abstract: Bayesian phylogeography is a framework that has enabled researchers to model the spatiotemporal diffusion of pathogens. In general, the framework assumes that discrete geographic sampling traits follow a continuous-time Markov chain process along the branches of an unknown phylogeny that is informed through nucleotide sequence data. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM) of predictors of interest to the pathogen. In this dissertation, I focus on these GLMs and describe their capabilities, limitations, and introduce a pipeline that may enable more researchers to utilize this framework. I first demonstrate how a GLM can be employed and how the support for the predictors can be measured using influenza A/H5N1 in Egypt as an example. Secondly, I compare the GLM framework to two alternative frameworks of Bayesian phylogeography: one that uses an advanced computational technique and one that does not. For this assessment, I model the diffusion of influenza A/H3N2 in the United States during the 2014-15 flu season with five methods encapsulated by the three frameworks. I summarize metrics of the phylogenies created by each and demonstrate their reproducibility by performing analyses on several random sequence samples under a variety of population growth scenarios. Next, I demonstrate how discretization of the location trait for a given sequence set can influence phylogenies and support for predictors. That is, I perform several GLM analyses on a set of sequences and change how the sequences are pooled, then show how aggregating predictors at four levels of spatial resolution will alter posterior support. Finally, I provide a solution for researchers that wish to use the GLM framework but may be deterred by the tedious file-manipulation requirements that must be completed to do so. My pipeline, which is publicly available, should alleviate concerns pertaining to the difficulty and time-consuming nature of creating the files necessary to perform GLM analyses. This dissertation expands the knowledge of Bayesian phylogeographic GLMs and will facilitate the use of this framework, which may ultimately reveal the variables that drive the spread of pathogens. / Dissertation/Thesis / Doctoral Dissertation Biomedical Informatics 2017

Aim: Public health systems have embraced health informatics and information technology as a potential transformational tool to improve real-time surveillance systems, communication, and sharing of information among various agencies. Global pandemic outbreaks like Zika and Ebola were quickly controlled due to electronic surveillance systems enabling efficient information access and exchange. However, there is the need for a more robust technology to enhance adequate epidemic forecasting, data sharing, and effective communication. The purpose of this review was to examine the use of informatics and information technology tools and its impact on public health delivery. Method: Investigators searched six electronic databases. These were MEDLINE, Cumulative Index to Nursing and Allied Health Literature (CINAHL) Complete, Cochrane Database of Systematic Reviews, COMPENDEX, Scopus, and Academic Search Premier from January 2000 to 31 March 2016. Results: A total of 60 articles met the eligibility criteria for inclusion. These studies were organized into three areas as (1) definition of the term public health informatics; (2) type of public health surveillance systems and implications for public health; and (3) electronic surveillance systems functionality, capability, training, and challenges. Our analysis revealed that due to the growing expectations to provide real-time response and population-centered evidence-based public health in this information-driven age there has been a surge in informatics and information technology adoption. Education and training programs are now available to equip public health students and professionals with skills in public health informatics. However, obstacles including interoperability, data standardization, privacy, and technology transfer persist. Conclusion: Re-engineering the delivery of public health is necessary to meet the demands of the 21st century and beyond. To meet this expectation, public health must invest in workforce development and capacity through education and training in informatics.

Indiana University-Purdue University Indianapolis (IUPUI) / Between 3.2 and 5.3 million U.S. civilians live with traumatic brain injury (TBI)-related disabilities. Although the post-acute phase of TBI has been recognized as both a discrete disease process and risk factor for chronic conditions, TBI is not recognized as a chronic disease. TBI epidemiology draws upon untimely, incomplete, cross-sectional, administrative datasets. The adoption of electronic health records (EHR) may supplement traditional datasets for public health surveillance and research. Methods Indiana constructed a state-wide clinical TBI registry from longitudinal (2004-2018) EHRs. This dissertation includes three distinct studies to enhance, evaluate, and apply the registry: 1) development and evaluation of a natural language processing algorithm for identification of TBI severity within free-text notes; 2) evaluation and comparison of the performance of the ICD-9-CM and ICD-10-CM surveillance definitions; and 3) estimating the effect of mild TBI (mTBI) on the risk of post-acute chronic conditions compared to individuals without mTBI. Results Automated extraction of Glasgow Coma Scale from clinical notes was feasible and demonstrated balanced recall and precision (F-scores) for classification of mild (99.8%), moderate (100%), and severe (99.9%) TBI. We observed poor sensitivity for ICD-10-CM TBI surveillance compared to ICD-9-CM (0.212 and 0.601, respectively), resulting in potentially 5-fold underreporting. ICD-10-CM was not statistically equivalent to ICD-9-CM for sensitivity (𝑑𝑑𝑑𝑑̂=0.389, 95% CI [0.388,0.405]) or positive predictive value (𝑑𝑑𝑑𝑑̂=-0.353, 95% CI [-0.362,-0.344]). Compared to a matched cohort, individuals with mTBI were more likely to be diagnosed with mental health, substance use, neurological, cardiovascular, and endocrine conditions. Conclusion ICD-9-CM and ICD-10-CM surveillance definitions were not equivalent, and the transition resulted in a underreporting incidence for mTBI. This has direct implications on existing and future TBI registries and the Report to Congress on Traumatic Brain Injury in the United States. The supplementation of state-based trauma registries with structured and unstructured EHR data is effective for studying TBI outcomes. Our findings support the classification of TBI as a chronic disease by funding bodies, which may improve public funding to replace legacy systems to improve standardization, timeliness, and completeness of the epidemiology and post-acute outcomes of TBI.

No description available.

A saúde mental é uma das áreas que envolve mais atenção, visto que as ações tomadas dentro da rede não podem ser reduzidas a sistemas fechados, sem comunicação com outros sistemas, mas a sistemas abertos, heterogêneos e articulados. Dessa maneira, torna-se necessário a busca de novas possibilidades para a realização do trabalho contínuo e articulado entre os diferentes níveis da rede de atenção em saúde mental. Diante deste contexto, o principal objetivo deste projeto é desenvolver e implantar um sistema de informação em saúde para gestão de pacientes que permite realizar o monitoramento do fluxo de pacientes com transtornos mentais. Para tal, o projeto contempla o desenvolvimento de um sistema web utilizando as tecnologias web PHP, HTML, JavaScript e CSS, Sistema Gerenciador de Banco de Dados MySQL e servidor web Apache. Um sistema baseado na arquitetura web, denominado SISAM 13, que permite acompanhar as consultas, solicitações de internação, internações e o movimento de pacientes na rede pública de saúde mental do Departamento Regional de Saúde XIII (DRS XIII), fornecendo relatórios de gestão, foi criado e implementado. Inicialmente, o sistema foi implantando como piloto e, após de 90 dias, entrou em funcionamento definitivo. De novembro de 2012 até outubro de 2014, foram cadastrados 4271 pacientes, 480 profissionais, 1483 agendamentos de consultas, 5938 solicitações de internação e 3239 internações. Evidenciou-se que a maioria dos municípios de procedência da solicitação de internação fazem parte do DRS XIII, confirmando a adequação da regionalização. Verificou-se que a alta proporção de solicitações provenientes dos serviços especializados em saúde mental mostrou a dificuldade de estabilização de pacientes com transtornos mentais por essas unidades, evidenciando a falta de organização desses serviços e a falta articulação com os demais serviços da rede. O sobrecarregamento da rede do DRS XIII pode ser justificado pelo alto tempo de espera por atendimento, e a redução do giro leito, prejudicando o fluxo de pacientes. A maioria da população atendida nos serviços de internação foi masculina, entre 20 a 39 anos, com diagnóstico de transtornos relacionados ao uso de substância(s) psicoativa(s) e internação com duração maior ou igual a 31 dias. O maior tempo de permanência pelas internações compulsórias em comparação com as internações voluntárias e involuntárias, ocasiona em redução no giro leito, refletindo para toda rede de saúde mental. A alta proporção de contrarreferências para serviços especializados em saúde mental pode contribuir para a continuidade do tratamento, todavia, verificou-se que apenas 54,92% das altas foram contrarreferencias. A baixa utilização da funcionalidade de consultas em conjunto com o número de ações de usuários com permissão de solicitadores menor que o de prestadores, sugere o aperfeiçoamento e/ou inclusão de funcionalidades no sistema para os serviços extra-hospitalares. O aumento de 13,16% do número total de ações de um ano para outro pode ser explicado pela incorporação do sistema no processo diário de trabalho, visto que os usuários do sistema foram vistos e reconhecidos como parte integrante na construção do sistema, permitindo o engajamento dos mesmos na sua utilização e melhoria. / Mental health is one of the areas that involves more attention, since the actions taken within the services network cannot be reduced to closed systems without communication with other systems, but with open, heterogeneous and articulated ones. Thus, a search for new possibilities for the realization of continuous and articulated work between different levels of mental health care network is necessary. Given this context, the main objective of this project is to develop and deploy a web based health information system for patient management in order to perform the monitoring of the flow of patients with mental disorders. To this end, the project will include the use of web technologies such as PHP, HTML, JavaScript and CSS, Database Management System MySQL, and Apache web server. A web based system called SISAM 13, that allows appointments, requests for hospitalizations, hospitalizations and the movement of patients in the public mental health network, providing management reports, was created. Initially, the system was implemented as a pilot, and after 90 days, it came into definitive operation. From November 2012 to October 2014, the system registered 4271 patients, 480 professionals, 1483 schedules appointments, 5938 request for hospitalizations and 3239 hospitalizations. Most origin municipalities of the requests was part of the Regional Health Department XIII (RHD XIII), confirming the adequacy of regionalization. It was found that the high proportion of requests from the mental health specialized services, showed the difficulty of stabilizing patients with mental disorders by these units, showing the lack of organization and coordination with other network services. The network overloading can be justified by the high waiting time for hospitalization, and the bed turnover decrease, damaging the network patients flow. It was shown that the majority of the population treated in hospital admissions was male, between 20 to 39 years, diagnosed with disorders related to the use of psychoactive(s) substance(s) use and length of stay more than or equal to 31 days. The longer length of stay by the compulsory admissions compared with voluntary and involuntary admissions, causes reduction in the bed turnover, reflecting on the entire mental health network. The high proportion of counter references to mental health specialist services can contribute to the continuity of care, however, it was found that only 54,92% of the discharges were counter referenced. The low level use of the appointments features along with the low number of user actions by requesters, suggests the improvement and / or inclusion of features in the system for outpatient services. The increase of 13,16% in the total number of actions from one year to another can be explained by the incorporation of the system in the daily working process, since users of the system were seen and recognized as an integral part in the system development, allowing their engagement in its use and improvement.

A saúde mental é uma das áreas que envolve mais atenção, visto que as ações tomadas dentro da rede não podem ser reduzidas a sistemas fechados, sem comunicação com outros sistemas, mas a sistemas abertos, heterogêneos e articulados. Dessa maneira, torna-se necessário a busca de novas possibilidades para a realização do trabalho contínuo e articulado entre os diferentes níveis da rede de atenção em saúde mental. Diante deste contexto, o principal objetivo deste projeto é desenvolver e implantar um sistema de informação em saúde para gestão de pacientes que permite realizar o monitoramento do fluxo de pacientes com transtornos mentais. Para tal, o projeto contempla o desenvolvimento de um sistema web utilizando as tecnologias web PHP, HTML, JavaScript e CSS, Sistema Gerenciador de Banco de Dados MySQL e servidor web Apache. Um sistema baseado na arquitetura web, denominado SISAM 13, que permite acompanhar as consultas, solicitações de internação, internações e o movimento de pacientes na rede pública de saúde mental do Departamento Regional de Saúde XIII (DRS XIII), fornecendo relatórios de gestão, foi criado e implementado. Inicialmente, o sistema foi implantando como piloto e, após de 90 dias, entrou em funcionamento definitivo. De novembro de 2012 até outubro de 2014, foram cadastrados 4271 pacientes, 480 profissionais, 1483 agendamentos de consultas, 5938 solicitações de internação e 3239 internações. Evidenciou-se que a maioria dos municípios de procedência da solicitação de internação fazem parte do DRS XIII, confirmando a adequação da regionalização. Verificou-se que a alta proporção de solicitações provenientes dos serviços especializados em saúde mental mostrou a dificuldade de estabilização de pacientes com transtornos mentais por essas unidades, evidenciando a falta de organização desses serviços e a falta articulação com os demais serviços da rede. O sobrecarregamento da rede do DRS XIII pode ser justificado pelo alto tempo de espera por atendimento, e a redução do giro leito, prejudicando o fluxo de pacientes. A maioria da população atendida nos serviços de internação foi masculina, entre 20 a 39 anos, com diagnóstico de transtornos relacionados ao uso de substância(s) psicoativa(s) e internação com duração maior ou igual a 31 dias. O maior tempo de permanência pelas internações compulsórias em comparação com as internações voluntárias e involuntárias, ocasiona em redução no giro leito, refletindo para toda rede de saúde mental. A alta proporção de contrarreferências para serviços especializados em saúde mental pode contribuir para a continuidade do tratamento, todavia, verificou-se que apenas 54,92% das altas foram contrarreferencias. A baixa utilização da funcionalidade de consultas em conjunto com o número de ações de usuários com permissão de solicitadores menor que o de prestadores, sugere o aperfeiçoamento e/ou inclusão de funcionalidades no sistema para os serviços extra-hospitalares. O aumento de 13,16% do número total de ações de um ano para outro pode ser explicado pela incorporação do sistema no processo diário de trabalho, visto que os usuários do sistema foram vistos e reconhecidos como parte integrante na construção do sistema, permitindo o engajamento dos mesmos na sua utilização e melhoria. / Mental health is one of the areas that involves more attention, since the actions taken within the services network cannot be reduced to closed systems without communication with other systems, but with open, heterogeneous and articulated ones. Thus, a search for new possibilities for the realization of continuous and articulated work between different levels of mental health care network is necessary. Given this context, the main objective of this project is to develop and deploy a web based health information system for patient management in order to perform the monitoring of the flow of patients with mental disorders. To this end, the project will include the use of web technologies such as PHP, HTML, JavaScript and CSS, Database Management System MySQL, and Apache web server. A web based system called SISAM 13, that allows appointments, requests for hospitalizations, hospitalizations and the movement of patients in the public mental health network, providing management reports, was created. Initially, the system was implemented as a pilot, and after 90 days, it came into definitive operation. From November 2012 to October 2014, the system registered 4271 patients, 480 professionals, 1483 schedules appointments, 5938 request for hospitalizations and 3239 hospitalizations. Most origin municipalities of the requests was part of the Regional Health Department XIII (RHD XIII), confirming the adequacy of regionalization. It was found that the high proportion of requests from the mental health specialized services, showed the difficulty of stabilizing patients with mental disorders by these units, showing the lack of organization and coordination with other network services. The network overloading can be justified by the high waiting time for hospitalization, and the bed turnover decrease, damaging the network patients flow. It was shown that the majority of the population treated in hospital admissions was male, between 20 to 39 years, diagnosed with disorders related to the use of psychoactive(s) substance(s) use and length of stay more than or equal to 31 days. The longer length of stay by the compulsory admissions compared with voluntary and involuntary admissions, causes reduction in the bed turnover, reflecting on the entire mental health network. The high proportion of counter references to mental health specialist services can contribute to the continuity of care, however, it was found that only 54,92% of the discharges were counter referenced. The low level use of the appointments features along with the low number of user actions by requesters, suggests the improvement and / or inclusion of features in the system for outpatient services. The increase of 13,16% in the total number of actions from one year to another can be explained by the incorporation of the system in the daily working process, since users of the system were seen and recognized as an integral part in the system development, allowing their engagement in its use and improvement.

Introdução: No Brasil, a maioria dos nascimentos é por cirurgia cesárea (CC), sendo amplamente utilizada no setor privado, mesmo com pesquisas indicando que quando as taxas de CC ultrapassam10-15%, os riscos adicionais superam os benefícios. A informação sobre benefícios e riscos das intervenções é fundamental para uma assistência segura e efetiva. É considerável o aumento de busca na web durante a gestação, no entanto, a qualidade das informações é questionável. Objetivo: avaliar a qualidade e abrangência das informações disponíveis sobre cesariana para leigos, em português, após um conjunto de políticas públicas para regular esta prática (2014/2015), na internet em geral e no site da Federação Brasileira de Associações de Ginecologia e Obstetrícia (FEBRASGO). Métodos: Trata-se de estudo documental observacional, transversal e analítico. A palavra \"cesárea\" e 25 sinônimos foram submetidos no campo de procura do site da FEBRASGO e em cinco motores de pesquisa para avaliar a preferência dos termos de busca. Os links catalogados foram analisados por dois pesquisadores independentes utilizando dois checklists: o DISCERN e um checklist específico para conteúdo. Adicionalmente, apresentou-se um debate sobre o sentido do nascimento, o ciberativismo e as políticas público no Brasil. Optou-se pela apresentação da tese no formato de três publicações, sendo duas já submetidas. Resultados: A palavra \"cesaria\" é a forma mais frequente, seguida de \"cesarea\". Na análise do conteúdo geral da internet, a produção de dado proveniente do Google.com.br representou apenas 45,5% (n = 235, 2018), sendo que este buscador tem a preferência de 94,5% dos brasileiros. Um terço do conteúdo esteve associado com informações relativas à recuperação da CC, resultado similar ao apontado pelo Google Trends com termos preferencias de busca na internet. As páginas Web foram melhor avaliadas em 2018 que em 2013, principalmente no critério de confiabilidade. O número páginas Web obtídos em 2018 foi 33% maior que em 2013, sendo que 93% eram inéditas. No site da FEBRASGO, foram observadas três fases distintas: 1) sem informação para leigos sobre CC, até 2014; 2) momento defensivo, onde os conteúdos estavam associados às medidas de redução de CC; 3) informativo, melhor redigido e autoral em 2018, porém, sem debater indicações, riscos e seu uso abusivo, no qual a CC é apenas citada dentro de outros temas. O debate sobre os ritos, mitos e as narrativas utilizadas no nascimento institucionalizado do Brasil traçou um paralelo teórico dos estudos entre o interacionismo simbólico de Mead e Blumer, com Davis Floyd e Diniz. Conclusões: Comparando os períodos de 2013 e 2018, nota-se melhora na confiabilidade da informação, porém, com uma queda do número de indicações e danos potenciais, e mais informação sobre recuperação. A cesárea é tratada frequentemente como fato consumado, tema que as gestantes estão mais interessadas. As associações médicas profissionais não tem promovido a devida informação sobre gravidez e parto, em linguagem apropriada para leigos, a Febrasgo poderia ocupar um lugar de referência na apomediação da relação médico-paciente, através de uma área dedicada a pacientes. O questionamento à epidemia de cesáreas se beneficiou da participação de iniciativas coletivas que representam narrativas independentes, como de grupos organizados de usuárias. Para a oferta de informações úteis à promoção de melhores resultados maternos e infantis, é necessária a mobilização em todas esferas sociais, públicas e privadas, e entre movimentos sociais, para a produção de conteúdo sobre CS com bases científicas, e uma orientação aos profissionais de saúde em recomendar páginas Web de qualidade às gestantes / Introduction: In Brazil, the majority of births are due to cesarean surgery (CC), being widely used in the private sector, even with research indicating that when CC rates exceed 10-15%, the additional risks outweigh the benefits. Information on benefits and risks of interventions is critical to safe and effective care. There is a growing trend for web research during pregnancy; however, the quality of information found is questionable. Objectives: This research aims to evaluate the quality and comprehensiveness of available information on CC for laypeople in Portuguese, following implementation of a set of public policies aimed at regulating this practice (2014/2015), on the internet in general and on the website of the Brazilian Federation of Associations of Gynecology and Obstetrics (FEBRASGO). Methods: An observational, transversal, analytical documentary research. The word \"cesarean\" and 25 synonyms were submitted in the search field of the FEBRASGO website and in five search engines to evaluate the preference of search terms.Two independent researchers using checklists to analyze the cataloged links: the DISCERN and a specific checklist for content.In addition, a debate was presented on the meaning of birth, cyberpolitics and public policies in Brazil.The thesis is presented in the article format, of the three publications, two already submitted.Results:The preliminary results on Internet search shows that the word \"cesaria\" is the most frequent form of the internet, followed by \"cesarea\". In the analysis of the general content of the internet, the production of data from Google.com.br represented only 45.5% (n = 235, 2018), and this search engine has the preference of 94.5% of Brazilians.One-third of the content was associated with CC recovery, a similar result to the one pointed out by Google Trends as preferences for internet search terms.The webpage (WP) number collected in 2018 was 33% higher than in 2013, and 93% of the previous were unpublished before. In 2018, WP were better endorsed than 2013 ones, particularly concerning the reliability criterion. On the FEBRASGO\'s website, analysis went through three phases: 1) no information for lay people about CC in 2014; 2) defensive texts associated with the CC reduction measures, in 2016; 3) a more informative, better written and authorial content in 2018, but with no debate on indications and abusive use of CC, only mentioned in other topic CC. The debate about the rites, myths and narratives used in the institutionalized birth of Brazil drew a theoretical parallel between the symbolic interactionism by Mead and Blumer and those by Davis Floyd and Diniz. Conclusions: When comparing the two periods, there is an improvement in the quality of information on CS, but with a decrease in the number of texts on indications and potential damages, as well as a rise on information about recovery from the surgery - often treated as a fait accompli - which is also a theme of great interest to pregnant women. Medical corporations have not promoted adequate information on pregnancy and childbirth in language appropriate for laypeople and need to be a reference in apomediation the physician-patient relationship through an area dedicated to patients. The questioning of the CS epidemy has benefited from the participation of collective initiatives that represent independent narratives, such as organized groups of healthcare consumers. To provide useful information that will improve the lives of mothers and infants, it\'s necessary to act in all social spheres, such as the public and the private, and across different social movements, producing CS related content based on scientific evidence, and guide healthcare professionals to recommending quality PW to pregnant women.