Hypothesis testing in semiparametric additive mixed models

We consider testing whether the nonparametric function in a semiparametric additive mixed model is a simple fixed degree polynomial, for example, a simple linear function. This test provides a goodness-of-fit test for checking parametric models against nonparametric models. It is based on the mixed-model representation of the smoothing spline estimator of the nonparametric function and the variance component score test by treating the inverse of the smoothing parameter as an extra variance component. We also consider testing the equivalence of two nonparametric functions in semiparametric additive mixed models for two groups, such as treatment and placebo groups. The proposed tests are applied to data from an epidemiological study and a clinical trial and their performance is evaluated through simulations.     

Protein family alignment annotation

For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins. This open-source software includes methods for viewing and aligning protein families, and for annotating sequence structure and residues with known functions. It offers new options to aid the study of proteins, and an extensible annotation tool for bioinformatics developers.     

Viewing and annotating sequence data with Artemis

Artemis is a widely used software tool for annotating and viewing sequence data. No database is required to use Artemis. Instead, individual sequence data files can be analysed with little or no formatting, making it particularly suited to the study of small genomes and chromosomes, and straightforward for a novice user to get started. Since its release in 1999, Artemis has been used to annotate a diverse collection of prokaryotic and eukaryotic genomes, ranging from Streptomyces coelicolor to, more recently, a large proportion of the Plasmodium falciparum genome. Artemis allows annotated genomes to be easily browsed and makes it simple to add useful biological information to raw sequence data. This paper gives an overview of some of the features of Artemis and includes how it facilitates manual gene prediction and can provide an overview of entire chromosomes or small compact genomes--useful for uncovering unusual features such as pathogenicity islands.     

Numerical computation of distortions in magnetic fields and induced currents in physiological solutions produced by microscope objectives

Identifying distortions produced by commonly employed microscope objectives and their components in uniform DC and 60 Hz AC magnetic fields is important in imaging studies involving exposure of cells to spatially uniform or nonuniform magnetic fields. In this study, DC and 60 Hz AC magnetic flux densities were numerically computed in the presence of finite element models of various components of commonly utilized microscope objectives, as well as a model of a complete objective. Also computed were the distortions in the current density induced by an applied time-varying magnetic field in a physiological buffer contained within a Petri dish. We show that the magnetic flux density could be increased up to 65% in the presence of the nickel-chrome plating of an objective housing and that the presence of ferromagnetic components like a screw or spring could produce peaks that are 7% higher than the undistorted value of magnetic flux density. In addition, a slight tilt of 1% in the objective with respect to the magnetic field could cause a 93% deviation in magnetic flux density from the unperturbed value. These results correlate well with previously published experimental measurements that showed the presence of significant and sometimes asymmetric distortions in both DC and 60 Hz magnetic fields. Moreover, this study further reports that induced current density changed up to 37% compared to values in the absence of the objective. The existence of distortions in applied magnetic fields and induced currents could affect the interpretation of results of cell function studies if it is assumed that the cells are exposed to uniform magnetic flux densities in the presence of a microscope objective. Such assumptions of uniform magnetic flux density could also account for the lack of reproducibility in several studies that examined changes in intracellular calcium by imaging techniques.     

Physiologic and Yield Responses of Shaded Cotton to the Plant Growth Regulator PGR-IV

The plant growth regulator PGR-IV has been reported to improve the growth, boll retention, and yield of cotton (Gossypium hirsutum L.) under optimum growing conditions. However, little is known about the response of cotton to PGR-IV under low light stress. A 3-year field study was conducted to determine if applying PGR-IV before an 8-day period of shade (63% light reduction) benefitted the growth and yield of shaded cotton. Shading during early squaring did not affect yield. Shading after the first flower stage significantly increased leaf chlorophyll concentration and fruit abscission and decreased the leaf photosynthetic rate, nonstructural carbohydrate concentrations, and lint yield. Foliar application of PGR-IV at 292 mL ha⁻¹ at early squaring and first flower did not improve the leaf photosynthetic rate of shaded cotton. However, shaded plants receiving PGR-IV had higher nonstructural carbohydrate concentrations in the floral buds and significantly lower fruit abscission than the shaded plants without PGR-IV. Applying PGR-IV to the foliage before shading resulted in a numeric increase (6–18%) in lint yield compared with shaded plants without PGR-IV. The decreased fruit abscission from the application of PGR-IV was associated with improved assimilate translocation. The yield enhancement from foliar application of PGR-IV was attributed to increased fruit retention. However, the average boll weight of shaded plants with PGR-IV tended to be lower than that of shaded plants without PGR-IV. Lint percentage was not affected by PGR-IV. Foliar application of PGR-IV appears beneficial for increasing the fruit retention of shaded cotton. Received June 12, 1997; accepted January 19, 1998     

海蛇乙醇浸出物的营养成分分析

目的分析四种海蛇蛇体乙醇浸出物（ＡＥＢＦＳＳ）的营养成分。方法采用自动氨基酸分析仪,高效液相色谱仪和原子吸收分光光度仪。结果ＡＥＢＦＳＳ含有大量蛋白质和糖类物质;含有１９种氨基酸和１６种矿物元素。结论海蛇浸酒具有药用及营养功效。     

Structure-function relations of heparin-mimetic sulfated xylan oligosaccharides: inhibition of Human Immunodeficiency Virus-1 infectivity in vitro

Heparins/heparan sulfates modulate the function of proteins and cell membranes in numerous biological systems including normal and disease processes in humans. Heparin has been used for many years as an anticoagulant, and anticoagulant heparin-mimetics were developed several decades ago by chemical sulfation of non-mammalian polysaccharides, e.g., an antithrombotic sulfated xylan. This pharmaceutical, which comprises a mixture of sulfated oligoxylans, also mimics most other biological actions of natural heparins in vitro, including inhibition of the human immunodeficiency virus, but the molecular basis for these actions has been unclear. Here, numerous Components of the sulfated oligoxylan mixture were isolated and when bioassayed in the case of anti-HIV-1 infectivity revealed that a structural specificity underlines the capacity of sulfated xylan to inhibit HIV-1, rather than a non-specific mechanism. Components were isolated by chromatographic fractionation through Bio-Gel P10 in 0.5M ammonium bicarbonate. This fractionation revealed an elution range associated with apparent molecular weights of 22 000 to <1500 relative to standard heparin and heparan sulfates and newly prepared sulfated oligosaccharide standards. Components were characterized by metachromatic absorption spectroscopy, ultracentrifugation, GlcA analysis, and potency against HIV-1 infectivity, both in the tetrazolium cytotoxicity assay and in syncytium-forming assays, in CD4-lymphocytes. Structural specificity was indicated by the differential potencies exhibited by the Components: Highest activity (cytotoxicity) was exhibited by Components in the chromatographic region 5500 in mass (50% effective (inhibitory) concentration=0.5–0.7 g ml–1 in the first fractionation series, and 0.1–0.5 g ml–1 in a second series). The potency declined sharply below 5400 in mass, but with an exception; a second structure exhibiting relatively high potency eluted among low-mass oligosaccharides which had an average size of a nonomer. Components displayed differential potencies also against the syncytium-forming infectivity of HIV-1. The high potency against syncytium-formation was retained by Components down to a minimum size of about 4500 in mass, smaller than the 5400 required above. One in ten of the 1,4-linked xyloses in the native xylan are substituted with a monomeric 1,2 DGlcA branch. We have speculated that pharmaceutical actions of sulfated xylan might be related to structures involving the -D linked substituents and this was examined using a space-filling model of a sulfated octaxylan and by analyses of Components for GlcA content. Understanding structure/function relations in the heparin-like actions of these agents would be of general significance for the careful examination of their potential clinical usefulness in many human processes modulated by heparins, including AIDS.     

Environmental change and the phenology of European aphids

Aphids, because of their short generation time and low developmental threshold temperatures, are an insect group expected to respond particularly strongly to environmental changes. Forty years of standardized, daily data on the abundance of flying aphids have been brought together from countries throughout Europe, through the EU Thematic Network 'EXAMINE'. Relationships between phenology, represented by date of first appearance in a year in a suction trap, of 29 aphid species and environmental data have been quantified using the residual maximum likelihood (REML) methodology. These relationships have been used with climate change scenario data to suggest plausible changes in aphid phenology. In general, the date of first record of aphid species in suction traps is expected to advance, the rate of advance varying with location and species, but averaging 8 days over the next 50 years. Strong relationships between aphid phenology and environmental variables have been found for many species, but they are notably weaker in species living all year on trees. Canonical variate analysis and principal coordinate analysis were used to determine ordinations of the 29 species on the basis of the presence/absence of explanatory variables in the REML models. There was strong discrimination between species with different life cycle strategies and between species feeding on herbs and trees, suggesting the possible value of trait-based groupings in predicting responses to environmental changes.     

ITMSQ: A software tool for N‐ and C‐terminal fragment ion pairs based isobaric tandem mass spectrometry quantification

Tandem MS (MS2) quantification using the series of N‐ and C‐terminal fragment ion pairs generated from isobaric‐labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64 and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solutionfor N‐ and C‐terminal fragment ion pairs based isobaric MS2 quantitative methods.