CAMCR: Computer assisted mixture model analysis for capture-recapture count data

Population size estimation with discrete or nonparametric mixture models is considered, and reliable ways of construction of the nonparametric mixture model estimator are reviewed and set into perspective. Construction of the maximum likelihood estimator of the mixing distribution is done for any number of components up to the global nonparametric maximum likelihood bound using the EM algorithm. In addition, the estimators of Chao and Zelterman are considered with some generalisations of Zelterman’s estimator. All computations are done with CAMCR, a special software developed for population size estimation with mixture models. Several examples and data sets are discussed and the estimators illustrated. Problems using the mixture model-based estimators are highlighted.

Modeling cumulative evidence for freedom from disease with applications to BSE surveillance trials

This investigation deals with the question of when a particular population can be considered to be disease-free. The motivation is the case of BSE where specific birth cohorts may present distinct disease-free subpopulations. The specific objective is to develop a statistical approach suitable for documenting freedom of disease, in particular, freedom from BSE in birth cohorts. The approach is based upon a geometric waiting time distribution for the occurrence of positive surveillance results and formalizes the relationship between design prevalence, cumulative sample size and statistical power. The simple geometric waiting time model is further modified to account for the diagnostic sensitivity and specificity associated with the detection of disease. This is exemplified for BSE using two different models for the diagnostic sensitivity. The model is furthermore modified in such a way that a set of different values for the design prevalence in the surveillance streams can be accommodated (prevalence heterogeneity) and a general expression for the power function is developed. For illustration, numerical results for BSE suggest that currently (data status September 2004) a birth cohort of Danish cattle born after March 1999 is free from BSE with probability (power) of 0.8746 or 0.8509, depending on the choice of a model for the diagnostic sensitivity.

Evaluation of the cumulative evidence for freedom from BSE in birth cohorts

Substantial resources are used for surveillance of bovine spongiform encephalopathy (BSE) despite an extremely low detection rate, especially in healthy slaughtered cattle. We have developed a method based on the geometric waiting time distribution to establish and update the statistical evidence for BSE-freedom for defined birth cohorts using continued surveillance data. The results suggest that currently (data included till September 2004) a birth cohort of Danish cattle born after March 1999 is free from BSE with probability (power) of 0.8746 or 0.8509, depending on the choice of a model for the diagnostic sensitivity. These results apply to an assumed design prevalence of 1 in 10,000 and account for prevalence heterogeneity. The age-dependent, diagnostic sensitivity for the detection of BSE has been identified as major determinant of the power. The incorporation of heterogeneity was deemed adequate on scientific grounds and led to improved power values. We propose our model as a decision tool for possible future modification of the BSE surveillance and discuss public health and international trade implications.

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Liquid ultraviolet matrix-assisted laser desorption/ionization - mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet -- matrix-assisted laser desorption/ionisation -- mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. The low-femtomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydroxybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and low-mass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

Rhodium assisted C-H activation of N-(2 '-hydroxyphenyl)benzaldimines. Synthesis, structure and electrochemical properties of a group of organorhodium complexes

Reaction of a group of N-(2'-hydroxyphenyl)benzaldimines, derived from 2-aminophenol and five para-substituted benzaldehydes (the para substituents are OCH3, CH3, H, Cl and NO2), with [Rh(PPh3)(3)Cl] in refluxing toluene in the presence of a base (NEW afforded a family of organometallic complexes of rhodium(III). The crystal structure of one complex has been determined by X-ray crystallography. In these complexes the benzaldimine ligands are coordinated to the metal center, via dissociation of the phenolic proton and the phenyl proton at the ortho position of the phenyl ring in the imine fragment, as dianionic tridentate C,N,O-donors, and the two PPh3 ligands are trans. The complexes are diamagnetic (low-spin d(6), S = 0) and show intense MLCT transitions in the visible region. Cyclic voltammetry shows a Rh(III)-Rh(IV) oxidation within 0.63-0.93 V vs SCE followed by an oxidation of the coordinated benzaldimine ligand. A reduction of the coordinated benzaldimine is also observed within -0.96 to -1.04 V vs SCE. Potential of the Rh(Ill)-Rh(IV) oxidation is found to be sensitive to the nature of the para-substituent. (c) 2006 Elsevier B.V. All rights reserved.

Liquid ultraviolet matrix-assisted laser desorption/ionization mass spectrometry for automated proteomic analysis

We have combined several key sample preparation steps for the use of a liquid matrix system to provide high analytical sensitivity in automated ultraviolet - matrix-assisted laser desorption/ ionisation - mass spectrometry (UV-MALDI-MS). This new sample preparation protocol employs a matrix-mixture which is based on the glycerol matrix-mixture described by Sze et al. U. Am. Soc. Mass Spectrom. 1998, 9, 166-174). The low-ferntomole sensitivity that is achievable with this new preparation protocol enables proteomic analysis of protein digests comparable to solid-state matrix systems. For automated data acquisition and analysis, the MALDI performance of this liquid matrix surpasses the conventional solid-state MALDI matrices. Besides the inherent general advantages of liquid samples for automated sample preparation and data acquisition the use of the presented liquid matrix significantly reduces the extent of unspecific ion signals in peptide mass fingerprints compared to typically used solid matrices, such as 2,5-dihydrox-ybenzoic acid (DHB) or alpha-cyano-hydroxycinnamic acid (CHCA). In particular, matrix and lowmass ion signals and ion signals resulting from cation adduct formation are dramatically reduced. Consequently, the confidence level of protein identification by peptide mass mapping of in-solution and in-gel digests is generally higher.

High-throughput proteomics using matrix-assisted laser desorption/ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Novel solid networks containing Sn-H as a greener replacement for soluble alkyl Sn-H reagents in radical assisted organic synthesis

DiGrignard reagents of the form XMg(CH2)(n)MgX, where X = Br or I and n = 6, 8, 10 or 12, were allowed to react with PhSnCl3 to produce highly cross-linked Ph-Sn polymeric networks. The Sn-H moiety was incorporated into these insoluble network polymers by treatment with Br-2 and NaBH4. Excellent accessibility of the Sn-H was displayed by these solvent penetrable but insoluble networks, giving them higher Sn-H loadings than all previously reported supported reagents. These reagents were totally regenerable in NaBH4 for radical assisted organic synthesis and no detectable leaching of the Sn into solution was observed during these reactions.

Solvent-Assisted Formation of Vesicles by a Self-Assembling Ni-3-Schiff Base Complex

A linear trinuclear Ni-Schiff base complex [Ni-3(salpen)(2)(PhCH2COO)(2)(EtOH)] has been synthesized by combining Ni(ClO4)(2)center dot 6H(2)O, phenyl acetic acid (C6H5CH2COOH), and the Schiff base ligand, N,N'-bis(salicylidene)-1,3-pentanediamine (H(2)salpen). This complex is self-assembled through hydrogen bonding and C-H-g interaction in the solid state to generate a sheet-like architecture, while in organic solvent (CH2Cl2), it forms vesicles with a mean diameter of 290 nm and fused vesicles, depending upon the concentration of the solution. These vesicles act as an excellent carrier of dye molecules in CH2Cl2. The morphology of the complex has been determined by scanning electron microscopy and transmission electron microscopy experiments, and the encapsulation of dye has been examined by confocal microscopic image and electronic absorption spectra.

Light-assisted synthesis of a Ru(VI) nitrido complex by the reaction of azide with a Ru(III) complex

Reaction of Ru(III)(L)(dmf)Cl-3 (1) (L = 4,4,4',4'-tetramethyl-2,2'- bisoxazoline, dmf = N,N-dimethylformamide) with an excess of sodium azide in a methanol-water mixture leads to the isolation of the sodium salt of a Ru( VI) nitrido complex of the tetraanion of N,N'-bis-(2,2-dimethyl-1-hydroxyethyl)-1,2-ethanediamide ( L'H-4; H a dissociable proton) of the formulation Na[Ru(L')(N)(H2O)].1.4H(2)O (2). Complex 2 is not generated in the absence of light. A tentative mechanism for the reaction is proposed and a Ru(IV) intermediate, Na[Ru(L')(N-3)(H2O)] . 2CH(3)OH.2H(2)O (3), isolated.

COMPUTER assisted technologies to enhance CONCURRENce in building DESIGN

Modern organisms are adapted to a wide variety of habitats and lifestyles. The processes of evolution have led to complex, interdependent, well-designed mechanisms of todays world and this research challenge is to transpose these innovative solutions to resolve problems in the context of architectural design practice, e.g., to relate design by nature with design by human. In a design by human environment, design synthesis can be performed with the use of rapid prototyping techniques that will enable to transform almost instantaneously any 2D design representation into a physical three-dimensional model, through a rapid prototyping printer machine. Rapid prototyping processes add layers of material one on top of another until a complete model is built and an analogy can be established with design by nature where the natural lay down of earth layers shapes the earth surface, a natural process occurring repeatedly over long periods of time. Concurrence in design will particularly benefit from rapid prototyping techniques, as the prime purpose of physical prototyping is to promptly assist iterative design, enabling design participants to work with a three-dimensional hardcopy and use it for the validation of their design-ideas. Concurrent design is a systematic approach aiming to facilitate the simultaneous involvment and commitment of all participants in the building design process, enabling both an effective reduction of time and costs at the design phase and a quality improvement of the design product. This paper presents the results of an exploratory survey investigating both how computer-aided design systems help designers to fully define the shape of their design-ideas and the extent of the application of rapid prototyping technologies coupled with Internet facilities by design practice. The findings suggest that design practitioners recognize that these technologies can greatly enhance concurrence in design, though acknowledging a lack of knowledge in relation to the issue of rapid prototyping.

The "freedom to frame questions... worth asking" or three stories and three (other) fragments of research

In our state of centralised control of the curriculum and high-stakes testing an examination subject's assessment objectives have become high profile. Some of the anomalous effects of this profile are shown in the teaching, question-setting, and marking of English literature. Glimpses of earlier times are revealed, all three secondary school key stages are considered, examination performances are discussed, and the views of beginning teachers about teaching to the test are sought.

Maternal depression and psychiatric outcomes in adolescent offspring: a13-year longitudinal study

Background: Maternal postnatal depression (PND) has been associated with adverse outcomes in young children, but an association with longer-term psychiatric disorder has not been demonstrated. We present the preliminary findings of a 13-year longitudinal study. Methods: In the course of a prospective longitudinal study, we examined DSM-IV Axis I disorders in 13-year-old adolescents who had (n=53) or had not (n=41) been exposed to maternal PND. We also detailed the occurrence of depression in mothers throughout the 13-year follow-up period. Results: Maternal PND was associated with higher rates of affective disorders in adolescent offspring. However, mothers who developed PND were also substantially more likely than those who did not to experience depression subsequently, a fact that contributed to the development of depressive disorder in offspring. Maternal PND was associated with increased risk for depression in adolescent offspring only if there had also been later episodes of maternal depression. In contrast, anxiety disorders in offspring were elevated in the maternal PND group regardless of the occurrence of subsequent maternal depression. Limitations: Due to the modest sample size and consequently limited power, findings must be regarded as preliminary. Conclusions: The particular association between early maternal depression and anxiety disorders in offspring was consistent with theories that emphasise the primacy of early environmental exposures. This position was not supported with respect to offspring depressive disorder, where overall duration of maternal depression was a significant factor. PND was associated with recurrent episodes of depression in the majority of cases, underlining the need for monitoring of this population beyond the postnatal period. (c) 2006 Elsevier B.V. All rights reserved.