses may be useful to identify relevant strategies for internal improvement, so the knowledge of threats can amortize factors that may have adverse
impacts beyond the control of the Mental Health Department. Better understanding of the strengths and the opportunities facilitates the achievement of the goals set in the project.
The first and not least upshot of this process has consisted in further integration between Primary and Mental Health Care, thus enabling the LHA to put the change into practice
Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble
into polydisperse semi-flexible chains due to hydrophobic stacking interactions
between terminal base pairs. Above a critical concentration, which depends on
temperature and duplex length, such chains order into liquid crystal phases.
Here, we investigate the self-assembly of such double-helical duplexes with a
combined numerical and theoretical approach. We simulate the bulk system
employing the coarse-grained DNA model recently proposed by Ouldridge et al. [
J. Chem. Phys. 134, 08501 (2011) ]. Then we evaluate the input quantities for
the theoretical framework directly from the DNA model. The resulting
parameter-free theoretical predictions provide an accurate description of the
simulation results in the isotropic phase. In addition, the theoretical
isotropic-nematic phase boundaries are in line with experimental findings,
providing a route to estimate the stacking free energy.Comment: 13 pages, 10 figure
Slow dynamics in a primitive tetrahedral network model
We report extensive Monte Carlo and event-driven molecular dynamics
simulations of the fluid and liquid phase of a primitive model for silica
recently introduced by Ford, Auerbach and Monson [J. Chem. Phys. 17, 8415
(2004)]. We evaluate the iso-diffusivity lines in the temperature-density plane
to provide an indication of the shape of the glass transition line. Except for
large densities, arrest is driven by the onset of the tetrahedral bonding
pattern and the resulting dynamics is strong in the Angell's classification
scheme. We compare structural and dynamic properties with corresponding results
of two recently studied primitive models of network forming liquids -- a
primitive model for water and a angular-constraint free model of
four-coordinated particles -- to pin down the role of the geometric constraints
associated to the bonding. Eventually we discuss the similarities between
"glass" formation in network forming liquids and "gel" formation in colloidal
dispersions of patchy particles.Comment: 9 pages, 10 figure
A molecular dynamics study of chemical gelation in a patchy particle model
We report event-driven molecular dynamics simulations of the irreversible
gelation of hard ellipsoids of revolution containing several associating
groups, characterizing how the cluster size distribution evolves as a function
of the extent of reaction, both below and above the gel point. We find that in
a very large interval of values of the extent of reaction, parameter-free
mean-field predictions are extremely accurate, providing evidence that in this
model the Ginzburg zone near the gel point, where non-mean field effects are
important, is very limited. We also find that the Flory's hypothesis for the
post-gelation regime properly describes the connectivity of the clusters even
if the long-time limit of the extent of reaction does not reach the fully
reacted state. This study shows that irreversibly aggregating asymmetric
hard-core patchy particles may provide a close realization of the mean-field
model, for which available theoretical predictions may help control the
structure and the connectivity of the gel state. Besides chemical gels, the
model is relevant to network-forming soft materials like systems with
bioselective interactions, functionalized molecules and patchy colloids.Comment: 6 pages, 4 figures, to be published in Soft Matte
Event-Driven Simulation of the Dynamics of Hard Ellipsoids
We introduce a novel algorithm to perform event-driven simulations of hard
rigid bodies of arbitrary shape, that relies on the evaluation of the geometric
distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we
perform molecular dynamics simulations varying the aspect-ratio X0 and the
packing fraction phi. We evaluate the translational Dtrans and the rotational
Drot diffusion coefficient and the associated isodiffusivity lines in the
phi-X0 plane. We observe a decoupling of the translational and rotational
dynamics which generates an almost perpendicular crossing of the Dtrans and
Drot isodiffusivity lines. While the self intermediate scattering function
exhibits stretched relaxation, i.e. glassy dynamics, only for large phi and X0
about equals to 1, the second order orientational correlator C2(t) shows
stretching only for large and small X0 values. We discuss these findings in the
context of a possible pre-nematic order driven glass transition.Comment: Proceedings of IWCS2007 Sendai (Japan
Classification and mapping of the woody vegetation of Gonarezhou National Park, Zimbabwe
Within the framework of the Great Limpopo Transfrontier Conservation Area (GLTFCA), the purpose of this study was to produce a classification of the woody vegetation of the Gonarezhou National Park, Zimbabwe, and a map of its potential distribution. Cover-abundance data of woody species were collected in 330 georeferenced relevés across the Park. These data were used to produce two matrices: the first one using the cover-abundance values as collected in five height layers and the second one based on merging the layers into a single cover value for each species. Automatic classifications were produced for both matrices to determine the optimal number of vegetation types. The two classification approaches both produced 14 types belonging to three macro-groups: mopane, miombo and alluvial woodlands. The results of the two classifications were compared looking at the constant, dominant and diagnostic species of each type. The classification based on separate layers was considered more effective and retained. A high-resolution map of the potential distribution of vegetation types for the whole study area was produced using Random Forest. In the model, the relationship between bioclimatic and topographic variables, known to be correlated to vegetation types, and the classified relevés was used. Identified vegetation types were compared with those of other national parks within the GLTFCA, and an evaluation of the main threats and pressures was conducted. Conservation implications: Vegetation classification and mapping are useful tools for multiple purposes including: surveying and monitoring plant and animal populations, communities and their habitats, and development of management and conservation strategies. Filling the knowledge gap for the Gonarezhou National Park provides a basis for standardised and homogeneous vegetation classification and mapping for the entire Great Limpopo Transfrontier Conservation Area
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