Van Der Laan Research Articles

Comparison of parametric and non-parametric methods for analysing genotype×environment interactions in safflower (Carthamus tinctoriusL.)

SUMMARYGenotype×environment interaction (GEI) is a major factor in the development of stable and high-yielding safflower cultivars under rain-fed conditions. In order to quantify GEI effects on the seed yield of 17 safflower genotypes and to identify stable genotypes, multi-environment yield trials (multi-environment trials (MET)) were conducted for four consecutive years in 33 different environments (year–location combinations) during 2003–06. The results indicated that GEI was significant using the Hildebrand (1980) procedure for non-crossover interaction (no change in genotypic rank) and by the Azzalini & Cox (1984) and the De Kroon & Van Der Laan (1981) tests for crossover interaction (change in genotypic rank). The rank-interaction was not significant when assessed using the Bredenkamp (1974) method. Fifteen univariate stability methods measuring different aspects of stability were used to determine stable genotypes. A principal component analysis based on rank correlation matrix separated those methods based on a dynamic concept of yield stability (change in genotypic performance corresponds to the predicted level for each environment) from those which are based on a static one (the lowest changes in genotypic performance across environments). The methods could be grouped into three distinct classes: (i) those which were associated with yield level and the dynamic concept of stability; (ii) those which were associated with environmental variance, which represents static stability; and (iii) those which were grouped with non-parametric stability statistics, which also represent static stability. The superiority index of cultivar performance, coefficient of regression, Rank-Sum (sum of ranks of yield and stability variance) and TOP (number of environments at which the cultivar occurred in the top third of the ranks) defined the dynamic stability.In this MET, the genotype PI-537598 was identified as the genotype with the highest yield and high stability of yield.

Immunization With a Bivalent Adenovirus-vectored Tuberculosis Vaccine Provides Markedly Improved Protection Over Its Monovalent Counterpart Against Pulmonary Tuberculosis

Recombinant virus-vectored vaccines hold great promise for tuberculosis (TB) vaccination strategies. However, there is a lack of side-by-side comparative investigations to dissect the functional differences and support the advantage of multivalent virus-vectored vaccine over its monovalent counterpart. We previously successfully developed a monovalent adenovirus (Ad)-vectored vaccine expressing Ag85a (AdAg85a) and demonstrated its superior protective efficacy in models of pulmonary TB. In this study, we have developed a bivalent Ad TB vaccine expressing Ag85a and TB10.4 antigens as a fusion protein (AdAg85a:TB10.4) and compared its T-cell-activating and immune protective efficacy with that by monovalent AdAg85a. A single intranasal (i.n.) administration of AdAg85a:TB10.4 induced robust T-cell responses toward the respective antigens within the airway lumen and spleen, although the level of Ag85a-specific T-cell responses in the airway lumen triggered by bivalent AdAg85a:TB10.4 was lower than that by its monovalent counterpart at earlier time points. Thus, a single i.n. delivery of AdAg85a:TB10.4 conferred a markedly improved and sustained level of protection in the lung against Mycobacterium tuberculosis (M.tb) challenge over that by AdAg85a or by conventional BCG immunization with similarly induced levels of protection in the spleen. Our results indicate a unique advantage of multivalent viral-vectored TB vaccines for immunization against pulmonary TB.

Why match? Investigating matched case-control study designs with causal effect estimation.

Matched case-control study designs are commonly implemented in the field of public health. While matching is intended to eliminate confounding, the main potential benefit of matching in case-control studies is a gain in efficiency. Methods for analyzing matched case-control studies have focused on utilizing conditional logistic regression models that provide conditional and not causal estimates of the odds ratio. This article investigates the use of case-control weighted targeted maximum likelihood estimation to obtain marginal causal effects in matched case-control study designs. We compare the use of case-control weighted targeted maximum likelihood estimation in matched and unmatched designs in an effort to explore which design yields the most information about the marginal causal effect. The procedures require knowledge of certain prevalence probabilities and were previously described by van der Laan (2008). In many practical situations where a causal effect is the parameter of interest, researchers may be better served using an unmatched design.

THE ANALYSIS OF AN EXTENDED AVERAGE COST INVENTORY MODEL FOR REVERSE LOGISTIC PLANNING

ABSTRACT Because of the increasing environmental consciousness and prevalence of resources reviving concept, promoting products reverse logistic system in order to carry out products recycling and remanufacturing has became a very important issue. This paper focuses on reverse logistic system planning by investigating end-of-life (EOL) product material flow and inventory management models. Based on the research of reverse logistic average cost inventory model by Teunter and van der Laan [6], we suggest an extended reverse logistic inventory model, which includes the operation of product decomposing in order to carry out parts and materials recycling, reusing and remanufacturing in the system. By adding such a capability, our goal is to conduct an extended inventory total cost model evaluation in order to achieve a better environmental awareness decision for reverse logistic planning. In the paper, the GA mathematic algorithm is used as a tool to analyze results of average cost inventory model for constructing a better reverse logistic planning decision model.

A revision of the cicadas of the genus Maua Distant (Hemiptera, Cicadidae) from Sundaland

The genus Maua was erected by Distant (1905) for Cicada quadrituberculata Signoret, 1847 and M. affinis Distant, 1905. The genus is currently placed in the tribe Dundubiini and the subtribe Leptopsaltriina (Duffels & Van der Laan 1985; Moulds 2005). In 1923, Moulton erected the new section Leptopsaltraria [sic] for the genera Leptopsaltria Stal, 1866, Maua Distant, 1905, Nabalua Moulton, 1923, Purana Stal, 1866 and Tanna Distant, 1905. The new section was characterised by the presence of one to three pairs of tubercles on the ventral side of the male abdomen. A revision of Nabalua was recently presented by Duffels (2004), and three, presumed monophyletic, groups of the genus Purana were revised: the P. nebulilinea group (Kos & Gogala 2000), the P. carmente group (Schouten & Duffels 2002) and the P. tigrina group (Duffels et al. 2007). In 1963, Metcalf added several genera, with and without abdominal tubercles, to the subtribe; none of these genera are recorded from Sundaland. This paper presents a revision of the genus Maua from Sundaland: the Malay Peninsula, Java, Sumatra, Borneo, Palawan and several smaller islands inbetween. Two species of Maua, M. borneensis from Borneo and M. palawanensis from Palawan and Balabac are described as new to science, and six species from Sundaland are redescribed: M affinis, M. albigutta (Walker, 1857), M. latilinea (Walker, 1868), M. linggana Moulton, 1923, M. platygaster Ashton, 1912, and M. quadrituberculata. Two species, M. ackermanni Schmidt, 1924 and M. dohrni Schmidt, 1912, both described from Sumatra, proved to be junior synonyms of respectively M. quadrituberculata and M. latilinea. Three species of Mau are not treated in this paper: M. albistigma (Walker, 1850) and M. fukienensis Liu, 1940 from China, and M. philippinensis Schmidt, 1924 from the Philippines. This study aims to contribute to a better knowledge of cicada biodiversity in Southeast Asia. Basic systematic studies providing illustrations and descriptions of species and keys to genera and species are regarded as a prerequisite for biodiversity studies. Biodiversity studies of cicadas in other tropical areas, such as Sulawesi, New Guinea, and the West Pacific, A revision of the cicadas of the genus Maua Distant (Hemiptera, Cicadidae) from Sundaland

Two Nonparametric Predictive Control Charts

Abstract Control charts based on distributional assumptions may be unsatisfactory if the assumptions are violated, as the average run length (ARL) might deviate from its anticipated value. Control limits for such charts are based on estimates of parameters, which might cause biased ARL. We introduced extrema charts based on nonparametric predictive inference (NPI) (Arts, Coolen and van der Laan, 2004), which do not suffer from these problems. Such charts use a reference set, and resulting inferences are exactly calibrated (Lawless and Fredette, 2005). It was shown that extrema charts perform well when compared to X charts, and they can quickly detect medium to large shifts. In this paper, we explore two alternative charts based on NPI, focussing on their data requirement and performance in detecting smaller shifts. We consider charts that use other order statistics than the extrema, and charts that use subsequent samples rather than single samples. The main conclusions are that the use of order statistics...

Diagnosis of Type III Endoleak and Endovascular Treatment with Aortouniiliac Stent-Graft

The present report describes a case of type III endoleak from a tear in the fabric of a Zenith bifurcated stent-graft approximately 6 months after implantation. The reason of the fabric tear was unknown. The complication was successfully treated by aortouniiliac stent-graft implantation followed by creation of a femorofemoral bypass.

Multiple Testing Procedures with Applications to Genomics by Sandrine Dudoit, Mark J. van der Laan

Multiple Testing Procedures with Applications to Genomics by Sandrine Dudoit, Mark J. van der Laan

Current status data with competing risks: Consistency and rates of convergence of the MLE

We study nonparametric estimation of the sub-distribution functions for current status data with competing risks. Our main interest is in the nonparametric maximum likelihood estimator (MLE), and for comparison we also consider a simpler “naive estimator.” Both types of estimators were studied by Jewell, van der Laan and Henneman [Biometrika (2003) 90 183–197], but little was known about their large sample properties. We have started to fill this gap, by proving that the estimators are consistent and converge globally and locally at rate n1/3. We also show that this local rate of convergence is optimal in a minimax sense. The proof of the local rate of convergence of the MLE uses new methods, and relies on a rate result for the sum of the MLEs of the sub-distribution functions which holds uniformly on a fixed neighborhood of a point. Our results are used in Groeneboom, Maathuis and Wellner [Ann. Statist. (2008) 36 1064–1089] to obtain the local limiting distributions of the estimators.

It Almost Takes a Village

production of this journal is truly a collaborative effort. Authors, referees, column editors, book reviewers, and production staff are all part of this community. Once again, an editorial year has passed by in the blink of an eye. As always, I am indebted to the RUSQ Editorial Advisory Board for their help with shaping content and direction. following individuals contributed many hours this past year through their service on this board: Judith M. Arnold, Gwen Arthur, Corinne Hill, Robert V. Labaree, Jessica E. Moyer, Kjerstine Nielsen, Amber A. Prentiss, Douglas Raber, Marianne Ryan, and Michael Stephens. Since a constant flow of manuscripts kept these board members busy, I am grateful for the willingness of the following experts to step in as needed to serve as occasional referees: Karen Antell, Lori Arp, Christine Avery, Anne Behler, Paula Contreras, Phillip Edwards, Linda Friend, Jennifer Gilley, Nancy Huling, M. Kathleen Kern, Daniel Mack, Charles Malenfant, Dale McNeill, Judith M. Nixon, Eric Novotny, Lisa O'Connor, Mary Popp, Emily Rimland, Kathleen A. Sullivan, Linda C. Smith, Amalia Strothmann, David Tyckoson, Barry Trott, Matthew Wayman, Beth S. Woodard, and Neal Wyatt. feedback to authors from these dedicated reviewers was instrumental in producing a collection of high-quality feature articles. following peer-reviewed feature articles were published in volume 47: Whatever Happened to 'Always Cite the Source?': Study of Source Citing and Other Issues Related to Telephone Reference, by Denise E. Agosto and Holly Anderton. Comparison of Retrieval Performance of Eleven Online Indexes Containing Information Related to Quaternary Research, An Interdisciplinary Science, by Lura E. Joseph. If My Mother Was Alive I'd Probably Have Called Her: Women's Search for Health Information in Rural Canada, by Roma Harris and Nadine Wathen. The Effects of Librarians' Behavioral Performance on User Satisfaction in Chat Services, by Nahyun Kwon and Vicki L. Gregory. Sociocultural Learning Theories and Information Literacy Teaching Activities in Higher Education, by Li Wang. Assessing User Interactions at the Desk Nearest the Front Door, by Pixey Anne Mosley. Determining Use of an Academic Library Collection: Report of a Study, by Jeannie Colson. Reference Transaction Handoffs: Factors Affecting the Transition from Chat to E-Mail, by Nora Wikoff. Cyberface or Face-to-Face: Teachable Moment and Changing Mediums, by Christine M. Desai and Stephanie J. Graves. Weeding Gone Wild: Planning and Implementing a Review of the Collection, by Carol A. Singer. 'But I Want a Real Book': An Investigation of Undergraduates' Usage and Attitudes toward Electronic Books, by Cynthia L. Gregory. A Generation in Transition: Study of the Usage and Attitudes toward Public Libraries by Generation 1.5 Composition Students, by Curt Asher and Emerson Case. Why Isn't Our Chat Used More?: Findings of Focus Group Discussions with Undergraduate Students, by Sharon Naylor, Bruce Stoffel, and Sharon Van Der Laan. Strategic Planning for in a Team Environment: Preferred Futuring Model, by Shahla Bahavar and Judy A. Truelson. Testing Classification Systems for Questions, by Deborah B. Henry and Tina M. Neville. It's All in the Marketing: Impact of a Virtual Marketing Campaign at Texas & M University, by Karen I. MacDonald, Wyoma vanDuinkerken, and Jane Stephens. Revitalizing the One-shot Instruction Session Using Problem-Based Learning, by Barbara Ferret Kenney. I am pleased that two issues of volume 47 contained editorials focusing on graduate programs in library and information science. Lisa O'Connor's thought provoking guest editorial, Nice Shoes, is written from the perspective of a practitioner who made the transition to library school educator. …

Yeast Pyruvate Dehydrogenase Complex Is Regulated by a Concerted Activity of Two Kinases and Two Phosphatases

The activity of yeast pyruvate dehydrogenase complex is regulated by reversible phosphorylation. Recently we identified two enzymes that are involved in the phosphorylation (Pkp1p) and dephosphorylation (Ppp1p) of Pda1p, the alpha-subunit of the pyruvate dehydrogenase complex. Here we provide evidence that two additional mitochondrial proteins, Pkp2p (Ygl059wp) and Ppp2p (Ycr079wp), are engaged in the regulation of this complex by affecting the phosphorylation state of Pda1p. Our data indicate complementary activities of the kinases and a redundant function for the phosphatases. Both proteins are associated with the complex. We propose a model for the role of the regulatory enzymes and the phosphorylation state of Pda1p in the assembly process of the pyruvate dehydrogenase complex.

An answer to a question by Herings et al.

We answer an open question by Herings et al. [J.J. Herings, G. van der Laan, D. Talman, Z. Yang, A fixed point theorem for discontinuous functions, Operations Research Letters 36 (1) (2008) 89–93], by proving that their fixed point theorem for discontinuous functions works for mappings defined on convex compact subset of R n , and not only polytopes. This rests on a fixed point result of Toussaint [S. Toussaint, On the existence of equilibria in economies with infinitely many commodities and without ordered preferences, Journal of Economic Theory 33 (1) (1984) 98–115].

Regression Analysis of a Disease Onset Distribution Using Diagnosis Data

We consider methods for estimating the effect of a covariate on a disease onset distribution when the observed data structure consists of right-censored data on diagnosis times and current status data on onset times amongst individuals who have not yet been diagnosed. Dunson and Baird (2001, Biometrics 57, 306-403) approached this problem using maximum likelihood, under the assumption that the ratio of the diagnosis and onset distributions is monotonic nondecreasing. As an alternative, we propose a two-step estimator, an extension of the approach of van der Laan, Jewell, and Petersen (1997, Biometrika 84, 539-554) in the single sample setting, which is computationally much simpler and requires no assumptions on this ratio. A simulation study is performed comparing estimates obtained from these two approaches, as well as that from a standard current status analysis that ignores diagnosis data. Results indicate that the Dunson and Baird estimator outperforms the two-step estimator when the monotonicity assumption holds, but the reverse is true when the assumption fails. The simple current status estimator loses only a small amount of precision in comparison to the two-step procedure but requires monitoring time information for all individuals. In the data that motivated this work, a study of uterine fibroids and chemical exposure to dioxin, the monotonicity assumption is seen to fail. Here, the two-step and current status estimators both show no significant association between the level of dioxin exposure and the hazard for onset of uterine fibroids; the two-step estimator of the relative hazard associated with increasing levels of exposure has the least estimated variance amongst the three estimators considered.

Comment: Improved Local Efficiency and Double Robustness

For missing data and causal inference problems, Rubin and van der Laan (2008) proposed estimators to achieve so-called improved local efficiency. We show that their estimators agree with existing estimators in the case of linear models, point out that one particular version of their estimators is also doubly robust, and suggest an extension for where the propensity score is estimated.

The Average Tree Solution for Cooperative Games with Communication Structure

This discussion paper resulted in a publication in 'Games and Economic Behavior', 2010, 68, 626-633. We study cooperative games with communication structure, represented by an undirected graph. Players in the game are able to cooperate only if they can form a network in the graph. A single-valued solution, the average tree solution, is proposed for this class of games. Given the graph structure we define a collection of spanning trees, where each spanning tree specifies a particular way by which players communicate and determines a payoff vector of marginal contributions of all the players. The average tree solution is defined to be the average of all these payoff vectors. It is shown that if a game has a complete communication structure, then the proposed solution coincides with the Shapley value, and that if the game has a cycle-free communication structure, it is the solution proposed by Herings, van der Laan and Talman (2008). We introduce the notion of link-convexity, under which the game is shown to have a non-empty core and the average tree solution lies in the core. In general, link-convexity is weaker than convexity. For games with a cycle-free communication structure, link-convexity is even weaker than super-additivity.

The Average Tree Solution for Cooperative Games with Communication Structure

We study cooperative games with communication structure, represented by an undirected graph. Players in the game are able to cooperate only if they can form a network in the graph. A single-valued solution, the average tree solution, is proposed for this class of games. Given the graph structure we define a collection of spanning trees, where each spanning tree specifies a particular way by which players communicate and determines a payoff vector of marginal contributions of all the players. The average tree solution is defined to be the average of all these payoff vectors. It is shown that if a game has a complete communication structure, then the proposed solution coincides with the Shapley value, and that if the game has a cycle-free communication structure, it is the solution proposed by Herings, van der Laan and Talman (2008). We introduce the notion of link-convexity, under which the game is shown to have a non-empty core and the average tree solution lies in the core. In general, link-convexity is weaker than convexity. For games with a cycle-free communication structure, link-convexity is even weaker than super-additivity.

Soft X-ray resonant magnetic scattering of magnetic nanostructures

Soft X-ray resonant magnetic scattering offers a unique element-, site- and valence-specific probe to study magnetic structures on the nanoscopic length scale. This new technique, which combines X-ray scattering with X-ray magnetic circular and linear dichroism, is ideally suited to investigate magnetic superlattices and magnetic domain structures. The theoretical analysis of the polarization dependence to determine the vector magnetization profile is presented. This is illustrated with examples studying the closure domains in self-organising magnetic domain structures, the magnetic order in patterned samples, and the local configuration of magnetic nano-objects using coherent X-rays. To cite this article: G. van der Laan, C. R. Physique 9 (2008).

Radiation Therapy Using A Simultaneously Integrated Boost For Early-Stage Breast Cancer

Evaluation of: van der Laan HP, Dolsma WV, Maduro JH et al.: Three-dimensional conformal simultaneously integrated boost technique for breast-conserving therapy. Int. J. Radiat. Oncol. Biol. Phys. 68(4), 1018–1023 (2007). Radiotherapy of 25 daily fractions of 2 Gy after breast-conserving surgery is effective in reducing the risk of a local recurrence. An extra boost dose of eight daily fractions of 2 Gy reduces this risk even further by a factor of 1.7. However, the extended treatment time is not patient friendly and is more labor intensive. With new, advanced equipment, it is now possible to use a so-called simultaneous integrated boost (SIB) technique to prevent these downsides. With this technique, the boost dose is integrated into the standard dose fractions, thus reducing the number of times a patient has to be irradiated. However, the initial implementation of this technique is very labor intensive and requires profound knowledge of the radiotherapy treatment planning system and treatment unit. In their article, van der Laan and colleagues present an SIB technique which is easier to implement than a sophisticated (inversely planned) SIB technique. Moreover, they are the first authors to present data on acute skin toxicity using this technique and fractionation schedule. Their work contributes significantly to the efforts of clinical physicists, radiation oncologists and radiation therapists worldwide to improve breast cancer patient care by the safe implementation of new, advanced radiotherapy technology. However, one has to realize that implementing such a technique still requires accurate knowledge of the target volume delineation and patient set-up accuracy in each institution. Also, boost volume changes may occur during treatment, which must be taken into account. Data are becoming available on this, and clinical trials investigating even higher boost doses or more conformal treatment techniques are being conducted.

History-adjusted Marginal Structural Models for Estimating Time-varying Effect Modification

Much of epidemiology and clinical medicine is focused on estimating the effects of treatments or interventions administered over time. In such settings of longitudinal treatment, time-dependent confounding is often an important source of bias. Marginal structural models (MSMs) are a powerful tool for estimating the causal effect of a treatment using observational data, particularly when time-dependent confounding is present. In recent statistical work, van der Laan et al. presented a generalized form of MSMs called "history-adjusted" MSMs (Int J Biostat 2005;1:article 4). Unlike standard MSMs, history-adjusted MSMs can be used to estimate modification of treatment effects by time-varying covariates. Estimation of time-dependent causal effect modification is frequently of great practical relevance. For example, clinical researchers are often interested in how the prognostic significance of a biomarker for treatment response can change over time. This article provides a practical introduction to the implementation and interpretation of history-adjusted MSMs. The method is illustrated using a clinical question drawn from the treatment of human immunodeficiency virus infection. Observational cohort data from San Francisco, California, collected between 2000 and 2004, are used to estimate the effect of time until switching antiretroviral therapy regimens among patients receiving a non suppressive regimen and how this effect differs depending on CD4-positive T-lymphocyte count.

Step-up and step-down procedures controlling the number and proportion of false positives

In multiple hypotheses testing, it is important to control the probability of rejecting “true” null hypotheses. A standard procedure has been to control the family-wise error rate (FWER), the probability of rejecting at least one true null hypothesis. For large numbers of hypotheses, using FWER can result in very low power for testing single hypotheses. Recently, powerful multiple step FDR procedures have been proposed which control the “false discovery rate” (expected proportion of Type I errors). More recently, van der Laan et al. [Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Statist. Appl. in Genetics and Molecular Biol. 3, 1–25] proposed controlling a generalized family-wise error rate k -FWER (also called gFWER ( k ) ), defined as the probability of at least ( k + 1 ) Type I errors ( k = 0 for the usual FWER). Lehmann and Romano [Generalizations of the familywise error rate. Ann. Statist. 33(3), 1138–1154] suggested both a single-step and a step-down procedure for controlling the generalized FWER. They make no assumptions concerning the p -values of the individual tests. The step-down procedure is simple to apply, and cannot be improved without violation of control of the k -FWER. In this paper, by limiting the number of steps in step-down or step-up procedures, new procedures are developed to control k -FWER (and the proportion of false positives) PFP. Using data from the literature, the procedures are compared with those of Lehmann and Romano [Generalizations of the familywise error rate. Ann. Statist. 33(3), 1138–1154], and, under the assumption of a multivariate normal distribution of the test statistics, show considerable improvement in the reduction of the number and PFP.