Simulation of the ambulatory processes in the biggest Brazilian cardiology hospital: a petri net approach

This paper presents a simulation of an ambulatory processes using timed Petri net (TPN). The simulation considers the flow of patients in the biggest Brazilian cardiology hospital. The TPN is used as a decision support system (DSS) to improve the processes, to reduce the waiting time of the patients in the ambulatory and in this way to assure a high-quality service to the patients. Simulations were carried out using the software Visual Object Net++. This is a free software and therefore the presented solution is a low-cost solution. Providing a low-cost solution has a huge importance in this work since the hospital is kept from the government efforts and operates with limited financial resources. The patients’ flow in the hospital can be faced as a service and the modelling and optimization of these services bring more efficiency to the system as well as improve the human factors involved. The results proved that some changes could be made in the processes to improve the performance of the system

Evaluating Resilience of Cyber-Physical-Social Systems

Nowadays, protecting the network is not the only security concern. Still, in cyber security, websites and servers are becoming more popular as targets due to the ease with which they can be accessed when compared to communication networks. Another threat in cyber physical social systems with human interactions is that they can be attacked and manipulated not only by technical hacking through networks, but also by manipulating people and stealing users’ credentials. Therefore, systems should be evaluated beyond cy- ber security, which means measuring their resilience as a piece of evidence that a system works properly under cyber-attacks or incidents. In that way, cyber resilience is increas- ingly discussed and described as the capacity of a system to maintain state awareness for detecting cyber-attacks. All the tasks for making a system resilient should proactively maintain a safe level of operational normalcy through rapid system reconfiguration to detect attacks that would impact system performance. In this work, we broadly studied a new paradigm of cyber physical social systems and defined a uniform definition of it. To overcome the complexity of evaluating cyber resilience, especially in these inhomo- geneous systems, we proposed a framework including applying Attack Tree refinements and Hierarchical Timed Coloured Petri Nets to model intruder and defender behaviors and evaluate the impact of each action on the behavior and performance of the system.Hoje em dia, proteger a rede não é a única preocupação de segurança. Ainda assim, na segurança cibernética, sites e servidores estão se tornando mais populares como alvos devido à facilidade com que podem ser acessados quando comparados às redes de comu- nicação. Outra ameaça em sistemas sociais ciberfisicos com interações humanas é que eles podem ser atacados e manipulados não apenas por hackers técnicos através de redes, mas também pela manipulação de pessoas e roubo de credenciais de utilizadores. Portanto, os sistemas devem ser avaliados para além da segurança cibernética, o que significa medir sua resiliência como uma evidência de que um sistema funciona adequadamente sob ataques ou incidentes cibernéticos. Dessa forma, a resiliência cibernética é cada vez mais discutida e descrita como a capacidade de um sistema manter a consciência do estado para detectar ataques cibernéticos. Todas as tarefas para tornar um sistema resiliente devem manter proativamente um nível seguro de normalidade operacional por meio da reconfi- guração rápida do sistema para detectar ataques que afetariam o desempenho do sistema. Neste trabalho, um novo paradigma de sistemas sociais ciberfisicos é amplamente estu- dado e uma definição uniforme é proposta. Para superar a complexidade de avaliar a resiliência cibernética, especialmente nesses sistemas não homogéneos, é proposta uma estrutura que inclui a aplicação de refinamentos de Árvores de Ataque e Redes de Petri Coloridas Temporizadas Hierárquicas para modelar comportamentos de invasores e de- fensores e avaliar o impacto de cada ação no comportamento e desempenho do sistema

Characterization of the longitudinal HIV-1 quasispecies evolution in HIV-1 infected individuals co-infected with Mycobacterium tuberculosis

One of the earliest and most striking observations made about HIV is the extensive genetic variation that the virus has within individual hosts, particularly in the hypervariable regions of the env gene which is divided into 5 variable regions (V1-V5) and 5 more constant (C1-C5) regions. HIV evolves at any time over the course of an individual’s infection and infected individuals harbours a population of genetically related but non-identical viruses that are under constant change and ready to adapt to changes in their environment. These genetically heterogeneous populations of closely related genomes are called quasispecies [65]. Tuberculosis or tubercle forming disease is an acute and/or chronic bacterial infection that primarily attacks the lungs, but which may also affect the kidneys, bones, lymph nodes, and brain. The disease is caused by Mycobacterium tuberculosis (MTB), a slow growing rod-shaped, acid fast bacterium. It is transmitted from person to person through inhalation of bacteria-carrying air droplets. Worldwide, one person out of three is infected with Mycobacterium tuberculosis – two billion people in total. TB currently holds the seventh place in the global ranking of causes of death [73]. In 2008, there were an estimated 9.4 (range, 8.9–9.9 million) million incident cases (equivalent to 139 cases per 100 000 population) of TB globally [75]. A complex biological interplay occurs between M. tuberculosis and HIV in coinfected host that results in the worsening of both pathologies. HIV promotes progression of M. tuberculosis either by endogenous reactivation or exogenous reinfection [77, 78] and, the course of HIV-1 infection is accelerated subsequent to the development of TB [80]. Active TB is associated with an increase in intra-patient HIV-1 diversity both systemically and at the infected lung sites [64,122]. The sustainability or reversal of the HIV-1 quasispecies heterogeneity after TB treatment is not known. Tetanus toxoid vaccinated HIV-1 infected patients developed a transient increase in HIV-1 heterogeneity which was reversed after few weeks [121]. Emergence of a heterogeneous HIV-1 population within a patient may be one of the mechanisms to escape strong immune or drug pressure [65,128]. The existence of better fitting and/or immune escape HIV-variants can lead to an increase in HIV-1 replication [129,130]. It might be that TB favourably selected HIV-1 variants which are sources for consistent HIV-1 replication. Understanding the mechanisms underlying the impacts of TB on HIV-1 is essential for the development of effective measures to reduce TB related morbidity and mortality in HIV-1 infected individuals. In the present study we studied whether the increase in HIV-1 quasispecies diversity during active TB is reversed or preserved throughout the course of antituberculous chemotherapy. For this purpose Two time point HIV-1 quasispecies were evaluated by comparing HIV-1 infected patients with active tuberculosis (HIV-1/TB) and HIV-1 infected patients without tuberculosis (HIV-1/non TB). Plasma samples were obtained from the Frankfurt HIV cohort and HIV-1 RNA was isolated. C2V5 env was amplified by PCR and molecular cloning was performed. Eight to twenty five clones were sequenced from each patient. Various phylogenetic analyses were performed including tree inferences, intra-patient viral diversity and divergence, selective pressure, co-receptor usage prediction and two time point identity of quasispecies comparison using Mantel’s test. We found out from this study that: 1) Active TB sustains HIV-1 quasispecies diversity for longer period 2. Active TB increases the rate of HIV-1 divergence 3) TB might slow down evolution of X4 variants And we concluded that active TB has an impact on HIV-1 viral diversity and divergence over time. The influence of active TB on longitudinal evolution of HIV- 1 may be predominant for R5 viruses. The use of CCR5-coreceptor inhibitors for HIV-1/TB patients as therapeutic approach needs further investigation.Eine der ersten und überraschenden Beobachtungen, welche bei der Analyse des HI-Virus gemacht wurden ist seine ausgeprägte Genetische Variabilität besonders die hypervariable Region des env Genes betreffen. Dieses wird in 5 variable Regionen (V1-V5) sowie 5 stärker konservierte Regionen (C1-C5) unterteilt. HIV wandelt sich zu jedem Zeitpunkt im Verlauf der Infektion und jedes infizierte Individuum ist Träger einer Population von genetisch verwandten jedoch nicht identischen Viren, welche sich kontinuierlich verändern und an die Erfordernisse innerhalb der Umgebung anpassen. Diese genetisch heterogenen, jedoch eng verwandten Populationen werden Quasispecies genannt. Tuberkulose ist eine mykobakterielle Infektion, welche sowohl akute als auch chronische Verläufe zeigt. Neben den Lungen als primärem Manifestationsort können auch die Nieren, Knochen und andere Organe befallen sein. Eine von drei Personen weltweit ist mit Mycobacterium tuberculosis infiziert, insgesamt 2 Milliarden Menschen. In HIV/TB Co-Inifzierten Menschen entsteht ein komplexes Zusammenspiel zwischen HIV und M. tuberculosis, welches zu einer Verschlechterung beider Krankheitsbilder führt. HIV führt durch endogene Rekativierung oder exogene Re-Infektion zu einer Progression der Tuberkulose, welche im weiteren Verlauf die Krankheitsprogression von HIV beschleunigt. Sowohl Morbidität als auch Mortalität sind in HIV-1/TB Co-Infizierten Menschen erhöht. Aktive Lungentuberkulose und Miliartuberkulose gehen mit dem Anstieg der Diversifität der HIV Viren innerhalb eines Wirtes einher. Wie lange diese erhöhte Heterogenität der HIV Quasispecies nach der erfolgreichen Behandlung einer Tuberkulose bestehen bleibt ist bisher noch unklar. Das Verständnis des dem Zusammenspiel von HIV und TB zugrundeliegenden Mechanismus ist essentiell für die Entwicklung von effektiven Massnahmen zur Senkung der Morbidität und Mortalität in HIV/TB Co-infizierten Menschen. Die gegenwärtige Forschungsarbeit folgte daher der Frage, ob wärend einer aktiven TB Infektion eine Zunahme der Diversität der HIV-1 Quasispecies zu beobachten ist und ob diese Diversität während einer TB Therapie erhalten bleibt oder sich zurück bildet. Hierfür wurden die HIV-1 Quasispecies zu zwei Zeitpunkten untersucht, wobei Proben von HIV-1 infizierten Patienten mit aktiver Tuberkulose (HIV-1/TB) und HIV infizierte Patienten ohne Tuberkulose (HIV-1/non TB) verglichen wurden. Aus Plasmaproben der Frankfurter HIV Cohorte wurde HIV-1 RNA isoliert. C2V5 env wurde durch PCR amplifiziert und molekular cloniert. Acht bis fünfundzwanzig Clone wurden für jeden Patienten sequenziert. Mehrere phylogenetische Analysen wurden durchgeführt, welche tree inferences, Intra-Patienten- und virale Diversität und Divergenz, Selektionsdruckanalysen, Vorhersage der Co-Rezeptornutzung sowie Zweipunktanalysen der Identität von Quasispecies mit Hilfe des Mantel’s Test miteinschlossen. Die Analysen ergaben die folgenden Ergebnisse: 1) Eine aktive TB erhält die Diversität von HIV-1 Quasispecies über einen längeren Zeitraum. 2. Eine aktive TB verstärkt die HIV -1 Divergenz 3) TB könnte zu einer langsameren Evolution von X4 Varianten führen. Schlussfolgerung: eine aktive TB beeinflusst die Entwicklung der viralen Diversität und Divergenz von HIV-1 im Verlauf der Krankheit. Der Einfluss der aktiven TB auf die longitudinale Evolution von HIV-1 könnte insbesondere R5 Viren betreffen. Der Einsatz von CCR5-Corezeptor Inhibitoren in HIV-1/TB coinifizerten Patienten sollte daher in Langzeitstudien untersucht werden

Process Mining Concepts for Discovering User Behavioral Patterns in Instrumented Software

Process Mining is a technique for discovering “in-use” processes from traces emitted to event logs. Researchers have recently explored applying this technique to documenting processes discovered in software applications. However, the requirements for emitting events to support Process Mining against software applications have not been well documented. Furthermore, the linking of end-user intentional behavior to software quality as demonstrated in the discovered processes has not been well articulated. After evaluating the literature, this thesis suggested focusing on user goals and actual, in-use processes as an input to an Agile software development life cycle in order to improve software quality. It also provided suggestions for instrumenting software applications to support Process Mining techniques

Context-Aware and Secure Workflow Systems

Businesses do evolve. Their evolution necessitates the re-engineering of their existing "business processes”, with the objectives of reducing costs, delivering services on time, and enhancing their profitability in a competitive market. This is generally true and particularly in domains such as manufacturing, pharmaceuticals and education). The central objective of workflow technologies is to separate business policies (which normally are encoded in business logics) from the underlying business applications. Such a separation is desirable as it improves the evolution of business processes and, more often than not, facilitates the re-engineering at the organisation level without the need to detail knowledge or analyses of the application themselves. Workflow systems are currently used by many organisations with a wide range of interests and specialisations in many domains. These include, but not limited to, office automation, finance and banking sector, health-care, art, telecommunications, manufacturing and education. We take the view that a workflow is a set of "activities”, each performs a piece of functionality within a given "context” and may be constrained by some security requirements. These activities are coordinated to collectively achieve a required business objective. The specification of such coordination is presented as a set of "execution constraints” which include parallelisation (concurrency/distribution), serialisation, restriction, alternation, compensation and so on. Activities within workflows could be carried out by humans, various software based application programs, or processing entities according to the organisational rules, such as meeting deadlines or performance improvement. Workflow execution can involve a large number of different participants, services and devices which may cross the boundaries of various organisations and accessing variety of data. This raises the importance of _ context variations and context-awareness and _ security (e.g. access control and privacy). The specification of precise rules, which prevent unauthorised participants from executing sensitive tasks and also to prevent tasks from accessing unauthorised services or (commercially) sensitive information, are crucially important. For example, medical scenarios will require that: _ only authorised doctors are permitted to perform certain tasks, _ a patient medical records are not allowed to be accessed by anyone without the patient consent and _ that only specific machines are used to perform given tasks at a given time. If a workflow execution cannot guarantee these requirements, then the flow will be rejected. Furthermore, features/characteristics of security requirement are both temporal- and/or event-related. However, most of the existing models are of a static nature – for example, it is hard, if not impossible, to express security requirements which are: _ time-dependent (e.g. A customer is allowed to be overdrawn by 100 pounds only up-to the first week of every month. _ event-dependent (e.g. A bank account can only be manipulated by its owner unless there is a change in the law or after six months of his/her death). Currently, there is no commonly accepted model for secure and context-aware workflows or even a common agreement on which features a workflow security model should support. We have developed a novel approach to design, analyse and validate workflows. The approach has the following components: = A modelling/design language (known as CS-Flow). The language has the following features: – support concurrency; – context and context awareness are first-class citizens; – supports mobility as activities can move from one context to another; – has the ability to express timing constrains: delay, deadlines, priority and schedulability; – allows the expressibility of security policies (e.g. access control and privacy) without the need for extra linguistic complexities; and – enjoy sound formal semantics that allows us to animate designs and compare various designs. = An approach known as communication-closed layer is developed, that allows us to serialise a highly distributed workflow to produce a semantically equivalent quasi-sequential flow which is easier to understand and analyse. Such re-structuring, gives us a mechanism to design fault-tolerant workflows as layers are atomic activities and various existing forward and backward error recovery techniques can be deployed. = Provide a reduction semantics to CS-Flow that allows us to build a tool support to animate a specifications and designs. This has been evaluated on a Health care scenario, namely the Context Aware Ward (CAW) system. Health care provides huge amounts of business workflows, which will benefit from workflow adaptation and support through pervasive computing systems. The evaluation takes two complementary strands: – provide CS-Flow’s models and specifications and – formal verification of time-critical component of a workflow

Process Mining Handbook

This is an open access book. This book comprises all the single courses given as part of the First Summer School on Process Mining, PMSS 2022, which was held in Aachen, Germany, during July 4-8, 2022. This volume contains 17 chapters organized into the following topical sections: Introduction; process discovery; conformance checking; data preprocessing; process enhancement and monitoring; assorted process mining topics; industrial perspective and applications; and closing

Washington University Record, August 23, 2002

https://digitalcommons.wustl.edu/record/1937/thumbnail.jp

Turku Centre for Computer Science – Annual Report 2013

Due to a major reform of organization and responsibilities of TUCS, its role, activities, and even structures have been under reconsideration in 2013. The traditional pillar of collaboration at TUCS, doctoral training, was reorganized due to changes at both universities according to the renewed national system for doctoral education. Computer Science and Engineering and Information Systems Science are now accompanied by Mathematics and Statistics in newly established doctoral programs at both University of Turku and &Aring;bo Akademi University. Moreover, both universities granted sufficient resources to their respective programmes for doctoral training in these fields, so that joint activities at TUCS can continue. The outcome of this reorganization has the potential of proving out to be a success in terms of scientific profile as well as the quality and quantity of scientific and educational results.&nbsp; International activities that have been characteristic to TUCS since its inception continue strong. TUCS&rsquo; participation in European collaboration through EIT ICT Labs Master&rsquo;s and Doctoral School is now more active than ever. The new double degree programs at MSc and PhD level between University of Turku and Fudan University in Shaghai, P.R.China were succesfully set up and are&nbsp; now running for their first year. The joint students will add to the already international athmosphere of the ICT House.&nbsp; The four new thematic reseach programmes set up acccording to the decision by the TUCS Board have now established themselves, and a number of events and other activities saw the light in 2013. The TUCS Distinguished Lecture Series managed to gather a large audience with its several prominent speakers. The development of these and other research centre activities continue, and&nbsp; new practices and structures will be initiated to support the tradition of close academic collaboration.&nbsp; The TUCS&rsquo; slogan Where Academic Tradition Meets the Exciting Future has proven true throughout these changes. Despite of the dark clouds on the national and European economic sky, science and higher education in the field have managed to retain all the key ingredients for success. Indeed, the future of ICT and Mathematics in Turku seems exciting.</p

Proceedings, MSVSCC 2012

Proceedings of the 6th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 19, 2012 at VMASC in Suffolk, Virginia