Review of Applied Spatial Data Analysis with R by R. S. Bivand, E. J. Pebesma, and V. Gomez-Rubio

Most authors struggle to pick a title that adequately conveys all of the material covered in a book. When I first saw Applied Spatial Data Analysis with R, I expected a review of spatial statistical models and their applications in packages (libraries) from the CRAN site of R. The authors’ title is not misleading, but I was very pleasantly surprised by how deep the word “applied” is here. The first half of the book essentially covers how R handles spatial data. To some statisticians this may be boring. Do you want, or need, to know the difference between S3 and S4 classes, how spatial objects in R are organized, and how various methods work on the spatial objects? A few years ago I would have said “no,” especially to the “want” part. Just let me slap my EXCEL spreadsheet into R and run some spatial functions on it. Unfortunately, the world is not so simple, and ultimately we want to minimize effort to get all of our spatial analyses accomplished. The first half of this book certainly convinced me that some extra effort in organizing my data into certain spatial class structures makes the analysis easier and less subject to mistakes. I also admit that I found it very interesting and I learned a lot.

Tests of the Dynamic Field Theory and the Spatial Precision Hypothesis: Capturing a Qualitative Developmental Transition in Spatial Working Memory

This study tested a dynamic field theory (DFT) of spatial working memory and an associated spatial precision hypothesis (SPH). Between 3 and 6 years of age, there is a qualitative shift in how children use reference axes to remember locations: 3-year-olds’ spatial recall responses are biased toward reference axes after short memory delays, whereas 6-year-olds’ responses are biased away from reference axes. According to the DFT and the SPH, quantitative improvements over development in the precision of excitatory and inhibitory working memory processes lead to this qualitative shift. Simulations of the DFT in Experiment 1 predict that improvements in precision should cause the spatial range of targets attracted toward a reference axis to narrow gradually over development, with repulsion emerging and gradually increasing until responses to most targets show biases away from the axis. Results from Experiment 2 with 3- to 5-year-olds support these predictions. Simulations of the DFT in Experiment 3 quantitatively fit the empirical results and offer insights into the neural processes underlying this developmental change.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Cross-cultural adaptation and assessment of the reliability and validity of the Core Outcome Measures Index (COMI) for the Brazilian-Portuguese language

The use of patient-orientated questionnaires is of utmost importance in assessing the outcome of spine surgery. Standardisation, using a common set of outcome measures, is essential to aid comparisons across studies/in registries. The Core Outcome Measures Index (COMI) is a short, multidimensional outcome instrument validated for patients with spinal disorders. This study aimed to produce a Brazilian-Portuguese version of the COMI. A cross-cultural adaptation of the COMI into Brazilian-Portuguese was carried out using established guidelines. 104 outpatients with chronic LBP (> 3 months) were recruited from a Public Health Spine Medical Care Centre. They completed a questionnaire booklet containing the newly translated COMI, and other validated symptom-specific questionnaires: Oswestry Disability Index (ODI) and Roland Morris disability scale (RM), and a pain visual analogue scale. All patients completed a second questionnaire within 7-10 days to assess reproducibility. The COMI summary score displayed minimal floor and ceiling effects. On re-test, the responses for each individual domain of the COMI were within 1 category in 98% patients for the domain 'function', 96% for 'symptom-specific well-being', 97% for 'general quality of life', 99% for 'social disability' and 100% for 'work disability'. The intraclass correlation coefficients (ICC2,1) for COMI pain and COMI summary scores were 0.91-0.96, which compared favourably with the corresponding values for the RM (ICC, 0.99) and ODI (ICC, 0.98). The standard error of measurement for the COMI was 0.6, giving a "minimum detectable change" (MDC95%) of approximately 1.7 points i.e., the minimum change to be considered "real change" beyond measurement error. The COMI scores correlated as hypothesised (Rho, 0.4-0.8) with the other symptom-specific questionnaires. The reproducibility of the Brazilian-Portuguese version of the COMI was comparable to that of other language versions. The COMI scores correlated in the expected manner with existing but longer symptom-specific questionnaires suggesting good convergent validity for the COMI. The Brazilian-Portuguese COMI represents a valuable tool for Brazilian study-centres in future multicentre clinical studies and surgical registries.

A Spatial Propensity Score Matching Evaluation of the Social Impacts of Sugarcane Growing on Municipalities in Brazil

The expansion of sugarcane growing in Brazil, spurred particularly by increased demand for ethanol, has triggered the need to evaluate the economic, social, and environmental impacts of this process, both on the country as a whole and on the growing regions. Even though the balance of costs and benefits is positive from an overall standpoint, this may not be so in specific producing regions, due to negative externalities. The objective of this paper is to estimate the effect of growing sugarcane on the human development index (HDI) and its sub-indices in cane producing regions. In the literature on matching effects, this is interpreted as the effect of the treatment on the treated. Location effects are controlled by spatial econometric techniques, giving rise to the spatial propensity score matching model. The authors analyze 424 minimum comparable areas (MCAs) in the treatment group, compared with 907 MCAs in the control group. The results suggest that the presence of sugarcane growing in these areas is not relevant to determine their social conditions, whether for better or worse. It is thus likely that public policies, especially those focused directly on improving education, health, and income generation/distribution, have much more noticeable effects on the municipal HDI.

Nanostructures on spin-coated polymer films controlled by solvent composition and polymer molecular weight

In this study we systematically investigated how the solvent composition used for polymer dissolution affects the porous structures of spin-coated polymers films. Cellulose acetate butyrate (CAB) and poly(methylmethacrylate) with low(PMMA-L) and high (PMMA-H) molecular weights were dissolved in mixtures of acetone (AC) and ethyl acetate (EA) at constant polymer concentration of 10 g/L The films were spin-coated at a relative air humidity of 55+/-5%, their thickness and index of refraction were determined by means of ellipsometry and their morphology was analyzed by atomic force microscopy. The dimensions and frequency of nanocavities on polymer films increased with the acetone content (phi(AC)) in the solvent mixture and decreased with increasing polymer molecular weight. Consequently, as the void content increased in the films, their apparent thicknesses increased and their indices of refraction decreased, creating low-cost anti-reflection surface. The void depth was larger for PMMA-L than for CAB. This effect was attributed to different activities of EA and AC in CAB or PMMA-L solution, the larger mobility of chains and the lower polarity of PMMA-L in comparison to CAB. (C) 2012 Elsevier B. V. All rights reserved.

Tráfego veicular e mortalidade por doenças do aparelho circulatório em homens adultos

OBJETIVO: Analisar a associação entre indicadores de exposição à poluição por tráfego veicular e mortalidade por doenças do aparelho circulatório em homens adultos. MÉTODOS: Foram analisadas informações sobre vias e volume de tráfego no ano de 2007 fornecidas pela companhia de engenharia de tráfego local. Mortalidade por doenças do aparelho circulatório no ano de 2005 entre homens ≥ 40 anos foram obtidas do registro de mortalidade do Programa de Aprimoramento de Informações de Mortalidade do Município de São Paulo, SP. Dados socioeconômicos do Censo 2000 e informações sobre a localização dos serviços de saúde também foram coletados. A exposição foi avaliada pela densidade de vias e volume de tráfego para cada distrito administrativo. Foi calculada regressão (α = 5%) entre esses indicadores de exposição e as taxas de mortalidade padronizadas, ajustando os modelos para variáveis socioeconômicas, número de serviços de saúde nos distritos e autocorrelação espacial. RESULTADOS: A correlação entre densidade de vias e volume de tráfego foi modesta (r² = 0,28). Os distritos do centro apresentaram os maiores valores de densidade de vias. O modelo de regressão espacial de densidade de vias indicou associação com mortalidade por doenças do aparelho circulatório (p = 0,017). Não se observou associação no modelo de volume de tráfego. Em ambos os modelos – vias e volume de tráfego (veículos leves/pesados) – a variável socioeconômica foi estatisticamente signifi cante. CONCLUSÕES: A associação entre mortalidade por doenças do aparelho circulatório e densidade de vias converge com a literatura e encoraja a realização de mais estudos epidemiológicos em nível individual e com métodos mais acurados de avaliação da exposição.

Influence of treatment with intranasal corticosteroids on the nasal mucosa, weight, and corticosteroid concentration in rats

Background: The effect of intranasal corticosteroids on the nasal epithelium mucosa is an important parameter of treatment safety. This study was designed to examine whether treatment with topical corticosteroids in patients with allergic rhinitis causes atrophic nasal mucosal changes, when compared with systemic corticosteroids, in rats. Methods: Male Wistar rats were treated daily during 7 weeks with topical administration with 10 microliters of normal saline (control group), 10 microliters of mometasone furoate group, 10 microliters of triamcinolone acetonide (T group), and 8 mg/kg of daily subcutaneous injections of methylprednisolone sodium succinate (MP group). Body weight was evaluated weekly. At the end of the treatment, rats were killed by decapitation to collect blood for determination of corticosterone levels and nasal cavities were prepared for histological descriptive analyses. Results: Treatment with T and MP decreased body weight. Plasma corticosterone concentration was significantly reduced by MP treatment and presented a clear tendency to decrease after T treatment. Histological changes observed in group T included ripples, cell vacuolization, increase in the number of nuclei, and decrease in the number of cilia in the epithelial cells. Conclusion: Growth and corticosterone concentration were impaired by T and MP at the same proportion, suggesting a role of this hormone in body gain. With the exception of T, intranasal or systemic treatment with the corticosteroids evaluated in this study did not affect nasal mucosa. (Am J Rhinol Allergy 26, e46-e49, 2012; doi: 10.2500/ajra.2012.26.3702)

Evaluation of the Concentration of Nonessential and Essential Elements in Chicken, Pork, and Beef Samples Produced in Brazil

Food safety is a global concern. Meat represents the most important protein source for humans. Thus, contamination of meat products by nonessential elements is a ready source of human exposure. In addition, knowledge of the concentration of essential elements is also relevant with respect to human nutrition. The aim of the present study was to determine the concentration of 17 elements in pork, beef, and chicken produced in Brazil. Meat samples were analyzed by inductively coupled plasma mass spectrometry. The estimated daily intake for nonessential elements including arsenic (As), cadmium (Cd), lead (Pb), mercury (Hg), and antimony (Sb) through meat consumption is below the toxicological reference values. However, high levels were detected for the nonessential element cesium (Cs), mainly in beef samples, an observation that deserves future studies to identify the source of contamination and potential adverse consequences.

Influence diagnostics in Gaussian spatial linear models

Spatial linear models have been applied in numerous fields such as agriculture, geoscience and environmental sciences, among many others. Spatial dependence structure modelling, using a geostatistical approach, is an indispensable tool to estimate the parameters that define this structure. However, this estimation may be greatly affected by the presence of atypical observations in the sampled data. The purpose of this paper is to use diagnostic techniques to assess the sensitivity of the maximum-likelihood estimators, covariance functions and linear predictor to small perturbations in the data and/or the spatial linear model assumptions. The methodology is illustrated with two real data sets. The results allowed us to conclude that the presence of atypical values in the sample data have a strong influence on thematic maps, changing the spatial dependence structure.

Evaluation of cytotoxic, genotoxic and antigenotoxic potential of Solanum lycocarpum fruits glicoalkaloid extract in V79 cells

Solanum lycocarpum St.-Hil (Solanaceae) is a hairy shrub or small much-branched tree of the Brazilian Cerrado, popularly known as "fruit-of-wolf". Considering that the induction of chromosomal mutations is involved in the process of carcinogenesis, and that S. lycocatpum is often used in folk medicine, it becomes relevant to study its effect on genetic material. In this sense, the aim of present study was to determine the possible cytotoxic, genotoxic and antigenotoxic potentials of S. lycocarpum fruits glycoalkaloid extract (SL) in Chinese hamster lung fibroblasts (V79 cells). The cytotoxicity was evaluated by the colony forming assay, apoptosis and necrosis assay. Trypan blue exclusion dye method and mitotic index. Genotoxic and antigenotoxic potential were evaluated by comet and chromosomal aberrations assays. Four concentrations of SL (4, 8, 16 and 32 mu g/mL) were used for the evaluation of its genotoxic potential. The DNA damage-inducing agent methyl methanesulfonate (MMS, 221 mu g/mL) was utilized in combination with extract to evaluate a possible protective effect. The results showed that SL was cytotoxic at concentrations above 32 mu g/mL by the colony forming assay. For apoptosis and necrosis assay, the concentration of 64 mu g/mL of SL showed statistically significant increase in cell death by apoptosis and necrosis, while the concentrations of 128 and 256 mu g/mL of SL demonstrated statistically significant increase in cell death by necrosis, compared with the control group. Analysis of cell viability by Trypan blue exclusion indicated >96% viability for treatments with concentrations up to 32 mu g/mL of SL No significant differences in MI were observed between cultures treated with different concentrations of 51 (4, 8, 16 and 32 mu g/mL) alone or in combination with MMS and the negative control, indicating that these treatments were not cytotoxic. The comet and chromosomal aberrations assays revealed that SL does not display genotoxic activity. Moreover, the different concentrations of SL showed protective effect against both genomic and chromosomal damages induced by MMS. (C) 2012 Elsevier Ltd. All rights reserved.

Cesarean section and increased body mass index in school children: two cohort studies from distinct socioeconomic background areas in Brazil

Abstract Background Recent studies have raised controversy regarding the association between cesarean section and later obesity in the offspring. The purpose of this study was to assess the association of cesarean section with increased body mass index (BMI) and obesity in school children from two Brazilian cities with distinct socioeconomic backgrounds. Methods Two birth cohorts respectively born in 1994 in Ribeirao Preto, a wealthy city in Southeast, and in 1997/98 in Sao Luis, a less wealthy city in Northeast of Brasil, were evaluated. After birth, 2,846 pairs of mothers-newborns were evaluated in Ribeirao Preto and 2,542 in Sao Luis. In 2004/05, 790 children aged 10/11 years were randomly reassessed in Ribeirao Preto and 673 at 7/9 years in Sao Luis. Information on type of delivery, maternal and child characteristics, socioeconomic position and anthropometric measurements were collected after birth and at school age. Obesity was defined as BMI ≥ 95th percentile at school age. Results Obesity rate was 13.0% in Ribeirao Preto and 2.1% in Sao Luis. Cesarean section was associated with obesity and remained significant after adjustment only in Ribeirao Preto [OR = 1.74 (95% CI: 1.04; 2.92)]. The association between cesarean section and BMI remained significant after adjustment for maternal schooling, maternal smoking during pregnancy, duration of breastfeeding, gender, birth weight and gestational age, type of school and, only in Sao Luis, pre-pregnancy maternal weight. In Ribeirao Preto children born by cesarean section had BMI 0.31 kg/m2 (95%CI: 0.11; 0.51) higher than those born by vaginal delivery. In Sao Luis BMI of children born by cesarean section was 0.28 kg/m2 higher (95%CI: 0.08; 0.49) than those born by vaginal delivery. Conclusion A positive association between cesarean section and increased BMI z-score was demonstrated in areas with different socioeconomic status in a middle-income country.

Inequalities in mortality of men by oral and pharyngeal cancer in Barcelona, Spain and São Paulo, Brazil, 1995–2003

Abstract Background Large inequalities of mortality by most cancers in general, by mouth and pharynx cancer in particular, have been associated to behaviour and geopolitical factors. The assessment of socioeconomic covariates of cancer mortality may be relevant to a full comprehension of distal determinants of the disease, and to appraise opportune interventions. The objective of this study was to compare socioeconomic inequalities in male mortality by oral and pharyngeal cancer in two major cities of Europe and South America. Methods The official system of information on mortality provided data on deaths in each city; general censuses informed population data. Age-adjusted death rates by oral and pharyngeal cancer for men were independently assessed for neighbourhoods of Barcelona, Spain, and São Paulo, Brazil, from 1995 to 2003. Uniform methodological criteria instructed the comparative assessment of magnitude, trends and spatial distribution of mortality. General linear models assessed ecologic correlations between death rates and socioeconomic indices (unemployment, schooling levels and the human development index) at the inner-city area level. Results obtained for each city were subsequently compared. Results Mortality of men by oral and pharyngeal cancer ranked higher in Barcelona (9.45 yearly deaths per 100,000 male inhabitants) than in Spain and Europe as a whole; rates were on decrease. São Paulo presented a poorer profile, with higher magnitude (11.86) and stationary trend. The appraisal of ecologic correlations indicated an unequal and inequitably distributed burden of disease in both cities, with poorer areas tending to present higher mortality. Barcelona had a larger gradient of mortality than São Paulo, indicating a higher inequality of cancer deaths across its neighbourhoods. Conclusion The quantitative monitoring of inequalities in health may contribute to the formulation of redistributive policies aimed at the concurrent promotion of wellbeing and social justice. The assessment of groups experiencing a higher burden of disease can instruct health services to provide additional resources for expanding preventive actions and facilities aimed at early diagnosis, standardized treatments and rehabilitation.

The relationship between training status, blood pressure and uric acid in adults and elderly

Abstract Background Hypertension can be generated by a great number of mechanisms including elevated uric acid (UA) that contribute to the anion superoxide production. However, physical exercise is recommended to prevent and/or control high blood pressure (BP). The purpose of this study was to investigate the relationship between BP and UA and whether this relationship may be mediated by the functional fitness index. Methods All participants (n = 123) performed the following tests: indirect maximal oxygen uptake (VO2max), AAHPERD Functional Fitness Battery Test to determine the general fitness functional index (GFFI), systolic and diastolic blood pressure (SBP and DBP), body mass index (BMI) and blood sample collection to evaluate the total-cholesterol (CHOL), LDL-cholesterol (LDL-c), HDL-cholesterol (HDL-c), triglycerides (TG), uric acid (UA), nitrite (NO2) and thiobarbituric acid reactive substances (T-BARS). After the physical, hemodynamic and metabolic evaluations, all participants were allocated into three groups according to their GFFI: G1 (regular), G2 (good) and G3 (very good). Results Baseline blood pressure was higher in G1 when compared to G3 (+12% and +11%, for SBP and DBP, respectively, p<0.05) and the subjects who had higher values of BP also presented higher values of UA. Although UA was not different among GFFI groups, it presented a significant correlation with GFFI and VO2max. Also, nitrite concentration was elevated in G3 compared to G1 (140±29 μM vs 111± 29 μM, for G3 and G1, respectively, p<0.0001). As far as the lipid profile, participants in G3 presented better values of CHOL and TG when compared to those in G1. Conclusions Taking together the findings that subjects with higher BP had elevated values of UA and lower values of nitrite, it can be suggested that the relationship between blood pressure and the oxidative stress produced by acid uric may be mediated by training status.

The nitrogen sufficiency index underlying estimates of nitrogen fertilization requirements of common bean

Chlorophyll determination with a portable chlorophyll meter can indicate the period of highest N demand of plants and whether sidedressing is required or not. In this sense, defining the optimal timing of N application to common bean is fundamental to increase N use efficiency, increase yields and reduce the cost of fertilization. The objectives of this study were to evaluate the efficiency of N sufficiency index (NSI) calculated based on the relative chlorophyll index (RCI) in leaves, measured with a portable chlorophyll meter, as an indicator of time of N sidedressing fertilization and to verify which NSI (90 and 95 %) value is the most appropriate to indicate the moment of N fertilization of common bean cultivar Perola. The experiment was carried out in the rainy and dry growing seasons of the agricultural year 2009/10 on a dystroferric Red Nitosol, in Botucatu, São Paulo State, Brazil. The experiment was arranged in a randomized complete block design with five treatments, consisting of N managements (M1: 200 kg ha-1 N (40 kg at sowing + 80 kg 15 days after emergence (DAE) + 80 kg 30 DAE); M2: 100 kg ha-1 N (20 kg at sowing + 40 kg 15 DAE + 40 kg 30 DAE); M3: 20 kg ha-1 N at sowing + 30 kg ha-1 when chlorophyll meter readings indicated NSI < 95 %; M4: 20 kg ha-1 N at sowing + 30 kg ha-1 N when chlorophyll meter readings indicated NSI < 90 % and, M5: control (without N application)) and four replications. The variables RCI, aboveground dry matter, total leaf N concentration, production components, grain yield, relative yield, and N use efficiency were evaluated. The RCI correlated with leaf N concentrations. By monitoring the RCI with the chlorophyll meter, the period of N sidedressing of common bean could be defined, improving N use efficiency and avoiding unnecessary N supply to common bean. The NSI 90 % of the reference area was more efficient to define the moment of N sidedressing of common bean, to increase N use efficiency.