Parameter recovery for a skew-normal IRT model under a Bayesian approach: hierarchical framework, prior and kernel sensitivity and sample size

Item response theory (IRT) comprises a set of statistical models which are useful in many fields, especially when there is an interest in studying latent variables (or latent traits). Usually such latent traits are assumed to be random variables and a convenient distribution is assigned to them. A very common choice for such a distribution has been the standard normal. Recently, Azevedo et al. [Bayesian inference for a skew-normal IRT model under the centred parameterization, Comput. Stat. Data Anal. 55 (2011), pp. 353-365] proposed a skew-normal distribution under the centred parameterization (SNCP) as had been studied in [R. B. Arellano-Valle and A. Azzalini, The centred parametrization for the multivariate skew-normal distribution, J. Multivariate Anal. 99(7) (2008), pp. 1362-1382], to model the latent trait distribution. This approach allows one to represent any asymmetric behaviour concerning the latent trait distribution. Also, they developed a Metropolis-Hastings within the Gibbs sampling (MHWGS) algorithm based on the density of the SNCP. They showed that the algorithm recovers all parameters properly. Their results indicated that, in the presence of asymmetry, the proposed model and the estimation algorithm perform better than the usual model and estimation methods. Our main goal in this paper is to propose another type of MHWGS algorithm based on a stochastic representation (hierarchical structure) of the SNCP studied in [N. Henze, A probabilistic representation of the skew-normal distribution, Scand. J. Statist. 13 (1986), pp. 271-275]. Our algorithm has only one Metropolis-Hastings step, in opposition to the algorithm developed by Azevedo et al., which has two such steps. This not only makes the implementation easier but also reduces the number of proposal densities to be used, which can be a problem in the implementation of MHWGS algorithms, as can be seen in [R.J. Patz and B.W. Junker, A straightforward approach to Markov Chain Monte Carlo methods for item response models, J. Educ. Behav. Stat. 24(2) (1999), pp. 146-178; R. J. Patz and B. W. Junker, The applications and extensions of MCMC in IRT: Multiple item types, missing data, and rated responses, J. Educ. Behav. Stat. 24(4) (1999), pp. 342-366; A. Gelman, G.O. Roberts, and W.R. Gilks, Efficient Metropolis jumping rules, Bayesian Stat. 5 (1996), pp. 599-607]. Moreover, we consider a modified beta prior (which generalizes the one considered in [3]) and a Jeffreys prior for the asymmetry parameter. Furthermore, we study the sensitivity of such priors as well as the use of different kernel densities for this parameter. Finally, we assess the impact of the number of examinees, number of items and the asymmetry level on the parameter recovery. Results of the simulation study indicated that our approach performed equally as well as that in [3], in terms of parameter recovery, mainly using the Jeffreys prior. Also, they indicated that the asymmetry level has the highest impact on parameter recovery, even though it is relatively small. A real data analysis is considered jointly with the development of model fitting assessment tools. The results are compared with the ones obtained by Azevedo et al. The results indicate that using the hierarchical approach allows us to implement MCMC algorithms more easily, it facilitates diagnosis of the convergence and also it can be very useful to fit more complex skew IRT models.

Landscape and soil regionalization in southern Brazilian Amazon and contiguous areas: methodology and relevance for ecological studies

Soils of a large tropical area with differentiated landscapes cannot be treated uniformly for ecological applications. We intend to develop a framework based on physiography that can be used in regional applications. The study region occupies more than 1.1 million km² and is located at the junction of the savanna region of Central Brazil and the Amazon forest. It includes a portion of the high sedimentary Central Brazil plateau and large areas of mostly peneplained crystalline shield on the border of the wide inner-Amazon low sedimentary plain. A first broad subdivision was made into landscape regions followed by a more detailed subdivision into soil regions. Mapping information was extracted from soil survey maps at scales of 1:250000-1:500000. Soil units were integrated within a homogenized legend using a set of selected attributes such as taxonomic term, the texture of the B horizon and the associated vegetation. For each region, a detailed inventory of the soil units with their area distribution was elaborated. Ten landscape regions and twenty-four soil regions were recognized and delineated. Soil cover of a region is normally characterized by a cluster composed of many soil units. Soil diversity is comparable in the landscape and the soil regions. Composition of the soil cover is quantitatively expressed in terms of area extension of the soil units. Such geographic divisions characterized by grouping soil units and their spatial estimates must be used for regional ecological applications.

Admissions due to pneumonia and biomass burning: a spatial approach

Objective: To identify spatial patterns in rates of admission for pneumonia among children and relate them to the number of fires reported in the state of Mato Grosso, Brazil. Methods: We conducted an ecological and exploratory study of data from the state of Mato Grosso for 2008 and 2009 on hospital admissions of children aged 0 to 4 years due to pneumonia and on fires in the same period. Admission rates were calculated and choropleth maps were plotted for rates and for fire outbreaks, Moran's I was calculated and the kernel estimator used to identify "hotspots." Data were analyzed using TerraView 3.3.1. Results: Fifteen thousand six hundred eighty-nine children were hospitalized (range zero to 2,315), and there were 161,785 fires (range 7 to 6,454). The average rate of admissions per 1,000 inhabitants was 2.89 (standard deviation [SD] = 5.18) and the number of fires per 1,000 inhabitants was 152.81 (SD = 199.91). Moran's I for the overall number of admissions was I = 0.02 (p = 0.26), the index for rate of admission was I = 0.02 (p = 0.21) and the index for the number of fires was I = 0.31 (p < 0.01). It proved possible to identify four municipalities with elevated rates of admissions for pneumonia. It was also possible to identify two regions with high admission densities. A clustering of fires was evident along what is known as the "arc of deforestation." Conclusions: This study identified municipalities in the state of Mato Grosso that require interventions to reduce rates of admission due to pneumonia and the number fires.

Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States

Background: Antigen B (AgB) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection. The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown, such as its subunit composition and oligomeric states. Methodology/Principal Findings: The subunit composition of E. granulosus AgB oligomers from individual bovine and human cysts was assessed by mass spectrometry associated with electrophoretic analysis. AgB8/1, AgB8/2, AgB8/3 and AgB8/4 subunits were identified in all samples analyzed, and an AgB8/2 variant (AgB8/2v8) was found in one bovine sample. The exponentially modified protein abundance index (emPAI) was used to estimate the relative abundance of the AgB subunits, revealing that AgB8/1 subunit was relatively overrepresented in all samples. The abundance of AgB8/3 subunit varied between bovine and human cysts. The oligomeric states formed by E. granulosus AgB and recombinant subunits available, rAgB8/1, rAgB8/2 and rAgB8/3, were characterized by native PAGE, light scattering and microscopy. Recombinant subunits showed markedly distinct oligomerization behaviors, forming oligomers with a maximum size relation of rAgB8/3 >rAgB8/2>rAgB8/1. Moreover, the oligomeric states formed by rAgB8/3 subunit were more similar to those observed for AgB purified from hydatid fluid. Pressure-induced dissociation experiments demonstrated that the molecular assemblies formed by the more aggregative subunits, rAgB8/2 and rAgB8/3, also display higher structural stability. Conclusions/Significance: For the first time, AgB subunit composition was analyzed in samples from single hydatid cysts, revealing qualitative and quantitative differences between samples. We showed that AgB oligomers are formed by different subunits, which have distinct abundances and oligomerization properties. Overall, our findings have significantly contributed to increase the current knowledge on AgB expression and structure, highlighting issues that may help to understand the parasite adaptive response during chronic infection.

The Young Mother and the Labor Market

Introduction - The Centro de Orientacao ao Adolescente of Campinas (Southeastern Brazil) maintains a program to qualify economically disadvantaged adolescent students aged 15 to 18 years to enter the labor market. Objective - To understand life projects of teenagers who became mothers while participating in the program, in the period from 2003 to 2008, aiming to find the place of professional life in their life trajectory before and after motherhood. Method - Eight young mothers were interviewed, and a qualitative methodology was applied to the analysis of the interviews. Results - The trajectories of study and work were discontinued or adapted due to motherhood. Four young mothers completed high school and none had entered university. Three did not return to work and the rest had diverse work experiences. The reported difficulties to enter the labor market were: inadequate instruments to support the children's care, low income, lack of work experience, presence of small children and little educational background. Final Considerations - Teenage motherhood did not indicate the exclusion of educational or work projects but indicated adjustments and the need for a family and social support network. It was noted the need for public policies targeted at the inclusion of youths in the labor market and at support services such as nurseries. Also, the need for a change in gender relations was demonstrated, with greater equality of rights as a precondition for the inclusion of women, especially those who are mothers, in the labor market.

IMPLEMENTATION OF PROTECTED AREAS FORCENTRAL CORRIDOR OF ATLANTIC FORESTIN BAHIA: CHALLENGES AND LIMITS

In Brazil, Protected Areas (PAs) are considered the cornerstone for development of national strategies for biodiversity conservation. Considering this point of view we analyzed thirty protected areas belonging to Atlantic Central Corridor of Atlantic Forest in Bahia, aiming to identify and analyze its current level of implementation. Lemos de Sa and Ferreira (2000) methodology which consist of applying a standard scale, where the variation of the level of implementation conforms to a range of 0 to 5 points was used, with appropriate adaptations. After obtaining the data from the implementation level we use the aggregation method of Ward to help visualize the dissimilarity between the protected areas studied. We used an international classification proposed by IUCN (International Union for Conservation of Nature) for that the UCs to be compared with works done in another countries, the UCs considered are in the groups Ia, II, V and VI da IUCN. As results, 50% of protected areas analyzed are reasonably implemented, 40% inadequately implemented, 6.7% are presented only on paper and only 3.3% can be classified as satisfactorily implemented. These areas presents problems in their regularization; deficiency in infrastructure, human and financial resources. Given the results its clear the recurrent fact that conservation areas under study must be effectively implemented and for this to occur environmental policies should be focused on actions to consolidate the goals of conservation strategy.

The EXTRIP (EXtracorporeal TReatments In Poisoning) workgroup: Guideline methodology

Extracorporeal treatments (ECTRs), such as hemodialysis and hemoperfusion, are used in poisoning despite a lack of controlled human trials demonstrating efficacy. To provide uniform recommendations, the EXTRIP group was formed as an international collaboration among recognized experts from nephrology, clinical toxicology, critical care, or pharmacology and supported by over 30 professional societies. For every poison, the clinical benefit of ECTR is weighed against associated complications, alternative therapies, and costs. Rigorous methodology, using the AGREE instrument, was developed and ratified. Methods rely on evidence appraisal and, in the absence of robust studies, on a thorough and transparent process of consensus statements. Twenty-four poisons were chosen according to their frequency, available evidence, and relevance. A systematic literature search was performed in order to retrieve all original publications regardless of language. Data were extracted on a standardized instrument. Quality of the evidence was assessed by GRADE as: High = A, Moderate = B, Low = C, Very Low = D. For every poison, dialyzability was assessed and clinical effect of ECTR summarized. All pertinent documents were submitted to the workgroup with a list of statements for vote (general statement, indications, timing, ECTR choice). A modified Delphi method with two voting rounds was used, between which deliberation was required. Each statement was voted on a Likert scale (1-9) to establish the strength of recommendation. This approach will permit the production of the first important practice guidelines on this topic.

RAND-like Appropriateness Methodology Consensus for Primary Open-Angle Glaucoma in Latin America

PURPOSE: To report the results of a Latin American consensus panel regarding the diagnosis and management of primary open-angle glaucoma and to compare these results with those from a similar panel in the United States. DESIGN: A RAND-like (Research and Development) appropriateness methodology was used to assess glaucoma practice in Latin America. METHODS: The 148 polling statements created for the RAND-like analysis in the United States and 10 additional statements specific to glaucoma care in Latin America were presented to a panel of Latin American glaucoma experts. Panelists were polled in private using the RAND-like methodology before and after the panel meeting. RESULTS: Consensus agreement or disagreement among Latin American experts was reached for 51.3% of statements before the meeting and increased to 66.5% in the private, anonymous meeting after polling (79.0% agreement, 21.0% disagreement). Although there was a high degree of concordance (111 of 148 statements; 75%) between the results of this Latin American panel and the United States panel, there were some notable exceptions relating to diagnostic and therapeutic decision making. CONCLUSIONS: This RAND-like consensus methodology provides a perspective of how Latin American glaucoma practitioners view many aspects of glaucoma and compares these results with those obtained using a similar methodology from practitioners in the United States. These findings may be helpful to ophthalmologists providing glaucoma care in Latin America and in other regions of the world. (Am J Ophthalmol 2012;154: 460-465. (C) 2012 by Elsevier Inc. All rights reserved.)

Intelligence systems methodology: a systemic approach to the organizational intelligence function

Organizational intelligence can be seen as a function of the viable structure of an organization. With the integration of the Viable System Model and Soft Systems Methodology (systemic approaches of organizational management) focused on the role of the intelligence function, it is possible to elaborate a model of action with a structured methodology to prospect, select, treat and distribute information to the entire organization that improves the efficacy and efficiency of all processes. This combination of methodologies is called Intelligence Systems Methodology (ISM) whose assumptions and dynamics are delimited in this paper. The ISM is composed of two simultaneous activities: the Active Environmental Mapping and the Stimulated Action Cycle. The elaboration of the formal ISM description opens opportunities for applications of the methodology on real situations, offering a new path for this specific issue of systems thinking: the intelligence systems. Knowledge Management Research & Practice (2012) 10, 141-152. doi:10.1057/kmrp.2011.44

Functional Magnetic Resonance Imaging Data Analysis by Autoregressive Estimator

The autoregressive (AR) estimator, a non-parametric method, is used to analyze functional magnetic resonance imaging (fMRI) data. The same method has been used, with success, in several other time series data analysis. It uses exclusively the available experimental data points to estimate the most plausible power spectra compatible with the experimental data and there is no need to make any assumption about non-measured points. The time series, obtained from fMRI block paradigm data, is analyzed by the AR method to determine the brain active regions involved in the processing of a given stimulus. This method is considerably more reliable than the fast Fourier transform or the parametric methods. The time series corresponding to each image pixel is analyzed using the AR estimator and the corresponding poles are obtained. The pole distribution gives the shape of power spectra, and the pixels with poles at the stimulation frequency are considered as the active regions. The method was applied in simulated and real data, its superiority is shown by the receiver operating characteristic curves which were obtained using the simulated data.

Speech Graphs Provide a Quantitative Measure of Thought Disorder in Psychosis

Background: Psychosis has various causes, including mania and schizophrenia. Since the differential diagnosis of psychosis is exclusively based on subjective assessments of oral interviews with patients, an objective quantification of the speech disturbances that characterize mania and schizophrenia is in order. In principle, such quantification could be achieved by the analysis of speech graphs. A graph represents a network with nodes connected by edges; in speech graphs, nodes correspond to words and edges correspond to semantic and grammatical relationships. Methodology/Principal Findings: To quantify speech differences related to psychosis, interviews with schizophrenics, manics and normal subjects were recorded and represented as graphs. Manics scored significantly higher than schizophrenics in ten graph measures. Psychopathological symptoms such as logorrhea, poor speech, and flight of thoughts were grasped by the analysis even when verbosity differences were discounted. Binary classifiers based on speech graph measures sorted schizophrenics from manics with up to 93.8% of sensitivity and 93.7% of specificity. In contrast, sorting based on the scores of two standard psychiatric scales (BPRS and PANSS) reached only 62.5% of sensitivity and specificity. Conclusions/Significance: The results demonstrate that alterations of the thought process manifested in the speech of psychotic patients can be objectively measured using graph-theoretical tools, developed to capture specific features of the normal and dysfunctional flow of thought, such as divergence and recurrence. The quantitative analysis of speech graphs is not redundant with standard psychometric scales but rather complementary, as it yields a very accurate sorting of schizophrenics and manics. Overall, the results point to automated psychiatric diagnosis based not on what is said, but on how it is said.

Reduced Population of Interstitial Cells of Cajal in Chagasic Megacolon

Background/Aims: In Chagasic megacolon, there is a reduction in the population of interstitial cells of Cajal. It was aimed to evaluate density of Cajal cells in the resected colon of Chagasic patients compared to control patients and to verify possible association between preoperative and postoperative bowel function of megacolon patients and cell count. Methodology: Sixteen megacolon patients (12 female; mean age 54.4 (31-73)) were operated on. Pre- and postoperative evaluation using Cleveland clinic constipation score was undertaken. Resected colons were examined. Cajal cells were identified by immunohistochemistry (anti-CD117). The mean cell number was compared to resected colons from 16 patients (7 female; mean age 62.8 (23-84)) with non-obstructive sigmoid cancer. Association between pre- and postoperative constipation scores and cell count for megacolon patients was evaluated using the Pearson test (r). Results: A reduced number of Cajal cells (per field: 2.84 (0-6.6) vs. 9.68 (4.3-13); p<0.001) were observed in the bowel of megacolon patients compared to cancer patients. No correlation between constipation score before (r=-0.205; p=0.45) or after surgery (r=0,291; p=0.28) and cell count in megacolon was observed. Conclusions: Patients with megacolon display marked reduction of interstitial cells of Cajal. An association of constipation severity and Cajal cells depopulation was not demonstrated.

Investigation of the pore blockage of a Brazilian dolomite during the sulfation reaction

The influence of the temperature and reaction time on the sulfation process of a dolomite is investigated in this paper. The sulfation effectiveness was evaluated and correlated with changes in the physical characteristics of a Brazilian dolomite during the reactive process. Calcination and sulfation experiments were performed under isothermal conditions for dolomite samples with average particle sizes of 545 mu m at temperatures of 750 degrees C, 850 degrees C and 950 degrees C at different times of sulfation. Thermogravimetric tests were applied to establish the reactivity variation of the dolomite in function of the time in the sulfation reaction and evaluate the methodology of the samples preparation. Porosimetry tests were performed to study the pore blockage of dolomite during the sulfation reaction. The highest values of BET surface area were 25.55 m(2)/g, 29.55 m(2)/g and 12.62 m(2)/g for calcined samples and after their sulfation processes, conversions of 51.5%, 61.9% and 42.8% were obtained at 750 degrees C, 850 degrees C and 950 degrees C, respectively. Considering the process as a whole, the best fit was provided by a first-order exponential decay equation. Moreover, the results have shown that it is possible to quantify the decreasing in the dolomite reactivity for sulfur dioxide sorption and understand the changes in the behavior of the sulfation process of limestones when applied to technologies, as fluidized bed combustor, in which sulfur dioxide is present. (C) 2011 Elsevier B. V. All rights reserved.

Evaluating different methods of microarray data normalization

Abstract Background With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration. Results Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets. Conclusion In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.

Effect of 2% chlorhexidine digluconate on bond strength of a glass-fibre post to root dentine

Aim: To assess the immediate influence of dentine bonding systems (DBS) associated with 2% chlorhexidine digluconate (CHX) on glass-fibre post-bond strength to root dentine, in terms of coronal, middle and apical thirds. Methodology: Sixty bovine roots were root filled and randomly assigned to 1 of 6 groups (n = 10): SBMP (3-step etch-and-rinse system, Scotchbond Multi-Purpose), SB (2-step etch-and-rinse system, Single Bond 2), SE (2-step self-etching system, Clearfil SE Bond) and SBMP-CHX, SB-CHX and SE-CHX, respectively, associated with CHX. For all groups, a glassfibre post was luted with a dual-cure resin cement, RelyX ARC. After 7-day storage, specimens were subjected to the push-out test. Failure modes were analysed under optical microscopy (40x). Bond strength values were statistically analysed by two-way ANOVA and Bonferroni tests (P < 0.05). Results: The effect of DBS was significant (P < 0.05), and SE reached higher bond strength in comparison with the other DBS tested. CHX association did not show improvement with any DBS (P > 0.05); rather, it negatively affected SE, which was detected for all thirds. There was no difference between thirds (P > 0.05), except for the SE-CHX, which presented lower values for the apical third (P < 0.05). Adhesive cement/dentine adhesive failure was predominant for all groups. CHX did not influence the failure mode for any DBS (P > 0.05). Conclusions: The performance of the dentine bonding systems was material dependent. CHX did not improve immediate bond strength; however, CHX negatively affected the bond strength of the self-etching system, especially in the third apical