A new tumour suppressor enters the network of intestinal progenitor cell homeostasis

In this issue of The EMBO Journal, Wilson et al (2012) elegantly discovered an important new axis for intestinal homeostasis and cancer, using an RNAi screen to enhance the RAS-induced multivulva (MUV) phenotype in Caenorhabditis elegans.     

Nonparametric estimation in a Markov "illness-death" process from interval censored observations with missing intermediate transition status

Summary .  In many clinical trials patients are intermittently assessed for the transition to an intermediate state, such as occurrence of a disease-related nonfatal event, and death. Estimation of the distribution of nonfatal event free survival time, that is, the time to the first occurrence of the nonfatal event or death, is the primary focus of the data analysis. The difficulty with this estimation is that the intermittent assessment of patients results in two forms of incompleteness: the times of occurrence of nonfatal events are interval censored and, when a nonfatal event does not occur by the time of the last assessment, a patient's nonfatal event status is not known from the time of the last assessment until the end of follow-up for death. We consider both forms of incompleteness within the framework of an "illness–death" model. We develop nonparametric maximum likelihood (ML) estimation in an "illness–death" model from interval-censored observations with missing status of intermediate transition. We show that the ML estimators are self-consistent and propose an algorithm for obtaining them. This work thus provides new methodology for the analysis of incomplete data that arise from clinical trials. We apply this methodology to the data from a recently reported cancer clinical trial ( Bonner et al., 2006 , New England Journal of Medicine 354, 567–578) and compare our estimation results with those obtained using a Food and Drug Administration recommended convention.     

Diagnosing Pancreatic Cancer: An Analysis of Several Strategies

The usefulness of a clinical examination was compared with several other procedures (ultrasonography, pancreatic function tests, endoscopic retrograde cholangiopancreatography and angiography) for diagnosing pancreatic cancer. We used a simplified form of decision analysis to show the effects of different strategies on direct diagnostic costs, missed diagnoses and false-positive diagnoses.Our analysis indicates that existing laboratory tests are either too non-specific or too invasive to be used successfully as screening tests for pancreatic cancer. To decrease the number of unnecessary laparotomies due to false-positive test findings, patients should have a high probability of pancreatic cancer, based on clinical criteria, before further testing is carried out. In fact, existing clinical criteria are both sensitive and specific for pancreatic cancer.     

NACOB presentation to ASB Young Scientist Award: Postdoctoral. The impact of boundary conditions and mesh size on the accuracy of cancellous bone tissue modulus determination using large-scale finite-element modeling. North American Congress on Biomechanics.

The apparent properties of cancellous bone are determined by a combination of both hard tissue properties and microstructural organization. A method is desired to extract the underlying hard tissue properties from simple mechanical tests, free from the complications of microstructure. It has been suggested that microCT voxel-based large-scale finite element models could be employed to accomplish this goal (van Rietbergen et al., 1995, Journal of Biomechanics, 28, 69-81). This approach has recently been implemented and it is becoming increasingly popular as finite element models increase in size and sophistication (Fyhrie et al., 1997, Proceedings of the 43rd Annual Meeting of the Orthopaedic Research Society, San Francisco, CA, p. 815; van Rietbergen et al., 1997, Proceedings of the 43rd Annual Meeting of the Orthopaedic Research Society, San Francisco, CA, p. 62). However, no direct quantitative measurements of the accuracy of this method applied to porous structures such as cancellous bone have been made. This project demonstrates the feasibility of this approach by quantifying its best-case accuracy in determining the trabecular hard tissue modulus of analogues fabricated of a material with known material properties determined independently by direct testing. In addition we were able to assess the impact of mesh size and boundary conditions on accuracy. We found that the assumption of a frictionless boundary condition in the parallel plate compression loading configuration was a significant source of error that could be overcome with the use of rigid end-caps similar to those used by Keaveny et al. (1997 Journal of Orthopaedic Research, 15(1), 101-110). In conclusion, we found that this approach is an effective method for determining the average trabecular hard tissue properties of human cancellous bone with an expected practical accuracy level better than 5%.     

Parameter estimation in longitudinal studies with outcome-dependent follow-up

In many observational studies, individuals are measured repeatedly over time, although not necessarily at a set of prespecified occasions. Instead, individuals may be measured at irregular intervals, with those having a history of poorer health outcomes being measured with somewhat greater frequency and regularity; i.e., those individuals with poorer health outcomes may have more frequent follow-up measurements and the intervals between their repeated measurements may be shorter. In this article, we consider estimation of regression parameters in models for longitudinal data where the follow-up times are not fixed by design but can depend on previous outcomes. In particular, we focus on general linear models for longitudinal data where the repeated measures are assumed to have a multivariate Gaussian distribution. We consider assumptions regarding the follow-up time process that result in the likelihood function separating into two components: one for the follow-up time process, the other for the outcome process. The practical implication of this separation is that the former process can be ignored when making likelihood-based inferences about the latter; i.e., maximum likelihood (ML) estimation of the regression parameters relating the mean of the longitudinal outcomes to covariates does not require that a model for the distribution of follow-up times be specified. As a result, standard statistical software, e.g., SAS PROC MIXED (Littell et al., 1996, SAS System for Mixed Models), can be used to analyze the data. However, we also demonstrate that misspecification of the model for the covariance among the repeated measures will, in general, result in regression parameter estimates that are biased. Furthermore, results of a simulation study indicate that the potential bias due to misspecification of the covariance can be quite considerable in this setting. Finally, we illustrate these results using data from a longitudinal observational study (Lipshultz et al., 1995, New England Journal of Medicine 332, 1738-1743) that explored the cardiotoxic effects of doxorubicin chemotherapy for the treatment of acute lymphoblastic leukemia in children.     

Quasi-likelihood estimation for relative risk regression models

For a prospective randomized clinical trial with two groups, the relative risk can be used as a measure of treatment effect and is directly interpretable as the ratio of success probabilities in the new treatment group versus the placebo group. For a prospective study with many covariates and a binary outcome (success or failure), relative risk regression may be of interest. If we model the log of the success probability as a linear function of covariates, the regression coefficients are log-relative risks. However, using such a log-linear model with a Bernoulli likelihood can lead to convergence problems in the Newton-Raphson algorithm. This is likely to occur when the success probabilities are close to one. A constrained likelihood method proposed by Wacholder (1986, American Journal of Epidemiology 123, 174-184), also has convergence problems. We propose a quasi-likelihood method of moments technique in which we naively assume the Bernoulli outcome is Poisson, with the mean (success probability) following a log-linear model. We use the Poisson maximum likelihood equations to estimate the regression coefficients without constraints. Using method of moment ideas, one can show that the estimates using the Poisson likelihood will be consistent and asymptotically normal. We apply these methods to a double-blinded randomized trial in primary biliary cirrhosis of the liver (Markus et al., 1989, New England Journal of Medicine 320, 1709-1713).     

Characterization of the mechanical properties of skin by inverse analysis combined with the indentation test

This study proposes a new method to determine the mechanical properties of human skin by the use of the indentation test [Pailler-Mattei, 2004. Caractérisation mécanique et tribologique de la peau humaine in vivo, Ph.D. Thesis, ECL-no. 2004-31; Pailler-Mattei, Zahouani, 2004. Journal of Adhesion Science and Technology 18, 1739-1758]. The principle of the measurements consists in applying an in vivo compressive stress [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222; Bosboom et al., 2001. Journal of Biomechanics 34, 1365-1368; Oomens et al., 1984. Selected Proceedings of Meetings of European Society of Biomechanics, pp. 227-232; Oomens et al., 1987. Journal of Biomechanics 20(9), 877-885] on the skin tissue of an individual's forearm. These measurements show an increase in the normal contact force as a function of the indentation depth. The interpretation of such results usually requires a long and tedious phenomenological study. We propose a new method to determine the mechanical parameters which control the response of skin tissue. This method is threefold: experimental, numerical, and comparative. It consists combining experimental results with a numerical finite elements model in order to find out the required parameters. This process uses a scheme of extended Kalman filters (EKF) [Gu et al., 2003. Materials Science and Engineering A345, 223-233; Nakamura et al., 2000. Acta Mater 48, 4293-4306; Leustean and Rosu, 2003. Certifying Kalman filters. RIACS Technical Report 03.02, 27pp. http://gureni.cs.uiuc.edu/~grosu/download/luta + leo.pdf; Welch and Bishop, An introduction to Kalman filter, University of North Carolina at Chapel Hill, 16p. http://www.cs.unc.edu/~welch/kalman/]. The first results presented in this study correspond to a simplified numerical modeling of the global system. The skin is assumed to be a semi-infinite layer with an isotropic linear elastic mechanical behavior [Zhang et al., 1994. Proceedings of the Institution of Mechanical Engineers 208, 217-222] This analysis will be extended to more realistic models in further works.     

快速脱腺苷酸化——miRNA抑制基因表达新机制

2006年3月14日,美国国家科学院院刊(ProcNatlAcadSciUSA)以封面论文形式刊载了纽约大学医学院研究者的最新发现:快速脱腺苷酸化是miRNA抑制基因表达的新机制.这一结果在理论上进一步丰富了对基因调控的认识,同时在药物设计及疾病治疗等实际应用中也有很大的潜力.     

Estimation of disease prevalence, true positive rate, and false positive rate of two screening tests when disease verification is applied on only screen-positives: a hierarchical model using multi-center data

Objectives: A model is proposed to estimate and compare cervical cancer screening test properties for third world populations when only subjects with a positive screen receive the gold standard test. Two fallible screening tests are compared, VIA and VILI. Methods: We extend the model of Berry et al. [1] to the multi-site case in order to pool information across sites and form better estimates for prevalences of cervical cancer, the true positive rates (TPRs), and false positive rates (FPRs). For 10 centers in five African countries and India involving more than 52,000 women, Bayesian methods were applied when gold standard results for subjects who screened negative on both tests were treated as missing. The Bayesian methods employed suitably correct for the missing screen negative subjects. The study included gold standard verification for all cases, making it possible to validate model-based estimation of accuracy using only outcomes of women with positive VIA or VILI result (ignoring verification of double negative screening test results) with the observed full data outcomes. Results: Across the sites, estimates for the sensitivity of VIA ranged from 0.792 to 0.917 while for VILI sensitivities ranged from 0.929 to 0.977. False positive estimates ranged from 0.056 to 0.256 for VIA and 0.085 to 0.269 for VILI. The pooled estimates for the TPR of VIA and VILI are 0.871 and 0.968, respectively, compared to the full data values of 0.816 and 0.918. Similarly, the pooled estimates for the FPR of VIA and VILI are 0.134 and 0.146, respectively, compared to the full data values of 0.144 and 0.146. Globally, we found VILI had a statistically significant higher sensitivity but no statistical difference for the false positive rates could be determined. Conclusion: Hierarchical Bayesian methods provide a straight forward approach to estimate screening test properties, prevalences, and to perform comparisons for screening studies where screen negative subjects do not receive the gold standard test. The hierarchical model with random effects used to analyze the sites simultaneously resulted in improved estimates compared to the single-site analyses with improved TPR estimates and nearly identical FPR estimates to the full data outcomes. Furthermore, higher TPRs but similar FPRs were observed for VILI compared to VIA.     

Superiority inferences on individual endpoints following noninferiority testing in clinical trials

We consider the problem of drawing superiority inferences on individual endpoints following non-inferiority testing. R?hmel et al. (2006) pointed out this as an important problem which had not been addressed by the previous procedures that only tested for global superiority. R?hmel et al. objected to incorporating the non-inferiority tests in the assessment of the global superiority test by exploiting the relationship between the two, since the results of the latter test then depend on the non-inferiority margins specified for the former test. We argue that this is justified, besides the fact that it enhances the power of the global superiority test. We provide a closed testing formulation which generalizes the three-step procedure proposed by R?hmel et al. for two endpoints. For the global superiority test, R?hmel et al. suggest using the L?uter (1996) test which is modified to make it monotone. The resulting test not only is complicated to use, but the modification does not readily extend to more than two endpoints, and it is less powerful in general than several of its competitors. This is verified in a simulation study. Instead, we suggest applying the one-sided likelihood ratio test used by Perlman and Wu (2004) or the union-intersection t(max) test used by Tamhane and Logan (2004).     

A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators

We developed a pharmacophore-based evolutionary approach for virtual screening. This tool, termed the Generic Evolutionary Method for molecular DOCKing (GEMDOCK), combines an evolutionary approach with a new pharmacophore-based scoring function. The former integrates discrete and continuous global search strategies with local search strategies to expedite convergence. The latter, integrating an empirical-based energy function and pharmacological preferences (binding-site pharmacological interactions and ligand preferences), simultaneously serves as the scoring function for both molecular docking and postdocking analyses to improve screening accuracy. We apply pharmacological interaction preferences to select the ligands that form pharmacological interactions with target proteins, and use the ligand preferences to eliminate the ligands that violate the electrostatic or hydrophilic constraints. We assessed the accuracy of our approach using human estrogen receptor (ER) and a ligand database from the comparative studies of Bissantz et al. (J Med Chem 2000;43:4759-4767). Using GEMDOCK, the average goodness-of-hit (GH) score was 0.83 and the average false-positive rate was 0.13% for ER antagonists, and the average GH score was 0.48 and the average false-positive rate was 0.75% for ER agonists. The performance of GEMDOCK was superior to competing methods such as GOLD and DOCK. We found that our pharmacophore-based scoring function indeed was able to reduce the number of false positives; moreover, the resulting pharmacological interactions at the binding site, as well as ligand preferences, were important to the screening accuracy of our experiments. These results suggest that GEMDOCK constitutes a robust tool for virtual database screening.     

Testing for association in the presence of population stratification: a simulation study comparing the S-TDT, STRAT and the GC

A novel approach for association testing in the presence of population stratification has been introduced by Pritchard et al. (2000a) and Pritchard et al. (2000b). The structured association approach is a two-tiered procedure that first estimates the population structure and then tests the null hypothesis H0: 'no association within subpopulations' in the second step. A power comparison of the stratified test for association (STRAT) (Pritchard et al., 2000b) and the Transmission-Disequilibrium-Test (TDT) (Spielman and Ewens, 1993a) in a simulation framework showed superiority of STRAT if allele frequencies or associations between allele and disease differ strongly in subpopulations. In more homogeneous situations, the TDT had greater power than STRAT. However, the TDT, based on family trios,that uses population controls, needs 50% more genotyping compared to STRAT. The Sib-Transmission-Disequilibrium-Test (S-TDT) needs the same amount of genotyping since it relays in its minimal configuration on pairs of siblings. This raises the question how the S-TDT (Spielman and Ewens, 1998a) performs compared to the population based methods STRAT and Genomic Controls (GC). In this paper, we present a simulation study accounting for two different models of population stratification in different settings of allele frequencies and under different risk models. The results showed that under a discrete as well as under an admixed population model, STRAT strongly outperformed the S-TDT and the GC when different alleles were associated in different subpopulations. In contrast, the S-TDT had greater power than STRAT when the same allele was associated in both subpopulations. Here, the GC was sometimes even more powerful than the S-TDT, depending on the population model and the allele frequency differences. A general recommendation for the use of one of the tests can therefore not be given.     

Model for the chemotactic response of a bacterial population.

We present a mathematical model for the motion of a bacterial population in prescribed attractant or repellent gradients. The model is suggested by the observations of Mesibov et al. (1973, J. Gen. Physiol. 62:203) and Brown and Berg (1974, Proc. Natl. Acad. Sci. U.S.A. 71:1388) who found that the sensitivity of the chemotactic response depends on the concentration of attractant. Predictions of the theory are in general agreement with the experiments of Dahlquist et al. (1972, Nat. New Biol. 236:120) and of Mesibov et al. on populations of motile bacteria in fixed attractant gradients. Additional tests of the model are proposed.     

Maximum likelihood analysis of logistic regression models with incomplete covariate data and auxiliary information

This article presents a new method for maximum likelihood estimation of logistic regression models with incomplete covariate data where auxiliary information is available. This auxiliary information is extraneous to the regression model of interest but predictive of the covariate with missing data. Ibrahim (1990, Journal of the American Statistical Association 85, 765-769) provides a general method for estimating generalized linear regression models with missing covariates using the EM algorithm that is easily implemented when there is no auxiliary data. Vach (1997, Statistics in Medicine 16, 57-72) describes how the method can be extended when the outcome and auxiliary data are conditionally independent given the covariates in the model. The method allows the incorporation of auxiliary data without making the conditional independence assumption. We suggest tests of conditional independence and compare the performance of several estimators in an example concerning mental health service utilization in children. Using an artificial dataset, we compare the performance of several estimators when auxiliary data are available.     

Chiroptical properties of diamino carboxylic acids

Diamino carboxylic acids have recently come to the attention of scientists working in the field of early life and its development. These are the monomers of a hypothetic early form of genetic material, the so-called Peptide Nucleic Acid (PNA) (Nielson et al., Proc Natl Acad Sci USA 2000;97:3868-3871). Since all biopolymers rely on a specific handedness of their building blocks, the question of symmetry breaking occurs in diamino acids and PNA in the same way as in amino acids and proteins. One possible mechanism for triggering this, is asymmetric photochemistry in interstellar/circumstellar matter by means of circularly polarized light (Bailey et al., Science 2005;281:672-674; Bailey, Orig Life Evol Biosphere 2001;21:167-183; Buscherm?hle, Astrophys J 2005;624:821-826; Meierhenrich, Angew Chem Int Ed Engl 2005;44:5630-5634). Here we have measured the CD-spectra of four chiral diamino carboxylic acids, three of which were found in the Murchison meteorite (Meierhenrich, Proc Natl Acad Sci USA 2004;101:9182-9186). The spectra show a uniform peak at 200 nm. These results and additional quantum mechanical calculations of the involved molecular orbitals support the assumption that the process of symmetry breaking in diamino acids does not depend significantly on the length of the side chain. This means that one process alone could suffice to lead to symmetry breaking in all four measured diamino carboxylic acids and might even to some extent be transferable to monoamino acids, the monomers of proteins.     

Adjusted regression trend test for a multicenter clinical trial

Studies using a series of increasing doses of a compound, including a zero dose control, are often conducted to study the effect of the compound on the response of interest. For a one-way design, Tukey et al. (1985, Biometrics 41, 295-301) suggested assessing trend by examining the slopes of regression lines under arithmetic, ordinal, and arithmetic-logarithmic dose scalings. They reported the smallest p-value for the three significance tests on the three slopes for safety assessments. Capizzi et al. (1992, Biometrical Journal 34, 275-289) suggested an adjusted trend test, which adjusts the p-value using a trivariate t-distribution, the joint distribution of the three slope estimators. In this paper, we propose an adjusted regression trend test suitable for two-way designs, particularly for multicenter clinical trials. In a step-down fashion, the proposed trend test can be applied to a multicenter clinical trial to compare each dose with the control. This sequential procedure is a closed testing procedure for a trend alternative. Therefore, it adjusts p-values and maintains experimentwise error rate. Simulation results show that the step-down trend test is overall more powerful than a step-down least significant difference test.     

NCAM is at the heart of reciprocal regulation of E-cadherin- and integrin-mediated adhesions via signaling modulation

New work by Lehembre et al. in The EMBO Journal reveals that the cell-adhesion molecule, NCAM, is at the heart of crosstalk between E-cadherin loss and reciprocal focal adhesion assembly during the epithelial to mesenchymal transition (EMT). NCAM upregulation induces the formation of novel signaling complexes that correlate with NCAM-dependent focal adhesion assembly, migration, and cancer cell invasion.     

Seasonal variation in Plasmodium prevalence in a population of blue tits Cyanistes caeruleus

1. Seasonal variation in environmental conditions is ubiquitous and can affect the spread of infectious diseases. Understanding seasonal patterns of disease incidence can help to identify mechanisms, such as the demography of hosts and vectors, which influence parasite transmission dynamics. 2. We examined seasonal variation in Plasmodium infection in a blue tit Cyanistes caeruleus population over 3 years using sensitive molecular diagnostic techniques, in light of Beaudoin et al.'s (1971; Journal of Wildlife Diseases, 7, 5-13) model of seasonal variation in avian malaria prevalence in temperate areas. This model predicts a within-year bimodal pattern of spring and autumn peaks with a winter absence of infection. 3. Avian malaria infections were mostly Plasmodium (24.4%) with occasional Haemoproteus infections (0.8%). Statistical nonlinear smoothing techniques applied to longitudinal presence/absence data revealed marked temporal variation in Plasmodium prevalence, which apparently showed a within-year bimodal pattern similar to Beaudoin et al.'s model. However, of the two Plasmodium morphospecies accounting for most infections, only the seasonal pattern of Plasmodium circumflexum supported Beaudoin et al.'s model. On closer examination there was also considerable age structure in infection: Beaudoin et al.'s seasonal pattern was observed only in first year and not older birds. Plasmodium relictum prevalence was less seasonally variable. 4. For these two Plasmodium morphospecies, we reject Beaudoin et al.'s model as it does not survive closer scrutiny of the complexities of seasonal variation among Plasmodium morphospecies and host age classes. Studies of host-parasite interactions should consider seasonal variation whenever possible. We discuss the ecological and evolutionary implications of seasonal variation in disease prevalence.     

Cost effectiveness of human papilloma virus testing in cervical cancer screening: a literature review

Human papilloma virus DNA testing may improve the cost effectiveness of cervical cancer screening programs. However, the circumstances to get this improvement are not the same between countries. The objective of this paper is to evaluate the cost effectiveness of introducing human papilloma virus testing in the current screening practice both in developed and developing countries. We conducted a review of published articles since January 2000 until December 2006 related to the cost effectiveness of introducing human papilloma virus testing in cervical cancer screening programs. A total of 17 original researches and six reviews were analyzed. Human papilloma virus testing is cost effective in developed countries only if it is a complementary test to Pap test and used to determine the management of women with atypical squamus cells of undetermined significance, the interval among tests is increased more than two years and it is performed in women over 30 years. On the other hand, developing countries should establish first organized screening programs and guarantee full coverage and access to diagnosis and treatment.     

The Evolution of a Kleptoparasitic System under Adaptive Dynamics

Kleptoparasitism, the stealing of food items, is a common biological phenomenon which has been modelled mathematically in a series of recent papers. A common assumption, following early work, was that mixed strategy solutions were not possible. In this paper we consider the evolution of mixed strategies under adaptive dynamics and show that such mixed strategies can be stable solutions under certain assumptions. In particular we revisit the recent paper of Broom et al. (Bull math Biol 66, 1645–1658, 2004) which assumed pure solutions only, and reanalyze the model under this new formulation. The second author was supported by the UNCG New Faculty Grant.