A Bayesian seamless phase I–II trial design with two stages for cancer clinical trials with drug combinations

The use of drug combinations in clinical trials is increasingly common during the last years since a more favorable therapeutic response may be obtained by combining drugs. In phase I clinical trials, most of the existing methodology recommends a one unique dose combination as “optimal,” which may result in a subsequent failed phase II clinical trial since other dose combinations may present higher treatment efficacy for the same level of toxicity. We are particularly interested in the setting where it is necessary to wait a few cycles of therapy to observe an efficacy outcome and the phase I and II population of patients are different with respect to treatment efficacy. Under these circumstances, it is common practice to implement two-stage designs where a set of maximum tolerated dose combinations is selected in a first stage, and then studied in a second stage for treatment efficacy. In this article we present a new two-stage design for early phase clinical trials with drug combinations. In the first stage, binary toxicity data is used to guide the dose escalation and set the maximum tolerated dose combinations. In the second stage, we take the set of maximum tolerated dose combinations recommended from the first stage, which remains fixed along the entire second stage, and through adaptive randomization, we allocate subsequent cohorts of patients in dose combinations that are likely to have high posterior median time to progression. The methodology is assessed with extensive simulations and exemplified with a real trial.     

Bayesian latent class models for capture–recapture in the presence of missing data

We propose a method for estimating the size of a population in a multiple record system in the presence of missing data. The method is based on a latent class model where the parameters and the latent structure are estimated using a Gibbs sampler. The proposed approach is illustrated through the analysis of a data set already known in the literature, which consists of five registrations of neural tube defects.     

Characterization of variant diphtheria toxin–interleukin-3 fusion protein,DTIL3K116W,for phase I clinical trials

We have produced clinical grade of DTIL3K116W, a variant diphtheria toxin–interleukin-3 fusion protein, for treatment of acute myeloid leukemia. The product was filter sterilized, aseptically vialed, and stored at ?80 °C. It was characterized by Coomassie-stained SDS-PAGE, endotoxin assay, cytotoxicity assay, sterility, mass spectroscopy, receptor binding affinity, ADP-ribosylation, inhibition of normal human CFU-GM, disulfide bond analysis, immunoblots, stability, size exclusion chromatography–HPLC, sequencing, and immunohistochemistry. Vialed product was sterile in 0.25 M NaCl/5 mM Tris, pH 7.9, and had a protein concentration of 1.08 mg/ml. Purity by SDS-PAGE was >99%. Aggregates by HPLC were <1%. Endotoxin levels were 0.296 EU/mg. Peptide mapping and mass spectroscopy confirmed its composition and molecular weight. The vialed drug kept reactivity with anti-IL3 and DT antibodies. Potency study revealed a 48-h EC₅₀ of 0.5 pM on TF1/H-ras cell. Its binding properties were confirmed by competitive experiments showing IC₅₀ of 1.4 nM. ADP-ribosylation activity was equivalent to DTGM-CSF. Drug did not react with tested frozen human tissue sections by immunohistochemistry. There was no evidence of loss of solubility, proteolysis aggregation, or loss of potency over 6 months at ?80 °C. Further, the drug was stable at 4 and 25 °C in the plastic syringe and administration tubing for 48 h.     

A phase II trial of murine monoclonal antibody 17-1A and interferon-γ: Clinical and immunological data

Summary A group of 15 patients with metastatic colorectal adenocarcinoma received a combination of interferon (0.1 mg/m², days 1–15) and the murine monoclonal antibody 17-1A (400 mg, days 5, 7, 9 and 12). The treatment was tolerated with minimal toxicity. Of the 14 evaluable patients, 13 developed human antibody to murine 17-1A, with 11 patients demonstrating antibody to the variable region of 17-1A (anti-idiotype). Antibody to the variable region was inhibited by 17-1A but not by mouse immunoglobulin. Sera from patients with substantial anti-idiotype reactivity were capable of inhibiting the binding of murine 17-1A to antigen expressing LS174-T cells thus indicating the presence of antibody directed against the 17-1A combining site (mirror-image anti-idiotype). The median survival of the whole group was 56 weeks and there was no correlation between clinical response/survival and the development of anti-idiotype antibody.Supported by the Veterans Administration Medical Center and by Public Health Services grant CA 45 232 from the National Cancer Institute, National Institutes of Health, Department of Health and Human Services     

The evolution of adult height across Spanish regions, 1950–1980: A new source of data

We present new evidence concerning the evolution of adult height across Spanish regions for the 1950–1980 male and female birth cohorts, using the augmented sample of the European Community Household Panel (ECHP) for Spain. This augmented sample, available only for the year 2000, contains self-reported height data representative at the Autonomous Community level. The average heights of these two sets of birth cohorts, female and male, are found to increase by 1.7 and 1.6 cm/decade, respectively. Making available a new dataset of quinquennial mean heights will allow researchers to study the determinants of population heights by means of a within-country analysis.     

How good are Bayesian belief networks for environmental management? A test with data from an agricultural river catchment

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A phase I/II trial of oxidized autologous tumor vaccines during the “watch and wait” phase of chronic lymphocytic leukemia

Based on their activity in patients with advanced stage chronic lymphocytic leukemia (CLL), a phase I/II study was designed to evaluate the feasibility, safety, and efficacy of autologous vaccines made from oxidized tumor cells in patients with earlier stage CLL, and to determine an optimal schedule of injections. Eighteen patients (at risk for disease progression and with white blood cell counts between 15 and 100×10⁶ cells/ml) were injected intramuscularly with 10 ml of oxidized autologous blood (composed mainly of CLL cells) either 12 times over 6 weeks (group 1), 12 times over 16 days (group 2), or 4 times over 6 weeks (group 3). Fourteen out of eighteen patients had Rai stage 0–II disease, while 4/18 had stage III–IV disease but did not require conventional treatment. Partial clinical responses, associated with enhanced anti-tumor T cell activity in vitro, were observed in 5/18 patients of whom three were in group 2. Stable disease was observed in six patients while disease progression appeared not to be affected in the remaining patients. Toxicity was minimal. Vaccination with oxidized autologous tumor cells appears worthy of further investigation and may be a potential alternative to a watch and wait strategy for selected CLL patients.     

Search for the possible role of ‘immunotherapy’ in operable bronchial non-small cell carcinoma (stage I and II): A phase I study with Corynebacterium parvum intrapleurally

Summary The possibility of giving C. parvum intrapleurally (i.p.) was investigated. C. parvum was given post-operatively either i.p. only or i.p. and intravenously (i.v.) simultaneously. The dose varied from 0.1–10 mg i.p. All patients had been operated for a bronchial carcinoma. Results: (1) Subjective complaints of either dyspnoea, thoracic pain, chills or nausea occured in 31 of 63 patients. No clear dose relation was found. A feeling of discomfort and fever could occur for another 3–4 days after the above more acute symptoms had disappeared. (2) Increased fever (0.5° C) occurred in 71% of the patients injected i.p. only. (3) No anaphylactic reaction was observed. (4) Increased total white blood cell counts (<20%) occurred in 38 patients. The WBC increase was mainly due to higher number of neutrocytes and granulocytes. Total lymphocyte, monocyte, eosinophilic, and basophilic granulocytes values per mm³ circulating blood remained unchanged, except at the dose of 7 mg C. parvum i.p. when monocyte values were increased significantly from 576±247 to 1100±578/mm³. (5) Moderate to severe effusions were observed radiologically in three patients after C. parvum intrapleurally.The study group is: M. Kaufmann, J. Stjernswärd (Ludwig Institut for Cancer Research, Lausanne Branch, Switzerland), M. Zelen, K. Stanley (Frontier Science and Technology Research Foundation, Inc. Amherst, New York, USA), D. S. Freestone, R. Bomford, M. T. Scott, T. Priestman (The Wellcome Research Laboratory, Beckenham, England), C. Mouritzen, G. Ahlbom (Dept. of Thoracic and Cardiovascular Surgery, Aarhus Kommunehospital, Aarhus, Denmark), N. Konietzko, D. Greschuchna (Ruhrland Klinic, Essen-Haidhausen, Germany), P. Hilgard (Innere Klinik und Poliklinik [Tumorforschung] Essen, Germany), J. Vogt-Moykopf, D. Zeidler, H. Toomes (Thoraxchirurgische Spezial-Klinik, Heidelberg-Rohrbach, Germany), F. Krause, R. Rios (Thoraxchirurgische Abt., Fachkrankenhaus für Lungen- und Bronchialerkrankungen, Löwenstein, Germany), J. Orel, M. Benedik, B. Hrabar (Clinical Center, Dept. of Thoracic Surgery, Ljubljana, Yugoslavia), S. Plesnicar (The Institute of Oncology, Ljubljana, Yugoslavia), H. A. Rostad, J. R. Vale (Rikshospital, Oslo, Norway), S. Hagen, S. Birkeland, (Ulleval Hospital, Oslo, Norway), T. Harbitz, R. Nissen-Meyer (Aker Hospital, Oslo, Norway), L. Rodriguez, V. O. Björk, K. Böök (Karolinska Sjukhuset, Thoracic Clinic, Stockholm, Sweden), E. Gradel, J. Hasse, P. Holbro (Kantonsspital, Thoraxchirurgische Klinik, Basel, Switzerland), L. Eckmann (Tiefenauspital, Chir. Univ.-Klinik, Bern, Switzerland), B. Nachbur, T. Liechti (Inselspital, Dept. of Thoracic and Cardiovascular Surgery, Bern, Switzerland), H. Cottier (Inst. of Pathology, Inselspital, Bern, Switzerland), W. Maurer, M. Kaufmann, P. Froelicher (Bürgerspital, Surgical Dept., Solothurn, Switzerland), H. Denck, N. Pridun (Krankenhaus der Stadt Wien-Lainz, Chir. Abt., Vienna, Austria), K. Karrer (Institute for Cancer Research, University of Vienna, Austria) Reprint requests should be addressed to any of the members listed above, or to the Ludwig Lung Cancer Trial, Operation Office, LICR, CH-1066 Epalinges, Switzerland. (For Current Contents, etc., please use above address)     

Flexible Phase I–II Design for Partially Ordered Regimens with Application to Therapeutic Cancer Vaccines

Statistics in Biosciences - Existing methodology for the design of Phase I–II studies has been intended to search for the optimal regimen, based on a tradeoff between toxicity and efficacy,...     

A New Function for the LDL Receptor: Transcytosis of LDL across the Blood–Brain Barrier

Lipoprotein transport across the blood–brain barrier (BBB) is of critical importance for the delivery of essential lipids to the brain cells. The occurrence of a low density lipoprotein (LDL) receptor on the BBB has recently been demonstrated. To examine further the function of this receptor, we have shown using an in vitro model of the BBB, that in contrast to acetylated LDL, which does not cross the BBB, LDL is specifically transcytosed across the monolayer. The C7 monoclonal antibody, known to interact with the LDL receptor-binding domain, totally blocked the transcytosis of LDL, suggesting that the transcytosis is mediated by the receptor. Furthermore, we have shown that cholesterol-depleted astrocytes upregulate the expression of the LDL receptor at the BBB. Under these conditions, we observed that the LDL transcytosis parallels the increase in the LDL receptor, indicating once more that the LDL is transcytosed by a receptor-mediated mechanism. The nondegradation of the LDL during the transcytosis indicates that the transcytotic pathway in brain capillary endothelial cells is different from the LDL receptor classical pathway. The switch between a recycling receptor to a transcytotic receptor cannot be explained by a modification of the internalization signals of the cytoplasmic domain of the receptor, since we have shown that LDL receptor messengers in growing brain capillary ECs (recycling LDL receptor) or differentiated cells (transcytotic receptor) are 100% identical, but we cannot exclude posttranslational modifications of the cytoplasmic domain, as demonstrated for the polymeric immunoglobulin receptor. Preliminary studies suggest that caveolae are likely to be involved in the potential transport of LDL from the blood to the brain.The maintenance of the homeostasis of brain interstitial fluid, which constitutes the special microenvironment for neurons, is established by the presence of the blood–brain barrier (BBB)¹ at the transition area from endothelial cells (ECs) to brain tissue. Of primary importance in the formation of a permeability barrier by these cells is the presence of continuous tight junctions that seal together the margins of the ECs and restrict the passage of substances from the blood to the brain. Furthermore, in contrast to ECs in many other organs, the brain capillary ECs contain no direct transendothelial passageways such as fenestrations or channels. But obviously, the BBB cannot be absolute. The brain is dependent upon the blood to deliver metabolic substrates and remove metabolic waste, and the BBB therefore facilitates the exchange of selected solutes. Carrier-mediated transport systems that facilitate the uptake of hexoses, amino acids, purine compounds, and mono-carboxylic acids have been revealed in the cerebral endothelium (Betz and Goldstein, 1978), but until now little information has come to light regarding the cerebral uptake of lipids.There is growing evidence that the brain is equipped with a relatively self-sufficient transport system for maintaining cholesterol and lipid homeostasis. The presence of a low density lipoprotein (LDL) receptor has been demonstrated by immunocytochemistry in rat and monkey brains; and apolipoprotein (apo) E and apo AI-containing particles have been detected in human cerebrospinal fluid (Pitas et al., 1987). Furthermore, enzymes involved in lipid metabolism have been located within the brain: LCAT mRNA has been shown to be expressed in rat brains and cholesteryl ester transfer protein, which plays a key role in cholesterol homeostasis, has been detected in human cerebrospinal fluid and seems to be synthesized in the brain (Albers et al., 1992). The distribution of the LDL receptor-related protein, a multifunctional receptor that binds apoE, is highly restricted and limited to the gray matter, primarily associated with neuronal cell population (Wolf et al., 1992). The difference in cellular expression of ligand (apoE) and receptor (LDL receptor-related protein) may provide a pathway for intracellular transport of apoE-containing lipoproteins in the central nervous system. All these data leave little doubt that the brain is equipped with a relatively self-sufficient transport system for cholesterol.Cholesterol could be derived from de novo synthesis within the brain and from plasma via the BBB. Malavolti et al. (1991) indicate the presence of unexpectedly close communications between extracerebral and brain cholesterol. Changes in the extracerebral cholesterol levels are readily sensed by the LDL receptor in the brain and promptly provoke appropriate modifications in its activity. Méresse et al. (1989a) provided direct evidence for the occurrence in vivo of an LDL receptor on the endothelium of brain capillaries. Furthermore, the fact that enzymes involved in the lipoprotein metabolism are present in the brain microvasculature (Brecher and Kuan, 1979) and that the entire fraction of the drug bound to lipoproteins is available for entry into the brain strongly suggest that this cerebral endothelial receptor plays a role in the interaction of plasma lipoproteins with brain capillaries. These results pinpoint the critical importance of the interactions between brain capillary ECs and lipoproteins. Owing to the fact that the neurological abnormalities that result from the inadequate absorption of dietary vitamin E can be improved by the oral administration of pharmacological doses of vitamin E, Traber and Kayden (1984) have suggested that LDL functions as a transport system for tocopherol to the brain. Furthermore, the trace amounts of apolipoprotein B that were detected by Salem et al. (1987) in cerebrospinal fluid from healthy patients using a very sensitive immunoblot technique confirm that, at most, small amounts of apolipoprotein B normally pass through the BBB. However, whether LDL is involved in the exchange is not known.Using an in vitro model of the BBB that imitates an in vivo situation by culturing capillary ECs and astrocytes on opposite sides of a filter (Dehouck et al., 1990a , 1992), we have demonstrated that in culture, like in vivo, in contrast to peripheral endothelium and in spite of the tight apposition of ECs and their contact with physiological concentrations of lipoproteins, brain capillary ECs express an LDL receptor (Méresse et al., 1991; Dehouck et al., 1994). The capacity of ECs to bind LDLs is greater when cocultured with astrocytes than in their absence. Futhermore, we have shown that the lipid requirement of astrocytes increases the expression of the LDL receptor on brain capillary ECs. Taken together, the presence of LDL receptors on brain capillary ECs and the modulation of the expression of these receptors by the lipid composition of astrocytes suggest that cholesterol used by cells in the central nervous system may be derived, at least in part, from the periphery via transport across the BBB.In the present study, we provide direct evidence that after binding to brain capillary ECs, there is a specific mechanism for the transport of LDL across the endothelial monolayer from the apical to the abluminal surface. This mechanism might be best explained by a process of receptor-mediated transcytosis. Preliminary results pinpoint the role of caveolae in the transcellular transport of LDL across the brain endothelium.     

A method for assessing the fit of a constitutive material model to experimental stress–strain data

Higher-order polynomial functions can be used as a constitutive model to represent the mechanical behaviour of biological materials. The goal of this study was to present a method for assessing the fit of a given constitutive three-dimensional material model. Goodness of fit was assessed using multiple parameters including the root mean square error and Hotelling's T ²-test. Specifically, a polynomial model was used to characterise the stress–strain data, varying the number of model terms used (45 combinations of between 3 and 11 terms) and the manner of optimisation used to establish model coefficients (i.e. determining coefficients either by parameterisation of all data simultaneously or averaging coefficients obtained by parameterising individual data trials). This framework for model fitting helps to ensure that a given constitutive formulation provides the best characterisation of biological material mechanics.     

A statistical methodology for tracking long-term change in reporting rates of birds from volunteer-collected presence–absence data

The ability to track change in biodiversity is essential to guide sustainable management and meet biodiversity monitoring, evaluation and reporting requirements, yet long-term data are usually scarce. Birds Australia has developed a simple survey methodology for use by their nationwide network of volunteers; it involves the collection of data on the presence–absence of species at repeatedly visited sites. Here we present a statistical methodology for use with these binary data to examine long-term change, using as an example records from a major bioregion of eastern Australia, 1999–2007. Regression splines were employed to model trend as a smooth nonlinear function of time within a generalised linear modelling framework. Confidence intervals based on bootstrap resampling provided a basis for assessing the significance of change, and a method was incorporated for identifying important change points in the trajectory from second derivatives of the curve. The methodology proved sensitive to change and the impact of extended dry periods was evident. The populations of several woodland species were found to be in significant decline. Two composite indices to track change common to a group of birds were developed and/or adapted from the existing literature. The results confirm the usefulness of repeated 2-ha presence–absence survey data to provide insight into patterns of long-term trends in bird populations. The statistical methodology described offers a means of tracking trends and identifying important time points and is particularly useful in situations where surveys of presence–absence of species are the most efficient way to gather long-term data.     

A Highly Sensitive Resonance Scattering Assay for Immunoglobulin M Using Ag(I)–Hydroquinone–Immunonanogold Catalytic Reaction

Ten-nanometer nanogold showed the strongest catalytic effect on the particle reaction between Ag(I) and hydroquinone to form nanosilver particles that exhibited the strongest resonance scattering (RS) peak at 350 nm. The enhanced RS intensity was linear to the nanogold concentration in the range of 30–5,700 nM Au. The nanogold was used to label goat antihuman immunoglobulin M (GIgM) to obtain an immunonanogold probe (AuGIgM) for immunoglobulin M (IgM). Based on the nanogold-labeled immunoreaction between IgM and AuGIgM, centrifugation, and AuGIgM–Ag(I)–hydroquinone nanocatalytic reaction, a highly sensitive and selective immunonanogold-catalytic Ag particle RS assay for 0.2–300 ng mL^?1 IgM was proposed, with a detection limit of 0.1 ng mL^?1. This assay was simple and sensitive and was applied to assay IgM in serum samples, with satisfactory results.     

A batch correction method for liquid chromatography–mass spectrometry data that does not depend on quality control samples

The need for reproducible and comparable results is of increasing importance in non-targeted metabolomic studies, especially when differences between experimental groups are small. Liquid chromatography–mass spectrometry spectra are often acquired batch-wise so that necessary calibrations and cleaning of the instrument can take place. However this may introduce further sources of variation, such as differences in the conditions under which the acquisition of individual batches is performed. Quality control (QC) samples are frequently employed as a means of both judging and correcting this variation. Here we show that the use of QC samples can lead to problems. The non-linearity of the response can result in substantial differences between the recorded intensities of the QCs and experimental samples, making the required adjustment difficult to predict. Furthermore, changes in the response profile between one QC interspersion and the next cannot be accounted for and QC based correction can actually exacerbate the problems by introducing artificial differences. “Background correction” methods utilise all experimental samples to estimate the variation over time rather than relying on the QC samples alone. We compare non-QC correction methods with standard QC correction and demonstrate their success in reducing differences between replicate samples and their potential to highlight differences between experimental groups previously hidden by instrumental variation.     

Age–age and trait–trait correlations for <Emphasis Type="Italic">Eucalyptus grandis</Emphasis> Hill ex Maiden and their implications for optimal selection age and design of clonal trials

Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported the a priori contention of sub-dividing them into three different environmental zones for testing and deployment. Within these zones, the determination of age-age genetic correlations for both height and mean annual increment (MAI) showed that strong age-age correlations are present for a rotation age of 6 years starting at 3 years age and, thereafter, suggesting this age as appropriate for selection. This biological selection age coincides with an "economical" age for selection based on discounted selection efficiency in perpetuity, considering a range of interest rates between 10% and 20%. High genetic correlations between wood density at 3 years and 6 years as well as the lack of genetic correlation between this trait and growth traits, also favors selection at age 3 and facilitates breeding strategies that consider the utilization of both traits for improvement. A simulation of optimal clonal test designs indicated that by using six locations and six blocks per location in a single-tree plot design, between 80% and 90% of the maximum selection efficiency could be obtained. This type of design allows testing of a large number of genotypes across a reasonable number of locations in a cost-effective manner.     

A coarse-grain MD (molecular dynamic) simulation of PCL–PEG and PLA–PEG aggregation as a computational model for prediction of the drug-loading efficacy of doxorubicin

Abstract

Formulating a hydrophobic drug that is water-soluble is a pharmaceutical challenge. One way is to incorporate the drug in an amphiphilic micelle composed from an aggregation of block copolymers. Design of a good nano-micelle requires many trial-and-error attempts. In this article, we developed a computational model based on a coarse-grained molecular dynamic (MD) simulation and correlated outputs with previous studies. A good correlation shows that this model reliably simulates poly-lactic acid–poly-ethylene glycol (PLA–PEG) and poly-caprolactone (PCL)–PEG aggregation in water with and without the presence of doxorubicin.

Communicated by Ramaswamy H. Sarma     

Using response surface methodology in combination with Plackett–Burman design for optimization of culture media and extracellular expression of Trichoderma reesei synthetic endoglucanase II in Escherichia coli

Molecular Biology Reports - Cellulases like endoglucanase II (EGII) from Trichoderma reesei are the industrial enzymes responsible for breakdown of cellulosic materials. Due to its importance for...