VizLattes: a tool for relevance analysis from scientific co-authorship networks

Social network data typically carry attribute information associated with the individuals and to their relationships. Such interconnected information can be useful to identify groups of individuals sharing common attribute properties and also to investigate the behaviour of particular individuals in a global network scenario. Different approaches have been introduced to extract and identify information of interest in social networks, and community identification is one of them. Some methods focus on identifying groups or communities of individuals based on their relationships, while others try to identify groups of individuals based on the common information they share. Integrating both approaches is not straightforward, as different mathematical and computational must be implemented and integrated into a unified framework. In this paper we approach this problem and propose a new method to identify underlying communities in a network, while highlighting the information shared by their components. Our solution relies on a single unified mathematical method. As a proof-of-concept, we have applied the proposed method to scientific co-authorship networks extracted from the wellknown Lattes Platform made available by CNPq, the Brazilian national science funding agency. We use textual information on the co-authors and their papers as focus attributes. We show that the method supports both community detection and also the identification of thematic paths, underlying topics and relevant authors characterizing distinct academic communities. The results presented show that this approach can be quite useful for exploration and understanding of academic collaboration networks.CAPESCNPqFAPES

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Global economic burden of unmet surgical need for appendicitis

Background: There is a substantial gap in provision of adequate surgical care in many low-and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods: Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results: Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion: For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Global variation in anastomosis and end colostomy formation following left-sided colorectal resection

Background End colostomy rates following colorectal resection vary across institutions in high-income settings, being influenced by patient, disease, surgeon and system factors. This study aimed to assess global variation in end colostomy rates after left-sided colorectal resection. Methods This study comprised an analysis of GlobalSurg-1 and -2 international, prospective, observational cohort studies (2014, 2016), including consecutive adult patients undergoing elective or emergency left-sided colorectal resection within discrete 2-week windows. Countries were grouped into high-, middle- and low-income tertiles according to the United Nations Human Development Index (HDI). Factors associated with colostomy formation versus primary anastomosis were explored using a multilevel, multivariable logistic regression model. Results In total, 1635 patients from 242 hospitals in 57 countries undergoing left-sided colorectal resection were included: 113 (6·9 per cent) from low-HDI, 254 (15·5 per cent) from middle-HDI and 1268 (77·6 per cent) from high-HDI countries. There was a higher proportion of patients with perforated disease (57·5, 40·9 and 35·4 per cent; P < 0·001) and subsequent use of end colostomy (52·2, 24·8 and 18·9 per cent; P < 0·001) in low- compared with middle- and high-HDI settings. The association with colostomy use in low-HDI settings persisted (odds ratio (OR) 3·20, 95 per cent c.i. 1·35 to 7·57; P = 0·008) after risk adjustment for malignant disease (OR 2·34, 1·65 to 3·32; P < 0·001), emergency surgery (OR 4·08, 2·73 to 6·10; P < 0·001), time to operation at least 48 h (OR 1·99, 1·28 to 3·09; P = 0·002) and disease perforation (OR 4·00, 2·81 to 5·69; P < 0·001). Conclusion Global differences existed in the proportion of patients receiving end stomas after left-sided colorectal resection based on income, which went beyond case mix alone

A fast method for analysis of contingency and selection in the context of preventive control of voltage stability

Nos últimos anos verificou-se um crescimento acentuado da complexidade da avaliação da segurança em Sistemas Elétricos de Potência (SEPs). O aumento das interligações, aliado à operação das redes com altos níveis de carregamento, aumenta a probabilidade de ocorrência de incidentes que podem levar o SEP à instabilidade de tensão, culminando com o colapso de tensão e grandes prejuízos à qualidade do fornecimento de energia elétrica. Neste trabalho foi proposta uma ferramenta rápida para a manutenção da segurança de SEPs no contexto da Estabilidade de Tensão (ET). Para tal, foi desenvolvida uma metodologia rápida para a análise de contingências. Selecionadas as críticas, a eliminação da criticalidade das mesmas é realizada via ações preventivas. Neste contexto, foram desenvolvidas duas abordagens para a seleção de ações preventivas. Na primeira procura-se minimizar o número de controles via técnicas de agrupamento de dados, para eliminar a criticalidade de uma contingência. Na segunda abordagem foi desenvolvida uma estratégia para obtenção de um grupo de controles para eliminar a criticalidade de todas as contingências. Ambas as abordagens baseiam-se em uma metodologia de análise de sensibilidade da margem de ET em relação aos controles preventivos que também foi proposta nesta tese. A eficácia da ferramenta foi comprovada por intermédio de simulações em um SEP. Os resultados foram bastante satisfatórios, os grupos de controles obtidos pela primeira abordagem representam um conjunto mínimo de ações preventivas para eliminar a criticalidade de uma contingência específica. Já na segunda abordagem, foi possível determinar um grupo de controles para a eliminar simultaneamente a criticalidade de todas as contingências. Como produto científico deste doutorado foram obtidas novas metodologias rápidas para a análise de segurança do SEP no contexto da ET.The complexity of the security assessment in Electric Power Systems (EPS) has received much attention from researches in recent years. The continuous growth in the number of interconnections, allied to networks operating with high loading levels, enhance the probability of incidents that can lead the EPS to voltage instability. Voltage collapse and considerably loss of the electric supply are the principal consequences of this scenery. In this study, we propose a fast tool for supporting the EPS security, in the context of Voltage Stability (VS). To this end, a fast methodology was developed for contingency analysis. Once the critical contingencies are selected, their criticalities are eliminated through the selection of preventive actions. In this context, two approaches were developed. In the first one, we aim at minimizing eh number of controls by using clustering techniques. In this case, the principal objective is to eliminate the criticality of a contingency. In the second approach, we developed a strategy for obtaining a groups of controls in order to eliminate the criticality of all contingencies. Both approaches are based on a methodology for sensitivity analysis of the VS margin with respect to preventive controls which is also proposed in this thesis. The effectiveness of the tool was corroborated by simulations in a EPS. We found the results satisfactory, since the groups of controls achieved by the first approach represent a minimum set of preventive actions that can be taken to eliminate the criticality of a specific contingency. In the second approach, it was possible to determine a minimum group of controls that eliminate the criticality of all contingencies simultaneously. New fast methodologies for security analysis of the EPS in the context of the VS is considered the main scientific product result of this doctorate

Algorithm for elaboration of plans for service restoration to large-scale distribution systems

A elaboração de planos de restabelecimento de energia (PRE) de forma rápida, para re-energização de sistemas de distribuição radiais (SDR), faz-se necessária para lidar com situações que deixam regiões dos SDR sem energia. Tais situações podem ser causadas por faltas permanentes ou pela necessidade de isolar zonas dos SDR para serviços de manutenção. Dentre os objetivos de um PRE, destacam-se: (i) reduzir o número de consumidores interrompidos (ou nenhum), e (ii) minimizar o número de manobras; que devem ser atendidos sem desrespeitar os limites operacionais dos equipamentos. Conseqüentemente, a obtenção de PRE em SDR é um problema com múltiplos objetivos, alguns conflitantes. As principais técnicas desenvolvidas para obtenção de PRE em SDR baseiam-se em algoritmos evolutivos (AE). A limitação da maioria dessas técnicas é a necessidade de simplificações na rede, para lidar com SDR de grande porte, que limitam consideravelmente a possibilidade de obtenção de um PRE adequado. Propõe-se, neste trabalho, o desenvolvimento e implantação computacional de um algoritmo para obtenção de PRE em SDR, que consiga lidar com sistemas de grande porte sem a necessidade de simplificações, isto é, considerando uma grande parte (ou a totalidade) de linhas, barras, cargas e chaves do sistema. O algoritmo proposto baseia-se em um AE multi-objetivo e na estrutura de dados, para armazenamento de grafos, denominada representação nó-profundidade (RNP), bem como em dois operadores genéticos que foram desenvolvidos para manipular de forma eficiente os dados armazenados na RNP. Em razão de se basear em um AE multi-objetivo, o algoritmo proposto possibilita uma investigação mais ampla do espaço de busca. Por outro lado, fazendo uso da RNP, para representar computacionalmente os SDR, e de seus operadores genéticos, o algoritmo proposto aumenta significativamente a eficiência da busca por adequados PRE. Isto porque aqueles operadores geram apenas configurações radiais, nas quais todos os consumidores são atendidos. Para comprovar a eficiência do algoritmo proposto, várias simulações computacionais foram realizadas, utilizando o sistema de distribuição real, de uma companhia brasileira, que possui 3.860 barras, 635 chaves, 3 subestações e 23 alimentadores.An elaborated and fast energy restoration plan (ERP) is required to deal with steady faults in radial distribution systems (RDS). That is, after a faulted zone has been identified and isolated by the relays, it is desired to elaborate a proper ERP to restore energy on that zone. Moreover, during the normal system operation, it is frequently necessary to elaborate ERP to isolate zones to execute routine tasks of network maintenance. Some of the objectives of an ERP are: (i) very few interrupted customers (or none), and (ii) operating a minimal number of switches, while at the same time respecting security constraints. As a consequence, the service restoration is a multiple objective problem, with some degree of conflict. The main methods developed for elaboration of ERP are based on evolutionary algorithms (EA). The limitation of the majority of these methods is the necessity of network simplifications to work with large-scale RDS. In general, these simplifications restrict the achievement of an adequate ERP. This work proposes the development and implementation of an algorithm for elaboration of ERP, which can deal with large-scale RDS without requiring network simplifications, that is, considering a large number (or all) of lines, buses, loads and switches of the system. The proposed algorithm is based on a multi-objective EA, on a new graph tree encoding called node-depth encoding (NDE), as well as on two genetic operators developed to efficiently manipulate a graph trees stored in NDEs. Using a multi-objective EA, the proposed algorithm enables a better exploration of the search space. On the other hand, using NDE and its operators, the efficiency of the search is increased when the proposed algorithm is used generating proper ERP, because those operators generate only radial configurations where all consumers are attended. The efficiency of the proposed algorithm is shown using a Brazilian distribution system with 3,860 buses, 635 switches, 3 substations and 23 feeders

Method for automatic determination of clades using community detection algorithm

Análises filogenéticas são bastante utilizadas para a compreensão das relações existentes entre objetos biológicos, beneficiando as investigações em vários campos das ciências da vida. Vários métodos computacionais para reconstruir filogenias tem sido desenvolvidos. Em geral, os métodos que fornecem filogenias mais confiáveis, requerem significativamente maior tempo computacional, restringindo a aplicação deles a conjuntos de dados relativamente pequenos. Por outro lado, a utilização de conjuntos de dados maiores é fundamental para proporcionar uma amostragem que seja suficiente, para restringir as incongruências na identificação de clados em uma filogenia. Este trabalho propõe uma abordagen (denominada CladeNet) de reamostragem de filogenias, obtidas por algoritmos relativamente eficientes, a fim de melhorar a identificação de clados. Experimentos com sete conjuntos de dados, que variam de dezenas a centenas de sequências de DNA mostram que, em geral, clados encontrados pela abordagem proposta tornam-se mais confiavéis, conforme os tamanhos dos conjuntos de sequências aumentam, com um moderado aumento do tempo computacional relativamente moderado. Além disso, o CladeNet é um método que também inova ao identificar clados de forma automáticamente por meio de um algoritmo de identificação de comunidades em redes.Phylogenies are useful for understanding relationships among biological objects, benefiting investigations in various fields of life sciences. Several computational methods for reconstructing phylogenies have been developed. In general, methods that provide more reliable phylogenies require significantly larger computing time, constraining their application to relatively small datasets of objects. On the other hand, the use of larger datasets is fundamental to provide enough samples in order to reduce incongruence in clade identification from a phylogeny. This work proposes an approach of resampling phylogenies (called CladeNet) obtained from relatively efficient algorithms, in order to improve clade identification. Experiments with seven datasets with sizes varying from dozens to hundreds of DNA sequences show that, in general, clades found by the proposed approach are more reliable as the dataset sizes augment, with relatively moderate increase of computing time. Moreover, CladeNet is a new method for identifying clades in an automatic way by means of community detection algorithm for networks

Surgical site infection after gastrointestinal surgery in children : an international, multicentre, prospective cohort study

Introduction Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings. Methods A multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI). Results Of 1159 children across 181 hospitals in 51 countries, 523 (45 center dot 1%) children were from high HDI, 397 (34 center dot 2%) from middle HDI and 239 (20 center dot 6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12 center dot 8% (51/397) in middle HDI and 24 center dot 7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI. Conclusion The odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.Peer reviewe