An Integrated Formulation for Comparing Treatments with Binary Response with a Control

The problem of comparing k(≧2) bernoulli rates of success with a control is considered. An one-stage decision procedure is proposed for either (1) choosing the best among several experimental treatments and the control treatment when the best is significantly superior or (2) selecting a random size subset that contains the best experimental treatment if it is better than the control when the difference between the best and the remaining treatments is not significant. We integrate two traditional formulations, namely, the indifference (IZ) approach and the subset selection (SS) approach, by seperating the parameter space into two disjoint sets, the preference zone (PZ) and the indifference zone (IZ). In the PZ we insist on selecting the best experimental treatment for a correct selection (CS₁) but in the IZ we define any selected subset to be correct (CS₂) if it contains the best experimental treatment which is also better than the control. We propose a procedure R to guarantee lower bounds P₁* for P(CS₁≧PZ) and P₂* for P(CS₂≧IZ) simultaneously. A brief table on the common sample size and the procedure parameters is presented to illustrate the procedure R.     

Genetic analysis of Karnal bunt (Neovossia indica) resistance in wheat

Embryos excised from seeds of six generations (P₁, P₂, F₁, BC₁, BC₂ and F₂) of a cross WH 283 x WH 533 were cultured on modified MS medium already inoculated with secondary sporidia ofNeovossia indica. Significant variations for callusing response (CR) (54.55–75.55%) were observed among generations but the presence or absence ofN. indicia did not affect callusing response. A clear inhibition zone (IZ) was formed around each embryo showing callusing. The diameter of IZ varied significantly among generations and was maximum in the resistant genotype, WH 283 (3.60 cm). Fresh weight and dry weight of calli, initiated from embryo cultured and inoculated withN. indica, varied significantly among generations. Coefficient of infection as well as percentage of infection reflected the overdominance of susceptibility. Generation mean analysis showed that the three parameter model was adequate for diameter of IZ only. Six-parameter model showed that additive (in presence ofN. indica), additive and additive x dominance (in absence ofN. indica) effects were also significant. Complementary type of epistasis for fresh weight of calli and dominance, and dominance x dominance effects for dry weight of calli were observed in the presence ofN. indica. Magnitude of additive effects was higher for diameter of IZ in three parameter model. Therefore, selection might assist in improving this trait and thus indirectly help in attaining the resistance towardsN. indica.     

Clade support measures and their adequacy

In addition to hypothesis optimality, the evaluation of clade (group, edge, split, node) support is an important aspect of phylogenetic analysis. Here we clarify the logical relationship between support and optimality and formulate adequacy conditions for support measures. Support, S, and optimality, O, are both empirical knowledge claims about the strength of hypotheses, h₁, h₂, …h_n, in relation to evidence, e, given background knowledge, b. Whereas optimality refers to the absolute strength of hypotheses, support refers to the relative strength of hypotheses. Consequently, support and optimality are logically related such that they vary in direct proportion to each other, S(h | e,b) ∝ O(h | e,b). Furthermore, in order for a support measure to be objective it must quantify support as a function of explanatory power. For example, Goodman–Bremer support and ratio of explanatory power (REP) support satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and calculate support as a function of explanatory power. As such, these are adequate measures of objective support. The equivalent measures for statistical optimality criteria are the likelihood ratio (or log‐likelihood difference) and likelihood difference support measures for maximum likelihood and the posterior probability ratio and posterior probability difference support measures for Bayesian inference. These statistical support measures satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and to that extent are internally consistent; however, they do not quantify support as a function of explanatory power and therefore are not measures of objective support. Neither the relative fit difference (RFD; relative GB support) nor any of the parsimony (bootstrap and jackknife character resampling) or statistical [bootstrap character resampling, Markov chain Monte Carlo (MCMC) clade frequencies] support measures based on clade frequencies satisfy the adequacy condition S(h | e,b) ∝ O(h | e,b) or calculate support as a function of explanatory power. As such, they are not adequate support measures. © The Willi Hennig Society 2008.     

A Selection Procedure for Selecting Good Exponential Populations

Consider k independent exponential populations with location parameters μ₁,…, μ_k and a common scale parameter or standard deviation θ. Let μ_(k) be the largest of the μ's and define a population to be good if its location parameter exceeds μ_(k) –Δ₁. A selection procedure is proposed to select a subset of the k populations which includes the good populations with probability at least P*, a pre-assigned value. Simultaneous confidence intervals, that can be derived with the proposed selection procedure, are discussed. Moreover, if populations with locations below μ_(k) –δ₂, (δ₂ > δ₁) are “bad”, a selection procedure is proposed and a sample size is determined so that the probability of omitting a “good” population or selecting a “bad” population is at most 1 – P*.     

Selecting the Best Population,Provided It Is Better than a Control: The Unequal Variance Case

Bechhofer and Turnbull (1978) proposed two procedures to compare k normal means with a standard and the procedures guarantee that (1) with probability at least P₀* (specified), no category is selected when the best experimental category is sufficiently worst than the standard, and (2) with probability at least P₁* (specified), the best experimental category is selected when it is sufficiently better than the second best and the standard. For the case of common known variance, they studied a single-stage procedure. For the case of common unknown variance, they studied a two-stage procedure. Under the same formulation of Bechhofer and Turnbull (1978) and for the same selection goals (1) and (2) described above, Wilcox (1984a) proposed a procedure to the case of unknown and unequal variances, and supplied a table of the necessary constants to implement the procedure. This paper considers the case of unknown and unequal variances for the same formulation of Bechhofer and Turnbull, and Wilcox, but assumes that μ₀ is an unknown control. A two-stage procedure is proposed to solve the problem. A lower bound of the probability of a correct selection is derived and it takes the same form as the double integral appeared in Rinott (1978) which was used for the lower bound of the probability of a correct selection for a different selection goal.     

Survival Chances of Mutants Starting With One Individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N mutants W_n^M(N) after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and W_n^S(N) after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction W_∞^S(0) are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N_p primary mutants and N_m of the new form W_n^M(N_p, N_m) after the multiplication phase M of the n-th generation (probability ε of an error in the replication of the primary mutant giving the new form) and W_n^S(N_p, N_m) after the following selection phase S (probabilities β_p and β_m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained.     

Conformational analysis of an EP24.15 inhibitor by NMR and molecular modelling

Summary The enzyme thimet oligopeptidase (EC3.4.24.15, EP24.15) is responsible for the hydrolysis of a number of neuropeptides. Despite much research examining its substrate specificity, little is known about the conformational requirements of its active site. We have used 1D¹H and 2D TOCSY NMR experiments to assign the proton resonances of the EP24.15 inhibitor,N-[1-(R, S)-carboxy-3-phenylpropyl]-Ala-Ala-Tyr-p-aminobenzoate (cFP), and 2D ROESY NMR to investigate whether cFP exhibits any conformational preferences in CD₃OD and in aqueous CD₃OD. Molecular modelling of charged cFP in the gaseous phase generated a number of conformations that were consistent with the NMR data obtained in CD₃OD. Analogous modelling on the uncharged cFP did not result in conformations consistent with any of the NMR data, but did suggest that, under non-polar conditions, cFP could adopt a hairpin conformation which would allow simultaneous coordination of the two carboxyl groups of cFP to the zinc ion in the active site of EP24.15.     

Solvent-mediated conformational transition in β-alanine containing cyclic peptides. VIII

In the present paper we describe the solution nmr structural analysis and restrained molecular dynamic simulation of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-β-Ala-β-Ala). The conformational analysis carried out in CD₃CN and dimethylsulfoxide (DMSO) solutions by nmr spectroscopy was based on interproton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. A restrained molecular dynamic simulation in vacuo was also performed to build refined molecular models. The molecule is present in both solvent systems as two slowly interconverting conformers, characterized by a cis-trans isomerism around the β-Ala⁵-Pro¹ peptide bond. In CD₃CN solution, the conformer with a cis peptide bond is quite similar to that observed in the solid state, while the conformer containing all trans peptide bonds is characterized by an intramolecular hydrogen bond stabilizing a C₁₀- and a C₁₃-ring structure. In DMSO solution, the trans isomer is partly similar to that observed in CD₃CN solution while the cis isomer is different from that observed in the solid state. The effect of the solvent in stabilizing different conformations was also investigated in DMSO-CD₃CN solvent mixtures. © 1996 John Wiley & Sons, Inc.     

Definitive Solution Structures for the 6-Formylated Versions of 1-(βD-Ribofuranosyl)-, 1-(2′-Deoxy-β-D-Ribofuranosyl)-, and 1-β-D-Arabinofuranosyluracil,and of Thymidine

Abstract

ROESY and NOESY NMR spectroscopic analyses of the ribofuranosyl (1a), 2′-deoxyribofuranosyl (1b), and arabinofuranosyl (1c) derivatives of 6-formyluracil in (CD₃)₂SO and D₂O solutions have established that each exclusive 7,05′-cyclic hemiacetal diastereomer of 1a,b and the major 7,O2′-cyclic hemiacetal diastereomer of 1c possess the 7R configuration. In addition, (7R)-1c has been shown to be thermodynamically more stable than (7S)-1c, contrary to our previous indication. A new, higher yielding synthetic route to 1a has been developed, 1b has been obtained for the first time in crystalline form, the route to 1c has been modified to better accommodate large scale preparations, and a new, fourth member of this class, 6-formylthymidine (1d), has been synthesized and its solution structures in (CD₃)₂SO, D₂O, and CD₃OD have been determined. Antitumor and antiviral evaluations of 1a-c have revealed no significant levels of activity.     

Micro-phase separation and configuration of ABC triblock copolymer in ultra-thin film by Monte Carlo simulation

A Monte Carlo simulation using the bond fluctuation and cavity diffusion algorithms was adopted to investigate the micro-phase separation of ABC triblock copolymer in ultra-thin film on simple cubic lattice. Simulations reveal that the morphologies of ABC copolymer films are dependent on not only the volume fraction of the middle block B (f _B) but also on the ratio of interaction between different kinds of blocks (?_(AC)/?_(AB)). As for the molecular orientation, the copolymers stretch parallel to the flat surface at lower f _B, but tend to align perpendicularly along z direction at higher f _B. Furthermore, the chain configuration was discussed in detail. Smaller ?_(AC)/?_(AB) is beneficial to the formation of a “loop” configuration, whereas, larger ?_(AC)/?_(AB) would result in a “bridge” configuration of ABC triblock copolymer chains. The formation of micro-phase structures was illustrated intuitively by the molecular orientation and the chain configuration.     

The morphological study on the adrenal gland of African ostrich chicks

The morphology of the adrenal gland has been studied for a number of animal species all over the world, yet the detailed data about ostrich chick has not been reported. In the present study, the morphological features of the adrenal gland in African ostrich chicks were investigated by means of gross anatomy, light and electron microscope. Differences between the left and right adrenal glands were found in shape, size and location. The interrenal tissue and chromaffin cell interdigitated irregularly. The interrenal tissue was divided into a peripheral zone (PZ) and a central inner zone (CZ), and the PZ was further distinguished into an outer area (subcapsular zone, SCZ) and an inner area (IZ). The cellular arrangement in these zones showed evident zonation that resembled the mammalian. This phenomenon had been previously described only for the pelicanus. The cytoplasm of interrenal cells in SCZ was stained lightly than in IZ and CZ, and contained several vacuoles. Additionally, unlike CZ cells, SCZ cells appeared to contain more mitochondria and less lipid droplets. Two types of chromaffin cells: epinephrine cells and norepinephrine cells could be detected. The type 1 granules possessed a central core and a variable distance between membrane and core; the type 2 granules had an eccentric core, which leant to one side of granule and sticked to the membrane, giving a lager lacouna appearance in another side of the granule.     

Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

Adaptation through natural selection may be the only means by which small and fragmented plant populations will persist through present day environmental change. A population's additive genetic variance for fitness (V_A(W)) represents its immediate capacity to adapt to the environment in which it exists. We evaluated this property for a population of the annual legume Chamaecrista fasciculata through a quantitative genetic experiment in the tallgrass prairie region of the Midwestern United States, where changing climate is predicted to include more variability in rainfall. To reduce incident rainfall, relative to controls receiving ambient rain, we deployed rain exclusion shelters. We found significant V_A(W) in both treatments. We also detected a significant genotype‐by‐treatment interaction for fitness, which suggests that the genetic basis of the response to natural selection will differ depending on precipitation. For the trait‐specific leaf area, we detected maladaptive phenotypic plasticity and an interaction between genotype and environment. Selection for thicker leaves was detected with increased precipitation. These results indicate capacity of this population of C. fasciculata to adapt in situ to environmental change.     

13C- and 1H-nmr evidence for all-cis peptide bonds in cyclic tetrapeptide cyclo(L-Pro-Sar)2

Conformations of the cyclic tetrapeptide cyclo(L -Pro-Sar)₂ in solution were studied by ¹H- and ¹³C-nmr spectrometry and model building. The nmr data provide definite evidence that this cyclic peptide exists chiefly in two conformations, namely, a C₂-symmetric conformation and an asymmetric structure. The former was demonstrated to be predominant in polar solvents (100% in Me₂SO-d₆). This structure contains all cis-peptide bond linkages and all trans′ Pro C^α?CO bonds. It represents the first cyclic tetrapeptide in which all four peptide bonds have been found in the cis-conformation. As the polarity of the solvent decreases, the population of C₂-symmetric conformers decreases (88% in CD₃CN and 65% in CDCl₃). At the same time, a minor asymmetric conformer, characterized by cis-cis-cis-trans peptide bond sequences (two cis Sar-Pro bonds, one cis Pro-Sar bond, and one trans Pro-Sar bond), is seen to increase (9% in CD₃CN and 30% in CDCl₃). A proposed predominant conformation in solution for cyclo(L -Pro-Sar)₂ was compared with a crystal structure, as reported in an accompanying paper. Both structures show striking overall similarities.     

RELATIONSHIPS AMONG SHOOT APICAL MERISTEM ONTOGENIC FEATURES IN TRICHOCEREUS PACHANOI AND MELOCACTUS MATANZANUS (CACTACEAE)

Various morphometric parameters of shoot apical meristems were measured during the ontogeny of Melocactus matanzanus and Trichocereus pachanoi. While some ontogenic features varied dramatically (i.e., apical surface curvature, dK/dl, varied by 0.15–0.17, while the apical volume increased from 10⁵ μm³ to 10⁷ or 10⁸ μm³), the percent volume of the central-mother-cell zone (CMCZ), pith-rib meristem (PRM), and the peripheral zone (PZ) showed remarkable intraspecific constancy: CMCZ = 9.2%, PRM = 10.4%, PZ = 80% for M. matanzanus, and CMCZ = 10%, PRM = 24.5%, PZ = 65% for T. pachanoi. Seedlings (2 plastochrons old) showed distinctly different percent volumes from older forms: CMCZ = 7.8%, PRM = 5.9%, PZ = 86% for M. matanzanus, and CMCZ = 8.9%, PRM = 13%, PZ = 77% for T. pachanoi. Geometric expressions of cell patterns within zones of the apex remained relatively constant throughout development. On the basis of intra- and interspecific comparisons of the percent volumes among 23 taxa and the chronology in the appearance of zones within the apex, it is concluded that while there are no apparent biological reasons for the actual percent volume values computed from our sample set, the constancy in zones reflects a high degree of homeostasis which is achieved early in ontogeny.     

A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species

Various aspects of the biochemistry of photosynthetic carbon assimilation in C₃ plants are integrated into a form compatible with studies of gas exchange in leaves. These aspects include the kinetic properties of ribulose bisphosphate carboxylase-oxygenase; the requirements of the photosynthetic carbon reduction and photorespiratory carbon oxidation cycles for reduced pyridine nucleotides; the dependence of electron transport on photon flux and the presence of a temperature dependent upper limit to electron transport. The measurements of gas exchange with which the model outputs may be compared include those of the temperature and partial pressure of CO₂(p(CO₂)) dependencies of quantum yield, the variation of compensation point with temperature and partial pressure of O₂(p(O₂)), the dependence of net CO₂ assimilation rate on p(CO₂) and irradiance, and the influence of p(CO₂) and irradiance on the temperature dependence of assimilation rate.Abbreviations RuP₂ ribulose bisphosphate - PGA 3-phosphoglycerate - C=p(CO₂) partial pressure of CO₂ - O=p(O₂) partial pressure of O₂ - PCR photosynthetic carbon reduction - PCO photorespiratory carbon oxidation     

Selection of a suitable plant for phytoremediation in mining artisanal zones

A study was undertaken with the aim of identifying a suitable plant for the phytoremediation of metal-polluted soil from an artisanal mining area in Ecuador. Three zones including a natural zone (NZ), abandoned zone (AZ) and intensively mined zone (IZ) were selected. Three common native plants grown in the three zones were identified and collected, including Miconia zamorensis, Axonopus compressus and Erato polymnioides. The percentage of arbuscular mycorrhizal colonization that benefits their own survival in polluted soil was analyzed in the root samples of these candidate species. Analysis of the soils and plants collected from the different zones showed that the concentrations of Pb, Zn, Cu and Cd were comparatively lower in the NZ, higher in the AZ and IZ, and highest in the AZ for all the metals. The concentration of all these metals in plant tissues was the highest in E. polymnioides. The data analysis including the metal accumulation index, bioconcentration factor and translocation factor strongly identified E. polymnioides as a hyperaccumulator plant suitable for phytoremediation.     

The effects of interelectrode distance over the innervation zone and normalization on the electromyographic amplitude and mean power frequency versus concentric,eccentric, and isometric torque relationships for the vastus lateralis muscle

The purpose of this study was to examine the influence of interelectrode distance (IED) over the estimated innervation zone (IZ) for the vastus lateralis muscle and normalization on the torque-related patterns of responses for electromyographic (EMG) amplitude and mean power frequency (MPF) during concentric isokinetic, eccentric isokinetic, and isometric muscle actions of the leg extensors. Eight men performed submaximal to maximal concentric isokinetic, eccentric isokinetic, and isometric muscle actions of the dominant leg extensors. Surface EMG signals were recorded simultaneously with two bipolar electrode arrangements in single differential configuration (20 and 40 mm IEDs) placed over the estimated IZ for the vastus lateralis muscle and a third electrode arrangement in single differential configuration (20 mm IED) placed distal to the estimated IZ. The results indicated that there were only a few (six of 90 statistical comparisons) significant (p < 0.05) mean differences among the three electrode arrangements for absolute EMG amplitude. There were no mean differences among the three electrode arrangements for absolute or normalized EMG MPF values or normalized EMG amplitude for the three types of muscle actions. Thus, it may be possible to reduce the potential influence of the IZ on amplitude and spectral parameters of the EMG signal through normalization.     

Immunomodulatory effects of <Emphasis Type="Italic">Caulerpa racemosa</Emphasis> var peltata polysaccharide and its selenizing product on T lymphocytes and NK cells in mice

A polysaccharide, CrvpPS, was isolated from Caulerpa racemosa var peltata. It was reacted with nano-selenium in distilled water containing ascorbic acid (Vit C) to form a stable CrvpPS-nano-Se complex. The immunomodulatory effects of CrvpPS and CrvpPS-nano-Se on T lymphocytes subgroups and NK cells in mice were investigated. After intragastric administration for 10 days separately, both CrvpPS and CrvpPS-nano-Se showed significant stimulatory functions to thymus gland of mice. Moreover, the CrvpPS-nano-Se induced the percentage of CD₃ ⁺, CD₃ ⁺CD₄ ⁺, NK cells and the CD₄ ⁺/CD₈ ⁺ value to increase significantly (P<0.05) when analyzed by flow cytometry, which is better than the CrvpPS, sucrose-nano-Se, and even the positive drug levamisole.     

ESTIMATING THE MATING BEHAVIOR OF A PAIR OF HYBRIDIZING HELICONIUS SPECIES IN THE WILD

Premating isolation between incipient species is rarely studied in nature, even though mating tests in captivity may give an inaccurate picture of natural hybridization. We studied premating barriers between the warningly colored butterflies Heliconius erato and H. himera (Lepidoptera) in a narrow contact zone in Ecuador, where hybrids are found at low frequency. Eggs obtained from wild-mated females, supplemented with eggs and young larvae collected from the wild, were reared to adulthood. Adult color patterns of these progeny were then used to infer how their parents must have mated. Likelihood was used to estimate both the frequencies of potential parental genotypes from adult phenotypes collected in the wild, and the degree of assortative mating from the inferred parents. The frequencies of parental genotypes varied across the hybrid zone, but our statistical method allowed estimates of hybrid deficit and assortative mating to be integrated across all sites sampled. The best estimate of the frequency of F₁ and backcross hybrid adults in the center of the hybrid zone was 10%, with support limits (7.1%, 13.0%; support limits are asymptotically equivalent to 95% confidence limits). Mating was highly assortative: in the center of the hybrid zone the cross-mating probability between H. erato and H. himera was only 5% (0.3%, 21.4%). Wild hybrids themselves mated with both pure forms, and the probabilities that they mated in any direction were not significantly lower than those among conspecifics. These results are consistent with earlier laboratory studies on mate choice, and suggest that selection against hybrids must be strong to prevent formation of a hybrid swarm. Unfortunately, the wide support limits on mating behavior precluded a measure of the strength of selection from these data alone. Our statistical approach provides a useful general method for estimating mate choice in the wild.