ELDA: extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays.

Human CD8+ memory- and effector-type T cells are poorly defined. We show here that, next to a naive compartment, two discrete primed subpopulations can be found within the circulating human CD8+ T cell subset. First, CD45RA−CD45R0+ cells are reminiscent of memory-type T cells in that they express elevated levels of CD95 (Fas) and the integrin family members CD11a, CD18, CD29, CD49d, and CD49e, compared to naive CD8+ T cells, and are able to secrete not only interleukin (IL) 2 but also interferon γ, tumor necrosis factor α, and IL-4. This subset does not exert cytolytic activity without prior in vitro stimulation but does contain virus-specific cytotoxic T lymphocyte (CTL) precursors. A second primed population is characterized by CD45RA expression with concomitant absence of expression of the costimulatory molecules CD27 and CD28. The CD8+CD45RA+CD27− population contains T cells expressing high levels of CD11a, CD11b, CD18, and CD49d, whereas CD62L (L-selectin) is not expressed. These T cells do not secrete IL-2 or -4 but can produce IFN-γ and TNF-α. In accordance with this finding, cells contained within this subpopulation depend for proliferation on exogenous growth factors such as IL-2 and -15. Interestingly, CD8+CD45RA+CD27− cells parallel effector CTLs, as they abundantly express Fas-ligand mRNA, contain perforin and granzyme B, and have high cytolytic activity without in vitro prestimulation. Based on both phenotypic and functional properties, we conclude that memory- and effector-type T cells can be separated as distinct entities within the human CD8+ T cell subset.

/pdf/phenotypic-and-functional-separation-of-memory-and-effector-27jcev1zp1.pdf

Phenotypic and Functional Separation of Memory and Effector Human CD8+ T Cells

https://www.bauer.uh.edu/gardner/docs/pdf/Exponential-Smoothing.pdf

Exponential smoothing: the state of the art, part ii

To gain more insight into the role of HIV-1-specific cytotoxic T lymphocytes (CTL) in the pathogenesis of AIDS, we investigated temporal relations between HIV-1 Gag-specific precursor CTL (CTLp), HIV-1 viral load, CD4+ T cell counts, and T cell function. Six HIV-1-infected subjects, who were asymptomatic for more than 8 yr with CD4+ counts > 500 cells/mm3, were compared with six subjects who progressed to AIDS within 5 yr after HIV-1 seroconversion. In the long-term asymptomatics, persistent HIV-1 Gag-specific CTL responses and very low numbers of HIV-1-infected CD4+ T cells coincided with normal and stable CD4+ counts and preserved CD3 mAb-induced T cell reactivity for more than 8 yr. In five out of six rapid progressors Gag-specific CTLp were also detected. However, early in infection the number of circulating HIV-1-infected CD4+ T cells increased despite strong and mounting Gag-specific CTL responses. During subsequent clinical progression to AIDS, loss of Gag-specific CTLp coincided with precipitating CD4+ counts and severe deterioration of T cell function. The possible relationships of HIV-1 Gag-specific CTLp to disease progression are discussed.

/pdf/kinetics-of-gag-specific-cytotoxic-t-lymphocyte-responses-ebfvvma34b.pdf

Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics.

The introduction and expression of genes in somatic cells is an innovative therapy for correcting genetic deficiency diseases and augmenting immune function. A potential obstacle to gene therapy is the elimination of such gene-modified cells by an immune response to novel protein products of the introduced genes. We are conducting an immunotherapy trial in which individuals seropositive for human immunodeficiency virus (HIV) receive CD8+ HIV-specific cytotoxic T cells modified by retroviral transduction to express a gene permitting positive and negative selection. However, five of six subjects developed cytotoxic T-lymphocyte responses specific for the novel protein and eliminated the transduced cytotoxic T cells. The rejection of genetically modified cells by these immunocompromised hosts suggests that strategies to render gene-modified cells less susceptible to host immune surveillance will be required for successful gene therapy of immunocompetent hosts.

T-cell mediated rejection of gene-modified HIV-specific cytotoxic T lymphocytes in HIV-infected patients

Limiting dilution assays Experimental design and statistical analysis

This paper examines the performance of two different (s, Q) inventory models, namely a simple and an advanced model, for spare parts in a production plant of a confectionery producer in the Netherlands. The simple approach is more or less standard: the undershoot of the reorder level is not taken into account and the normal distribution is used as the distribution of demand during lead-time. The advanced model takes undershoots into account, differentiates between zero and nonzero demands during lead-time, and utilises the gamma distribution for the demand distribution. Both models are fed with parameters estimated by a procedure that forecasts demand sizes and time between demand occurrences separately (intermittent demand). The results show that the advanced approach yields a service level close to the desired one under many circumstances, while the simple approach is not consistent, in that it leads to much larger inventories in meeting the desired service level for all spare parts.

/pdf/a-combined-forecast-inventory-control-procedure-for-spare-1g6v52wfd8.pdf

A Combined Forecast-Inventory Control Procedure for Spare Parts

Two computer programs are presented which can be used for the determination of the design and the statistical evaluation of data in the context of limiting and serial dilution analysis. The first program (DESIGN) gives the experimenter the opportunity to set up different designs, to improve a design according to several suggestions, to make a picture of a design and to evaluate the results of artificial data, obtained from a random experiment corresponding with the chosen design, until (s)he is convinced of having a suitable design for a particular experiment. The second program (EVALUATE) evaluates the experimental data. The design method and the statistical methods used in the programs have been chosen on practical and theoretical grounds.

Computer aided design and evaluation of limiting and serial dilution experiments

On the interaction between forecasting and stock control: The case of non-stationary demand

For the familiar (R, s, S) inventory control system only approximate expressions exist for the fill rate, ie the fraction of demand that can be satisfied from stock. Best-known are the approximations derived from renewal theory, holding under specific conditions; in particular, S–s should be reasonably large. Here, an exact expression for the fill rate is derived, holding generally in the situation that demand has a gamma distribution with known integer-valued shape parameter, while lead time is constant. These exact results allow a check of the renewal theory based approximations. In addition, an extremely fast simulation program was written, obviously holding for general shape parameter values.

/pdf/exact-fill-rates-for-r-s-s-inventory-control-with-gamma-4q2o9goh36.pdf

Leo Strijbosch

Papers

Limiting dilution assays Experimental design and statistical analysis

A Combined Forecast-Inventory Control Procedure for Spare Parts

Computer aided design and evaluation of limiting and serial dilution experiments

On the interaction between forecasting and stock control: The case of non-stationary demand

Exact fill rates for (R, s, S) inventory control with gamma distributed demand