基于串级质谱信息进行蛋白质数据库搜索的结果可靠性分析

SEQUEST与Mascot为目前蛋白组学分析研究中使用最为广泛的蛋白质库搜索工具.尝试将Mascot与SEQUEST搜索结果进行比较,进而采用不同多变量判别方法对二者的搜索结果进行判别分析,以降低其结果的假阳性率.通过对Mascot与SEQUEST搜索结果进行比较,发现所得结果差异很大;利用多变量判别分析方法对Mascot及SEQUEST搜索结果进行判别分析,可有效提高SEQUEST结果中假阳性结果与正确结果之间的区分能力.对于Mascot搜索结果,采用多变量判别分析方法仍无法显著降低其假阳性结果,利用Decoy库搜索结果进行估计时亦存在导致错误估计的风险.     

Performance Test of Vitamin B6 Test Kit Candidate

Vitamin B6 test kit was designed as an alternative, affordable and user-friendly analysis tool for small and medium enterprises which process bananas. Its performance was evaluated twice with 70 respondents and the measurements considered satisfying when the results were laid in the range of one square deviation from the real value that determined by spectrophotometer. Performance tests results then compared to pH measurement using pH indicator, the more familiar test kit that also rely on human ability to distinguish color. The first performance test to respondents that closely related to chemical measurement got 33 success results and 29 respondents gave satisfying results which was comparable to pH measurement that gave 31 of 33 satisfying results. The second performance test was conducted by 70 respondents which involving respondents with background that unrelated to chemical measurement. As much as 34 success results for both measurements from the related group but only 32 and 27 success measurements for pH measurement and Vitamin B6 measurement using kit, respectively, from the unrelated group. The second performance test results for pH measurement did not give significant difference with the second one, 34 of 35 satisfying results from closely related group and 27 of 32 from unrelated group. Second performance test results for Vitamin B6 was significantly different from the first one since the respondents required to conduct the measurement twice and the results were reported as average values. Vitamin B6 kit gave 23 of 61 satisfying results with 15 of 34 were from the closely related group and 8 of 27 from the unrelated group. Data from closely related group from second performance test were further analyzed by considered as two separated measurements and compared to the results from the first performance test. It was found that measurement conducted first gave only 2 of 34 satisfying results compared to 22 of 34 from measurement conducted at second. The results were also recapitulated and analyzed based on background and gender. Closely related group gave 44.12%, 29.41%, 26.47% satisfying, query and unsatisfied measurement results, respectively. These results were better compare to the unrelated group that only gave 29.63%, 25.93% and 44.44%. Female respondents gave 36.36%, 36.36%, 27.27% satisfying, query and unsatisfied measurement results, respectively, which better than male respondents that gave 41.18%, 5.88% and 52.94%. Vitamin B6 kit had good performance as a test kit candidate but still required many improvements so the measurement results doesn’t affected by gender, user background and number of conducted measurement. Better design of color chart was a proposed improvement to reduce the fatigue of eye's conical cell that will be conducted in the next study.     

Structure of amorphous poly-(ethylmethacrylate): a wide-angle x-ray scattering study

The local, temperature dependent structure of poly-(ethylmethacrylate) was studied with wide-angle x-ray scattering. The results were set into context to recent wide-angle neutron scattering results as well as to the results from a multitude of studies of the dynamics of this polymer. The temperature dependence of the wide angle x-ray results point to the development of local order which is backed by the neutron scattering results and which is connected to characteristic temperatures of the relaxation dynamic T(g) and T(c). The poly-(ethylmethacrylate) was studied in its predominantly syndiotactic as well as predominantly isotactic state displaying vastly different local structures as manifested in the x-ray results.     

COMPUTER SIMULATION OF POLYMER SOLUTION THERMODYNAMICS

The statistical counting method for the computer simulation of the ther-modynamic quantities of polymer solution has been reviewed. The calculating results fora single athermal chain confirm the theory of the renormalization group. The results forthe athermal solution are consistent with the scaling law of the osmotic pressure with theexponent 2.25. The results for a single chain with the segmental interaction are in a goodagreement with the exact results obtained by the direct counting method. The results forthe polymer solution show us that the Flory-Huggins parameter is strongly dependent onboth the polymer concentration and the interaction energy between segments. Monte carlo simulation; Polymer solution; Thermodynamic quantities;Translational entropy; Conformational entropy; Scaling law     

Extremal Catacondensed Benzenoids

Some results with respect to Hosoya index and Merrifield–Simmons index of tree-type hexagonal systems (catacondensed hydrocarbons) are shown. Using the results, the tree-type hexagonal systems with minimum, second minimum Hosoya index and maximum, second maximum Merrifield–Simmons index are determined. These results generalize some known results on extremal hexagonal chains.     

Use of glassy carbon as a working electrode in controlled potential coulometry

Glassy carbon has been used as the working electrode in controlled potential coulometry. The results of coulometric investigations of chromium, copper, iron, uranium and neptunium are compared with results obtained with platinum or mercury working electrodes. The accuracy of results with the glassy carbon electrode compares favourably with the results obtainable with the other electrodes, but the precision is poorer.     

AB initio molecular orbital calculations on the pentadienyl radical

In this publication we present the results of ab initio Gaussian orbital calculations of ESR coupling constants in the pentadienyl radical. The results are compared with experiment and with the results of similar semi-empirical calculations.     

L'analyse thermique differentielle est-ce encore bien raisonnable

Through two simple and well-known examples, there are shown the limits and defects of DTA method of investigation in comparison of results obtained recently with true and moderns calorimeters. Today we must not confuse the true calorimetrical results with the DSC results (or DTA masked results) which give only an estimated value of temperature and heat about the phenomenon.     

Phase behavior of short-range square-well model

Various Monte Carlo techniques are used to determine the complete phase diagrams of the square-well model for the attractive ranges lambda = 1.15 and lambda = 1.25. The results for the latter case are in agreement with earlier Monte Carlo simulations for the fluid-fluid coexistence curve and yield new results for the liquidus-solidus lines. Our results for lambda = 1.15 are new. We find that the fluid-fluid critical point is metastable for both cases, with the case lambda = 1.25 being just below the threshold value for metastability. We compare our results with prior studies and with experimental results for the gamma(II)-crystallin.     

Full CI benchmark calculations for molecular properties

Full CI calculations of first- and second-order properties are presented to provide benchmark results for comparisons with other methods, such as multireference CI(MRCI). The full CI(FCI) polarizability of F^– is computed using a double zeta plus polarization plus diffuse basis set. These FCI results are compared to those obtained at other levels of theory; the CASSCF/MRCI with Davidson correction results are in excellent agreement with the FCI. Differences between the polarizability results computed as a (numerical) second derivative of the energy or as an induced dipole moment are also discussed. FCI calculations are presented for the dipole moment and polarizability of HF, CH₂ and SiH₂ using a DZP basis set. Again, the CASSCF/MRCI values are in excellent agreement with the FCI results, whereas SDCI values, whether computed as an expectation value or as an energy derivative, are much worse. The results obtained using the CPF approach are in considerably better agreement with the FCI results than SDCI, and are similar in quality to the SDCI energy derivative results with the inclusion of Davidson's correction.     

A review of the relationship between quality control and donor sample results obtained from serological assays used for screening blood donations for anti-HIV and hepatitis B surface antigen

Quality control principles, initially designed for manufacturing, have been applied to clinical chemistry and later to serological testing for infectious diseases. Methods for setting control limits have been included using the effects of assay performance on clinical outcomes. However, this approach assumes that the reactivity of patient samples change proportionally with the results of quality control samples tested in the same assay. Although this may be the case for clinical chemistry, this assumption has never been tested for serological assays. During a 9-month period, 177910 and 185684 donor test results for HBsAg and anti-HIV, respectively, were analysed and compared with 712 HBsAg and 710 anti-HIV results obtained from a single batch of a multimarker quality control sample obtained from the same assays. Results of the analysis showed that the negative donor results did not change in proportion with the changes experienced by the quality control sample results as determined by regression coefficients, particularly when results obtained from different reagent batches were compared. There were insufficient results obtained from positive samples for a similar analysis. However, investigations show that, even if the reactivity of positive donor samples changed in proportion with the change in reactivity of the quality control sample, few false-negative donor test results would have occurred.     

Thermoluminescence detection of irradiated fruits and vegetables: international interlaboratory trial

An international interlaboratory trial was conducted to validate thermoluminescence methods for detecting irradiated fruits and vegetables. Five products were used in this study. This paper presents the results from prestudy material, homogeneity testing, details of sample preparation, and participants' results. Prestudy results provided a basis for cross comparison of instruments in different laboratories. A wide range of sensitivities, reproducibilities, and signal-to-background ratios were observed. Homogeneity testing showed that the method can distinguish between nonirradiated and irradiated products, including those bleached with 100 J/cm2 artificial daylight, provided that sensitivity rejection criteria are rigorously applied. Blind results were returned by 9 participants in the form of first and second glow integrals and glow ratios for all samples and a qualitative classification for each product. Of the 387 results reported, 327 valid results were obtained from participants. Where valid data were obtained, correct qualitative identifications were made by participants in all cases. Participants' results and homogeneity testing both confirm the validity of the thermoluminescence method for detecting irradiated fruits and vegetables.     

Assessment of uncertainty in pesticide multiresidue analytical methods: main sources and estimation

The estimation of the uncertainty associated to analytical methods is necessary in order to establish the comparability of results. Multiresidue analytical methods lack very often of information about uncertainty of results with likely implications when results are compared with maximum residue levels (MRL) established by regulations. An adequate identification and estimation of each uncertainty source allows to laboratories to establish the accuracy of results and to balance with time-consuming and costs.     

The application of computer curve fitting techniques to regnault-pfaundler calculations of calorimetric data

A curve fitting programme, using a cubic-spline technique, is described for fitting the results from reaction calorimetry. The coefficients from the technique are used to determine the mean resistance and other correction terms in a Regnault-Pfaundler analysis; the results agree with hand-worked results to better the 0.5%. The difficulties of using polynomial techniques are discussed and the importance is noted of computer plotting of results in checking the behaviour of the techniques.     

On the conductivity of an 0.01D aqueous potassium chloride solution

In a recent paper in this Journal, Saulnier and Barthel presented results for the electrolytic conductivity of 0.01 D potassium chloride solutions which they measured in a new type of conductance cell capable of absolute measurements at 0, 18 and 25°C. Their results disagreed by more than they expected from the results of Jones and Bradshaw at 18 and 25°C after they corrected the Jones and Bradshaw results to the absolute ohm and to the IPTS 1968. However their conversion was in error. The correct conversion is given and a recomparison is made with the Jones and Bradshaw results.     

Comparability and compatibility of proficiency testing results in schemes with a limited number of participants

Comparability and compatibility of proficiency testing (PT) results are discussed for schemes with a limited number of participants (less than 20–30) based on the use of reference materials (RMs) as test items. Since PT results are a kind of measurement/analysis/test result, their comparability is a property conditioned by traceability to measurement standards applied in the measurement process. At the same time, metrological traceability of the certified value of the RM (sent to PT participants as test items) is also important, since the PT results are compared with the RM certified value. The RM position in the calibration hierarchy of measurement standards sets the degree of comparability for PT results, which can be assessed in the scheme. However, this assessment is influenced by commutability (adequacy or match) of the matrix RM used for PT and routine samples. Compatibility of PT results is a characteristic of the collective (group) performance of the laboratories participating in PT that can be expressed as closeness of the distribution of the PT results to the distribution of the RM data. Achieving quality-of-measurement/analysis/test results in the framework of the concept “tested once, accepted everywhere” requires both comparability and compatibility of the test results.     

Modelling and measuring the thermal conductivity of multi-metallic Zn/Cu nanofluid

A metallic nanofluid is a suspension of metallic nanoparticles in a base fluid. Multi-metallic nanoparticles are a combination of two or more types of metallic particles. Such multi-metallic nanoparticles were suspended in water using an ultrasonic vibrator for different total volume fractions and different ratios of metallic/metallic nanoparticles. A transient hot wire setup was built to measure the thermal conductivity of the nanofluid at different temperatures. The experimental results were in good agreement with the results in the literature. Then, the experimental results were used as input data for an adaptive neural fuzzy inference system (ANFIS) to predict the thermal conductivity of the multi-metallic nanofluid. The maximum deviation between the ANFIS results and experimental measurements was 1 %. The predicted results and the experimental data were compared with other models. The ANFIS model was found to have good ability to predict the thermal conductivity of the multi-metallic nanofluid over the range of the experimental results.     

Calculation of diffusion coefficients for carbon dioxide + solute system near the critical conditions by non-equilibrium molecular dynamics simulation

A non-equilibrium molecular dynamics simulation was adopted to calculate the diffusion coefficients for a pseudo-binary system of carbon dioxide and for a carbon dioxide + solute system at 308.2 and 318.2 K. The calculated results were compared with the self- and tracer diffusion coefficients calculated by an equilibrium molecular dynamics simulation. The simulated results for the pseudo-binary system of carbon dioxide by the non-equilibrium molecular dynamics simulation are in good agreement with the results of self diffusion coefficients for pure carbon dioxide by the equilibrium molecular dynamics simulation. The simulated results of mutual diffusion coefficients for the carbon dioxide + solute system by the non-equilibrium molecular dynamics simulation are slightly lower than the results of the tracer diffusion coefficients by the equilibrium molecular dynamics simulation. The anomalous behavior of diffusion coefficients near the critical concentration was represented by the results of the non-equilibrium molecular dynamics simulation.     

Screening of hydrodynamic interactions in Brownian rod suspensions

We present the details and results of a simulation study addressing the dynamics and rheology of rod suspensions over a wide regime of concentrations ranging from dilute to concentrated systems. Our study compares the results of two complementary simulation methods. The first method adapts a recently proposed explicit solvent simulation strategy and incorporates both hydrodynamical effects and steric interactions between the rod units. We compare the results of such a method with those obtained from a Brownian dynamics simulation approach which retains the steric interactions but neglects the effects of hydrodynamic interactions. Overall, our results in the context of the translational and rotational diffusivities are in agreement with the hydrodynamical predictions in the dilute regime and the corresponding results of the tube model and its extensions thereof in the semidilute regimes. The latter results suggest that effects of hydrodynamic interactions on the translational and rotational diffusivities are secondary relative to the steric interactions and at best lead only to a small correction to the results of the classical tube model. Our results in the context of linear viscoelasticity also broadly confirms the predictions of the tube model for the storage and loss moduli and allows us to extract for the first time the independent hydrodynamic and Brownian contributions to the zero shear viscosity. While the relative magnitudes of these contributions are consistent with the theoretical predictions, the quantitative magnitudes are quite different from the theoretical predictions. Overall, these results confirm the validity of the hydrodynamic "screening" hypothesis and ratify the neglect of hydrodynamical stresses in quantifying the linear rheology of Brownian rod suspensions.     

The kinetics and molecular modeling of the complexation of tenoxicam with cyclodextrins in solution

The effect of cyclodextrins on photodegradation of tenoxicam (TEN) was studied at pH 4, 7 and 10. After 60 min of irradiation with UV light, the photodegradation was extensive. All cyclodextrins (alpha, beta, or gamma) stabilize TEN and reduce the rate of photodegradation. The largest effect of cyclodextrins is at pH 7. Molecular modeling results help to explain and manipulate the results. The results are discussed and compared with other results from previous studies.