Missing data mechanisms and their implications on the analysis of categorical data

We review some issues related to the implications of different missing data mechanisms on statistical inference for contingency tables and consider simulation studies to compare the results obtained under such models to those where the units with missing data are disregarded. We confirm that although, in general, analyses under the correct missing at random and missing completely at random models are more efficient even for small sample sizes, there are exceptions where they may not improve the results obtained by ignoring the partially classified data. We show that under the missing not at random (MNAR) model, estimates on the boundary of the parameter space as well as lack of identifiability of the parameters of saturated models may be associated with undesirable asymptotic properties of maximum likelihood estimators and likelihood ratio tests; even in standard cases the bias of the estimators may be low only for very large samples. We also show that the probability of a boundary solution obtained under the correct MNAR model may be large even for large samples and that, consequently, we may not always conclude that a MNAR model is misspecified because the estimate is on the boundary of the parameter space.

Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers

Facioscapulohumeral muscular dystrophy (FSHD) is a progressive muscle disorder that has been associated with a contraction of 3.3-kb repeats on chromosome 4q35. FSHD is characterized by a wide clinical inter- and intrafamilial variability, ranging from wheelchair-bound patients to asymptomatic carriers. Our study is unique in comparing the gene expression profiles from related affected, asymptomatic carrier, and control individuals. Our results suggest that the expression of genes on chromosome 4q is altered in affected and asymptomatic individuals. Remarkably, the changes seen in asymptomatic samples are largely in products of genes encoding several chemokines, whereas the changes seen in affected samples are largely in genes governing the synthesis of GPI-linked proteins and histone acetylation. Besides this, the affected patient and related asymptomatic carrier share the 4qA161 haplotype. Thus, these polymorphisms by themselves do not explain the pathogenicity of the contracted allele. Interestingly, our results also suggest that the miRNAs might mediate the regulatory network in FSHD. Together, our results support the previous evidence that FSHD may be caused by transcriptional dysregulation of multiple genes, in cis and in trans, and suggest some factors potentially important for FSHD pathogenesis. The study of the gene expression profiles from asymptomatic carriers and related affected patients is a unique approach to try to enhance our understanding of the missing link between the contraction in D4Z4 repeats and muscle disease, while minimizing the effects of differences resulting from genetic background.

Cytochrome-b variation in Apis mellifera samples and its association with COI-COII patterns

Five Mbo I (Mbo-A, Mbo-M, Mbo-C(1), Mbo-C(2) and Mbo-C(3)) and Hinf I (Hinf-1 to Hinf-5) patterns were observed in Apis mellifera samples after restriction of a 485 bp fragment of the mitochondrial cytochrome-b (cyt-b) gene. Associating the cyt-b Restriction fragment length polymorphism (RFLP) pattern of each sample to its respective previously established COI-COII (Dra I sites) pattern, five restriction patterns (Mbo-C(1), Mbo-C(2), Mbo-C(3), Hinf-1 and Hinf-4) were observed in samples of maternal origin associated to the evolutionary branch C. No deletions or insertions were observed and the nucleotide substitution rate was estimated at 5.4%. Higher nucleotide diversity was observed among the branch C-haplotypes when compared with A and M lineages. Further studies are needed to confirm if the cyt-b + COI-COII haplotypes help to assign certain phylogeographic patterns to the branch C and to clarify phylogenetic relationships among A. mellifera subspecies.

Next Generation Sequencing of Pooled Samples Reveals New SNRNP200 Mutations Associated with Retinitis Pigmentosa

The gene SNRNP200 is composed of 45 exons and encodes a protein essential for pre-mRNA splicing, the 200 kDa helicase hBrr2. Two mutations in SNRNP200 have recently been associated with autosomal dominant retinitis pigmentosa (adRP), a retinal degenerative disease, in two families from China. In this work we analyzed the entire 35-Kb SNRNP200 genomic region in a cohort of 96 unrelated North American patients with adRP. To complete this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products. We then validated the detected DNA changes by Sanger sequencing of individual samples from this cohort and from an additional one of 95 patients. One of the two previously known mutations (p.S1087L) was identified in 3 patients, while 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals, indicating that the prevalence of SNRNP200-associated adRP is relatively high. We also took advantage of this research to evaluate the pool-and-sequence method, especially with respect to the generation of false positive and negative results. We conclude that, although this strategy can be adopted for rapid discovery of new disease-associated variants, it still requires extensive validation to be used in routine DNA screenings. (C) 2011 Wiley-Liss, Inc.

Effects of gamma-radiation on the fungus Alternaria alternata in artificially inoculated cereal samples

The objective of this study was to evaluate the effects of different gamma-radiation doses on the growth of Alternaria alternata in artificially inoculated cereal samples. Seeds and grains were divided into four groups: Control Group (not irradiated), and Groups 1, 2 and 3, inoculated with an A. alternata spore suspension (1 x 10(6) spores/mL) and exposed to 2, 5 and 10 kGy, respectively. Serial dilutions of the samples were prepared and seeded on DRBC (dichloran rose bengal chloramphenicol agar) and DCMA (dichloran chloramphenicol malt extract agar) media, after which the number of colony-forming units per gram was determined in each group. In addition, fungal morphology after irradiation was analyzed by scanning electron microscopy (SEM). The results showed that ionizing radiation at a dose of 5 kGy was effective in reducing the growth of A. alternata. However, a dose of 10 kGy was necessary to inhibit fungal growth completely. SEM made it possible to visualize structural alterations induced by the different gamma-radiation doses used. (C) 2009 Elsevier Ltd. All rights reserved.

Evaluation of laccases and melanization in clinical and environmental Cryptococcus neoformans samples by non-denaturing PAGE

The increased incidence of infections caused by the opportunistic pathogen Cryptococcus neoformans, which mainly affects immunocompromised patients but can also infect immunocompetent individuals, has needed additional studies on this micro-organism`s pathogenicity and factors related to virulence, such as enzyme production, for a better understanding of the aetiology of cryptococcosis. The aim of this study was to verify the applicability of non-denaturing PAGE for analysis of laccases by quantification of the amount of melanin pigment produced by clinical and environmental strains of C. neoformans. After incubation of the gel with the substrate L-dopa, strains produced melanin spots of a bright brown to black colour. Quantification of these spots was performed by densitometry analysis and the amount of melanin produced was calculated and compared among the strains. All strains showed laccase activity. Serotype B strains showed a higher melanin intensity than serotype A strains. Over half of the clinical strains (56.2%) showed the lowest melanin intensities, suggesting that melanin production may not be the main virulence factor against host defence. The clinical strain ICB 88 revealed two melanin spots on the gel, indicating the presence of two laccase isoforms. The environmental strains showed the highest values of melanin intensity, which may be related to previous exposure to environmental stress conditions.

Study of DNA damage with a new system for irradiation of samples in a nuclear reactor

In this paper, we report results of a quantitative analysis of the effects of neutrons on DNA, and, specifically, the production of simple and double breaks of plasmid DNA in aqueous solutions with different concentrations of free-radical scavengers. The radiation damage to DNA was evaluated by electrophoresis through agarose gels. The neutron and gamma doses were measured separately with thermoluminescent detectors. In this work, we have also demonstrated usefulness of a new system for positioning and removing samples in channel BH#3 of the IEA-R1 reactor at the Instituto de Pesquisas Energeticas e Nucleares (Brazil) without necessity of interrupting the reactor operation. (C) 2010 Elsevier Ltd. All rights reserved.

New mechanical samples positioning system for irradiations on a radial channel at nuclear research reactor in a full-power continuous operation

This paper describes a new mechanical samples positioning system that allows the safe placement and removal of biological samples for prolonged irradiation, in a nuclear reactor during full-power continuous operation. Also presented herein the materials of construction and operating principles. Additionally, this sample positioning system is compared with an existing pneumatic and automated transfer system, already available at the research reactors. The system consists of a mechanical arm with a claw, which can deliver the samples for irradiations without reactor shutdown. It was installed in the lEA-R1 research reactor at Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, Brazil, and for the past 5 years, the system has successfully operated and allowed the conducting of important experiments. As a result of its introduction, the facility has been in a position to positively respond to the increased demand in studies of biology, medicine, physics, engineering, detector/dosimeter calibrations, etc. It is one example of the appropriated technologies that save energy and resources. (C) 2010 Elsevier Ltd. All rights reserved.

Temperature Dependence of the Intergranular Critical Current Density in Uniaxially Pressed Bi(1.65)Pb(0.35)Sr(2)Ca(2)Cu(3)O(10+delta) Samples

We have studied the normal and superconducting transport properties of Bi(1.65)Pb(0.35)Sr(2)Ca(2)Cu(3)O(10+delta) (Bi-2223) ceramic samples. Four samples, from the same batch, were prepared by the solid-state reaction method and pressed uniaxially at different compacting pressures, ranging from 90 to 250 MPa before the last heat treatment. From the temperature dependence of the electrical resistivity, combined with current conduction models for cuprates, we were able to separate contributions arising from both the grain misalignment and microstructural defects. The behavior of the critical current density as a function of temperature at zero applied magnetic field, J (c) (T), was fitted to the relationship J (c) (T)ae(1-T/T (c) ) (n) , with na parts per thousand 2 in all samples. We have also investigated the behavior of the product J (c) rho (sr) , where rho (sr) is the specific resistance of the grain-boundary. The results were interpreted by considering the relation between these parameters and the grain-boundary angle, theta, with increasing the uniaxial compacting pressure. We have found that the above type of mechanical deformation improves the alignment of the grains. Consequently the samples exhibit an enhance in the intergranular properties, resulting in a decrease of the specific resistance of the grain-boundary and an increase in the critical current density.

Intergranular properties of uniaxially pressed YBa(2)Cu(3)O(7-delta) ceramic samples

We performed measurements of electrical resistivity as a function of temperature, rho(T), in polycrystalline samples of YBa(2)Cu(3)O(7-delta) (Y-123) subjected to different uniaxial compacting pressures. We observed by using X-ray diffractometry that samples have a very similar composition. Most of the identified peaks are related to the superconducting Y-123 phase. Also, from the X-ray diffraction patterns performed, in powder and pellet samples, we estimated the Lotgering factor along the (00l) direction, F((00l)). The results indicate that F((00l)) increases from 0.13 to 0.16. From electrical resistivity measurements as a function of temperature, we were able to separate contributions arising from both the grain misalignment and microstructural defects. We found appreciable degradation in the normal-state transport properties of samples with an increase in uniaxial compacting pressure. It seems that this type of behavior is associated with an increase in the influence of microstructural defects at the intergranular level. The experimental results are analyzed in the framework of a current conduction model of granular samples.

Enhanced visualization of histological samples with an adjustable RGB contrast system with application for tissue used in photodynamic therapy

The analysis of histological sections has long been a valuable tool in the pathological studies. The interpretation of tissue conditions, however, relies directly on visual evaluation of tissue slides, which may be difficult to interpret because of poor contrast or poor color differentiation. The Chromatic Contrast Visualization System (CCV) combines an optical microscope with electronically controlled light-emitting diodes (LEDs) in order to generate adjustable intensities of RGB channels for sample illumination. While most image enhancement techniques rely on software post-processing of an image acquired under standard illumination conditions, CCV produces real-time variations in the color composition of the light source itself. The possibility of covering the entire RGB chromatic range, combined with the optical properties of the different tissues, allows for a substantial enhancement in image details. Traditional image acquisition methods do not exploit these visual enhancements which results in poorer visual distinction among tissue structures. Photodynamic therapy (PDT) procedures are of increasing interest in the treatment of several forms of cancer. This study uses histological slides of rat liver samples that were induced to necrosis after being exposed to PDT. Results show that visualization of tissue structures could be improved by changing colors and intensities of the microscope light source. PDT-necrosed tissue samples are better differentiated when illuminated with different color wavelengths, leading to an improved differentiation of cells in the necrosis area. Due to the potential benefits it can bring to interpretation and diagnosis, further research in this field could make CCV an attractive technique for medical applications.

Comparing diagnostic tests with missing data

When missing data occur in studies designed to compare the accuracy of diagnostic tests, a common, though naive, practice is to base the comparison of sensitivity, specificity, as well as of positive and negative predictive values on some subset of the data that fits into methods implemented in standard statistical packages. Such methods are usually valid only under the strong missing completely at random (MCAR) assumption and may generate biased and less precise estimates. We review some models that use the dependence structure of the completely observed cases to incorporate the information of the partially categorized observations into the analysis and show how they may be fitted via a two-stage hybrid process involving maximum likelihood in the first stage and weighted least squares in the second. We indicate how computational subroutines written in R may be used to fit the proposed models and illustrate the different analysis strategies with observational data collected to compare the accuracy of three distinct non-invasive diagnostic methods for endometriosis. The results indicate that even when the MCAR assumption is plausible, the naive partial analyses should be avoided.

Testing hypotheses in the Birnbaum-Saunders distribution under type-II censored samples

The two-parameter Birnbaum-Saunders distribution has been used successfully to model fatigue failure times. Although censoring is typical in reliability and survival studies, little work has been published on the analysis of censored data for this distribution. In this paper, we address the issue of performing testing inference on the two parameters of the Birnbaum-Saunders distribution under type-II right censored samples. The likelihood ratio statistic and a recently proposed statistic, the gradient statistic, provide a convenient framework for statistical inference in such a case, since they do not require to obtain, estimate or invert an information matrix, which is an advantage in problems involving censored data. An extensive Monte Carlo simulation study is carried out in order to investigate and compare the finite sample performance of the likelihood ratio and the gradient tests. Our numerical results show evidence that the gradient test should be preferred. Further, we also consider the generalized Birnbaum-Saunders distribution under type-II right censored samples and present some Monte Carlo simulations for testing the parameters in this class of models using the likelihood ratio and gradient tests. Three empirical applications are presented. (C) 2011 Elsevier B.V. All rights reserved.

Prevalence of Human Papillomaviruses in Urine Samples of Male Patients Infected With HIV-1 in Sao Paulo, Brazil

Human papillomavirus is a DNA virus that includes 118 genotypes. HPV16 is responsible for 80% of cervical cancer in women. Men are important reservoirs and major transmitters of HPV to their partners. The aim of this study was to detect HPV DNA and to determine the prevalence of HPV types 6, 11, 16, and 18 in urine samples of men infected with HIV-1. This study included 223 patients infected with HIV-1 from the Center of Reference on HIV/AIDS (CRT-SP) and an outpatient clinic of HIV. Urine samples were collected and after DNA extraction real-time PCR was performed for detection of HPV DNA. Positive samples were then tested by conventional PCR using type-specific primers for the four HPV types. A total of 223 men infected with HIV-1 were tested, 81% of whom were on HAART. Four (5.8%) were positive for HPV6, 18 (26.1%) were positive for HPV11, 22 (31.9%) were positive for HPV16 and five (7.2%) were positive for HPV18 by conventional PCR. Twenty (29%) patients had other HPV types and five patients (1.5%) had multiple types. The mean T CD4+cells count was 517 and 441 cells/mm(3) (P=0.30), in HPV negative and positive men, respectively. The HIV viral load was higher in the HPV negative group than for in the men with HPV (P=0.0002). A 30.9% prevalence of HPV was found in asymptomatic urine samples of men infected with HIV-1. This study suggests that urine may be a useful specimen for HPV screening. J. Med. Virol 81:2007-2011, 2009. (C) 2009 Wiley-Liss, Inc.

Development of a sequential injection-square wave voltammetry method for determination of paraquat in water samples employing the hanging mercury drop electrode

This work describes the development and optimization of a sequential injection method to automate the determination of paraquat by square-wave voltammetry employing a hanging mercury drop electrode. Automation by sequential injection enhanced the sampling throughput, improving the sensitivity and precision of the measurements as a consequence of the highly reproducible and efficient conditions of mass transport of the analyte toward the electrode surface. For instance, 212 analyses can be made per hour if the sample/standard solution is prepared off-line and the sequential injection system is used just to inject the solution towards the flow cell. In-line sample conditioning reduces the sampling frequency to 44 h(-1). Experiments were performed in 0.10 M NaCl, which was the carrier solution, using a frequency of 200 Hz, a pulse height of 25 mV, a potential step of 2 mV, and a flow rate of 100 mu L s(-1). For a concentration range between 0.010 and 0.25 mg L(-1), the current (i(p), mu A) read at the potential corresponding to the peak maximum fitted the following linear equation with the paraquat concentration (mg L(-1)): ip = (-20.5 +/- 0.3) Cparaquat -(0.02 +/- 0.03). The limits of detection and quantification were 2.0 and 7.0 mu g L(-1), respectively. The accuracy of the method was evaluated by recovery studies using spiked water samples that were also analyzed by molecular absorption spectrophotometry after reduction of paraquat with sodium dithionite in an alkaline medium. No evidence of statistically significant differences between the two methods was observed at the 95% confidence level.