Consultation for Teachers and Children's Language and Literacy Development during Pre-Kindergarten

MyTeachingPartner (MTP) is a teacher professional development program designed to improve the quality of teacher-child interactions in pre-kindergarten classrooms and children's language and literacy development. The program includes language/literacy activities and two Web-based resources—video exemplars of effective interactions and individualized consultation—designed to support teachers' high quality implementation of these activities. This study examined the impacts of the MTP Web-based resources on the language and literacy development of 1,165 children during pre-kindergarten. Children whose teachers were randomly assigned to receive access to both the video exemplars and participated in consultation (MTP Consultancy n = 65) made greater gains in receptive language skills during pre-kindergarten compared to children whose teachers were randomly assigned to receive access to the video exemplars only (MTP Video Library n = 69). Further, among MTP Consultancy teachers, more hours of participating in the consultation process was positively associated with children's receptive language development, and more hours implementing the language/literacy activities was positively associated with children's language and literacy development. Implications for improving children's school readiness and promoting teachers' participation in professional development programs are discussed.     

A New Algorithm for Explicit Determination of Variance Component Estimations in Mixed Models and Mixed Classifications of Balanced ANOVA

This paper deals with the balanced case of the analysis of variance. The use of a classification function leads to an easy determination of all possible sources of variation of any mixed classification. For mixed models a new method is derived, which allows to represent explicit the ANOVA-estimations of the variance components respectively the estimation of the mean sum of squares of the fixed effects for all sources of variation. Thereby the corresponding F-quotients and the approximate confidence intervals of variance components are received in a simple way.     

Content Analysis of Printed News Media Related to Drowning Incidents in Turkey

Drowning is a major public health problem in Turkey as it is for other countries. According to the latest statistics, the annual average number of people who drowned in the rivers, lakes, or seas of Turkey is 642. An examination of the language and the presentation style that the media use while covering the news about drowning cases may help us to determine the risk factors of the drowning cases and reduce the number. This study aims to show the awareness level of the Turkish print media on preventing drowning incidents and to discuss the steps to be taken in the Turkish media in order to prevent drowning. To this end, attitudes and presentations of three best-selling newspapers in Turkey—Zaman, Posta, and Hürriyet—and a less-selling one, Cumhuriyet, were studied in accordance with the content analysis method. The results show that the awareness of the Turkish media to prevent drowning incidents is inadequate. The number of drowning cases covered by these newspapers are very few, and they emphasis the forensic aspect of the incidents by using dramatic language without background information.     

Diminished Confidence Levels in the Interval Estimation of an Unknown Regressor in Model I of Linear Regression

For the model y=β₀ + β₁ x + e (model I of linear regression) in the literature confidence estimators of an unknown position x₀ are given at which either the expectation of y is given (see FIELLER, 1944; FINNEY, 1952), or realizations of y are given (see GRAYBILL, 1961). These confidence regions with level 1—α need not be intervals. The occurrence of interval shape is a random event. Its probability is equal to the power of the t test for the examination of the hypothesis H: β₁ = 0. The papers mentioned above claim to provide confidence intervals with level 1 ? α. But because of the restriction of (1 —α)—confidence regions to intervals the true confidence probability is the conditional probability W_c: W_c = P (the confidence region covers x₀| the region has interval shape). Here this conditional probability is shown to be less than 1 —α. Evidence on the possible deviations from 1 —α has been obtained by simulations.     

A new method for analyzing gene expression based on frequency analysis of RT-PCR products obtained with degenerate primers

This paper presents a new method of gene expression analysis: frequency analysis of RT-PCR products obtained with degenerate primers (FAPP). The main advantage of the new approach compared to the present methods of gene expression analysis is that it is applicable to non-model plant objects whose gene sequences are unknown. The advantages and disadvantages of FAPP are described in detail using data on calcium-dependent protein kinase, stilbene synthase, and phenylalanine ammonia-lyase gene expression in two cell cultures of Vitis amurensis. We compared the expression profiles obtained by FAPP to those obtained by real-time PCR and expressed sequence tags.     

The Use of Discrete Characters in Discriminant Analysis for Diagnosis of Pulmonary Tuberculosis and for Classification of Patients Differing in Treatment Efficiency Based on Polymorphisms at Nine Codominant Loci: HP,GC, TF,PI, PGM1, GLO1, C3, ACP1, and ESD

Discriminant analysis was used to differentiate patients with pulmonary tuberculosis (N = 106) from healthy individuals (N = 328) and patients whose treatment was efficient (N = 71) from those whose treatment was inefficient (N = 35). The analysis involved the data on nine polymorphic codominant loci: HP, GC, TF, PI, PGM1, GLO1, C3, ACP1, and ESD. The loci were selected by significance of differences in genotype frequencies between tuberculosis patients and healthy controls (GC, TF, PI, C3, ACP1) or between the two groups of patients differing in treatment efficiency (HP, GC, PI, PGM1, C3, ESD). Discrimination was based on a graphic method of Bayes classification procedure with a single-variate nomograph allowing easy estimation of the a posteriori probabilities for an individual to be classified. The two groups of patients proved to be discriminated sufficiently well (probability of misclassification P _err = 0.24), whereas discrimination between tuberculosis patients and healthy individuals was less efficient (P _err = 0.33). The method was proposed as a means of predicting the efficiency of treatment in pulmonary tuberculosis. Along with clinical, roentgenological, and laboratory examination, discriminant analysis may be employed as an accessory test in diagnostics of pulmonary tuberculosis, especially when the diagnosis is questionable.     

Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution

A new method for the mathematical analysis of large metabolic networks is presented. Based on the fact that the occurrence of a metabolic reaction generally requires the existence of other reactions providing its substrates, series of metabolic networks are constructed. In each step of the corresponding expansion process those reactions are incorporated whose substrates are made available by the networks of the previous generations. The method is applied to the set of all metabolic reactions included in the KEGG database. Starting with one or more seed compounds, the expansion results in a final network whose compounds define the scope of the seed. Scopes of all metabolic compounds are calculated and it is shown that large parts of cellular metabolism can be considered as the combined scope of simple building blocks. Analyses of various expansion processes reveal crucial metabolites whose incorporation allows for the increase in network complexity. Among these metabolites are common cofactors such as NAD⁺, ATP, and coenzyme A. We demonstrate that the outcome of network expansion is in general very robust against elimination of single or few reactions. There exist, however, crucial reactions whose elimination results in a dramatic reduction of scope sizes. It is hypothesized that the expansion process displays characteristics of the evolution of metabolism such as the temporal order of the emergence of metabolic pathways. [Reviewing Editor : Dr. David Pollock]     

Development of a Genotyping Method for Potato Scab Pathogens Based on Multiplex PCR

Scab disease significantly damages potato and other root crops. Streptomyces scabiei, S. acidiscabiei, and S. turgidiscabiei are the best-known causal agents of this disease. We have developed a novel genotyping method for these potato scab pathogens using multiplex PCR, whose benefits include rapid and easy detection of multiple species. We designed a species-specific primer set (6 primers, 3 pairs) for the 16S rRNA genes and 16S–23S ITS regions of these potato scab pathogens. The specificity of the primer set was confirmed by testing 18 strains containing potato scab pathogens, other Streptomyces species, and strains of other genera. The application of the developed method to potato field soil and potato tissue samples resulted in the clear detection and identification of pathogens. Since this method is applicable to a large number of environmental samples, it is expected to be useful for a high-throughput analysis of soil and plant tissues of scab disease.     

基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块

前列腺癌病因及发病机理研究有助于前列腺癌预防和治疗.目前,前列腺癌生化试验研究方法成本高、耗时,而基于网络计算方法容易受基因表达谱数据不完整、噪声高及实验样本数量少等约束.为此,本文提出一种基于节点-模块置信度及局部模块度的双重约束算法(命名为NMCOM),挖掘前列腺癌候选疾病模块.NMCOM算法不依赖基因表达谱数据,采用候选基因与致病表型之间一致性得分,候选基因与致病基因之间语义相似性得分融合排序策略,选取起始节点,并基于节点-模块置信度及局部模块度双重约束挖掘前列腺癌候选疾病模块.通过对挖掘出的模块进行富集分析,最终得到18个有显著意义的候选疾病基因模块.与单一打分排序方法及随机游走重开始方法相比,NMCOM融合排序策略的平均排名比小、AUC值大,且挖掘出结果明显优于其他模块挖掘算法,模块生物学意义显著.NMCOM算法不仅能准确有效地挖掘前列腺癌候选疾病模块,且可扩展挖掘其他疾病候选模块.     

A Method to Rank Multiple Trait Performance of Biological Entities

Performance of biological entities are defined, in general by k inter-dependent traits whose error variances are heterogeneous. A method of arriving at “Performance Scores” for the entities along with a multivariate test of significance of k-trait differences is described. They are used to compute, for each entity, a “Performance Index” on which a ranking of the relative performance is obtained. The improvement in the present method over an earlier one is illustrated with a numerical example.     

Order patterns recurrence plots in the analysis of ERP data

Recurrence quantification analysis (RQA) is an established tool for data analysis in various behavioural sciences. In this article we present a refined notion of RQA based on order patterns. The use of order patterns is commonplace in time series analysis. Exploiting this concept in combination with recurrence plots (RP) and their quantification (RQA) allows for advances in contemporary EEG research, specifically in the analysis of event related potentials (ERP), as the method is known to be robust against non-stationary data. The use of order patterns recurrence plots (OPRPs) on EEG data recorded during a language processing experiment exemplifies the potentials of the method. We could show that the application of RQA to ERP data allows for a considerable reduction of the number of trials required in ERP research while still maintaining statistical validity.     

Eye morphology and visual acuity in the pipevine swallowtail (Battus philenor) studied with a new method of measuring interommatidial angles

Because of the important role sensory systems play in the behaviour of animals, information on sensory capabilities is of great value to behavioural ecologists in the development of hypotheses to explain behaviour. In compound eyes, interommatidial angles are a key determinant of visual acuity but methods for measuring these angles are often demanding and limited to live animals with a pseudopupil. Here we present a new technique for measuring interommatidial angles that is less demanding in terms of technology than other techniques but still accurate. It allows measurements in eyes without a pseudopupil such as dark eyes or even museum specimens. We call this technique the radius of curvature estimation (RCE) method. We describe RCE and validate the method by comparing results from RCE with those from pseudopupil analysis for the butterfly Asterocampa leilia. As an application of RCE we measure the eyes of the butterfly Battus philenor, a species whose visually guided behaviour is well known but whose eye structure and visual acuity are unknown. We discuss the results of the eye morphology in B. philenor in relation to their behaviour and ecology. We contend that RCE fills a gap in the repertoire of techniques available to study peripheral determinants of spatial resolution in compound eyes, because it can be applied on species with dark eyes. RCE then opens up for sampling a larger number of specimens, which, in combination with being able to use museum specimens, makes it possible to quantitatively test ecologically and evolutionarily driven hypotheses about vision in animals in a new way.     

Mid‐P confidence intervals for group testing based on the total number of positive groups

In the estimation of proportions by group testing, unequal sized groups results in an ambiguous ordering of the sample space, which complicates the construction of exact confidence intervals. The total number of positive groups is shown to be a suitable statistic for ordering outcomes, provided its ties are broken by the MLE. We propose an interval estimation method based on this quantity, with a mid‐P correction. Coverage is evaluated using group testing problems in plant disease assessment and virus transmission by insect vectors. The proposed method provides good coverage in a range of situations, and compares favorably with existing exact methods.     

Establishing bioequivalence of racemic venlafaxine formulations using stereoselective assay method: Is it necessary?

A bioequivalence study for venlafaxine generic formulation was conducted as an open label, balanced, randomized, two‐way crossover, single‐dose study. In this study, a comparison of various pharmacokinetic parameters of venlafaxine hydrochloride 150 mg modified release capsules of Ranbaxy and EFEXOR®‐XR 150 mg capsules of Wyeth, in healthy, adult, male, human subjects under fasting condition was performed to conclude bioequivalence. Venlafaxine and its major active metabolite O‐desmethylvenlafaxine (ODV) are racemates. The “(S)‐(+)” and “(R)‐(−)” enantiomers of venlafaxine and ODV are established as being active. Hence, subject samples were analyzed using nonstereoselective and stereoselective assay methods. Both (S)‐(+) and (R)‐(−) enantiomers of venlafaxine and ODV showed similar absorption and disposition. The 90% confidence intervals for venlafaxine, (R)‐(−)‐venlafaxine as well as (S)‐(+)‐venlafaxine were within acceptance range concluding bioequivalence. The results obtained by stereoselective assay were comparable to the nonstereoselective analysis, as sum of concentrations of (S)‐(+)‐ and (R)‐(−)‐enantiomers of venlafaxine and ODV. The mean (S)‐(+)/(R)‐(−) ratios of the enantiomers of venlafaxine and ODV at various time points were consistent in the study subjects. Therefore, the estimation of venlafaxine and ODV using nonstereoselective assay method is effective in distinguishing formulation differences (if any) in bioequivalence studies in a cost‐effective manner. Chirality, 2011. © 2011 Wiley‐Liss, Inc.     

Confidence intervals for directly standardized rates using mid‐p gamma intervals

Directly standardized rates continue to be an integral tool for presenting rates for diseases that are highly dependent on age, such as cancer. Statistically, these rates are modeled as a weighted sum of Poisson random variables. This is a difficult statistical problem, because there are k observed Poisson variables and k unknown means. The gamma confidence interval has been shown through simulations to have at least nominal coverage in all simulated scenarios, but it can be overly conservative. Previous modifications to that method have closer to nominal coverage on average, but they do not achieve the nominal coverage bound in all situations. Further, those modifications are not central intervals, and the upper coverage error rate can be substantially more than half the nominal error. Here we apply a mid‐p modification to the gamma confidence interval. Typical mid‐p methods forsake guaranteed coverage to get coverage that is sometimes higher and sometimes lower than the nominal coverage rate, depending on the values of the parameters. The mid‐p gamma interval does not have guaranteed coverage in all situations; however, in the (not rare) situations where the gamma method is overly conservative, the mid‐p gamma interval often has at least nominal coverage. The mid‐p gamma interval is especially appropriate when one wants a central interval, since simulations show that in many situations both the upper and lower coverage error rates are on average less than or equal to half the nominal error rate.     

Temporal-method estimates of Ne from highly polymorphic loci

The temporal method is used widely to estimategenetic effective population size (N _e), a parameter of fundamental interestto studies of evolutionary and conservationbiology. The statistical properties oftemporal-method estimates have not beenexplored for highly polymorphic DNA markersthat often contain many alleles occurring invery low frequencies. We used a Monte Carlosimulation approach to assess accuracy andprecision of the temporal method whenimplemented with haplotypic/allelic data atmitochondrial (mt)DNA and nuclear-encodedmicrosatellite DNA loci. Estimates of N _e were between 2%–106% greater thantheir true values in 48 simulationsparameterized using different demographicscenarios, models of mutation, and samplesizes. Overestimation of N _e resultsfrom a bias in the approximation used by Waples(1989) to derive the relationship between theexpected temporal variance (F) and N _e when allele frequencies are very closeto 0 or 1. Our results show that one commonlyapplied solution to this problem, binning oflow-frequency alleles, results in a trade-offof accuracy and precision in some cases. Weshow that both chi-square and normalapproximations are appropriate for estimating95% confidence intervals of N _e andwe develop a power analysis based on thechi-square distribution to estimate samplesizes and allelic diversity required toevaluate specific hypotheses. For highlypolymorphic loci like mtDNA andmicrosatellites, the increased precisionafforded by the presence of rare allelesoutweighs the upward bias in temporal-methodestimates of N _e.     

On the Concept of Code in Linguistics and Biosemiotics

Biosemioticians use language and linguistic concepts as a window onto phenomena and processes on all levels of life. Like most biologists, some biosemioticians use language and linguistic concepts as metaphors for phenomena and processes on the cellular level. Even mainstream biologists may be aware that with concepts like code, information or communication on the level of the cell, they are anthropomorphizing the living things they study. The paradox of linguistics is that the object of study is at the same time the cognitive tool for its analysis. Like everyone else, biologists depend on the species-specific cognitive tool of language to study the laws and phenomena of all kinds of living organisms. Biosemioticians face both paradoxes and the challenge of mediating between the terminologies of the disciplines they navigate. At the 11^th Gatherings in Biosemiotics in New York, several papers commented on inadequate concepts in the field of linguistics and the failure of the discipline of linguistics as a whole. In this paper, I comment on some of the claims that were made specifically about the distinctive feature and the notion of code in linguistics.     

Susceptible-infected-removed epidemic models with dynamic partnerships

The author extends the classical, stochastic, Susceptible-Infected-Removed (SIR) epidemic model to allow for disease transmission through a dynamic network of partnerships. A new method of analysis allows for a fairly complete understanding of the dynamics of the system for small and large time. The key insight is to analyze the model by tracking the configurations of all possible dyads, rather than individuals. For large populations, the initial dynamics are approximated by a branching process whose threshold for growth determines the epidemic threshold, R ₀, and whose growth rate, , determines the rate at which the number of cases increases. The fraction of the population that is ever infected, , is shown to bear the same relationship to R ₀ as in models without partnerships. Explicit formulas for these three fundamental quantities are obtained for the simplest version of the model, in which the population is treated as homogeneous, and all transitions are Markov. The formulas allow a modeler to determine the error introduced by the usual assumption of instantaneous contacts for any particular set of biological and sociological parameters. The model and the formulas are then generalized to allow for non-Markov partnership dynamics, non-uniform contact rates within partnerships, and variable infectivity. The model and the method of analysis could also be further generalized to allow for demographic effects, recurrent susceptibility and heterogeneous populations, using the same strategies that have been developed for models without partnerships.     

A confidence interval for the unknown value of the regressor with given expectation of the regressand in model I of linear regression

In the case of model I of linear regression there is derived a confidence interval for that x_o where the “true line” will reach a given value y_o. The interval can be given by the intersections between the line y = y_o and the hyperbolas providing pointwise confidence intervals of the expectations of y.