Spatial and management factors associated with exposure of smallholder dairy cattle in Tanzania to tick-borne pathogens

A cross-sectional study of serum antibody responses of cattle to tick-borne pathogens (Theileria parva, Theileria mutans, Anaplasma marginale, Babesia bigemina and Babesia bovis) was conducted on smallholder dairy farms in Tanga and Iringa Regions of Tanzania. Seroprevalence was highest for T. parva (48% in Iringa and 23% in Tanga) and B. bigemina (43% in Iringa and 27% in Tanga) and lowest for B. bovis (12% in Iringa and 6% in Tanga). We use spatial and non-spatial models, fitted using classical and Bayesian methods, to explore risk factors associated with seroprevalence. These include both fixed effects (age, grazing history and breeding status) and random effects (farm and local spatial effects). In both regions, seroprevalence for all tick-borne pathogens increased significantly with age. Animals pasture grazed in the 3 months prior to the start of the sampling period were significantly more likely to be seropositive for Theileria spp. and Babesia spp. Pasture grazed animals were more likely to be seropositive than zero-grazed animals for A. marginale, but the relationship was weaker than that observed for the other four pathogens. This study did not detect any significant differences in seroprevalence associated with other management-related variables, including the method or frequency of acaricide application. After adjusting for age, there was weak evidence of localised (< 5 km) spatial correlation in exposure to some of the tick borne diseases. However, this was small compared with the 'farm-effect', suggesting that risk factors specific to the farm were more important than those common to the local neighbourhood. Many animals were seropositive for more than one pathogen and the correlation between exposure to the different pathogens remained after adjusting for the identified risk factors. Identifying the determinants of exposure to multiple tick-borne pathogens and characterizing local variation in risk will assist in the development of more effective control strategies for smallholder dairy farms. (c) 2005 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Phylogeny, biogeography, and ecology of Ficus section Malvanthera (Moraceae)

We conducted the first molecular phylogenetic study of Ficus section Malvanthera (Moraceae; subgenus Urostigma) based on 32 Malvanthera accessions and seven outgroups representing other sections of Ficus subgenus Urostigma. We used DNA sequences from the nuclear ribosomal internal and external transcribed spacers (ITS and ETS), and the glyceraldehyde-3-phosphate dehydrogenase (G3pdh) region. Phylogenetic analysis using maximum parsimony, maximum likelihood and Bayesian methods recovered a monophyletic section Malvanthera to the exclusion of the rubber fig, Ficus elastica. The results of the phylogenetic analyses do not conform to any previously proposed taxonomic subdivision of the section and characters used for previous classification are homoplasious. Geographic distribution, however, is highly conserved and Melanesian Malvanthera are monophyletic. A new subdivision of section Malvanthera reflecting phylogenetic relationships is presented. Section Malvanthera likely diversified during a period of isolation in Australia and subsequently colonized New Guinea. Two Australian series are consistent with a pattern of dispersal out of rainforest habitat into drier habitats accompanied by a reduction in plant height during the transition from hemi-epiphytic trees to lithophytic trees and shrubs. In contradiction with a previous study of Pleistodontes phylogeny suggesting multiple changes in pollination behaviour, reconstruction of changes in pollination behaviour on Malvanthera, suggests only one or a few gains of active pollination within the section. (C) 2008 Elsevier Inc. All rights reserved.

A phylogenetic reappraisal of the Peltophorum group (Caesalpinieae: Leguminosae) based on the chloroplast trnL-F, rbcL and rps16 sequence data

The monophyly of the Peltophorum group, one of nine informal groups recognized by Polhill in the Caesalpinieae, was tested using sequence data from the trnL-F, rbcL, and rps16 regions of the chloroplast genome. Exemplars were included from all 16 genera of the Peltophorum group, and from 15 genera representing seven of the other eight informal groups in the tribe. The data were analyzed separately and in combined analyses using parsimony and Bayesian methods. The analysis method had little effect on the topology of well-supported relationships. The molecular data recovered a generally well-supported phylogeny with many intergeneric relationships resolved. Results show that the Peltophorum group as currently delimited is polyphyletic, but that eight genera plus one undescribed genus form a core Peltophorum group, which is referred to here as the Peltophorum group sensu stricto. These genera are Bussea, Conzattia, Colvillea, Delonix, Heteroflorum (inedit.), Lemuropisum, Parkinsonia, Peltophorum, and Schizolobium. The remaining eight genera of the Peltophorum group s.l. are distributed across the Caesalpinieae. Morphological support for the redelimited Peltophorum group and the other recovered clades was assessed, and no unique synapomorphy was found for the Peltophorum group s.s. A proposal for the reclassification of the Peltophorum group s.l. is presented.

Expressing medicine side effects: assessing the effectiveness of absolute risk, relative risk, and number needed to harm, and the provision of baseline risk information

Objective: To assess the effectiveness of absolute risk, relative risk, and number needed to harm formats for medicine side effects, with and without the provision of baseline risk information. Methods: A two factor, risk increase format (relative, absolute and NNH) x baseline (present/absent) between participants design was used. A sample of 268 women was given a scenario about increase in side effect risk with third generation oral contraceptives, and were required to answer written questions to assess their understanding, satisfaction, and likelihood of continuing to take the drug. Results: Provision of baseline information significantly improved risk estimates and increased satisfaction, although the estimates were still considerably higher than the actual risk. No differences between presentation formats were observed when baseline information was presented. Without baseline information, absolute risk led to the most accurate performance. Conclusion: The findings support the importance of informing people about baseline level of risk when describing risk increases. In contrast, they offer no support for using number needed to harm. Practice implications: Health professionals should provide baseline risk information when presenting information about risk increases or decreases. More research is needed before numbers needed to harm (or treat) should be given to members of the general populations. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Experimental and modeled UV erthemal irradiance under overcast conditions: the role of cloud optical depth

This paper evaluates the relationship between the cloud modification factor (CMF) in the ultraviolet erythe- mal range and the cloud optical depth (COD) retrieved from the Aerosol Robotic Network (AERONET) "cloud mode" algorithm under overcast cloudy conditions (confirmed with sky images) at Granada, Spain, mainly for non-precipitating, overcast and relatively homogenous water clouds. Empirical CMF showed a clear exponential dependence on experimental COD values, decreasing approximately from 0.7 for COD=10 to 0.25 for COD=50. In addition, these COD measurements were used as input in the LibRadtran radia tive transfer code allowing the simulation of CMF values for the selected overcast cases. The modeled CMF exhibited a dependence on COD similar to the empirical CMF, but modeled values present a strong underestimation with respect to the empirical factors (mean bias of 22 %). To explain this high bias, an exhaustive comparison between modeled and experimental UV erythemal irradiance (UVER) data was performed. The comparison revealed that the radiative transfer simulations were 8 % higher than the observations for clear-sky conditions. The rest of the bias (~14 %) may be attributed to the substantial underestimation of modeled UVER with respect to experimental UVER under overcast conditions, although the correlation between both dataset was high (R2 ~ 0.93). A sensitive test showed that the main reason responsible for that underestimation is the experimental AERONET COD used as input in the simulations, which has been retrieved from zenith radiances in the visible range. In this sense, effective COD in the erythemal interval were derived from an iteration procedure based on searching the best match between modeled and experimental UVER values for each selected overcast case. These effective COD values were smaller than AERONET COD data in about 80 % of the overcast cases with a mean relative difference of 22 %.

Cloud clearing techniques over land for land surface temperature retrieval from the Advanced Along Track Scanning Radiometer

We present five new cloud detection algorithms over land based on dynamic threshold or Bayesian techniques, applicable to the Advanced Along Track Scanning Radiometer (AATSR) instrument and compare these with the standard threshold based SADIST cloud detection scheme. We use a manually classified dataset as a reference to assess algorithm performance and quantify the impact of each cloud detection scheme on land surface temperature (LST) retrieval. The use of probabilistic Bayesian cloud detection methods improves algorithm true skill scores by 8-9 % over SADIST (maximum score of 77.93 % compared to 69.27 %). We present an assessment of the impact of imperfect cloud masking, in relation to the reference cloud mask, on the retrieved AATSR LST imposing a 2 K tolerance over a 3x3 pixel domain. We find an increase of 5-7 % in the observations falling within this tolerance when using Bayesian methods (maximum of 92.02 % compared to 85.69 %). We also demonstrate that the use of dynamic thresholds in the tests employed by SADIST can significantly improve performance, applicable to cloud-test data to provided by the Sea and Land Surface Temperature Radiometer (SLSTR) due to be launched on the Sentinel 3 mission (estimated 2014).

Taxonomic and Phylogenetic Relationships Between Species of the Genus Culex (Diptera: Culicidae) From Brazil Inferred From the Cytochrome c Oxidase I Mitochondrial Gene

Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

The toucan genus Ramphastos (Piciformes: Ramphastidae) has been a model in the formulation of Neotropical paleobiogeographic hypotheses. Weckstein (2005) reported on the phylogenetic history of this genus based on three mitochondrial genes, but some relationships were weakly supported and one of the subspecies of R. vitellinus (citreolaemus) was unsampled. This study expands on Weckstein (2005) by adding more DNA sequence data (including a nuclear marker) and more samples, including R v. citreolaemus. Maximum parsimony, maximum likelihood, and Bayesian methods recovered similar trees, with nodes showing high support. A monophyletic R. vitellinus complex was strongly supported as the sister-group to R. brevis. The results also confirmed that the southeastern and northern populations of R. vitellinus ariel are paraphyletic. X v. citreolaemus is sister to the Amazonian subspecies of the vitellinus complex. Using three protein-coding genes (COI, cytochrome-b and ND2) and interval-calibrated nodes under a Bayesian relaxed-clock framework, we infer that ramphastid genera originated in the middle Miocene to early Pliocene, Ramphastos species originated between late Miocene and early Pleistocene, and intra-specific divergences took place throughout the Pleistocene. Parsimony-based reconstruction of ancestral areas indicated that evolution of the four trans-Andean Ramphastos taxa (R. v. citreolaemus, R. a. swainsonii, R. brevis and R. sulfuratus) was associated with four independent dispersals from the cis-Andean region. The last pulse of Andean uplift may have been important for the evolution of R. sulfuratus, whereas the origin of the other trans-Andean Ramphastos taxa is consistent with vicariance due to drying events in the lowland forests north of the Andes. Estimated rates of molecular evolution were higher than the ""standard"" bird rate of 2% substitutions/site/million years for two of the three genes analyzed (cytochrome-b and ND2). (C) 2009 Elsevier Inc. All rights reserved.

On the influence of imputation in classification: practical issues

The substitution of missing values, also called imputation, is an important data preparation task for many domains. Ideally, the substitution of missing values should not insert biases into the dataset. This aspect has been usually assessed by some measures of the prediction capability of imputation methods. Such measures assume the simulation of missing entries for some attributes whose values are actually known. These artificially missing values are imputed and then compared with the original values. Although this evaluation is useful, it does not allow the influence of imputed values in the ultimate modelling task (e.g. in classification) to be inferred. We argue that imputation cannot be properly evaluated apart from the modelling task. Thus, alternative approaches are needed. This article elaborates on the influence of imputed values in classification. In particular, a practical procedure for estimating the inserted bias is described. As an additional contribution, we have used such a procedure to empirically illustrate the performance of three imputation methods (majority, naive Bayes and Bayesian networks) in three datasets. Three classifiers (decision tree, naive Bayes and nearest neighbours) have been used as modelling tools in our experiments. The achieved results illustrate a variety of situations that can take place in the data preparation practice.

Study of bulk matter properties through strange quark hadrons with the STAR experiment

Relativistic heavy ion collisions are the ideal experimental tool to explore the QCD phase diagram. Several results show that a very hot medium with a high energy density and partonic degrees of freedom is formed in these collisions, creating a new state of matter. Measurements of strange hadrons can bring important information about the bulk properties of such matter. The elliptic flow of strange hadrons such as phi, K(S)(0), Lambda, Xi and Omega shows that collectivity is developed at partonic level and at intermediate p(T) the quark coalescence is the dominant mechanism of hadronization. The nuclear modification factor is an another indicator of the presence of a very dense medium. The comparison between measurements of Au+Au and d+Au collisions, where only cold nuclear matter effects are expected, can shed more light on the bulk properties. In these proceedings, recent results from the STAR experiment on bulk matter properties are presented.

Inferential Implications of Over-Parametrization: A Case Study in Incomplete Categorical Data

P>In the context of either Bayesian or classical sensitivity analyses of over-parametrized models for incomplete categorical data, it is well known that prior-dependence on posterior inferences of nonidentifiable parameters or that too parsimonious over-parametrized models may lead to erroneous conclusions. Nevertheless, some authors either pay no attention to which parameters are nonidentifiable or do not appropriately account for possible prior-dependence. We review the literature on this topic and consider simple examples to emphasize that in both inferential frameworks, the subjective components can influence results in nontrivial ways, irrespectively of the sample size. Specifically, we show that prior distributions commonly regarded as slightly informative or noninformative may actually be too informative for nonidentifiable parameters, and that the choice of over-parametrized models may drastically impact the results, suggesting that a careful examination of their effects should be considered before drawing conclusions.Resume Que ce soit dans un cadre Bayesien ou classique, il est bien connu que la surparametrisation, dans les modeles pour donnees categorielles incompletes, peut conduire a des conclusions erronees. Cependant, certains auteurs persistent a negliger les problemes lies a la presence de parametres non identifies. Nous passons en revue la litterature dans ce domaine, et considerons quelques exemples surparametres simples dans lesquels les elements subjectifs influencent de facon non negligeable les resultats, independamment de la taille des echantillons. Plus precisement, nous montrons comment des a priori consideres comme peu ou non-informatifs peuvent se reveler extremement informatifs en ce qui concerne les parametres non identifies, et que le recours a des modeles surparametres peut avoir sur les conclusions finales un impact considerable. Ceci suggere un examen tres attentif de l`impact potentiel des a priori.

Genética do acamamento em trigo (Triticum aestivum L.) e a identificação do caráter para seleção

O problema do acamamento em trigo tem chamado a atenção dos melhoristas devido à severidade dos danos causados as plantas com reflexo no rendimento e na qualidade dos grãos. É um caráter difícil de ser estudado diretamente, dados a múltiplas interações com o ambiente. Muitos trabalhos foram desenvolvidos procurando identificar métodos para seleção indireta. A estatura de planta foi exaustivamente estudada por ser um caráter de alta herdabilidade e fortemente correlacionado com o acamamento; entretanto, plantas com estatura abaixo de 70 cm são inadequadas para o cultivo devido a sua pouca competitividade com as ervas daninhas e por apresentarem dificuldades para a colheita mecanizada. Neste sentido, no presente trabalho foram testados os vários caracteres relacionados com o acamamento e métodos indiretos que possibilitem maiores ganhos na seleção. Foi identificado o coeficiente de resistência do colmo, método internacionalmente conhecido com cLr, como sendo a metodologia mais eficiente para seleção indireta em populações segregantes. Foi também mensurada a dissimilaridade genética entre dez cultivares de trigo recomendadas para cultivo no Rio Grande do Sul e Santa Catarina, no ano 2000, e mais os genótipos IAC 5 e TB 951. A genética do caráter cLr foi estudada através da Análise de Gerações, metodologia também conhecida como Teste de Escala Conjunta. Foram avaliadas a natureza e a magnitude dos efeitos gênicos envolvidos o que ficou determinado que a aditividade e dominância atuam de maneira similar. Não foram encontrados efeitos epistáticos e a herdabilidade no sentido restrito foi de mediana a alta. O caráter cLr parece ser controlado por dois genes independentes com dois alelos cada, sendo que o genótipo duplamente recessivo (aabb) expressou fenotipicamente os valores mais altos para resistência ao acamamento.

Estudo de caso para ensino: “Errar é humano: um desafio na busca da segurança do paciente em unidade pública de saúde.”

A preocupação com a segurança do paciente, fator importante na dimensão da qualidade do cuidado de saúde, é, atualmente, um tema de grande relevância entre pesquisadores do todo o mundo. Os “erros” ocorrem em qualquer local onde se prestam cuidados de saúde e na maioria das situações são passíveis de medidas preventivas. O objetivo deste estudo de caso para ensino é desvelar, através de uma revisão bibliográfica, o debate em torno do tema da segurança do paciente a partir do século XXI, enfocando sua relevância enquanto problema global de saúde pública. Além disso, este estudo discorre sobre os desafios relacionados às lacunas e perspectivas neste tema e sua abordagem na realidade brasileira. Os resultados da análise sugerem que a investigação sobre a segurança do paciente apresenta falhas nas suas abordagens a serem melhor definidas e estabelecidas. Foram identificadas ainda, as barreiras, como grande demanda dos prontos-socorros das grandes cidades, o medo do profissional que cometeu o erro, adesão de todos os profissionais e dos gestores, e desafios para serem enfrentados, como o desenvolvimento de estratégias e ações políticas de saúde específicas, tanto para a pesquisa na área de saúde quanto para a literatura de saúde pública em gestão pública.

Estimação de parâmetros genéticos em caprinos leiteiros por meio de análise de regressão aleatória utilizando-se a Amostragem de Gibbs

Modelos de regressão aleatória foram utilizados neste estudo para estimar parâmetros genéticos da produção de leite no dia do controle (PLDC) em caprinos leiteiros da raça Alpina, por meio da metodologia Bayesiana. As estimativas geradas foram comparadas às obtidas com análise de regressão aleatória, utilizando-se o REML. As herdabilidades encontradas pela análise Bayesiana variaram de 0,18 a 0,37, enquanto, pelo REML, variaram de 0,09 a 0,32. As correlações genéticas entre dias de controle próximos se aproximaram da unidade, decrescendo gradualmente conforme a distância entre os dias de controle aumentou. Os resultados obtidos indicam que: a estrutura de covariâncias da PLDC em caprinos ao longo da lactação pode ser modelada adequadamente por meio da regressão aleatória; a predição de ganhos genéticos e a seleção de animais geneticamente superiores é viável ao longo de toda a trajetória da lactação; os resultados gerados pelas análises de regressão aleatória utilizando-se a Amostragem de Gibbs e o REML foram semelhantes, embora as estimativas das variâncias genéticas e das herdabilidades tenham sido levemente superiores na análise Bayesiana, utilizando-se a Amostragem de Gibbs.

Use of Poisson spatiotemporal regression models for the Brazilian Amazon Forest: malaria count data

INTRODUÇÃO: A malaria é uma doença endêmica na região da Amazônia Brasileira, e a detecção de possíveis fatores de risco pode ser de grande interesse às autoridades em saúde pública. O objetivo deste artigo é investigar a associação entre variáveis ambientais e os registros anuais de malária na região amazônica usando métodos bayesianos espaço-temporais. MÉTODOS: Utilizaram-se modelos de regressão espaço-temporais de Poisson para analisar os dados anuais de contagem de casos de malária entre os anos de 1999 a 2008, considerando a presença de alguns fatores como a taxa de desflorestamento. em uma abordagem bayesiana, as inferências foram obtidas por métodos Monte Carlo em cadeias de Markov (MCMC) que simularam amostras para a distribuição conjunta a posteriori de interesse. A discriminação de diferentes modelos também foi discutida. RESULTADOS: O modelo aqui proposto sugeriu que a taxa de desflorestamento, o número de habitants por km² e o índice de desenvolvimento humano (IDH) são importantes para a predição de casos de malária. CONCLUSÕES: É possível concluir que o desenvolvimento humano, o crescimento populacional, o desflorestamento e as alterações ecológicas associadas a estes fatores estão associados ao aumento do risco de malária. Pode-se ainda concluir que o uso de modelos de regressão de Poisson que capturam o efeito temporal e espacial em um enfoque bayesiano é uma boa estratégia para modelar dados de contagem de malária.