Bayesian design and analysis of two-arm cluster randomized trials using assurance

We consider the design of a two-arm superiority cluster randomized controlled trial (RCT) with a continuous outcome. We detail Bayesian inference for the analysis of the trial using a linear mixed-effects model. The treatment is compared to control using the posterior distribution for the treatment effect. We develop the form of the assurance to choose the sample size based on this analysis, and its evaluation using a two loop Monte Carlo sampling scheme. We assess the proposed approach, considering the effect of different forms of prior distribution, and the number of Monte Carlo samples needed in both loops for accurate determination of the assurance and sample size. Based on this assessment, we provide general advice on each of these choices. We apply the approach to the choice of sample size for a cluster RCT into poststroke incontinence, and compare the resulting sample size to that from assurance based on a Wald test for the treatment effect. The Bayesian approach to design and analysis developed in this article can offer advantages in terms of an increase in the robustness of the chosen sample size to parameter mis-specification and reduced sample sizes if prior information indicates the treatment effect is likely to be larger than the minimal clinically important difference.

Sample size determination for point-of-care COVID-19 diagnostic tests: a Bayesian approach

BACKGROUND

In a pandemic setting, it is critical to evaluate and deploy accurate diagnostic tests rapidly. This relies heavily on the sample size chosen to assess the test accuracy (e.g. sensitivity and specificity) during the diagnostic accuracy study. Too small a sample size will lead to imprecise estimates of the accuracy measures, whereas too large a sample size may delay the development process unnecessarily. This study considers use of a Bayesian method to guide sample size determination for diagnostic accuracy studies, with application to COVID-19 rapid viral detection tests. Specifically, we investigate whether utilising existing information (e.g. from preceding laboratory studies) within a Bayesian framework can reduce the required sample size, whilst maintaining test accuracy to the desired precision.

METHODS

The method presented is based on the Bayesian concept of assurance which, in this context, represents the unconditional probability that a diagnostic accuracy study yields sensitivity and/or specificity intervals with the desired precision. We conduct a simulation study to evaluate the performance of this approach in a variety of COVID-19 settings, and compare it to commonly used power-based methods. An accompanying interactive web application is available, which can be used by researchers to perform the sample size calculations.

RESULTS

Results show that the Bayesian assurance method can reduce the required sample size for COVID-19 diagnostic accuracy studies, compared to standard methods, by making better use of laboratory data, without loss of performance. Increasing the size of the laboratory study can further reduce the required sample size in the diagnostic accuracy study.

CONCLUSIONS

The method considered in this paper is an important advancement for increasing the efficiency of the evidence development pathway. It has highlighted that the trade-off between lab study sample size and diagnostic accuracy study sample size should be carefully considered, since establishing an adequate lab sample size can bring longer-term gains. Although emphasis is on its use in the COVID-19 pandemic setting, where we envisage it will have the most impact, it can be usefully applied in other clinical areas.

Multilevel emulation for stochastic computer models with application to large offshore wind farms

Renewable energy projects, such as large offshore wind farms, are critical to achieving low-emission targets set by governments. Stochastic computer models allow us to explore future scenarios to aid decision making while considering the most relevant uncertainties. Complex stochastic computer models can be prohibitively slow, and thus an emulator may be constructed and deployed to allow for efficient computation. We present a novel heteroscedastic Gaussian Process emulator that exploits cheap approximations to a stochastic offshore wind farm simulator. We also conduct a probabilistic sensitivity analysis to understand the influence of key parameters in the wind farm model, which will help us to plan a probability elicitation in the future.

Bayesian sample size determination for diagnostic accuracy studies

The development of a new diagnostic test ideally follows a sequence of stages which, among other aims, evaluate technical performance. This includes an analytical validity study, a diagnostic accuracy study, and an interventional clinical utility study. In this article, we propose a novel Bayesian approach to sample size determination for the diagnostic accuracy study, which takes advantage of information available from the analytical validity stage. We utilize assurance to calculate the required sample size based on the target width of a posterior probability interval and can choose to use or disregard the data from the analytical validity study when subsequently inferring measures of test accuracy. Sensitivity analyses are performed to assess the robustness of the proposed sample size to the choice of prior, and prior‐data conflict is evaluated by comparing the data to the prior predictive distributions. We illustrate the proposed approach using a motivating real‐life application involving a diagnostic test for ventilator associated pneumonia. Finally, we compare the properties of the approach against commonly used alternatives. The results show that, when suitable prior information is available, the assurance‐based approach can reduce the required sample size when compared to alternative approaches.

Comparative diagnostic accuracy studies with an imperfect reference standard - a comparison of correction methods

BACKGROUND

Staquet et al. and Brenner both developed correction methods to estimate the sensitivity and specificity of a binary-response index test when the reference standard is imperfect and its sensitivity and specificity are known. However, to our knowledge, no study has compared the statistical properties of these methods, despite their long application in diagnostic accuracy studies.

AIM

To compare the correction methods developed by Staquet et al. and Brenner.

METHODS

Simulations techniques were employed to compare the methods under assumptions that the new test and the reference standard are conditionally independent or dependent given the true disease status of an individual. Three clinical datasets were analysed to understand the impact of using each method to inform clinical decision-making.

RESULTS

Under the assumption of conditional independence, the Staquet et al. correction method outperforms the Brenner correction method irrespective of the prevalence of disease and whether the performance of the reference standard is better or worse than the index test. However, when the prevalence of the disease is high (> 0.9) or low (< 0.1), the Staquet et al. correction method can produce illogical results (i.e. results outside [0,1]). Under the assumption of conditional dependence; both methods failed to estimate the sensitivity and specificity of the index test especially when the covariance terms between the index test and the reference standard is not close to zero.

CONCLUSION

When the new test and the imperfect reference standard are conditionally independent, and the sensitivity and specificity of the imperfect reference standard are known, the Staquet et al. correction method outperforms the Brenner method. However, where the prevalence of the target condition is very high or low or the two tests are conditionally dependent, other statistical methods such as latent class approaches should be considered.

Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions

Diseases are characterized by distinct changes in tissue molecular distribution. Molecular analysis of intact tissues traditionally requires preexisting knowledge of, and reagents for, the targets of interest. Conversely, label-free discovery of disease-associated tissue analytes requires destructive processing for downstream identification platforms. Tissue-based analyses therefore sacrifice discovery to gain spatial distribution of known targets or sacrifice tissue architecture for discovery of unknown targets. To overcome these obstacles, we developed a multimodality imaging platform for discovery-based molecular histology. We apply this platform to a model of disseminated infection triggered by the pathogen Staphylococcus aureus, leading to the discovery of infection-associated alterations in the distribution and abundance of proteins and elements in tissue in mice. These data provide an unbiased, three-dimensional analysis of how disease affects the molecular architecture of complex tissues, enable culture-free diagnosis of infection through imaging-based detection of bacterial and host analytes, and reveal molecular heterogeneity at the host-pathogen interface.

Abstract B01: BLU-667: A highly selective RET inhibitor to target RET-driven NSCLC

Activating RET fusions have been observed in 1-2% of non-small cell lung adenocarcinomas (NSCLC). These tumors often occur in non-smokers and lack other driver mutations, similar to NSCLC driven by activation of the tyrosine kinases EGFR, ALK or ROS. Multi-kinase inhibitors (mKIs) with in vitro activity against RET, such as cabozantinib and vandetanib, have been tested in RET-rearranged NSCLC, but without the high response rate often seen with targeted therapies in genetically-defined NSCLC, likely a result of off-toxicities that limit the ability to fully inhibit RET kinase activation. BLU-667 is a next-generation kinase inhibitor specifically tailored to target the activated forms of RET, while sparing kinases that contribute to dose-limiting toxicities, such as VEGFR-2. BLU-667 potently inhibited both RET fusion activity (IC50 = 0.4 nM) and demonstrated 88-fold selectivity over VEGFR-2 in enzymatic assays. In a cellular setting, BLU 667 inhibited the most prevalent RET fusion observed in NSCLC, KIF5B-RET, over 20X more potently than the multikinase inhibitors cabozantinib, vandetanib or RXDX-105. KIF5B-RET autophosphorylation and proliferation driven by RET fusions was inhibited with BLU-667 in the low nanomolar range (4 – 15 nM). In vivo oral administration of BLU 667 was well tolerated in mice at all doses and exhibited dose-dependent modulation of oncogenic RET kinase activity in all in vivo models tested, including a KIF5B-RET NSCLC PDX, as well as a KIF5B-RET V804L-driven tumor model with a mutation at the gatekeeper position, a position susceptible to on-target mutation in many oncogenic kinases. Notably, BLU-667, but not cabozantinib, induced tumor growth inhibition without impacting biomarkers of VEGFR-2 inhibition, providing strong evidence that selective inhibition of RET alone is sufficient for antitumor activity in vivo. By sparing off-target kinases with known toxicity profiles, BLU-667 is predicted to robustly inhibit RET at clinically achievable doses. Moreover, with activity against predicted resistance mutations such as those at the gatekeeper position, BLU-667 may prevent or delay the emergence of resistance and therefore provide patients with RET-driven malignancies an opportunity for more durable and effective therapies. As such, BLU-667 is currently in the dose-escalation segment of a first-in-human phase 1 trial for patients with RET-driven solid tumors with activating RET alterations (NCT03037385).

Citation Format: Rami Rahal, Michelle Maynard, Wei Hu, Jason Brubaker, Qiangfang Cao, Joseph L. Kim, Michael P. Sheets, Douglas P. Wilson, Kevin J. Wilson, Lucian DiPietro, Timothy LaBranche, Beni Wolf, Timothy Guzi, Christoph Lengauer, Erica K. Evans. BLU-667: A highly selective RET inhibitor to target RET-driven NSCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr B01.

Evaluation of a novel fluorescent nanobeacon for targeted imaging of Thomsen-Friedenreich associated colorectal cancer

The Thomsen-Friedenreich (TF) antigen represents a prognostic biomarker of colorectal carcinoma. Here, using a nanobeacon, the surface of which was fabricated with peanut agglutinin as TF-binding molecules, we demonstrate that the nanobeacon is able to detect TF antigen in frozen and freshly biopsied polyps using fluorescence microscopy. Our results provide important clues about how to detect aberrant colonic tissues in the most timely fashion. Given the versatile application method for this topical nanobeacon, the protocol used in this work is amenable to clinical colonoscopy. Moreover, the prospects of clinical translation of this technology are evident.

Isolation of sterol mutants inChlamydomonas reinhardi: Chromatographic analyses

Several sterol mutants ofChlamydomonas reinhardi were isolated by selecting for single colonies resistant to the polyene antibiotic, nystatin. The sterol profiles of three isolates-KD7, KD16, and KD21-as well as a wild type strain (137C) were determined by gas liquid chromatography and mass spectrometry. The wild type strain contained ergosterol (C28-5,7,22-triene) as the predominant sterol, with smaller amounts of a C28-5,7-diene, a C28-7-ene, and C-24 ethyl analogs of these three sterols. The three mutants had altered sterol composition, but none required exogenous sterol for growth. KD7 contained a C28-5,7,22,25-tetraene, a C28-5,7,25-triene, a C28-7,25-diene, and three C-24 ethyl analogs. The lesion in KD7 is apparently an inability to reduce the C-25 double bond required for the biosynthesis of ergosterol and an ethyl analog. The predominant sterols accumulated by KD16 and KD21 were a C28-5,7-diene, a C28-7-ene, and C-24 ethyl versions of these two sterols, suggesting that these strains are 22(23)-desaturase mutants.

Approximate Uncertainty Modeling in Risk Analysis with Vine Copulas

Many applications of risk analysis require us to jointly model multiple uncertain quantities. Bayesian networks and copulas are two common approaches to modeling joint uncertainties with probability distributions. This article focuses on new methodologies for copulas by developing work of Cooke, Bedford, Kurowica, and others on vines as a way of constructing higher dimensional distributions that do not suffer from some of the restrictions of alternatives such as the multivariate Gaussian copula. The article provides a fundamental approximation result, demonstrating that we can approximate any density as closely as we like using vines. It further operationalizes this result by showing how minimum information copulas can be used to provide parametric classes of copulas that have such good levels of approximation. We extend previous approaches using vines by considering nonconstant conditional dependencies, which are particularly relevant in financial risk modeling. We discuss how such models may be quantified, in terms of expert judgment or by fitting data, and illustrate the approach by modeling two financial data sets.

Co-registration of multi-modality imaging allows for comprehensive analysis of tumor-induced bone disease

Bone metastases are a clinically significant problem that arises in approximately 70% of metastatic breast cancer patients. Once established in the bone, tumor cells induce changes in the bone microenvironment that lead to bone destruction, pain, and significant morbidity. While much is known about the later stages of bone disease, less is known about the earlier stages or the changes in protein expression in the tumor micro-environment. Due to promising results of combining magnetic resonance imaging (MRI) and Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry (MALDI IMS) ion images in the brain, we developed methods for applying these modalities to models of tumor-induced bone disease in order to better understand the changes in protein expression that occur within the tumor-bone microenvironment. Specifically, we integrated 3-dimensional-volume reconstructions of spatially resolved MALDI IMS with high-resolution anatomical and diffusion weighted MRI data and histology in an intratibial model of breast tumor-induced bone disease. This approach enables us to analyze proteomic profiles from MALDI IMS data with corresponding in vivo imaging and ex vivo histology data. To the best of our knowledge, this is the first time that these three modalities have been rigorously registered in the bone. The MALDI mass-to-charge ratio peaks indicate differential expression of calcyclin, ubiquitin, and other proteins within the tumor cells, while peaks corresponding to hemoglobin A and calgranulin A provided molecular information that aided in the identification of areas rich in red and white blood cells, respectively. This multi-modality approach will allow us to comprehensively understand the bone-tumor microenvironment and thus may allow us to better develop and test approaches for inhibiting bone metastases.

A Bayes linear Bayes method for estimation of correlated event rates

Typically, full Bayesian estimation of correlated event rates can be computationally challenging since estimators are intractable. When estimation of event rates represents one activity within a larger modeling process, there is an incentive to develop more efficient inference than provided by a full Bayesian model. We develop a new subjective inference method for correlated event rates based on a Bayes linear Bayes model under the assumption that events are generated from a homogeneous Poisson process. To reduce the elicitation burden we introduce homogenization factors to the model and, as an alternative to a subjective prior, an empirical method using the method of moments is developed. Inference under the new method is compared against estimates obtained under a full Bayesian model, which takes a multivariate gamma prior, where the predictive and posterior distributions are derived in terms of well-known functions. The mathematical properties of both models are presented. A simulation study shows that the Bayes linear Bayes inference method and the full Bayesian model provide equally reliable estimates. An illustrative example, motivated by a problem of estimating correlated event rates across different users in a simple supply chain, shows how ignoring the correlation leads to biased estimation of event rates.

Early assessment of breast cancer response to neoadjuvant chemotherapy by semi-quantitative analysis of high-temporal resolution DCE-MRI: preliminary results

PURPOSE

To evaluate whether semi-quantitative analysis of high temporal resolution dynamic contrast-enhanced MRI (DCE-MRI) acquired early in treatment can predict the response of locally advanced breast cancer (LABC) to neoadjuvant chemotherapy (NAC).

MATERIALS AND METHODS

As part of an IRB-approved prospective study, 21 patients with LABC provided informed consent and underwent high temporal resolution 3T DCE-MRI before and after 1cycle of NAC. Using measurements performed by two radiologists, the following parameters were extracted for lesions at both examinations: lesion size (short and long axes, in both early and late phases of enhancement), radiologist's subjective assessment of lesion enhancement, and percentages of voxels within the lesion demonstrating progressive, plateau, or washout kinetics. The latter data were calculated using two filters, one selecting for voxels enhancing ≥50% over baseline and one for voxels enhancing ≥100% over baseline. Pretreatment imaging parameters and parameter changes following cycle 1 of NAC were evaluated for their ability to discriminate patients with an eventual pathological complete response (pCR).

RESULTS

All 21 patients completed NAC followed by surgery, with 9 patients achieving a pCR. No pretreatment imaging parameters were predictive of pCR. However, change after cycle 1 of NAC in percentage of voxels demonstrating washout kinetics with a 100% enhancement filter discriminated patients with an eventual pCR with an area under the receiver operating characteristic curve (AUC) of 0.77. Changes in other parameters, including lesion size, did not predict pCR.

CONCLUSION

Semi-quantitative analysis of high temporal resolution DCE-MRI in patients with LABC can discriminate patients with an eventual pCR after one cycle of NAC.

Imaging analysis of hepatoblastoma resectability across neoadjuvant chemotherapy

PURPOSE

Hepatoblastomas often require neoadjuvant chemotherapy to facilitate partial hepatectomy, which necessitates freedom of tumor borders from the confluence of hepatic veins (COHV), portal vein bifurcation (PVB), and retrohepatic inferior vena cava (IVC). This study aimed to clarify the effect of incremental neoadjuvant cycles on the AHEP0731 protocol criteria of hepatoblastoma resectability.

METHODS

Hepatoblastoma responses to neoadjuvant chemotherapy were analyzed among patients (n=23) treated at two children's hospitals between 1996 and 2010. Using digital imaging data, ellipsoid and point-based models were created to measure tumor volume regression and respective distances from tumor borders nearest to the COHV, PVB, and IVC.

RESULTS

Hepatoblastoma volumes regressed with incremental neoadjuvant chemotherapy cycles (p<0.001). Although tumor borders regressed away from the COHV (p=0.008), on average only 1.1mm was gained. No change from tumor borders to the PVB was detected (p=0.102). Distances from tumor borders to the IVC remained stable at one hospital (p=0.612), but increased only 0.15 mm every 10 days of therapy at the other (p=0.002). Neoadjuvant chemotherapy induced slightly more tumors to meet the threshold vascular margin of 1cm (baseline to completion): COHV, 11 (47.8%) to 17 (73.9%; p=0.058); PVB, 11 (47.8%) to 15 (65.2%; p=0.157); and IVC, 4 (17.4%) to 10 (43.5%; p=0.034). No differences were detected in demographic or disease-specific characteristics between patients who did or did not achieve this 1-cm margin after conclusion of chemotherapy.

CONCLUSION

Hepatoblastoma volumes regress significantly with increasing neoadjuvant chemotherapy cycles. However, tumors often remain anchored to the major hepatic vasculature, showing marginal improvement in resectability criteria.

The radial diffusivity and magnetization transfer pool size ratio are sensitive markers for demyelination in a rat model of type III multiple sclerosis (MS) lesions

Determining biophysical sensitivity and specificity of quantitative magnetic resonance imaging is essential to develop effective imaging metrics of neurodegeneration. Among these metrics, apparent pool size ratio (PSR) from quantitative magnetization transfer (qMT) imaging and radial diffusivity (RD) from diffusion tensor imaging (DTI) are both known to relate to histological measure of myelin density and integrity. However their relative sensitivities towards quantitative myelin detection are unknown. In this study, we correlated high-resolution quantitative magnetic resonance imaging measures of subvoxel tissue structures with corresponding quantitative myelin histology in a lipopolysaccharide (LPS) mediated animal model of MS. Specifically, we acquired quantitative magnetization transfer (qMT) and diffusion tensor imaging (DTI) metrics (on the same tissue sample) in an animal model system of type III oligodendrogliopathy which lacked prominent lymphocytic infiltration, a system that had not been previously examined with quantitative MRI. We find that the qMT measured apparent pool size ratio (PSR) showed the strongest correlation with a histological measure of myelin content. DTI measured RD showed the next strongest correlation, and other DTI and relaxation parameters (such as the longitudinal relaxation rate (R1f) or fractional anisotropy (FA)) showed considerably weaker correlations with myelin content.

Multifunctional nanobeacon for imaging Thomsen-Friedenreich antigen-associated colorectal cancer

This research aimed to validate the specificity of the newly developed nanobeacon for imaging the Thomsen-Friedenreich (TF) antigen, a potential biomarker of colorectal cancer. The imaging agent is comprised of a submicron-sized polystyrene nanosphere encapsulated with a Coumarin 6 dye. The surface of the nanosphere was modified with peanut agglutinin (PNA) and poly(N-vinylacetamide (PNVA) moieties. The former binds to Gal-β(1-3)GalNAc with high affinity while the latter enhances the specificity of PNA for the carbohydrates. The specificity of the nanobeacon was evaluated in human colorectal cancer cells and specimens, and the data were compared with immunohistochemical staining and flow cytometric analysis. Additionally, distribution of the nanobeacon in vivo was assessed using an "intestinal loop" mouse model. Quantitative analysis of the data indicated that approximately 2 μg of PNA were detected for each milligram of the nanobeacon. The nanobeacon specifically reported colorectal tumors by recognizing the tumor-specific antigen through the surface-immobilized PNA. Removal of TF from human colorectal cancer cells and tissues resulted in a loss of fluorescence signal, which suggests the specificity of the probe. Most importantly, the probe was not absorbed systematically in the large intestine upon topical application. As a result, no registered toxicity was associated with the probe. These data demonstrate the potential use of this novel nanobeacon for imaging the TF antigen as a biomarker for the early detection and prediction of the progression of colorectal cancer at the molecular level.

Monitoring the inflammatory response to infection through the integration of MALDI IMS and MRI

Systemic bacterial infection is characterized by a robust whole-organism inflammatory response. Analysis of the immune response to infection involves technologies that typically focus on single organ systems and lack spatial information. Additionally, the analysis of individual inflammatory proteins requires antibodies specific to the protein of interest, limiting the panel of proteins that can be analyzed. Herein we describe the application of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) to mice systemically infected with Staphylococcus aureus to identify inflammatory protein masses that respond to infection throughout an entire infected animal. Integrating the resolution afforded by magnetic resonance imaging (MRI) with the sensitivity of MALDI IMS provides three-dimensional spatially resolved information regarding the distribution of innate immune proteins during systemic infection, allowing comparisons to in vivo structural information and soft-tissue contrast via MRI. Thus, integrating MALDI IMS with MRI provides a systems-biology approach to study inflammation during infection.

Structural basis for selective small molecule kinase inhibition of activated c-Met

The receptor tyrosine kinase c-Met is implicated in oncogenesis and is the target for several small molecule and biologic agents in clinical trials for the treatment of cancer. Binding of the hepatocyte growth factor to the cell surface receptor of c-Met induces activation via autophosphorylation of the kinase domain. Here we describe the structural basis of c-Met activation upon autophosphorylation and the selective small molecule inhibiton of autophosphorylated c-Met. MK-2461 is a potent c-Met inhibitor that is selective for the phosphorylated state of the enzyme. Compound 1 is an MK-2461 analog with a 20-fold enthalpy-driven preference for the autophosphorylated over unphosphorylated c-Met kinase domain. The crystal structure of the unbound kinase domain phosphorylated at Tyr-1234 and Tyr-1235 shows that activation loop phosphorylation leads to the ejection and disorder of the activation loop and rearrangement of helix αC and the G loop to generate a viable active site. Helix αC adopts a orientation different from that seen in activation loop mutants. The crystal structure of the complex formed by the autophosphorylated c-Met kinase domain and compound 1 reveals a significant induced fit conformational change of the G loop and ordering of the activation loop, explaining the selectivity of compound 1 for the autophosphorylated state. The results highlight the role of structural plasticity within the kinase domain in imparting the specificity of ligand binding and provide the framework for structure-guided design of activated c-Met inhibitors.

Diversity of Rhizobia Nodulating Phaseolus vulgaris L. in Two Kenyan Soils with Contrasting pHs

Rhizobia were isolated from two Kenyan soils with pHs of 4.5 and 6.8 and characterized on the basis of their host ranges for nodulation and nitrogen fixation, colony morphologies, restriction fragment fingerprints, and hybridization with a nifH probe. The populations of rhizobia nodulating Phaseolus vulgaris in the two soils were similar in numbers and in effectiveness of N(inf2) fixation but were markedly different in composition. The population in the Naivasha soil (pH 6.8) was dominated by isolates specific in host range for nodulation to P. vulgaris; these all had multiple copies, in most cases four, of the structural nitrogenase gene nifH. Only one of the isolates from this soil formed effective nodules on Leucaena leucocephala, and this isolate had only a single copy of nifH. By contrast, the population in the acid Daka-ini soil (pH 4.5) was composed largely of broad-host-range isolates which had single copies of nifH. The isolates from the Daka-ini soil which were specific to P. vulgaris generally had three copies of nifH, although one isolate had only two copies. These rhizobial isolates are indigenous to Kenyan soils and yet have marked similarities to previously described Rhizobium species from other continents.

Repeatability of DTI-based skeletal muscle fiber tracking

Diffusion tensor imaging (DTI)-based muscle fiber tracking enables the measurement of muscle architectural parameters, such as pennation angle (theta) and fiber tract length (L(ft)), throughout the entire muscle. Little is known, however, about the repeatability of either the muscle architectural measures or the underlying diffusion measures. Therefore, the goal of this study was to investigate the repeatability of DTI fiber tracking-based measurements and theta and L(ft). Four DTI acquisitions were performed on two days that allowed for between acquisition, within day, and between day analyses. The eigenvalues and fractional anisotropy were calculated at the maximum cross-sectional area of, and fiber tracking was performed in, the tibialis anterior muscle of nine healthy subjects. The between acquisitions condition had the highest repeatability for the DTI indices and the architectural parameters. The overall inter class correlation coefficients (ICC's) were greater than 0.6 for both theta and L(ft) and the repeatability coefficients were theta < 10.2 degrees and L(ft) < 50 mm. In conclusion, under the experimental and data analysis conditions used, the repeatability of the diffusion measures is very good and repeatability of the architectural measurements is acceptable. Therefore, this study demonstrates the feasibility for longitudinal studies of alterations in muscle architecture using DTI-based fiber tracking, under similar noise conditions and with similar diffusion characteristics.

An automated algorithm to improve the precision of basilar artery diameter measurements before and after subarachnoid hemorrhage-induced vasospasm in an animal model

OBJECTIVE

Quantifying vasospasm has traditionally been performed manually, a method prone to imprecision and user bias. An alternative approach is to use computerized image analysis techniques to define and quantify the diameter of a vessel. The goal of this article is to demonstrate a novel automated vessel measurement algorithm specific to the needs of vasospasm studies and to compare it with traditional manual measurements in an animal model of vasospasm.

METHODS

A total of 576 arterial diameter measurements were collected by 4 independent, blinded examiners from 24 angiograms in a rabbit subarachnoid hemorrhage (SAH) model. Measurements were taken from 3 segments of the basilar artery in anteroposterior and lateral projections, both before SAH and after SAH-induced vasospasm. Means and standard deviations of 288 manual measurements were compared with 288 automated measurements.

RESULTS

The precision of automated measurements was significantly improved compared with standardized manual measurements (85.7% decrease in variation; P < .001). When using automated measurements, the precision was not affected by vessel size, but when using manual measurements, smaller arteries were less precise (P = .04). There was no significant difference in precision between 2 different contrast concentrations (P = .32).

CONCLUSION

Automated measurements of basilar artery diameters are more precise than manual measurements, both before and after SAH-induced vasospasm. The variability in the manual group worsens when the artery is smaller secondary to vasospasm, indicating a need for the use of this segmentation method.

Quantitative assessment of DTI-based muscle fiber tracking and optimal tracking parameters

Diffusion tensor imaging-based fiber tracking in skeletal muscle has been used to reconstruct and quantify muscle architecture. In addition, the consistent pattern of muscle fiber geometry enables a quantitative assessment of the fiber tracking. This work describes a method to determine the accuracy of individual muscle fiber tracts based on the location at which the fibers terminate, the fiber path, and similarity to the neighboring fibers. In addition, the effect of different stop criteria settings on this quantitative assessment was investigated. Fiber tracking was performed on the tibialis anterior muscle of nine healthy subjects. Complete fiber tracts covered 89.4 +/- 9.6% and 75.0 +/- 15.2% of the aponeurosis area in the superficial and deep compartments, respectively. Applications of the method include the exclusion of erroneous fiber-tracking results, quantitative assessment of data set quality, and the assessment of fiber-tracking stop criteria.

2,5-Disubstituted pyridines: the discovery of a novel series of 5-HT2A ligands

This report describes the effect of replacing the central basic amine present in many known 5-HT(2A) ligands with an aromatic residue. We targeted the isomeric phenethylpyridines 2 and 3 and these compounds proved to be excellent leads, possessing good 5-HT(2A) receptor binding affinity and selectivity over the 5-HT(2C) subtype. Optimization of one isomer led to the identification of 25, a compound with sub-nanomolar 5-HT(2A) affinity and selectivity over 5-HT(2C) of greater than 4600-fold.

Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon)

In this study, microsatellite markers were developed for the genetic linkage mapping and breeding program of the black tiger shrimp Penaeus monodon. A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified from 10 100 EST sequences in the P. monodon EST database. AT-rich microsatellite types were predominant in the EST sequences. Homology searching by the blastn and blastx programs revealed that these 997 ESTs represented 8.6% known gene products, 27.8% hypothetical proteins and 63.6% unknown gene products. Characterization of 50 markers on a panel of 35-48 unrelated shrimp indicated an average number of alleles of 12.6 and an average polymorphic information content of 0.723. These EST microsatellite markers along with 208 other markers (185 amplified fragment length polymorphisms, one exon-primed intron-crossing, six single strand conformation polymorphisms, one single nucleotide polymorphism, 13 non-EST-associated microsatellites and two EST-associated microsatellites) were analysed across the international P. monodon mapping family. A total of 144 new markers were added to the P. monodon maps, including 36 of the microsatellite-containing ESTs. The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome.

Predictors for non-adherence to antiretroviral therapy

Objectives: To determine the risk factors for non-adherence to antiretroviral therapy. Methods: Two hundred clients attending the Melbourne Sexual Health Centre completed a questionnaire about lifestyle, self-efficacy, depression, drug or alcohol use, social supports, and attitudes to health care. Self-reported adherence (SRA) was measured by missed doses in the last 4, 7 and 28 days. Routinely collected viral load levels were reviewed. Results: Two hundred (85%) out of 231 eligible clients participated in the study. Viral load was most strongly associated with SRA for the last 28 days (P < 0.001). Non-adherence was defined as <98.2% SRA. Non-adherence was most strongly associated with having regular daily routines [odds ratio and 95% confidence interval = 0.4 (0.2, 0.7], having set times for getting up and going to bed [0.5 (0.3, 1.0)], using marijuana more than 4 times per week [0.4 (0.2, 1.0)] and lower self-efficacy which included; being sure that you will be able to take medications as directed [0.2 (0.1, 0.6)] and being sure that missing doses of HIV medication will result in drug resistance [0.4 (0.2, 0.7)]. When significant questions were combined into a composite score to screen for non-adherence, the sensitivity to predict non-adherence was as high as 71% with a specificity of 59%. Conclusions : This study showed that a 10-min questionnaire was associated with clients past non-adherence to antiretroviral therapy and may be useful for predicting future adherence.

Structure-Based design, synthesis and sAR of a novel series of thiopheneamidine urokinase plasminogen activator inhibitors

The serine protease urokinase plasminogen activator (uPA) is thought to play a central role in tumor metastasis and angiogenesis. Molecular modeling studies suggest that 5-thiomethylthiopheneamidine inhibits uPA by binding at the S1 pocket of the active site. Further structure based elaboration of this residue resulted in a novel class of potent and selective inhibitors of uPA.

Synthesis of thiophene-2-carboxamidines containing 2-aminothiazoles and their biological evaluation as urokinase inhibitors

The serine protease urokinase (uPa) has been implicated in the progression of both breast and prostate cancer. Utilizing structure based design, the synthesis of a series of substituted 4-[2-amino-1,3-thiazolyl]-thiophene-2-carboxamidines is described. Further optimization of this series by substitution of the terminal amine yielded urokinase inhibitors with excellent activities.

Research and development to improve naval shipboard waste management using a compact closed-loop-controlled waste incinerator

Research has been conducted into the application of forced acoustics for enhancing the performance of a pyrolyzed waste afterburner configured as a dump combustor. Subscale studies showed that acoustic forcing of an air jet entering a dump chamber could trigger the formation of coherent vortices generated by entrainment of ambient gases. Subsequent studies showed that combustible gases could be introduced into the coherent vortices, and with additional modulation this configuration would lead to an enhanced combustion rate with low emissions of pollutants. The acoustically forced burner concept was scaled up to practical levels and tested as an afterburner on a commercial waste incinerator operating in pyrolysis mode. Results show that the afterburner can promote both compactness, due to the rapid combustion rate, and low pollutant emissions resulting from enhanced mixing prior to combustion.

Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile

Molecular techniques were employed to document the microbial diversity associated with the marine sponge Rhopaloeides odorabile. The phylogenetic affiliation of sponge-associated bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rDNA analysis. The community structure was extremely diverse with representatives of the Actinobacteria, low-G+C gram-positive bacteria, the beta- and gamma-subdivisions of the Proteobacteria, Cytophaga/Flavobacterium, green sulfur bacteria, green nonsulfur bacteria, planctomycetes, and other sequence types with no known close relatives. FISH probes revealed the spatial location of these bacteria within the sponge tissue, in some cases suggesting possible symbiotic functions. The high proportion of 16S rRNA sequences derived from novel actinomycetes is good evidence for the presence of an indigenous marine actinomycete assemblage in R. odorabile. High microbial diversity was inferred from low duplication of clones in a library with 70 representatives. Determining the phylogenetic affiliation of sponge-associated microorganisms by 16S rRNA analysis facilitated the rational selection of culture media and isolation conditions to target specific groups of well-represented bacteria for laboratory culture. Novel media incorporating sponge extracts were used to isolate bacteria not previously recovered from this sponge.

Five Crustacean Hyperglycemic Family Hormones of Penaeus monodon: Complementary DNA Sequence and Identification in Single Sinus Glands by Electrospray Ionization-Fourier Transform Mass Spectrometry

Five novel neuropeptides, designated Pm-sgp-I to -V, of the crustacean hyperglycemic hormone (CHH) family have been identified from the giant tiger prawn Penaeus monodon by isolation of the preprohormone genes from an eyestalk complementary DNA library. On the basis of sequence similarity, the encoded peptides have been classified as CHH-like type I hormones, which include all known CHHs and the molt-inhibiting hormone (MIH) of the lobster Homarus americanus. Consistent with CHH type I preprohormones, the Pm-sgp precursors include a signal peptide, a CHH precursor-related peptide (CPRP), and the CHH-like hormone. Analysis by electrospray ionization-Fourier transform mass spectrometry enabled the neuropeptide complement of individual sinus glands to be resolved. It also confirmed the presence of the five Pm-sgp neuropeptides within the sinus gland of an individual animal, in that the masses observed were consistent with those predicted from the gene sequence of the Pm-sgps after posttranslational modification. These modifications included cleavage of the signal peptide and precursor protein, carboxy-terminal amidation, and formation of three disulfide bridges. Analysis of crude extracts of single sinus glands from different animals revealed variation in neuropeptide content and will provide a tool for determining whether the content varies as a function of the physiological state of the animal.

Tissue-Specific Expressed Sequence Tags from the Black Tiger Shrimp Penaeus monodon

: Expressed sequence tag data were generated from complementary DNA libraries created from cephalothorax, eyestalk, and pleopod tissue of the black tiger shrimp (Penaeus monodon). Significant database matches were found for 48 of 83 nuclear genes sequenced from the cephalothorax library, 22 of 55 nuclear genes from the eyestalk library, and 6 of 13 nuclear genes from the pleopod library. The putative identities of these genes reflected the expected tissue specificity. For example, genes for digestive enzymes were identified from the cephalothorax library and genes involved in the visual and neuroendocrine system from the eyestalk library. A few sequences matched anonymous EST or genomic sequences, and others contained mini-satellite or microsatellite repeat sequences. The remainder, 31 from the cephalothorax library, 25 from the eyestalk library, and 5 from the pleopod library, were sequences of high nucleotide complexity with no matches in any database searched and thus may represent novel genes.

Prediction of peptide affinity to HLA DR molecules

A method to quantitatively predict peptide binding to HLA DRB1*0401, B1*0101, and B1*1501 has been developed using a dataset of the relative contributions of each of the naturally occurring amino acids in the context of a simplified peptide backbone. The prediction assumed that the relative role of each of the peptide sidechains could be treated independently and could be measured by assaying each of the twenty naturally occurring amino acids at the central eleven positions of a 13 residue peptide previously shown to contain the minimal requirements for high affinity binding to HLA DR proteins. Three separate databases were generated. They were shown to have predictive value when tested on a set of 13 unrelated peptides known to bind the DR proteins with a wide range of apparent affinity. The DRB1*0401 database was tested further by analyzing myelin basic protein. All 13 amino acid peptides containing a hydrophobic amino acid at the third position were synthesized and assayed for binding purified DRB1*0401. In every case, the measured affinity correlated with the predictive values within the experimental error of the assays. Finally, the ability to predict peptide binding to MHC class II molecules was shown to help in identifying T cell determinants. The specificity of DRB1*0401 restricted T cell hybridomas against human serum albumin corresponded to two peptides, predicted, and shown to bind the class II protein with high affinity.

Down-regulation of poison ivy/oak-induced contact sensitivity by treatment with a class II MHC binding peptide:hapten conjugate

Immune regulation of contact sensitivity to the poison ivy/oak catechol was studied at the level of class II MHC-restricted T cell recognition of hapten:peptide conjugates. In this study we have shown that 1) T cells from C3H/HeN (H-2k) mice, immunized with a synthetic I-Ak binding peptide coupled to 3-pentadecyl-catechol (PDC; a representative catechol in urushiol), recognized peptides derived from syngeneic cells linked to the same catechol; 2) T cells from draining lymph nodes of C3H/HeN mice skin-painted with PDC proliferated in response to a peptide carrier:PDC conjugate only when it was linked at the 7th, but not the 4th or the 10th, position on the peptide carrier; and 3) tolerization studies confirmed down-regulation of PDC-induced delayed-type hypersensitivity following treatment with a single I-Ak binding peptide carrying PDC covalently bound to a lysine residue at the middle (7th) TCR contact position. Tolerization with peptide:PDC conjugate resulted in abrogation of hapten-specific T cell proliferative responses that correlated with diminished IL-2 secretion. On the basis of these data we propose that it may be sufficient to couple the hapten at a single, well-chosen position on a carrier peptide to target a relevant population of T cells involved in contact sensitivity.

Effect of ovariectomy and steroid hormone replacement on the recovery of arterial blood pressure following haemorrhage in anaesthetized Brattleboro rats

There is increasing evidence that ovarian steroids inhibit vascular responsiveness to the neurohypophysial hormone vasopressin. The present study examined the recovery of the arterial blood pressure following a single (2 ml/100 g body weight) haemorrhage in ovariectomized (OVX) Brattleboro rats with hereditary hypothalamic diabetes insipidus (BDI) and rats of the parent Long Evans (LE) strain. Some groups of OVX rats received subcutaneous implants of either 17 beta-oestradiol (E2) or progesterone 7 days prior to haemorrhage. The arterial blood pressure recovery immediately following haemorrhage was significantly impaired in both groups of steroid-treated OVX LE rats compared with the OVX controls (both comparisons P < 0.05). The impairment in blood pressure recovery seen in the steroid-replaced OVX LE rats was similar to that seen in pro-oestrous rats (when ovarian steroid levels are raised) compared with male rats of this strain (P < 0.05). In contrast, ovariectomy with or without steroid replacement in BDI rats had no further effect on the already attenuated recovery of arterial blood pressure after haemorrhage in this strain. Heart rate responses to haemorrhage also showed strain differences, which were dependent on steroid treatment. Pro-oestrous female LE rats showed a small decrease in heart rate after haemorrhage, followed by a recovery process, and this initial bradycardia was markedly enhanced in the OVX steroid-treated animals. In contrast, untreated OVX LE rats showed an initial and sustained increase in heart rate which was significantly higher than in the steroid-treated OVX animals (P < 0.05). All BDI rats, irrespective of treatment, consistently showed an increased heart rate after haemorrhage. In conclusion, ovarian steroid replacement in OVX LE, but not vasopressin-deficient BDI, rats was associated with an attenuated pressor recovery after haemorrhage. This provides further evidence for the existence of an important inhibitory interaction between ovarian steroids and vasopressin. The initial decrease in heart rate observed in pro-oestrous and steroid-treated OVX LE rats after haemorrhage also appears to be related to an ovarian steroid-vasopressin interaction.

Down-regulation of poison ivy/oak-induced contact sensitivity by treatment with a class II MHC binding peptide:hapten conjugate

Immune regulation of contact sensitivity to the poison ivy/oak catechol was studied at the level of class II MHC-restricted T cell recognition of hapten:peptide conjugates. In this study we have shown that 1) T cells from C3H/HeN (H-2k) mice, immunized with a synthetic I-Ak binding peptide coupled to 3-pentadecyl-catechol (PDC; a representative catechol in urushiol), recognized peptides derived from syngeneic cells linked to the same catechol; 2) T cells from draining lymph nodes of C3H/HeN mice skin-painted with PDC proliferated in response to a peptide carrier:PDC conjugate only when it was linked at the 7th, but not the 4th or the 10th, position on the peptide carrier; and 3) tolerization studies confirmed down-regulation of PDC-induced delayed-type hypersensitivity following treatment with a single I-Ak binding peptide carrying PDC covalently bound to a lysine residue at the middle (7th) TCR contact position. Tolerization with peptide:PDC conjugate resulted in abrogation of hapten-specific T cell proliferative responses that correlated with diminished IL-2 secretion. On the basis of these data we propose that it may be sufficient to couple the hapten at a single, well-chosen position on a carrier peptide to target a relevant population of T cells involved in contact sensitivity.

Simultaneous detection of different Rhizobium strains marked with either the Escherichia coli gusA gene or the Pyrococcus furiosus celB gene

A new marker system for gram-negative bacteria was developed on the basis of the celB gene from the hyperthermophilic archaeon Pyrococcus furiosus, which encodes a thermostable beta-glucosidase with a high level of beta-galactosidase activity. The celB gene is highly suitable as a marker for studying plant-bacterium interaction because endogenous background beta-glucosidase and beta-galactosidase enzyme activity can readily be inactivated by heat and because inexpensive substrates for detection are commercially available. Two celB-expressing transposons were constructed for use in ecological studies of a variety of gram-negative bacteria. The combined use of the gusA marker gene and celB allowed the simultaneous detection of several Rhizobium strains on a plant, and multiple-strain occupancy of individual modules also could be easily detected.

Differential stability of HLA-DR alleles independent of endogenous peptides

Purified HLA DRB1*0101 was shown to be inherently more stable to dissociation than DRB1*0401. The residues responsible for the differential stability were defined by constructing hybrid molecules, which contained a small number of residues from DRB1*0101 substituted into the framework of DRB1*0401. One of the hybrid molecules, containing six substituted amino acids, was as stable as DRB1*0101, but exhibited the binding specificity of DRB1*0401. This result indicated that the differential stability between the alleles arose from structural differences, and was not due solely to varying populations of endogenous peptides.

Differential stability of HLA-DR alleles independent of endogenous peptides

Purified HLA DRB1*0101 was shown to be inherently more stable to dissociation than DRB1*0401. The residues responsible for the differential stability were defined by constructing hybrid molecules, which contained a small number of residues from DRB1*0101 substituted into the framework of DRB1*0401. One of the hybrid molecules, containing six substituted amino acids, was as stable as DRB1*0101, but exhibited the binding specificity of DRB1*0401. This result indicated that the differential stability between the alleles arose from structural differences, and was not due solely to varying populations of endogenous peptides.

beta-Glucuronidase (GUS) transposons for ecological and genetic studies of rhizobia and other gram-negative bacteria

A series of transposons are described which contain the gusA gene, encoding beta-glucuronidase (GUS), expressed from a variety of promoters, both regulated and constitutive. The regulated promoters include the tac promoter which can be induced by IPTG, and nifH promoters which are symbiotically activated in legume nodules. One transposon contains gusA with a strong Shine-Dalgarno translation initiation context, but no promoter, and thus acts as a promoter-probe transposon. In addition, a gus operon deletion strain of Escherichia coli, and a transposon designed for use in chromosomal mapping using PFGE, are described. The GUS transposons are constructed in a mini-Tn5 system which can be transferred to Gram-negative bacteria by conjugation, and will form stable genomic insertions. Due to the absence of GUS activity in plants and many bacteria of economic importance, these transposons constitute powerful new tools for studying the ecology and population biology of bacteria in the environment and in association with plants, as well as for studies of the fundamental molecular basis of such interactions. The variety of assays available for GUS enable both quantitative assays and spatial localization of marked bacteria to be carried out.