Linear Rank Tests Derived from a Superpopulation Model

A superpopulation model generates the probabilities of a Bernouilli random variable. The ranks of the involved variables are considered as survey weights. The distribution f each linear rank statistic is derived under the null hypothesis for the two sample problem and for the case k2 when a simple random sampling or stratified sampling is used. The growth of a population of insects and the behavior of patients with imsomnia are studied using these procedures.     

Applications of a Vectorized MANOVA-Model

If the observation matrix of n independent p-dimensional normal vectors with common covariance matrix is transformed into an np-vector, linear models and hypotheses on the expectations can be formulated, that are not attainable in standard MANOVA or GMANOVA models. The distribution of an earlier proposed test procedure for this vectorized model is derived for p = 2, and its application is demonstrated for crossover and repeated measurement designs. Numerical results are compared in situations, in which both the standard and the vectorized model are applicable.     

Frequency responses of cat rapidly adapting mechanoreceptive fibers

The frequency responses of 11 rapidly adapting (RA) fibers in cat were studied by representing the average firing rate as a function of sinusoidal stimulus amplitude and stimulus frequency. Specifically, rate-intensity functions at different stimulation frequencies were fitted by four-parameter (a₀, a₁, a₂, a₃), piece-wise linear functions using nonlinear regression (n = 59; R² > 0.877). Rate-intensity functions at intermediate frequencies were found by linear interpolation. The result of this analysis is rate–amplitude–frequency functions plotted as two-dimensional surfaces. The surfaces consist of five regions separated and sufficiently defined by four space curves. At 14 different frequencies, the statistical distribution of each rate-intensity-function parameter could be approximated by a particular lognormal distribution (n = 56; R² > 0.796). The Kolmogorov–Smirnov test fails to reject this hypothesis for each combination of frequency and parameter (56 tests; p > 0.39). Therefore, at a given frequency, the variation of the parameters can be represented by lognormal distributions with specific means and standard deviations. Responses of six RA fibers, which are different from the data-set used for modeling, were compared with the stochastic model at different frequencies. The parameters of those fibers were tested against the null hypotheses that they were sampled from the particular parameter distributions dictated by the model. The Kolmogorov–Smirnov test fails to reject all the hypotheses at the α = 0.05 level (44 tests). At the α = 0.10 level, only a few test parameters were found to be departing from the model (a₀ and a₁ at 5?Hz; a₂ at 20?Hz; a₂ and a₃ at 50?Hz). The remaining test parameters could be accurately described by the model. Having confirmed the validity of the model, the logarithmic means and the logarithmic standard deviations of the lognormally distributed rate-intensity-function parameters were estimated in the frequency range of 4–200?Hz. The rate–amplitude–frequency surfaces sampled from the established stochastic model completely characterize the rate responses of RA fibers to sinusoidal stimuli and are superior to tuning curves which require selecting criterion responses. The current rate-response model is promising for future computational work, especially on population modeling.     

One-Way Classification ANOVA Model for the Mixture of Two Multivariate Normal Populations

When a sample of size n is available from a mixture of two normal populations with different mean vectors and a common covariance matrix, SRIVASTAVA and AWAN (1982) develop one-way ANOVA analysis for testing a certain composite linear hypothesis. They show that the error and hypothesis sum of products matrices have independent noncentral Wishart densities of rank unity each. However, they do not obtain the necessary Wilks' λ for testing the desired hypothesis. The present paper obtains the density of λ. This density is doubly noncentral multivariate beta density. The derivation is based on generalized Sverdrup's lemmas, KABE (1965), (1974).     

International Society of Chronobiology: Membership Information

Most variables of interest in laboratory medicine show predictable changes with several frequencies in the span of time investigated. The waveform of such nonsinusoidal rhythms can be well described by the use of multiple components rhythmometry, a method that allows fitting a linear model with several cosine functions. The method, originally described for analysis of longitudinal time series, is here extended to allow analysis of hybrid data (time series sampled from a group of subjects, each represented by an individual series). Given k individual series, we can fit the same linear model with m different frequencies (harmonics or not from one fundamental period) to each series. This fit will provide estimations for 2m + 1 parameters, namely, the amplitude and acrophase of each component, as well as the rhythm-adjusted mean. Assuming that the set of parameters obtained for each individual is a random sample from a multivariate normal population, the corresponding population parameter estimates can be based on the means of estimates obtained from individuals in the sample. Their confidence intervals depend on the variability among individual parameter estimates. The vari-ance-covariance matrix can then be estimated on the basis of the sample covariances. Confidence intervals for the rhythm-adjusted mean, as well as for the amplitude-acrophase pair, of each component can then be computed using the estimated covariance matrix. The p-values for testing the zero-amplitude assumption for each component, as well as for the global model, can finally be derived using those confidence intervals and the t and F distributions. The method, validated by a simulation study and illustrated by an example of modeling the circadian variation of heart rate, represents a new step in the development of statistical procedures in chronobiology.     

A Mixed Model for Binary Data: The Modified X2-test

In this paper, a statistical model for clinical trials is presented for the special situation that a varying and unstructered number of binary responses is obtained from each subject. The assumptions of the model are the following: 1.) For each subject there is a (constant) individual Bernoulli parameter determining the distribution of the binary responses of this subject. 2.) The Bernoulli parameters associated with the subjects are realizations of independent random variables with distributions P_g in treatment group g(g = 1, 2, …, G). 3.) Given the value of the Bernoulli parameter, the observations are stochastically independent within each subject. Under these assumptions, a test statistic is derived to test the hypothesis H₀:E(P₁) = E(P₂) = … = E(P_G). It is proven and demonstrated by simulations, that the test statistic asymptotically (i.e. for a large number of subjects) follows the X²-distribution.     

Oxygen transfer coefficients by dynamic model moment analysis

A new method to estimate the oxygen transfer coefficient (K_La) from the experimental dynamic response data is presented. Employing a linear model which allows for gas phase, diffusion film, and oxygen electrode dynamics, the first moment of the response curve is simply related to the sum of the model parameters. Two separate experiments are used to characterize the measurement dynamics and to measure the unknown K_La parameter. The simple calculation procedure involves only measuring the area above the response curves.     

One-Step Preparation of a TA-cloning Vector from a Specially Designed Parent Plasmid Containing a Dual <Emphasis Type="Italic">lacZ</Emphasis> Gene System

A high-yield method was developed for producing a TA-cloning vector suitable for blue/white colony selection from a unique parent plasmid containing a dual lacZ gene system through a one-step restriction enzyme digestion, which creates a single-base 3′-overhang. The dual lacZ gene system was realized by inserting an inner lacZ gene between two single-base 3′-overhangs, creating restriction enzyme sites within the reading-frame-adjusted outer lacZ gene sequence in the parent plasmid. The proposed method overcomes problems, such as the inefficient digestion frequently observed when generating a TA-cloning vector and the difficulty of purifying TA-cloning vectors from the digestion mixture, while maintaining the applicability of blue/white colony selection. Moreover, the use of TA-cloning vector prepared by the proposed method can provide the distinguish tool of transformants carrying the cloning product from those carrying contaminating parent plasmids, recircularized plasmids derived from incompletely digested parent plasmid fragments, or intra-molecularly ligated TA-cloning vectors derived from T-overhangs missing TA-cloning vectors (instability of the T-overhangs is another important consideration when designing TA-cloning vectors) by making all colonies except those carrying the cloning product appear blue during blue/white colony selection.     

Development of a photosynthesis model with an emphasis on ecological applications

Summary A physiologically based steady-state model of whole leaf photosynthesis (WHOLEPHOT) is detailed which describes the functional dependence of net photosynthesis in C ₃ leaves on [CO₂], [O₂], incident radiant flux (PhAR), and leaf temperature. The model simulates among other phenomena a) observed [CO₂], [O₂], and temperature effects on the initial slope of light response curves, b) a C ₃ type temperature response curve of net photosynthesis, c) a shift of the optimum temperature of net photosynthesis to higher temperatures with increasing light intensity, and d) observed temperature and [O₂] effects on the CO₂ compensation point. Model parameters are derived from published response data of several C ₃ species. Simulations also demonstrate that parameter changes based on literature data result in acclimation-like changes in net photosynthesis response with respect to light intensity and temperature. The advantages of this model are that the number of parameters is minimized in order to focus on environmental effects and that all parameters can be determined from measured net photosynthesis responses.     

Model Construction and Model Examination on the Basis of Simulated Selection

By reason nonlinear relations founded between selection differential and realised selection response we have been made investigations about variants of the genetic-statistical model, which include this nonlinearity. The variations of the model would not only referred to the postulate pattern of the connection between phenotype, genotype and environment but also enclosed the postulate assumption about the distribution of the variates. In an investigated special case the linear model equation P = G ± e was held, however the distributions of P and G were defined over a limited range in one direction. For P we have defined a modified normal distribution and the distribution of the random vector (G, e) non normal regarded with cov (G, e) ≠ 0, By means of a solution set of an integral equation a density function of the random vector (P, G) has been received, in which the expectation of the selection response of the usual genetic-statistical model approximate is included as a special case. The genetical parameters has been derived, which result from changed model. However their representation was only possible partially as an integral function. A subsequent paper informs of the examination this mode! variants, which depend on a parameter of the nonlinearity c.     

Neural circuitry underlying linear representation of wind information in a nonspiking local interneuron of the cockroach

In the cercal system of the cockroach Periplaneta americana, primary sensory interneurons exhibiting a sharp directional sensitivity respond to wind in a linear manner whereas those exhibiting an omnidirectional sensitivity respond nonlinearly. For example, the wind-evoked response in an identifiable, nonspiking local interneuron, 101, which responds preferentially to wind from the left versus the right, is characterized exclusively by a differential first-order (linear) kernel. However, the slow potential response in a cercal giant interneuron, GI-1, is omnidirectional, and characterized by a second-order (nonlinear) kernel with an elongated depolarizing peak on the diagonal with two off-diagonal valleys. We here examined the neural circuitry underlying the linear and nonlinear representations of wind information by the deprivation of inputs from particular sets of cercal hair afferents. Electrical stimulation of the ipsilateral (related to the soma) cercal nerve elicited a depolarizing potential in 101, which was followed by delayed hyperpolarization. A continuous flow of 10^–4 M picrotoxin, which selectively blocked this delayed hyperpolarization, resulted in a significant change in the 101 response from linear to nonlinear. Because no frequency-doubling response was observed, the nonlinearity is due to signal compression (or rectification) that reflects the mechanical property of cercal afferents. This is consistent with the hypothesis that the linear representation in 101 is based on a subtraction process between two subsets of particular column hairs, whose best optimal directions are opposite to each other.Abbreviations GABA -aminobutyric acid - GI(s) giant interneuron(s) - GI-1, GI-2, GI-3, GI-4 giant interneuron 1,2,3,4 - ipsi ipsilateral - cont contralateral - MSE(s) mean square error(s)     

Electrophysiological studies of gustation in lepidopterous larvae

Summary Comparisons were made of the eleotrophysiological responses of the maxillary gustatory receptors of the following categories of caterpillars: (1) three closely related species (Papilio polyxenes L.,P. troilus L., andP. glaucus L.) each of which feeds on a different group of plants; (2) two unrelated oligophagous species (P. glaucus L. andMalacosoma americana Fabr.) that have one preferred food plant in common; (3) three unrelated monophagous species (Danaus plexippus L.,Euchaetias egle Drury, andPygarctia eglenensis Clemens) that share the same plant. Materials tested included sodium chloride, carbohydrates, amino acids, glycosides, and the saps ofDaucus carota L. andFoeniculum vulgare Mill. (the food plants ofP. polyxenes),Sassafras albidum (Nutt.) andLindera Benzoin (L.) (the food plants ofP. troilus),Prunus virginiana L. (a favored food ofP. glaucus andM. americana),Asclepias syriaca L. andApocynum androsaemifolium L. (eaten byD. plexippus,E. egle, andP. eglenensis), andBrassica oleraceae L. (food plant ofPieris rapae).The following conclusions were drawn: (1) no species of caterpillar gives a single standard electrophysiological response to all of the plants it rejects; that is, rejection is not a unitary modality; (2) a plant that is unacceptable to several species of caterpillars does not elicit the same pattern of response from each; (3) a food plant that is shared by several species of caterpillars does not elicit the same pattern of response from each; (4) a species of caterpillar that has more than one food plant does not generate the same sensory pattern to each; (5) there is no universal difference between sensory patterns for acceptance and those for rejection.A model based upon the hypothesis of across-fiber patterning is proposed to explain these results. The essence of this model is that the receptors have unique but overlapping action spectra and that each compound or mixture of compounds in leaf saps that can be discriminated generates a unique total pattern of response. Whether or not a plant is ingested depends, therefore, not on the presence or absence of a single stimulant or deterrent but upon the total sensory impression derived from integrated response to multiple plant components. Prior to the first bite a caterpillar makes its first discrimination on the basis of olfactory clues.This work was supported by National Science Foundation Grant GB 1472 and the Class of 1877 Professorship of Princeton University.     

A framework for incorporating 3D hyperelastic vascular wall models in 1D blood flow simulations

We present a novel framework for investigating the role of vascular structure on arterial haemodynamics in large vessels, with a special focus on the human common carotid artery (CCA). The analysis is carried out by adopting a three-dimensional (3D) derived, fibre-reinforced, hyperelastic structural model, which is coupled with an axisymmetric, reduced order model describing blood flow. The vessel transmural pressure and lumen area are related via a Holzapfel–Ogden type of law, and the residual stresses along the thickness and length of the vessel are also accounted for. After a structural characterization of the adopted hyperelastic model, we investigate the link underlying the vascular wall response and blood-flow dynamics by comparing the proposed framework results against a popular tube law. The comparison shows that the behaviour of the model can be captured by the simpler linear surrogate only if a representative value of compliance is applied. Sobol’s multi-variable sensitivity analysis is then carried out in order to identify the extent to which the structural parameters have an impact on the CCA haemodynamics. In this case, the local pulse wave velocity (PWV) is used as index for representing the arterial transmission capacity of blood pressure waveforms. The sensitivity analysis suggests that some geometrical factors, such as the stress-free inner radius and opening angle, play a major role on the system’s haemodynamics. Subsequently, we quantified the differences in haemodynamic variables obtained from different virtual CCAs, tube laws and flow conditions. Although each artery presents a distinct vascular response, the differences obtained across different flow regimes are not significant. As expected, the linear tube law is unable to accurately capture all the haemodynamic features characterizing the current model. The findings from the sensitivity analysis are further confirmed by investigating the axial stretching effect on the CCA fluid dynamics. This factor does not seem to alter the pressure and flow waveforms. On the contrary, it is shown that, for an axially stretched vessel, the vascular wall exhibits an attenuation in absolute distension and an increase in circumferential stress, corroborating the findings of previous studies. This analysis shows that the new model offers a good balance between computational complexity and physics captured, making it an ideal framework for studies aiming to investigate the profound link between vascular mechanobiology and blood flow.

     

UNDESIRABLE CONSEQUENCES OF NEGLECTING NONLINEARITY: RESPONSE TO COMMENTS BY LIEFTING ET AL. (2013) ON ROCHA & KLACZKO (2012)

In response to our previous study, Liefting et al. argue, in defense of their work on latitudinal variation of developmental‐rate reaction norms (RNs), that (1) developmental rate (the reciprocal of development time: rate = time^?1) is a more biologically relevant variable than development time; (2) the linear RN model is a valid approximation; and (3) three experimental points suffice to estimate RN parameters. Here, we reply to their comments. First, we give evidence that the complexity of actual development challenges the appealing simplicity of developmental rate. Using the same analysis as Liefting et al. to test their hypothesis with development time, instead of rate, reveals a pattern that is the opposite of their conclusion. Second, we show that a quadratic model is consistent with the whole development‐time RNs and explains this contradiction. Third, with the quadratic model, we introduce two parameters to study plasticity: the RN shape (the quadratic coefficient) and RN local plasticity (the derivative of the RN function). The first showed a statistically significant correlation with latitude; and the second showed a continuous variation pattern where all localized patterns can be found (positive, negative, or nonsignificant correlations with latitude) but certainly cannot be generalized.     

A Stochastic Compartmental Model with Long Lasting Infusion

Most of the compartmental models in current use to model pharmacokinetic systems are deterministic. Stochastic formulations of pharmacokinetic compartmental models introduce stochasticity through either a probabilistic transfer mechanism or the randomization of the transfer rate constants. In this paper we consider a linear stochastic differential equation (LSDE) which represents a stochastic version of a one‐compartment linear model when input function undergoes random fluctuations. The solution of the LSDE, its mean value and covariance structure are derived. An explicit likelihood function is obtained either when the process is observed continuously over a period of time or when sampled data are available, as it is generally feasible. We discuss some asymptotic properties of the maximum likelihood estimators for the model parameters. Furthermore we develop expressions for two random variables of interest in pharmacokinetics: the area under the time‐concentration curve, M₀(T), and the plateau concentration, x_ss. Finally the estimation procedure is illustrated by an application to real data.     

Molecular cloning of resistance genes and architecture of a linked gene cluster involved in biosynthesis of oxytetracycline by Streptomyces rimosus

Summary The isolation of mutants of Streptomyces rimosus which were blocked in oxytetracycline (OTC) production was described previously. The genes for the early steps of antibiotic biosynthesis mapped together. Genomic DNA fragments of S. rimosus which conferred resistance to OTC and complemented all of these non-producing mutants have been cloned. The cloned DNA is physically linked within approximately 30 kb of the genome of S. rimosus. The gene cluster is flanked at each end by a resistance gene each of which, independently, can confer resistance to the antibiotic. In OTC-sensitive strains of S. rimosus, the entire gene cluster including both resistance genes has been deleted. Complementation of blocked mutants by cloned DNA fragments in multi-copy vectors was often masked by a secondary effect of switching off antibiotic productions in strains othersise competent to produce OTC. This adverse effect on OTC production was not observed with recombinants using low copy-number vectors.     

CRISPR Cas9- and Cas12a-mediated gusA editing in transgenic blueberry

To develop an effective genome editing tool for blueberry breeding, CRISPR-Cas9 and CRISPR-Cas12a were evaluated for their editing efficiencies of a marker gene, beta-glucuronidase (gusA), which was previously introduced into two blueberry cultivars each a single-copy transgene. Four expression vectors were built, with CRISPR-Cas9 and CRISPR-Cas12a each driven by a 35S promoter or AtUbi promoter. Each vector contained two editing sites in the gusA. These four vectors were respectively transformed into the leaf explants of transgenic gusA blueberry and the resulting transgenic calli were induced under hygromycin selection. GUS staining showed that some small proportions of the hygromycin-resistant calli had non-GUS stained sectors, suggesting some possible occurrences of gusA editing. We sequenced GUS amplicons spanning the two editing sites in three blueberry tissues and found about 5.5% amplicons having editing features from the calli transformed with the 35S-Cas9 vector. Further, we conducted a second round of shoot regeneration from leaf explants derived from the initial Cas9- and Cas12a-containing calli (T₀) and analyzed amplicons of the target editing region. Of the newly induced shoots, 15.5% for the 35S-Cas9 and 5.3% for the AtUbi-Cas9 showed non-GUS staining, whereas all of the shoots containing the Cas12a vectors showed blue staining. Sanger sequencing confirmed the editing-induced mutations in two representative non-GUS staining lines. Clearly, the second round of regeneration had enriched editing events and enhanced the production of edited shoots. The results and protocol described will be helpful to facilitating high-precision breeding of blueberries using CRISPR Cas technologies.

     

A Legumain-based minigene vaccine targets the tumor stroma and suppresses breast cancer growth and angiogenesis

Tumor associated macrophages (TAMs) are well known to play a very important role in tumor angiogenesis and metastasis. The suppression of TAMs in the tumor-microenvironment (TME) provides a novel strategy to inhibit tumor growth and dissemination by remodeling the tumor’s stroma. Here, we tested our hypothesis that suppression of TAMs can be achieved in syngeneic BALB/c mice with oral minigene vaccines against murine MHC class I antigen epitopes of Legumain, an asparaginyl endopeptidase and a member of the C13 family of cystine proteases which is overexpressed on TAMs in the tumor stroma. Vaccine vectors were constructed and transformed into attenuated Salmonella typhimurium (Dam ⁻ , AroA ⁻ ) for oral delivery. Groups of mice received either the expression vectors encoding the Legumain H-2D or 2K epitopes or the control empty vector by gavage. The efficacy of the minigene vaccines was determined by their ability to protect mice from lethal tumor cell challenges, the induction of a specific CTL response as well as IFN-γ release, and inhibition of tumor angiogenesis. We demonstrated that the Legumain minigene vaccine provided effective protection against tumor cell challenge by inducing a specific CD8⁺ T-cell response against Legumain⁺ TAMs in our breast tumor model. The protection, induced by this T-cell response, mediated by the Legumain Kd minigene, is also responsible for lysing D2F2 breast carcinoma cells in syngeneic BALB/c mice and for suppressing tumor angiogenesis. Importantly, in a prophylactic setting, the minigene vaccine proved to be of similar anti-tumor efficacy as a vaccine encoding the entire Legumain gene. Together, our findings establish proof of concept that a Legumain minigene vaccine provides a more flexible alternative to the whole gene vaccine, which may facilitate the future design and clinical applications of such a vaccine for cancer prevention.     

A biogeographic–ecological approach to disentangle reticulate evolution in the Triatoma phyllosoma species group (Heteroptera: Triatominae), vectors of Chagas disease

Introgression and incomplete lineage sorting (ILS) are two of the main sources of gene‐tree incongruence; both can confound the assessment of phylogenetic relationships among closely related species. The Triatoma phyllosoma species group is a clade of partially co‐distributed and cross‐fertile Chagas disease vectors. Despite previous efforts, the phylogeny of this group remains unresolved, largely because of substantial gene‐tree incongruence. Here, we sequentially address introgression and ILS to provide a robust phylogenetic hypothesis for the T. phyllosoma species group. To identify likely instances of introgression prior to molecular scrutiny, we assessed biogeographic data and information on fertility of inter‐specific crosses. We first derived a few explicit hybridization hypotheses by considering the degree of spatial overlap within each species pair. Then, we assessed the plausibility of these hypotheses in the light of each species pair's cross‐fertility. Using this contextual information, we evaluated mito‐nuclear (cyt b, ITS‐2) gene‐tree incongruence and found evidence suggesting introgression within two species pairs. Finally, we modeled ILS using a Bayesian multispecies coalescent approach and either (a) a “complete” dataset with all the specimens in our sample, or (b) a “filtered” dataset without putatively introgressed specimens. The “filtered tree” had higher posterior‐probability support, as well as more plausible topology and divergence times, than the “complete tree.” Detecting and filtering out introgression and modeling ILS allowed us to derive an improved phylogenetic hypothesis for the T. phyllosoma species group. Our results illustrate how biogeographic and ecological‐reproductive contextual information can help clarify the systematics and evolution of recently diverged taxa prone to introgression and ILS.