Second-Order Designs in Two Stages

This study examines the comparative information intrinsic to each stage of a two-stage experiment. Aliasing at the first stage, possible confounding of effects between stages, and efficiency comparisons for the two stages are determined directly from the analysis. A practical advantage is that runs to be assigned prospectively to the first and second stages may be evaluated beforehand, independently of empirical data. Motivated by studies in the digestion of seafood wastes, a case study develops a central composite design in k = 3 regressors, first on augmenting a 2³ design with center run, then on augmenting a small composite design with center run. Other augmentations are considered as well. The study concludes with some minimal augmentations to a 2³ design with center run, so as to ensure full estimability in a second-order model in three regressors.     

Surveying Hard-to-Reach Groups Through Sampled Respondents in a Social Network

The sampling frame in most social science surveys misses members of certain groups, such as the homeless or individuals living with HIV. These groups are known as hard-to-reach groups. One strategy for learning about these groups, or subpopulations, involves reaching hard-to-reach group members through their social network. In this paper we compare the efficiency of two common methods for subpopulation size estimation using data from standard surveys. These designs are examples of mental link tracing designs. These designs begin with a randomly sampled set of network members (nodes) and then reach other nodes indirectly through questions asked to the sampled nodes. Mental link tracing designs cost significantly less than traditional link tracing designs, yet introduce additional sources of potential bias. We examine the influence of one such source of bias using simulation studies. We then demonstrate our findings using data from the General Social Survey collected in 2004 and 2006. Additionally, we provide survey design suggestions for future surveys incorporating such designs.     

A Simple Procedure for Constructing Experiment Designs with Incomplete Blocks of Sizes 2 and 3

In order to maximize control of heterogeneity within complete blocks, an experimenter could use incomplete blocks of size k = 2 or 3. In certain situations, incomplete blocks of this nature would eliminate the need for such spatial types of analyses as nearest neighbor. The intrablock efficiency factors for such designs are relatively low. However, with recovery of interblock information, FEDERER and SPEED (1987) have presented measures of design efficiency factors which demonstrate that efficiency factors approach unity for certain ratios of the intrablock and interblock variance components. Hence with recovery of interblock information, even incomplete block designs with k = 2 or 3 have relatively high efficiency factors. The reduction in the intrablock error variance over the complete block error variance in many situations will provide designs with high efficiency. A simple procedure for constructing incomplete blocks of sizes 2 and 3 is presented. It is shown how to obtain additional zero-one association confounding arrangements when v = 4 t, t an integer, and for v = pk, k ≤ p. It is indicated how to do the statistical analysis for these designs.     

Statistical Inference for a Two‐Stage Outcome‐Dependent Sampling Design with a Continuous Outcome

Summary The two‐stage case–control design has been widely used in epidemiology studies for its cost‐effectiveness and improvement of the study efficiency ( White, 1982 , American Journal of Epidemiology 115, 119–128; Breslow and Cain, 1988 , Biometrika 75, 11–20). The evolution of modern biomedical studies has called for cost‐effective designs with a continuous outcome and exposure variables. In this article, we propose a new two‐stage outcome‐dependent sampling (ODS) scheme with a continuous outcome variable, where both the first‐stage data and the second‐stage data are from ODS schemes. We develop a semiparametric empirical likelihood estimation for inference about the regression parameters in the proposed design. Simulation studies were conducted to investigate the small‐sample behavior of the proposed estimator. We demonstrate that, for a given statistical power, the proposed design will require a substantially smaller sample size than the alternative designs. The proposed method is illustrated with an environmental health study conducted at National Institutes of Health.     

Optimal nested row-column designs with specified components

We consider nested row-column designs where each of the rowand column component designs is specified. For the case thateach of the component designs has second-order balance, we definesuch a nested row-column design to be special if it is generallybalanced, with the smallest possible number of canonical treatmentcontrasts having the lower canonical efficiency factor in bothcomponents. We show that if any special row-column design existsthen it is A-optimal over all nested row-column designs withthe given components.     

Construction and Analysis of an Augmented Lattice Square Design

Augmented designs are useful for screening experiments involving large numbers of new and untried treatments. Since resolvable row‐column designs are useful for controlling extraneous variation, it is desirable to use such designs for the check or standard treatments to construct augmented lattice square experiment designs. A simple procedure is described for constructing such designs using c = 2k and c = 3k check treatments and n = rk(k ‐— 2) and n = rk(k — 3) new treatments, respectively, r being the number of complete blocks. A trend analysis for these designs, which allows for solutions of fixed effects, is presented. The random effects case is also discussed. A SAS computer code and the output from this code illustrated with a small numerical example are available from the author.     

Survival of Lactic Acid Bacteria in Seawater: A Factorial Study

A feasibility study of lactic bacteria as potential probiotics in larval cultures of marine fish was performed by investigating the survival of five strains of lactic bacteria in seawater by readily standardized procedures at different temperatures and salinities. These conditions were chosen in such a way that their combinations define a complete first-order factorial design. Depending on the strain and the ambient conditions, the survival adhered to first-order kinetics in some cases, and to the Gompertz equation in others. The half lives (t _0.5) calculated from these models were subsequently introduced as responses to the factorial designs, estimating the coefficients of empirical equations that describe the group effect of temperature and salinity on t _0.5. Simply additive effects were found in two cases, a negative first-order interaction in another case, while another two required second-order models.     

A note on the karyotypes and chromosome associations of the Hylobatidae, with special reference to Hylobates (Nomascus) concolor

The somatic chromosomes, obtained from short term leukocyte cultures, were studied of four species of the Hylobatidae: Hylobates lar, H. agilis, H. (Nomascus) concolor and Symphalangus syndactylus. In accordance with earlier observations by others, the diploid chromosome numbers were found to be 44 in both Hylobates lar and H. agilis, 52 in H. concolor and 50 in Symphalangus syndactylus. The chromosome associations observed in metaphase spreads are clearly different in the three types of chromosome complements. In Hylobates lar and H. agilis associations are found between both members of the marked chromosome pair. In Symphalangus syndactylus the only two acrocentric elements of the karyo-type, which are of medium size, associate frequently. In H. concolor finally, the members of three pairs of small acrocentrics are involved in chromosome associations. G-banding patterns (obtained by trypsin treatment) showed that in a male individual of this species also the small acrocentric Y chromosome sometimes participates in these associations. The evolutionary aspects of these observations are briefly discussed.     

EVOLUTIONARY PREDICTABILITY IN NATURAL POPULATIONS: DO MATING SYSTEM AND NONADDITIVE GENETIC VARIANCE INTERACT TO AFFECT HERITABILITIES IN PLANTAGO LANCEOLATA?

Quantitative genetics has been an immensely powerful tool in manipulating the phenotypes of domesticated plants and animals. Much of the predictive power of quantitative genetics depends on the breeder's control over the context in which phenotype and mating are being expressed. In the natural world, these contexts are often difficult to describe, let alone control. We are left, therefore, with a poor understanding of the limits of quantitative genetics in natural populations. One of the crucial contextual elements for assessing breeding value is the genetic background in which an individual's genes are being assessed. When interacting genes are polymorphic within a population, the degree of mating among relatives can influence the correlations among mates and the predictions of a response to selection. Population structure can strongly influence the degree to which dominance and epistasis influences additive genetic variance and heritability. The extent of inbreeding can also influence heritabilities through its effect on the environmental component of phenotypic variance. The applicability of standard quantitative genetic breeding designs to the measurement of heritabilities in natural populations therefore depends in part on: (1) the mating system of the population; and (2) the importance of gene interactions in determining phenotypic variation. We tested for an effect of mating structure on the partitioning of phenotypic variance and heritability by comparing two breeding designs in a common environment. Both breeding designs used 139 pollen parents taken from mapped locations in a population of Plantago lanceolata L., and crossed to 280 seed parents from the same population. One design was random-mating, the second was biased toward near-neighbor matings to an extent determined by field measure of pollen-mediated gene flow distances. The offspring were grown randomly mixed in a common garden. Nine traits were measured: central corm diameter, number of leaves, area of the most recently fully expanded leaf, density of hairs (cm^-2) on the leaves, dry weight per unit leaf area, photosynthetic capacity, transpiration rates, water use efficiency, and reproductive dry weight. Heritabilities and variance components from the two designs were compared using randomization tests. None of the variance components or the heritabilities differed significantly between breeding designs at the 0.05 level. The test could distinguish differences between the heritabilities measured in the two breeding designs as small as 0.11, on average. Thus, for the degree of inbreeding normally exhibited in P. lanceolata there is insufficient gene interaction present within populations to influence the partitioning of variance between additive and nonadditive components or to influence heritability estimates to a meaningful extent. We suggest that for Plantago other sources of variation in heritability estimates, such as maternal effects and genotype × environment interactions, are more important influences than the interaction between inbreeding and gene interactions, and standard heritability estimate based on random breeding is as accurate as one taking the natural mating structure into account.     

Eye Attached Hemipollinaria in the Hawkmoth and Settling Moth Pollination of Habenaria (Orchidaceae): A Study on Functional Morphology in 5 Species from Subtropical South America

Morphological adaptations to sphingophily and pollination by moths was studied in 5 South American Habenaria species. For H. gourlieana and H. hieronymi direct evidence of hawkmoth (Agrius cingulatus and Manduca sexta) and settling moth (Rachiplusia nu) pollination, respectively, by hemipollinaria attachment on the eyes, is presented. In two other species (H. paucofilia, H. rupicola) pollination by settling moths and eye attachment of the hemipollinaria can be inferred by indirect evidence (placement of scales and massulae on the flowers) and by flower structure. For the fifth species (H. montevidensis) pollination by small moths or mosquitoes with hemipollinaria attachment on the proboscis is postulated. A comparative study in floral features revealed clear morphological divergence between sphingophilous and phalaenophilous species. In addition to deeper spurs the former have slender, exerted, and upturned petal lobes (acting as mechanical guide to the hovering visitors), a much developed median rostellar lobe (acting as deflecting surface of the hawkmoths towards the viscidia), flexible and sinuous hemipollinarium caudicles (appropriate for frontal strikes against the stigma when hemipollinaria are brought by the hawkmoths dangling against the flower). Male efficiency was compared between 4 species with overlapping flowering time in the same area. Male efficiency factors were unexpectedly low in all species. Only in one species (H. hieronymi) each pollen donation accounted for more than one pollination. H. gourlieana is part of a more or less rich sphingophilous flora interacting with the same two long-tongued hawkmoth species. Interspecific competition for pollen placement on the pollinator's body surface is probably low on account of different pollination mechanisms.     

Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies

The use of bispecific antibodies (BsAbs) to treat human diseases is on the rise. Increasingly complex and powerful therapeutic mechanisms made possible by BsAbs are spurring innovation of novel BsAb formats and methods for their production. The long‐lived in vivo pharmacokinetics, optimal biophysical properties and potential effector functions of natural IgG monoclonal (and monospecific) antibodies has resulted in a push to generate fully IgG BsAb formats with the same quaternary structure as monoclonal IgGs. The production of fully IgG BsAbs is challenging because of the highly heterogeneous pairing of heavy chains (HCs) and light chains (LCs) when produced in mammalian cells with two IgG HCs and two LCs. A solution to the HC heterodimerization aspect of IgG BsAb production was first discovered two decades ago; however, addressing the LC mispairing issue has remained intractable until recently. Here, we use computational and rational engineering to develop novel designs to the HC/LC pairing issue, and particularly for κ LCs. Crystal structures of these designs highlight the interactions that provide HC/LC specificity. We produce and characterize multiple fully IgG BsAbs using these novel designs. We demonstrate the importance of specificity engineering in both the variable and constant domains to achieve robust HC/LC specificity within all the BsAbs. These solutions facilitate the production of fully IgG BsAbs for clinical use.     

13C-13C Homonuclear Recoupling in Solid-State Nuclear Magnetic Resonance at a Moderately High Magic-Angle-Spinning Frequency

Two-dimensional ¹³C-¹³C correlation experiments are widely employed in structure determination of protein assemblies using solid-state nuclear magnetic resonance. Here, we investigate the process of ¹³C-¹³C magnetisation transfer at a moderate magic-angle-spinning frequency of 30 kHz using some of the prominent second-order dipolar recoupling schemes. The effect of isotropic chemical-shift difference and spatial distance between two carbons and amplitude of radio frequency on ¹H channel on the magnetisation transfer efficiency of these schemes is discussed in detail.     

Salt-Sensitive and Auxotrophic Mutants of Halomonas elongata and H. meridiana by Use of Hydroxylamine Mutagenesis

The killing action and induced mutagenicity in hydroxylamine (HA)-treated cells of two moderately halophilic species of the genus Halomonas, H. elongata and H. meridiana, were investigated. A high sensitivity of H. elongata and especially of H. meridiana to HA was found. The efficiency of the mutagenicity obtained with the HA treatment was tested at different salinities. Optimal experimental conditions for HA mutagenesis of these two moderate halophiles were determined. A clear, efficient mutagenicity of both H. elongata and H. meridiana after HA mutagenesis was achieved. The optimal procedures yielded a number of useful auxotrophic mutants of H. elongata as well as different salt-sensitive mutants of H. elongata and H. meridiana for further studies. Some of these latter mutants appeared to be affected in the synthesis of compatible solutes. Received: 11 June 1996 / Accepted: 19 July 1996     

Size variation in the postcranium ofAustralopithecus afarensis and extant species of hominoidea

The postcranial sample ofA. afarensis can be divided into two size groups. Among the best preserved elements which are represented by both morphs are the distal femur, proximal ulna, and capitate. The difference between the large and small fossil femora is similar to the difference between average male and femaleG. gorilla andP. pygmaeus. The distal femora ofH. sapiens are less sexually dimorphic while those ofP. paniscus, P. troglodytes, andH. lar are not significantly dimorphic at all. Large and small capitates and proximal ulnae ofA. afarensis differ slightly more than the highly dimorphic species of extant Hominoidea. In my sample of Amerindians, the capitate and proximal ulna are also strongly dimorphic. The two species ofPan have insignificant sexual dimorphism in these traits. There results imply that strong sexual dimorphism in body size is the primitive condition for the large bodied hominoids.     

Optimization of extraction process by response surface methodology and preliminary structural analysis of polysaccharides from defatted peanut (Arachis hypogaea) cakes

In this work, response surface methodology was used to determine optimum conditions for extraction of polysaccharides from defatted peanut cake. A central composite design including independent variables, such as extraction temperature (x₁), extraction time (x₂), and ethanol concentration (x₃) was used. Selected response which evaluates the extraction process was polysaccharide yield, and the second-order model obtained for polysaccharide yield revealed coefficient of determination of 97.81%. The independent variable with the largest effect on response was ethanol concentration (x₃). The optimum extraction conditions were found to be extraction temperature 48.7 °C, extraction time 1.52 h, and ethanol concentration of 61.9% (v/v), respectively. Under these conditions, the extraction efficiency of polysaccharide can increase to 25.89%. The results of structural analysis showed that the main composition of defatted peanut cake polysaccharide was α-galactose.     

Two new species of Heligmoptera Nadtochiy, 1977 (Nematoda: Trichostrongylina: Heligmosomoidea) from myospalacine rodents in China (Gansu), with a redefinition of the genus

Two species, Heligmoptera giraudouxi n. sp. and H. querei n. sp., are described. These are co-parasites of the small intestine of Myospalax fontanierii in China (Gansu). H. giraudouxi is closely related to the only existing species of the genus, H. myospalaxi (Nadtochiy, 1970), a parasite of Myospalax psilurus in the Primor'e Region of Russia. It is distinguished by the pattern of the left lateral lobe. H. querei differs from the two other species by possessing a long dorsal ray and from H. giraudouxi by the length of the left ala. From a phylogenetic point of view, these three species may form a small clade, adapted to Myospalax spp., derived from related forms in Insectivora, this capture resulting in the appearance of monodelphy.     

Planting Seedlings in Tree Islands Versus Plantations as a Large‐Scale Tropical Forest Restoration Strategy

Planting tree seedlings in small patches (islands) has been proposed as a method to facilitate forest recovery that is less expensive than planting large areas and better simulates the nucleation process of recovery. We planted seedlings of four tree species at 12 formerly agricultural sites in southern Costa Rica in two designs: plantation (entire 50 × 50 m area planted) and island (six patches of three sizes). We monitored seedling survival, height, and canopy area over 3 years. To elucidate mechanisms influencing survival and growth, we measured soil and foliar nutrients, soil compaction, and photosynthesis. Survival of all species was similar in the two planting designs. Seedling height and canopy area were greater in plantations than islands at most sites, and more seedlings in islands decreased in height due to damage incurred during plot maintenance. Survival, height, and canopy area were both site‐ and species‐specific with the two N‐fixing species (Inga edulis and Erythrina poeppigiana) greater than the other species (Terminalia amazonia and Vochysia guatemalensis). Foliar N was higher in Terminalia and Vochysia in sites where Inga growth was greater. Soil nutrients, however, explained a small amount of the large differences in growth across sites. Leaf mass per area was higher in islands, and P use efficiency was higher in plantations. Our results show advantages (good seedling survival, cheaper) and disadvantages (more seedling damage, slightly lower growth) to the island planting design. Our study highlights the importance of replicating restoration strategies at several sites to make widespread management recommendations.     

Differential uptake of summer precipitation among co-occurring trees and shrubs in a pinyon-juniper woodland

Measurements of the ratio of deuterium to hydrogen (D/H) in stem xylem water were used to determine the relative uptake of summer precipitation by four co-occurring plant species in southern Utah. The species compared included two trees, Juniperus osteosperma and Pinus edulis, and two shrubs, Artemisia tridentata and Chrysothamnus nauseousus. There were significant differences among species in the relative use of summer precipitation. Chrysothamnus nauseosus had stem water D/H ratios in May through August 1990 that were not significantly different from that of groundwater. In contrast, the other three species had stem water D/H ratios that were intermediate between the groundwater value and summer precipitation values, indicating that a mixture of both precipitation and groundwater was being used by these species. The two tree species generally had higher D/H values than did A. tridentata indicating a higher average uptake of summer precipitation, although the roots of J. osteosperma and P. edulis may not be as responsive to small precipitation events as A. tridentata. There was a strong negative correlation between stem water D/H ratios and predawn water potential, which suggests a relationship between plant rooting pattern and water source use. In addition, water-use efficiency during photosynthetic gas exchange, calculated from leaf carbon isotope composition, differed among species and was strongly correlated with differences in the relative uptake of summer precipitation.     

Morphological and isozyme divergence in Korean Hepatica sensu stricto (Ranunculaceae)

 Morphological and electrophoretic data were studied to examine species delimitation, patterns of morphological and genetic variation in three Korean Hepatica including two endemics, H.␣maxima and H. insularis. Based on a phenogram using 15 morphological characters, taxa were distinct; it was consistent with the phenogram based on genetic distance. In the enzyme electrophoresis study, the genetic identities suggested that three taxa were genetically divergent enough to be recognized as different species, falling within the range expected␣for congeners. The genetic identity between H.␣asiatica and H. insularis was higher than the values between these two taxa and H.␣maxima, a restricted endemic of Ulleung Island. The least genetic variation was found in H. maxima and the greatest in widespread H. asiatica. These data are consistent with theoretical expectations that small populations are more likely to be genetically depauperate. Received November 13, 2001; accepted May 10, 2002 Published online: December 11, 2002     

Anomalous change in the specific conductivity in lipoproteins at around physiologic temperatures

Studying the temperature dependence of conductivity sigma of rat and human lipoproteins and apoprotein A-I fractions revealed an anomalous region in the range of temperatures (35-38) +/- 0.5 degree C. The activation energy delta H and temperature coefficient sigma (delta sigma/delta T) on both sides of Tc and the heat of transition (delta H of transition) were calculated. In high-density human lipoproteins and apoA-I, the delta H value was found to be very low. Some mechanisms of interaction of hydrocortizone with high-density lipoproteins and apoA-I were studied by using IR-spectroscopy and conductometry were studied. It was found that the hormone considerably increases the portion of alpha-helices and beta-structures in these proteins (coil<-->alpha-helix and coil<-->beta-structure transitions). In this case, delta H value of the transition increases 13-fold; in addition, the abnormal region in apoA-I shifts 1-2 degrees C downwards. The anomalous changes in conductivity in the range of physiological temperatures in all lipoprotein fractions including apoA-I are probably related to structural phase transitions both in proteins and in phospholipids. Since the delta H value of the transition in human high-density lipoproteins is small, it is assumed that, in phospholipids of these particles, an orientation transition of the A<-->C smectic type takes place, which is assigned to the second-order phase transition. The structural transition in apoA-I can probably also be assigned to the second-order phase transition since the enthalpia of the transition is very small; presumably, this transition is related to changes in symmetry due to changes in the secondary structure (coil<-->beta-tructure transition).