Logistic regression with Markov chains as covariates

The tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is an obvious carcinogen for lung cancer. Since CBMN (Cytokinesis-blocked micronucleus) has been found to be extremely sensitive to NNK-induced genetic damage, it is a potential important factor to predict the lung cancer risk. However, the association between lung cancer and NNK-induced genetic damage measured by CBMN assay has not been rigorously examined. ^ This research develops a methodology to model the chromosomal changes under NNK-induced genetic damage in a logistic regression framework in order to predict the occurrence of lung cancer. Since these chromosomal changes were usually not observed very long due to laboratory cost and time, a resampling technique was applied to generate the Markov chain of the normal and the damaged cell for each individual. A joint likelihood between the resampled Markov chains and the logistic regression model including transition probabilities of this chain as covariates was established. The Maximum likelihood estimation was applied to carry on the statistical test for comparison. The ability of this approach to increase discriminating power to predict lung cancer was compared to a baseline "non-genetic" model. ^ Our method offered an option to understand the association between the dynamic cell information and lung cancer. Our study indicated the extent of DNA damage/non-damage using the CBMN assay provides critical information that impacts public health studies of lung cancer risk. This novel statistical method could simultaneously estimate the process of DNA damage/non-damage and its relationship with lung cancer for each individual.^

Age -period -cohort analysis: An extension of Cox's lifetable regression with time -dependent covariates

It is well known that an identification problem exists in the analysis of age-period-cohort data because of the relationship among the three factors (date of birth + age at death = date of death). There are numerous suggestions about how to analyze the data. No one solution has been satisfactory. The purpose of this study is to provide another analytic method by extending the Cox's lifetable regression model with time-dependent covariates. The new approach contains the following features: (1) It is based on the conditional maximum likelihood procedure using a proportional hazard function described by Cox (1972), treating the age factor as the underlying hazard to estimate the parameters for the cohort and period factors. (2) The model is flexible so that both the cohort and period factors can be treated as dummy or continuous variables, and the parameter estimations can be obtained for numerous combinations of variables as in a regression analysis. (3) The model is applicable even when the time period is unequally spaced.^ Two specific models are considered to illustrate the new approach and applied to the U.S. prostate cancer data. We find that there are significant differences between all cohorts and there is a significant period effect for both whites and nonwhites. The underlying hazard increases exponentially with age indicating that old people have much higher risk than young people. A log transformation of relative risk shows that the prostate cancer risk declined in recent cohorts for both models. However, prostate cancer risk declined 5 cohorts (25 years) earlier for whites than for nonwhites under the period factor model (0 0 0 1 1 1 1). These latter results are similar to the previous study by Holford (1983).^ The new approach offers a general method to analyze the age-period-cohort data without using any arbitrary constraint in the model. ^

Model parameter

Interannual environmental variability in Peru is dominated by the El Niño Southern Oscillation (ENSO). The most dramatic changes are associated with the warm El Niño (EN) phase (opposite the cold La Niña phase), which disrupts the normal coastal upwelling and affects the dynamics of many coastal marine and terrestrial resources. This study presents a trophic model for Sechura Bay, located at the northern extension of the Peruvian upwelling system, where ENSO-induced environmental variability is most extreme. Using an initial steady-state model for the year 1996, we explore the dynamics of the ecosystem through the year 2003 (including the strong EN of 1997/98 and the weaker EN of 2002/03). Based on support from literature, we force biomass of several non-trophically-mediated 'drivers' (e.g. Scallops, Benthic detritivores, Octopus, and Littoral fish) to observe whether the fit between historical and simulated changes (by the trophic model) is improved. The results indicate that the Sechura Bay Ecosystem is a relatively inefficient system from a community energetics point of view, likely due to the periodic perturbations of ENSO. A combination of high system productivity and low trophic level target species of invertebrates (i.e. scallops) and fish (i.e. anchoveta) results in high catches and an efficient fishery. The importance of environmental drivers is suggested, given the relatively small improvements in the fit of the simulation with the addition of trophic drivers on remaining functional groups' dynamics. An additional multivariate regression model is presented for the scallop Argopecten purpuratus, which demonstrates a significant correlation between both spawning stock size and riverine discharge-mediated mortality on catch levels. These results are discussed in the context of the appropriateness of trophodynamic modeling in relatively open systems, and how management strategies may be focused given the highly environmentally influenced marine resources of the region.

Proposal of an Alternative Model for Speed-Flow Relationship in Two-Lane Highways

A research has been carried out in two-lanehighways in the Madrid Region to propose an alternativemodel for the speed-flowrelationship using regular loop data. The model is different in shape and, in some cases, slopes with respect to the contents of Highway Capacity Manual (HCM). A model is proposed for a mountainous area road, something for which the HCM does not provide explicitly a solution. The problem of a mountain road with high flows to access a popular recreational area is discussed, and some solutions are proposed. Up to 7 one-way sections of two-lanehighways have been selected, aiming at covering a significant number of different characteristics, to verify the proposed method the different classes of highways on which the Manual classifies them. In order to enunciate the model and to verify the basic variables of these types of roads a high number of data have been used. The counts were collected in the same way that the Madrid Region Highway Agency performs their counts. A total of 1.471 hours have been collected, in periods of 5 minutes. The models have been verified by means of specific statistical test (R2, T-Student, Durbin-Watson, ANOVA, etc.) and with the diagnostics of the contrast of assumptions (normality, linearity, homoscedasticity and independence). The model proposed for this type of highways with base conditions, can explain the different behaviors as traffic volumes increase, and follows a polynomial multiple regression model of order 3, S shaped. As secondary results of this research, the levels of service and the capacities of this road have been measured with the 2000 HCM methodology, and the results discussed. © 2011 Published by Elsevier Ltd.

Efficiency analysis of information technology and online social networks management : an integrated DEA-Model assessment

This paper analyses the relationship between productive efficiency and online-social-networks (OSN) in Spanish telecommunications firms. A data-envelopment-analysis (DEA) is used and several indicators of business ?social Media? activities are incorporated. A super-efficiency analysis and bootstrapping techniques are performed to increase the model?s robustness and accuracy. Then, a logistic regression model is applied to characterise factors and drivers of good performance in OSN. Results reveal the company?s ability to absorb and utilise OSNs as a key factor in improving the productive efficiency. This paper presents a model for assessing the strategic performance of the presence and activity in OSN.

Propuestas regulatorias para el diseño de un mercado ibérico a plazo eficiente de la energía = Regulatory proposals for the development of an efficient iberian energy forward market

El mercado ibérico de futuros de energía eléctrica gestionado por OMIP (“Operador do Mercado Ibérico de Energia, Pólo Português”, con sede en Lisboa), también conocido como el mercado ibérico de derivados de energía, comenzó a funcionar el 3 de julio de 2006. Se analiza la eficiencia de este mercado organizado, por lo que se estudia la precisión con la que sus precios de futuros predicen el precio de contado. En dicho mercado coexisten dos modos de negociación: el mercado continuo (modo por defecto) y la contratación mediante subasta. En la negociación en continuo, las órdenes anónimas de compra y de venta interactúan de manera inmediata e individual con órdenes contrarias, dando lugar a operaciones con un número indeterminado de precios para cada contrato. En la negociación a través de subasta, un precio único de equilibrio maximiza el volumen negociado, liquidándose todas las operaciones a ese precio. Adicionalmente, los miembros negociadores de OMIP pueden liquidar operaciones “Over-The-Counter” (OTC) a través de la cámara de compensación de OMIP (OMIClear). Las cinco mayores empresas españolas de distribución de energía eléctrica tenían la obligación de comprar electricidad hasta julio de 2009 en subastas en OMIP, para cubrir parte de sus suministros regulados. De igual manera, el suministrador de último recurso portugués mantuvo tal obligación hasta julio de 2010. Los precios de equilibrio de esas subastas no han resultado óptimos a efectos retributivos de tales suministros regulados dado que dichos precios tienden a situarse ligeramente sesgados al alza. La prima de riesgo ex-post, definida como la diferencia entre los precios a plazo y de contado en el periodo de entrega, se emplea para medir su eficiencia de precio. El mercado de contado, gestionado por OMIE (“Operador de Mercado Ibérico de la Energía”, conocido tradicionalmente como “OMEL”), tiene su sede en Madrid. Durante los dos primeros años del mercado de futuros, la prima de riesgo media tiende a resultar positiva, al igual que en otros mercados europeos de energía eléctrica y gas natural. En ese periodo, la prima de riesgo ex-post tiende a ser negativa en los mercados de petróleo y carbón. Los mercados de energía tienden a mostrar niveles limitados de eficiencia de mercado. La eficiencia de precio del mercado de futuros aumenta con el desarrollo de otros mecanismos coexistentes dentro del mercado ibérico de electricidad (conocido como “MIBEL”) –es decir, el mercado dominante OTC, las subastas de centrales virtuales de generación conocidas en España como Emisiones Primarias de Energía, y las subastas para cubrir parte de los suministros de último recurso conocidas en España como subastas CESUR– y con una mayor integración de los mercados regionales europeos de energía eléctrica. Se construye un modelo de regresión para analizar la evolución de los volúmenes negociados en el mercado continuo durante sus cuatro primeros años como una función de doce indicadores potenciales de liquidez. Los únicos indicadores significativos son los volúmenes negociados en las subastas obligatorias gestionadas por OMIP, los volúmenes negociados en el mercado OTC y los volúmenes OTC compensados por OMIClear. El número de creadores de mercado, la incorporación de agentes financieros y compañías de generación pertenecientes a grupos integrados con suministradores de último recurso, y los volúmenes OTC compensados por OMIClear muestran una fuerte correlación con los volúmenes negociados en el mercado continuo. La liquidez de OMIP está aún lejos de los niveles alcanzados por los mercados europeos más maduros (localizados en los países nórdicos (Nasdaq OMX Commodities) y Alemania (EEX)). El operador de mercado y su cámara de compensación podrían desarrollar acciones eficientes de marketing para atraer nuevos agentes activos en el mercado de contado (p.ej. industrias consumidoras intensivas de energía, suministradores, pequeños productores, compañías energéticas internacionales y empresas de energías renovables) y agentes financieros, captar volúmenes del opaco OTC, y mejorar el funcionamiento de los productos existentes aún no líquidos. Resultaría de gran utilidad para tales acciones un diálogo activo con todos los agentes (participantes en el mercado, operador de mercado de contado, y autoridades supervisoras). Durante sus primeros cinco años y medio, el mercado continuo presenta un crecimento de liquidez estable. Se mide el desempeño de sus funciones de cobertura mediante la ratio de posición neta obtenida al dividir la posición abierta final de un contrato de derivados mensual entre su volumen acumulado en la cámara de compensación. Los futuros carga base muestran la ratio más baja debido a su buena liquidez. Los futuros carga punta muestran una mayor ratio al producirse su menor liquidez a través de contadas subastas fijadas por regulación portuguesa. Las permutas carga base liquidadas en la cámara de compensación ubicada en Madrid –MEFF Power, activa desde el 21 de marzo de 2011– muestran inicialmente valores altos debido a bajos volúmenes registrados, dado que esta cámara se emplea principalmente para vencimientos pequeños (diario y semanal). Dicha ratio puede ser una poderosa herramienta de supervisión para los reguladores energéticos cuando accedan a todas las transacciones de derivados en virtud del Reglamento Europeo sobre Integridad y Transparencia de los Mercados de Energía (“REMIT”), en vigor desde el 28 de diciembre de 2011. La prima de riesgo ex-post tiende a ser positiva en todos los mecanismos (futuros en OMIP, mercado OTC y subastas CESUR) y disminuye debido a la curvas de aprendizaje y al efecto, desde el año 2011, del precio fijo para la retribución de la generación con carbón autóctono. Se realiza una comparativa con los costes a plazo de generación con gas natural (diferencial “clean spark spread”) obtenido como la diferencia entre el precio del futuro eléctrico y el coste a plazo de generación con ciclo combinado internalizando los costes de emisión de CO2. Los futuros eléctricos tienen una elevada correlación con los precios de gas europeos. Los diferenciales de contratos con vencimiento inmediato tienden a ser positivos. Los mayores diferenciales se dan para los contratos mensuales, seguidos de los trimestrales y anuales. Los generadores eléctricos con gas pueden maximizar beneficios con contratos de menor vencimiento. Los informes de monitorización por el operador de mercado que proporcionan transparencia post-operacional, el acceso a datos OTC por el regulador energético, y la valoración del riesgo regulatorio pueden contribuir a ganancias de eficiencia. Estas recomendaciones son también válidas para un potencial mercado ibérico de futuros de gas, una vez que el hub ibérico de gas –actualmente en fase de diseño, con reuniones mensuales de los agentes desde enero de 2013 en el grupo de trabajo liderado por el regulador energético español– esté operativo. El hub ibérico de gas proporcionará transparencia al atraer más agentes y mejorar la competencia, incrementando su eficiencia, dado que en el mercado OTC actual no se revela precio alguno de gas. ABSTRACT The Iberian Power Futures Market, managed by OMIP (“Operador do Mercado Ibérico de Energia, Pólo Português”, located in Lisbon), also known as the Iberian Energy Derivatives Market, started operations on 3 July 2006. The market efficiency, regarding how well the future price predicts the spot price, is analysed for this energy derivatives exchange. There are two trading modes coexisting within OMIP: the continuous market (default mode) and the call auction. In the continuous trading, anonymous buy and sell orders interact immediately and individually with opposite side orders, generating trades with an undetermined number of prices for each contract. In the call auction trading, a single price auction maximizes the traded volume, being all trades settled at the same price (equilibrium price). Additionally, OMIP trading members may settle Over-the-Counter (OTC) trades through OMIP clearing house (OMIClear). The five largest Spanish distribution companies have been obliged to purchase in auctions managed by OMIP until July 2009, in order to partly cover their portfolios of end users’ regulated supplies. Likewise, the Portuguese last resort supplier kept that obligation until July 2010. The auction equilibrium prices are not optimal for remuneration purposes of regulated supplies as such prices seem to be slightly upward biased. The ex-post forward risk premium, defined as the difference between the forward and spot prices in the delivery period, is used to measure its price efficiency. The spot market, managed by OMIE (Market Operator of the Iberian Energy Market, Spanish Pool, known traditionally as “OMEL”), is located in Madrid. During the first two years of the futures market, the average forward risk premium tends to be positive, as it occurs with other European power and natural gas markets. In that period, the ex-post forward risk premium tends to be negative in oil and coal markets. Energy markets tend to show limited levels of market efficiency. The price efficiency of the Iberian Power Futures Market improves with the market development of all the coexistent forward contracting mechanisms within the Iberian Electricity Market (known as “MIBEL”) – namely, the dominant OTC market, the Virtual Power Plant Auctions known in Spain as Energy Primary Emissions, and the auctions catering for part of the last resort supplies known in Spain as CESUR auctions – and with further integration of European Regional Electricity Markets. A regression model tracking the evolution of the traded volumes in the continuous market during its first four years is built as a function of twelve potential liquidity drivers. The only significant drivers are the traded volumes in OMIP compulsory auctions, the traded volumes in the OTC market, and the OTC cleared volumes by OMIClear. The amount of market makers, the enrolment of financial members and generation companies belonging to the integrated group of last resort suppliers, and the OTC cleared volume by OMIClear show strong correlation with the traded volumes in the continuous market. OMIP liquidity is still far from the levels reached by the most mature European markets (located in the Nordic countries (Nasdaq OMX Commodities) and Germany (EEX)). The market operator and its clearing house could develop efficient marketing actions to attract new entrants active in the spot market (e.g. energy intensive industries, suppliers, small producers, international energy companies and renewable generation companies) and financial agents as well as volumes from the opaque OTC market, and to improve the performance of existing illiquid products. An active dialogue with all the stakeholders (market participants, spot market operator, and supervisory authorities) will help to implement such actions. During its firs five and a half years, the continuous market shows steady liquidity growth. The hedging performance is measured through a net position ratio obtained from the final open interest of a month derivatives contract divided by its accumulated cleared volume. The base load futures in the Iberian energy derivatives exchange show the lowest ratios due to good liquidity. The peak futures show bigger ratios as their reduced liquidity is produced by auctions fixed by Portuguese regulation. The base load swaps settled in the clearing house located in Spain – MEFF Power, operating since 21 March 2011, with a new denomination (BME Clearing) since 9 September 2013 – show initially large values due to low registered volumes, as this clearing house is mainly used for short maturity (daily and weekly swaps). The net position ratio can be a powerful oversight tool for energy regulators when accessing to all the derivatives transactions as envisaged by European regulation on Energy Market Integrity and Transparency (“REMIT”), in force since 28 December 2011. The ex-post forward risk premium tends to be positive in all existing mechanisms (OMIP futures, OTC market and CESUR auctions) and diminishes due to the learning curve and the effect – since year 2011 – of the fixed price retributing the indigenous coal fired generation. Comparison with the forward generation costs from natural gas (“clean spark spread”) – obtained as the difference between the power futures price and the forward generation cost with a gas fired combined cycle plant taking into account the CO2 emission rates – is also performed. The power futures are strongly correlated with European gas prices. The clean spark spreads built with prompt contracts tend to be positive. The biggest clean spark spreads are for the month contract, followed by the quarter contract and then by the year contract. Therefore, gas fired generation companies can maximize profits trading with contracts of shorter maturity. Market monitoring reports by the market operator providing post-trade transparency, OTC data access by the energy regulator, and assessment of the regulatory risk can contribute to efficiency gains. The same recommendations are also valid for a potential Iberian gas futures market, once an Iberian gas hub – currently in a design phase, with monthly meetings amongst the stakeholders in a Working Group led by the Spanish energy regulatory authority since January 2013 – is operating. The Iberian gas hub would bring transparency attracting more shippers and improving competition and thus its efficiency, as no gas price is currently disclosed in the existing OTC market.

Bayesian model selection methodology for road safety

Road accidents are a very relevant issue in many countries and macroeconomic models are very frequently applied by academia and administrations to reduce their frequency and consequences. The selection of explanatory variables and response transformation parameter within the Bayesian framework for the selection of the set of explanatory variables a TIM and 3IM (two input and three input models) procedures are proposed. The procedure also uses the DIC and pseudo -R2 goodness of fit criteria. The model to which the methodology is applied is a dynamic regression model with Box-Cox transformation (BCT) for the explanatory variables and autorgressive (AR) structure for the response. The initial set of 22 explanatory variables are identified. The effects of these factors on the fatal accident frequency in Spain, during 2000-2012, are estimated. The dependent variable is constructed considering the stochastic trend component.

Análise genética da produção in vitro de embriões em bovinos Guzerá

O objetivo dessa pesquisa foi avaliar aspectos genéticos que relacionados à produção in vitro de embriões na raça Guzerá. O primeiro estudo focou na estimação de (co) variâncias genéticas e fenotípicas em características relacionadas a produção de embriões e na detecção de possível associação com a idade ao primeiro parto (AFC). Foi detectada baixa e média herdabilidade para características relacionadas à produção de oócitos e embriões. Houve fraca associação genética entre características ligadas a reprodução artificial e a idade ao primeiro parto. O segundo estudo avaliou tendências genéticas e de endogamia em uma população Guzerá no Brasil. Doadoras e embriões produzidos in vitro foram considerados como duas subpopulações de forma a realizar comparações acerca das diferenças de variação anual genética e do coeficiente de endogamia. A tendência anual do coeficiente de endogamia (F) foi superior para a população geral, sendo detectado efeito quadrático. No entanto, a média de F para a sub- população de embriões foi maior do que na população geral e das doadoras. Foi observado ganho genético anual superior para a idade ao primeiro parto e para a produção de leite (305 dias) entre embriões produzidos in vitro do que entre doadoras ou entre a população geral. O terceiro estudo examinou os efeitos do coeficiente de endogamia da doadora, do reprodutor (usado na fertilização in vitro) e dos embriões sobre resultados de produção in vitro de embriões na raça Guzerá. Foi detectado efeito da endogamia da doadora e dos embriões sobre as características estudadas. O quarto (e último) estudo foi elaborado para comparar a adequação de modelos mistos lineares e generalizados sob método de Máxima Verossimilhança Restrita (REML) e sua adequação a variáveis discretas. Quatro modelos hierárquicos assumindo diferentes distribuições para dados de contagem encontrados no banco. Inferência foi realizada com base em diagnósticos de resíduo e comparação de razões entre componentes de variância para os modelos em cada variável. Modelos Poisson superaram tanto o modelo linear (com e sem transformação da variável) quanto binomial negativo à qualidade do ajuste e capacidade preditiva, apesar de claras diferenças observadas na distribuição das variáveis. Entre os modelos testados, a pior qualidade de ajuste foi obtida para o modelo linear mediante transformação logarítmica (Log10 X +1) da variável resposta.

Relação espacial dos óbitos e internações por tuberculose com indicadores sociais em Ribeirão Preto (SP)

Objetivo: Propôs-se analisar a relação espacial dos óbitos e internações evitáveis por TB com indicadores sociais em Ribeirão Preto/SP. Métodos: Trata-se de um estudo ecológico em que foram considerados os casos de óbitos e internações, tendo como causa básica do óbito e motivo principal da internação, a tuberculose (CID A15.0 a A19.9), ocorridos na zona urbana de Ribeirão Preto e registrados respectivamente no Sistema de Informação sobre Mortalidade e no Sistema de Internação Hospitalar do Sistema Único de Saúde no período de 2006 a 2012. Foi realizada a análise univariada das variáveis sociodemográficas e operacionais dos casos investigados. Para construção dos indicadores sociais utilizou-se a análise de componentes principais, sendo selecionados dados das áreas de abrangência do município, considerando os dados do Censo Demográfico de 2010. A geocodificação dos casos foi processada no TerraView versão 4.2.2. Recorreu-se à regressão linear múltipla, pelo método dos mínimos quadrados e à regressão espacial para análise da relação de dependência espacial entre os indicadores sociais e as taxas de mortalidade e de internações por TB. A autocorrelação nos resíduos da regressão linear múltipla foi testada por meio do Teste Global de Moran, as análises foram realizadas considerando os softwares Arcgis-versão 10.1, Statistica versão 12.0, OpenGeoDa versão 1.0 e R versão 3.2.3. Para o diagnóstico do melhor modelo de regressão espacial, utilizou-se o teste Multiplicador de Lagrange. Em todos os testes, foi fixado o nivel de significancia de alfa em 5% (p< 0,05). Resultados: Foram registrados 50 casos de óbitos e 196 casos de internações por TB. A maioria dos casos registrados em ambos os sistemas se deu em pessoas do sexo masculino (n=41; 82%/n=146; 74,5%) e com a forma clínica pulmonar (n=44; 80,0%/n=138; 67,9%). Na construção dos indicadores sociais, três novas variáveis surgiram, apresentando respectivamente variância total de 46,2%, 18,7% e 14,6% sendo denominadas como indicadores de renda, desigualdade social e equidade social. Na modelagem para verificar relação espacial entre os óbitos e os indicadores sociais observou-se que a equidade social foi indicador estatisticamente significativo (p=0,0013) com relação negativa a mortalidade, sendo o Modelo da Defasagem Espacial o melhor método para testar a dependência espacial, com valor de ? (rho) estimado em 0,53 e altamente significativo (p=0,0014). Já na modelagem da relação espacial entre as internações por tuberculose e os indicadores sociais, o indicador de renda apresentou-se estatisticamente significativo (p=0,015) com relação negativa a internação e o melhor método para testar a dependência espacial também foi o Modelo da Defasagem Espacial com valor de ? (rho) estimado em 0,80 e altamente significativo (p<0,0001). Conclusão: O estudo contribuiu no avanço do conhecimento de que a mortalidade e as internações por tuberculose são eventos socialmente determinados, o que sugere investimento por parte da gestão

Determinant factors of senior tourists’ length of stay

The current tendency to undertake more trips, but of shorter duration, throughout the year, has meant that the tourist industry has started to show greater interest in attracting those market segments that opt for more prolonged stays, as they are especially profitable. One of these segments is that of seniors. Given the aging demographic of the population worldwide, which is particularly noticeable in Spain, the object of this study is to identify the variables that determine the length of stay of Spanish seniors at their destination. The Negative Binomial model was adapted to the context of length of stay by Spanish seniors and the determinant factors identified were: age, travel purpose, climate, type of accommodation, group size, trip type and the activities carried out at the destination. This study is a contribution to this field from an empirical point of view, given the scarcity of studies of this type and their eminently descriptive character; as well as from a practical level, with interesting implications for the sector.

WGTTEST: Stata module to test the impact of sampling weights in regression analysis

wgttest performs a test proposed by DuMouchel and Duncan (1983) to evaluate whether the weighted and unweighted estimates of a regression model are significantly different.

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study.

BACKGROUND Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis. However, detailed information about the microbial composition of the respiratory tract in infants with this disorder is scarce. We aimed to undertake longitudinal in-depth characterisation of the upper respiratory tract microbiota in infants with cystic fibrosis during the first year of life. METHODS We did this prospective cohort study at seven cystic fibrosis centres in Switzerland. Between Feb 1, 2011, and May 31, 2014, we enrolled 30 infants with a diagnosis of cystic fibrosis. Microbiota characterisation was done with 16S rRNA gene pyrosequencing and oligotyping of nasal swabs collected every 2 weeks from the infants with cystic fibrosis. We compared these data with data for an age-matched cohort of 47 healthy infants. We additionally investigated the effect of antibiotic treatment on the microbiota of infants with cystic fibrosis. Statistical methods included regression analyses with a multivariable multilevel linear model with random effects to correct for clustering on the individual level. FINDINGS We analysed 461 nasal swabs taken from the infants with cystic fibrosis; the cohort of healthy infants comprised 872 samples. The microbiota of infants with cystic fibrosis differed compositionally from that of healthy infants (p=0·001). This difference was also found in exclusively antibiotic-naive samples (p=0·001). The disordering was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae in infants with cystic fibrosis compared with healthy infants (multivariable linear regression model stratified by age and adjusted for season; second month: coefficient 16·2 [95% CI 0·6-31·9]; p=0·04; third month: 17·9 [3·3-32·5]; p=0·02; fourth month: 21·1 [7·8-34·3]; p=0·002). Oligotyping analysis enabled differentiation between Staphylococcus aureus and coagulase-negative Staphylococci. Whereas the analysis showed a decrease in S aureus at and after antibiotic treatment, coagulase-negative Staphylococci increased. INTERPRETATION Our study describes compositional differences in the microbiota of infants with cystic fibrosis compared with healthy controls, and disordering of the microbiota on antibiotic administration. Besides S aureus, coagulase-negative Staphylococci also contributed to the disordering identified in these infants. These findings are clinically important in view of the crucial role that bacterial pathogens have in the disease progression of cystic fibrosis in early life. Our findings could be used to inform future studies of the effect of antibiotic treatment on the microbiota in infants with cystic fibrosis, and could assist in the prevention of early disease progression in infants with this disorder. FUNDING Swiss National Science Foundation, Fondation Botnar, the Swiss Society for Cystic Fibrosis, and the Swiss Lung Association Bern.

Transmission dynamics of the Echinococcus granulosus sheep-dog strain (G1 genotype) in camels in Tunisia

Cystic echinococcosis, caused by Echinococcus grantilosus, is highly endemic in North Africa and the Middle East. This paper examines the abundance and prevalence of infection of E. granulosus in camels in Tunisia. No cysts were found in 103 camels from Kebili, whilst 19 of 188 camels from Benguerden (10.1%) were infected. Of the cysts found 95% were considered fertile with the presence of protoscolices and 80% of protoscolices were considered viable by their ability to exclude aqueous eosin. Molecular techniques were used on cyst material from camels and this demonstrated that the study animals were infected with the G1 sheep strain of E. granulosus. Observed data were fitted to a mathematical model by maximum likelihood techniques to define the parameters and their confidence limits and the negative binomial distribution was used to define the error variance in the observed data. The infection pressure to camels was somewhat lower in comparison to sheep reported in an earlier study. However, because camels are much longer-lived animals, the results of the model fit suggested that older camels have a relatively high prevalence rate, reaching a most likely value of 32% at age 15 years. This could represent an important source of transmission to dogs and hence indirectly to man of this zonotic strain. In common with similar studies on other species, there was no evidence of parasite-induced immunity in camels. (C) 2004 Elsevier B.V. All rights reserved.

Determinants of exercise capacity in patients with type 2 diabetes

OBJECTIVE - Type 2 diabetes is associated with reduced exercise capacity, but the cause of this association is unclear. We sought the associations of impaired exercise capacity in type 2 diabetes. RESEARCH DESIGN AND METHODS - Subclinical left ventricular (LV) dysfunction was sought from myocardial strain rate and the basal segmental diastolic velocity (Em) of each wall in 170 patients with type 2 diabetes (aged 56 +/- 10 years, 91 men), good quality echocardiographic images, and negative exercise echocardiograms. The same measurements were made in 56 control subjects (aged 53 +/- 10 years, 29 men). Exercise capacity was calculated in metabolic equivalents, and heart rate recovery (HRR) was measured as the heart rate difference between peak and 1 min after exercise. In subjects with type 2 diabetes, exercise capacity was correlated with clinical, therapeutic, biochemical, and echocardiographic variables, and significant independent associations were sought using a multiple linear regression model. RESULTS - Exercise capacity, strain rate, Em, and HRR were significantly reduced in type 2 diabetes. Exercise capacity was associated with age (r- = -0.37, P < 0.001), male sex (r = 0.26, P = 0.001), BMI (r = -0.19, P = 0.012), HbA(1c) (AlC; r = -0.22, P = 0.009), Em (r = 0.43, P < 0.001), HRR (r = 0.42, P < 0.001), diabetes duration (r = -0.18, P = 0.021), and hypertension history (r = -0.28, P < 0.001). Age (P < 0.001), male sex (P = 0.007), BMI (P = 0.001), Em (P = 0.032), HRR (P = 0.013), and AlC (P = 0.0007) were independent predictors of exercise capacity. CONCLUSIONS - Reduced exercise capacity in patients with type 2 diabetes is associated with diabetes control, subclinical LV dysfunction, and impaired HRR.

Multi-level zero-inflated Poisson regression modelling of correlated count data with excess zeros

Count data with excess zeros relative to a Poisson distribution are common in many biomedical applications. A popular approach to the analysis of such data is to use a zero-inflated Poisson (ZIP) regression model. Often, because of the hierarchical Study design or the data collection procedure, zero-inflation and lack of independence may occur simultaneously, which tender the standard ZIP model inadequate. To account for the preponderance of zero counts and the inherent correlation of observations, a class of multi-level ZIP regression model with random effects is presented. Model fitting is facilitated using an expectation-maximization algorithm, whereas variance components are estimated via residual maximum likelihood estimating equations. A score test for zero-inflation is also presented. The multi-level ZIP model is then generalized to cope with a more complex correlation structure. Application to the analysis of correlated count data from a longitudinal infant feeding study illustrates the usefulness of the approach.