Improving generalized regression analysis for the spatial prediction of forest communities

Aim This study used data from temperate forest communities to assess: (1) five different stepwise selection methods with generalized additive models, (2) the effect of weighting absences to ensure a prevalence of 0.5, (3) the effect of limiting absences beyond the environmental envelope defined by presences, (4) four different methods for incorporating spatial autocorrelation, and (5) the effect of integrating an interaction factor defined by a regression tree on the residuals of an initial environmental model. Location State of Vaud, western Switzerland. Methods Generalized additive models (GAMs) were fitted using the grasp package (generalized regression analysis and spatial predictions, http://www.cscf.ch/grasp). Results Model selection based on cross-validation appeared to be the best compromise between model stability and performance (parsimony) among the five methods tested. Weighting absences returned models that perform better than models fitted with the original sample prevalence. This appeared to be mainly due to the impact of very low prevalence values on evaluation statistics. Removing zeroes beyond the range of presences on main environmental gradients changed the set of selected predictors, and potentially their response curve shape. Moreover, removing zeroes slightly improved model performance and stability when compared with the baseline model on the same data set. Incorporating a spatial trend predictor improved model performance and stability significantly. Even better models were obtained when including local spatial autocorrelation. A novel approach to include interactions proved to be an efficient way to account for interactions between all predictors at once. Main conclusions Models and spatial predictions of 18 forest communities were significantly improved by using either: (1) cross-validation as a model selection method, (2) weighted absences, (3) limited absences, (4) predictors accounting for spatial autocorrelation, or (5) a factor variable accounting for interactions between all predictors. The final choice of model strategy should depend on the nature of the available data and the specific study aims. Statistical evaluation is useful in searching for the best modelling practice. However, one should not neglect to consider the shapes and interpretability of response curves, as well as the resulting spatial predictions in the final assessment.

Estudo do Ruído Sísmico no Arquipélago de Cabo Verde

Traditionally the study of Earth's internal structure has been based on analysis of seismic waves recorded during the occurrence of earthquakes. Recently, some researchers have shown to be possible to use ambient seismic noise (generally generated by ocean storms) to obtain dispersion curves with satisfactory results. Moreover, the use of ambient seismic noise measurement has advantages because they are independent of the earthquake-station geometry. This study aims to determine the dispersion curves of Rayleigh waves from the analysis of ambient seismic noise records, obtained in Cape Verde archipelago, whose origin and structure has attracted interest from several researchers. Analyzing the data collected between November 2007 and September 2008, Green's functions were determined. The analysis of these functions allowed to construct energy diagrams and to measure dispersion curves of group velocities between pairs of stations.

Predição da hidroquímica da água (qualidade de água) usando sondagens electromagnéticas transientes (TEM)

This work aims the applicability of the Transient electromagnetic method at an arid and semiarid environmental condition in the Santiago Island – Cape Verde. Some seashore areas of this island show an increasing salt contamination of the groundwater. The main objective of present work is to relate this water-quality condition with parameters taken from the transient sounding’s data. In this context, transient soundings have been acquired from 2005 through 2009, at several chosen valleys near the sea, in a mean rate of one field campaign each year. The first phase of this work was the understanding of the geophysical method details, problems and applicability, as the chosen and acquired equipment was the first one to be permanently available to the Portuguese geosciences community. This first phase was also accomplished with field tests. Interpretation of the transient sounding’s data curves were done by application of 1-D inversion methods already developed and published, as also with quasi 2-D and quasi 3-D inversion algorithms, where applicability was feasible. This was the second phase. The 2-D and 3-D approximation results are satisfactory and promising; although a higher spatial sounding’s density should certainly allow for better results. At phase three, these results have been compared against the available lithologic, hydrologic and hydrochemical data, in the context of Santiago’s island settings. The analyses of these merged data showed that two distinct origins for the observed inland groundwater salinity are possible; seashore shallow mixing with contemporary seawater and mixing with a deep and older salty layer from up flow groundwater. Relations between the electric resistivity and the salt water content distribution were found for the surveyed areas. To this environment condition, the electromagnetic transient method proved to be a reliable and powerful technique. The groundwater quality can be accessed beyond the few available watershed points, which have an uneven distribution.

Label-free cytotoxicity screening assay by digital holographic microscopy

Abstract We introduce a label-free technology based on digital holographic microscopy (DHM) with applicability for screening by imaging, and we demonstrate its capability for cytotoxicity assessment using mammalian living cells. For this first high content screening compatible application, we automatized a digital holographic microscope for image acquisition of cells using commercially available 96-well plates. Data generated through both label-free DHM imaging and fluorescence-based methods were in good agreement for cell viability identification and a Z'-factor close to 0.9 was determined, validating the robustness of DHM assay for phenotypic screening. Further, an excellent correlation was obtained between experimental cytotoxicity dose-response curves and known IC values for different toxic compounds. For comparable results, DHM has the major advantages of being label free and close to an order of magnitude faster than automated standard fluorescence microscopy.

Fermat's treatise on quadrature: A new reading

The Treatise on Quadrature of Fermat (c. 1659), besides containing the first known proof of the computation of the area under a higher parabola, R x+m/n dx, or under a higher hyperbola, R x-m/n dx with the appropriate limits of integration in each case , has a second part which was not understood by Fermat s contemporaries. This second part of the Treatise is obscure and difficult to read and even the great Huygens described it as'published with many mistakes and it is so obscure (with proofs redolent of error) that I have been unable to make any sense of it'. Far from the confusion that Huygens attributes to it, in this paper we try to prove that Fermat, in writing the Treatise, had a very clear goal in mind and he managed to attain it by means of a simple and original method. Fermat reduced the quadrature of a great number of algebraic curves to the quadrature of known curves: the higher parabolas and hyperbolas of the first part of the paper. Others, he reduced to the quadrature of the circle. We shall see how the clever use of two procedures, quite novel at the time: the change of variables and a particular case of the formulaof integration by parts, provide Fermat with the necessary tools to square very easily curves as well-known as the folium of Descartes, the cissoid of Diocles or the witch of Agnesi.

Evolutionary rates of Jurassic ammonites in relation to sea-level fluctuations

An analysis is presented of the diversity and faunal turnover of Jurassic ammonites related to transgressive /regressive events. The data set contained 400 genera and 1548 species belonging to 67 ammonite zones covering the entire Jurassic System. These data were used in the construction of faunal turnover curves and ammonite diversities, that correlate with sea-level fluctuation curves. Twenty-four events of ammonite faunal turnover are analyzed throughout the Jurassic. The most important took place at the Sinemurian-Carixian boundary, latest Carixian-Middle Domerian, Domerian-Toarcian boundary, latest Middle Toarcian-Late Toarcian, Toarcian-Aalenian boundary, latest Aalenian-earliest Bajocian, latest Early Bajocian-earliest Late Bojocian, Early Bathonian-Middle Bathonian boundary, latest Middle Bathonian-earliest Late Bathonian, latest Bathonian-Early Callovian, earliest Early Oxfordian-Middle Oxfordian, earliest Late Oxfordian-latest Oxfordian, latest Early Kimmeridgian, Late Kimmeridgian, middle Early Tithonian and Early Tithonian-Late Tithonian boundary. More than 75 percent of these turnovers correlate with regressive-transgressive cycles in the Exxon, and /or Hallam's sea-level curves. Inmost cases the extinction events coincide with regressive intervals, whereas origination and radiation events are related to transgressive cycles. The turnovers frequently coincide with major or minor discontinuities in the Subbetic basin (Betic Cordillera).

Giffen goods and market making

This paper shows that information effects per se are not responsible forthe Giffen goods anomaly affecting competitive traders demands in multi-asset, noisy rational expectations equilibrium models. The role thatinformation plays in traders strategies also matters. In a market withrisk averse, uninformed traders, informed agents havea dual motive for trading: speculation and market making. Whilespeculation entails using prices to assess the effect of private signalerror terms, market making requires employing them to disentangle noisetraders effects in traders aggregate orders. In a correlated environment,this complicates a trader s signal-extraction problem and maygenerate upward-sloping demand curves. Assuming either (i) that competitive,risk neutral market makers price the assets, or that (ii) the risktolerance coefficient of uninformed traders grows without bound, removesthe market making component from informed traders demands, rendering themwell behaved in prices.

Automated quantitative pupillometry for the prognostication of coma after cardiac arrest.

BACKGROUND: Sedation and therapeutic hypothermia (TH) delay neurological responses and might reduce the accuracy of clinical examination to predict outcome after cardiac arrest (CA). We examined the accuracy of quantitative pupillary light reactivity (PLR), using an automated infrared pupillometry, to predict outcome of post-CA coma in comparison to standard PLR, EEG, and somato-sensory evoked potentials (SSEP). METHODS: We prospectively studied over a 1-year period (June 2012-June 2013) 50 consecutive comatose CA patients treated with TH (33 °C, 24 h). Quantitative PLR (expressed as the % of pupillary response to a calibrated light stimulus) and standard PLR were measured at day 1 (TH and sedation; on average 16 h after CA) and day 2 (normothermia, off sedation: on average 46 h after CA). Neurological outcome was assessed at 90 days with Cerebral Performance Categories (CPC), dichotomized as good (CPC 1-2) versus poor (CPC 3-5). Predictive performance was analyzed using area under the ROC curves (AUC). RESULTS: Patients with good outcome [n = 23 (46 %)] had higher quantitative PLR than those with poor outcome [n = 27; 16 (range 9-23) vs. 10 (1-30) % at day 1, and 20 (13-39) vs. 11 (1-55) % at day 2, both p < 0.001]. Best cut-off for outcome prediction of quantitative PLR was <13 %. The AUC to predict poor outcome was higher for quantitative than for standard PLR at both time points (day 1, 0.79 vs. 0.56, p = 0.005; day 2, 0.81 vs. 0.64, p = 0.006). Prognostic accuracy of quantitative PLR was comparable to that of EEG and SSEP (0.81 vs. 0.80 and 0.73, respectively, both p > 0.20). CONCLUSIONS: Quantitative PLR is more accurate than standard PLR in predicting outcome of post-anoxic coma, irrespective of temperature and sedation, and has comparable prognostic accuracy than EEG and SSEP.

Longevity and fecundity of Dichroplus maculipennis (Orthoptera, Acrididae) at non-outbreaking and outbreaking situations

Dichroplus maculipennis is one of the most characteristic and damaging grasshopper species of Argentina, mainly in areas of the Pampas and Patagonia regions. We estimated and compared the longevity and fecundity of adult female D. maculipennis under controlled conditions (30ºC, 14L:10D, 40% RH) from individuals collected as last instar nymphs (VI) in the field and with a known recent history of low and high density conditions. Densities of D. maculipennis at the collecting sites were 0.95 individuals per m² in 2006 and 46 ind/m² in 2009, representing non-outbreaking and outbreaking situations, respectively. Adult female longevity in 2006 (67.96 ± 3.2 days) was significantly higher (p < 0.05) than in 2009 (37.44 ± 1.98 days). The number of egg-pods per female was 3.32 ± 0.44 for 2006 and 1.62 ± 0.26 for 2009. The average fecundity in 2006 (89.29 ± 11.9 eggs/female) was significantly greater (p < 0.05) than that in 2009 (36.27 ± 5.82 eggs/female). While it was observed that the oviposition rate was higher in 2006, this difference was not significant (p > 0.05). The fecundity curves showed that the highest values were at weeks 11 and 13 for the 2006 females, and at week 6 for those of 2009. Since the daily oviposition rate at low and high densities was not significantly different, the diminished fecundity rate at high density is attributable to their reduced longevity.

Validation procedures in radiological diagnostic models. Neural network and logistic regression

The objective of this paper is to compare the performance of twopredictive radiological models, logistic regression (LR) and neural network (NN), with five different resampling methods. One hundred and sixty-seven patients with proven calvarial lesions as the only known disease were enrolled. Clinical and CT data were used for LR and NN models. Both models were developed with cross validation, leave-one-out and three different bootstrap algorithms. The final results of each model were compared with error rate and the area under receiver operating characteristic curves (Az). The neural network obtained statistically higher Az than LR with cross validation. The remaining resampling validation methods did not reveal statistically significant differences between LR and NN rules. The neural network classifier performs better than the one based on logistic regression. This advantage is well detected by three-fold cross-validation, but remains unnoticed when leave-one-out or bootstrap algorithms are used.

Diversity of Ephemeroptera (Insecta) of the Serra da Mantiqueira and Serra do Mar, southeastern Brazil

The aim of this study was to inventory the mayfly fauna, based on nymphal and alate stages, in Serra da Mantiqueira and in Serra do Mar, São Paulo State, as well as to present information about habitats used by the genera. Nymphs were collected in several streams and mesohabitats with a Surber sampler and the winged stages with light attraction methods, entomological nets, and Malaise traps. In all, eight families and 33 genera were recorded, representing a very significant portion of the Brazilian fauna (80% of families and 49% of genera). Furthermore, it was possible to identify 11 species, of which two are new records for the state: Tricorythodes santarita Traver and Caenis reissi Malzacher. Despite the high diversity recorded, the accumulation curves presented an ascending form, indicating an increase in the number of genera with additional sampling effort. The high richness found in these areas are in agreement with the high biodiversity of the Atlantic Forest biome and the sampling effort employed, which included the use of different methods, the collection of both nymphs and winged stages, and the sampling of a large area with diverse streams and habitats.

The IFNL3/4 ΔG variant increases susceptibility to cytomegalovirus retinitis among HIV-infected patients.

BACKGROUND: Cytomegalovirus (CMV) retinitis is a major cause of visual impairment and blindness among patients with uncontrolled HIV infections. Whereas polymorphisms in interferon-lambda 3 (IFNL3, previously named IL28B) strongly influence the clinical course of hepatitis C, few studies examined the role of such polymorphisms in infections due to viruses other than hepatitis C virus. OBJECTIVES: To analyze the association of newly identified IFNL3/4 variant rs368234815 with susceptibility to CMV-associated retinitis in a cohort of HIV-infected patients. DESIGN AND METHODS: This retrospective longitudinal study included 4884 white patients from the Swiss HIV Cohort Study, among whom 1134 were at risk to develop CMV retinitis (CD4 nadir <100 /μl and positive CMV serology). The association of CMV-associated retinitis with rs368234815 was assessed by cumulative incidence curves and multivariate Cox regression models, using the estimated date of HIV infection as a starting point, with censoring at death and/or lost follow-up. RESULTS: A total of 40 individuals among 1134 patients at risk developed CMV retinitis. The minor allele of rs368234815 was associated with a higher risk of CMV retinitis (log-rank test P = 0.007, recessive mode of inheritance). The association was still significant in a multivariate Cox regression model (hazard ratio 2.31, 95% confidence interval 1.09-4.92, P = 0.03), after adjustment for CD4 nadir and slope, HAART and HIV-risk groups. CONCLUSION: We reported for the first time an association between an IFNL3/4 polymorphism and susceptibility to AIDS-related CMV retinitis. IFNL3/4 may influence immunity against viruses other than HCV.

Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data.

BACKGROUND: Prognosis prediction for resected primary colon cancer is based on the T-stage Node Metastasis (TNM) staging system. We investigated if four well-documented gene expression risk scores can improve patient stratification. METHODS: Microarray-based versions of risk-scores were applied to a large independent cohort of 688 stage II/III tumors from the PETACC-3 trial. Prognostic value for relapse-free survival (RFS), survival after relapse (SAR), and overall survival (OS) was assessed by regression analysis. To assess improvement over a reference, prognostic model was assessed with the area under curve (AUC) of receiver operating characteristic (ROC) curves. All statistical tests were two-sided, except the AUC increase. RESULTS: All four risk scores (RSs) showed a statistically significant association (single-test, P < .0167) with OS or RFS in univariate models, but with HRs below 1.38 per interquartile range. Three scores were predictors of shorter RFS, one of shorter SAR. Each RS could only marginally improve an RFS or OS model with the known factors T-stage, N-stage, and microsatellite instability (MSI) status (AUC gains < 0.025 units). The pairwise interscore discordance was never high (maximal Spearman correlation = 0.563) A combined score showed a trend to higher prognostic value and higher AUC increase for OS (HR = 1.74, 95% confidence interval [CI] = 1.44 to 2.10, P < .001, AUC from 0.6918 to 0.7321) and RFS (HR = 1.56, 95% CI = 1.33 to 1.84, P < .001, AUC from 0.6723 to 0.6945) than any single score. CONCLUSIONS: The four tested gene expression-based risk scores provide prognostic information but contribute only marginally to improving models based on established risk factors. A combination of the risk scores might provide more robust information. Predictors of RFS and SAR might need to be different.

Early multimodal outcome prediction after cardiac arrest in patients treated with hypothermia.

OBJECTIVES: Therapeutic hypothermia and pharmacological sedation may influence outcome prediction after cardiac arrest. The use of a multimodal approach, including clinical examination, electroencephalography, somatosensory-evoked potentials, and serum neuron-specific enolase, is recommended; however, no study examined the comparative performance of these predictors or addressed their optimal combination. DESIGN: Prospective cohort study. SETTING: Adult ICU of an academic hospital. PATIENTS: One hundred thirty-four consecutive adults treated with therapeutic hypothermia after cardiac arrest. MEASUREMENTS AND MAIN RESULTS: Variables related to the cardiac arrest (cardiac rhythm, time to return of spontaneous circulation), clinical examination (brainstem reflexes and myoclonus), electroencephalography reactivity during therapeutic hypothermia, somatosensory-evoked potentials, and serum neuron-specific enolase. Models to predict clinical outcome at 3 months (assessed using the Cerebral Performance Categories: 5 = death; 3-5 = poor recovery) were evaluated using ordinal logistic regressions and receiving operator characteristic curves. Seventy-two patients (54%) had a poor outcome (of whom, 62 died), and 62 had a good outcome. Multivariable ordinal logistic regression identified absence of electroencephalography reactivity (p < 0.001), incomplete recovery of brainstem reflexes in normothermia (p = 0.013), and neuron-specific enolase higher than 33 μg/L (p = 0.029), but not somatosensory-evoked potentials, as independent predictors of poor outcome. The combination of clinical examination, electroencephalography reactivity, and neuron-specific enolase yielded the best predictive performance (receiving operator characteristic areas: 0.89 for mortality and 0.88 for poor outcome), with 100% positive predictive value. Addition of somatosensory-evoked potentials to this model did not improve prognostic accuracy. CONCLUSIONS: Combination of clinical examination, electroencephalography reactivity, and serum neuron-specific enolase offers the best outcome predictive performance for prognostication of early postanoxic coma, whereas somatosensory-evoked potentials do not add any complementary information. Although prognostication of poor outcome seems excellent, future studies are needed to further improve prediction of good prognosis, which still remains inaccurate.

Pesca exploratoria y experimental con red de cerco artesanal en la Región Tumbes.2005

Se evaluó la utilización de la malla de 50 mm (2”) en redes de cerco artesanal de la Región Tumbes en una pesquería multiespecífica. Se trabajó con una red control de tamaño de malla de 38 mm (1,5”) y la red experimental de 50 mm (2,0”), con un porcentaje de embande de 0,65 y 0,77, respectivamente. Se determinó diferencia entre las curvas de profundidad de calado del cuerpo central de las redes (tc= 46,670, t*= 1,98, p= 0) la red experimental tuvo mayor profundidad de velado; entre las curvas de velocidad de caída del cuerpo central de las redes, hubo diferencia significativa (tc= 7,790, t*= 1,98, p = 0,000), debido al mayor lastre y filtrado de las mallas de la red experimental. El coeficiente abertura horizontal (μ1) de las mallas en la franja superior durante el máximo velado de la red y el gareteo fue en las mallas del cabecero o copo, parte central y ultimo cuerpo de la red, en promedio 0,71; 0,74 y 0,73 respectivamente; (valores cercanos al coeficiente de armado ideal para el escape de ciertos peces fusiformes). El promedio de μ1 obtenidos en la región de las mallas centrales en el cabecero, centro y ultimo cuerpo de la red fue 0,85; 0,85 y 0,84 respectivamente; lo que indicó una mayor abertura horizontal de las mallas por encima del valor del coeficiente de armado que no permitiría el escape de los peces. Se concluyó que por la condición de las mallas de la red de cerco experimental (tamaño de malla 50 mm) no es óptima para gran parte de la estructura de la red, esto no permitiría la selectividad por tamaños.