Asymmetric regression models with limited responses with an application to antibody response to vaccine

We develop regression models for limited and censored data based on the mixture between the log‐power‐normal and Bernoulli‐type distributions. A likelihood‐based approach is implemented for parameter estimation and a small‐scale simulation study is conducted to evaluate parameter recovery, with emphasis on bias estimation. The main conclusion is that the approach is very much satisfactory for moderate and large sample sizes. A real data example, the safety and immunogenecity study of measles vaccine in Haiti, is presented to illustrate how different models can be used to fit this type of data. As shown, the asymmetric models considered seem to present the best fit for the data set under study, revealing significance of the explanatory variable sex, which is not found significant with the log‐normal model.     

From sextant to GPS: Twenty‐five years of mapping the genome with ChIP

Since its inception, ChIP technology has evolved immensely. Technological advances have improved its specificity and sensitivity, its scale has expanded to a genome‐wide level, and its relative ease of use has made it a virtually ubiquitous tool. This year marks the 25th anniversary of the development of ChIP. In honor of this milestone, we briefly revisit its history, offer a review of recent articles employing ChIP on a genome‐wide scale, and lay out our views for the future of ChIP. J. Cell. Biochem. 107: 6–10, 2009. © 2009 Wiley‐Liss, Inc.     

How to Deal with Resource Productivity

Resource productivity enhancement stands at the center of tackling issues on environmental pollution and resource scarcity. Identifying influential socioeconomic factors should be the first step in establishing and improving resource management policy. This study compares and analyzes data from multiple countries to construct a resource productivity simulation model. The socioeconomic factors and their characteristic patterns are discussed in detail. The results demonstrate that the major factors influencing resource productivity include income level, population density, economic structure, energy structure, and raw material trade. Among these factors, the three most important are income level, population density, and economic structure. The influencing patterns can be summarized as follows: (1) Resource productivity increases with increasing income levels. (2) Countries with high population density are inclined to demonstrate high resource productivity. (3) The economic structure shows a biphase influence on resource productivity, that is, during industrialization, decreased agricultural activity and increased industrial activity lead to higher resource productivity. On the other hand, after industrialization, decreasing industrial activity and an expanding service sector become the major impetus of resource productivity enhancement. (4) Raw material export demonstrates a negative effect on resource productivity. Countries that depend heavily on raw material export show a unique resource productivity evolution pattern. For these countries, relatively high resource productivity in low income phases and relatively low resource productivity in high income phases show only small increases in resource efficiency and economic growth. Finally, insights from the study are transformed into suggestions for sustainable resource management and resource productivity enhancement.     

Sensitivity of lysosomal enzymes to the plant alkaloid sanguinarine: comparison with other SH-specific agents

The influence of the benzo[c]phenanthridine alkaloid sanguinarine on some lysosomal enzyme activities was investigated. Sanguinarine inhibits lysosomal hydrolases in homogenates of cultured mouse fibroblasts. After incubation of mouse fibroblasts in culture with 100 microM sanguinarine an approximately 50% decrease in the activities of N-acetyl-beta,D-glucosaminidase (NAGA), beta-galactosidase (GAL), arylsulfatase and acid lipase was observed. Because the biological activity of sanguinarine might arise from the interaction of its iminium cation with enzyme thiol groups, we compared its effect on NAGA, GAL and acid phosphatase (AcP) activities with the effects of SH-specific reagents p-chloromercuribenzoic acid (CPMA) and N-ethylmaleimide (NEM). Treatment of lysosomal fractions with millimolar concentrations of sanguinarine induces a dose-dependent inhibition of the enzymes; for example, 0.6 mM sanguinarine causes approximately a 40% decrease in AcP and NAGA activities. NEM has similar effects, and increasing the preincubation temperature from 0 degrees C to 37 degrees C intensifies the inhibition due to both agents. CPMA also inhibits the activity of GAL (IC50 0.7 microM), AcP (IC50 12.5 microM) and NAGA (IC50 6.8 microM) in a dose-dependent manner but is more potent than sanguinarine or NEM. Comparative analysis of the primary structures of these enzymes using the program BLAST reveals the presence of highly conserved cysteine residues, which confirms the importance of thiol-groups for their activities. Thus, both the experimental observations obtained in this study and the literature data imply a significant role of redox-based mechanisms in regulating lysosomal functional activity.     

Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts

Successful protein expression, purification, and crystallization for challenging targets typically requires evaluation of a multitude of expression constructs. Often many iterations of truncations and point mutations are required to identify a suitable derivative for recombinant expression. Making and characterizing these variants is a significant barrier to success. We have developed a rapid and efficient cloning process and combined it with a protein microscreening approach to characterize protein suitability for structural studies. The Polymerase Incomplete Primer Extension (PIPE) cloning method was used to rapidly clone 448 protein targets and then to generate 2143 truncations from 96 targets with minimal effort. Proteins were expressed, purified, and characterized via a microscreening protocol, which incorporates protein quantification, liquid chromatography mass spectrometry and analytical size exclusion chromatography (AnSEC) to evaluate suitability of the protein products for X-ray crystallography. The results suggest that selecting expression constructs for crystal trials based primarily on expression solubility is insufficient. Instead, AnSEC scoring as a measure of protein polydispersity was found to be predictive of ultimate structure determination success and essential for identifying appropriate boundaries for truncation series. Overall structure determination success was increased by at least 38% by applying this combined PIPE cloning and microscreening approach to recalcitrant targets.     

Liposomes surface conjugated with human hemoglobin target delivery to macrophages

Current strategies to deliver therapeutic molecules to specific cell and tissue types rely on conjugation of antibodies and other targeting ligands directly to the therapeutic molecule itself or its carrier. This work describes a novel strategy to deliver therapeutic molecules into macrophages that takes advantage of the native hemoglobin (Hb) scavenging activity of plasma haptoglobin (Hp) and the subsequent uptake of the Hb-Hp complex into macrophages via CD163 receptor-mediated endocytosis. The drug delivery system described in this work consists of Hb decorated liposomes that can encapsulate any therapeutic molecule of interest, in this case the model fluorescent dye calcein was used in this study. The results of this study clearly demonstrate that this delivery system is specific towards macrophages and demonstrates the feasibility of using this approach in targeted drug delivery.     

A Lithium Amide‐Borohydride Solid‐State Electrolyte with Lithium‐Ion Conductivities Comparable to Liquid Electrolytes

High ionic conductivity of up to 6.4 × 10^?3 S cm^?1 near room temperature (40 °C) in lithium amide‐borohydrides is reported, comparable to values of liquid organic electrolytes commonly employed in lithium‐ion batteries. Density functional theory is applied coupled with X‐ray diffraction, calorimetry, and nuclear magnetic resonance experiments to shed light on the conduction mechanism. A Li₄Ti₅O₁₂ half‐cell battery incorporating the lithium amide‐borohydride electrolyte exhibits good rate performance up to 3.5 mA cm^?2 (5 C) and stable cycling over 400 cycles at 1 C at 40 °C, indicating high bulk and interfacial stability. The results demonstrate the potential of lithium amide‐borohydrides as solid‐state electrolytes for high‐power lithium‐ion batteries.     

Curvature factor and membrane solubilization, with particular reference to membrane rafts

The composition of membrane rafts (cholesterol/sphingolipid-rich domains) cannot be fully deduced from the analysis of a detergent-resistant membrane fraction after solubilization in Triton X-100 at 4°C. It is hypothesized that the membrane curvature-dependent lateral distribution of membrane components affects their solubilization. The stomatocytogenic, Triton X-100, cannot effectively solubilize membrane components, especially with regard to the outward membrane curvature.     

An approach to the conditional error rate principle with nuisance parameters

In the presence of nuisance parameters, the conditional error rate principle is difficult to apply because of the dependency of the conditional error function of the preplanned test on nuisance parameters. To use the conditional error rate principle with nuisance parameters, we propose to search among tests that guarantee overall error control for the test that maximizes a weighted combination of the conditional error rates over possible values of the nuisance parameters. We show that the optimization problem that defines such a test can be solved efficiently by existing algorithms.     

Non-homogeneous Markov process models with informative observations with an application to Alzheimer's disease

Identifying risk factors for transition rates among normal cognition, mildly cognitive impairment, dementia and death in an Alzheimer's disease study is very important. It is known that transition rates among these states are strongly time dependent. While Markov process models are often used to describe these disease progressions, the literature mainly focuses on time homogeneous processes, and limited tools are available for dealing with non-homogeneity. Further, patients may choose when they want to visit the clinics, which creates informative observations. In this paper, we develop methods to deal with non-homogeneous Markov processes through time scale transformation when observation times are pre-planned with some observations missing. Maximum likelihood estimation via the EM algorithm is derived for parameter estimation. Simulation studies demonstrate that the proposed method works well under a variety of situations. An application to the Alzheimer's disease study identifies that there is a significant increase in transition rates as a function of time. Furthermore, our models reveal that the non-ignorable missing mechanism is perhaps reasonable.     

Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts

The intermolecular contact regions between monomers of the homodimeric DNA binding protein ParR and the interaction between the glycoproteins CD28 and CD80 were investigated using a strategy that combined chemical cross-linking with differential MALDI-MS analyses. ParR dimers were modified in vitro with the thiol-cleavable cross-linker 3,3'-dithio-bis(succinimidylproprionate) (DTSSP), proteolytically digested with trypsin and analyzed by MALDI-MS peptide mapping. Comparison of the peptide maps obtained from digested cross-linked ParR dimers in the presence and absence of a thiol reagent strongly supported a "head-to-tail" arrangement of the monomers in the dimeric complex. Glycoprotein fusion constructs CD28-IgG and CD80-Fab were cross-linked in vitro by DTSSP, characterized by nonreducing SDS-PAGE, digested in situ with trypsin and analyzed by MALDI-MS peptide mapping (+/- thiol reagent). The data revealed the presence of an intermolecular cross-link between the receptor regions of the glycoprotein constructs, as well as a number of unexpected but nonetheless specific interactions between the fusion domains of CD28-IgG and the receptor domain of CD80-Fab. The strategy of chemical cross-linking combined with differential MALDI-MS peptide mapping (+ thiol reagent) enabled localization of the interface region(s) of the complexes studied and clearly demonstrates the utility of such an approach to obtain structural information on interacting noncovalent complexes.     

Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments

With the recent development of genomic resources and high‐throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C₄ grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype–phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.     

Assessing Equivalence Tests with Respect to their Expected p‐Value

Monte‐Carlo simulation methods are commonly used for assessing the performance of statistical tests under finite sample scenarios. They help us ascertain the nominal level for tests with approximate level, e.g. asymptotic tests. Additionally, a simulation can assess the quality of a test on the alternative. The latter can be used to compare new tests and established tests under certain assumptions in order to determinate a preferable test given characteristics of the data. The key problem for such investigations is the choice of a goodness criterion. We expand the expected p‐value as considered by Sackrowitz and Samuel‐Cahn (1999) to the context of univariate equivalence tests. This presents an effective tool to evaluate new purposes for equivalence testing because of its independence of the distribution of the test statistic under null‐hypothesis. It helps to avoid the often tedious search for the distribution under null‐hypothesis for test statistics which have no considerable advantage over yet available methods. To demonstrate the usefulness in biometry a comparison of established equivalence tests with a nonparametric approach is conducted in a simulation study for three distributional assumptions.     

Competitiveness and life‐history characteristics of Daphnia with respect to susceptibility to a bacterial pathogen

Costs of resistance, i.e. trade‐offs between resistance to parasites or pathogens and other fitness components, may prevent the fixation of resistant genotypes and therefore explain the maintenance of genetic polymorphism for resistance in the wild. Using two approaches, the cost of resistance to a sterilizing bacterial pathogen were tested for in the crustacean Daphnia magna. First, groups of susceptible and resistant hosts from each of four natural populations were compared in terms of their life‐history characteristics. Secondly, we examined the competitiveness of nine clones from one population for which more detailed information on genetic variation for resistance was known. In no case did the results show that competitiveness or life history characteristics of resistant Daphnia systematically differed from susceptible ones. These results suggest that costs of resistance are unlikely to explain the maintenance of genetic variation in D. magna populations. We discuss methods for measuring fitness and speculate on which genetic models of host‐parasite co‐evolution may apply to the Daphnia‐microparasite system.     

Regression analysis of multivariate interval-censored failure time data with application to tumorigenicity experiments

This paper discusses multivariate interval-censored failure time data that occur when there exist several correlated survival times of interest and only interval-censored data are available for each survival time. Such data occur in many fields. One is tumorigenicity experiments, which usually concern different types of tumors, tumors occurring in different locations of animals, or together. For regression analysis of such data, we develop a marginal inference approach using the additive hazards model and apply it to a set of bivariate interval-censored data arising from a tumorigenicity experiment. Simulation studies are conducted for the evaluation of the presented approach and suggest that the approach performs well for practical situations.     

Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0

With the advent of next‐generation sequencing technologies, large data sets of several thousand loci from multiple conspecific individuals are available. Such data sets should make it possible to obtain accurate estimates of population genetic parameters, even for complex models of population history. In the analyses of large data sets, it is difficult to consider finite‐sites mutation models (FSMs). Here, we use extensive simulations to demonstrate that the inclusion of FSMs is necessary to avoid severe biases in the estimation of the population mutation rate θ, population divergence times, and migration rates. We present a new version of Jaatha, an efficient composite‐likelihood method for estimating demographic parameters from population genetic data and evaluate the usefulness of Jaatha in two biological examples. For the first application, we infer the speciation process of two wild tomato species, Solanum chilense and Solanum peruvianum. In our second application example, we demonstrate that Jaatha is readily applicable to NGS data by analyzing genome‐wide data from two southern European populations of Arabidopsis thaliana. Jaatha is now freely available as an R package from the Comprehensive R Archive Network (CRAN).     

Monitoring codling moth (Lepidoptera: Tortricidae) with a four‐component volatile blend compared to a sex pheromone‐based blend

Monitoring adult codling moth, Cydia pomonella (L.), is a crucial component in implementing effective integrated management programmes in apple, Malus domestica Borkhausen. Use of sex pheromone lures to track male populations has been the traditional approach, but their use in orchards treated with sex pheromone for mating disruption (MD) has been problematic. Development of kairomone and kairomone–pheromone combination lures has allowed the catch of female moths and has benefited several aspects of codling moth management through improved spray timings and action thresholds. Recently, a new four‐component volatile blend (4‐K) comprised of pear ester, (E,Z)‐2,4‐ethyl decadienoate (PE), (E)‐11 4,8‐dimethyl‐1,3,7‐nonatriene, all isomers of pyranoid linalool oxide and acetic acid (AA) has been characterized that has increased female moth catch threefold versus any previous blend. Field trapping studies were conducted to compare moth catches in traps baited with 4‐K versus the use of sex pheromone, (E,E)‐8,10‐dodecadien‐1‐ol (PH) in combination with PE and AA. Trials were conducted in orchards left either untreated, or treated with PH or PH + PE. Traps baited with 4‐K and 4‐K + PH lures caught significantly more females than traps baited with PH + PE + AA lures. Traps baited with 4‐K + PH lures caught significantly more total moths than traps baited with PH + PE + AA lures in all three orchards. Adding a PH lure to traps with the 4‐K lure did not affect female catch, but significantly increased male and total moth catches. These studies demonstrate that codling moth can be trapped effectively in apple under MD without the use of sex pheromone lures. The significant increase in female codling moth catch with the 4‐K lure suggests that efforts to improve spray timings and action threshold determinations as well as mass trapping might be enhanced with this new lure.     

Mouse translation elongation factor eEF1A-2 interacts with Prdx-I to protect cells against apoptotic death induced by oxidative stress

eEF1A-1 and eEF1A-2 are two isoforms of translation elongation factor eEF1A. In adult mammalian tissues, isoform eEF1A-1 is present in all tissues except neurons, cardiomyocytes, and myotubes, where its isoform, eEF1A-2, is the only form expressed. Both forms of eEF1A have been characterized to function in the protein elongation step of translation, and eEF1A-1 is shown to possess additional non-canonical roles in actin binding/bundling, microtubule bundling/severing, and cellular transformation processes. To study whether eEF1A-2 has similar non-canonical functions, we carried out a yeast two-hybrid screening using a full sequence of mouse eEF1A-2 as bait. A total of 78 hits, representing 23 proteins, were identified and validated to be true positives. We have focused on the protein with the highest frequency of hits, peroxiredoxin I (Prdx-I), for in-depth study of its functional implication for eEF1A-2. Here we show that Prdx-I coimmunoprecipitates with eEF1A-2 from extracts of both cultured cells and mouse tissues expressing this protein, but it does not do so with its isoform, eEF1A-1, even though the latter is abundantly present. We also report that an eEF1A-2 and Prdx-I double transfectant increases resistance to peroxide-induced cell death as high as 1 mM peroxide treatment, significantly higher than do single transfectants with either gene alone; this protection is correlated with reduced activation of caspases 3 and 8, and with increased expression of pro-survival factor Akt. Thus, our results suggest that eEF1A-2 interacts with Prdx-I to functionally provide cells with extraordinary resistance to oxidative stress-induced cell death.