Quantifying the limits of CAR T-cell delivery in mice and men

CAR (Chimeric Antigen Receptor) T cells have demonstrated clinical success for the treatment of multiple lymphomas and leukaemias, but not for various solid tumours, despite promising data from murine models. Lower effective CAR T-cell delivery rates to human solid tumours compared to haematological malignancies in humans and solid tumours in mice might partially explain these divergent outcomes. We used anatomical and physiological data for human and rodent circulatory systems to calculate the typical perfusion of healthy and tumour tissues, and estimated the upper limits of immune cell delivery rates across different organs, tumour types and species. Estimated maximum delivery rates were up to 10 000-fold greater in mice than humans yet reported CAR T-cell doses are typically only 10–100-fold lower in mice, suggesting that the effective delivery rates of CAR T cells into tumours in clinical trials are far lower than in corresponding mouse models. Estimated delivery rates were found to be consistent with published positron emission tomography data. Results suggest that higher effective human doses may be needed to drive efficacy comparable to mouse solid tumour models, and that lower doses should be tested in mice. We posit that quantitation of species and organ-specific delivery and homing of engineered T cells will be key to unlocking their potential for solid tumours.     

Extensive direct-tandem organization of a long repeat DNA sequence on the Y chromosome of chinook salmon (Oncorhynchus tshawytscha)

A long repetitive DNA sequence (OtY8) has been cloned from male chinook salmon and its genomic organization has been characterized. The repeat has a unit length of 8 kb and is present approximately 300 times per diploid male nucleus. All internal fragments within the 8-kb repeat segregate from father to son, suggesting that the entire repeat unit is located on the Y chromosome. The organization of this sequence into an 8-kb repeat unit is restricted to the Y chromosome, as are several male-specific repeat subtypes identified on the basis of restriction-site variation. The repeat possesses only weak internal sequence similarities, suggesting that OtY8 has not arisen by duplication of a smaller repeat unit, as is the case for other long tandem arrays found in eukaryotes. Based on a laddered pattern arising from partial digestion of genomic DNA with a restriction enzyme which cuts only once per repeat unit, this sequence is not dispersed on the Y chromosome but is organized as a head-to-tail tandem array. Pulse-gel electrophoresis reveals that the direct-tandem repeats are organized into at least six separate clusters containing approximately 12 to 250 copies, comprising some 2.4 Mb of Y-chromosomal DNA in total. Related sequences with nucleotide substitutions and DNA insertions relative to the Y-chromosomal fragment are found elsewhere in the genome but at much lower copy number and, although similar sequences are also found in other salmonid species, the amplification of the repeat into a Y-chromosome-linked tandem array is only observed in chinook salmon. The OtY8 repetitive sequence is genetically tightly associated with the sex-determination locus and provides an opportunity to examine the evolution of the Y chromosome and sex determination process in a lower vertebrate.     

iSAX: disk-aware mining and indexing of massive time series datasets

Current research in indexing and mining time series data has produced many interesting algorithms and representations. However, the algorithms and the size of data considered have generally not been representative of the increasingly massive datasets encountered in science, engineering, and business domains. In this work, we introduce a novel multi-resolution symbolic representation which can be used to index datasets which are several orders of magnitude larger than anything else considered in the literature. To demonstrate the utility of this representation, we constructed a simple tree-based index structure which facilitates fast exact search and orders of magnitude faster, approximate search. For example, with a database of one-hundred million time series, the approximate search can retrieve high quality nearest neighbors in slightly over a second, whereas a sequential scan would take tens of minutes. Our experimental evaluation demonstrates that our representation allows index performance to scale well with increasing dataset sizes. Additionally, we provide analysis concerning parameter sensitivity, approximate search effectiveness, and lower bound comparisons between time series representations in a bit constrained environment. We further show how to exploit the combination of both exact and approximate search as sub-routines in data mining algorithms, allowing for the exact mining of truly massive real world datasets, containing tens of millions of time series.     

Dimensionality Reduction for Fast Similarity Search in Large Time Series Databases

The problem of similarity search in large time series databases has attracted much attention recently. It is a non-trivial problem because of the inherent high dimensionality of the data. The most promising solutions involve first performing dimensionality reduction on the data, and then indexing the reduced data with a spatial access method. Three major dimensionality reduction techniques have been proposed: Singular Value Decomposition (SVD), the Discrete Fourier transform (DFT), and more recently the Discrete Wavelet Transform (DWT). In this work we introduce a new dimensionality reduction technique which we call Piecewise Aggregate Approximation (PAA). We theoretically and empirically compare it to the other techniques and demonstrate its superiority. In addition to being competitive with or faster than the other methods, our approach has numerous other advantages. It is simple to understand and to implement, it allows more flexible distance measures, including weighted Euclidean queries, and the index can be built in linear time. Received 16 May 2000 / Revised 18 December 2000 / Accepted in revised form 2 January 2001     

Total System Reliability: Integrated Model for Growth and Test Termination

Reliability demonstration testing is not the most efficient method of assuring product reliability prior to shipment. It is costly, time consuming and has inherent technical and social limitations. The dilemma facing the reliability and quality engineer is whether to continue demonstration testing and risk shipping a product late or ship the product and risk warranty and field service returns. Either option can cause the company to lose significant market share and profit. This paper sets out to solve this dilemma by meeting both the time to market constraints and the product reliability goals. The weaknesses of existing reliability demonstration techniques are explored and a comprehensive methodology is introduced involving controlled development processes, stress testing, root cause determination and process change feedback mechanisms. All prototype products are manufactured on the final volume process line resulting in the early identification and correction of process‐related problems. Testing commences on the first available prototypes with system stress/robust testing being employed to stimulate failures, determine their root cause and correct them. Reliability growth modelling assesses the ongoing improvements occurring in reliability during the development cycle, while a statistical stopping rule is used to determine the optimal product release time without risking product warranty. The approach is applicable to systems incorporating both hardware and software elements. The methodology has been validated on three development projects of telecommunication systems comprising hardware and software. In addition to enhancing team behaviour and performance, the development times have been reduced by 14% and the ramp‐up time to full worldwide product shipments has been reduced by 50%. Copyright © 2005 John Wiley & Sons, Ltd.     

Defining the outcome of immunosuppression withdrawal after liver transplantation

Successful immunosuppression withdrawal should benefit the natural history of organ transplantation patients. To identify the clinical hazards of removing drug treatment and possible characteristics that predict a favorable outcome in long-term liver recipients, immunosuppression was withdrawn completely and the clinicopathological outcome documented in 18 liver recipients. Indication for transplantation, HLA matching, early rejection history, and presence of microchimerism were examined as predictors of outcome. Chimerism was determined by polymerase chain reaction-based examination for donor-specific HLA-DRB1 alleles and Y-gene-specific nucleotide sequences. At 3 years, 5 patients (28%) remained completely off immunosuppression; 12 patients (67%) experienced histological graft changes: acute rejection in 4, portal tract inflammation/hepatitis in 7, and necrosis in 1. Hepatitis B or C viral infections did not account for the nonrejection patterns. Unmasking of systemic disorders occurred. Chimerism, demonstrated in 7 patients (39%), with skin the optimal tissue, was not associated with tolerance. Parameters associated with successful drug withdrawal were transplantation for non-immune-mediated liver disorders, fewer donor-recipient HLA A, B, and DR mismatches, and a low incidence of early rejection. Immunosuppression withdrawal is a feasible option in a proportion of selected liver recipients, but identification of tolerant patients remains imprecise.     

Bacteria for the nineties

Staphylococcus aureus and Enterococci have gained prominence as the causes of wound infections during this decade. Methicillin-resistant Staphylococcus aureus (MRSA) became commonplace in the United States during the 1980s. In Canada, infections with MRSA have been increasing in frequency since 1995. MRSA develops resistance by producing an altered penicillin-binding protein, PBP 2a, coded for by the mecA gene. Vancomycin is the usual drug of choice. Recently, strains with intermediate resistance to vancomycin (VISA) have been isolated from patients in Japan and the United States. Interim guidelines for their control have been developed by the Centers for Disease Control. Enterococci have developed a resistance to a variety of antimicrobials during the past three decades, including beta-lactams and aminoglycosides. Recently, strains resistant to vancomycin (VRE) have been found in the United States and Canada. They are particularly difficult to treat, although some success has been achieved with experimental drugs. These microorganisms have the ability to escape control by antimicrobials almost as soon as they are developed. Thus, we must practice good infection control and reserve antimicrobials only for clear cases of infection if we are to prevent or delay the emergence of resistance.