A Note on Binary Contingency Tables

This paper considers contingency tables in which the marginal frequencies for one variable are all 1. This could occur with two-category binary data or when a continuous variable is treated in categorical fashion. Some results concerning the expectation of goodness-of-fit statistics are reported. In particular it is noted that the expectation of the Pearson statistic is independent of the model being fitted.     

Sublethal effects of pyriproxyfen,a juvenile hormone analogue,on Plutella xylostella (Lepidoptera: Plutellidae): life table study

The sublethal effects of pyriproxyfen (PYR, a juvenile hormone analogue) were investigated for two consecutive generations on life-history parameters, such as developmental time, pupal weight, fecundity, fertility and longevity of the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae). After topical application bioassay of third instar larvae, the LC₂₅ and LC₅₀ values (as sublethal doses) were determined to be 1.49 and 2.01 μg/μl, respectively. The results showed that the egg incubation period, larval and pupal duration times and oviposition period were increased in treated groups compared with the control (treated with distilled water). Pupal weight, adult longevity, fecundity and fertility were significantly reduced in the treatment groups compared with the control. Using the age-stage, two-sex life table analysis, we found that the intrinsic rate of increase (r), finite rate of increase (λ), gross reproduction rate (GRR) and net reproductive rate (R ₀) significantly decreased while the mean generation time (T) and doubling time (DT) increased in two treatment groups compared with the control. In addition, administration of PYR induced morphogenetic abnormalities including untanned pupae, larval–pupal intermediates and various defective adults. The LC₅₀ value was more effective on all of the above biological characteristics than the LC₂₅ for both generations, although parents were more affected than the offspring. In general, our results revealed that PYR was highly effective against P. xylostella in the laboratory both directly (causing mortality) and indirectly (disruption of normal growth and development). We conclude that PYR is an excellent candidate for suppressing populations of P. xylostella through its sublethal effects.     

Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues.

Amino acid substitution tables are calculated for residues in membrane proteins where the side chain is accessible to the lipid. The analysis is based upon the knowledge of the three-dimensional structures of two homologous bacterial photosynthetic reaction centers and alignments of their sequences with the sequences of related proteins. The patterns of residue substitutions show that the lipid-accessible residues are less conserved and have distinctly different substitution patterns from the inaccessible residues in water-soluble proteins. The observed substitutions obtained from sequence alignments of transmembrane regions (identified from, e.g., hydrophobicity analysis) can be compared with the patterns derived from the substitution tables to predict the accessibility of residues to the lipid. A Fourier transform method, similar to that used for the calculation of a hydrophobic moment, is used to detect periodicity in the predicted accessibility that is compatible with the presence of an alpha-helix. If the putative transmembrane region is identified as helical, then the buried and exposed faces can be discriminated. The presence of charged residues on the lipid-exposed face can help to identify the regions that are in contact with the polar environment on the borders of the bilayer, and the construction of a meaningful three-dimensional model is then possible. This method is tested on an alignment of bacteriorhodopsin and two related sequences for which there are structural data at near atomic resolution.     

Asymptotical Tests on the Equivalence,Substantial Difference and Non‐inferiority Problems with Two Proportions

Let d = p₂ ? p₁ be the difference between two binomial proportions obtained from two independent trials. For parameter d, three pairs of hypothesis may be of interest: H₁: d ≤ δ vs. K₁: d > δ; H₂: d ? (δ₁, δ₂) vs. K₂: d ∈ (δ₁, δ₂); and H₃: d ∈ [δ₁, δ₂] vs. K₃: d ? [δ₁, δ₂], where H_i is the null hypothesis and K_i is the alternative hypothesis. These tests are useful in clinical trials, pharmacological and vaccine studies and in statistics generally. The three problems may be investigated by exact unconditional tests when the sample sizes are moderate. Otherwise, one should use approximate (or asymptotical) tests generally based on a Z‐statistics like those suggested in the paper. The article defines a new procedure for testing H₂ or H₃, demonstrates that this is more powerful than tests based on confidence intervals (the classic TOST – two one sided tests – test), defines two corrections for continuity which reduce the liberality of the three tests, and selects the one that behaves better. The programs for executing the unconditional exact and asymptotic tests described in the paper can be loaded at http://www.ugr.es/~bioest/software.htm. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment

The discovery that the functions of most eukaryotic gene products are mediated through multi-protein complexes makes the prediction of protein interactions one of the most important current challenges in structural biology. Rigid-body docking methods can generate a large number of alternative candidates, but it is difficult to discriminate the near-native interactions from the large number of false positives. Many different scoring functions have been developed for this purpose, but in most cases, experimental and biological information is still required for accurate predictions. We explore here the use of evolutionary restraints in evaluating rigid-body docking geometries. In order to identify potential interface residues we identify functional residues based on the comparison of observed amino acid substitutions with those predicted from local environment. The interface residues identified by this method are correctly located in 85% of the cases. These predicted interface residues are used to define distance restraints that help to score rigid-body docking solutions. We have developed the pyDockRST software, which uses the percentage of satisfied distance restraints, together with the electrostatics and desolvation binding energy, to identify correct docking orientations. This methodology dramatically improves the docking results when compared to the use of energy criteria alone, and is able to find the correct orientation within the top 20 docking solutions in 80% of the cases.     

云龟履硕蚧的生物学及其自然种群生命表

云龟履硕蚧Perissopneumonxyliae (Ayyar)主要分布于云南玉溪、曲靖、楚雄等地 (州 )的板栗产区 ,是板栗的主要害虫之一。该虫在云南易门每年发生 1代 ,幼虫有 3龄 ,以 3龄若虫在树皮缝隙或树干基部越冬。高温、雨水冲刷、瓢虫捕食、紫胶白虫Eublemmaamabilis捕食和白蜡虫花翅跳小蜂Microterysericeri寄生是其主要的自然控制因子     

A life table study on three genetic strains of Ophryotrocha diadema (Polychaeta,Dorvilleidae)

A life-table study was performed on three strains of Ophryotrocha diadema. The wild type strain, YY (yellow eggs), was compared with a recessive mutant strain, ww (white eggs), and the F₁, hybrid, Yw.

The viability of the YY strain was greater than that of the ww strain. The hybrids were intermediate. Expectation of life. e., of zygotes were: YY 27.9, Yw 19.1, and ww 15.1 wk, respectively. The total outcome of reproduction followed the same pattern; the net reproductive rates, R ₀, were related as 1:0.62:0.47 for YY: Yw: ww.

Reproduction began in the fourth week. A maximum reproductive output during the next 4 wk was followed by a fast decline. The intrinsic rate of natural increase, r, was 0.880 per week for the YY strain, 0.903 for the Yw strain and 0.872 for the ww strain. For all strains, the first 7 wk of reproduction contributed more than 99% of the Lotka equation σ e ^?rx l _x m _x = l, i.e., l _x m _x values at older ages would not substantially affect population growth. In this 7–wk period (and the previous nonreproductive weeks), mortality differences were small among strains. During the period of maximum reproduction the average size of egg masses was approximately the same in all strains. The heterozygote superiority was due to shorter intervals between successive spawnings.

It is suggested that in the opportunistic species O. diadema deviations from an r–selected reproductive pattern are due to small adult size and to its ancestry from a mainly K–selected, very old polychaete group.

O. diadema has proven to be a useful test animal for marine pollution research. Observed effects on survival and reproduction have been summarized in a model to demonstrate population consequences of sublethal pollutant levels.     

Competing risk analysis for life table data with known observation times

"Several models have been proposed for the analysis of cohort mortality in the presence of competing risks.... This paper describes a maximum likelihood approach to the analysis of follow up data in life table format for the case of two competing risks--a specific cause and its competing complement. The model developed uses a robust survivorship assumption--the piecewise exponential--and takes into account information on time to death and time to withdrawal." (summary in GER)