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4-1BB and OX40 act independently to facilitate robust CD8 and CD4 recall responses.

Mice deficient in OX40 or 4-1BB costimulatory pathways show defects in T cell recall responses, with predominant effects on CD4 vs CD8 T cells, respectively. However, OX40L can also stimulate CD8 T cells and 4-1BBL can influence CD4 T cells, raising the possibility of redundancy between the two TNFR family costimulators. To test this possibility, we generated mice deficient in both 4-1BBL and OX40L. In an adoptive transfer model, CD4 T cells expressed 4-1BB and OX40 sequentially in response to immunization, with little or no overlap in the timing of their expression. Under the same conditions, CD8 T cells expressed 4-1BB, but no detectable OX40. Thus, in vivo expression of 4-1BB and OX40 can be temporally and spatially segregated. In the absence of OX40L, there were decreased CD4 T cells late in the primary response and no detectable secondary expansion of adoptively transferred CD4 T cells under conditions in which primary expansion was unaffected. The 4-1BBL had a minor effect on the primary response of CD4 T cells in this model, but showed larger effects on the secondary response, although 4-1BBL(-/-) mice show less impairment in CD4 secondary responses than OX40L(-/-) mice. The 4-1BBL(-/-) and double knockout mice were similarly impaired in the CD8 T cell response, whereas OX40L(-/-) and double knockout mice were similarly impaired in the CD4 T cell response to both protein Ag and influenza virus. Thus, 4-1BB and OX40 act independently and nonredundantly to facilitate robust CD4 and CD8 recall responses.

4-1BB Ligand↗

Retinoic acid and polyriboinosinic:polyribocytidylic acid stimulate robust anti-tetanus antibody production while differentially regulating type 1/type 2 cytokines and lymphocyte populations.

Retinoic acid (RA), a bioactive retinoid, and polyriboinosinic:polyribocytidylic acid (PIC) are known to promote immunity in vitamin A-deficient animals. In this study, we hypothesized that RA, PIC, and the combination can provide significant immunoadjuvant activity even in the vitamin A-adequate state. Six-week-old C57BL/6 mice were immunized with tetanus toxoid (TT) and treated with RA and/or PIC at priming in three independent studies of short and long duration. RA and PIC differentially regulated both primary and secondary anti-TT IgG isotypes, whereas the combination of RA + PIC stimulated the highest level of anti-TT IgG production and, concomitantly, a ratio of IgG1 to IgG2a similar to that of the control group. The regulation of Ab response was strongly associated with type 1/type 2 cytokine gene expression. Whereas RA reduced type 1 cytokines (IFN-gamma and IL-12), PIC enhanced both type 1 and type 2 cytokines (IL-4 and IL-12) and cytokine-related transcription factors. Despite the presence of PIC, the IL-4:IFN-gamma ratio was significantly elevated by RA. In addition, RA and/or PIC modulated NK/NKT cell populations and the level of expression of the costimulatory molecules CD80/CD86, evident 3 days after priming. Notably, the NKT:NK and CD80:CD86 ratios were correlated with the IL-4:IFN-gamma ratio, indicative of multiple converging modes of regulation. Overall, RA, PIC, and RA + PIC rapidly and differentially shaped the anti-tetanus Ig response. The robust, durable, and proportionate increase in all anti-TT IgG isotypes induced by RA + PIC suggests that this combination is promising as a means to enhance the Ab response to TT and similar vaccines.

Adjuvants, Immunologic↗

Strong TCR signaling, TLR ligands, and cytokine redundancies ensure robust development of type 1 effector T cells.

T cell effector function is a central mechanism of adaptive immunity, and accordingly, protection of the host against pathogens. One of the primary effector molecules produced by T cells in response to such pathogens is the cytokine, IFN-gamma. Although the signaling pathways associated with the production of IFN-gamma are well established, disparate in vivo and in vitro results indicate that distinct pathways may become more prominent dependent upon the nature of the infection, inflammatory milieu and tissue localization. We have examined the roles and requirements of the major IFN-gamma-inducing pathways in vivo and in vitro, specifically: strength of TCR signal; paracrine release of IL-12, IL-23, and IL-18; and autocrine production of IFN-gamma. Our data show a dynamic interaction between these activation pathways, which allows the host a degree of flexibility and redundancy in the induction of IFN-gamma. Upon strong signaling through the TCR, IL-12, IL-18, and IL-23 play negligible roles in the induction of IFN-gamma, whereas autocrine IFN-gamma is an important component in sustaining its own secretion. However, the absence of any one of these factors during a weaker TCR signal, results in strikingly impaired T cell IFN-gamma production. Of note, TLR-activated dendritic cells (DCs) were capable of overcoming the absence of a strong TCR signal, IL-12, IL-23, or IL-18 revealing an important additional mechanism for ensuring a robust IFN-gamma response. Our findings clarify the hierarchical requirements of the major IFN-gamma inducing pathways and highlight the important role TLR ligand-activated DCs have to preserve them.

Animals↗

[Robustness of the analytic/holistic processing strategies in various cognitive tasks].

Robustness of the analytic/holistic processing strategies was examined in various cognitive tasks. The tasks in Experiment I were to classify facial patterns and verbal materials of different category structures into two categories. Stimuli were presented either with (thematization condition) or without a theme. Three types of strategies were discerned; consistently-analytic, consistently-holistic and optimal shifting. Experiment II was designed to test their performance in the Kagan type perceptual and memory identification tasks. The results from the two experiments showed that about 30% of the subjects adhered to either analytic or holistic strategy across tasks and experiments. They exhibited responses similar to the reflective and impulsive types. Approximately 40% of the subjects adjusted their strategies according to the task demands.

Acoustic Stimulation↗

An efficient, robust and unified method for mapping complex traits (III): combined linkage/linkage-disequilibrium analysis.

Extending the method for linkage analysis [Zhao et al., 1998a: Am. J. Med. Genet. 77:366-383; 1998b: Am. J. Med. Genet. 79:49-61], this article describes a method for the linkage-disequilibrium analysis, and for combining linkage and linkage-disequilibrium analyses. As highly dense markers are increasingly used in genome scans, one or more markers are not only linked with the disease genes if they exist, but also likely in linkage-disequilibrium with those putative genes. Hence, linkage-disequilibrium analysis potentially offers additional information about positions of putative disease genes. Combining both linkage and linkage-disequilibrium signals, this approach is able to improve positional signals. As before, the proposed method is a model-based approach, but semiparametric via the estimating equation technique. Under the assumptions of penetrance and allele frequency, this method efficiently estimates recombination fractions for linkage analysis and odds ratios for linkage-disequilibrium analysis. As described in two previous papers, this method is relatively more robust than the lod score methods, since it requires weaker assumption than conditional independence. While the estimated recombination fractions are used for inference as part of linkage analysis, the estimated odds ratios are used for linkage-disequilibrium inference and combined linkage, and linkage-disequilibrium parameters can be used to test combined linkage/linkage-disequilibrium analysis. This approach has been implemented, named gSCAN, and its compiled version is available for trial on request via the web site (http:/lynx.fhcrc.org/qge). We applied this new approach to affected sib-pair data collected for the genome scan to localize type 1 diabetes genes. Under an assumed autosomal dominant gene model, the linkage analysis confirms an earlier suggestion of one major gene around D6S281. Interestingly, the linkage-disequilibrium analysis suggests several additional signals around D6S250, GATA30, D6S311, D6S441, D6S442, D6S415, D6S411, D6S305, and a290xh9. The linkage analysis, on the other hand, suggests a signal around D6S281, while providing supporting evidence for several other marker loci. However, the combined analysis did not provide strong support for any of the findings, implying that linkage and linkage-disequilibrium findings are not consistent.

Alleles↗

Computing minimum description length for robust linear regression model selection.

A minimum description length (MDL) and stochastic complexity approach for model selection in robust linear regression is studied in this paper. Computational aspects and implementation of this approach to practical problems are the focuses of the study. Particularly, we provide both algorithms and a package of S language programs for computing the stochastic complexity and proceeding with the associated model selection. A simulation study is then presented for illustration and comparing the MDL approach with the commonly used AIC and BIC methods. Finally, an application is given to a physiological study of triathlon athletes.

Algorithms↗

Robust estimation of parasite component community richness.

The performance of 2 nonparametric estimators of species richness, the bootstrap (S(B)) and kth-order jackknife (S(Jk)), are compared using simulated parasite communities. The parameters of the simulation match those of an earlier comparison that favored S(B) as an estimator but did not include S(Jk). S(Jk) is the least biased of the 2 estimators. Whereas the bias of S(B) is significantly affected by true species richness and the proportion of rare species, the bias of S(Jk) is relatively insensitive to changes in these parameters, and is, therefore, recommended as a robust estimator of species richness.

Analysis of Variance↗

Robust regeneration of adult sensory axons in degenerating white matter of the adult rat spinal cord.

We have recently reported that minimally disturbed adult CNS white matter can support regeneration of adult axons by using a novel microtransplantation technique to inject minute volumes of dissociated adult rat dorsal root ganglion neurons directly into adult rat CNS pathways (Davies et al., 1997). This atraumatic injection procedure minimized scarring and allowed considerable numbers of regenerating adult axons immediate access to the adult CNS glial terrain where they rapidly extended for long distances. A critical question remained as to whether degenerating white matter at acute and chronic stages (up to 3 months) after injury could still support regeneration. To investigate this, we have microtransplanted adult sensory neurons into degenerating white matter of the adult rat spinal cord several millimeters rostral to a severe lesion of the dorsal columns. Regeneration of donor sensory axons in both directions away from the site of transplantation was robust even within white matter undergoing fulminant Wallerian degeneration despite intimate contact with myelin. Along their route, the regrowing axons extended large numbers of collaterals into the adjacent dorsal horn. However, after entering the lesion, the rapidly extending growth cones stopped and became dystrophic within high concentrations of reactive glial matrix. Our results offer compelling evidence that the major environmental impediment to regeneration in the adult CNS is the molecular barrier that forms directly at the lesion site, and that degenerating white matter beyond the glial scar has a far greater intrinsic ability to support axon regeneration than previously thought possible.

Animals↗

Robust assessment of statistical significance in the use of unbound/intrinsic pharmacokinetic parameters in quantitative structure-pharmacokinetic relationships with lipophilicity.

The optimization of pharmacokinetic properties remains one of the most challenging aspects of drug design. Key parameters, clearance and volume of distribution, are multifactorial, which makes deriving structure-pharmacokinetic relationships difficult. The correction of clearance and volume of distribution for the unbound fraction in plasma is one approach taken that has enabled quantitative structure-pharmacokinetic relationships to be derived. Three published data-sets where unbound parameters have been correlated with lipophilicity have been reanalyzed. The reanalysis has shown that high correlation coefficients can be achieved without any true correlation in the data and can lead to misinterpretation of the ways in which lipophilicity influences pharmacokinetics. Randomization procedures are proposed as a more robust method of assessing significance.

Algorithms↗

Free-Tree--freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of genus Frenkelia.

The Win95 program for computation of distance matrixes and construction of phylogenetic or phenetic trees on the basis of RAPD, RFLP and allozyme data was presented. In contrast with other presently available software, the program FreeTree can also assess the robustness of the tree topology by bootstrap, jackknife or OTU-jackknife analysis. Moreover, the program can be used also for an analysis of data obtained in several independent experiments performed with nonidentical subsets of taxa. The function of the program was demonstrated by an analysis of RAPD data from 22 strains of Frenkelia. The program is available as an autoextractive archive containing the installation files of FreeTree and TreeView, manual in MS Word format and a sample of the input file at http://www.natur.cuni.cz/flegr/programs/+ ++freetree.

Animals↗

Rapid and robust olfactory conditioning with milk before suckling experience: promotion of nipple attachment in the newborn rat.

An olfactory conditioning paradigm tested the hypothesis that newborn rats are able to learn about events associated with their first experience with milk as early as 3-5 hr after birth. Exposure to lemon odor (conditioned stimulus, [CS]) paired with intraoral milk infusions (unconditioned stimulus, [US]) resulted in strong conditioning: In the presence of the CS, sustained attachment occurred to an empty nipple as if it provided milk, whereas pups in control conditions showed little attachment. A single CS-US pairing was sufficient for strong conditioning, which was evident with a trace interval as long as 60 s. Conditioning was robust enough to promote attachment to a nipple providing saline, which is aversive to the newborn rat, and comparably strong conditioning occurred with sucrose or saccharin as the US. These findings suggest that olfactory conditioning has the potential to modify suckling behavior.

Animals↗

Robust outcome prediction for intensive-care patients.

Missing data are a major plague of medical databases in general, and of Intensive Care Unit databases in particular. The time pressure of work in an Intensive Care Unit pushes the physicians to omit randomly or selectively record data. These different omission strategies give rise to different patterns of missing data and the recommended approach of completing the database using median imputation and fitting a logistic regression model can lead to significant biases. This paper applies a new classification method, called robust Bayes classifier, which does not rely on any particular assumption about the pattern of missing data and compares it to the median imputation approach using a database of 324 Intensive Care Unit patients.

Bayes Theorem↗

Human anti-mouse antibodies: pitfalls in tumor marker measurement and strategies for enhanced assay robustness; including results with Elecsys CEA.

Therapies using monoclonal antibodies may have undesirable consequences for the diagnostic use of tumor markers. These effects can be minimised by employing chimeric antibodies as well as special interference eliminating reagents. Human Anti-Mouse Antibodies (HAMA) are produced as a result of the immune response of a patient to treatment with murine monoclonal antibodies. The interaction of HAMA with the murine monoclonal antibodies of a tumor marker assay can simulate (false) positive or negative results leading to misdiagnosis and to inadequate disease management of a patient. To avoid HAMA-interferences "Roche Diagnostics" established a three-component-system: The use of chimeric antibodies, the interference elimination, which is realised in the parameters most frequently used like CEA and TSH. By employing such a chimeric antibody, Elecsys CEA proved to be extremely robust against HAMA-interferences. With 20 clinical relevant samples from different Mab-approaches, no HAMA-interference was observed. By fragmentation of the antibodies, i.e., elimination of the constant region and using monovalent fab-fragments (antigen binding fragment) combined with the addition of special blocking reagents all not-chimerized, Elecsys assays showed comparable results to chimerisation. This could also be shown with 20 clinical relevant samples.

Animals↗

Force transducer design: a new approach combining nonlinear finite element analysis and robust design.

Designing a strain gage based force transducer is considered more of an art than an engineering process. Only general guidelines are available, and many trial and error iterations are needed to optimize the geometry and minimize the errors caused by nonlinear behavior of the structure. A new method, based on nonlinear finite element analysis and robust design principles, is proposed. A matrix of experiments considers relevant geometric and loading parameters. The behavior of the structure under different combinations of these parameters is determined by calculating the strain at different locations (suitable for strain gage installation) using finite element models. The nonlinear behavior of the transducer is identified by comparing the results of the nonlinear finite element analysis with those obtained using a linear finite element analysis. A signal-to-noise ratio is defined to quantify the nonlinearities and how the considered parameters affect them. An analysis of variance is employed to determine their relative influence. Based on the results of the statistical analysis, it is possible to identify the best value for each geometric parameter that would reduce, if not eliminate the nonlinearities. Once these optimal geometric parameters are chosen, a prototype can be built, instrumented with strain gages, and tested, to validate the obtained design. To illustrate this new proposed methodology, and appreciate its advantages over current practice of designing a force transducer, an example of the step-by-step procedure is illustrated considering a thin-wall cylindrical transducer.

Equipment Design↗

Utility of semivariogram for spatial variation of soil nutrients and the robust analysis of semivariogram.

The spatial variation of soil nutrients in topsoil (0-20 cm) was analyzed using semivariogram in the Zunhua County of Hebei Province, China. The effect on semivariogram with randomly deleted data and kriged estimates using various reduced sample sizes was also analyzed. The semivariograms of available N, total N, available P, organic matter were best described by a spherical model, except for available K, which best fitted a complex structure of exponential model and linear with sill model. The ratio of nugget to total sample variance ranged from 34.4% to 68.4%, indicating the spatial correlation of tested soil nutrients on a large scale was moderately dependent. Among five soil nutrients, available nitrogen and available phosphorus had the shortest spatial correlation range (5 km and 5.5 km), available K had the longest range (25.5 km), whereas total nitrogen and organic matter had intermediate spatial correlation range (14.5 km and 8.5 km). The semivariograms of available N, total N, available P, and organic matter were insensitive to a 50%-60% reduction in original sampling density, while for available K, it is up to 70%. The estimated spatial distributions of total N by kriging, under various reduced sample sizes, all correlated significantly (P = 0.001) with those obtained from original data. The results showed that the semivariogram was a relatively robust tool when used in a large region and sufficient spatial variation information could be retained regardless of a higher deletion proportion of the original data. The original sample data could be reduced by kriging and the estimates showed no loss of spatial information, however, the results may be unreliable unless a clearly identified semivariogram model could be obtained. The results may provide useful information for determining the appropriate sampling densities for these scales of soil survey.

Environmental Monitoring↗

Evaluation of the Gammarus pulex in situ feeding assay as a biomonitor of water quality: robustness, responsiveness, and relevance.

Biomonitoring using benthic macroinvertebrates has been used to assess water quality in Europe since the early 20th century. Most methods use community-level measurements, and the use of single-species responses has been limited, despite their potential benefits as sensitive, early warning indicators. Here we evaluate a single-species in situ assay in which the response is feeding inhibition of the freshwater amphipod Gammarus pulex. The assay was deployed in uncontaminated reference sites to quantify background variability in feeding rates and to elucidate sources of this variation. The ability of the assay to detect impacts of point-source discharges was assessed and the ecological relevance of the assay determined by comparing assay responses to aspects of community structure and functioning. Water temperature accounted for 76% of the variation in the feeding rate of animals deployed at uncontaminated sites, and summer deployments had a >90% power to detect a 30% inhibition in feeding. Inhibition of the situ feeding rate of G. pulex deployed downstream of a variety of point-source discharges ranged from 27 to 99.6%. Gammarus pulex is an important detritivore in stream communities, and a strong positive correlation existed between in situ feeding rate measured over 6 d and leaf decomposition measured over 28 d. A positive correlation also existed between in situ feeding and macroinvertebrate diversity and a biotic index. The G. pulex in situ feeding assay is a short-term sublethal biomonitor of water quality that is indicative of community- and ecosystem-level responses occurring over longer time periods. It is robust, responsive, and relevant.

Animals↗

Robustness and economic measures as control benchmark performance criteria.

The objective of this paper was to investigate the usefulness of new multi-criteria measures to evaluate a control strategy through the Benchmark protocol. Using a case study in which respirometry-based control strategies are evaluated, the proposed measures were calculated. An economic index including weighted investment and operating costs (termed Total Cost Index--TCI) appears more powerful than a grey-scale presentation approach. Using the latter approach, it is hard to reflect the relative importance of the criteria investigated, which makes practical decisions rather difficult. In addition, a Robustness Index (RI) is proposed that allows us to evaluate the transferability of control strategies to situations different from the ones defined in the benchmark protocol. Finally, the case study shows that it may be advisable to replace the currently used open loop benchmark reference by a plant in which dissolved oxygen is controlled in all aerated reactors. This quite simple strategy also turned out to be the best one among all evaluated strategies.

Algorithms↗

Development and validation of a cost-effective, efficient, and robust liquid chromatographic method for the simultaneous determination of the acetyl and succinoyl content in hydroxypropyl methylcellulose acetate succinate polymer.

A reversed-phase liquid chromatographic method was developed and validated for the determination of the content of free acetic acid, free succinic acid, acetyl substituents, and succinoyl substituents in hydroxypropyl methylcellulose acetate succinate (HPMCAS; Chemical Abstracts Service Registry No. 71138-97-1) polymer. This single new method gave accurate and precise measurement of both acetyl and succinoyl substituents, which had previously required 3 Japanese Pharmaceutical Excipients (JPE) methods to accomplish. Consequently, analysis time and turnaround time are decreased significantly. Furthermore, this method can also separate and determine the free acetic and succinic acids in HPMCAS polymer, a task that the corresponding JPE method cannot achieve. The values for accuracy (average recovery from 12 standard samples) were 99.9% for acetic acid and 99.8% for succinic acid. The values for injection precision (relative standard deviation [RSD]) were 0.11% for acetic acid and 0.28% for succinic acid. The values for intermediate precision (RSD) were 1.25% for determination of the acetyl content at the 8.78% (w/w) level and 1.33% for determination of the succinoyl content at the 10.9% (w/w) level. The values for intermediate precision (RSD) were 5.98% for determination of free acetic acid at the 0.12% (w/w) level and 5.13% for determination of free succinic acid at the 0.029% (w/w) level. The method was proven to be robust with respect to variation in the pH of the mobile phase, the concentration of potassium dihydrogen phosphate, and the flow rate. The method is well suited for quality control in today's fast-paced pharmaceutical laboratories.

Acetates↗