Measuring healthcare integration: Operationalization of a framework for a systems evaluation of palliative care structures, processes, and outcomes

BACKGROUND: Healthcare integration is a priority in many countries, yet there remains little direction on how to systematically evaluate this construct to inform further development. The examination of community-based palliative care networks provides an ideal opportunity for the advancement of integration measures, in consideration of how fundamental provider cohesion is to effective care at end of life.

AIM: This article presents a variable-oriented analysis from a theory-based case study of a palliative care network to help bridge the knowledge gap in integration measurement.

DESIGN: Data from a mixed-methods case study were mapped to a conceptual framework for evaluating integrated palliative care and a visual array depicting the extent of key factors in the represented palliative care network was formulated.

SETTING/PARTICIPANTS: The study included data from 21 palliative care network administrators, 86 healthcare professionals, and 111 family caregivers, all from an established palliative care network in Ontario, Canada.

RESULTS: The framework used to guide this research proved useful in assessing qualities of integration and functioning in the palliative care network. The resulting visual array of elements illustrates that while this network performed relatively well at the multiple levels considered, room for improvement exists, particularly in terms of interventions that could facilitate the sharing of information.

CONCLUSION: This study, along with the other evaluative examples mentioned, represents important initial attempts at empirically and comprehensively examining network-integrated palliative care and healthcare integration in general.

Techno-Economic Feasibility of Selective CO2 Capture Processes from Biogas Streams using Ionic Liquids as Physical Absorbents

Biogas from anaerobic digestion of sewage sludge is a renewable resource with high energy content, which is formed mainly of CH4 (40-75 vol.%) and CO2 (15-60 vol.%) Other components such as water (H2O, 5-10 vol.%) and trace amounts of hydrogen sulfide and siloxanes can also be present. A CH4-rich stream can be produced by removing the CO2 and other impurities so that the upgraded bio-methane can be injected into the natural gas grid or used as a vehicle fuel. The main objective of this paper is to develop a new modeling methodology to assess the technical and economic performance of biogas upgrading processes using ionic liquids which physically absorb CO2. Three different ionic liquids, namely the 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, 1-hexyl-3-methylimidazoliumbis[(trifluoromethyl)sulfonyl]imide and trihexyl(tetradecyl)phosphonium bis[(trifluoromethyl)sulfonyl]imide, are considered for CO2 capture in a pressure-swing regenerative absorption process. The simulation software Aspen Plus and Aspen Process Economic Analyzer is used to account for mass and energy balances as well as equipment cost. In all cases, the biogas upgrading plant consists of a multistage compressor for biogas compression, a packed absorption column for CO2 absorption, a flash evaporator for solvent regeneration, a centrifugal pump for solvent recirculation, a pre-absorber solvent cooler and a gas turbine for electricity recovery. The evaluated processes are compared in terms of energy efficiency, capital investment and bio-methane production costs. The overall plant efficiency ranges from 71-86 % whereas the bio-methane production cost ranges from £6.26-7.76 per GJ (LHV). A sensitivity analysis is also performed to determine how several technical and economic parameters affect the bio-methane production costs. The results of this study show that the simulation methodology developed can predict plant efficiencies and production costs of large scale CO2 capture processes using ionic liquids without having to rely on gas solubility experimental data.

Protein phosphatases acting on the replication checkpoint

A génese de um cancro está dependente da acumulação de mutações genéticas que dão origem a instabilidade genómica, que por sua vez resulta na proliferação descontrolada. Para prevenir a acumulação destas mutações, as células têm mecanismos de controlo (checkpoints) que suspendem o ciclo celular e accionam as vias de reparação do ADN. Estes eventos são muitas vezes regulados por dinâmicas de (des)fosforilação de proteínas. As proteínas fosfatases (PPs), enzimas responsáveis pela remoção do grupo fosfato de resíduos fosforilados, desempenham funções cruciais na regulação de muitos mecanismos celulares. Enquanto que no início do projecto as cinases envolvidas no checkpoint da replicação estavam bem estabelecidas, as PPs envolvidas não eram conhecidas. A Chk1, um componente da maquinaria do checkpoint da replicação, é exemplo dessa regulação por (des)fosforilação, como sejam nos resíduos Ser317 e Ser345. Assim, como primeira abordagem para determinar quais os grupos de PPs envolvidos na regulação do checkpoint da replicação, decidimos investigar o seu papel na regulação da fosforilação da Chk1. A primeira conclusão é que a desfosforilação da Chk1 ao longo do tempo, tanto in vivo como in vitro, ocorre com uma dinâmica bi-fásica. Em segundo, a abordagem in vitro sugere que as famílias PP1, PP2A e PP2C estão envolvidas na desfosforilação da Chk1. Uma vez que a família PP2A foi a que mostrou a maior acção nesta reacção, decidimos investigar outros membros da família in vivo, primeiro com uma abordagem geral (tratando com OA ou sobreexpressando a PME-1), e depois com o knockdown específico da PP4 e PP6 (através de siRNA). Os resultados mostram que a inibição das PPs afectam tanto a desfosforilação como o estado de activação da Chk1 em resposta a tratamento com Hidroxiureia (HU). Todas as PPs testadas in vivo pareceram ser capazes de regular, a níveis diferentes, tanto a fosforilação como a desfosforilação da Chk1. A função das PPs foi também investigada ao nível: da regulação do disparo das origens de replicação, e da recuperação da suspensão da replicação, induzida pela HU. No último caso, os dados indicam que na situação simultânea de knockdown da PP4 com tratamento de HU, há um atraso do ciclo celular na resolução da transição de G2/M. No ensaio de replicação por pulse-chase, os resultamos mostram que tanto o tratamento com OA, como a sobre-expressão de I-2 ou PME-1, atrasam a cronologia do disparo programado das origens de replicação. No entanto, nenhum dos tratamentos efectuados parece desregular o início do checkpoint da replicação. Um rastreio de 2-híbrido de levedura com uma biblioteca de cDNA de testículo humano foi realizado, usando a Chk1 como isco, no sentido de descobrir novos interactores e definir novas possíveis funções para a Chk1 no contexto da meiose. Com base nos resultados do rastreio, duas novas funções são sugeridas: a interacção com a GAGE12 sugere uma função na recombinação genómica/vigilância do genoma durante a meiose, e as interacções com a EEF1α1 e a RPS5 sugerem uma função na regulação da síntese proteíca. Estas experiências fornecem um visão geral para a compreensão da diversidade de funções das proteínas fosfatases envolvidas no checkpoint da replicação, bem como, abre novos caminhos para o desenvolvimento de novas drogas para o tratamento do cancro.

Novel critical phenomena in optimization driven processes on networks

The work presented in this Ph.D thesis was developed in the context of complex network theory, from a statistical physics standpoint. We examine two distinct problems in this research field, taking a special interest in their respective critical properties. In both cases, the emergence of criticality is driven by a local optimization dynamics. Firstly, a recently introduced class of percolation problems that attracted a significant amount of attention from the scientific community, and was quickly followed up by an abundance of other works. Percolation transitions were believed to be continuous, until, recently, an 'explosive' percolation problem was reported to undergo a discontinuous transition, in [93]. The system's evolution is driven by a metropolis-like algorithm, apparently producing a discontinuous jump on the giant component's size at the percolation threshold. This finding was subsequently supported by number of other experimental studies [96, 97, 98, 99, 100, 101]. However, in [1] we have proved that the explosive percolation transition is actually continuous. The discontinuity which was observed in the evolution of the giant component's relative size is explained by the unusual smallness of the corresponding critical exponent, combined with the finiteness of the systems considered in experiments. Therefore, the size of the jump vanishes as the system's size goes to infinity. Additionally, we provide the complete theoretical description of the critical properties for a generalized version of the explosive percolation model [2], as well as a method [3] for a precise calculation of percolation's critical properties from numerical data (useful when exact results are not available). Secondly, we study a network flow optimization model, where the dynamics consists of consecutive mergings and splittings of currents flowing in the network. The current conservation constraint does not impose any particular criterion for the split of current among channels outgoing nodes, allowing us to introduce an asymmetrical rule, observed in several real systems. We solved analytically the dynamic equations describing this model in the high and low current regimes. The solutions found are compared with numerical results, for the two regimes, showing an excellent agreement. Surprisingly, in the low current regime, this model exhibits some features usually associated with continuous phase transitions.

Integer-valued APARCH processes in the analysis of time series of counts

The Asymmetric Power Arch representation for the volatility was introduced by Ding et al.(1993) in order to account for asymmetric responses in the volatility in the analysis of continuous-valued financial time series like, for instance, the log-return series of foreign exchange rates, stock indices or share prices. As reported by Brannas and Quoreshi (2010), asymmetric responses in volatility are also observed in time series of counts such as the number of intra-day transactions in stocks. In this work, an asymmetric power autoregressive conditional Poisson model is introduced for the analysis of time series of counts exhibiting asymmetric overdispersion. Basic probabilistic and statistical properties are summarized and parameter estimation is discussed. A simulation study is presented to illustrate the proposed model. Finally, an empirical application to a set of data concerning the daily number of stock transactions is also presented to attest for its practical applicability in data analysis.

Knowledge representation for data integration and exploration in translational medicine

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Modeling and simulation of spray drying processes based on quality by design principles

Tese de doutoramento, Farmácia (Tecnologia Farmacêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

Role of plasmodium translationally repressed gene products in malaria transmission

Tese de doutoramento, Ciências Biomédicas (Microbiologia e Parasitologia), Universidade de Lisboa, Faculdade de Medicina, 2015

Planning and management of marine protected areas : methodological approaches to cope with data scarcity

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2015

Effects of fluvial and marine processes on nearshore suspended sediment concentrations off the Elwha River

Senior thesis written for Oceanography 444

A Meteorological and Snow observational data set from Snoqualmie Pass (921 m), Washington Cascades, U.S.

We introduce a quality controlled observational atmospheric, snow, and soil data set from Snoqualmie Pass, Washington, U.S.A., to enable testing of hydrometeorological and snow process representations within a rain-snow transitional climate where existing observations are sparse and limited. Continuous meteorological forcing (including air temperature, total precipitation, wind speed, specific humidity, air pressure, short- and longwave irradiance) are provided at hourly intervals for a 24-year historical period (water years 1989-2012) and at half-hourly intervals for a more-recent period (water years 2013-2015), separated based on the availability of observations. Additional observations include 40-years of snow board new snow accumulation, multiple measurements of total snow depth, and manual snow pits, while more recent years include sub-daily surface temperature, snowpack drainage, soil moisture and temperature profiles, and eddy co-variance derived turbulent heat flux. This data set is ideal for testing hypotheses about energy balance, soil and snow processes in the rain-snow transition zone. Plots of live data can be found here: http://depts.washington.edu/mtnhydr/cgi/plot.cgi

Analyzing drifter designs and data gathering methods in complex estuarine environments

Senior thesis written for Oceanography 445

Tidal flow over a sill in Muchalat Inlet, Nootka Sound, and the resultant mixing processes

Senior thesis written for Oceanography 445

New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach

Malaria, caused by Plasmodium falciparum (P. falciparum), ranks as one of the most baleful infectious diseases worldwide. New antimalarial treatments are needed to face existing or emerging drug resistant strains. Protein degradation appears to play a significant role during the asexual intraerythrocytic developmental cycle (IDC) of P. falciparum. Inhibition of the ubiquitin proteasome system (UPS), a major intracellular proteolytic pathway, effectively reduces infection and parasite replication. P. falciparum and erythrocyte UPS coexist during IDC but the nature of their relationship is largely unknown. We used an approach based on Tandem Ubiquitin-Binding Entities (TUBEs) and 1D gel electrophoresis followed by mass spectrometry to identify major components of the TUBEs-associated ubiquitin proteome of both host and parasite during ring, trophozoite and schizont stages. Ring-exported protein (REX1), a P. falciparum protein located in Maurer's clefts and important for parasite nutrient import, was found to reach a maximum level of ubiquitylation in trophozoites stage. The Homo sapiens (H. sapiens) TUBEs associated ubiquitin proteome decreased during the infection, whereas the equivalent P. falciparum TUBEs-associated ubiquitin proteome counterpart increased. Major cellular processes such as DNA repair, replication, stress response, vesicular transport and catabolic events appear to be regulated by ubiquitylation along the IDC P. falciparum infection.

Ontologies for reusing data cleaning knowledge

The emergence of new business models, namely, the establishment of partnerships between organizations, the chance that companies have of adding existing data on the web, especially in the semantic web, to their information, led to the emphasis on some problems existing in databases, particularly related to data quality. Poor data can result in loss of competitiveness of the organizations holding these data, and may even lead to their disappearance, since many of their decision-making processes are based on these data. For this reason, data cleaning is essential. Current approaches to solve these problems are closely linked to database schemas and specific domains. In order that data cleaning can be used in different repositories, it is necessary for computer systems to understand these data, i.e., an associated semantic is needed. The solution presented in this paper includes the use of ontologies: (i) for the specification of data cleaning operations and, (ii) as a way of solving the semantic heterogeneity problems of data stored in different sources. With data cleaning operations defined at a conceptual level and existing mappings between domain ontologies and an ontology that results from a database, they may be instantiated and proposed to the expert/specialist to be executed over that database, thus enabling their interoperability.