Presmoothing the transition probabilities in the illness-death model

One major goal in clinical applications of multi-state models is the estimation of transition probabilities. In a recent paper, Meira-Machado et al. (2006) introduce a substitute for the Aalen-Johansen estimator in the case of a non-Markov illness-death model. The idea behind their estimator is to weight the data by the Kaplan-Meier weights pertaining to the distribution of the total survival time of the process. In this paper we propose a modification of Meira-Machado et al. (2006) estimator based on presmoothing. Consistency is established. We investigate the finite sample performance of the new estimator through simulations. Data from a study on colon cancer are used for illustration purposes.     

Tests of ordered hypotheses in linkage in heredity

The asymptotic null distribution of the likelihood ratio test for two cases of ordered hypotheses in a particular genetic model is considered. A simple iterative process is proposed in order to get the restricted estimates. It is shown that both tests have asymptotically a chi-bar squared distribution and the same size. A simulation study is also conducted in order to compare the usual unrestricted test with the corresponding one of ordered hypotheses. Finally, the results are extended to some special cases.     

Multiwalled carbon nanotube modified screen-printed electrodes for the detection of p-aminophenol: optimisation and application in alkaline phosphatase-based assays

Carboxylated multiwalled carbon nanotubes (MWCNT-COOH) were used to modify the working electrode surface of different screen-printed electrodes. The effect of this modification on the electrodic characteristics (double layer capacitance, electroactive area and heterogeneous rate constants for the electron transfer) was evaluated and optimized for the cyclic voltammetric determination of p-aminophenol. The enzymatic hydrolysis of p-aminophenylphosphate was employed for the quantification of alkaline phosphatase, one of the most important label enzymes in immunoassays. Finally, ELISA assays were carried out to quantify pneumolysin using this enzymatic system. Results obtained indicated that low superficial densities of MWCNT-COOH (0.03-0.06 μg mm⁻²) yielded the same electrodic improvements but with better analytical properties.     

Application of X-ray fluorescence analytical techniques in phytoremediation and plant biology studies

Phytoremediation is an emerging technology that employs the use of higher plants for the clean-up of contaminated environments. Progress in the field is however handicapped by limited knowledge of the biological processes involved in plant metal uptake, translocation, tolerance and plant–microbe–soil interactions; therefore a better understanding of the basic biological mechanisms involved in plant/microbe/soil/contaminant interactions would allow further optimization of phytoremediation technologies. In view of the needs of global environmental protection, it is important that in phytoremediation and plant biology studies the analytical procedures for elemental determination in plant tissues and soil should be fast and cheap, with simple sample preparation, and of adequate accuracy and reproducibility. The aim of this study was therefore to present the main characteristics, sample preparation protocols and applications of X-ray fluorescence-based analytical techniques (energy dispersive X-ray fluorescence spectrometry—EDXRF, total reflection X-ray fluorescence spectrometry—TXRF and micro-proton induced X-ray emission—micro-PIXE). Element concentrations in plant leaves from metal polluted and non-polluted sites, as well as standard reference materials, were analyzed by the mentioned techniques, and additionally by instrumental neutron activation analysis (INAA) and atomic absorption spectrometry (AAS). The results were compared and critically evaluated in order to assess the performance and capability of X-ray fluorescence-based techniques in phytoremediation and plant biology studies. It is the EDXRF, which is recommended as suitable to be used in the analyses of a large number of samples, because it is multi-elemental, requires only simple preparation of sample material, and it is analytically comparable to the most frequently used instrumental chemical techniques. The TXRF is compatible to FAAS in sample preparation, but relative to AAS it is fast, sensitive and multi-elemental. The micro-PIXE technique requires rather expensive instrumentation, but offers multi-elemental analysis on the tissue and cellular level.     

Chemical Approach to the Optimization of Conditions Using HS-SPME/GC–MS for Characterization of Volatile Compounds in Eugenia brasiliensis Fruit

Grumixama (Eugenia brasiliensis Lam.) is a native fruit of the Brazilian Atlantic Forest, belonging to the Myrtaceae family, which designatesthe most significant number of species with food potential. It stands out due to its phytochemical characteristics because of the presence of polyphenols and volatile organic compounds. Volatile compounds are substances released by foods that give off an aroma and influence flavor. Solid-phase microextraction is a technique that allows for low-cost, fast, and solvent-free extraction, has an affinity for numerous analytes, and is easily coupled to gas chromatography. The objectives of this work were to evaluate the efficiency of different fibers of SPME (solid-phase microextraction) in the extraction of volatile organic compounds from grumixama pulp; optimize a method for extraction time, temperature, and sample weight; and to determine the characteristic volatile profile of this fruit. For the extraction of volatile compounds, three fibers of different polarities were used: polar polyacrylate (PA) fibers, divinylbenzene/carboxyne/polydimethylsiloxane (DVB/CAR/PDMS) semipolar fibers, and polydimethylsiloxane/divinylbenzene (PDMS/DVB). Fourteen volatile organic compounds (VOCs) were identified by DVB/CAR/PDMS, six by PA, and seven by PDMS/DVB through solid-phase microextraction in the headspace mode (SPME-HS). Considering the total number of compounds identified, regardless of the fiber used, and the optimization of the method, Eugenia brasiliensis presented sesquiterpene fractions (85.7%, 83.3%, and 85.7% of total VOCs) higher than the monoterpene fractions (14.3%, 16.7%, and 14.3%) for DVB/CAR/PDMS, PA, and PDMS/DVB, respectively in its composition. In addition, it was possible to verify that the fiber DVB/CAR/PDMS presented a better efficiency due to the larger chromatographic area observed when the grumixama pulp was subjected to conditions of 75 °C, 2.0 g, and an adsorption time of 20 min.     

Analytical selenoamino acid studies by chromatography with interfaced atomic mass spectrometry and atomic emission spectral detection

Consumption of selenium enriched plants or yeast-based nutritional supplements has been reported to provide anticarcinogenic benefits which are selenium compound dependent. Separation and identification of these selenium compounds is critical to understand the activity. Plants and yeast convert inorganic selenium in the soil or growth media into organoselenium compounds, probably following a route similar to the sulfur assimilatory pathway. Non-volatile selenium compounds produced include selenoamino acids, some of which have shown anticarcinogenic activity. Volatile compounds produced by chemical reaction of involatile precursors have also been found. An ion pair chromatographic method with ICP-MS detection for the separation of selenoamino acid standards potentially present in real samples is given. The method allows separation of selenoamino acids including such analytes as the cis-trans isomers of Se-1-propenyl-dl-selenocysteine. The method also provides the capability of determining the presence of selenoxides and possibly selenones, and tracking of other functionalities and reactions by selective derivatization. Alternatively, selenoamino acids are treated with ethylchloroformate to produce stable volatile derivatives which are amenable to GC separation with element specific atomic emission detection (GC-AED). Results of total selenium determination and speciation of selenium enriched yeast-based nutritional supplements, selenium enriched allium vegetables and bioremediation samples are presented.     

Chromotropic acid-functionalized polyurethane foam: A new sorbent for on-line preconcentration and determination of cobalt and nickel in lettuce samples

A chromotropic acid-functionalized polyurethane foam has been developed for use in an on-line preconcentration system for cobalt and nickel determination. The packing material was prepared by covalent coupling of chromotropic acid with the polyurethane foam through an azo group. Co and Ni ions were sorbed in the mini-column, from which they could be eluted directly to the nebulizer-burner system of a flame atomic absorption spectrometer. Elution of cobalt and nickel from the mini-column can be accomplished with 0.50 and 0.75 M HCl solutions, respectively. The enrichment factors obtained were 22 (Co) and 27 (Ni), for 60 s preconcentration time, and 57 (Co) and 59 (Ni), if a preconcentration time of 180 s was used. Under the optimum conditions, the proposed procedure allowed the determination of metals with detection limits of 0.43 (cobalt) and 0.52 microg/L (nickel), respectively, on using preconcentration periods of 180 s. The accuracy of the developed procedure was evaluated by analysis of the certified reference materials NIST 1515 Apple Leaves and NIST 1570a Spinach Leaves. The method was applied to the analysis of lettuce samples. The contents of cobalt in the samples analyzed varied from 0.75 to 0.98 microg/g. Nickel was not detected in the lettuce samples.     

New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor

To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.